Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 21 of 135
Found at i:5773379 original size:12 final size:12
Alignment explanation
Indices: 5773364--5773397 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5773354 TCAATTCCAA
5773364 TTTCACTTTTAC
1 TTTCACTTTTAC
*
5773376 TTTCACTTTCAC
1 TTTCACTTTTAC
*
5773388 TTTCAATTTT
1 TTTCACTTTT
5773398 TATCACAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTCACTTTTAC
Found at i:5776757 original size:7 final size:7
Alignment explanation
Indices: 5776749--5776787 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
5776739 GTTAATGCAT
*
5776749 ATGGCAT
1 ATGGCAC
*
5776756 ATGGCAT
1 ATGGCAC
5776763 ATGGCAC
1 ATGGCAC
5776770 ATGGCAC
1 ATGGCAC
5776777 ATGGCAC
1 ATGGCAC
5776784 ATGG
1 ATGG
5776788 GGTTCATCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (7 bp):
ATGGCAC
Found at i:5776764 original size:14 final size:14
Alignment explanation
Indices: 5776745--5776787 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
5776735 ATCAGTTAAT
*
5776745 GCATATGGCATATG
1 GCATATGGCACATG
5776759 GCATATGGCACATG
1 GCATATGGCACATG
*
5776773 GCACATGGCACATG
1 GCATATGGCACATG
5776787 G
1 G
5776788 GGTTCATCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (14 bp):
GCATATGGCACATG
Found at i:5790104 original size:6 final size:6
Alignment explanation
Indices: 5790081--5790113 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
5790071 GGACTAGAAG
5790081 CACGGA CACAGG- CACGGA CACGGA CACGGA CAC
1 CACGGA CAC-GGA CACGGA CACGGA CACGGA CAC
5790114 ACAGCACGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.08
6 21 0.84
7 2 0.08
ACGTcount: A:0.33, C:0.36, G:0.30, T:0.00
Consensus pattern (6 bp):
CACGGA
Found at i:5792337 original size:31 final size:31
Alignment explanation
Indices: 5792302--5792372 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
5792292 ATAATGATCA
5792302 TCTCTTAAAATTTTCAAAATTATTTTTAATT
1 TCTCTTAAAATTTTCAAAATTATTTTTAATT
5792333 TCTCTTAAAATTTTCAAAATTATTTTTAATT
1 TCTCTTAAAATTTTCAAAATTATTTTTAATT
*
5792364 T-TTTTAAAA
1 TCTCTTAAAA
5792373 AAATTAAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 7 0.18
31 32 0.82
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (31 bp):
TCTCTTAAAATTTTCAAAATTATTTTTAATT
Found at i:5796519 original size:24 final size:26
Alignment explanation
Indices: 5796478--5796531 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
5796468 GTGTGTCTCG
* * *
5796478 TATTTTTCTTTCAGTTAAA-TTTTTT
1 TATTTTTCTTCCAATTAAACTTTTAT
5796503 TATTTTT-TTCCAATTAAACTTTTAT
1 TATTTTTCTTCCAATTAAACTTTTAT
5796528 TATT
1 TATT
5796532 CTAGCAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTTTTCTTCCAATTAAACTTTTAT
Found at i:5801666 original size:124 final size:124
Alignment explanation
Indices: 5801505--5801746 Score: 317
Period size: 123 Copynumber: 2.0 Consensus size: 124
5801495 TTTAATGATC
* * * **
5801505 AAAATGTCAATAATTAATAATAATAGTGACTCTATCATAATTTTTTTTAAGTTTGATGAACACGA
1 AAAATGTCAAGAATTAATAATAATAATGACTCTATCATAA-TTTTTTAAAGTTTGATGAACAAAA
* * *
5801570 TGTAATTTAAACTATACATAAGTGATCTAATTCAT-AGTTTACCCTAATAATAAGTTACT
65 TGTAATTTAAACCACACATAAGTGATCCAATTCATAAGTTTACCCTAATAATAAGTTACT
* **
5801629 AAAATGTCAAGAATTGATAATCCTAATGAC-CATATCATAATTTTTTAAAGTTTGATGAACAAAA
1 AAAATGTCAAGAATTAATAATAATAATGACTC-TATCATAATTTTTTAAAGTTTGATGAACAAAA
* ** *
5801693 TGTAATTTAAACCACACATGAGTGATCCAATTTGTAATTTTACCCTAATAATAA
65 TGTAATTTAAACCACACATAAGTGATCCAATTCATAAGTTTACCCTAATAATAA
5801747 TCAGTTAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
123 51 0.50
124 50 0.50
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.36
Consensus pattern (124 bp):
AAAATGTCAAGAATTAATAATAATAATGACTCTATCATAATTTTTTAAAGTTTGATGAACAAAAT
GTAATTTAAACCACACATAAGTGATCCAATTCATAAGTTTACCCTAATAATAAGTTACT
Found at i:5803390 original size:20 final size:20
Alignment explanation
Indices: 5803367--5803416 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5803357 CTAAACTTAA
5803367 CATTGATTTAACATTTAA-AT
1 CATTG-TTTAACATTTAAGAT
*
5803387 CATTCTTTAAACATTTAAGAT
1 CATTGTTT-AACATTTAAGAT
5803408 C-TTGTTTAA
1 CATTGTTTAA
5803417 ATGAATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 18 0.69
21 3 0.12
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (20 bp):
CATTGTTTAACATTTAAGAT
Found at i:5813948 original size:14 final size:14
Alignment explanation
Indices: 5813924--5813956 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5813914 CGTAATTTGA
5813924 GTTTT-TTTTTAAT
1 GTTTTATTTTTAAT
5813937 GTTTTATTTTTAAT
1 GTTTTATTTTTAAT
5813951 -TTTTAT
1 GTTTTAT
5813957 GCTTATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (14 bp):
GTTTTATTTTTAAT
Found at i:5815218 original size:20 final size:21
Alignment explanation
Indices: 5815173--5815218 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
5815163 AAAAACTAGC
5815173 AAATGTATTTTATAGTTTTTAT
1 AAAT-TATTTTATAGTTTTTAT
5815195 -AATTATTTTA-A-TTTGTTAT
1 AAATTATTTTATAGTTT-TTAT
5815214 AAATT
1 AAATT
5815219 GAGTCACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 3 0.14
19 5 0.23
20 11 0.50
21 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (21 bp):
AAATTATTTTATAGTTTTTAT
Found at i:5817119 original size:12 final size:12
Alignment explanation
Indices: 5817102--5817126 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5817092 CTATGCCCAT
5817102 TTCCATTTAATC
1 TTCCATTTAATC
5817114 TTCCATTTAATC
1 TTCCATTTAATC
5817126 T
1 T
5817127 AAACATTGAA
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:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCCATTTAATC
Found at i:5821582 original size:31 final size:29
Alignment explanation
Indices: 5821521--5821594 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 29
5821511 TCAATAACTT
*
5821521 TAACTTAAA-AAAAAATTTAGTATTTCAA
1 TAACTTAAATAAAAAATTTAATATTTCAA
5821549 TAACTTAAATAAAAATATTTTAATAATTT-AA
1 TAACTTAAATAAAAA-A-TTTAAT-ATTTCAA
5821580 TAACTTAAATAAAAA
1 TAACTTAAATAAAAA
5821595 CTTTCAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 9 0.22
29 5 0.12
30 1 0.02
31 22 0.54
32 4 0.10
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.36
Consensus pattern (29 bp):
TAACTTAAATAAAAAATTTAATATTTCAA
Found at i:5821605 original size:31 final size:32
Alignment explanation
Indices: 5821542--5821607 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
5821532 AAAATTTAGT
**
5821542 ATTTCAATAACTTAAATAAAAATATTTTAATA
1 ATTTCAATAACTTAAATAAAAATATTCAAATA
5821574 ATTT-AATAACTTAAATAAAAACT-TTCAAATA
1 ATTTCAATAACTTAAATAAAAA-TATTCAAATA
5821605 ATT
1 ATT
5821608 ACATACTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (32 bp):
ATTTCAATAACTTAAATAAAAATATTCAAATA
Found at i:5830816 original size:58 final size:59
Alignment explanation
Indices: 5830714--5830824 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 59
5830704 ATTAATATTA
*
5830714 AAAAAGATTAAGTACCAAATTAAGAAAAAGAGTCAAGTTCAGGTACCAAATTAGAACCC
1 AAAAAGATTAAATACCAAATTAAGAAAAAGAGTCAAGTTCAGGTACCAAATTAGAACCC
* * * * *
5830773 AAAAAGTTTAAATACCAACTTAA-AAAAAGTGTCAAGTTTAGGTATCAAATTA
1 AAAAAGATTAAATACCAAATTAAGAAAAAGAGTCAAGTTCAGGTACCAAATTA
5830825 AAAAAAATTG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 26 0.57
59 20 0.43
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (59 bp):
AAAAAGATTAAATACCAAATTAAGAAAAAGAGTCAAGTTCAGGTACCAAATTAGAACCC
Found at i:5838676 original size:15 final size:16
Alignment explanation
Indices: 5838656--5838685 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5838646 TGAATACAAA
5838656 AGAATAAGAT-TTAAG
1 AGAATAAGATGTTAAG
5838671 AGAATAAGATGTTAA
1 AGAATAAGATGTTAA
5838686 CTAAGATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (16 bp):
AGAATAAGATGTTAAG
Found at i:5841115 original size:5 final size:5
Alignment explanation
Indices: 5841107--5841142 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
5841097 AAATGTAATG
* *
5841107 TTGGT TTGGT TTGGT TTGGC TTGGT TTTGT TTGGT T
1 TTGGT TTGGT TTGGT TTGGT TTGGT TTGGT TTGGT T
5841143 GCGCAGCCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.36, T:0.61
Consensus pattern (5 bp):
TTGGT
Found at i:5852408 original size:85 final size:84
Alignment explanation
Indices: 5852268--5852452 Score: 291
Period size: 85 Copynumber: 2.2 Consensus size: 84
5852258 TTTTTATAAT
5852268 TTTTTAGTAAGTTTTAATAGCTTTTAATAATTTCTAAATTTTGGTTGAAATTATAATATTTTTAT
1 TTTTT-GTAAGTTTTAATAGCTTTTAATAATTTCTAAATTTTGGTTGAAATTATAATATTTTTAT
*
5852333 -TTATTTTTTACATATTTAAA
65 CGT-TTTTTTACATATTTAAA
*
5852353 TTTTTGTAAGTTTTAATAGCTTTTAATAATTTTTAAAATTTTGGTTGAAATTATAATATTTTTAT
1 TTTTTGTAAGTTTTAATAGCTTTTAATAATTTCT-AAATTTTGGTTGAAATTATAATATTTTTAT
5852418 CGGTTTTTTTACATATTTAAA
65 C-GTTTTTTTACATATTTAAA
* *
5852439 TTTTTATAAATTTT
1 TTTTTGTAAGTTTT
5852453 TACATTGATC
Statistics
Matches: 93, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
84 28 0.30
85 35 0.38
86 29 0.31
87 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (84 bp):
TTTTTGTAAGTTTTAATAGCTTTTAATAATTTCTAAATTTTGGTTGAAATTATAATATTTTTATC
GTTTTTTTACATATTTAAA
Found at i:5858088 original size:15 final size:15
Alignment explanation
Indices: 5858068--5858121 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
5858058 ATATTACAAA
5858068 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
5858083 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
5858100 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
5858117 ATATT
1 ATATT
5858122 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:5858314 original size:13 final size:14
Alignment explanation
Indices: 5858298--5858326 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5858288 ATTGAAAAAT
5858298 ATAATATTTT-ATA
1 ATAATATTTTAATA
5858311 ATAATATTTTAATA
1 ATAATATTTTAATA
5858325 AT
1 AT
5858327 TTTAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATATTTTAATA
Found at i:5858324 original size:21 final size:19
Alignment explanation
Indices: 5858299--5858341 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
5858289 TTGAAAAATA
5858299 TAAT-ATTTTATAATAATATTT
1 TAATAATTTTA-AAT-AT-TTT
5858320 TAATAATTTTAAATATTTT
1 TAATAATTTTAAATATTTT
5858339 TAA
1 TAA
5858342 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 7 0.33
22 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATAATTTTAAATATTTT
Found at i:5859396 original size:27 final size:27
Alignment explanation
Indices: 5859363--5859417 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
5859353 ATTTTATGAT
5859363 TAAAATT-TAGATTGATATTCAAAAAAA
1 TAAAATTAT-GATTGATATTCAAAAAAA
* *
5859390 TAAAATTATGATTGATATTTAAATAAA
1 TAAAATTATGATTGATATTCAAAAAAA
5859417 T
1 T
5859418 TTAAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (27 bp):
TAAAATTATGATTGATATTCAAAAAAA
Found at i:5873413 original size:15 final size:15
Alignment explanation
Indices: 5873393--5873421 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5873383 TGTATACAAC
5873393 GATGTATAATTAAAT
1 GATGTATAATTAAAT
5873408 GATGTATAATTAAA
1 GATGTATAATTAAA
5873422 GTAATTTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (15 bp):
GATGTATAATTAAAT
Found at i:5876043 original size:28 final size:30
Alignment explanation
Indices: 5875998--5876068 Score: 112
Period size: 28 Copynumber: 2.5 Consensus size: 30
5875988 GTGATCTACG
*
5875998 TGTATTTAGCACTTTGTGTGCTCTCTGTT-
1 TGTAATTAGCACTTTGTGTGCTCTCTGTTC
5876027 T-TAATTAGCACTTTGTGTGCTCTCTGTTC
1 TGTAATTAGCACTTTGTGTGCTCTCTGTTC
5876056 TGTAA-TAGCACTT
1 TGTAATTAGCACTT
5876069 CGGTGCTTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 26 0.67
29 10 0.26
30 3 0.08
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.48
Consensus pattern (30 bp):
TGTAATTAGCACTTTGTGTGCTCTCTGTTC
Found at i:5877102 original size:16 final size:17
Alignment explanation
Indices: 5877081--5877112 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5877071 TTAAAAATTA
5877081 TAAAAA-TATAATCTAT
1 TAAAAATTATAATCTAT
5877097 TAAAAATTATAATCTA
1 TAAAAATTATAATCTA
5877113 ATTTTGACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATTATAATCTAT
Found at i:5877945 original size:34 final size:34
Alignment explanation
Indices: 5877907--5877971 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
5877897 AGAAGCTATG
5877907 TTTGTATTCAGTTTAATTGCCCCATCAATATCTT
1 TTTGTATTCAGTTTAATTGCCCCATCAATATCTT
5877941 TTTGTATTCAGTTTAATTGCCCCATCAATAT
1 TTTGTATTCAGTTTAATTGCCCCATCAATAT
5877972 TCAAAAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (34 bp):
TTTGTATTCAGTTTAATTGCCCCATCAATATCTT
Found at i:5883426 original size:57 final size:57
Alignment explanation
Indices: 5883353--5883517 Score: 162
Period size: 57 Copynumber: 2.9 Consensus size: 57
5883343 TTTTCAAAAA
* *
5883353 TTTTGGGTGTTGGCCATCAAATGACCGACACCCCCTTTTCTCGAAAAAAAATTGTATT
1 TTTTAGGTGTTGGCCATCAAATGACCGACACCCCCTTTTCTCGAAAAAAAATTGCA-T
* *
5883411 TTTTA-GTGTTGGCCATCAAAT-AGCCGACACTCCCTATT-TC--AAAAAAA-TGCAT
1 TTTTAGGTGTTGGCCATCAAATGA-CCGACACCCCCTTTTCTCGAAAAAAAATTGCAT
* *** * *
5883463 TTTTAGGTGTTGACCATTGCATGATCGACACCTCCTATTTCTCGAGAAAAAAATT
1 TTTTAGGTGTTGGCCATCAAATGACCGACACCCCCT-TTTCTCGA-AAAAAAATT
5883518 TCAAATTTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
52 6 0.07
53 24 0.28
54 10 0.12
55 2 0.02
56 3 0.03
57 29 0.34
58 11 0.13
59 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (57 bp):
TTTTAGGTGTTGGCCATCAAATGACCGACACCCCCTTTTCTCGAAAAAAAATTGCAT
Found at i:5883643 original size:61 final size:61
Alignment explanation
Indices: 5883541--5883888 Score: 370
Period size: 61 Copynumber: 5.7 Consensus size: 61
5883531 GTGTCGGTCA
* * *
5883541 TTTTCTCGAGAAAACAAAATCAAATTTTTTTAGTGTTGGCCATTGCATGGCCGACACACCCC
1 TTTTCTCGAGAAAA-AAATTCAAATTTTTTTGGTGTTGGCCATTGAATGGCCGACACACCCC
* ** **
5883603 TTTTCTCGAG-AAAAAATTCCAAATTTTTTTTGTGTTGGCCATCAAATGGCCGACACCTACCTT
1 TTTTCTCGAGAAAAAAATT-CAAATTTTTTTGGTGTTGGCCATTGAATGGCCGACA-C-ACCCC
* * * * *
5883666 TTTTCTCGAGAAAAAAATTTAAAATTTTTTGGTGTTAGCCATTGCATGGCCG--ACATCCC
1 TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATTGAATGGCCGACACACCCC
* * * **
5883725 TCTTTCTTGAGAAAAAAATTTAAATTTTTTTGGTGTAGGCCATCAAATGGCCGACAC-CTCCC
1 T-TTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATTGAATGGCCGACACAC-CCC
* *
5883787 TTTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTGGCCA-TCAGATGGCTGACAC-CCCC
1 TTTTCTCGAG-AAAAAAATTCAAATTTTTTTGGTGTTGGCCATTGA-ATGGCCGACACACCCC
* *
5883848 TTTTCTCGAG-AAAAAATTCACA-TTTTTGGGTGTTGGCCATT
1 TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATT
5883889 TTCCTCGGAT
Statistics
Matches: 242, Mismatches: 33, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
58 16 0.07
59 15 0.06
60 49 0.20
61 58 0.24
62 57 0.24
63 39 0.16
64 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (61 bp):
TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATTGAATGGCCGACACACCCC
Found at i:5883770 original size:123 final size:122
Alignment explanation
Indices: 5883541--5883887 Score: 438
Period size: 122 Copynumber: 2.8 Consensus size: 122
5883531 GTGTCGGTCA
* *
5883541 TTTTCTCGAGAAAACAAAATCAAATTTTTTTAGTGTTGGCCATTGCATGGCCGACACACCCCTTT
1 TTTTCTCGAGAAAA-AAATTCAAATTTTTTTGGTGTTGGCCATTGCATGGCCGACAC-CCCCTTT
* * *
5883606 TCTCGAG-AAAAAATTCCAAATTTTTTTTGTGTTGGCCATCAAATGGCCGACACCTACCTT
64 TCTCGAGAAAAAAATTCCAAATTTTTTTGGTGTAGGCCATCAAATGGCCGACACCT-CC-C
* * * *
5883666 TTTTCTCGAGAAAAAAATTTAAAATTTTTTGGTGTTAGCCATTGCATGGCCGACA-TCCCTCTTT
1 TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCCT-TTT
* *
5883730 CTTGAGAAAAAAATT-TAAATTTTTTTGGTGTAGGCCATCAAATGGCCGACACCTCCC
65 CTCGAGAAAAAAATTCCAAATTTTTTTGGTGTAGGCCATCAAATGGCCGACACCTCCC
* *
5883787 TTTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAG-ATGGCTGACACCCCCTTT
1 TTTTCTCGAG-AAAAAAATTCAAATTTTTTTGGTGTTGGCCAT-TGCATGGCCGACACCCCCTTT
* * *
5883851 TCTCGAG-AAAAAATT-CACA-TTTTTGGGTGTTGGCCAT
64 TCTCGAGAAAAAAATTCCAAATTTTTTTGGTGTAGGCCAT
5883888 TTTCCTCGGA
Statistics
Matches: 195, Mismatches: 22, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
120 16 0.08
121 20 0.10
122 52 0.27
123 49 0.25
124 44 0.23
125 14 0.07
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (122 bp):
TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTC
TCGAGAAAAAAATTCCAAATTTTTTTGGTGTAGGCCATCAAATGGCCGACACCTCCC
Found at i:5883818 original size:62 final size:61
Alignment explanation
Indices: 5883541--5883887 Score: 402
Period size: 62 Copynumber: 5.7 Consensus size: 61
5883531 GTGTCGGTCA
* * ***
5883541 TTTTCTCGAGAAAACAAAATCAAATTTTTTTAGTGTTGGCCATTGCATGGCCGACACAC-CCC
1 TTTTCTCGAGAAAA-AAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACAC-CTCCC
* *
5883603 TTTTCTCGAG-AAAAAATTCCAAATTTTTTTTGTGTTGGCCATCAAATGGCCGACACCTACCTT
1 TTTTCTCGAGAAAAAAATT-CAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCT-CC-C
* * * ***
5883666 TTTTCTCGAGAAAAAAATTTAAAATTTTTTGGTGTTAGCCATTGCATGGCCGACA--TCCC
1 TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCC
* * *
5883725 TCTTTCTTGAGAAAAAAATTTAAATTTTTTTGGTGTAGGCCATCAAATGGCCGACACCTCCC
1 T-TTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCC
* *
5883787 TTTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAGATGGCTGACACC-CCC
1 TTTTCTCGAG-AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCC
* *
5883848 TTTTCTCGAG-AAAAAATTCACA-TTTTTGGGTGTTGGCCAT
1 TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCAT
5883888 TTTCCTCGGA
Statistics
Matches: 248, Mismatches: 28, Indels: 22
0.83 0.09 0.07
Matches are distributed among these distances:
58 17 0.07
59 12 0.05
60 54 0.22
61 58 0.23
62 60 0.24
63 39 0.16
64 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (61 bp):
TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCC
Found at i:5884847 original size:30 final size:32
Alignment explanation
Indices: 5884788--5884869 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 32
5884778 AGAAAAAAAA
* *
5884788 TTAAAATATACAACAAAAAATAGAAATTAAAT
1 TTAAAATATAAAACAAAAAATACAAATTAAAT
*
5884820 TTAAAATA-AAAAC-AAAATTACAAATTAAAT
1 TTAAAATATAAAACAAAAAATACAAATTAAAT
*
5884850 TTAAAATGT-AAACGAAAAAA
1 TTAAAATATAAAAC-AAAAAA
5884870 AATCAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
30 26 0.62
31 4 0.10
32 12 0.29
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.24
Consensus pattern (32 bp):
TTAAAATATAAAACAAAAAATACAAATTAAAT
Found at i:5885014 original size:24 final size:24
Alignment explanation
Indices: 5884985--5885038 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
5884975 GGCATTACAT
5884985 TGGTGTTCGTCGGCTCATCCTCGG
1 TGGTGTTCGTCGGCTCATCCTCGG
5885009 TGGTGTTCGTCGGCTCATCCTCGG
1 TGGTGTTCGTCGGCTCATCCTCGG
5885033 TGGTGT
1 TGGTGT
5885039 CAACGTTGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.04, C:0.26, G:0.35, T:0.35
Consensus pattern (24 bp):
TGGTGTTCGTCGGCTCATCCTCGG
Found at i:5885391 original size:64 final size:62
Alignment explanation
Indices: 5885277--5885410 Score: 209
Period size: 64 Copynumber: 2.1 Consensus size: 62
5885267 AATCATGAAG
5885277 AAAAAAAATTTGAAATTTTTTTCTCGAGAAAAAGGAGTGTCGGCCATGCAATGGCCAACACA
1 AAAAAAAATTTGAAATTTTTTTCTCGAGAAAAAGGAGTGTCGGCCATGCAATGGCCAACACA
*
5885339 AAAAAAAATTT-AAA-TTTTTTCTCGAGAAAAAAAGGGGGGTGTCGGCCATGCAATGGCCAACAC
1 AAAAAAAATTTGAAATTTTTTTCTCGAG--AAAAA--GGAGTGTCGGCCATGCAATGGCCAACAC
5885402 A
62 A
5885403 AAAAAAAA
1 AAAAAAAA
5885411 AAACAAAAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
60 12 0.18
61 3 0.04
62 16 0.24
64 36 0.54
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (62 bp):
AAAAAAAATTTGAAATTTTTTTCTCGAGAAAAAGGAGTGTCGGCCATGCAATGGCCAACACA
Found at i:5885510 original size:57 final size:56
Alignment explanation
Indices: 5885415--5885553 Score: 190
Period size: 57 Copynumber: 2.4 Consensus size: 56
5885405 AAAAAAAAAC
* * * *
5885415 AAAAATGCAATTTTTTTTGAAATAGGGGGTGTCGGCCATTTGATGGCCAACACC-A
1 AAAAATGTAATTTTTTTTGAAAAAGGGAGTGTCGGCCATTTGATAGCCAACACCTA
5885470 AAAAATGTAATTTTTTTTCGAGAAAAGGGAGTGTCGGCCATTTGATAGCCAACACCTA
1 AAAAATGTAATTTTTTTT-GA-AAAAGGGAGTGTCGGCCATTTGATAGCCAACACCTA
*
5885528 AAAAATTTGAATTTTTTTTGACAAAA
1 AAAAATGT-AATTTTTTTTGA-AAAA
5885554 AAGATGTGTC
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
55 17 0.23
56 2 0.03
57 31 0.42
58 14 0.19
59 10 0.14
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (56 bp):
AAAAATGTAATTTTTTTTGAAAAAGGGAGTGTCGGCCATTTGATAGCCAACACCTA
Found at i:5885570 original size:59 final size:57
Alignment explanation
Indices: 5885450--5885584 Score: 157
Period size: 59 Copynumber: 2.3 Consensus size: 57
5885440 GGGGTGTCGG
* ** **
5885450 CCATTTGATGGCCAACACCAAAAAATGTAATTTTTTTTCGAGAAAAGGGAGTGTCGG
1 CCATTTGATGGCCAACACCAAAAAATGTAATTTTTTTTCGACAAAAAAGAGTGTCAA
* *
5885507 CCATTTGATAGCCAACACCTAAAAAATTTGAATTTTTTTT-GACAAAAAAGATGTGTCAA
1 CCATTTGATGGCCAACACC-AAAAAATGT-AATTTTTTTTCGACAAAAAAGA-GTGTCAA
5885566 CCA-TTGCATGGCCAACACC
1 CCATTTG-ATGGCCAACACC
5885585 CCAAATTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 18 0.27
58 19 0.29
59 29 0.44
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (57 bp):
CCATTTGATGGCCAACACCAAAAAATGTAATTTTTTTTCGACAAAAAAGAGTGTCAA
Found at i:5886725 original size:15 final size:16
Alignment explanation
Indices: 5886707--5886744 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5886697 AATAAAAAAT
*
5886707 ATATAAAAATATTA-A
1 ATATAAAAATAATATA
*
5886722 ATATTAAAATAATATA
1 ATATAAAAATAATATA
5886738 ATATAAA
1 ATATAAA
5886745 TATTTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAAAATAATATA
Found at i:5886767 original size:29 final size:28
Alignment explanation
Indices: 5886680--5886770 Score: 80
Period size: 31 Copynumber: 3.1 Consensus size: 28
5886670 TAAAATGATT
*
5886680 ATATAAAAATTTCAATAAA-TAAAAAAT-
1 ATATAAAAATTT-AAAAAATTAAAAAATA
*
5886707 ATATAAAAATATT-AAATATTAAAATAATATA
1 ATATAAAAAT-TTAAAAAATT-AAA-AA-ATA
*
5886738 ATATAAATATTTAAAAAAATTAAAAAATA
1 ATATAAAAATTT-AAAAAATTAAAAAATA
5886767 ATAT
1 ATAT
5886771 GGAGAGACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
26 3 0.06
27 11 0.21
28 5 0.10
29 9 0.17
30 6 0.12
31 12 0.23
32 6 0.12
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (28 bp):
ATATAAAAATTTAAAAAATTAAAAAATA
Found at i:5887621 original size:14 final size:14
Alignment explanation
Indices: 5887597--5887630 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5887587 TAGGTTACGT
5887597 TTTTCTCTTTCTTTC
1 TTTT-TCTTTCTTTC
5887612 TTTTTCTTTCTTTC
1 TTTTTCTTTCTTTC
5887626 TTTTT
1 TTTTT
5887631 TGGTAACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCTTTCTTTC
Found at i:5902943 original size:26 final size:27
Alignment explanation
Indices: 5902893--5902950 Score: 91
Period size: 26 Copynumber: 2.1 Consensus size: 27
5902883 ATGAAATTTG
5902893 TAGGTCACCTAGCTCCACGGCACCATTA
1 TAGGTCACCTAGC-CCACGGCACCATTA
*
5902921 TAGGTCACCTAG-CCACGGCACCATTG
1 TAGGTCACCTAGCCCACGGCACCATTA
5902947 TAGG
1 TAGG
5902951 AGGCGTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 17 0.59
28 12 0.41
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.21
Consensus pattern (27 bp):
TAGGTCACCTAGCCCACGGCACCATTA
Found at i:5903491 original size:31 final size:31
Alignment explanation
Indices: 5903456--5903521 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
5903446 AAAAAAACTT
* *
5903456 AATAGCTCAGTGACTTAAATAAAAACTTTTG
1 AATAGCTCAGCGACTTAAATAAAAACTTTCG
* * *
5903487 AATAGTTTAGCGACTTAAATGAAAACTTTCG
1 AATAGCTCAGCGACTTAAATAAAAACTTTCG
5903518 AATA
1 AATA
5903522 ATTCAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (31 bp):
AATAGCTCAGCGACTTAAATAAAAACTTTCG
Found at i:5904695 original size:16 final size:16
Alignment explanation
Indices: 5904674--5904715 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
5904664 ACAAAAATTA
5904674 AATATAAAATTAATAG
1 AATATAAAATTAATAG
5904690 AATATAAAATTAATAG
1 AATATAAAATTAATAG
5904706 AATATAAAAT
1 AATATAAAAT
5904716 ACAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (16 bp):
AATATAAAATTAATAG
Found at i:5904847 original size:30 final size:30
Alignment explanation
Indices: 5904813--5905162 Score: 228
Period size: 30 Copynumber: 11.8 Consensus size: 30
5904803 ATTTGAGATG
* *
5904813 AAAATGAAATTTTAGAGAAA-TTCGAGGGTC
1 AAAATGTAATTTTAGAGAAAGTT-GAGGGTT
* * *
5904843 AAAATGTGATTTTGAAAAAAAGTTAGAGGGTT
1 AAAATGTAATTTT-AGAGAAAGTT-GAGGGTT
*
5904875 AAAATGTAATTTTA-AGAAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAGAAAGTTGA-GGGTT
* * *
5904905 AAAATGCAATTTTAG-GAAAGTTTAGTGATT
1 AAAATGTAATTTTAGAGAAAGTTGAG-GGTT
* * *
5904935 AAAATGTAATTTTGGA-AAAATT-TGGGTT
1 AAAATGTAATTTTAGAGAAAGTTGAGGGTT
* * * *
5904963 AAAATATGA-TTTGGA-AAAGTTTAAGGGTT
1 AAAATGTAATTTTAGAGAAAG-TTGAGGGTT
* *
5904992 AAAATGTAATTTTGGA-AAAGTTTAGGGATT
1 AAAATGTAATTTTAGAGAAAGTTGAGGG-TT
*
5905022 AAAATGTAATTTTAGA-AAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAGAAAGTTGA-GGGTT
*
5905052 AAAATGTAATTTTAGA-AAGGTTTTG-GGGTT
1 AAAATGTAATTTTAGAGAAAG--TTGAGGGTT
* * * *
5905082 AAAATATGA-TTTGGA-AAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAGAAAGTTGA-GGGTT
*
5905111 AAAATGTAATTTT--AGAAAGATTTAGGGGTT
1 AAAATGTAATTTTAGAGAAAG-TTGA-GGGTT
* *
5905141 AAAATATAATTTTA-AAAAAGTT
1 AAAATGTAATTTTAGAGAAAGTT
5905163 TGGTGACCTT
Statistics
Matches: 266, Mismatches: 35, Indels: 38
0.78 0.10 0.11
Matches are distributed among these distances:
27 11 0.04
28 13 0.05
29 45 0.17
30 161 0.61
31 14 0.05
32 22 0.08
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTAGAGAAAGTTGAGGGTT
Found at i:5905119 original size:59 final size:58
Alignment explanation
Indices: 5904860--5905152 Score: 351
Period size: 60 Copynumber: 5.0 Consensus size: 58
5904850 GATTTTGAAA
**
5904860 AAAAG-TTAGAGGGTTAAAATGTAATTTTAAGAAAGTTTAGGGGTTAAAATGCAATTTTAGG
1 AAAAGTTTAG-GGGTTAAAATGTAATTTT-AGAAAGTTTAGGGGTTAAAATATAA-TTT-GG
* * * * *
5904921 -AAAGTTTAGTGATTAAAATGTAATTTTGGAAAAATTT--GGGTTAAAATATGATTTGG
1 AAAAGTTTAGGGGTTAAAATGTAATTTTAG-AAAGTTTAGGGGTTAAAATATAATTTGG
* * * * *
5904977 AAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGATTAAAATGTAATTTTAG
1 AAAAGTTTAGGGGTTAAAATGTAATTTTAG-AAAGTTTAGGGGTTAAAATATAA-TTTGG
* *
5905037 AAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAGGTTTTGGGGTTAAAATATGATTTGG
1 AAAAGTTTAGGGGTTAAAATGTAATTTTAGAAA-GTTTAGGGGTTAAAATATAATTTGG
5905096 AAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAGATTTAGGGGTTAAAATATAATTT
1 AAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAG-TTTAGGGGTTAAAATATAATTT
5905153 TAAAAAAGTT
Statistics
Matches: 200, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
56 2 0.01
57 36 0.18
58 12 0.06
59 72 0.36
60 74 0.37
61 4 0.02
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (58 bp):
AAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAGTTTAGGGGTTAAAATATAATTTGG
Found at i:5907991 original size:17 final size:19
Alignment explanation
Indices: 5907960--5907999 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5907950 TACAAATAAA
*
5907960 TTTTCATTTCAATTCT-AT
1 TTTTCATATCAATTCTCAT
5907978 TTTTCATATC-ATTCTCAT
1 TTTTCATATCAATTCTCAT
5907996 TTTT
1 TTTT
5908000 GTCCCATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTCATATCAATTCTCAT
Found at i:5913230 original size:6 final size:6
Alignment explanation
Indices: 5913219--5913258 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
5913209 CTTCCCCTTC
* *
5913219 CTCTAA CACTAA CTCTGA CTCTAA CTCTAA CTCTAA CTCT
1 CTCTAA CTCTAA CTCTAA CTCTAA CTCTAA CTCTAA CTCT
5913259 TGTCCTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.33
Consensus pattern (6 bp):
CTCTAA
Found at i:5919297 original size:58 final size:57
Alignment explanation
Indices: 5919232--5919350 Score: 184
Period size: 58 Copynumber: 2.1 Consensus size: 57
5919222 AAAAAAAGTT
* * *
5919232 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTCGGGTTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTATATTTGGG-TTAAAAATATTCAGGTTTA
* *
5919290 GTTTATGAGTATTTTTTAAGAATAAAATTATATTTGGGTTAAAAATATTTAGGTTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTATATTTGGGTTAAAAATATTCAGGTTTA
5919347 GTTT
1 GTTT
5919351 GTTAATGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 21 0.38
58 35 0.62
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (57 bp):
GTTTATGAGTATTATTTAAGAATAAAATTATATTTGGGTTAAAAATATTCAGGTTTA
Found at i:5919364 original size:57 final size:58
Alignment explanation
Indices: 5919246--5919365 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 58
5919236 ATGAGTGTTA
* * * **
5919246 TTTAGGAATAAAATTATATTTGGGTTTAAAAATATTCGGGTTTAGTTTATGAGTATTT
1 TTTAAGAATAAAATTATATTTGGGTTTAAAAATATTCAGGTTTAGTTTATGAATAGGT
* * * *
5919304 TTTAAGAATAAAATTATATTTGGG-TTAAAAATATTTAGGTTTAGTTTGTTAATGGGT
1 TTTAAGAATAAAATTATATTTGGGTTTAAAAATATTCAGGTTTAGTTTATGAATAGGT
5919361 TTTAA
1 TTTAA
5919366 ATATTAGGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
57 30 0.57
58 23 0.43
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (58 bp):
TTTAAGAATAAAATTATATTTGGGTTTAAAAATATTCAGGTTTAGTTTATGAATAGGT
Found at i:5920535 original size:26 final size:26
Alignment explanation
Indices: 5920505--5920559 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
5920495 AATGTAATAT
*
5920505 GTATGATAGATGTCCATATGAACTTA
1 GTATGATAGATGCCCATATGAACTTA
*
5920531 GTATGATAGATGCCCGTATGAACTTA
1 GTATGATAGATGCCCATATGAACTTA
5920557 GTA
1 GTA
5920560 ATAGGTTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (26 bp):
GTATGATAGATGCCCATATGAACTTA
Found at i:5925246 original size:24 final size:23
Alignment explanation
Indices: 5925227--5925286 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
5925217 ATTATTCATC
5925227 TTATATTTTTTTAAT-ATATTA-
1 TTATATTTTTTTAATAATATTAT
* *
5925248 TTATGA-TTATATAATAATATTTAT
1 TTAT-ATTTTTTTAATAATA-TTAT
5925272 TTATATTTTTTTAAT
1 TTATATTTTTTTAAT
5925287 TTTATAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 11 0.37
22 4 0.13
23 4 0.13
24 11 0.37
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTATATTTTTTTAATAATATTAT
Found at i:5926021 original size:34 final size:34
Alignment explanation
Indices: 5925978--5926045 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
5925968 TATTTGACTG
*
5925978 TATCTAAACAGGAGAATGGGGTTGATGGTTATTT
1 TATCTAAACAGGAGAATGGGGTTGACGGTTATTT
5926012 TATCTAAACAGGAGAATGGGGTTGACGGTTATTT
1 TATCTAAACAGGAGAATGGGGTTGACGGTTATTT
5926046 GGTGTCGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.34
Consensus pattern (34 bp):
TATCTAAACAGGAGAATGGGGTTGACGGTTATTT
Found at i:5926468 original size:16 final size:17
Alignment explanation
Indices: 5926437--5926469 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5926427 GAGTCTAAAA
*
5926437 TATTTATTTTTTAATAT
1 TATTTATTTATTAATAT
5926454 TATTT-TTTATTAATAT
1 TATTTATTTATTAATAT
5926470 CAAAATTCAA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATTTATTAATAT
Found at i:5937311 original size:23 final size:23
Alignment explanation
Indices: 5937285--5937330 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5937275 TGATACCAAA
*
5937285 GCACTTTCAAGTCTACCTATAAT
1 GCACTTTCAAGTCTAACTATAAT
* *
5937308 GCACTTTGAAGTTTAACTATAAT
1 GCACTTTCAAGTCTAACTATAAT
5937331 TGCATGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (23 bp):
GCACTTTCAAGTCTAACTATAAT
Found at i:5942332 original size:14 final size:14
Alignment explanation
Indices: 5942313--5942341 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5942303 CGAAAAGGGC
5942313 TACATTACATCCCT
1 TACATTACATCCCT
5942327 TACATTACATCCCT
1 TACATTACATCCCT
5942341 T
1 T
5942342 TCTTATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (14 bp):
TACATTACATCCCT
Found at i:5942864 original size:378 final size:377
Alignment explanation
Indices: 5942027--5943157 Score: 1358
Period size: 378 Copynumber: 3.0 Consensus size: 377
5942017 GATTATTTTT
* * * * *
5942027 TTTTTATTTAGGT-TGCTCTTGTTTGTTATTTGTTATTCTTGACCCTTAATCCTTAGCTGGTTTA
1 TTTTTATCTA-GTCTGCTCTTGTATGTCATTTGTTACTCTTG-CCCTCAATCCTTAGCTGGTTTA
* * * * * *
5942091 TTACGA-TGGCACAAGATGTAAAATTAAATATGTTGCCAAACATTTATATGTTTAACATTTGATA
64 CTACAATTGGCATAAGATGTAAAATTAAATATGTTGCAAAACATTTATATGTTTCACATTTGGTA
* * *
5942155 AATTCAATTTCAAGTAAAGTTTTTTTTTTTATTTGCTAAAAAAATTAATTTTGGAGAATTGACAG
129 AATTCAATTTCAAGTAAAG--TTTCTTTTTATTTG-TTAAAAAATTAATTTTGGAGAATTGACGG
* * * * *
5942220 TTATAGTGTCACTGATCACGTAACGACTGATAGAGAGATTGAATCATAAACAGTCAAGAGTAAAA
191 TTATAATGTCATTGATCACGTAACGACTGAGAGAGAGATTGAGTCATAGACAGTCAAGAGTAAAA
* * * *
5942285 TGACCATAATCACTCTAACGAAAAGGGCTACATTACATCCCTTACATTACATCCCTTTCTTATAT
256 AGACCATAATCACCCTAACGAAAAGGG------------CC--ACATTACATCCCTTTCTTAAAC
* * *
5942350 TGTTAACAATTGCAAATAAGCGATGCTACATGT--TTAGAGAGTTGTTGGCTTATTATTGGATTG
307 TGTCAACAATTGCAAATAAACGATGCTACATGTCATTAGAAAGTTGTTGGCTTATTATTGGATTG
5942413 GTGTCC
372 GTGTCC
* * *
5942419 TTTTTATCTAGTCTGCTCTTGTATGTCATTTGTTACTCTTGCCCCTCAATACTTAACTTGTTTAC
1 TTTTTATCTAGTCTGCTCTTGTATGTCATTTGTTACTCTTG-CCCTCAATCCTTAGCTGGTTTAC
*
5942484 TACAATTGGCATAAAATGTAAAATTAAATATGTTGCAAAACATTTATATGTTTCACATTTGGTAA
65 TACAATTGGCATAAGATGTAAAATTAAATATGTTGCAAAACATTTATATGTTTCACATTTGGTAA
* * ** *
5942549 ATTCAATTTCAAATAAAGTTTCTTTTTATTTGTTAAAATATTAATTTTGGAGACCTGATGGTTAT
130 ATTCAATTTCAAGTAAAGTTTCTTTTTATTTGTTAAAAAATTAATTTTGGAGAATTGACGGTTAT
** * *
5942614 AATGTCATTGATTGCGTAACGACTGAGAGAGAGATTGAGTTACAGACAGTCAAGAGTAAAAAGAC
195 AATGTCATTGATCACGTAACGACTGAGAGAGAGATTGAGTCATAGACAGTCAAGAGTAAAAAGAC
* * **
5942679 CATAATTACCCTAGCGAAAAGGGCCACATTACATCCCTTTCTTAAACTGTCAACAATTGCGGATA
260 CATAATCACCCTAACGAAAAGGGCCACATTACATCCCTTTCTTAAACTGTCAACAATTGCAAATA
** *
5942744 ATTGATGCTACATGTCATTAGAAAGTTGTTGACTTATTATTGGATTGGTGTCC
325 AACGATGCTACATGTCATTAGAAAGTTGTTGGCTTATTATTGGATTGGTGTCC
*
5942797 TTTTTATCTAAG-CTGCTCTTGTATGTCATTTGTTACTCTTGCCTCTCAATCCTTAGCCGGTTTA
1 TTTTTATCT-AGTCTGCTCTTGTATGTCATTTGTTACTCTTGCC-CTCAATCCTTAGCTGGTTTA
** * * * *
5942861 CTACAATTGATATAAGATGTAAAATTAAATATGTTACGAAACATTTATATGTTTCACCTTTTGTA
64 CTACAATTGGCATAAGATGTAAAATTAAATATGTTGCAAAACATTTATATGTTTCACATTTGGTA
* * * *
5942926 AATCCAATTTCAAGTAAAATTTCTTTTTATTTGCTAAAAAATTAATTTGGGAGAATTGACGGTTA
129 AATTCAATTTCAAGTAAAGTTTCTTTTTATTTGTTAAAAAATTAATTTTGGAGAATTGACGGTTA
* * * * *
5942991 TAATGTCATTGATCACGTAATGATTGAGAGAGAGACTG-GATCATAGACA-ACTGAGAGTAAAAA
194 TAATGTCATTGATCACGTAACGACTGAGAGAGAGATTGAG-TCATAGACAGTC-AAGAGTAAAAA
* * * * * * * *
5943054 GATCAAAATCACCCTAAAGAAAAAGGTCACATTATATCCCTTTCTTAGACTGTCAACAATTGAAA
257 GACCATAATCACCCTAACGAAAAGGGCCACATTACATCCCTTTCTTAAACTGTCAACAATTGCAA
*
5943119 ATAAACGATGCTACATGTCATTAGAAAATTGTTGGCTTA
322 ATAAACGATGCTACATGTCATTAGAAAGTTGTTGGCTTA
5943158 GCTATCCATT
Statistics
Matches: 640, Mismatches: 91, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
376 48 0.08
377 4 0.01
378 342 0.53
379 2 0.00
390 102 0.16
391 15 0.02
392 56 0.09
393 71 0.11
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (377 bp):
TTTTTATCTAGTCTGCTCTTGTATGTCATTTGTTACTCTTGCCCTCAATCCTTAGCTGGTTTACT
ACAATTGGCATAAGATGTAAAATTAAATATGTTGCAAAACATTTATATGTTTCACATTTGGTAAA
TTCAATTTCAAGTAAAGTTTCTTTTTATTTGTTAAAAAATTAATTTTGGAGAATTGACGGTTATA
ATGTCATTGATCACGTAACGACTGAGAGAGAGATTGAGTCATAGACAGTCAAGAGTAAAAAGACC
ATAATCACCCTAACGAAAAGGGCCACATTACATCCCTTTCTTAAACTGTCAACAATTGCAAATAA
ACGATGCTACATGTCATTAGAAAGTTGTTGGCTTATTATTGGATTGGTGTCC
Found at i:5943290 original size:6 final size:6
Alignment explanation
Indices: 5943272--5943319 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
5943262 AAACTTTTCT
* *
5943272 TTTAAA GTTTAAA TTTAAA -TTAAA GTTTAAA TTTAAA ATTGAA TTTAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAA
5943320 TTAAATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 5 0.14
6 19 0.54
7 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:5943319 original size:18 final size:18
Alignment explanation
Indices: 5943273--5943308 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5943263 AACTTTTCTT
5943273 TTAAAGTTTAAATTTAAA
1 TTAAAGTTTAAATTTAAA
5943291 TTAAAGTTTAAATTTAAA
1 TTAAAGTTTAAATTTAAA
5943309 ATTGAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TTAAAGTTTAAATTTAAA
Found at i:5943992 original size:19 final size:18
Alignment explanation
Indices: 5943959--5944001 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
5943949 TAAATGGCAT
* *
5943959 TAATAATAATTTTATTAG
1 TAATAATAATATTATTAA
5943977 TAATAATTAATATTATTAA
1 TAATAA-TAATATTATTAA
5943996 TAATAA
1 TAATAA
5944002 CGTCTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAATAATAATATTATTAA
Found at i:5945307 original size:29 final size:28
Alignment explanation
Indices: 5945261--5945434 Score: 201
Period size: 29 Copynumber: 6.1 Consensus size: 28
5945251 ACCCTTTAAC
* *
5945261 CCCT-AAACTTCTCCAAAATTATATTTTAA
1 CCCTAAAACTTC-CAAAAATTACATTTT-A
**
5945290 CCCTAAAACTTTTAAAAATTACATTTTGA
1 CCCTAAAACTTCCAAAAATTACATTTT-A
5945319 CCCTAAAACTTCCAAAAATTACATTTTA
1 CCCTAAAACTTCCAAAAATTACATTTTA
***
5945347 CCCCCGAACTTCCAAAAATTACATTTTTA
1 CCCTAAAACTTCCAAAAATTACA-TTTTA
*
5945376 ACCTCAAAACTTCCAAAAATTACATTTTA
1 CCCT-AAAACTTCCAAAAATTACATTTTA
5945405 CCC--AAACTTCCAAAAATTACATTTTTA
1 CCCTAAAACTTCCAAAAATTACA-TTTTA
5945432 CCC
1 CCC
5945435 CCGAGTGTCC
Statistics
Matches: 126, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
26 18 0.14
27 8 0.06
28 21 0.17
29 56 0.44
30 23 0.18
ACGTcount: A:0.40, C:0.26, G:0.01, T:0.33
Consensus pattern (28 bp):
CCCTAAAACTTCCAAAAATTACATTTTA
Found at i:5945356 original size:28 final size:28
Alignment explanation
Indices: 5945235--5945436 Score: 183
Period size: 29 Copynumber: 7.0 Consensus size: 28
5945225 GTAGGTCCTT
* * * *
5945235 AAACTGTCTAAAAATTACCCTTTAACCCCT
1 AAACT-TCCAAAAATTA-CATTTTACCCCC
* * **
5945265 AAACTTCTCCAAAATTATATTTTAACCCTA
1 AAACTTC-CAAAAATTACATTTT-ACCCCC
** **
5945295 AAACTTTTAAAAATTACATTTTGACCCTA
1 AAACTTCCAAAAATTACATTTT-ACCCCC
5945324 AAACTTCCAAAAATTACATTTTACCCCC
1 AAACTTCCAAAAATTACATTTTACCCCC
* * *
5945352 GAACTTCCAAAAATTACATTTTTAACCTCA
1 AAACTTCCAAAAATTACA-TTTT-ACCCCC
5945382 AAACTTCCAAAAATTACATTTTA--CCC
1 AAACTTCCAAAAATTACATTTTACCCCC
5945408 AAACTTCCAAAAATTACATTTTTACCCCC
1 AAACTTCCAAAAATTACA-TTTTACCCCC
5945437 GAGTGTCCAA
Statistics
Matches: 143, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
26 19 0.13
27 5 0.03
28 22 0.15
29 54 0.38
30 43 0.30
ACGTcount: A:0.40, C:0.26, G:0.01, T:0.33
Consensus pattern (28 bp):
AAACTTCCAAAAATTACATTTTACCCCC
Found at i:5948840 original size:319 final size:316
Alignment explanation
Indices: 5947735--5950160 Score: 2305
Period size: 320 Copynumber: 7.7 Consensus size: 316
5947725 ACATTTGAAT
* * * * * *
5947735 AAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCATGCAACGATTGGGAGAGAAATTG
1 AAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACGACTGAGAGAGAGACTG
* * * * * * **
5947800 GATCACAGACAGTCAAGAGTAAAATGACTATAATCGCCCTAATGAAAAGGGTTACATTACATCCC
66 GACCACAGACAATCGAGAGTAAAAAGACCATAATCGCCCTAGTGAAAAGGGCCACATTACATCCC
* * ** * *
5947865 TTTCTTAGACTGTTAACAATTACAAATAAACGATGCTACATGTTGTTAGAAAGTTGTTAGCTTAG
131 TTTCTTAGACTGTCAACAATTACAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCTTAA
* *
5947930 CTACCCATTGTGTAGCAA--ATATATATATA-----TATGTTGCCATATATTTCCTTAAACATTT
196 CTACCCATTGTGTAGCAATTATATATATATATTTTGTATGTGGCCAAATATTTCCTTAAACATTT
* * *
5947988 ATATGATTCACATTTGGTAAATTCAATTTCAAGTTATGTTTGTTTTATTTGCTAAA
261 ATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTGTTTTATTTGCTAAA
* * * * *
5948044 ATAA-TAATTTTGTAGAATTGACAGTTATAGTGTCACCGATCACGTAACGACTAAGAGAAAGATT
1 A-AATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACGACTGAGAGAGAGACT
* *
5948108 GGACCACAGACAATCGAGAGTAAAAAGACCATAATCACCCTAGTGAAAAGGGCCACATTACAGCC
65 GGACCACAGACAATCGAGAGTAAAAAGACCATAATCGCCCTAGTGAAAAGGGCCACATTACATCC
* * * *
5948173 CTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCAATAGAAAATTGCTGGCTTA
130 CTTTCTTAGACTGTCAACAATTACAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCTTA
* *
5948238 ACTACCCATTGTGTAGCAATTATATATATAATGTGTGTGTGTATGTGGCCAAATATTTCCCTAAA
195 ACTACCCATTGTGTAGCAATTATATATAT-ATAT-T-T-TGTATGTGGCCAAATATTTCCTTAAA
*
5948303 CATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAATGTTTGTTTTATTTGCTAAA
256 CATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTGTTTTATTTGCTAAA
* * * * *
5948364 TAATTAATTTTGGAGAATTAACAGTTATAGTGTCACGGATCACGTAATGACTGTGAGAGAGACTG
1 AAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACGACTGAGAGAGAGACTG
* * * *
5948429 GACCACAGACAGTCGAGAGAAAAAAGATCATAATCACCCTAGTGAAAAGGGCCACATTACATCCC
66 GACCACAGACAATCGAGAGTAAAAAGACCATAATCGCCCTAGTGAAAAGGGCCACATTACATCCC
* * *
5948494 TTTCTTAGACCT-TCAACAATTACAAATAAACGATGCTACATGTCATTAGAAAGCTATTGGCTTA
131 TTTCTTAGA-CTGTCAACAATTACAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCTTA
* * * * *
5948558 ACTGCACATTCTATAGCAATTATATATATAATATGTGTTTGTATGTGGCCAAATATTTCCCTAAA
195 ACTACCCATTGTGTAGCAATTATATATAT-ATA--T-TTTGTATGTGGCCAAATATTTCCTTAAA
* *
5948623 CATTTATATGTTTCACATTTGATAAATTCAATTTCAAGTAAAG-TTCTTTTATTTGCTAAA
256 CATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTGTTTTATTTGCTAAA
* * * *
5948683 AAATTATTTTTGGAGAATTGACAGTTATAGTGTCATTGATCACGTAACGACTGAGACAGAGATTG
1 AAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACGACTGAGAGAGAGACTG
* * *
5948748 AGA-CACAGACAATCGAGAGTAGAAAGACCATTATCGCTCTAGTGAAAAGGGCCACATTACATCC
66 -GACCACAGACAATCGAGAGTAAAAAGACCATAATCGCCCTAGTGAAAAGGGCCACATTACATCC
* * * * * *
5948812 CTTTCTTAGACTGTAAACAATTACAAATAAGCGATGATGCGTGTCATTAAAAAGTTGTTGGATTA
130 CTTTCTTAGACTGTCAACAATTACAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCTTA
* ** * *
5948877 GCTACCCATTACGTAGTAA-T-TATATATATA---TG--T-T-GCCAAGTATTTCCTTAAACATT
195 ACTACCCATTGTGTAGCAATTATATATATATATTTTGTATGTGGCCAAATATTTCCTTAAACATT
* * * * * *
5948933 TATATGTTTCACAATTGATAAATTTAATTTCAAGTAAAATTTATTTTTATTTGCAAAA
260 TATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTT-GTTTTATTTGCTAAA
* * ** * * * * * * *
5948991 AAATTAATTTTGAAAAATTGATGGTTACAATTTCATTGATCACGTAA-TAATGGAAAGAGAGACT
1 AAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACGACT-GAGAGAGAGACT
* ** ** * * * * * *
5949055 AGACTTCAGACAGGCGAGAGTAAAAAGATCATAATCGGCCTAGTAAAAAGGGCTACATAACGTCC
65 GGACCACAGACAATCGAGAGTAAAAAGACCATAATCGCCCTAGTGAAAAGGGCCACATTACATCC
* * * * * * *
5949120 ATTTCTTAGATTGTCAACCATTACAAATAAGCGATGCTACATATCAATAAAAAATTGTTGGCTTA
130 CTTTCTTAGACTGTCAACAATTACAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCTTA
* *
5949185 GCTACCCATTGTGTAG----TA-AT-TATATA-----TAT-T-GCGAAATATTTCCTTAAACATT
195 ACTACCCATTGTGTAGCAATTATATATATATATTTTGTATGTGGCCAAATATTTCCTTAAACATT
* *
5949237 TATATGTTTCACATTTGGTAAATTCAATTTCAATTAATGTTTGTTTTATTTGCTAAA
260 TATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTGTTTTATTTGCTAAA
* * * ** *
5949294 AAATTAATTTTGAAGAATTGACAATTATAATGTCACTGATCACGTAATAATTGAGAGAGAGACTG
1 AAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACGACTGAGAGAGAGACTG
* * * * * * *
5949359 GATCATAGA-TAGCGGAGAGTAAAAAGACCATAATTGCCCTAATGAAAAGGCCCACATTACATCC
66 GACCACAGACAATC-GAGAGTAAAAAGACCATAATCGCCCTAGTGAAAAGGGCCACATTACATCC
* * * *
5949423 TTTTCTTAGAGTGTCAACAATTGCAAATAAGTGATGCTACATGTCATTAGAAAGTTGTTGGCTTA
130 CTTTCTTAGACTGTCAACAATTACAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCTTA
* *****
5949488 ACTACCCATTGTGTAGCAATTATATATATATATATATATTATATATGTGTGTGTGTGTATGTGT-
195 ACTACCCATTGTGTAGC-A--AT-TATATATATATAT-TT-TGTATGTG-G-CCAAATAT-T-TC
* *** ** * * * * * * * * *
5949552 ATGTGGCCAAATATTTCTTTAAACATCTATATGTTTCACATTTGTTAAATTCAATTTCAAGTAAA
250 CT-TAAACATTTATATGTTT---CA-C-ATTTG-GT-A-A-AT-TCAATTTCAA-GTAAAGT---
* *
5949617 GTTTTTTTTATTTGCTAAA
300 TTGT--TTTATTTGCTAAA
* * * *
5949636 AAATTAATTTTGAAGAATTGACAGTTATAGTATCACTGATCACGTAACAATTGAGAGAGAGACTG
1 AAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACGACTGAGAGAGAGACTG
* * * * * * *
5949701 GACCACA-AGCAATCGGGAGTAAAAAAATCATAATCGCCGTAGCGAAAATGGCTACATTACAT-C
66 GACCACAGA-CAATCGAGAGTAAAAAGACCATAATCGCCCTAGTGAAAAGGGCCACATTACATCC
* * * *
5949764 CTTGTCTTAGATTGTCAACAATTGCAAATAAGCGATGTTCCATGTCATTAGAAAGTTGTTGGCTT
130 CTT-TCTTAGACTGTCAACAATTACAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCTT
* * * * *
5949829 AATTACCCATTGTGTAACAATTATATTTTTATATCTATGTATATGTGGCCAAATATTTCCTTAAA
194 AACTACCCATTGTGTAGCAATTATATATATATAT-T-T-TGTATGTGGCCAAATATTTCCTTAAA
* * *
5949894 CATTTATATGTTTCACATGTGGTAAATTCAATTTCAAGTAAAATATT-TTTTATTTGCAAAA
256 CATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGT-TTGTTTTATTTGCTAAA
* * * * * *
5949955 AAAATAATTTTGGAAAATTGACA---AT-TTGTCACTAATTACGTAACGACTATGAAAGAGAGAC
1 AAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACGAC--TGAGAGAGAGAC
* * * * * ** *
5950016 TGAACCACAAACAGTCAAGAGTAAAAAGATCATAATCGCCCTAACGAAAACGGCCACATTACAAT
64 TGGACCACAGACAATCGAGAGTAAAAAGACCATAATCGCCCTAGTGAAAAGGGCCACATTAC-AT
* * * * * *
5950081 -CCTTTCTTAGAGTGTCAACAATTGCAAATAAACGATGTTCCATGTCATTAGAAAATTGTTGGCT
128 CCCTTTCTTAGACTGTCAACAATTACAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCT
5950145 TAAC-ACCCATTGTGTA
193 TAACTACCCATTGTGTA
5950161 ACAAGTGCTT
Statistics
Matches: 1756, Mismatches: 285, Indels: 145
0.80 0.13 0.07
Matches are distributed among these distances:
302 2 0.00
303 181 0.10
304 66 0.04
305 3 0.00
306 56 0.03
307 7 0.00
308 178 0.10
309 181 0.10
310 4 0.00
311 10 0.01
312 4 0.00
313 6 0.00
315 16 0.01
316 17 0.01
317 129 0.07
318 10 0.01
319 225 0.13
320 348 0.20
321 5 0.00
322 5 0.00
323 1 0.00
324 7 0.00
325 10 0.01
326 12 0.01
327 1 0.00
328 1 0.00
329 3 0.00
330 5 0.00
331 5 0.00
332 3 0.00
333 1 0.00
334 1 0.00
335 12 0.01
336 10 0.01
337 8 0.00
338 13 0.01
339 11 0.01
340 2 0.00
341 5 0.00
342 190 0.11
343 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (316 bp):
AAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACGACTGAGAGAGAGACTG
GACCACAGACAATCGAGAGTAAAAAGACCATAATCGCCCTAGTGAAAAGGGCCACATTACATCCC
TTTCTTAGACTGTCAACAATTACAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCTTAA
CTACCCATTGTGTAGCAATTATATATATATATTTTGTATGTGGCCAAATATTTCCTTAAACATTT
ATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTGTTTTATTTGCTAAA
Found at i:5949843 original size:342 final size:315
Alignment explanation
Indices: 5949545--5950164 Score: 879
Period size: 317 Copynumber: 2.0 Consensus size: 315
5949535 TGTGTGTGTG
* * * *
5949545 TATGTGTATGTGGCCAAATATTTCTTTAAACATCTATATGTTTCACATTTGTTAAATTCAATTTC
1 TATGTATATGTGGCCAAATATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTC
*
5949610 AAGTAAAGTTTTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGACAGTTATAGTATCACTGA
66 AAGTAAAGTTTTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGACAATTATAGT-TCACTGA
* *
5949675 TCACGTAACAATTGAGAGAGAGACTGGACCACAAGCAATCGGGAGTAAAAAAATCATAATCGCCG
130 TCACGTAACAATTGAGAGAGAGACTGGACCACAAGCAATCGGGAGTAAAAAGATCATAATCGCCC
* * *
5949740 TAGCGAAAATGGCTACATTACATCCTTGTCTTAGATTGTCAACAATTGCAAATAAGCGATGTTCC
195 TAACGAAAA-GGCCACATTACATCCTT-TCTTAGAGTGTCAACAATTGCAAATAAGCGATGTTCC
*
5949805 ATGTCATTAGAAAGTTGTTGGCTTAATTACCCATTGTGTAACAATTATATTTTTATATC
258 ATGTCATTAGAAAGTTGTTGGCTTAA-TACCCATTGTGTAACAATTATATTTTTATATA
*
5949864 TATGTATATGTGGCCAAATATTTCCTTAAACATTTATATGTTTCACATGTGGTAAATTCAATTTC
1 TATGTATATGTGGCCAAATATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTC
* * * * *
5949929 AAGTAAAATATTTTTTATTTGCAAAAAAAATAATTTTGGAA-AATTGACAATT-T-G-TCACTAA
66 AAGTAAAGTTTTTTTTATTTGCTAAAAAATTAATTTT-GAAGAATTGACAATTATAGTTCACTGA
* * * * * * **
5949990 TTACGTAACGACTATGAAAGAGAGACTGAACCACAAACAGTCAAGAGTAAAAAGATCATAATCGC
130 TCACGTAAC-AAT-TGAGAGAGAGACTGGACCACAAGCAATCGGGAGTAAAAAGATCATAATCGC
*
5950055 CCTAACGAAAACGGCCACATTACAATCCTTTCTTAGAGTGTCAACAATTGCAAATAAACGATGTT
193 CCTAACGAAAA-GGCCACATTAC-ATCCTTTCTTAGAGTGTCAACAATTGCAAATAAGCGATGTT
* *
5950120 CCATGTCATTAGAAAATTGTTGGCTTAACACCCATTGTGTAACAA
256 CCATGTCATTAGAAAGTTGTTGGCTTAATACCCATTGTGTAACAA
5950165 GTGCTTGAGT
Statistics
Matches: 269, Mismatches: 28, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
315 14 0.05
316 18 0.07
317 124 0.46
318 7 0.03
319 103 0.38
320 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (315 bp):
TATGTATATGTGGCCAAATATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTC
AAGTAAAGTTTTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGACAATTATAGTTCACTGAT
CACGTAACAATTGAGAGAGAGACTGGACCACAAGCAATCGGGAGTAAAAAGATCATAATCGCCCT
AACGAAAAGGCCACATTACATCCTTTCTTAGAGTGTCAACAATTGCAAATAAGCGATGTTCCATG
TCATTAGAAAGTTGTTGGCTTAATACCCATTGTGTAACAATTATATTTTTATATA
Found at i:5953865 original size:20 final size:18
Alignment explanation
Indices: 5953829--5953878 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 18
5953819 AAATTATAAA
5953829 AATAAAAATCAATAATTGTT
1 AATAAAAAT-AATAATT-TT
5953849 -ATAAAAATAATTAAATTTT
1 AATAAAAATAA-T-AATTTT
5953868 AATAAAAATAA
1 AATAAAAATAA
5953879 AAAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
20 14 0.52
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
AATAAAAATAATAATTTT
Found at i:5953883 original size:19 final size:19
Alignment explanation
Indices: 5953829--5953888 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
5953819 AAATTATAAA
* *
5953829 AATAAAAATCAATAATTGTT
1 AATAAAAATAAAAAATT-TT
*
5953849 -ATAAAAATAATTAAATTTT
1 AATAAAAATAA-AAAATTTT
*
5953868 AATAAAAATAAAAAATATT
1 AATAAAAATAAAAAATTTT
5953887 AA
1 AA
5953889 AAATTAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AATAAAAATAAAAAATTTT
Found at i:5953919 original size:20 final size:20
Alignment explanation
Indices: 5953877--5953920 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5953867 TAATAAAAAT
* *
5953877 AAAAAATATTAAAAATTAGA
1 AAAAAATATGAAAAAGTAGA
5953897 AAAAAATATGAAGAAAGTA-A
1 AAAAAATATGAA-AAAGTAGA
5953917 AAAA
1 AAAA
5953921 TTATAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (20 bp):
AAAAAATATGAAAAAGTAGA
Found at i:5954145 original size:10 final size:9
Alignment explanation
Indices: 5954126--5954235 Score: 68
Period size: 9 Copynumber: 12.0 Consensus size: 9
5954116 TTTTGGTACG
5954126 ATAATTTTT
1 ATAATTTTT
5954135 ATAATTTTTT
1 ATAA-TTTTT
5954145 ATGAA-TTTT
1 AT-AATTTTT
5954154 AT-ATTTTT
1 ATAATTTTT
* *
5954162 ACATTTTTT
1 ATAATTTTT
5954171 ATAATTTTT
1 ATAATTTTT
*
5954180 -TACGA-CTTT
1 ATA--ATTTTT
5954189 ATAAATTTTT
1 AT-AATTTTT
5954199 ATAATTTTT
1 ATAATTTTT
* *
5954208 TTATATTTCT
1 ATA-ATTTTT
5954218 AT-ATGTTTT
1 ATAAT-TTTT
*
5954227 ATGATTTTT
1 ATAATTTTT
5954236 CTAAAATTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
7 1 0.01
8 9 0.11
9 44 0.56
10 22 0.28
11 3 0.04
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5954151 original size:11 final size:10
Alignment explanation
Indices: 5954126--5954208 Score: 56
Period size: 10 Copynumber: 9.0 Consensus size: 10
5954116 TTTTGGTACG
5954126 ATAA-TTTTT
1 ATAATTTTTT
5954135 ATAATTTTTT
1 ATAATTTTTT
5954145 ATGAA--TTTT
1 AT-AATTTTTT
5954154 AT-A-TTTTT
1 ATAATTTTTT
*
5954162 A-CATTTTTT
1 ATAATTTTTT
5954171 ATAATTTTTT
1 ATAATTTTTT
** *
5954181 ACGA--CTTT
1 ATAATTTTTT
*
5954189 ATAAATTTTT
1 ATAATTTTTT
5954199 ATAATTTTTT
1 ATAATTTTTT
5954209 TATATTTCTA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
7 1 0.02
8 11 0.19
9 16 0.28
10 28 0.48
11 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:5954175 original size:36 final size:38
Alignment explanation
Indices: 5954126--5954208 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 38
5954116 TTTTGGTACG
* *
5954126 ATAA-TTTTTATAATTTTTTATGAATTT-TATATTTTT
1 ATAATTTTTTATAATTTTTTACGAATTTATAAATTTTT
* *
5954162 A-CATTTTTTATAATTTTTTACGACTTTATAAATTTTT
1 ATAATTTTTTATAATTTTTTACGAATTTATAAATTTTT
5954199 ATAATTTTTT
1 ATAATTTTTT
5954209 TATATTTCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
35 1 0.03
36 22 0.56
37 9 0.23
38 7 0.18
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (38 bp):
ATAATTTTTTATAATTTTTTACGAATTTATAAATTTTT
Found at i:5954226 original size:28 final size:27
Alignment explanation
Indices: 5954150--5954235 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
5954140 TTTTTATGAA
* *
5954150 TTTTATATTTTTACATTTTTTATAA-TT
1 TTTTATATTTATA-AATTTTTATAATTT
*
5954177 TTTTACGACTTTATAAATTTTTATAATTT
1 TTTTA-TA-TTTATAAATTTTTATAATTT
* * *
5954206 TTTTATATTTCTATATGTTTTATGATTT
1 TTTTATATTTATAAAT-TTTTATAATTT
5954234 TT
1 TT
5954236 CTAAAATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
27 12 0.25
28 24 0.50
29 12 0.25
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (27 bp):
TTTTATATTTATAAATTTTTATAATTT
Found at i:5956105 original size:23 final size:23
Alignment explanation
Indices: 5956076--5956122 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5956066 TTATGACAAT
5956076 TTTATGCAACATAGTTTAAAATA
1 TTTATGCAACATAGTTTAAAATA
5956099 TTTATGCAACATAGTTTAAAATA
1 TTTATGCAACATAGTTTAAAATA
5956122 T
1 T
5956123 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (23 bp):
TTTATGCAACATAGTTTAAAATA
Found at i:5960843 original size:18 final size:18
Alignment explanation
Indices: 5960820--5960856 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5960810 TTTGTGATCA
5960820 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
5960838 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
5960856 A
1 A
5960857 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:5965110 original size:53 final size:53
Alignment explanation
Indices: 5965030--5965133 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 53
5965020 GACTTGATTC
*
5965030 TGATAAGAAAACACCTAAATCCACTCAATTACTTAAGATAAAATTGTGTGATA
1 TGATAAGAAAACACCTAAATCCACTCAATCACTTAAGATAAAATTGTGTGATA
* * * *
5965083 TGATAAGAAAACACGTAGATTCGCTCAATCACTTAAGATAAAATTGTGTGA
1 TGATAAGAAAACACCTAAATCCACTCAATCACTTAAGATAAAATTGTGTGA
5965134 GAAATTGACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.28
Consensus pattern (53 bp):
TGATAAGAAAACACCTAAATCCACTCAATCACTTAAGATAAAATTGTGTGATA
Found at i:5973863 original size:6 final size:6
Alignment explanation
Indices: 5973838--5973876 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5973828 ACAATTCATA
* * *
5973838 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
5973877 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:5973897 original size:21 final size:21
Alignment explanation
Indices: 5973871--5973919 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
5973861 TTCACTTTCA
5973871 CTTTCAATTTTGATCACAAAT
1 CTTTCAATTTTGATCACAAAT
5973892 CTTTCAATTTTGATCACAAAT
1 CTTTCAATTTTGATCACAAAT
*
5973913 CATTCAA
1 CTTTCAA
5973920 ATTCAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (21 bp):
CTTTCAATTTTGATCACAAAT
Found at i:5977091 original size:16 final size:16
Alignment explanation
Indices: 5977070--5977129 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
5977060 TATAAAAGAA
5977070 AAAATATTAGAAAATT
1 AAAATATTAGAAAATT
* *
5977086 AAAATATTATCTTAAAAAT
1 AAAATATTA---GAAAATT
5977105 AAAATATTAGAAAATT
1 AAAATATTAGAAAATT
5977121 AAAATATTA
1 AAAATATTA
5977130 TCTTAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
16 23 0.62
19 14 0.38
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (16 bp):
AAAATATTAGAAAATT
Found at i:5977107 original size:19 final size:19
Alignment explanation
Indices: 5977080--5977144 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
5977070 AAAATATTAG
*
5977080 AAAATTAAAATATTATCTT
1 AAAAATAAAATATTATCTT
*
5977099 AAAAATAAAATATTA---G
1 AAAAATAAAATATTATCTT
*
5977115 AAAATTAAAATATTATCTT
1 AAAAATAAAATATTATCTT
*
5977134 AATAA-AAAATA
1 AAAAATAAAATA
5977145 AAAATATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
16 14 0.38
18 6 0.16
19 17 0.46
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAATAAAATATTATCTT
Found at i:5977109 original size:35 final size:34
Alignment explanation
Indices: 5977068--5977144 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 34
5977058 CATATAAAAG
5977068 AAAAAATATTAGAAAATTAAAATATTATCTTAAA
1 AAAAAATATTAGAAAATTAAAATATTATCTTAAA
*
5977102 AATAAAATATTAGAAAATTAAAATATTATCTTAAT
1 AA-AAAATATTAGAAAATTAAAATATTATCTTAAA
5977137 AAAAAATA
1 AAAAAATA
5977145 AAAATATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 8 0.20
35 33 0.80
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (34 bp):
AAAAAATATTAGAAAATTAAAATATTATCTTAAA
Found at i:5978835 original size:18 final size:19
Alignment explanation
Indices: 5978814--5978855 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
5978804 ATATTTTAAA
5978814 CAAATTTAAT-TTTTTATT
1 CAAATTTAATATTTTTATT
5978832 CAAATTTAATATTTTTATT
1 CAAATTTAATATTTTTATT
*
5978851 TAAAT
1 CAAAT
5978856 CTTCTGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
CAAATTTAATATTTTTATT
Found at i:5979196 original size:6 final size:5
Alignment explanation
Indices: 5979158--5979217 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
5979148 ATACGATGCA
* ** * *
5979158 TTTAT TTTAT TTTAT TTTAT ATTAT AATAT TATTAT TATAT TTAAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT
5979209 TATTAT TTT
1 T-TTAT TTT
5979218 TTTATATTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
5 36 0.80
6 9 0.20
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (5 bp):
TTTAT
Found at i:5979199 original size:26 final size:23
Alignment explanation
Indices: 5979159--5979226 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 23
5979149 TACGATGCAT
5979159 TTATT-TTATTTTATTTTATATTA
1 TTATTATTA-TTTATTTTATATTA
5979182 TAATATTATTA-TTATATTTA-ATT-
1 T--TATTATTATTTAT-TTTATATTA
5979205 TTATTATTATTT-TTTTATATTA
1 TTATTATTATTTATTTTATATTA
5979227 ATTACAAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
20 4 0.11
21 12 0.32
22 2 0.05
23 2 0.05
24 7 0.18
25 8 0.21
26 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTATTATTATTTATTTTATATTA
Found at i:5979203 original size:18 final size:19
Alignment explanation
Indices: 5979169--5979214 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
5979159 TTATTTTATT
5979169 TTATT-TTATATTATAATA
1 TTATTATTATATTATAATA
*
5979187 TTATTATTATATT-TAATT
1 TTATTATTATATTATAATA
5979205 TTATTATTAT
1 TTATTATTAT
5979215 TTTTTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTATTATATTATAATA
Found at i:5987627 original size:20 final size:21
Alignment explanation
Indices: 5987602--5987657 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
5987592 AAATATAAAA
5987602 TTTGAATTTTTTATAAA-TAT
1 TTTGAATTTTTTATAAATTAT
* *
5987622 TTTGAAATTTTGA-AAATTAT
1 TTTGAATTTTTTATAAATTAT
5987642 TTTG-ATTATTTTATAA
1 TTTGAATT-TTTTATAA
5987658 TTTTGCTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 5 0.17
20 22 0.76
21 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTGAATTTTTTATAAATTAT
Found at i:5990575 original size:3 final size:3
Alignment explanation
Indices: 5990567--5990615 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
5990557 GGGTCTTTTA
5990567 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5990615 T
1 T
5990616 GTAAATTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5994249 original size:7 final size:7
Alignment explanation
Indices: 5994234--5994290 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
5994224 TATATTTTTA
*
5994234 TTAAGAT
1 TTAATAT
5994241 TTAATAT
1 TTAATAT
5994248 TTAATAT
1 TTAATAT
5994255 TTAATA-
1 TTAATAT
*
5994261 -TATTAT
1 TTAATAT
*
5994267 TTATTAT
1 TTAATAT
5994274 TTAA-AT
1 TTAATAT
*
5994280 TT-GTAT
1 TTAATAT
5994286 TTAAT
1 TTAAT
5994291 TTATGTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 4 0.10
6 8 0.20
7 29 0.71
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (7 bp):
TTAATAT
Found at i:5994267 original size:19 final size:19
Alignment explanation
Indices: 5994245--5994290 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5994235 TAAGATTTAA
5994245 TATTTAATATTTAATATAT-
1 TATTTAATATTTAA-ATATG
* *
5994264 TATTTATTATTTAAATTTG
1 TATTTAATATTTAAATATG
5994283 TATTTAAT
1 TATTTAAT
5994291 TTATGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTAATATTTAAATATG
Found at i:5996635 original size:21 final size:21
Alignment explanation
Indices: 5996610--5996673 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
5996600 AAATTTCAGT
* *
5996610 AGCAATCTATAGATTTCCAAA
1 AGCAATCTGTAGATTTTCAAA
* *
5996631 AGCAAACTGCAGATTTTCAAA
1 AGCAATCTGTAGATTTTCAAA
5996652 AGCAAAT-TGTAGATTTTCAAA
1 AGC-AATCTGTAGATTTTCAAA
5996673 A
1 A
5996674 TAAAACTGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (21 bp):
AGCAATCTGTAGATTTTCAAA
Found at i:6008607 original size:35 final size:35
Alignment explanation
Indices: 6008561--6008627 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
6008551 GGTTGCTCGA
*
6008561 TAAATGGTTAATTATAAAATGTGTTTTATTTTCGG
1 TAAATGGTTAATTATAAAATGTGTTTCATTTTCGG
6008596 TAAATGGTTAATTATAAAATGTGTTTCATTTT
1 TAAATGGTTAATTATAAAATGTGTTTCATTTT
6008628 TTTAGTGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (35 bp):
TAAATGGTTAATTATAAAATGTGTTTCATTTTCGG
Found at i:6021240 original size:20 final size:20
Alignment explanation
Indices: 6021215--6021255 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6021205 TGCCATTGAG
6021215 AATCATCTTCATATGATTAT
1 AATCATCTTCATATGATTAT
*
6021235 AATCATCTTCGTATGATTAT
1 AATCATCTTCATATGATTAT
6021255 A
1 A
6021256 GATTATTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (20 bp):
AATCATCTTCATATGATTAT
Found at i:6028962 original size:7 final size:7
Alignment explanation
Indices: 6028952--6028982 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
6028942 CCATGGCCAT
6028952 TGGCAAA
1 TGGCAAA
6028959 TGGCAAA
1 TGGCAAA
6028966 TGGCAAA
1 TGGCAAA
6028973 TGGCAAA
1 TGGCAAA
6028980 TGG
1 TGG
6028983 ACTGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.32, T:0.16
Consensus pattern (7 bp):
TGGCAAA
Found at i:6030418 original size:44 final size:44
Alignment explanation
Indices: 6030355--6030444 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
6030345 GAGATAAGCG
6030355 ATCAAGTGGTTTAATAGATAAATGTCTTTGTATTATTTTATTTT
1 ATCAAGTGGTTTAATAGATAAATGTCTTTGTATTATTTTATTTT
6030399 ATCAAGTGGTTTAATAGATAAATGTCTTTGTATTATTTTATTTT
1 ATCAAGTGGTTTAATAGATAAATGTCTTTGTATTATTTTATTTT
6030443 AT
1 AT
6030445 ATTAAGTGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.52
Consensus pattern (44 bp):
ATCAAGTGGTTTAATAGATAAATGTCTTTGTATTATTTTATTTT
Found at i:6033953 original size:42 final size:42
Alignment explanation
Indices: 6033894--6033980 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
6033884 ACATTTGAAC
6033894 TAAACAACCGATTGTCCTAATTCATTCCAAAAGTATTTTTAG
1 TAAACAACCGATTGTCCTAATTCATTCCAAAAGTATTTTTAG
6033936 TAAACAACCGATTGTCCTAATTCATTCCAAAAGTATTTTTAG
1 TAAACAACCGATTGTCCTAATTCATTCCAAAAGTATTTTTAG
6033978 TAA
1 TAA
6033981 GTTTATATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (42 bp):
TAAACAACCGATTGTCCTAATTCATTCCAAAAGTATTTTTAG
Found at i:6034223 original size:10 final size:11
Alignment explanation
Indices: 6034203--6034252 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 11
6034193 TATTTTGTAA
6034203 ATATATTTATTT
1 ATAT-TTTATTT
*
6034215 AT-TTTTATTA
1 ATATTTTATTT
6034225 AT-TTTTATTTT
1 ATATTTTA-TTT
6034236 ATATTTT-TTT
1 ATATTTTATTT
6034246 ATATTTT
1 ATATTTT
6034253 TCAAAATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 23 0.68
11 5 0.15
12 6 0.18
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATATTTTATTT
Found at i:6034250 original size:17 final size:17
Alignment explanation
Indices: 6034204--6034252 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 17
6034194 ATTTTGTAAA
*
6034204 TATATTTATTTAT-TTT
1 TATATTTTTTTATATTT
**
6034220 TAT-TAATTTT-TATTT
1 TATATTTTTTTATATTT
6034235 TATATTTTTTTATATTT
1 TATATTTTTTTATATTT
6034252 T
1 T
6034253 TCAAAATAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
14 1 0.04
15 10 0.40
16 8 0.32
17 6 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TATATTTTTTTATATTT
Found at i:6034699 original size:17 final size:18
Alignment explanation
Indices: 6034667--6034700 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6034657 AAATTTAAAC
*
6034667 TTTTAAATATTAAAATAA
1 TTTTAAATAATAAAATAA
6034685 TTTTAAA-AATAAAATA
1 TTTTAAATAATAAAATA
6034701 CAAGTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTTAAATAATAAAATAA
Found at i:6034828 original size:30 final size:29
Alignment explanation
Indices: 6034794--6034850 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
6034784 TATTCTCTTA
*
6034794 TTTAAAGATTA-AAAAAAAACTATAAATAAT
1 TTTAAACATTATAAAAAAAA-TA-AAATAAT
*
6034824 TTTAAACATTATATAAAAAATAAAATA
1 TTTAAACATTATAAAAAAAATAAAATA
6034851 CAAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 12 0.50
31 7 0.29
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (29 bp):
TTTAAACATTATAAAAAAAATAAAATAAT
Found at i:6038244 original size:21 final size:21
Alignment explanation
Indices: 6038218--6038277 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
6038208 AAAATTCAAA
6038218 AAAAATTATAAAAATTACTTT
1 AAAAATTATAAAAATTACTTT
*
6038239 AAAAATTA-AAAATCATTATTTT
1 AAAAATTATAAAA--ATTACTTT
*
6038261 ACAAAA-AATAAAAATTA
1 A-AAAATTATAAAAATTA
6038278 TAATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 4 0.12
21 12 0.36
22 9 0.27
23 8 0.24
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATTATAAAAATTACTTT
Found at i:6038256 original size:22 final size:22
Alignment explanation
Indices: 6038217--6038275 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
6038207 TAAAATTCAA
6038217 AAAAAATTATAAAA-ATTACTTT
1 AAAAAATTA-AAAATATTACTTT
*
6038239 -AAAAATTAAAAATCATTATTTT
1 AAAAAATTAAAAAT-ATTACTTT
*
6038261 ACAAAAAATAAAAAT
1 A-AAAAATTAAAAAT
6038276 TATAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 4 0.13
21 8 0.26
22 7 0.23
24 12 0.39
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAAATTAAAAATATTACTTT
Found at i:6041025 original size:21 final size:21
Alignment explanation
Indices: 6040999--6041045 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6040989 AATTTTCAAT
6040999 AATTTTT-ATAATTATTTATA
1 AATTTTTAATAATTATTTATA
* * *
6041019 AATTTTTAATATTTTTTTATG
1 AATTTTTAATAATTATTTATA
6041040 AATTTT
1 AATTTT
6041046 ATAGTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
AATTTTTAATAATTATTTATA
Found at i:6041143 original size:31 final size:31
Alignment explanation
Indices: 6041103--6041180 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
6041093 TTACTTAAAT
*
6041103 AATCAATTAAACTCTCATAAAATAATAAAAA
1 AATCAATTAAACCCTCATAAAATAATAAAAA
** * * *
6041134 TTTCAATTAAGCCCTCGTAAAATGATAAAAA
1 AATCAATTAAACCCTCATAAAATAATAAAAA
*
6041165 AATCAATTAAGCCCTC
1 AATCAATTAAACCCTC
6041181 CACATCATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (31 bp):
AATCAATTAAACCCTCATAAAATAATAAAAA
Found at i:6052264 original size:43 final size:43
Alignment explanation
Indices: 6052203--6052288 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
6052193 ATTCTACTTT
*
6052203 GGCAGATGGATTTATTTACTTGTCATTTTCATAGTGGAACATA
1 GGCAGATGGATTTATTTACTTGTCACTTTCATAGTGGAACATA
6052246 GGCAGATGGATTTATTTACTTGTCACTTTCATAGTGGAACATA
1 GGCAGATGGATTTATTTACTTGTCACTTTCATAGTGGAACATA
6052289 CATTAACCCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (43 bp):
GGCAGATGGATTTATTTACTTGTCACTTTCATAGTGGAACATA
Found at i:6055013 original size:26 final size:26
Alignment explanation
Indices: 6054983--6055034 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6054973 ATTTACTTAA
6054983 TCTTATTCATTATAATGTGTAAAAAT
1 TCTTATTCATTATAATGTGTAAAAAT
6055009 TCTTATTCATTATAATGTGTAAAAAT
1 TCTTATTCATTATAATGTGTAAAAAT
6055035 AGTAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (26 bp):
TCTTATTCATTATAATGTGTAAAAAT
Found at i:6060156 original size:29 final size:28
Alignment explanation
Indices: 6060124--6060566 Score: 180
Period size: 29 Copynumber: 15.2 Consensus size: 28
6060114 AAATGGTAAT
6060124 TTTTGGTGAAATCGGGGTTGAAAAAGGAA
1 TTTTGGTGAAATCGGGGTT-AAAAAGGAA
* * * *
6060153 TTTTGG-AAAATTTAGGGG-T-AAATGGTAC
1 TTTTGGTGAAA--TCGGGGTTAAAAAGG-AA
6060181 TTTTGGTGAAATCGGGGTTAAAAATGGAA
1 TTTTGGTGAAATCGGGGTTAAAAA-GGAA
* * * *
6060210 TTTTGG-GAAGTTTGGGG-TAAAATGGTCA
1 TTTTGGTGAA-ATCGGGGTTAAAAAGG-AA
6060238 TTTTGGTGAAATCGGGGTTAAAAATGGAA
1 TTTTGGTGAAATCGGGGTTAAAAA-GGAA
* * * *
6060267 TTTTGG-GAATTTTAGGGG-TAAAATGGTATT
1 TTTTGGTGAA--ATCGGGGTTAAAAAGG-A-A
**
6060297 TTTTGGTGAAATCGCAGTTAAAAATGGAA
1 TTTTGGTGAAATCGGGGTTAAAAA-GGAA
* * * *
6060326 TCTT-G-GAAAGTTTGAGGG-TAAAATGGTCA
1 TTTTGGTGAAA--TCG-GGGTTAAAAAGG-AA
*
6060355 TTTTGGTGAAATCGGGATTAAAAATGGAA
1 TTTTGGTGAAATCGGGGTTAAAAA-GGAA
* ** *
6060384 TTTTGG-GAAGTTTAAGGG-TAAAATGGTAA
1 TTTTGGTGAA--ATCGGGGTTAAAAAGG-AA
*
6060413 TTTTTGGTGAAGTCGGGGTTAAAAATGGAA
1 -TTTTGGTGAAATCGGGGTTAAAAA-GGAA
* * *
6060443 TTTT--AGAAAGTTCAGGGG-TAAAATGGTCAT
1 TTTTGGTGAAA--TC-GGGGTTAAAAAGG--AA
*
6060473 TTTTGGTGAAATCGAGGTTAAAAATGGAA
1 TTTTGGTGAAATCGGGGTTAAAAA-GGAA
* * * *
6060502 TTTTGG-GAAGTTTGGGGGTAAAATGGTAA
1 TTTTGGTGAA-ATCGGGGTTAAAAAGG-AA
*
6060531 TTTTTGGTGAAGTCGGGGTTAAAAATGGAA
1 -TTTTGGTGAAATCGGGGTTAAAAA-GGAA
6060561 TTTTGG
1 TTTTGG
6060567 AAGTTCGGGG
Statistics
Matches: 303, Mismatches: 63, Indels: 96
0.66 0.14 0.21
Matches are distributed among these distances:
27 19 0.06
28 53 0.17
29 126 0.42
30 80 0.26
31 21 0.07
32 4 0.01
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (28 bp):
TTTTGGTGAAATCGGGGTTAAAAAGGAA
Found at i:6060176 original size:58 final size:59
Alignment explanation
Indices: 6060113--6060595 Score: 685
Period size: 59 Copynumber: 8.3 Consensus size: 59
6060103 TTGCGATGGC
* *
6060113 AAAATGGTAATTTTTGGTGAAATCGGGGTTGAAAAA-GGAATTTTGGAAAATTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAAATGGAATTTTGGGAAGTTTAGGGGT
*
6060172 -AAATGGT-ACTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTT-GGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
* *
6060228 AAAATGGTCA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAATTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
* ** * *
6060286 AAAATGGTATTTTTTGGTGAAATCGCAGTTAAAAATGGAATCTTGGAAAGTTT-GAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAG-GGGT
* * *
6060345 AAAATGGTCA-TTTTGGTGAAATCGGGATTAAAAATGGAATTTTGGGAAGTTTAAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
* * * *
6060403 AAAATGGTAATTTTTGGTGAAGTCGGGGTTAAAAATGGAATTTTAGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
* * *
6060462 AAAATGGTCATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
* **
6060521 AAAATGGTAATTTTTGGTGAAGTCGGGGTTAAAAATGGAATTTT-GGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
6060579 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
6060596 ACAGTCCAGG
Statistics
Matches: 379, Mismatches: 37, Indels: 17
0.88 0.09 0.04
Matches are distributed among these distances:
56 10 0.03
57 83 0.22
58 102 0.27
59 184 0.49
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
Found at i:6060376 original size:117 final size:117
Alignment explanation
Indices: 6060113--6060592 Score: 693
Period size: 117 Copynumber: 4.1 Consensus size: 117
6060103 TTGCGATGGC
* * *
6060113 AAAATGGTAATTTTTGGTGAAATCGGGGTTGAAAAA-GGAATTTTGGAAAATTTAGGGGT-AAAT
1 AAAATGGTCA-TTTTGGTGAAATCGGGGTT-AAAAATGGAATTTTGGGAAGTTTAGGGGTAAAAT
* *
6060176 GGT-ACTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTG-GGGT
64 GGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
*
6060228 AAAATGGTCATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAATTTTAGGGGTAAAATGG
1 AAAATGGTCATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAAATGG
* ** *
6060293 TATTTTTTGGTGAAATCGCAGTTAAAAATGGAATCTTGGAAAGTTTGAGGGT
66 TAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
* *
6060345 AAAATGGTCATTTTGGTGAAATCGGGATTAAAAATGGAATTTTGGGAAGTTTAAGGGTAAAATGG
1 AAAATGGTCATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAAATGG
* * *
6060410 TAATTTTTGGTGAAGTCGGGGTTAAAAATGGAATTTTAGAAAG-TTCAGGGGT
66 TAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGA-GGGT
* *
6060462 AAAATGGTCATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGGAAGTTTGGGGGTAAAATG
1 AAAATGGTCA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAAATG
* * *
6060527 GTAATTTTTGGTGAAGTCGGGGTTAAAAATGGAATTTTGG-AAGTTCGGGGGT
65 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
*
6060579 AAAATGGTAATTTT
1 AAAATGGTCATTTT
6060593 TGGACAGTCC
Statistics
Matches: 330, Mismatches: 28, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
113 5 0.02
114 40 0.12
115 16 0.05
116 46 0.14
117 133 0.40
118 90 0.27
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.34
Consensus pattern (117 bp):
AAAATGGTCATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAAATGG
TAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
Found at i:6060809 original size:161 final size:162
Alignment explanation
Indices: 6060635--6061000 Score: 506
Period size: 162 Copynumber: 2.3 Consensus size: 162
6060625 CCAAGAAAGG
* *
6060635 GTGACACGTGGCAGCCCCACAG-GCA-TCTAGA-AGTCAAAGGACGAATTTGTAAATCTTGAAAA
1 GTGACACGTGGCAGCCCC-CAGTGCAGTC-AAACAGTCAAAGGACGAATTTATAAATCTTGAAAA
* *
6060697 ATTCTCGGGCCAATTTTGTAATTAAGTAGAAGTTGATTTGAA-GATTAAATTAAAACAAATTAAA
64 ATTCTCGGGCCAATTTTGTAATTAAATAAAAGTTGATTT-AAGGATTAAATTAAAACAAATTAAA
* *
6060761 AATGACAGGGACTAGATACGTAAATAAACCAAAAA
128 AATGACAGGGAATAGATACATAAATAAACCAAAAA
* ** ***
6060796 GTGACACGTGGCAGCCTCTGGTGCAGTCAAACAGTCAAAGGGTTAATTTATAAATCTTGAAAAAT
1 GTGACACGTGGCAGCCCCCAGTGCAGTCAAACAGTCAAAGGACGAATTTATAAATCTTGAAAAAT
*
6060861 TCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAAT
66 TCTCGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAAT
** *
6060926 GACAGGGAATAGATACATAAATAAGGCAAAAG
131 GACAGGGAATAGATACATAAATAAACCAAAAA
* **
6060958 GTGACACGTGGCAGCCTCTGGTGCAGTCAAACAGTCAAAGGAC
1 GTGACACGTGGCAGCCCCCAGTGCAGTCAAACAGTCAAAGGAC
6061001 TAAATTGAAA
Statistics
Matches: 183, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
160 1 0.01
161 24 0.13
162 158 0.86
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (162 bp):
GTGACACGTGGCAGCCCCCAGTGCAGTCAAACAGTCAAAGGACGAATTTATAAATCTTGAAAAAT
TCTCGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAAT
GACAGGGAATAGATACATAAATAAACCAAAAA
Found at i:6060852 original size:162 final size:162
Alignment explanation
Indices: 6060678--6060998 Score: 545
Period size: 162 Copynumber: 2.0 Consensus size: 162
6060668 TCAAAGGACG
* * *
6060678 AATTTGTAAATCTTGAAAAATTCTCGGGCCAATTTTGTAATTAAGTAGAAGTTGATTTGAA-GAT
1 AATTTATAAATCTTGAAAAATTCTCGGGCCAATTTTGTAATTAAATAAAAGTTGATTT-AAGGAT
* *
6060742 TAAATTAAAACAAATTAAAAATGACAGGGACTAGATACGTAAATAAACCAAAAAGTGACACGTGG
65 TAAATTAAAACAAATTAAAAATGACAGGGAATAGATACATAAATAAACCAAAAAGTGACACGTGG
6060807 CAGCCTCTGGTGCAGTCAAACAGTCAAAGGGTT
130 CAGCCTCTGGTGCAGTCAAACAGTCAAAGGGTT
*
6060840 AATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAAGGATT
1 AATTTATAAATCTTGAAAAATTCTCGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAAGGATT
** *
6060905 AAATTAAAACAAATTAAAAATGACAGGGAATAGATACATAAATAAGGCAAAAGGTGACACGTGGC
66 AAATTAAAACAAATTAAAAATGACAGGGAATAGATACATAAATAAACCAAAAAGTGACACGTGGC
6060970 AGCCTCTGGTGCAGTCAAACAGTCAAAGG
131 AGCCTCTGGTGCAGTCAAACAGTCAAAGG
6060999 ACTAAATTGA
Statistics
Matches: 149, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
161 2 0.01
162 147 0.99
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (162 bp):
AATTTATAAATCTTGAAAAATTCTCGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAAGGATT
AAATTAAAACAAATTAAAAATGACAGGGAATAGATACATAAATAAACCAAAAAGTGACACGTGGC
AGCCTCTGGTGCAGTCAAACAGTCAAAGGGTT
Found at i:6061912 original size:18 final size:19
Alignment explanation
Indices: 6061889--6061934 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
6061879 AATATTAATA
6061889 TTATTATTAGTAAA-ACAT
1 TTATTATTAGTAAAGACAT
* *
6061907 TTATTATTATTAAAGATAT
1 TTATTATTAGTAAAGACAT
6061926 TTATTATTA
1 TTATTATTA
6061935 ATAATATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
TTATTATTAGTAAAGACAT
Found at i:6061929 original size:19 final size:18
Alignment explanation
Indices: 6061870--6061934 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 18
6061860 GTTTTCTTTT
6061870 TTATTATTAAATATTAATATTA
1 TTATTATTAAA-A-T-AT-TTA
* *
6061892 TTATTAGTAAAACATTTA
1 TTATTATTAAAATATTTA
6061910 TTATTATTAAAGATATTTA
1 TTATTATTAAA-ATATTTA
6061929 TTATTA
1 TTATTA
6061935 ATAATATCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 13 0.34
19 14 0.37
21 1 0.03
22 10 0.26
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (18 bp):
TTATTATTAAAATATTTA
Found at i:6062762 original size:6 final size:6
Alignment explanation
Indices: 6062751--6062827 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
6062741 TTAAATTTGG
* * * *
6062751 TTAAAT TTAAAT ATAAA- ATAAAT TTAAAT AAGTAAAT TTAAA- TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
* *
6062799 ATAAAT TTAAA- ATAAAT TTAAACT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA-T TTAAA
6062828 AGCCCAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
5 14 0.25
6 31 0.55
7 6 0.11
8 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:6062774 original size:17 final size:16
Alignment explanation
Indices: 6062752--6062828 Score: 77
Period size: 17 Copynumber: 4.7 Consensus size: 16
6062742 TAAATTTGGT
6062752 TAAATTTAAATATAAAA
1 TAAATTTAAA-ATAAAA
*
6062769 TAAATTT-AAAT-AAG
1 TAAATTTAAAATAAAA
*
6062783 TAAATTTAAATTAAAAA
1 TAAATTTAAAAT-AAAA
*
6062800 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAA-A
6062817 TAAACTTTAAAA
1 TAAA-TTTAAAA
6062829 GCCCAAGCCC
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.18
15 5 0.10
16 5 0.10
17 24 0.48
18 7 0.14
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (16 bp):
TAAATTTAAAATAAAA
Found at i:6062778 original size:11 final size:11
Alignment explanation
Indices: 6062758--6062820 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
6062748 TGGTTAAATT
*
6062758 TAAATATAAAA
1 TAAATTTAAAA
6062769 TAAATTT-AAA
1 TAAATTTAAAA
* *
6062779 T-AA-GTAAATT
1 TAAATTTAAA-A
*
6062789 TAAATTAAAAA
1 TAAATTTAAAA
6062800 TAAATTTAAAA
1 TAAATTTAAAA
6062811 TAAATTTAAA
1 TAAATTTAAA
6062821 CTTTAAAAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
8 1 0.02
9 4 0.10
10 5 0.12
11 28 0.68
12 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:6066193 original size:31 final size:31
Alignment explanation
Indices: 6066135--6066193 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
6066125 GATTCAAAAG
* * *
6066135 AAGTAGTATTCCATCCTAACAATCGATTCAA
1 AAGTAGTATTCCAACATAACAAACGATTCAA
*
6066166 AAGTAGTATTCCAACATGACAAACGATT
1 AAGTAGTATTCCAACATAACAAACGATT
6066194 TAAACATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (31 bp):
AAGTAGTATTCCAACATAACAAACGATTCAA
Found at i:6068039 original size:19 final size:19
Alignment explanation
Indices: 6068011--6068054 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
6068001 TTAGATTTTA
* *
6068011 AAATTTAATTACATTTAGT
1 AAATTAAATTACATTGAGT
**
6068030 AAATTAAATTTTATTGAGT
1 AAATTAAATTACATTGAGT
6068049 AAATTA
1 AAATTA
6068055 CACTCATAAG
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:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (19 bp):
AAATTAAATTACATTGAGT
Found at i:6070600 original size:6 final size:6
Alignment explanation
Indices: 6070575--6070613 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
6070565 ACAATTCATA
* * *
6070575 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
6070614 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:6076347 original size:13 final size:14
Alignment explanation
Indices: 6076309--6076346 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
6076299 TCGAAAAAGT
6076309 AATTCATTTTTCAGA
1 AATT-ATTTTTCAGA
*
6076324 AATTATTTTTCGGA
1 AATTATTTTTCAGA
6076338 AATTATTTT
1 AATTATTTT
6076347 CAGTCAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (14 bp):
AATTATTTTTCAGA
Found at i:6085252 original size:28 final size:28
Alignment explanation
Indices: 6085221--6085298 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
6085211 AGAATTTTTC
6085221 AAAAAATGTAAAAAAATATTAAAAT-AT
1 AAAAAATGTAAAAAAATATTAAAATGAT
*
6085248 AAAAAA--TAATAAAAATATTAGAAATGGT
1 AAAAAATGTAA-AAAAATATTA-AAATGAT
*
6085276 AAAATATTGT--AAAAATATTAAAA
1 AAAA-AATGTAAAAAAATATTAAAA
6085299 AATGAGAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
25 3 0.07
26 10 0.23
27 13 0.30
28 15 0.35
29 1 0.02
31 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (28 bp):
AAAAAATGTAAAAAAATATTAAAATGAT
Found at i:6085261 original size:26 final size:27
Alignment explanation
Indices: 6085232--6085298 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 27
6085222 AAAAATGTAA
6085232 AAAAATATTAAAAT-ATAAAAAATAAT
1 AAAAATATTAAAATGATAAAAAATAAT
* * **
6085258 AAAAATATTAGAAATGGTAAAATATTGT
1 AAAAATATTA-AAATGATAAAAAATAAT
6085286 AAAAATATTAAAA
1 AAAAATATTAAAA
6085299 AATGAGAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.29
27 7 0.20
28 18 0.51
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (27 bp):
AAAAATATTAAAATGATAAAAAATAAT
Found at i:6085262 original size:18 final size:18
Alignment explanation
Indices: 6085222--6085265 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6085212 GAATTTTTCA
*
6085222 AAAAATGTAAAAAAATAT
1 AAAAATATAAAAAAATAT
*
6085240 TAAAATAT-AAAAAATAAT
1 AAAAATATAAAAAAAT-AT
6085258 AAAAATAT
1 AAAAATAT
6085266 TAGAAATGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAATATAAAAAAATAT
Found at i:6085301 original size:10 final size:9
Alignment explanation
Indices: 6085232--6085299 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
6085222 AAAAATGTAA
6085232 AAAAATATT
1 AAAAATATT
*
6085241 -AAAATATA
1 AAAAATATT
*
6085249 AAAAATAAT
1 AAAAATATT
6085258 AAAAATATT
1 AAAAATATT
* **
6085267 AGAAATGGT
1 AAAAATATT
6085276 -AAAATATTGT
1 AAAAATA-T-T
6085286 AAAAATATT
1 AAAAATATT
6085295 AAAAA
1 AAAAA
6085300 ATGAGAATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
8 11 0.24
9 26 0.58
10 2 0.04
11 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (9 bp):
AAAAATATT
Found at i:6085625 original size:34 final size:33
Alignment explanation
Indices: 6085587--6085701 Score: 81
Period size: 34 Copynumber: 3.3 Consensus size: 33
6085577 TAAACCCTAA
6085587 GGTTCAGGGTTTGTATTCTGGATTTAAAATTTCG
1 GGTTC-GGGTTTGTATTCTGGATTTAAAATTTCG
* * * *
6085621 GGTTCGGGTTTAG-ATTTCTAGAACCTT-AAATCTCAA
1 GGTTCGGGTTT-GTA-TTCT-GGA-TTTAAAATTTC-G
* * * *
6085657 GGTTCAAGGTTTGTATTCGGGATTTAAAGTTTAG
1 GGTTC-GGGTTTGTATTCTGGATTTAAAATTTCG
6085691 GGTTCGGGTTT
1 GGTTCGGGTTT
6085702 AGATTTTGGA
Statistics
Matches: 60, Mismatches: 13, Indels: 17
0.67 0.14 0.19
Matches are distributed among these distances:
33 12 0.20
34 17 0.28
35 14 0.23
36 11 0.18
37 6 0.10
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (33 bp):
GGTTCGGGTTTGTATTCTGGATTTAAAATTTCG
Found at i:6085694 original size:70 final size:70
Alignment explanation
Indices: 6085572--6085707 Score: 211
Period size: 70 Copynumber: 1.9 Consensus size: 70
6085562 TAAAACTCAA
* * *
6085572 AACCTTAAACCCTAAGGTTCAGGGTTTGTATTCTGGATTTAAAATTTCGGGTTCGGGTTTAGATT
1 AACCTTAAACCCTAAGGTTCAAGGTTTGTATTCGGGATTTAAAATTTAGGGTTCGGGTTTAGATT
6085637 TCTAG
66 TCTAG
* *
6085642 AACCTTAAA-TCTCAAGGTTCAAGGTTTGTATTCGGGATTTAAAGTTTAGGGTTCGGGTTTAGAT
1 AACCTTAAACCCT-AAGGTTCAAGGTTTGTATTCGGGATTTAAAATTTAGGGTTCGGGTTTAGAT
6085706 TT
65 TT
6085708 TGGATTCGAG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 2 0.03
70 58 0.97
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (70 bp):
AACCTTAAACCCTAAGGTTCAAGGTTTGTATTCGGGATTTAAAATTTAGGGTTCGGGTTTAGATT
TCTAG
Found at i:6085729 original size:20 final size:19
Alignment explanation
Indices: 6085657--6085730 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
6085647 TAAATCTCAA
* *
6085657 GGTTCAAGGTTTGTATTCG
1 GGTTTAAGGTTTGGATTCG
* *
6085676 GGATTTAAAGTTTAGGGTTCG
1 GG-TTTAAGGTTT-GGATTCG
*
6085697 GGTTT-AGATTTTGGATTCG
1 GGTTTAAG-GTTTGGATTCG
6085716 AGGTTTAAGGTTTGG
1 -GGTTTAAGGTTTGG
6085731 TTCAAGATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
19 9 0.21
20 24 0.57
21 9 0.21
ACGTcount: A:0.19, C:0.05, G:0.34, T:0.42
Consensus pattern (19 bp):
GGTTTAAGGTTTGGATTCG
Done.