Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 6 of 145
Found at i:2534464 original size:4 final size:4
Alignment explanation
Indices: 2534455--2534515 Score: 95
Period size: 4 Copynumber: 15.2 Consensus size: 4
2534445 TTTGCAGTGC
*
2534455 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TGGT
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT
* *
2534503 TTGC TTGC TTGT T
1 TTGT TTGT TTGT T
2534516 CTCATTCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.00, C:0.03, G:0.26, T:0.70
Consensus pattern (4 bp):
TTGT
Found at i:2541234 original size:31 final size:31
Alignment explanation
Indices: 2541189--2541247 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2541179 ATCATTAAAT
2541189 TATTCGAAAATTTTTATTTAAGTCACTGAAC
1 TATTCGAAAATTTTTATTTAAGTCACTGAAC
2541220 TATTC-AAAACTTTTTATTTAAGTCACTG
1 TATTCGAAAA-TTTTTATTTAAGTCACTG
2541248 GAAGTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (31 bp):
TATTCGAAAATTTTTATTTAAGTCACTGAAC
Found at i:2542802 original size:14 final size:14
Alignment explanation
Indices: 2542765--2542807 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2542755 GTTCAAGATG
2542765 TAATTAATTTAAAATTT
1 TAATTAA-TT-AAA-TT
2542782 TAATTAATTAAATT
1 TAATTAATTAAATT
*
2542796 TATTTAATTAAA
1 TAATTAATTAAA
2542808 AACCTATTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 13 0.52
15 3 0.12
16 2 0.08
17 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATTAATTAAATT
Found at i:2556051 original size:40 final size:39
Alignment explanation
Indices: 2556007--2556141 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 39
2555997 CGTTTGGACA
*
2556007 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTTAT
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTAT
* ** * * *
2556047 AAAAACGCTGCTAAAGGTAGAGAATTAGCGGCGC-TTAAC
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTAT
* * *
2556086 AGAAAACGCCGCTAAAAATTAGCATTAGCGGTG-TTTTCT
1 A-AAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTAT
2556125 AAAAATCGCCGC-AAAAA
1 AAAAA-CGCCGCTAAAAA
2556142 GCCTAAGCCA
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
38 9 0.12
39 24 0.32
40 42 0.56
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTAT
Found at i:2556423 original size:84 final size:84
Alignment explanation
Indices: 2556282--2557570 Score: 2578
Period size: 84 Copynumber: 15.3 Consensus size: 84
2556272 CGCTTCTTAT
2556282 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2556347 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2556366 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2556431 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2556450 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2556515 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2556534 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2556599 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2556618 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2556683 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2556702 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2556767 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2556786 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2556851 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2556870 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2556935 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2556954 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2557019 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2557038 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2557103 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2557122 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2557187 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2557206 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2557271 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2557290 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2557355 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2557374 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2557439 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2557458 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
2557523 CTTAGTGGCGTTTTTGGTC
66 CTTAGTGGCGTTTTTGGTC
2557542 TAGCGCCGCTAATGGTATGTGTTTTTAGC
1 TAGCGCCGCTAATGGTATGTGTTTTTAGC
2557571 GGCGTTTTCA
Statistics
Matches: 1205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 1205 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.36
Consensus pattern (84 bp):
TAGCGCCGCTAATGGTATGTGTTTTTAGCAAAATACAACGGCGTCGTTTTGTGGCCTTCAGTGGC
CTTAGTGGCGTTTTTGGTC
Found at i:2575235 original size:43 final size:43
Alignment explanation
Indices: 2575102--2575238 Score: 132
Period size: 43 Copynumber: 3.2 Consensus size: 43
2575092 GTGGTCGAAC
* * **
2575102 CGCCGCTATAGATCAGGGTCTATTGCGGCATTTTAGGGGAAAG
1 CGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGAAAAAG
* * * * * **
2575145 CGCCGCTAAAGATTAGGTTCT-TTAGTGGCGTTTGTGGTCAAAG
1 CGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAGGAAAAAG
* * *
2575188 CGCCGCTATAGATCAGGGTCTATTCCGGCGTTTGAGAAAAAAA
1 CGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGAAAAAG
2575231 CGCCGCTA
1 CGCCGCTA
2575239 AAGACCCTGA
Statistics
Matches: 73, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
42 2 0.03
43 69 0.95
44 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26
Consensus pattern (43 bp):
CGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGAAAAAG
Found at i:2575235 original size:86 final size:87
Alignment explanation
Indices: 2575060--2575242 Score: 278
Period size: 86 Copynumber: 2.1 Consensus size: 87
2575050 NNNNNNNNNN
*
2575060 CCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAACCGCCGCTATAGATCAGGGTCTAT
1 CCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAACCGCCGCTATAGATCAGGGTCTAT
* * *** *
2575125 TGCGGCATTTTAGGGGAAAGCG
66 TCCGGCATTTGAGAAAAAAACG
*
2575147 CCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTAT
1 CCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAACCGCCGCTATAGATCAGGGTCTAT
*
2575211 TCCGGCGTTTGAGAAAAAAACG
66 TCCGGCATTTGAGAAAAAAACG
2575233 CCGCTAAAGA
1 CCGCTAAAGA
2575243 CCCTGATCTA
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 59 0.68
87 28 0.32
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (87 bp):
CCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAACCGCCGCTATAGATCAGGGTCTAT
TCCGGCATTTGAGAAAAAAACG
Found at i:2575511 original size:22 final size:22
Alignment explanation
Indices: 2575484--2575526 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2575474 TCTGCGGCGC
*
2575484 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
*
2575506 AAAAAGCGCCGTTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
2575527 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:2576553 original size:18 final size:20
Alignment explanation
Indices: 2576530--2576566 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
2576520 TCGAAACCAG
2576530 TCGGTTAA-C-AAAAAATTT
1 TCGGTTAACCGAAAAAATTT
2576548 TCGGTTAACCGAAAAAATT
1 TCGGTTAACCGAAAAAATT
2576567 AATAAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
TCGGTTAACCGAAAAAATTT
Found at i:2576617 original size:13 final size:13
Alignment explanation
Indices: 2576599--2576628 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2576589 AGCCCAAACT
2576599 CAATTACCCAACC
1 CAATTACCCAACC
2576612 CAATTACCCAACC
1 CAATTACCCAACC
2576625 CAAT
1 CAAT
2576629 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:2588690 original size:19 final size:20
Alignment explanation
Indices: 2588664--2588711 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
2588654 CAAGTATTAT
* *
2588664 ATTTAAAATTTTAATAAAAA
1 ATTTAAAATATTAAAAAAAA
2588684 A-TTAAAA-ATTAAAAAAAA
1 ATTTAAAATATTAAAAAAAA
2588702 ATTTAAAATA
1 ATTTAAAATA
2588712 AAATTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 10 0.42
19 12 0.50
20 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTAAAATATTAAAAAAAA
Found at i:2588700 original size:18 final size:18
Alignment explanation
Indices: 2588674--2588714 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2588664 ATTTAAAATT
*
2588674 TTAATAAAAAATTAAAAA
1 TTAAAAAAAAATTAAAAA
*
2588692 TTAAAAAAAAATTTAAAA
1 TTAAAAAAAAATTAAAAA
2588710 -TAAAA
1 TTAAAA
2588715 TTAAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
TTAAAAAAAAATTAAAAA
Found at i:2588715 original size:96 final size:97
Alignment explanation
Indices: 2588615--2588812 Score: 389
Period size: 96 Copynumber: 2.1 Consensus size: 97
2588605 ACATCACATA
2588615 AAAATTAAATATATAATAATATATAATACTATTACTTGTCAAGTATTATATTTAAAATTTTAATA
1 AAAATTAAATATATAATAATATATAATACTATTACTTGTCAAGTATTATATTTAAAATTTTAATA
2588680 AAAAATTAAAAATTAAAAAAAAAT-TTAAAAT
66 AAAAATTAAAAATTAAAAAAAAATATTAAAAT
2588711 AAAATTAAATATATAATAATATATAATACTATTACTTGTCAAGTATTATATTTAAAATTTTAATA
1 AAAATTAAATATATAATAATATATAATACTATTACTTGTCAAGTATTATATTTAAAATTTTAATA
2588776 AAAAATTAAAAATTAAAAAAAAATATTAAAAT
66 AAAAATTAAAAATTAAAAAAAAATATTAAAAT
2588808 AAAAT
1 AAAAT
2588813 GTATAAAATA
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 89 0.88
97 12 0.12
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (97 bp):
AAAATTAAATATATAATAATATATAATACTATTACTTGTCAAGTATTATATTTAAAATTTTAATA
AAAAATTAAAAATTAAAAAAAAATATTAAAAT
Found at i:2588786 original size:19 final size:20
Alignment explanation
Indices: 2588762--2588807 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2588752 AGTATTATAT
* *
2588762 TTAAAATTTTAATAAAAA-A
1 TTAAAATTTAAAAAAAAATA
*
2588781 TTAAAAATTAAAAAAAAATA
1 TTAAAATTTAAAAAAAAATA
2588801 TTAAAAT
1 TTAAAAT
2588808 AAAATGTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAATTTAAAAAAAAATA
Found at i:2588793 original size:13 final size:13
Alignment explanation
Indices: 2588777--2588825 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
2588767 ATTTTAATAA
2588777 AAAATTAAAA-ATT
1 AAAA-TAAAATATT
*
2588790 AAAAAAAAATATT
1 AAAATAAAATATT
*
2588803 AAAATAAAATGTAT
1 AAAATAAAATAT-T
2588817 AAAATAAAA
1 AAAATAAAA
2588826 CTTAGCACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 4 0.13
13 17 0.55
14 10 0.32
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (13 bp):
AAAATAAAATATT
Found at i:2590093 original size:74 final size:74
Alignment explanation
Indices: 2590006--2590149 Score: 261
Period size: 74 Copynumber: 1.9 Consensus size: 74
2589996 GCCTTGTGGT
* *
2590006 GAAGATGTCAAGTGAAGTGTCACCAAGGAAGCATAAGCCCCATCGGTTATATTCATCAACGTATC
1 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
2590071 GTGTCTACC
66 GTGTCTACC
*
2590080 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTTATCAACGTATC
1 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
2590145 GTGTC
66 GTGTC
2590150 GACCTTTCTC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (74 bp):
GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCGGTAATATTCATCAACGTATC
GTGTCTACC
Found at i:2596029 original size:21 final size:21
Alignment explanation
Indices: 2595986--2596026 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2595976 CTTTTTAAAA
*
2595986 AATTAATTACCAAAAAATAAT
1 AATTAATTAACAAAAAATAAT
*
2596007 AATTAAATTAACAATAAATA
1 AATT-AATTAACAAAAAATA
2596027 TAAATATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTAATTAACAAAAAATAAT
Found at i:2598271 original size:7 final size:7
Alignment explanation
Indices: 2598240--2598264 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2598230 GTGATGATTA
2598240 TTTTTCT
1 TTTTTCT
2598247 TTTTTCT
1 TTTTTCT
2598254 TTTTTCT
1 TTTTTCT
2598261 TTTT
1 TTTT
2598265 CTATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:2598271 original size:14 final size:15
Alignment explanation
Indices: 2598238--2598272 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
2598228 ACGTGATGAT
2598238 TATTTTTCTTTTTTC
1 TATTTTTCTTTTTTC
2598253 T-TTTTTC-TTTTTC
1 TATTTTTCTTTTTTC
2598266 TATTTTT
1 TATTTTT
2598273 ATCCAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 11 0.58
15 1 0.05
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (15 bp):
TATTTTTCTTTTTTC
Found at i:2599541 original size:18 final size:17
Alignment explanation
Indices: 2599504--2599543 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
2599494 TTACATGTCT
**
2599504 AATTGATAAAAGGACCA
1 AATTGATAAAAGGAAAA
2599521 AATTGCATAAAAGGAAAA
1 AATTG-ATAAAAGGAAAA
2599539 AATTG
1 AATTG
2599544 GGTTCTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.20
Consensus pattern (17 bp):
AATTGATAAAAGGAAAA
Found at i:2600272 original size:21 final size:21
Alignment explanation
Indices: 2600239--2600282 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2600229 AAGATGTGAC
**
2600239 TTGTATTGGATTGAATG-TAAA
1 TTGTATTAAATTG-ATGTTAAA
2600260 TTGTATTAAATTGATGTTAAA
1 TTGTATTAAATTGATGTTAAA
2600281 TT
1 TT
2600283 TACTCGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (21 bp):
TTGTATTAAATTGATGTTAAA
Found at i:2600886 original size:49 final size:49
Alignment explanation
Indices: 2600730--2600892 Score: 127
Period size: 49 Copynumber: 3.3 Consensus size: 49
2600720 GTAGCTCTTA
* * * * * *
2600730 TGAGCGTCCCGTTATATGGCTCTTCATGATCTTCCCAATTATAGGCTCTTTA
1 TGAGCTTCCCGTTA-ATTGCTCTTCA-GAAC-TACCAGTTATAGGCTCTTTG
* * * * *
2600782 TGGGCTTCCCGTTAA-TGCTCACTT--GAACTTCCCGTTATATGGCTATTCG
1 TGAGCTTCCCGTTAATTGCT--CTTCAGAACTACCAGTTATA-GGCTCTTTG
* *
2600831 -GTGCTTCCCGTTAATTGCTCTTCAGAGCTACCAGTTATAGGCTCTTTG
1 TGAGCTTCCCGTTAATTGCTCTTCAGAACTACCAGTTATAGGCTCTTTG
2600879 TGAGCTTCCCGTTA
1 TGAGCTTCCCGTTA
2600893 TAGTGCTTGA
Statistics
Matches: 87, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
47 3 0.03
48 28 0.32
49 37 0.43
50 3 0.03
51 1 0.01
52 15 0.17
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (49 bp):
TGAGCTTCCCGTTAATTGCTCTTCAGAACTACCAGTTATAGGCTCTTTG
Found at i:2600892 original size:25 final size:25
Alignment explanation
Indices: 2600723--2600895 Score: 106
Period size: 25 Copynumber: 7.0 Consensus size: 25
2600713 GCACATCGTA
*
2600723 GCTC-TTATGAGCGTCCCGTTATATG
1 GCTCTTTATGAGCTTCCCGTTATA-G
* * *
2600748 GCTCTTCATGATCTTCCCAATTATAG
1 GCTCTTTATGAGCTTCCC-GTTATAG
* *
2600774 GCTCTTTATGGGCTTCCCGTTA-AT
1 GCTCTTTATGAGCTTCCCGTTATAG
** *
2600798 GCTCACT-TGAACTTCCCGTTATATG
1 GCTCTTTATGAGCTTCCCGTTATA-G
* ** * *
2600823 GCT-ATTCGGTGCTTCCCGTTA-ATT
1 GCTCTTTATGAGCTTCCCGTTATA-G
* * *
2600847 GCTCTTCA-GAGCTACCAGTTATAG
1 GCTCTTTATGAGCTTCCCGTTATAG
*
2600871 GCTCTTTGTGAGCTTCCCGTTATAG
1 GCTCTTTATGAGCTTCCCGTTATAG
2600896 TGCTTGAGAG
Statistics
Matches: 110, Mismatches: 30, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
23 12 0.11
24 30 0.27
25 37 0.34
26 26 0.24
27 5 0.05
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (25 bp):
GCTCTTTATGAGCTTCCCGTTATAG
Found at i:2602574 original size:21 final size:22
Alignment explanation
Indices: 2602536--2602583 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
2602526 TTAGTAGACT
*
2602536 CATCTTGGCTATTTGTCAAGTG
1 CATCTTGGCTATTTGTCAAGTA
2602558 CATCTTGGCTA-TTGTCAAGTA
1 CATCTTGGCTATTTGTCAAGTA
2602579 CATCT
1 CATCT
2602584 CGTGATAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
CATCTTGGCTATTTGTCAAGTA
Found at i:2613197 original size:18 final size:18
Alignment explanation
Indices: 2613174--2613208 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2613164 TTTTATATGT
* *
2613174 TATAAATTATATAATATA
1 TATAAATAACATAATATA
2613192 TATAAATAACATAATAT
1 TATAAATAACATAATAT
2613209 GCGGAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAAATAACATAATATA
Found at i:2617533 original size:114 final size:114
Alignment explanation
Indices: 2617330--2617829 Score: 682
Period size: 114 Copynumber: 4.4 Consensus size: 114
2617320 TAAATTATAT
2617330 TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
1 TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* *
2617395 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGTTTTCTCAAAAACGCCGC
66 GACGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCTCAAAAACGCCGC
*
2617444 TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCCGAAAGCTCAGAAAAC
1 TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* * * * *
2617509 GATGTCGTTGAGCTTAGGTTTTTTTGTGGCGCTTTCACAAAAACGCCGC
66 GACGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCTCAAAAACGCCGC
* * * *
2617558 TAAAGT-TCTGA-CTATTAGCGGCGCATACTTAAAAACGCCACTAAATCCCTGAAAGCTCAGGAA
1 TAAA-TCCCTGAGC-ATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAA
* * * *
2617621 ACGGCGTCGTTGGGCTTAGGTATTTTTGCGGTGC-TTCCCAAAAAACGTCGC
64 ACGACGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCTC-AAAAACGCCGC
* * * * *
2617672 AAAAGCCCTGAGCATTAGCGGGGCATACTTAAAAACGCCACTGAATCCCCGAAAGCTCAGAAAAC
1 TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* * **
2617737 GATGTCGTTGGGCTTAGGTTTTTTTGTAGCGCTTTCTCAAAAACGCCGC
66 GACGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCTCAAAAACGCCGC
* * ** *
2617786 TAAAGCCCTGAGCATTAGCGGCGCTTTCTGGAAAACGCCGCTAA
1 TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAA
2617830 TGCCTATTTT
Statistics
Matches: 336, Mismatches: 44, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
113 5 0.01
114 325 0.97
115 6 0.02
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (114 bp):
TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
GACGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCTCAAAAACGCCGC
Found at i:2617823 original size:228 final size:228
Alignment explanation
Indices: 2617330--2617829 Score: 761
Period size: 228 Copynumber: 2.2 Consensus size: 228
2617320 TAAATTATAT
*
2617330 TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* * * *
2617395 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGTTTTCTCAAAAACGCCGCTAAATCCCTGAGCATT
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGTCTTCCCAAAAACGCCGCAAAAGCCCTGAGCATT
* *
2617460 AGCGGCGCTTACTTAAAAATGCCACTAAATCCCCGAAAGCTCAGAAAACGATGTCGTTGAGCTTA
131 AGCGGCGCATACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGATGTCGTTGAGCTTA
*
2617525 GGTTTTTTTGTGGCGCTTTCACAAAAACGCCGC
196 GGTTTTTTTGTAGCGCTTTCACAAAAACGCCGC
** * * *
2617558 TAAAGTTCTGA-CTATTAGCGGCGCATACTTAAAAACGCCACTAAATCCCTGAAAGCTCAGGAAA
1 TAAAGCCCTGAGC-ATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAA
* *
2617622 CGGCGTCGTTGGGCTTAGGTATTTTTGCGGTG-CTTCCCAAAAAACGTCGCAAAAGCCCTGAGCA
65 CGGCGTCGTTGGGCTTAGGTATTTTTGCGGCGTCTTCCC-AAAAACGCCGCAAAAGCCCTGAGCA
* * *
2617686 TTAGCGGGGCATACTTAAAAACGCCACTGAATCCCCGAAAGCTCAGAAAACGATGTCGTTGGGCT
129 TTAGCGGCGCATACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGATGTCGTTGAGCT
*
2617751 TAGGTTTTTTTGTAGCGCTTTCTCAAAAACGCCGC
194 TAGGTTTTTTTGTAGCGCTTTCACAAAAACGCCGC
* ** *
2617786 TAAAGCCCTGAGCATTAGCGGCGCTTTCTGGAAAACGCCGCTAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAA
2617830 TGCCTATTTT
Statistics
Matches: 243, Mismatches: 26, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
227 5 0.02
228 237 0.98
229 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (228 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGTCTTCCCAAAAACGCCGCAAAAGCCCTGAGCATT
AGCGGCGCATACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGATGTCGTTGAGCTTA
GGTTTTTTTGTAGCGCTTTCACAAAAACGCCGC
Found at i:2620719 original size:18 final size:19
Alignment explanation
Indices: 2620672--2620720 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
2620662 CATTATGTAT
2620672 AATTTTATTGCTAGCATGAA
1 AATTTTA-TGCTAGCATGAA
* * *
2620692 AGTTTCATGCTA-CTTGAA
1 AATTTTATGCTAGCATGAA
2620710 AATTTTATGCT
1 AATTTTATGCT
2620721 TAATTACTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 14 0.58
19 5 0.21
20 5 0.21
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (19 bp):
AATTTTATGCTAGCATGAA
Found at i:2622925 original size:19 final size:19
Alignment explanation
Indices: 2622903--2622945 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2622893 TAATTGAAAT
*
2622903 AAAATTAATTTATATT-TAA
1 AAAATTAA-ATATATTCTAA
2622922 AAAA-TAAATATATTCTAA
1 AAAATTAAATATATTCTAA
2622940 AAAATT
1 AAAATT
2622946 TGCGTTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 10 0.48
19 5 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTAAATATATTCTAA
Found at i:2627235 original size:14 final size:14
Alignment explanation
Indices: 2627216--2627255 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2627206 TTGTTTGCCA
2627216 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
2627230 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
2627244 GAAAAATGTTTT
1 GTAAAATGTTTT
2627256 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:2627264 original size:20 final size:20
Alignment explanation
Indices: 2627239--2627278 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2627229 CGTAAAATGA
*
2627239 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
2627259 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
2627279 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:2627268 original size:34 final size:35
Alignment explanation
Indices: 2627224--2627290 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2627214 CAGTAAAATG
*
2627224 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
2627258 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
2627291 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:2627355 original size:32 final size:32
Alignment explanation
Indices: 2627269--2627355 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
2627259 TTTCTGTAAA
* *
2627269 ATGATTTACTGGAAAATATTTTCTGGTGTTTGG
1 ATGATTTCCT-GAAAATATTTTCTGCTGTTTGG
* *
2627302 ATGA-ATCTATGTAAAATATTTTCTGCTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGCTGTTTGG
2627335 CA-GATTTCCTGAAAATATTTT
1 -ATGATTTCCTGAAAATATTTT
2627356 TCGAAAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
32 12 0.27
33 29 0.66
34 3 0.07
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGCTGTTTGG
Found at i:2632676 original size:24 final size:24
Alignment explanation
Indices: 2632619--2632677 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2632609 CACAAAAAAA
2632619 ATAAAAATATGTGTAATGATGTAT
1 ATAAAAATATGTGTAATGATGTAT
* * *
2632643 ATATATATATGTGTGTAT-ATGTAT
1 ATAAAAATATGTGT-AATGATGTAT
2632667 ATAAAAATATG
1 ATAAAAATATG
2632678 AAATGTATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (24 bp):
ATAAAAATATGTGTAATGATGTAT
Found at i:2632999 original size:3 final size:3
Alignment explanation
Indices: 2632991--2633049 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
2632981 TGTACATAGC
*
2632991 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AACT AATT AAT -TT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT
*
2633036 AGT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
2633050 AACAACGGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 3 0.06
3 41 0.84
4 5 0.10
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2634407 original size:22 final size:22
Alignment explanation
Indices: 2634381--2634426 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2634371 AAATAAATTT
2634381 ACCCTTTTTGTTTAAAATCTCA
1 ACCCTTTTTGTTTAAAATCTCA
2634403 ACCCTTTTTGTTTAAAATCTCA
1 ACCCTTTTTGTTTAAAATCTCA
2634425 AC
1 AC
2634427 TATAACCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.43
Consensus pattern (22 bp):
ACCCTTTTTGTTTAAAATCTCA
Found at i:2641542 original size:7 final size:7
Alignment explanation
Indices: 2641530--2641556 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2641520 TAATCCATAT
2641530 TATTTAA
1 TATTTAA
2641537 TATTTAA
1 TATTTAA
2641544 TATTTAA
1 TATTTAA
2641551 TATTTA
1 TATTTA
2641557 TGAATATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTTAA
Found at i:2642339 original size:13 final size:13
Alignment explanation
Indices: 2642317--2642367 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
2642307 TTTAGTATTA
2642317 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
2642330 TTTTTTAAAAGTG
1 CTTTTGAAAAGTG
*
2642343 CTTTTCAGAAA-TG
1 CTTTTGA-AAAGTG
2642356 CTTTTGAAAAGT
1 CTTTTGAAAAGT
2642368 TTTGTTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 3 0.10
13 25 0.81
14 3 0.10
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:2643529 original size:24 final size:24
Alignment explanation
Indices: 2643497--2643550 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2643487 AAAGAGAGAG
*
2643497 AAAATTTTA-AAGAATATAAAACAA
1 AAAAATTTATAAGAAT-TAAAACAA
**
2643521 AAAAATTTATATTAATTAAAACAA
1 AAAAATTTATAAGAATTAAAACAA
2643545 AAAAAT
1 AAAAAT
2643551 ACAGAGATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAAATTTATAAGAATTAAAACAA
Found at i:2653910 original size:3 final size:3
Alignment explanation
Indices: 2653902--2653953 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2653892 TAATCCCTAT
2653902 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2653950 TTA T
1 TTA T
2653954 ATATACATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2658620 original size:24 final size:24
Alignment explanation
Indices: 2658588--2658641 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2658578 AAAGAGAGAG
*
2658588 AAAATTTTA-AAGAATATAAAACAA
1 AAAAATTTATAAGAAT-TAAAACAA
**
2658612 AAAAATTTATATTAATTAAAACAA
1 AAAAATTTATAAGAATTAAAACAA
2658636 AAAAAT
1 AAAAAT
2658642 ACAGAGATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAAATTTATAAGAATTAAAACAA
Found at i:2662216 original size:34 final size:32
Alignment explanation
Indices: 2662178--2662256 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 32
2662168 TTTCAATCTG
*
2662178 AAATTATTTAATAATTTTTAAATGTTTAATGATA
1 AAATTATTTAATAATGTTTAAATGTTT--TGATA
* * * *
2662212 AAATTAGTTACTAATGTTTACATGTTTTGTTA
1 AAATTATTTAATAATGTTTAAATGTTTTGATA
2662244 AAATTATCTTAAT
1 AAATTAT-TTAAT
2662257 TGTATATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 10 0.27
33 4 0.11
34 23 0.62
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (32 bp):
AAATTATTTAATAATGTTTAAATGTTTTGATA
Found at i:2663137 original size:24 final size:24
Alignment explanation
Indices: 2663110--2663161 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2663100 TTAGTAAGTC
* *
2663110 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2663134 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2663158 AAAT
1 AAAT
2663162 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2664536 original size:51 final size:51
Alignment explanation
Indices: 2664384--2664551 Score: 160
Period size: 51 Copynumber: 3.3 Consensus size: 51
2664374 TTCGATGGTT
* ** * *
2664384 TGCACATAGTACCACCCATGTGACCATTGTC-ATCCGATACATGTAGTAGCC
1 TGCACATAGTACTACAAATGTGACCATTATCTAT-CGATACACGTAGTAGCC
* * * * *** * * *
2664435 TACACATAGTACTACACACGTGATCAAGCTTTAT-GGTTCACGTAGTAGCC
1 TGCACATAGTACTACAAATGTGACCATTATCTATCGATACACGTAGTAGCC
*
2664485 TGCACATAATACTACAAATGTGACCATTATCTATCGATACACGTAGTAGCC
1 TGCACATAGTACTACAAATGTGACCATTATCTATCGATACACGTAGTAGCC
*
2664536 TGCACTTAGTACTACA
1 TGCACATAGTACTACA
2664552 CACGTGTTCA
Statistics
Matches: 90, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
50 38 0.42
51 50 0.56
52 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (51 bp):
TGCACATAGTACTACAAATGTGACCATTATCTATCGATACACGTAGTAGCC
Found at i:2667735 original size:23 final size:23
Alignment explanation
Indices: 2667709--2667759 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
2667699 ATTCGAATAT
2667709 TGTAATATCC-CAAAAATTACTAC
1 TGTAATA-CCTCAAAAATTACTAC
2667732 TGTAATACCTCAAAAATTACTAC
1 TGTAATACCTCAAAAATTACTAC
*
2667755 AGTAA
1 TGTAA
2667760 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (23 bp):
TGTAATACCTCAAAAATTACTAC
Found at i:2671102 original size:27 final size:27
Alignment explanation
Indices: 2671070--2671121 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
2671060 TCGATGATTC
2671070 TAAGTAAGGTTATTTGTTTTGGTATTG
1 TAAGTAAGGTTATTTGTTTTGGTATTG
2671097 TAAGTAAGGTTATTTGTTTTGGTAT
1 TAAGTAAGGTTATTTGTTTTGGTAT
2671122 GTACATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (27 bp):
TAAGTAAGGTTATTTGTTTTGGTATTG
Found at i:2679284 original size:100 final size:99
Alignment explanation
Indices: 2679111--2679302 Score: 375
Period size: 100 Copynumber: 1.9 Consensus size: 99
2679101 TTTCGAACTG
2679111 CACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTCTTCTTTTCCCCTTCAGATT
1 CACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTCTTCTTTTCCCCTTCAGATT
2679176 TGTTTCACTCTGCTGATTCTGCATGTAATCGTTTC
66 TGTTTCACTCTGCTG-TTCTGCATGTAATCGTTTC
2679211 CACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTCTTCTTTTCCCCTTCAGATT
1 CACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTCTTCTTTTCCCCTTCAGATT
2679276 TGTTTCACTCTGCTGTTCTGCATGTAA
66 TGTTTCACTCTGCTGTTCTGCATGTAA
2679303 ATATTATAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 12 0.13
100 80 0.87
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (99 bp):
CACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTCTTCTTTTCCCCTTCAGATT
TGTTTCACTCTGCTGTTCTGCATGTAATCGTTTC
Found at i:2694571 original size:2 final size:2
Alignment explanation
Indices: 2694564--2694588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2694554 ATGTTCTTTT
2694564 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2694589 TTGGTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2699620 original size:27 final size:27
Alignment explanation
Indices: 2699563--2699624 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
2699553 GCTATTTGAT
* * *
2699563 AGGCGCAACTAGTTGAGCCTATCTAAC
1 AGGCGCGACTAATTGAGCCTAACTAAC
* * *
2699590 AGGCGCGACTAATTGTGCCTAACTCAG
1 AGGCGCGACTAATTGAGCCTAACTAAC
2699617 AGGCGCGA
1 AGGCGCGA
2699625 ATGGTGGGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.19
Consensus pattern (27 bp):
AGGCGCGACTAATTGAGCCTAACTAAC
Found at i:2701991 original size:113 final size:114
Alignment explanation
Indices: 2701858--2702084 Score: 447
Period size: 113 Copynumber: 2.0 Consensus size: 114
2701848 AAATTATATA
2701858 ATGCGGATTCAATTATTAATAATAAAAAATAAATAAAATTTTTAATAAAAGGAACAAAATATAAT
1 ATGCGGATTCAATTATTAATAATAAAAAATAAATAAAATTTTTAATAAAAGGAACAAAATATAAT
2701923 CTAATTTTCAGGATTTTTCACTTCCCTTTCCGTATTT-CTACACAAAAT
66 CTAATTTTCAGGATTTTTCACTTCCCTTTCCGTATTTCCTACACAAAAT
2701971 ATGCGGATTCAATTATTAATAATAAAAAATAAATAAAATTTTTAATAAAAGGAACAAAATATAAT
1 ATGCGGATTCAATTATTAATAATAAAAAATAAATAAAATTTTTAATAAAAGGAACAAAATATAAT
2702036 CTAATTTTCAGGATTTTTCACTTCCCTTTCCGTATTTCCTACACAAAAT
66 CTAATTTTCAGGATTTTTCACTTCCCTTTCCGTATTTCCTACACAAAAT
2702085 CTACATATTA
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 102 0.90
114 11 0.10
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (114 bp):
ATGCGGATTCAATTATTAATAATAAAAAATAAATAAAATTTTTAATAAAAGGAACAAAATATAAT
CTAATTTTCAGGATTTTTCACTTCCCTTTCCGTATTTCCTACACAAAAT
Found at i:2710050 original size:29 final size:29
Alignment explanation
Indices: 2710008--2710064 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
2709998 TTAACAATTA
2710008 ATCCTAATGTGGGTGGATTTGGTAAGGGG
1 ATCCTAATGTGGGTGGATTTGGTAAGGGG
2710037 ATCCTAATGTGGGTGGATTTGGTAAGGG
1 ATCCTAATGTGGGTGGATTTGGTAAGGG
2710065 AGATGCAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.07, G:0.40, T:0.32
Consensus pattern (29 bp):
ATCCTAATGTGGGTGGATTTGGTAAGGGG
Found at i:2710158 original size:2 final size:2
Alignment explanation
Indices: 2710153--2710177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2710143 GTAAAAAAGA
2710153 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2710178 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2710182 original size:2 final size:2
Alignment explanation
Indices: 2710177--2710227 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
2710167 TCTCTCTCTC
* * *
2710177 TA TA TA TA TA TA TA TA TA TA -A TA TG TGA TA TA TA TC TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
*
2710219 TA TT TA TA T
1 TA TA TA TA T
2710228 GTTGTGTCTG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2717794 original size:260 final size:261
Alignment explanation
Indices: 2717333--2717855 Score: 1039
Period size: 260 Copynumber: 2.0 Consensus size: 261
2717323 GATGCATTTC
2717333 ATCCAAGTGAGGCTGCCAATGTGATCATTGGGAGGAGATCCTACAGCGCTCAATCTCCTACCGAT
1 ATCCAAGTGAGGCTGCCAATGTGATCATTGGGAGGAGATCCTACAGCGCTCAATCTCCTACCGAT
2717398 GCTTACCCCATTGATATCCGCCGTCTTGCTCAGCTCTGAAACTGAAAGTCGACGAGGTTTTTTAT
66 GCTTACCCCATTGATATCCGCCGTCTTGCTCAGCTCTGAAACTGAAAGTCGACGAGGTTTTTTAT
2717463 GGGAATTTATAGATAATTAATTGAATCGTTGTAGAATTCTTTCTATATTTGTGTCGTTTTGAATT
131 GGGAATTTATAGATAATTAATTGAATCGTTGTAGAATTCTTTCTATATTTGTGTCGTTTTGAATT
2717528 GTGTAACAGCTTACAATCATAAGTGTCATTGTTCTAAGGGAAGTGGCAAGCAATA-ATATATATA
196 GTGTAACAGCTTACAATCATAAGTGTCATTGTTCTAAGGGAAGTGGCAAGCAATATATATATATA
2717592 T
261 T
2717593 ATCCAAGTGAGGCTGCCAATGTGATCATTGGGAGGAGATCCTACAGCGCTCAATCTCCTACCGAT
1 ATCCAAGTGAGGCTGCCAATGTGATCATTGGGAGGAGATCCTACAGCGCTCAATCTCCTACCGAT
2717658 GCTTACCCCATTGATATCCGCCGTCTTGCTCAGCTCTGAAACTGAAAGTCGACGAGGTTTTTTAT
66 GCTTACCCCATTGATATCCGCCGTCTTGCTCAGCTCTGAAACTGAAAGTCGACGAGGTTTTTTAT
2717723 GGGAATTTATAGATAATTAATTGAATCGTTGTAGAATTCTTTCTATATTTGTGTCGTTTTGAATT
131 GGGAATTTATAGATAATTAATTGAATCGTTGTAGAATTCTTTCTATATTTGTGTCGTTTTGAATT
2717788 GTGTAACAGCTTACAATCATAAGTGTCATTGTTCTAAGGGAAGTGGCAAGCAATATATATATATA
196 GTGTAACAGCTTACAATCATAAGTGTCATTGTTCTAAGGGAAGTGGCAAGCAATATATATATATA
2717853 T
261 T
2717854 AT
1 AT
2717856 ATATATATGC
Statistics
Matches: 262, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
260 250 0.95
261 12 0.05
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (261 bp):
ATCCAAGTGAGGCTGCCAATGTGATCATTGGGAGGAGATCCTACAGCGCTCAATCTCCTACCGAT
GCTTACCCCATTGATATCCGCCGTCTTGCTCAGCTCTGAAACTGAAAGTCGACGAGGTTTTTTAT
GGGAATTTATAGATAATTAATTGAATCGTTGTAGAATTCTTTCTATATTTGTGTCGTTTTGAATT
GTGTAACAGCTTACAATCATAAGTGTCATTGTTCTAAGGGAAGTGGCAAGCAATATATATATATA
T
Found at i:2718053 original size:23 final size:22
Alignment explanation
Indices: 2718006--2718051 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2717996 TATTTAATTA
* *
2718006 TTAATTTTTTCGATTTAACTAT
1 TTAATTTTTTCGAATTAAATAT
2718028 TTAA-TTTTTCGAGATTAAATAT
1 TTAATTTTTTCGA-ATTAAATAT
2718050 TT
1 TT
2718052 TAGTCATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (22 bp):
TTAATTTTTTCGAATTAAATAT
Found at i:2718641 original size:31 final size:32
Alignment explanation
Indices: 2718606--2718675 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
2718596 GCTAAATTCC
* ** *
2718606 TAATCAATTCT-AGTTCTTCAAGGGTTTGTAT
1 TAATCAATCCTAAGTTCTTCAAGAATTTGCAT
*
2718637 TAATCAATCCTAATTTCTTCAAGAATTTGCAT
1 TAATCAATCCTAAGTTCTTCAAGAATTTGCAT
2718669 TAATCAA
1 TAATCAA
2718676 CCTCTAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (32 bp):
TAATCAATCCTAAGTTCTTCAAGAATTTGCAT
Found at i:2728382 original size:2 final size:2
Alignment explanation
Indices: 2728375--2728456 Score: 150
Period size: 2 Copynumber: 42.0 Consensus size: 2
2728365 AAGCCAAGAA
2728375 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2728417 -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2728457 TTTAATTATA
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2734492 original size:59 final size:59
Alignment explanation
Indices: 2734371--2734492 Score: 129
Period size: 59 Copynumber: 2.1 Consensus size: 59
2734361 TTGCATCCCG
* ** * **
2734371 AACAAAGTGACAATCCACCTCAATTGCAATATGTAAAGCAAATTGTTTATTGCATCTTA
1 AACAAAGTGACAATCCACCTCAATTGCAATATGCAAAGCAAATTGACTATGGCATCGAA
* * * * *
2734430 AACAAAGTGACAATCCACTTCAATTTCAATCTGCAACA-CAGATTGACTATGGCCTCGAA
1 AACAAAGTGACAATCCACCTCAATTGCAATATGCAA-AGCAAATTGACTATGGCATCGAA
2734489 AACA
1 AACA
2734493 TCGTTCTTCT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 50 0.98
60 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26
Consensus pattern (59 bp):
AACAAAGTGACAATCCACCTCAATTGCAATATGCAAAGCAAATTGACTATGGCATCGAA
Found at i:2735030 original size:21 final size:22
Alignment explanation
Indices: 2735004--2735060 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
2734994 AATAGGGAAT
*
2735004 ATATATAATATTTTCCT-AAAG
1 ATATATAATATATTCCTAAAAG
2735025 ATATATAATATATTCCTAAAAG
1 ATATATAATATATTCCTAAAAG
2735047 ATATATAATATATT
1 ATATATAATATATT
2735061 TAGATATTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (22 bp):
ATATATAATATATTCCTAAAAG
Found at i:2738602 original size:3 final size:3
Alignment explanation
Indices: 2738594--2738624 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2738584 CATTATATCT
2738594 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
2738625 ATGTAATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:2739903 original size:7 final size:7
Alignment explanation
Indices: 2739887--2739916 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2739877 TTAATAACCG
2739887 AAAAAG-
1 AAAAAGA
2739893 AAAAAGA
1 AAAAAGA
2739900 AAAAAGA
1 AAAAAGA
2739907 AAAAAGA
1 AAAAAGA
2739914 AAA
1 AAA
2739917 CCAAACCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:2746284 original size:29 final size:30
Alignment explanation
Indices: 2746221--2746299 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
2746211 ATTTCAAAAC
*
2746221 TATACATAAACTTTGGTTTAATATGCAATTG
1 TATACATAAACTTTGATTT-ATATGCAATTG
* *
2746252 TATACATGAACTTTGATTT-TATGCAATTT
1 TATACATAAACTTTGATTTATATGCAATTG
* *
2746281 TATATATCAAATTTTGATT
1 TATACAT-AAACTTTGATT
2746300 CAAACCAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.37
30 9 0.22
31 17 0.41
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (30 bp):
TATACATAAACTTTGATTTATATGCAATTG
Found at i:2751974 original size:19 final size:19
Alignment explanation
Indices: 2751929--2751983 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
2751919 TAAAAAAAAT
*
2751929 TATTTTTTAAACATTTTTA
1 TATTTTTTTAACATTTTTA
* *
2751948 TATATTTTTAAGATTTCTTA
1 TATTTTTTTAACATTT-TTA
2751968 -ATTTTTTT--CATTTTTA
1 TATTTTTTTAACATTTTTA
2751984 AAATTTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
19 20 0.67
20 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTTTTTAACATTTTTA
Found at i:2753640 original size:3 final size:3
Alignment explanation
Indices: 2753632--2753664 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2753622 TTCATCAACC
2753632 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2753665 GATTTTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2760474 original size:16 final size:17
Alignment explanation
Indices: 2760433--2760477 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 17
2760423 TAAGCAAGTT
2760433 TAATATTTTTGTCCAAACC
1 TAATATTTTTG--CAAACC
2760452 T-AT-TTTTTG-AAACC
1 TAATATTTTTGCAAACC
2760466 TAATATTTTTGC
1 TAATATTTTTGC
2760478 CCAAGATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 6 0.26
17 6 0.26
18 2 0.09
19 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (17 bp):
TAATATTTTTGCAAACC
Found at i:2761580 original size:32 final size:31
Alignment explanation
Indices: 2761521--2761597 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
2761511 ATCAACAAGT
2761521 TTAATTAA-TTAGTATGAGTTATCAAATTAAA
1 TTAATTAATTTA-TATGAGTTATCAAATTAAA
* *
2761552 TTAATTAATTTATCATGAGTTATTAAATTTAA
1 TTAATTAATTTAT-ATGAGTTATCAAATTAAA
* *
2761584 GTAATTAGTTTATA
1 TTAATTAATTTATA
2761598 AGGTTCTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 10 0.25
32 30 0.75
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.47
Consensus pattern (31 bp):
TTAATTAATTTATATGAGTTATCAAATTAAA
Found at i:2761909 original size:16 final size:16
Alignment explanation
Indices: 2761888--2761927 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
2761878 TCAATTTTAG
2761888 TATTATAA-GAAAATAT
1 TATTATAATGAAAA-AT
2761904 TATTATAATGAAAAAT
1 TATTATAATGAAAAAT
2761920 TATTATAA
1 TATTATAA
2761928 AGAGGTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
TATTATAATGAAAAAT
Found at i:2762352 original size:7 final size:7
Alignment explanation
Indices: 2762336--2762374 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
2762326 TATTTTTTTT
*
2762336 ACCTTAA
1 ACCTTGA
2762343 ACCTTGA
1 ACCTTGA
*
2762350 ACCTTAA
1 ACCTTGA
2762357 ACCTTGA
1 ACCTTGA
*
2762364 ATCTTGA
1 ACCTTGA
2762371 ACCT
1 ACCT
2762375 GGTTCAAGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (7 bp):
ACCTTGA
Found at i:2762355 original size:14 final size:14
Alignment explanation
Indices: 2762336--2762374 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2762326 TATTTTTTTT
2762336 ACCTTAAACCTTGA
1 ACCTTAAACCTTGA
2762350 ACCTTAAACCTTGA
1 ACCTTAAACCTTGA
* *
2762364 ATCTTGAACCT
1 ACCTTAAACCT
2762375 GGTTCAAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (14 bp):
ACCTTAAACCTTGA
Found at i:2763014 original size:7 final size:7
Alignment explanation
Indices: 2763002--2763033 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2762992 ATTAATCATA
2763002 AAAAGAT
1 AAAAGAT
2763009 AAAAGAT
1 AAAAGAT
2763016 AAAAGAT
1 AAAAGAT
2763023 AAAAGAT
1 AAAAGAT
2763030 AAAA
1 AAAA
2763034 AATATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAGAT
Found at i:2769701 original size:4 final size:4
Alignment explanation
Indices: 2769692--2769721 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2769682 ATCATCGTGA
*
2769692 TATG TATG TATG AATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
2769722 GAGTTACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:2772994 original size:31 final size:30
Alignment explanation
Indices: 2772945--2773004 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
2772935 GAGACAATTG
* * *
2772945 TGACCGATTATAAGGTATGAAAATGCAAATA
1 TGACCAATTACAAAGTATG-AAATGCAAATA
*
2772976 TGACCAATTACAAAGTATGATATGCAAAT
1 TGACCAATTACAAAGTATGAAATGCAAAT
2773005 GTGAATGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (30 bp):
TGACCAATTACAAAGTATGAAATGCAAATA
Found at i:2799300 original size:37 final size:37
Alignment explanation
Indices: 2799250--2799325 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
2799240 AAGCTCATTG
2799250 TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
1 TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
2799287 TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
1 TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
2799324 TC
1 TC
2799326 TTTAAGTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.26, C:0.33, G:0.13, T:0.28
Consensus pattern (37 bp):
TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
Found at i:2801325 original size:32 final size:34
Alignment explanation
Indices: 2801288--2801359 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 34
2801278 TATTACACAT
*
2801288 TAATTTTAA-TTTAG-TGCATTAAAATATTTTAC
1 TAATTTTAATTTTAGTTACATTAAAATATTTTAC
***
2801320 TAATTTTAATTTTAGTTACATTTTCATATTTTAC
1 TAATTTTAATTTTAGTTACATTAAAATATTTTAC
2801354 TAATTT
1 TAATTT
2801360 CATTGTCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 9 0.26
33 5 0.15
34 20 0.59
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (34 bp):
TAATTTTAATTTTAGTTACATTAAAATATTTTAC
Found at i:2801359 original size:17 final size:16
Alignment explanation
Indices: 2801311--2801359 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
2801301 GTGCATTAAA
2801311 ATATTTTACTAATTTT
1 ATATTTTACTAATTTT
*
2801327 A-ATTTTAGTTACATTTT
1 ATATTTTA-CTA-ATTTT
2801344 CATATTTTACTAATTT
1 -ATATTTTACTAATTT
2801360 CATTGTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 6 0.22
16 3 0.11
17 9 0.33
18 3 0.11
19 6 0.22
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (16 bp):
ATATTTTACTAATTTT
Found at i:2833800 original size:16 final size:16
Alignment explanation
Indices: 2833779--2833811 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2833769 ATAAAATATT
2833779 TAAAAAA-ATTATAAAA
1 TAAAAAATATTA-AAAA
2833795 TAAAAAATATTAAAAA
1 TAAAAAATATTAAAAA
2833811 T
1 T
2833812 TCAATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAAATATTAAAAA
Found at i:2835470 original size:14 final size:15
Alignment explanation
Indices: 2835448--2835523 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 15
2835438 CAATCAAACA
2835448 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
2835462 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
2835477 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
2835497 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
2835511 ACGGAAAA-CATTT
1 CCAGAAAATCATTT
2835524 CACTGGCTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.43
15 14 0.29
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:2835489 original size:20 final size:20
Alignment explanation
Indices: 2835464--2835503 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2835454 AATATTTTCC
*
2835464 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2835484 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2835504 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2835509 original size:34 final size:35
Alignment explanation
Indices: 2835452--2835518 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2835442 CAAACACCAG
*
2835452 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2835487 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2835519 CATTTCACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2836248 original size:135 final size:136
Alignment explanation
Indices: 2836097--2836368 Score: 537
Period size: 135 Copynumber: 2.0 Consensus size: 136
2836087 ATTGTAAATT
2836097 TAGTCCATATAGTTTAATTTGTTCTTTTTTATTTTTCATATATTTTTTTAAATTTTGAAATTTCA
1 TAGTCCATATAGTTTAATTTGTTCTTTTTTATTTTTCATATATTTTTTTAAATTTTGAAATTTCA
2836162 ATTTTTTATCAAATTACCGGCAATTAAATTCGTCAGGGGTAAGACAACATTTAGTCTATAAA-TT
66 ATTTTTTATCAAATTACCGGCAATTAAATTCGTCAGGGGTAAGACAACATTTAGTCTATAAAGTT
2836226 GACAGC
131 GACAGC
2836232 TAGTCCATATAGTTTAATTTGTTCTTTTTTATTTTTCATATATTTTTTTAAATTTTGAAATTTCA
1 TAGTCCATATAGTTTAATTTGTTCTTTTTTATTTTTCATATATTTTTTTAAATTTTGAAATTTCA
2836297 ATTTTTTATCAAATTACCGGCAATTAAATTCGTCAGGGGTAAGACAACATTTAGTCTATAAAGTT
66 ATTTTTTATCAAATTACCGGCAATTAAATTCGTCAGGGGTAAGACAACATTTAGTCTATAAAGTT
2836362 GACAGC
131 GACAGC
2836368 T
1 T
2836369 TTTCTCAATT
Statistics
Matches: 136, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
135 127 0.93
136 9 0.07
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (136 bp):
TAGTCCATATAGTTTAATTTGTTCTTTTTTATTTTTCATATATTTTTTTAAATTTTGAAATTTCA
ATTTTTTATCAAATTACCGGCAATTAAATTCGTCAGGGGTAAGACAACATTTAGTCTATAAAGTT
GACAGC
Found at i:2839623 original size:6 final size:6
Alignment explanation
Indices: 2839614--2839641 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2839604 AAAAAAGTAA
2839614 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
2839642 TCTGTAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:2850077 original size:15 final size:15
Alignment explanation
Indices: 2850057--2850087 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2850047 CACTTTCAAC
2850057 ATTTTATTCTATTTT
1 ATTTTATTCTATTTT
*
2850072 ATTTTATTGTATTTT
1 ATTTTATTCTATTTT
2850087 A
1 A
2850088 AAATTTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTATTCTATTTT
Found at i:2857269 original size:31 final size:31
Alignment explanation
Indices: 2857234--2857302 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
2857224 CTCAACAATC
*
2857234 CAATGACTTAAATAAAAACTAGTGGATAATT
1 CAATGACTTAAATAAAAACTAGTGAATAATT
* ** *
2857265 CAATGACTTCAATAAAAACTTTTGAATAGTT
1 CAATGACTTAAATAAAAACTAGTGAATAATT
2857296 CAATGAC
1 CAATGAC
2857303 CACTTTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (31 bp):
CAATGACTTAAATAAAAACTAGTGAATAATT
Found at i:2864231 original size:28 final size:28
Alignment explanation
Indices: 2864199--2864290 Score: 98
Period size: 28 Copynumber: 3.2 Consensus size: 28
2864189 GTTCAAACAC
2864199 ACTCATAATAAAAATCAGGGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAA
* *
2864227 ACTCAAGGTCACTAAATAATTA--GTAAACTAA
1 ACTC-A--T-AATAAA-AATCAGGGTAAACTAA
*
2864258 TCTCATAATAAAAATCAGGGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAA
2864286 ACTCA
1 ACTCA
2864291 ATGTCACTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.08
27 5 0.10
28 18 0.35
29 1 0.02
30 1 0.02
31 13 0.25
32 5 0.10
33 4 0.08
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (28 bp):
ACTCATAATAAAAATCAGGGTAAACTAA
Found at i:2864253 original size:31 final size:30
Alignment explanation
Indices: 2864218--2864312 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
2864208 AAAAATCAGG
2864218 GTAAACTAAACTCAAGGTCACTAAATAATTA
1 GTAAACTAAACTCAA-GTCACTAAATAATTA
* * *
2864249 GTAAACTAATCTC-A-T-AATAAA-AATCA
1 GTAAACTAAACTCAAGTCACTAAATAATTA
2864275 GGGTAAACTAAACTCAATGTCACTAAATAATTA
1 --GTAAACTAAACTCAA-GTCACTAAATAATTA
2864308 GTAAA
1 GTAAA
2864313 TTTACATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.08
27 5 0.10
28 13 0.25
29 1 0.02
30 1 0.02
31 18 0.35
32 5 0.10
33 4 0.08
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.26
Consensus pattern (30 bp):
GTAAACTAAACTCAAGTCACTAAATAATTA
Found at i:2864271 original size:59 final size:59
Alignment explanation
Indices: 2864200--2864312 Score: 217
Period size: 59 Copynumber: 1.9 Consensus size: 59
2864190 TTCAAACACA
2864200 CTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAACTAAT
1 CTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAACTAAT
*
2864259 CTCATAATAAAAATCAGGGTAAACTAAACTCAATGTCACTAAATAATTAGTAAA
1 CTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAA
2864313 TTTACATTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.26
Consensus pattern (59 bp):
CTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAACTAAT
Found at i:2864396 original size:31 final size:31
Alignment explanation
Indices: 2864355--2864420 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
2864345 CAAATGATCG
*
2864355 TTGAACTATTCAAAAGTTTTCATTTAAGTTA
1 TTGAACTATTCAAAAGTTTTCATTTAAGTCA
* *
2864386 TTGAATTATTCAAAAGTTTTTATTTAAGTCA
1 TTGAACTATTCAAAAGTTTTCATTTAAGTCA
2864417 TTGA
1 TTGA
2864421 GTTGTTAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (31 bp):
TTGAACTATTCAAAAGTTTTCATTTAAGTCA
Found at i:2865165 original size:19 final size:21
Alignment explanation
Indices: 2865127--2865176 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
2865117 TCAAAAGATA
**
2865127 TATAAAAGATATTTTTAAAAA-
1 TATAAAA-ATATTTAAAAAAAG
2865148 T-TAAAAATATTTAAAAAAAG
1 TATAAAAATATTTAAAAAAAG
2865168 TATAAAAAT
1 TATAAAAAT
2865177 TACAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 11 0.44
20 6 0.24
21 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
TATAAAAATATTTAAAAAAAG
Found at i:2875371 original size:27 final size:26
Alignment explanation
Indices: 2875341--2875404 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 26
2875331 TTTATCGAGG
2875341 TTATTAATTTATCGATAAATTAATATT
1 TTATTAATTTATCGATAAATTAATA-T
2875368 TTATTAATTTATCGATAAATTAATAT
1 TTATTAATTTATCGATAAATTAATAT
*
2875394 TCATTAATTTA
1 TTATTAATTTA
2875405 GAGAATATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 11 0.31
27 25 0.69
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.52
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATTAATAT
Found at i:2875551 original size:36 final size:35
Alignment explanation
Indices: 2875486--2875557 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
2875476 TGAATCAACG
*
2875486 TTAATTGGTTCATGTATAAAAAAAAAAAGAGTTAA
1 TTAATTGATTCATGTATAAAAAAAAAAAGAGTTAA
*
2875521 TTAATTGATTCATGTA-ACCAAAAAGAAAAGAGTTAA
1 TTAATTGATTCATGTATA--AAAAAAAAAAGAGTTAA
2875557 T
1 T
2875558 GATTTCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 1 0.03
35 15 0.45
36 17 0.52
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.31
Consensus pattern (35 bp):
TTAATTGATTCATGTATAAAAAAAAAAAGAGTTAA
Found at i:2885623 original size:7 final size:7
Alignment explanation
Indices: 2885605--2885639 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2885595 AATTAACCAA
*
2885605 AATAAAT
1 AATATAT
2885612 AATATAT
1 AATATAT
*
2885619 TATATAT
1 AATATAT
2885626 AATATAT
1 AATATAT
2885633 AATATAT
1 AATATAT
2885640 TTTTTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATATAT
Found at i:2887425 original size:31 final size:31
Alignment explanation
Indices: 2887377--2887440 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
2887367 AAAATTTTAA
* *
2887377 TTTAGTAAAGATAAAATTATACTTTGATCTT
1 TTTAGTAAAGATAAAATTATAATTTAATCTT
* *
2887408 TTTAG-AAATGATGAAATTTTAATTTAATCTT
1 TTTAGTAAA-GATAAAATTATAATTTAATCTT
2887439 TT
1 TT
2887441 AAAAATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (31 bp):
TTTAGTAAAGATAAAATTATAATTTAATCTT
Found at i:2891698 original size:14 final size:15
Alignment explanation
Indices: 2891678--2891719 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2891668 ATAATGTAAC
2891678 ATATATTTTAATGTT
1 ATATATTTTAATGTT
* *
2891693 -TATATTATAGTGTT
1 ATATATTTTAATGTT
2891707 ATATATTATTAAT
1 ATATATT-TTAAT
2891720 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 12 0.57
15 6 0.29
16 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
ATATATTTTAATGTT
Found at i:2903501 original size:30 final size:31
Alignment explanation
Indices: 2903426--2903512 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
2903416 AAACTTTATG
*
2903426 GGTTTTAGTGAGAATTTTCAAAAATTTTGGTA
1 GGTTTTA-TGAAAATTTTCAAAAATTTTGGTA
* * * * *
2903458 GGTCTAATTAAAATTTTCAAAATTTTTTG-A
1 GGTTTTATGAAAATTTTCAAAAATTTTGGTA
*
2903488 GGTTTTATGAAAATTTATAAAAAAT
1 GGTTTTATGAAAATTT-TCAAAAAT
2903513 GAAGAGTCTA
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
30 14 0.33
31 24 0.56
32 5 0.12
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (31 bp):
GGTTTTATGAAAATTTTCAAAAATTTTGGTA
Found at i:2910466 original size:15 final size:14
Alignment explanation
Indices: 2910439--2910466 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2910429 AATTAGTGTT
2910439 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
2910453 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
2910467 TGGGGGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
GAAAACTAAAAAAA
Found at i:2916925 original size:31 final size:30
Alignment explanation
Indices: 2916889--2917001 Score: 104
Period size: 31 Copynumber: 3.6 Consensus size: 30
2916879 GATTGACTAA
2916889 AATTTTTAAAAATTTTGAAGGTTTTAATGAG
1 AATTTTTAAAAATTTTGAAGG-TTTAATGAG
* * *
2916920 AATTTTTAAACAATTTTGTATGTTTAACT-AA
1 AATTTTTAAA-AATTTTGAAGGTTTAA-TGAG
**
2916951 AACTTTCAAAAAAATTTTTGAATGGTTTAATGAG
1 AA-TTT-TTAAAAA-TTTTGAA-GGTTTAATGAG
2916985 AA-TTTTAAAAATTTTGA
1 AATTTTTAAAAATTTTGA
2917002 GTGGGCTAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
30 6 0.09
31 23 0.35
32 17 0.26
33 10 0.15
34 9 0.14
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.44
Consensus pattern (30 bp):
AATTTTTAAAAATTTTGAAGGTTTAATGAG
Found at i:2917027 original size:65 final size:64
Alignment explanation
Indices: 2916896--2917027 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 64
2916886 TAAAATTTTT
**
2916896 AAAAATTTTGAAGGTTTTAATGAGAATTTTTAAACAATTTTGTATGTTTAACTAAAACTTTCAA
1 AAAAATTTTGAAGGTTTTAATGAGAATTTTTAAACAATTTTGTATGGCTAACTAAAACTTTCAA
* *
2916960 AAAAATTTTTGAATGG-TTTAATGAGAA-TTTTAAA-AATTTTG-AGTGGGCTAATTAAAATTTT
1 AAAAA-TTTTGAA-GGTTTTAATGAGAATTTTTAAACAATTTTGTA-T-GGCTAACTAAAACTTT
2917021 CAA
62 CAA
2917024 AAAA
1 AAAA
2917028 TGTATAATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
62 1 0.02
63 8 0.13
64 31 0.52
65 18 0.30
66 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (64 bp):
AAAAATTTTGAAGGTTTTAATGAGAATTTTTAAACAATTTTGTATGGCTAACTAAAACTTTCAA
Found at i:2926156 original size:100 final size:103
Alignment explanation
Indices: 2926019--2926290 Score: 371
Period size: 104 Copynumber: 2.7 Consensus size: 103
2926009 AAAATTACAT
*
2926019 TAAAAAATCACAAAACAC-TAAACT-AACACTAACAATTTATATAACCTAATCATAAATTACAAA
1 TAAAAAATCACAAAACACAT-AACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAA
**
2926082 CAAAATAACTATAAAA-TTATTT-ATTAAA-TACATTAC
65 CAAAATAACTATAAAATTTATTTAAAAAAAGTACATTAC
2926118 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
1 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
* *
2926183 AAAATAATTATAAAATTTTTTTAAAAAAAGTTACATTAC
66 AAAATAACTATAAAATTTATTTAAAAAAAG-TACATTAC
* * *
2926222 TAAAAGATCACAAAAC-CATATACTAAACACTAACAA-TT-TGTAACCTAATCCCATAAATTATT
1 TAAAAAATCACAAAACACATA-ACTAAACACTAACAATTTATATAACCTAAT--CATAAATTACT
2926284 AACAAAA
63 AACAAAA
2926291 ATAAATAACT
Statistics
Matches: 156, Mismatches: 8, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
99 22 0.14
100 54 0.35
101 5 0.03
102 14 0.09
103 6 0.04
104 55 0.35
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (103 bp):
TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
AAAATAACTATAAAATTTATTTAAAAAAAGTACATTAC
Found at i:2926248 original size:104 final size:99
Alignment explanation
Indices: 2926008--2926290 Score: 355
Period size: 100 Copynumber: 2.8 Consensus size: 99
2925998 TACATTATAT
2926008 AAAAATTACATTA--AAAAATCACAAAA-CACTAAACT-AACACTAACAATTTATATAACCTAAT
1 AAAAATTACATTACTAAAAATCACAAAACCA-T-AACTAAACACTAACAATTTATATAACCTAAT
*
2926069 CATAAATTACAAACAAAATAACTATAAAATTATTTA
64 CATAAATTACTAACAAAATAACTATAAAATTATTTA
**
2926105 TTAAA-TACATTACTAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAAT
1 AAAAATTACATTACT-AAAAATCACAAAAC-CATAACTAAACACTAACAATTTATATAACCTAAT
* *
2926169 CATAAATTACTAACAAAATAATTATAAAATTTTTTTAA
64 CATAAATTACTAACAAAATAACTATAAAA-TTATTT-A
*
2926207 AAAAAGTTACATTACTAAAAGATCACAAAACCATATACTAAACACTAACAA-TT-TGTAACCTAA
1 AAAAA-TTACATTACTAAAA-ATCACAAAACCATA-ACTAAACACTAACAATTTATATAACCTAA
*
2926270 TCCCATAAATTATTAACAAAA
63 T--CATAAATTACTAACAAAA
2926291 ATAAATAACT
Statistics
Matches: 163, Mismatches: 9, Indels: 21
0.84 0.05 0.11
Matches are distributed among these distances:
96 7 0.04
97 3 0.02
99 17 0.10
100 54 0.33
101 7 0.04
102 14 0.09
103 10 0.06
104 51 0.31
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (99 bp):
AAAAATTACATTACTAAAAATCACAAAACCATAACTAAACACTAACAATTTATATAACCTAATCA
TAAATTACTAACAAAATAACTATAAAATTATTTA
Found at i:2926775 original size:17 final size:17
Alignment explanation
Indices: 2926750--2926783 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2926740 AAAATAATAC
*
2926750 ATTACTTTTTTTTTCTT
1 ATTACTTTTATTTTCTT
*
2926767 ATTATTTTTATTTTCTT
1 ATTACTTTTATTTTCTT
2926784 CTCCTTTCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTACTTTTATTTTCTT
Found at i:2926973 original size:28 final size:26
Alignment explanation
Indices: 2926916--2926979 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
2926906 TATCTATGCA
* *
2926916 GCAGAGGGGCGTAGGGGGGCTGTATG
1 GCAGAGGGGCGCAGGGGGGCTGTAGG
*
2926942 GCAGAGGGGCGCAGGGGGGCTGTGCGGG
1 GCAGAGGGGCGCAGGGGGGCTGT--AGG
2926970 GCAGAGGGGC
1 GCAGAGGGGC
2926980 ACAAGGGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 22 0.67
28 11 0.33
ACGTcount: A:0.14, C:0.16, G:0.61, T:0.09
Consensus pattern (26 bp):
GCAGAGGGGCGCAGGGGGGCTGTAGG
Found at i:2933731 original size:26 final size:26
Alignment explanation
Indices: 2933702--2933754 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2933692 TTTCAACCAG
2933702 TTTGTACTAATTTACGAGTCAAAAAA
1 TTTGTACTAATTTACGAGTCAAAAAA
2933728 TTTGTACTAATTTACGAGTCAAAAAA
1 TTTGTACTAATTTACGAGTCAAAAAA
2933754 T
1 T
2933755 CAGCCAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (26 bp):
TTTGTACTAATTTACGAGTCAAAAAA
Found at i:2935858 original size:13 final size:13
Alignment explanation
Indices: 2935840--2935865 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2935830 GCTTCAATAA
2935840 ATGTTTTGACAAT
1 ATGTTTTGACAAT
2935853 ATGTTTTGACAAT
1 ATGTTTTGACAAT
2935866 CAATACAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATGTTTTGACAAT
Found at i:2940825 original size:11 final size:11
Alignment explanation
Indices: 2940809--2940841 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2940799 GGGTGAATTG
2940809 ATCTTTCTCTT
1 ATCTTTCTCTT
*
2940820 ATCTTTTTCTT
1 ATCTTTCTCTT
2940831 ATCTTTCTCTT
1 ATCTTTCTCTT
2940842 TAATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (11 bp):
ATCTTTCTCTT
Found at i:2942081 original size:19 final size:19
Alignment explanation
Indices: 2942057--2942094 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2942047 TTTGATTATT
2942057 TGAAAACCTATTTTAATGA
1 TGAAAACCTATTTTAATGA
2942076 TGAAAACCTATTTTAATGA
1 TGAAAACCTATTTTAATGA
2942095 AAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
TGAAAACCTATTTTAATGA
Found at i:2942100 original size:19 final size:19
Alignment explanation
Indices: 2942059--2942100 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2942049 TGATTATTTG
**
2942059 AAAACCTATTTTAATGATG
1 AAAACCTATTTTAATGAAA
2942078 AAAACCTATTTTAATGAAA
1 AAAACCTATTTTAATGAAA
2942097 AAAA
1 AAAA
2942101 AAATCTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (19 bp):
AAAACCTATTTTAATGAAA
Found at i:2943338 original size:66 final size:65
Alignment explanation
Indices: 2943232--2943362 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 65
2943222 TCGACTAAAC
2943232 CCAAATAATACAAAACCAAAAGGAGAAAGACATGTAAAGCCTCGCGCAAGGGACCAACAACACCC
1 CCAAATAATACAAAACCAAAAGGAGAAAGACATGTAAAGCCTCG-GCAAGGGACCAACAACACCC
2943297 T
65 T
* *
2943298 CCAAATAATACAAAACCAAAAGTAGAAAGAGATGTAAAGCCTCGGCAAGGGACCAACAACACCCT
1 CCAAATAATACAAAACCAAAAGGAGAAAGACATGTAAAGCCTCGGCAAGGGACCAACAACACCCT
2943363 TTATAAGGCT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 21 0.33
66 42 0.67
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.10
Consensus pattern (65 bp):
CCAAATAATACAAAACCAAAAGGAGAAAGACATGTAAAGCCTCGGCAAGGGACCAACAACACCCT
Found at i:2948473 original size:23 final size:24
Alignment explanation
Indices: 2948429--2948473 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
2948419 ATTTTCCCGA
* *
2948429 TAAAAATTTGATTAATTTTATTGT
1 TAAAAATTTAATTAATTCTATTGT
*
2948453 TAAAAA-TTAATTTATTCTATT
1 TAAAAATTTAATTAATTCTATT
2948474 TATGATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAAAAATTTAATTAATTCTATTGT
Found at i:2948774 original size:11 final size:11
Alignment explanation
Indices: 2948758--2948782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2948748 ACAGCAATGG
2948758 CCAATGTTCAT
1 CCAATGTTCAT
2948769 CCAATGTTCAT
1 CCAATGTTCAT
2948780 CCA
1 CCA
2948783 TCAGAGGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (11 bp):
CCAATGTTCAT
Found at i:2971705 original size:31 final size:32
Alignment explanation
Indices: 2971639--2971705 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 32
2971629 ACGTGATTTT
* *
2971639 AAAAAAAATACATCAAAATCTAACAATATACA
1 AAAAAAAAAACATCAAAATATAACAATATACA
* *
2971671 AAAAAAAAAACA-C-AAATATACACATTATATA
1 AAAAAAAAAACATCAAAATATA-ACAATATACA
2971702 AAAA
1 AAAA
2971706 TGCATGAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 6 0.20
31 13 0.43
32 11 0.37
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (32 bp):
AAAAAAAAAACATCAAAATATAACAATATACA
Found at i:2971859 original size:22 final size:21
Alignment explanation
Indices: 2971834--2971890 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
2971824 TTAAAATATT
2971834 AAATTAAATTTTTATTATTT-TA
1 AAATTAAA-TTTTATT-TTTATA
2971856 AAATGT-AATTTTATTTTTATA
1 AAAT-TAAATTTTATTTTTATA
*
2971877 AATTTAAAATTTTA
1 AAATT-AAATTTTA
2971891 AAATACTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
20 4 0.13
21 12 0.40
22 13 0.43
23 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AAATTAAATTTTATTTTTATA
Found at i:2974188 original size:15 final size:16
Alignment explanation
Indices: 2974168--2974201 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2974158 ATCATTCAAA
2974168 AAATTACAAAAAT-AT
1 AAATTACAAAAATAAT
*
2974183 AAATTACTAAAATAAT
1 AAATTACAAAAATAAT
2974199 AAA
1 AAA
2974202 ATTATATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATTACAAAAATAAT
Found at i:2980106 original size:15 final size:15
Alignment explanation
Indices: 2980073--2980106 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2980063 TTACAATAAG
* *
2980073 AAAAATAAAAATTTT
1 AAAAATAAAAATATA
2980088 AAAAATAAAAATATA
1 AAAAATAAAAATATA
2980103 AAAA
1 AAAA
2980107 TTAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAAAATATA
Found at i:2980444 original size:6 final size:6
Alignment explanation
Indices: 2980428--2980462 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
2980418 TCATGTATTG
*
2980428 TGTGTA CGTGTA TGTGTA TGTGTA TGTGTA TGTGT
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGT
2980463 GTGGGTGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.03, G:0.34, T:0.49
Consensus pattern (6 bp):
TGTGTA
Found at i:2983118 original size:13 final size:13
Alignment explanation
Indices: 2983102--2983131 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2983092 TGGTATGAGT
2983102 TTATGGGTTTTGG
1 TTATGGGTTTTGG
2983115 TTATGGGTTTTGG
1 TTATGGGTTTTGG
2983128 TTAT
1 TTAT
2983132 AGGCAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.33, T:0.57
Consensus pattern (13 bp):
TTATGGGTTTTGG
Found at i:2983291 original size:25 final size:26
Alignment explanation
Indices: 2983263--2983312 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
2983253 AGAAGAAAGT
2983263 TTAAAGAACATAAAA-GAAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAAA
** *
2983288 TTAAATTACTTAAAACGAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
2983313 TATGGGGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (26 bp):
TTAAAGAACATAAAACGAAAAAAAAA
Found at i:2983817 original size:43 final size:43
Alignment explanation
Indices: 2983757--2983851 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
2983747 AATGATGATA
*
2983757 TAAAATT-ATACAAATATAAATTATTTTATTTTATATGTCTTT
1 TAAAATTAAAACAAATATAAATTATTTTATTTTATATGTCTTT
*
2983799 TAAAATTAAAACAAATATAAATTATTTTATTTTGTATGTCTTT
1 TAAAATTAAAACAAATATAAATTATTTTATTTTATATGTCTTT
2983842 TAAAATTAAA
1 TAAAATTAAA
2983852 GGAAACAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 7 0.14
43 43 0.86
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (43 bp):
TAAAATTAAAACAAATATAAATTATTTTATTTTATATGTCTTT
Found at i:2987290 original size:27 final size:27
Alignment explanation
Indices: 2987252--2987316 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
2987242 ATTGATAAGG
*
2987252 ACGTAAAATTTTAGTGGGTTACACTAC
1 ACGTAAAATTTTAGTGGGTTAAACTAC
2987279 ACGTAAAATTTTAGTGGGTTAAACTAC
1 ACGTAAAATTTTAGTGGGTTAAACTAC
*
2987306 ACATAAGAATT
1 ACGTAA-AATT
2987317 GATAAGAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 31 0.89
28 4 0.11
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (27 bp):
ACGTAAAATTTTAGTGGGTTAAACTAC
Found at i:2988162 original size:110 final size:110
Alignment explanation
Indices: 2987969--2988188 Score: 422
Period size: 110 Copynumber: 2.0 Consensus size: 110
2987959 TTTTGTGGCG
2987969 TTTGGACGGAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCAAAAAATAAAACGCCGCAAAATA
1 TTTGGACGGAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCAAAAAATAAAACGCCGCAAAATA
2988034 TATAGCAGTAGCGGCGCTTCAAGCAAAACGCAGTAAAAGAACATA
66 TATAGCAGTAGCGGCGCTTCAAGCAAAACGCAGTAAAAGAACATA
*
2988079 TTTGGACGGAAAACGCCGCTAAAAATCGAGCATTAGTGGCGCAAAAAATAAAACGCCGCAAAATA
1 TTTGGACGGAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCAAAAAATAAAACGCCGCAAAATA
*
2988144 TATAGCAGTAGCGGCGCTTCAAGCAAAACGCCGTAAAAGAACATA
66 TATAGCAGTAGCGGCGCTTCAAGCAAAACGCAGTAAAAGAACATA
2988189 ATTAGCAGCG
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (110 bp):
TTTGGACGGAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCAAAAAATAAAACGCCGCAAAATA
TATAGCAGTAGCGGCGCTTCAAGCAAAACGCAGTAAAAGAACATA
Found at i:2990244 original size:45 final size:45
Alignment explanation
Indices: 2990194--2990284 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
2990184 TGTTGCGTCC
* * *
2990194 TTCTTGCCCAATTTCTTGAATTCCCAAATCCGTAAATCGCCTCCT
1 TTCTTGCCCAATTTCTTAAAATCCCAAATCCCTAAATCGCCTCCT
* *
2990239 TTCTTGCCTAATTTCTTAAAATCCGAAATCCCTAAATCGCCTCCT
1 TTCTTGCCCAATTTCTTAAAATCCCAAATCCCTAAATCGCCTCCT
2990284 T
1 T
2990285 CCTCCTTCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (45 bp):
TTCTTGCCCAATTTCTTAAAATCCCAAATCCCTAAATCGCCTCCT
Done.