Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 98 of 163
Found at i:27562596 original size:15 final size:15
Alignment explanation
Indices: 27562562--27562594 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
27562552 TTTCAAAATA
27562562 TTTCCAGATCTGGGT
1 TTTCCAGATCTGGGT
27562577 TTTCCTAGATCTGGGT
1 TTTCC-AGATCTGGGT
27562593 TT
1 TT
27562595 CCAAATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.45
Consensus pattern (15 bp):
TTTCCAGATCTGGGT
Found at i:27563516 original size:6 final size:6
Alignment explanation
Indices: 27563498--27563606 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
27563488 TTAAATTGAT
* *
27563498 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA
* ** *
27563545 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAACA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA-A
*
27563594 TTAAAAA TTTAAA
1 TT-TAAA TTTAAA
27563607 AGCCCAATGT
Statistics
Matches: 83, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 50 0.60
7 15 0.18
8 6 0.07
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:27563528 original size:17 final size:15
Alignment explanation
Indices: 27563502--27563566 Score: 78
Period size: 17 Copynumber: 4.1 Consensus size: 15
27563492 ATTGATTTTA
27563502 AATTTATTTAAATTT
1 AATTTATTTAAATTT
27563517 AGATTTATTTTAAATTT
1 A-ATTTA-TTTAAATTT
*
27563534 AA-ATATTTAAATTT
1 AATTTATTTAAATTT
27563548 AATTTGAATTTAAATTT
1 AATTT--ATTTAAATTT
27563565 AA
1 AA
27563567 ATAAAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.26
15 4 0.09
16 6 0.14
17 22 0.51
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
AATTTATTTAAATTT
Found at i:27563544 original size:31 final size:31
Alignment explanation
Indices: 27563506--27563569 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
27563496 ATTTTAAATT
*
27563506 TATTTAAATTTAGATTT-ATTTTAAATTTAAA
1 TATTTAAATTTA-ATTTGAATTTAAATTTAAA
27563537 TATTTAAATTTAATTTGAATTTAAATTTAAA
1 TATTTAAATTTAATTTGAATTTAAATTTAAA
27563568 TA
1 TA
27563570 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TATTTAAATTTAATTTGAATTTAAATTTAAA
Found at i:27563552 original size:11 final size:11
Alignment explanation
Indices: 27563488--27563568 Score: 64
Period size: 11 Copynumber: 7.5 Consensus size: 11
27563478 GACTTTTGAG
* *
27563488 TTAAATTGATT
1 TTAAATTTAAT
27563499 TTAAATTT-AT
1 TTAAATTTAAT
27563509 TTAAATTTAGAT
1 TTAAATTTA-AT
*
27563521 TT-ATTTTAAAT
1 TTAAATTT-AAT
27563532 TTAAA--T-AT
1 TTAAATTTAAT
27563540 TTAAATTTAAT
1 TTAAATTTAAT
*
27563551 TTGAATTTAAAT
1 TTAAATTT-AAT
27563563 TTAAAT
1 TTAAAT
27563569 AAAAATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 7 0.12
10 11 0.20
11 24 0.43
12 14 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:27563565 original size:42 final size:41
Alignment explanation
Indices: 27563498--27563591 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 41
27563488 TTAAATTGAT
* ** * *
27563498 TTTAAATTT-ATTTAAATTTAGATTTATTTTAAATTTAAATA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAA-A
*
27563539 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
27563580 TATTAAATTTAA
1 T-TTAAATTTAA
27563592 CATTAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 11 0.24
42 34 0.76
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (41 bp):
TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
Found at i:27563605 original size:20 final size:18
Alignment explanation
Indices: 27563554--27563606 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
27563544 ATTTAATTTG
*
27563554 AATTTAAATTTAAATAAA
1 AATTAAAATTTAAATAAA
*
27563572 AATTAAAATATTAAATTTAA
1 AATTAAAAT-TTAAA-TAAA
*
27563592 CATTAAAAATTTAAA
1 AATT-AAAATTTAAA
27563607 AGCCCAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 8 0.28
19 5 0.17
20 11 0.38
21 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAAATTTAAATAAA
Found at i:27564278 original size:3 final size:3
Alignment explanation
Indices: 27564263--27564319 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
27564253 TCATAACATT
* * * *
27564263 TAA TAA CAA TAA TAA TAA TAT TAA TTAA TAA CAT TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
*
27564308 AAA TAA TAA TAA
1 TAA TAA TAA TAA
27564320 AAAATGAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:27565469 original size:30 final size:30
Alignment explanation
Indices: 27565430--27565730 Score: 433
Period size: 30 Copynumber: 10.0 Consensus size: 30
27565420 CCCTAAATTG
* **
27565430 TCCAGAAATTACATTTTAACAATAAAACTTT
1 TCCA-AAATTACATTTTGACCCTAAAACTTT
*
27565461 TCTAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
**
27565491 TCCAAAATTATGTTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
** *
27565521 TCCAAAATTATGTTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
*
27565551 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
* *
27565581 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
* *
27565611 TCTAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
*
27565641 TCCAAAATTACATTTTGACCCTAAACCTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
27565671 TCCAAAATTACATTTTGA-CCTCAAAACTTT
1 TCCAAAATTACATTTTGACCCT-AAAACTTT
*
27565701 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
27565731 CTTAAATCCC
Statistics
Matches: 250, Mismatches: 18, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
29 3 0.01
30 242 0.97
31 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCTAAAACTTT
Found at i:27566890 original size:10 final size:10
Alignment explanation
Indices: 27566871--27566899 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
27566861 TAAACCGATG
27566871 TTTT-AACGT
1 TTTTAAACGT
27566880 TTTTAAACGT
1 TTTTAAACGT
27566890 TTTTAAACGT
1 TTTTAAACGT
27566900 ATTGTTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (10 bp):
TTTTAAACGT
Found at i:27567072 original size:30 final size:30
Alignment explanation
Indices: 27567021--27567248 Score: 242
Period size: 30 Copynumber: 7.8 Consensus size: 30
27567011 CGACAGTCCA
27567021 AAAATTACATTTTGA-CCCAAAACTTTCTG
1 AAAATTACATTTTGACCCCAAAACTTTCTG
*
27567050 AAAGTT-CTATTTTGACCCCAAAACTTTCTG
1 AAAATTAC-ATTTTGACCCCAAAACTTTCTG
**
27567080 AAAATTACATTTCAACCCCAAAACTTTTCCT-
1 AAAATTACATTTTGACCCCAAAAC-TTT-CTG
* *
27567111 -AAATTACATTTCGA-CCCAAAACTTT-TCC
1 AAAATTACATTTTGACCCCAAAACTTTCT-G
**
27567139 AAAATTACATTTTGACCTTAAAACTTTC--
1 AAAATTACATTTTGACCCCAAAACTTTCTG
*
27567167 AAAATTATATTTTGACCCCAAAACTTTCTG
1 AAAATTACATTTTGACCCCAAAACTTTCTG
* * *
27567197 GAAATTACATTTTGACCCTAAAACTTT-TCC
1 AAAATTACATTTTGACCCCAAAACTTTCT-G
27567227 AAAATTACATTTTGA-CCCAAAA
1 AAAATTACATTTTGACCCCAAAA
27567249 TTCAAAAAAA
Statistics
Matches: 169, Mismatches: 17, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
26 1 0.01
28 29 0.17
29 40 0.24
30 93 0.55
31 4 0.02
32 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTCTG
Found at i:27567091 original size:59 final size:57
Alignment explanation
Indices: 27567021--27567248 Score: 232
Period size: 59 Copynumber: 3.9 Consensus size: 57
27567011 CGACAGTCCA
27567021 AAAATTACATTTTGACCCAAAACTTTCTGAAAGTTCTATTTTGACCCCAAAACTTTCTG
1 AAAATTACATTTTGACCCAAAACTTTCT-AAA-TTCTATTTTGACCCCAAAACTTTCTG
** * *
27567080 AAAATTACATTTCAACCCCAAAACTTTTCCTAAATTAC-ATTTCGA-CCCAAAACTTT-TCC
1 AAAATTACATTTTGA-CCCAAAAC-TTT-CTAAATT-CTATTTTGACCCCAAAACTTTCT-G
* * *
27567139 AAAATTACATTTTGACCTTAAAACTTTCAAAATTATATTTTGACCCCAAAACTTTCTG
1 AAAATTACATTTTGACC-CAAAACTTTCTAAATTCTATTTTGACCCCAAAACTTTCTG
* *
27567197 GAAATTACATTTTGACCCTAAAACTTTTCCAAAATTAC-ATTTTGA-CCCAAAA
1 AAAATTACATTTTGACCC-AAAAC-TTT-CTAAATT-CTATTTTGACCCCAAAA
27567249 TTCAAAAAAA
Statistics
Matches: 142, Mismatches: 14, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
57 12 0.08
58 38 0.27
59 53 0.37
60 30 0.21
61 7 0.05
62 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (57 bp):
AAAATTACATTTTGACCCAAAACTTTCTAAATTCTATTTTGACCCCAAAACTTTCTG
Found at i:27567190 original size:117 final size:117
Alignment explanation
Indices: 27567021--27567248 Score: 350
Period size: 117 Copynumber: 1.9 Consensus size: 117
27567011 CGACAGTCCA
* *
27567021 AAAATTACATTTTGACCCAAAACTTTCTGAAAGTTCTATTTTGACCCCAAAACTTTCTGAAAATT
1 AAAATTACATTTTGACCCAAAACTTTC-GAAAATTATATTTTGACCCCAAAACTTTCTGAAAATT
*
27567086 ACATTTCAACCCCAAAACTTTTCCTAAATTACATTTCGACCCAAAACTTTTCC
65 ACATTTCAACCCCAAAACTTTTCCAAAATTACATTTCGACCCAAAACTTTTCC
* *
27567139 AAAATTACATTTTGACCTTAAAACTTTC-AAAATTATATTTTGACCCCAAAACTTTCTGGAAATT
1 AAAATTACATTTTGACC-CAAAACTTTCGAAAATTATATTTTGACCCCAAAACTTTCTGAAAATT
** * *
27567203 ACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCAAAA
65 ACATTTCAACCCCAAAACTTTTCCAAAATTACATTTCGACCCAAAA
27567249 TTCAAAAAAA
Statistics
Matches: 100, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
117 74 0.74
118 17 0.17
119 9 0.09
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (117 bp):
AAAATTACATTTTGACCCAAAACTTTCGAAAATTATATTTTGACCCCAAAACTTTCTGAAAATTA
CATTTCAACCCCAAAACTTTTCCAAAATTACATTTCGACCCAAAACTTTTCC
Found at i:27579271 original size:68 final size:68
Alignment explanation
Indices: 27579069--27579837 Score: 1317
Period size: 68 Copynumber: 11.3 Consensus size: 68
27579059 ATTATTTCCT
**
27579069 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAA
27579134 CGTC
65 CGTC
* **
27579138 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAA
27579203 CGTC
65 CGTC
* *
27579207 ATCCTTTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATCGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
27579272 GTC
66 GTC
27579275 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
27579340 GTC
66 GTC
* * * *
27579343 ATCCTCTTGAAATTGAAGTAGAGTAGATAACAAGTCTTTTTCTCTGAAATCGAAGTAAGAGTAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
27579408 GTC
66 GTC
27579411 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
27579476 GTC
66 GTC
*
27579479 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATCGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
27579544 GTC
66 GTC
*
27579547 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTC-TTTTCTCTGAAATCGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
27579611 GTC
66 GTC
* *
27579614 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTTTGAAATCGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
27579679 GTC
66 GTC
27579682 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
27579747 GTC
66 GTC
**
27579750 AT-CTACTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 ATCCT-CTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCA
27579814 ACGTC
64 ACGTC
* *
27579819 ATCCTTTTGGAATTGAAGT
1 ATCCTCTTGAAATTGAAGT
27579838 GAAGTGGGAT
Statistics
Matches: 672, Mismatches: 24, Indels: 8
0.95 0.03 0.01
Matches are distributed among these distances:
67 69 0.10
68 455 0.68
69 146 0.22
70 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (68 bp):
ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:27580152 original size:6 final size:6
Alignment explanation
Indices: 27580143--27580209 Score: 63
Period size: 6 Copynumber: 12.0 Consensus size: 6
27580133 TTAAATTGAT
27580143 TTTAAA TTT--A TTTAAA TTTAAA TTTAAA -TT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
27580186 ATTAAA ATTAAA ATTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
27580210 AATGAAATAC
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
3 1 0.02
4 6 0.11
5 2 0.04
6 46 0.84
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:27580156 original size:21 final size:20
Alignment explanation
Indices: 27580132--27580209 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 20
27580122 GACTTTTTGT
* *
27580132 TTTAAATTGATTTTAAATTTA
1 TTTAAATTAAATTTAAA-TTA
27580153 TTTAAATTTAAATTTAAATTA
1 TTTAAA-TTAAATTTAAATTA
*
27580174 TTTAAATTTAAAATTAAA--A
1 TTTAAA-TTAAATTTAAATTA
* *
27580193 TTAAAATTAAAATTAAA
1 TTTAAATTAAATTTAAA
27580210 AATGAAATAC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
18 11 0.21
19 6 0.12
21 26 0.50
22 9 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
TTTAAATTAAATTTAAATTA
Found at i:27580210 original size:6 final size:6
Alignment explanation
Indices: 27580175--27580230 Score: 67
Period size: 6 Copynumber: 9.0 Consensus size: 6
27580165 TTTAAATTAT
* * *
27580175 TTAAAT TTAAAA TTAAAA TTAAAA TTAAAA TTAAAAA TGAAATA CTAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT-AAAA TTAAA-A TTAAAA
27580225 TTAAAA
1 TTAAAA
27580231 AGTCCAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
6 34 0.79
7 9 0.21
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (6 bp):
TTAAAA
Found at i:27582084 original size:30 final size:30
Alignment explanation
Indices: 27582031--27582353 Score: 285
Period size: 30 Copynumber: 10.8 Consensus size: 30
27582021 AAATTGTCCA
*
27582031 AAAATTACATTTTAACCCCAAAACTTTTTG
1 AAAATTACATTTTGACCCCAAAACTTTTTG
* * * *
27582061 AAAGTT-CTATTTTGACCCAAAAACTTTCTA
1 AAAATTAC-ATTTTGACCCCAAAACTTTTTG
* ** **
27582091 AAAATTACATGTCAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTTG
* * * **
27582121 TAAATTACATTTTAACCCTAAAACTTTTCA
1 AAAATTACATTTTGACCCCAAAACTTTTTG
* * *
27582151 AAAATTATATTTTGACCCCAACACTTTCT-
1 AAAATTACATTTTGACCCCAAAACTTTTTG
** **
27582180 AGAAATTACATTTCAACCCCAAAACTTTTCC
1 A-AAATTACATTTTGACCCCAAAACTTTTTG
**
27582211 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTTG
* * *
27582241 AAAATTATATTTTGACCCTAAAACTTTCT-
1 AAAATTACATTTTGACCCCAAAACTTTTTG
*
27582270 AGAAATTACATTTTGACCCTAAAACTTTTCT-
1 A-AAATTACATTTTGACCCCAAAACTTTT-TG
* **
27582301 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTTG
* *
27582331 AAAATCATATTTTGACCCCAAAA
1 AAAATTACATTTTGACCCCAAAA
27582354 TTTCAAAAAA
Statistics
Matches: 243, Mismatches: 43, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
29 3 0.01
30 236 0.97
31 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTTG
Found at i:27582108 original size:60 final size:58
Alignment explanation
Indices: 27582029--27582353 Score: 332
Period size: 60 Copynumber: 5.4 Consensus size: 58
27582019 CTAAATTGTC
* *
27582029 CAAAAATTACATTTTAACCCCAAAACTTTTTGAAAGTT-CTATTTTGACCCAAAAAC-TTT
1 CAAAAATTACATTTTGACCCCAAAACTTTTT-AAA-TTAC-ATTTTGACCCTAAAACTTTT
* ** *
27582088 CTAAAAATTACATGTCAACCCCAAAACTTTTCCTAAATTACATTTTAACCCTAAAACTTTT
1 C-AAAAATTACATTTTGACCCCAAAACTTTT--TAAATTACATTTTGACCCTAAAACTTTT
* * * ** *
27582149 CAAAAATTATATTTTGACCCCAACACTTTCTAGAAATTACATTTCAACCCCAAAACTTTT
1 CAAAAATTACATTTTGACCCCAAAACTTT-T-TAAATTACATTTTGACCCTAAAACTTTT
* * *
27582209 CCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAAC-TTT
1 CAAAAATTACATTTTGACCCCAAAACTTTT--TAAATTACATTTTGACCCTAAAACTTTT
* *
27582268 CTAGAAATTACATTTTGACCCTAAAACTTTTCTAAAATTACATTTTGACCCTAAAACTTTT
1 C-AAAAATTACATTTTGACCCCAAAACTTTT-T-AAATTACATTTTGACCCTAAAACTTTT
* * *
27582329 CCAAAATCATATTTTGACCCCAAAA
1 CAAAAATTACATTTTGACCCCAAAA
27582354 TTTCAAAAAA
Statistics
Matches: 224, Mismatches: 32, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
59 7 0.03
60 203 0.91
61 13 0.06
62 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (58 bp):
CAAAAATTACATTTTGACCCCAAAACTTTTTAAATTACATTTTGACCCTAAAACTTTT
Found at i:27582186 original size:90 final size:90
Alignment explanation
Indices: 27582032--27582357 Score: 458
Period size: 90 Copynumber: 3.6 Consensus size: 90
27582022 AATTGTCCAA
** * * * *
27582032 AAATTACATTTTAACCCCAAAACTTTTTGAAAGTTCTATTTTGACCCAAAAACTTTCTAAAAATT
1 AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCTAGAAATT
*
27582097 ACATGTCAACCCCAAAACTTTTCCT
66 ACATTTCAACCCCAAAACTTTTCCT
* * *
27582122 AAATTACATTTTAACCCTAAAACTTTTCAAAAATTATATTTTGACCCCAACACTTTCTAGAAATT
1 AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCTAGAAATT
*
27582187 ACATTTCAACCCCAAAACTTTTCCA
66 ACATTTCAACCCCAAAACTTTTCCT
* *
27582212 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCTAGAAATT
1 AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCTAGAAATT
** *
27582277 ACATTTTGACCCTAAAACTTTT-CT
66 ACATTTCAACCCCAAAACTTTTCCT
* * *
27582301 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATCATATTTTGACCCCAAAA-TTTC
1 -AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTC
27582358 AAAAAAATTG
Statistics
Matches: 213, Mismatches: 22, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
89 5 0.02
90 208 0.98
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (90 bp):
AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCTAGAAATT
ACATTTCAACCCCAAAACTTTTCCT
Found at i:27582373 original size:30 final size:30
Alignment explanation
Indices: 27582030--27582401 Score: 278
Period size: 30 Copynumber: 12.4 Consensus size: 30
27582020 TAAATTGTCC
* **
27582030 AAAAATTACATTTTAACCCCAAAACTTTTT
1 AAAAATTACATTTTGACCCCAAAACTTTCA
* * * *
27582060 GAAAGTT-CTATTTTGACCCAAAAACTTTCT
1 AAAAATTAC-ATTTTGACCCCAAAACTTTCA
* **
27582090 AAAAATTACATGTCAACCCCAAAACTTTTC-
1 AAAAATTACATTTTGACCCCAAAAC-TTTCA
** * *
27582120 CTAAATTACATTTTAACCCTAAAACTTTTC-
1 AAAAATTACATTTTGACCCCAAAAC-TTTCA
* * *
27582150 AAAAATTATATTTTGACCCCAACACTTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCA
* **
27582180 AGAAATTACATTTCAACCCCAAAACTTTTC-
1 AAAAATTACATTTTGACCCCAAAAC-TTTCA
*
27582210 CAAAATTACATTTTGACCCCAAAACTTTTC-
1 AAAAATTACATTTTGACCCCAAAAC-TTTCA
* * * *
27582240 CAAAATTATATTTTGACCCTAAAACTTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCA
* *
27582270 AGAAATTACATTTTGACCCTAAAACTTTTC-
1 AAAAATTACATTTTGACCCCAAAAC-TTTCA
* *
27582300 TAAAATTACATTTTGACCCTAAAACTTTTC-
1 AAAAATTACATTTTGACCCCAAAAC-TTTCA
* * *
27582330 CAAAATCATATTTTGACCCCAAAA-TTTCAA
1 AAAAATTACATTTTGACCCCAAAACTTTC-A
* * *
27582360 AAAAATTGCATTTT-ACCCCGAAGCTTTC-
1 AAAAATTACATTTTGACCCCAAAACTTTCA
27582388 AAAAATTATCATTT
1 AAAAATTA-CATTT
27582402 CACCCTCAAA
Statistics
Matches: 282, Mismatches: 49, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
28 11 0.04
29 21 0.07
30 237 0.84
31 13 0.05
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCAAAACTTTCA
Found at i:27590944 original size:4 final size:4
Alignment explanation
Indices: 27590935--27590960 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
27590925 GGAGAAACGT
27590935 AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AG
27590961 GTAGGCCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:27593972 original size:18 final size:18
Alignment explanation
Indices: 27593949--27593986 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
27593939 ACGAATAAAC
27593949 TTGTCGATATTATTGCTA
1 TTGTCGATATTATTGCTA
27593967 TTGTCGATATTATTGCTA
1 TTGTCGATATTATTGCTA
27593985 TT
1 TT
27593987 AAGAGTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.53
Consensus pattern (18 bp):
TTGTCGATATTATTGCTA
Found at i:27595864 original size:23 final size:23
Alignment explanation
Indices: 27595830--27595881 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
27595820 AATTTTGTCA
27595830 ATTTTAACTTG-TATTAAAAAAAT
1 ATTTTAACTTGTTA-TAAAAAAAT
* **
27595853 ATTTTAATTTGTTATATCAAAAT
1 ATTTTAACTTGTTATAAAAAAAT
27595876 ATTTTA
1 ATTTTA
27595882 TCAAATAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (23 bp):
ATTTTAACTTGTTATAAAAAAAT
Found at i:27600016 original size:5 final size:5
Alignment explanation
Indices: 27600002--27600041 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
27599992 ATATAAATAT
27600002 TTTTC TTTTTC TTTTC TTTTC TTTTC TTCTTC TTTT- TTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTT
27600042 ATATATGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 19 0.58
6 10 0.30
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:27600023 original size:16 final size:17
Alignment explanation
Indices: 27600002--27600041 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
27599992 ATATAAATAT
27600002 TTTTCTTTTTCTT-TTC
1 TTTTCTTTTTCTTCTTC
27600018 TTTTC-TTTTCTTCTTC
1 TTTTCTTTTTCTTCTTC
27600034 TTTT-TTTT
1 TTTTCTTTT
27600042 ATATATGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTTCTTCTTC
Found at i:27600028 original size:21 final size:20
Alignment explanation
Indices: 27600002--27600041 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
27599992 ATATAAATAT
*
27600002 TTTTCTTTTTCTTTTCTTTTC
1 TTTTCTTCTTCTTTT-TTTTC
27600023 TTTTCTTCTTCTTTTTTTT
1 TTTTCTTCTTCTTTTTTTT
27600042 ATATATGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTCTTCTTCTTTTTTTTC
Found at i:27616474 original size:11 final size:11
Alignment explanation
Indices: 27616455--27616518 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
27616445 CCACGTCAGC
*
27616455 AAATGATTTTA
1 AAATTATTTTA
27616466 AAATTATTTTTTA
1 AAATTA--TTTTA
*
27616479 AAA--A-TATA
1 AAATTATTTTA
27616487 AAATTATTTTA
1 AAATTATTTTA
*
27616498 AAATTAATTTA
1 AAATTATTTTA
*
27616509 GAATTATTTT
1 AAATTATTTT
27616519 TTAAAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
8 6 0.14
10 1 0.02
11 27 0.64
13 8 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:27617438 original size:29 final size:27
Alignment explanation
Indices: 27617400--27617498 Score: 127
Period size: 29 Copynumber: 3.7 Consensus size: 27
27617390 TTAAAATATT
27617400 AAAATAATTTTAATAATTTTATATTTTA
1 AAAATAATTTTAATAA-TTTATATTTTA
27617428 AAAATTAATTTTAA-AA--TA-ATTTT-
1 AAAA-TAATTTTAATAATTTATATTTTA
27617451 AAAATAATTTTAATAATTTATATTTTAAA
1 AAAATAATTTTAATAATTTATATTTT--A
27617480 AAAATAATTTTAATAATTT
1 AAAATAATTTTAATAATTT
27617499 TAAAATCATT
Statistics
Matches: 63, Mismatches: 0, Indels: 15
0.81 0.00 0.19
Matches are distributed among these distances:
22 9 0.14
23 6 0.10
24 5 0.08
25 4 0.06
26 5 0.08
28 6 0.10
29 28 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AAAATAATTTTAATAATTTATATTTTA
Found at i:27617463 original size:51 final size:49
Alignment explanation
Indices: 27617390--27617509 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 49
27617380 ATGATGATGA
* *
27617390 TTAA-AATATTAAAATAATTTTAATAATTTTATATTTT-AAAAATTAATT
1 TTAATAATTTTAAAATAATTTTAATAA-TTTATATTTTAAAAAAATAATT
27617438 TTAAAATAATTTTAAAATAATTTTAATAATTTATATTTTAAAAAAATAATT
1 TT--AATAATTTTAAAATAATTTTAATAATTTATATTTTAAAAAAATAATT
*
27617489 TTAATAATTTTAAAATCATTT
1 TTAATAATTTTAAAATAATTT
27617510 GCTGATGTGG
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
48 2 0.03
49 18 0.28
50 12 0.18
51 33 0.51
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (49 bp):
TTAATAATTTTAAAATAATTTTAATAATTTATATTTTAAAAAAATAATT
Found at i:27617981 original size:17 final size:16
Alignment explanation
Indices: 27617933--27617995 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
27617923 TAAAATGACC
*
27617933 CAAAGCCAAAATAATT
1 CAAACCCAAAATAATT
* * *
27617949 TAAAGCCGAAATTAATT
1 CAAA-CCCAAAATAATT
*
27617966 CAAACCCAAAACTAATG
1 CAAACCCAAAA-TAATT
27617983 C-AACCCAAAATAA
1 CAAACCCAAAATAA
27617996 GTTTGAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
15 3 0.08
16 17 0.46
17 17 0.46
ACGTcount: A:0.54, C:0.22, G:0.06, T:0.17
Consensus pattern (16 bp):
CAAACCCAAAATAATT
Found at i:27619724 original size:15 final size:15
Alignment explanation
Indices: 27619704--27619733 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27619694 CAATTTTAGG
27619704 TGGTGGTGGTGGAGA
1 TGGTGGTGGTGGAGA
27619719 TGGTGGTGGTGGAGA
1 TGGTGGTGGTGGAGA
27619734 AGTAGAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.60, T:0.27
Consensus pattern (15 bp):
TGGTGGTGGTGGAGA
Found at i:27622599 original size:21 final size:21
Alignment explanation
Indices: 27622575--27622615 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27622565 AATTTAAAAA
*
27622575 TAAA-TGAAATCATAAATGGAT
1 TAAATTGAAAT-AAAAATGGAT
27622596 TAAATTGAAATAAAAATGGA
1 TAAATTGAAATAAAAATGGA
27622616 GTTTTAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.27
Consensus pattern (21 bp):
TAAATTGAAATAAAAATGGAT
Found at i:27624563 original size:191 final size:192
Alignment explanation
Indices: 27624223--27625235 Score: 1138
Period size: 191 Copynumber: 5.3 Consensus size: 192
27624213 TGGTATAGAA
* ** ** *
27624223 GCTTCTCTCCATTCCACTATAACCTCAAGGACATTGAGATAAGCTTTTTTTGTGTTAATCCGACC
1 GCTTCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTGC-TTCATTGTTTTAATCCGACC
* * * * * * *
27624288 CAGTACAACTTCAGGGGTATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGTAACCTCAGG
65 CACTACAAC-TCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCTCAAG
*
27624353 GACATTGAGATCTGTTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGT
129 GACATTGAGATCCGTTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGT
* ** *
27624417 GCTTCACTCCATTCCACTGTAACCTCAAGGACATTGA-ATCTGCTTCATTGTTTTAATCTAACTC
1 GCTTCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTGCTTCATTGTTTTAATCCGACCC
* * * * *
27624481 ACTATAACTCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCTATTCCACTTTAGCCTCAAGGA
66 ACTACAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCTCAAGGA
* ** * *
27624546 CATTGAGATCCGTTACTCATTTTGATTTGATCCACTACAACTTCAGGGATATAGAATATGGT
131 CATTGAGATCCGTTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGT
* * * * * * ** *
27624608 GCTTCACTCTACTCCATTGTAACCTTAAGGACATTGAGATATATTTCATTGTTTTAATCCAACCC
1 GCTTCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTGCTTCATTGTTTTAATCCGACCC
* * * * * * *
27624673 ACAACAAGTCAGGGGTATGGGATTTTATGTTGTAACTTCTCTCCATTCCACACTAACTTTAGGGA
66 ACTACAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCTCAAGGA
* *
27624738 CATTGAGATTCATTACTCATTTTGATCTGATCCACTGTAACTT-AGGGATATAGGATCTGGT
131 CATTGAGATCCGTTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGT
** * * * * *
27624799 GCTTCACTTTAGTCTACTATAACCTCAGGGACATTGAGATCTTCTTCATTGTTTTAATCTGACCC
1 GCTTCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTGCTTCATTGTTTTAATCCGACCC
* ** * * * *
27624864 ACTGCAAGACAGGGGTATGGGATTTGATATTGTAACTTCTTTCCATTCCACACTAACTTCAAGGA
66 ACTACAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCTCAAGGA
* * * * * * ** *
27624929 CATTAAGATTCATTACTCGTTTTGATCCGATCCAGTACAACTTTAGGGATATAGGATCTGGT
131 CATTGAGATCCGTTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGT
* * * *
27624991 GCTTTACTCCATTCAAC-AGTAACCTCAATGACATTGAGATCTGCTTCGTTGTTTTAATCCGACC
1 GCTTCACTCCATTCCACTA-TAACCTCAAGGACATTGAGATCTGCTTCATTGTTTTAATCCGACC
* ** * * * *
27625055 TACTGTAACTCATGGATATGGGATTTGA-GATTGTAACTTCTCTCCATTCCACTGTAACCTCTAG
65 CACTACAACTCAGGGGTATGGGATTTGATG-TTGTAACTTCTCTCCATTCCACTCTAACCTCAAG
* * * * * *
27625119 GATATTGAGAT-CGATTACTCATTTTGACCCGATCCATTGTAACTTCA-GGATATAAGATTTGGT
129 GACATTGAGATCCG-TTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGT
* * *
27625182 GCTTCACTCCATTCGACTATAACCTCAAGGACATTGAGATTTGCTTCGTTGTTT
1 GCTTCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTGCTTCATTGTTT
27625236 CAGTCTACTT
Statistics
Matches: 697, Mismatches: 116, Indels: 15
0.84 0.14 0.02
Matches are distributed among these distances:
191 366 0.53
192 292 0.42
193 4 0.01
194 35 0.05
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (192 bp):
GCTTCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTGCTTCATTGTTTTAATCCGACCC
ACTACAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTCTAACCTCAAGGA
CATTGAGATCCGTTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGT
Found at i:27625015 original size:383 final size:384
Alignment explanation
Indices: 27624223--27625235 Score: 1209
Period size: 383 Copynumber: 2.6 Consensus size: 384
27624213 TGGTATAGAA
* ** *
27624223 GCTTCTCTCCATTCCACTA-TAACCTCAAGGACATTGAGATA-AGCTTTTTTTGTGTTAATCCGA
1 GCTTCACTCCATTCCAC-AGTAACCTCAAGGACATTGAGATATA--TTTCATTGTTTTAATCCGA
* * * * * * *
27624286 CCCAGTACAACTTCAGGGGTATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGTAACCTCA
63 CCCACTACAAC-TCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACTTTA
27624351 GGGACATTGAGATCTG-TTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTG
127 GGGACATTGAGATC-GATTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTG
* *
27624415 GTGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGA-ATCTGCTTCATTGTTTTAATCTAAC
191 GTGCTTCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTTCTTCATTGTTTTAATCTAAC
* * * * * ** *
27624479 TCACTATAACTCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCTATTCCACTTTAGCCTCAAG
256 CCACTACAACACAAGGGTATGGGATTTGATATTGTAACTTCTCTCCATTCCACACTAACCTCAAG
* * **
27624544 GACATTGAGATCCGTTACTCATTTTGATTTGATCCACTACAACTTCAGGGATATAGAATATGGT
321 GACATTAAGATCCATTACTCATTTTGATCCGATCCACTACAACTTCAGGGATATAGAATATGGT
* * ** * *
27624608 GCTTCACTCTACTCCATTGTAACCTTAAGGACATTGAGATATATTTCATTGTTTTAATCCAACCC
1 GCTTCACTCCATTCCACAGTAACCTCAAGGACATTGAGATATATTTCATTGTTTTAATCCGACCC
* * * **
27624673 ACAACAAGTCAGGGGTATGGGATTTTATGTTGTAACTTCTCTCCATTCCACACTAACTTTAGGGA
66 ACTACAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACTTTAGGGA
27624738 CATTGAGATTC-ATTACTCATTTTGATCTGATCCACTGTAACTT-AGGGATATAGGATCTGGTGC
131 CATTGAGA-TCGATTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGTGC
** * * * *
27624801 TTCACTTTAGTCTACTATAACCTCAGGGACATTGAGATCTTCTTCATTGTTTTAATCTGACCCAC
195 TTCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTTCTTCATTGTTTTAATCTAACCCAC
* * * * *
27624866 TGCAAGACAGGGGTATGGGATTTGATATTGTAACTTCTTTCCATTCCACACTAACTTCAAGGACA
260 TACAACACAAGGGTATGGGATTTGATATTGTAACTTCTCTCCATTCCACACTAACCTCAAGGACA
* * * * * *
27624931 TTAAGATTCATTACTCGTTTTGATCCGATCCAGTACAACTTTAGGGATATAGGATCTGGT
325 TTAAGATCCATTACTCATTTTGATCCGATCCACTACAACTTCAGGGATATAGAATATGGT
* * * * ** * *
27624991 GCTTTACTCCATTCAACAGTAACCTCAATGACATTGAGATCTGCTTCGTTGTTTTAATCCGACCT
1 GCTTCACTCCATTCCACAGTAACCTCAAGGACATTGAGATATATTTCATTGTTTTAATCCGACCC
** * * *
27625056 ACTGTAACTCATGGATATGGGATTTGA-GATTGTAACTTCTCTCCATTCCACTGTAACCTCTA-G
66 ACTACAACTCAGGGGTATGGGATTTGATG-TTGTAACTTCTCTCCATTCCACTGTAA-CTTTAGG
* * * * * *
27625119 GATATTGAGATCGATTACTCATTTTGACCCGATCCATTGTAACTTCA-GGATATAAGATTTGGTG
129 GACATTGAGATCGATTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGTG
* *
27625183 CTTCACTCCATTCGACTATAACCTCAAGGACATTGAGAT-TTGCTTCGTTGTTT
194 CTTCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTT-CTTCATTGTTT
27625236 CAGTCTACTT
Statistics
Matches: 529, Mismatches: 89, Indels: 22
0.83 0.14 0.03
Matches are distributed among these distances:
382 54 0.10
383 410 0.78
384 30 0.06
385 34 0.06
386 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (384 bp):
GCTTCACTCCATTCCACAGTAACCTCAAGGACATTGAGATATATTTCATTGTTTTAATCCGACCC
ACTACAACTCAGGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACTTTAGGGA
CATTGAGATCGATTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGTGCT
TCACTCCATTCCACTATAACCTCAAGGACATTGAGATCTTCTTCATTGTTTTAATCTAACCCACT
ACAACACAAGGGTATGGGATTTGATATTGTAACTTCTCTCCATTCCACACTAACCTCAAGGACAT
TAAGATCCATTACTCATTTTGATCCGATCCACTACAACTTCAGGGATATAGAATATGGT
Found at i:27625635 original size:50 final size:50
Alignment explanation
Indices: 27625402--27625647 Score: 207
Period size: 49 Copynumber: 5.0 Consensus size: 50
27625392 TCATCTTTAG
* ** * * *
27625402 TCGTTGCGGCTTCAATCTTTCCCTTCACAT-TTCCGAGGTGTAAGGTTCG
1 TCGTTGCGGCTTCAATCTTTCCCTTCATATCTTCTAAGGTATAAGATTCC
* * * * * *
27625451 TCGTTGCGGCTTCAACCTTTTCCTCCACATC-TCTAGGGTATAAGGTTCAC
1 TCGTTGCGGCTTCAATCTTTCCCTTCATATCTTCTAAGGTATAAGATTC-C
* * * * **
27625501 -CGTTGCGGCTTCAACCTTTCCCTCCATATC-TCTAGGGTACAAGATTTG
1 TCGTTGCGGCTTCAATCTTTCCCTTCATATCTTCTAAGGTATAAGATTCC
* * *
27625549 TCATTGTGGCTTCAATCTTTCCCTAT-ATAT-TCTCTAATGTATAAGATTCC
1 TCGTTGCGGCTTCAATCTTTCCCT-TCATATCT-TCTAAGGTATAAGATTCC
* * *
27625599 TCGTTGCAGCTTCAATCTTTCCCTTCATGTCTTCTAAGGTATATGATTC
1 TCGTTGCGGCTTCAATCTTTCCCTTCATATCTTCTAAGGTATAAGATTC
27625648 AACGTTTCCT
Statistics
Matches: 160, Mismatches: 29, Indels: 15
0.78 0.14 0.07
Matches are distributed among these distances:
49 107 0.67
50 52 0.32
51 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (50 bp):
TCGTTGCGGCTTCAATCTTTCCCTTCATATCTTCTAAGGTATAAGATTCC
Found at i:27634271 original size:23 final size:23
Alignment explanation
Indices: 27634245--27634298 Score: 87
Period size: 20 Copynumber: 2.5 Consensus size: 23
27634235 AAAATAGTGG
27634245 CAAAAATAACAGCAAAACAACAA
1 CAAAAATAACAGCAAAACAACAA
27634268 C--AAA-AACAGCAAAACAACAA
1 CAAAAATAACAGCAAAACAACAA
27634288 CAAAAATAACA
1 CAAAAATAACA
27634299 TCTTCAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 17 0.61
21 3 0.11
22 3 0.11
23 5 0.18
ACGTcount: A:0.70, C:0.22, G:0.04, T:0.04
Consensus pattern (23 bp):
CAAAAATAACAGCAAAACAACAA
Found at i:27634327 original size:11 final size:11
Alignment explanation
Indices: 27634247--27634292 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
27634237 AATAGTGGCA
* *
27634247 AAAATAACAGC
1 AAAACAACAAC
27634258 AAAACAACAAC
1 AAAACAACAAC
*
27634269 -AAA-AACAGC
1 AAAACAACAAC
27634278 AAAACAACAAC
1 AAAACAACAAC
27634289 AAAA
1 AAAA
27634293 ATAACATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 5 0.17
10 6 0.21
11 18 0.62
ACGTcount: A:0.72, C:0.22, G:0.04, T:0.02
Consensus pattern (11 bp):
AAAACAACAAC
Found at i:27634350 original size:22 final size:22
Alignment explanation
Indices: 27634325--27634423 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 22
27634315 AAACAACATC
*
27634325 AAACAGCAACCAAAATAGT-AA
1 AAACAGCAACCAAAACAGTAAA
27634346 AAA-A-C--CCAAAACAGTAAA
1 AAACAGCAACCAAAACAGTAAA
* * * *
27634364 AAA-ACCAACACCAAAATAGCATA
1 AAACAGC-A-ACCAAAACAGTAAA
*
27634387 AAACAACAACCAAAACAGTAAA
1 AAACAGCAACCAAAACAGTAAA
27634409 AAACAGC-ACCAAAAC
1 AAACAGCAACCAAAAC
27634424 TATAATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
17 9 0.15
18 6 0.10
19 2 0.03
20 1 0.02
21 11 0.18
22 17 0.27
23 14 0.23
24 2 0.03
ACGTcount: A:0.64, C:0.24, G:0.06, T:0.06
Consensus pattern (22 bp):
AAACAGCAACCAAAACAGTAAA
Found at i:27634356 original size:17 final size:17
Alignment explanation
Indices: 27634332--27634371 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
27634322 ATCAAACAGC
*
27634332 AACCAAAATAGTAAAAA
1 AACCAAAACAGTAAAAA
*
27634349 ACCCAAAACAGTAAAAA
1 AACCAAAACAGTAAAAA
27634366 AACCAA
1 AACCAA
27634372 CACCAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (17 bp):
AACCAAAACAGTAAAAA
Found at i:27634960 original size:31 final size:30
Alignment explanation
Indices: 27634925--27635034 Score: 93
Period size: 30 Copynumber: 3.7 Consensus size: 30
27634915 AACTTGTCAC
27634925 TTTTTCCTAATTTGGTACCTAAACTTGAATT
1 TTTTTCCTAATTTGGTACCTAAACTT-AATT
* * *
27634956 TTTTT-TTAAGTTGGTACTTAAACTT--TT
1 TTTTTCCTAATTTGGTACCTAAACTTAATT
*** * *
27634983 TGGGTCC-AATTTGGTACCTGAACTTAACTC
1 TTTTTCCTAATTTGGTACCTAAACTTAA-TT
*
27635013 TTTTTCCTAATTTGGTATCTAA
1 TTTTTCCTAATTTGGTACCTAA
27635035 TCTTTTTAAT
Statistics
Matches: 58, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
27 19 0.33
30 22 0.38
31 17 0.29
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (30 bp):
TTTTTCCTAATTTGGTACCTAAACTTAATT
Found at i:27635007 original size:88 final size:88
Alignment explanation
Indices: 27634868--27635034 Score: 214
Period size: 88 Copynumber: 1.9 Consensus size: 88
27634858 GAACTTGACA
* ** **
27634868 TTTTTTTAATGTGGTATCTAAATTTTTTTTGTCCAATTTGGTACTCAAACTTGTCACTTTTTCCT
1 TTTTTTTAATGTGGTATCTAAACTTTTTGGGTCCAATTTGGTACTCAAACTTAACACTTTTTCCT
27634933 AATTTGGTACCTAAACTTGAATT
66 AATTTGGTACCTAAACTTGAATT
* *
27634956 TTTTTTTAA-GTTGGTA-CTTAAACTTTTTGGGTCCAATTTGGTAC-CTGAACTTAACTCTTTTT
1 TTTTTTTAATG-TGGTATC-TAAACTTTTTGGGTCCAATTTGGTACTC-AAACTTAACACTTTTT
*
27635018 CCTAATTTGGTATCTAA
63 CCTAATTTGGTACCTAA
27635035 TCTTTTTAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
87 3 0.04
88 65 0.96
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (88 bp):
TTTTTTTAATGTGGTATCTAAACTTTTTGGGTCCAATTTGGTACTCAAACTTAACACTTTTTCCT
AATTTGGTACCTAAACTTGAATT
Found at i:27635280 original size:58 final size:58
Alignment explanation
Indices: 27635200--27635368 Score: 207
Period size: 58 Copynumber: 2.9 Consensus size: 58
27635190 AATTGAATCT
* *
27635200 AAAAAAAGTTTAGGTTCTAAATTAGGAAAAAATGCCAAGTTCAGGTACCAAATT-GGTC
1 AAAAAAAGTTTAAGTTC-AAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTC
* ** *
27635258 CAAAAAAGTTTAAGTGTCAAATTAGGAAAATGTGTCAAGTTTAGGTACCAAATTGGGTC
1 AAAAAAAGTTTAAGT-TCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTC
* * *
27635317 AAAAAAAGTTTAAGTACCAAATTA-AAAAAAAGTATCAAGTTCAGGTACCAAA
1 AAAAAAAGTTTAAGT-TCAAATTAGGAAAAAA-TGTCAAGTTCAGGTACCAAA
27635369 CGTTATATTA
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
58 49 0.52
59 45 0.48
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (58 bp):
AAAAAAAGTTTAAGTTCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTC
Found at i:27635355 original size:59 final size:58
Alignment explanation
Indices: 27635200--27635368 Score: 205
Period size: 59 Copynumber: 2.9 Consensus size: 58
27635190 AATTGAATCT
* * * *
27635200 AAAAAAAGTTTAGGTTCTAAATTAGGAAAAAA-TGCCAAGTTCAGGTACCAAATTGGTC
1 AAAAAAAGTTTAAGTACCAAATTA-GAAAAAAGTGTCAAGTTCAGGTACCAAATTGGTC
* ** * * *
27635258 CAAAAAAGTTTAAGTGTCAAATTAGGAAAATGTGTCAAGTTTAGGTACCAAATTGGGTC
1 AAAAAAAGTTTAAGTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATT-GGTC
* *
27635317 AAAAAAAGTTTAAGTACCAAATTAAAAAAAAGTATCAAGTTCAGGTACCAAA
1 AAAAAAAGTTTAAGTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAA
27635369 CGTTATATTA
Statistics
Matches: 92, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
57 5 0.05
58 39 0.42
59 48 0.52
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (58 bp):
AAAAAAAGTTTAAGTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATTGGTC
Found at i:27651202 original size:3 final size:3
Alignment explanation
Indices: 27651194--27651227 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
27651184 CATCTCTTCC
*
27651194 TCA TCA TCA TCA TCA TCA TCA TTA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
27651228 TGGAATCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:27653893 original size:89 final size:87
Alignment explanation
Indices: 27653749--27653953 Score: 261
Period size: 89 Copynumber: 2.3 Consensus size: 87
27653739 TCAAACTTTC
* * ** * *
27653749 TCAAAAAAAGCAATTAAGTTCCTTTTTTTTTTTTGTATTCATTGGAGTACTTGAACTTTCAAAAT
1 TCAAAAAAAGCAATTAAG-CCCCTACTTTTTTTTGCACTCATTGGAGTACTTGAACTTTCAAAAT
* *
27653814 GCATTAAAAAGGCCCTAAAACATT
65 GCATAAAAAAGACCCTAAAAC-TT
*
27653838 GTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCAATTGG-GTACTTGAACTTTTAAAA
1 -TCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTC-ATTGGAGTACTTGAACTTTCAAAA
*
27653902 TGCATAAAAAAGACCCTCAAACTT
64 TGCATAAAAAAGACCCTAAAACTT
*
27653926 T-AAAAAAAACAATTAAGCCCCTACTTTT
1 TCAAAAAAAGCAATTAAGCCCCTACTTTT
27653954 ATTAAAAAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
86 26 0.25
87 1 0.01
88 2 0.02
89 51 0.50
90 23 0.22
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (87 bp):
TCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCATTGGAGTACTTGAACTTTCAAAATG
CATAAAAAAGACCCTAAAACTT
Found at i:27654021 original size:20 final size:19
Alignment explanation
Indices: 27653998--27654054 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
27653988 TTATAAATAT
27653998 TATTAAATTTTAATAAAAAA
1 TATTAAATTTTAA-AAAAAA
** *
27654018 TATTAAAAATTAGAAAAAA
1 TATTAAATTTTAAAAAAAA
*
27654037 TATAAAAATTTTAAAAAA
1 TAT-TAAATTTTAAAAAA
27654055 TATAAAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TATTAAATTTTAAAAAAAA
Found at i:27654042 original size:18 final size:18
Alignment explanation
Indices: 27654012--27654062 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
27654002 AAATTTTAAT
27654012 AAAAAATATTAAAAATTAG
1 AAAAAATA-TAAAAATTAG
**
27654031 AAAAAATATAAAAATTTT
1 AAAAAATATAAAAATTAG
27654049 AAAAAATATAAAAA
1 AAAAAATATAAAAA
27654063 ATTGTGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 22 0.73
19 8 0.27
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAAATATAAAAATTAG
Found at i:27654827 original size:89 final size:87
Alignment explanation
Indices: 27654533--27654830 Score: 345
Period size: 90 Copynumber: 3.4 Consensus size: 87
27654523 ATAAGAGCAA
* * *
27654533 GGACTTAATTGCTGTTTTGAAAAATTTTGAGGATCTTTTTGATGCA-TTTGAAAGTTCAAGTACC
1 GGACTTAATTGCTTTTTTG-AAAAGTTTGAGGATCTTTTTAATGCATTTTGAAAGTTCAAGTACC
* *
27654597 TAAATGAGTG-AAAAAAAAGCAG
65 TCAATGAGTGCAAAAAAAAGAAG
* * *
27654619 GGGCTTAATTGCTTTTTTGAAGAAGTTTTAGGGTAT-TTTTTTATGCATTTTGAAAGTTCAAGT-
1 GGACTTAATTGCTTTTTTGAA-AAGTTTGA-GG-ATCTTTTTAATGCATTTTGAAAGTTCAAGTA
*
27654682 GCTCAATTGAGTGCAAAAAAAAAGAATG
63 CCTCAA-TGAGTGC-AAAAAAAAGAA-G
*
27654710 GG-CTTAATTGCTTTTTTTGAAAAGGTTTGAGGATCTTTTTAATGCATTTTAAAAGTTCAAGTAC
1 GGACTTAATTGC-TTTTTTGAAAA-GTTTGAGGATCTTTTTAATGCATTTTGAAAGTTCAAGTAC
* *
27654774 CCCAATGAGTGCAAAAAAAAGGAG
64 CTCAATGAGTGCAAAAAAAAGAAG
*
27654798 GGACTTAATTACTTTTTTTGAGAAAGTTTGAGG
1 GGACTTAATTGC-TTTTTTGA-AAAGTTTGAGG
27654831 GATTTTTACA
Statistics
Matches: 183, Mismatches: 15, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
85 2 0.01
86 23 0.13
87 16 0.09
88 26 0.14
89 37 0.20
90 58 0.32
91 21 0.11
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (87 bp):
GGACTTAATTGCTTTTTTGAAAAGTTTGAGGATCTTTTTAATGCATTTTGAAAGTTCAAGTACCT
CAATGAGTGCAAAAAAAAGAAG
Found at i:27665038 original size:29 final size:29
Alignment explanation
Indices: 27664975--27665038 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
27664965 CATTCTAATC
* *
27664975 ATTTATATTTGAAATATTACATTTTAGTA
1 ATTTATATTTAAAATATTACAATTTAGTA
* * * *
27665004 ACTTATATTTAAAATGTTATAATTTAGTT
1 ATTTATATTTAAAATATTACAATTTAGTA
27665033 ATTTAT
1 ATTTAT
27665039 GTTATTATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (29 bp):
ATTTATATTTAAAATATTACAATTTAGTA
Found at i:27665142 original size:18 final size:16
Alignment explanation
Indices: 27665110--27665153 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
27665100 ATGGAATGAG
27665110 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
27665126 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
27665140 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
27665154 ACTTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:27671698 original size:23 final size:22
Alignment explanation
Indices: 27671575--27671721 Score: 100
Period size: 23 Copynumber: 6.5 Consensus size: 22
27671565 AGTACTGGGA
*
27671575 AAATAGTAAGCACACACAGTGC
1 AAATAGTAAGCACACAAAGTGC
* * *
27671597 -AATCCAATAGGCACACACAGTGC
1 AAAT--AGTAAGCACACAAAGTGC
* * * *
27671620 -AATCAGTAGGCGCACATAGCGC
1 AAAT-AGTAAGCACACAAAGTGC
* *
27671642 AAATCAGTAGGCACACAAGGTGC
1 AAAT-AGTAAGCACACAAAGTGC
* *
27671665 AAAACAATAAGCACACAAAGTGC
1 -AAATAGTAAGCACACAAAGTGC
27671688 GAAATAGTAAGCACACAAAGTGC
1 -AAATAGTAAGCACACAAAGTGC
*
27671711 GAAACAGTAAG
1 -AAATAGTAAG
27671722 TGCGCTAGCG
Statistics
Matches: 103, Mismatches: 18, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
21 3 0.03
22 15 0.15
23 82 0.80
24 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.12
Consensus pattern (22 bp):
AAATAGTAAGCACACAAAGTGC
Found at i:27678877 original size:23 final size:22
Alignment explanation
Indices: 27678845--27678924 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
27678835 AAGTACTTAA
* *
27678845 CAGTAAGCACACCCAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
27678867 CCAGTAGGCACACACAGT-CAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
27678889 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
27678912 CAGTAGGCACACA
1 CAGTAGGCACACA
27678925 AGGTACGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.29
22 5 0.10
23 30 0.61
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:27678938 original size:23 final size:23
Alignment explanation
Indices: 27678912--27678967 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
27678902 TAGCGCAAAT
* *
27678912 CAGTAGGCACACAAGGTACGAAA
1 CAGTAAGCACACAAAGTACGAAA
*
27678935 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAAGCACACAAAGTACGAAA
* *
27678958 TAGCAAGCAC
1 CAGTAAGCAC
27678968 GCTAGTGTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACAAAGTACGAAA
Found at i:27686563 original size:13 final size:14
Alignment explanation
Indices: 27686545--27686574 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27686535 GTCAACACAA
27686545 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
27686558 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
27686572 TCA
1 TCA
27686575 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:27703753 original size:37 final size:37
Alignment explanation
Indices: 27703689--27703761 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
27703679 AATGTCACTG
* **
27703689 CATGAGCACTTCTAGATTGTGCCCAAAACTGTCGCCA
1 CATGAGCACTTCCAGATTGCACCCAAAACTGTCGCCA
* *
27703726 CATGAGCACTTCCAGATTGCACTCAAAATTGTCGCC
1 CATGAGCACTTCCAGATTGCACCCAAAACTGTCGCC
27703762 GCAGGAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
CATGAGCACTTCCAGATTGCACCCAAAACTGTCGCCA
Found at i:27703808 original size:37 final size:38
Alignment explanation
Indices: 27703767--27703866 Score: 109
Period size: 38 Copynumber: 2.7 Consensus size: 38
27703757 TCGCCGCAGG
27703767 AATATT-TCCAGAA-TGCATCCAAG-ACTATCACTGCATA
1 AATATTCTCCA-AATTGCAT-CAAGAACTATCACTGCATA
* *
27703804 AATATTCTTCAAATTGTATCAAGAACTATCACTGCATA
1 AATATTCTCCAAATTGCATCAAGAACTATCACTGCATA
* *
27703842 AGTATTCTTC-AATTGCACTCAAGAA
1 AATATTCTCCAAATTGCA-TCAAGAA
27703867 TGTCGCTGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
37 18 0.33
38 37 0.67
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (38 bp):
AATATTCTCCAAATTGCATCAAGAACTATCACTGCATA
Found at i:27703838 original size:38 final size:38
Alignment explanation
Indices: 27703786--27703866 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
27703776 AGAATGCATC
*
27703786 CAAG-ACTATCACTGCATAAATATTCTTCAAATTGTA-T
1 CAAGAACTATCACTGCATAAATATTCTTC-AATTGCACT
*
27703823 CAAGAACTATCACTGCATAAGTATTCTTCAATTGCACT
1 CAAGAACTATCACTGCATAAATATTCTTCAATTGCACT
27703861 CAAGAA
1 CAAGAA
27703867 TGTCGCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
37 10 0.25
38 30 0.75
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (38 bp):
CAAGAACTATCACTGCATAAATATTCTTCAATTGCACT
Found at i:27707404 original size:37 final size:37
Alignment explanation
Indices: 27707349--27707419 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
27707339 TAATGTTGCT
* *
27707349 GCATGAGCACTTCTAGATTGCGCCCAAAACTGTCGCC
1 GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCC
27707386 GCATGAGCACTTCCAGATTGCACCCAAAACTGTC
1 GCATGAGCACTTCCAGATTGCACCCAAAACTGTC
27707420 TTCGTATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.21
Consensus pattern (37 bp):
GCATGAGCACTTCCAGATTGCACCCAAAACTGTCGCC
Found at i:27707497 original size:38 final size:38
Alignment explanation
Indices: 27707441--27707514 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
27707431 ATTTCTGGAA
* *
27707441 TGCATCCAAGACTGTCGCTCCATAAATATTCTTCAAAT
1 TGCATCCAAGACTATCGCTACATAAATATTCTTCAAAT
*
27707479 TGCATCC-AGAACTATCGCTACATAAGTATTCTTCAA
1 TGCATCCAAG-ACTATCGCTACATAAATATTCTTCAA
27707515 TTGTACCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 2 0.06
38 30 0.94
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (38 bp):
TGCATCCAAGACTATCGCTACATAAATATTCTTCAAAT
Found at i:27707562 original size:26 final size:26
Alignment explanation
Indices: 27707528--27707581 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
27707518 TACCAAGGAA
27707528 TGTCCCTGCATGAACATATCTAGAAT
1 TGTCCCTGCATGAACATATCTAGAAT
* * *
27707554 TGTCGCTGCATGAACGTGTCTAGAAT
1 TGTCCCTGCATGAACATATCTAGAAT
27707580 TG
1 TG
27707582 CACCCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (26 bp):
TGTCCCTGCATGAACATATCTAGAAT
Found at i:27708965 original size:40 final size:40
Alignment explanation
Indices: 27708921--27709023 Score: 143
Period size: 40 Copynumber: 2.6 Consensus size: 40
27708911 GGTATTTCCG
***
27708921 AATAAATGAAAAGGTTGAAAAAGATATTATTTGGAAGGAT
1 AATAAATGAAAAGGTTGAAAAAGATATTATTCAAAAGGAT
* *
27708961 AATAAATGAAAAGGTTGAAAAGGATGTTATTCAAAAGGAT
1 AATAAATGAAAAGGTTGAAAAAGATATTATTCAAAAGGAT
* *
27709001 AATAAATGAAAAGGGTCAAAAAG
1 AATAAATGAAAAGGTTGAAAAAG
27709024 GTAAATTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.52, C:0.02, G:0.22, T:0.23
Consensus pattern (40 bp):
AATAAATGAAAAGGTTGAAAAAGATATTATTCAAAAGGAT
Found at i:27718206 original size:11 final size:11
Alignment explanation
Indices: 27718185--27718229 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
27718175 AAAGAAGCTT
27718185 ATTCAATGATTG
1 ATTC-ATGATTG
*
27718197 ACTCATGATTG
1 ATTCATGATTG
*
27718208 ATTTGATGATTG
1 A-TTCATGATTG
27718220 ATTCATGATT
1 ATTCATGATT
27718230 TTTTAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 16 0.57
12 12 0.43
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (11 bp):
ATTCATGATTG
Found at i:27718817 original size:14 final size:14
Alignment explanation
Indices: 27718798--27718827 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27718788 TTTTTTTGAC
27718798 TTATTAAATTAATT
1 TTATTAAATTAATT
*
27718812 TTATTAAATTAGTT
1 TTATTAAATTAATT
27718826 TT
1 TT
27718828 TTATAAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
TTATTAAATTAATT
Found at i:27725808 original size:29 final size:28
Alignment explanation
Indices: 27725776--27725842 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
27725766 TCATAAAACG
27725776 TTTTATTTTAATGAATTACTACTATATAA
1 TTTTATTTTAATGAATTAC-ACTATATAA
* * * *
27725805 TTTTATTTTATTGTATTACATTTTATAA
1 TTTTATTTTAATGAATTACACTATATAA
27725833 TTTT-TTTTAA
1 TTTTATTTTAA
27725843 AAGGATATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 5 0.15
28 11 0.33
29 17 0.52
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTTATTTTAATGAATTACACTATATAA
Found at i:27730322 original size:4 final size:5
Alignment explanation
Indices: 27730284--27730314 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
27730274 AAAACAGATT
27730284 AAAGG -AAGG AAAGG AAAGG AAAGG AAAGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
27730315 GAAAGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:27733842 original size:20 final size:20
Alignment explanation
Indices: 27733808--27733849 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
27733798 TCCAAACACC
27733808 AAAAAATATTAATTTTTTCAG
1 AAAAAATATTAA-TTTTTCAG
*
27733829 AAAAAA-ATTCATTTTTCAG
1 AAAAAATATTAATTTTTCAG
27733848 AA
1 AA
27733850 TTCATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 4 0.20
21 6 0.30
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAAAATATTAATTTTTCAG
Found at i:27737167 original size:26 final size:27
Alignment explanation
Indices: 27737138--27737188 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
27737128 AAAATTACAC
27737138 TTTAACCTTTT-AAAATAATAAAAAAA
1 TTTAACCTTTTAAAAATAATAAAAAAA
* *
27737164 TTTAATCTTTTAAAAATTATAAAAA
1 TTTAACCTTTTAAAAATAATAAAAA
27737189 TACATATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (27 bp):
TTTAACCTTTTAAAAATAATAAAAAAA
Found at i:27738906 original size:14 final size:15
Alignment explanation
Indices: 27738881--27738909 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27738871 TTTGTTTTAA
27738881 TTAAATTTAGGGTTT
1 TTAAATTTAGGGTTT
27738896 TTAAA-TTAGGGTTT
1 TTAAATTTAGGGTTT
27738910 AGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTAAATTTAGGGTTT
Found at i:27738912 original size:21 final size:21
Alignment explanation
Indices: 27738886--27738930 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
27738876 TTTAATTAAA
*
27738886 TTTAGGGTTTTT-AAATTAGGG
1 TTTA-GGTTTTTAAAATTAGAG
27738907 TTTAGGTTTTTAAAATTAGAG
1 TTTAGGTTTTTAAAATTAGAG
27738928 TTT
1 TTT
27738931 TAGTATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (21 bp):
TTTAGGTTTTTAAAATTAGAG
Found at i:27738939 original size:21 final size:21
Alignment explanation
Indices: 27738898--27738939 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
27738888 TAGGGTTTTT
*
27738898 AAATTAGGGTTTAGGTTTTTA
1 AAATTAGGGTTTAGGTATTTA
*
27738919 AAATTAGAGTTTTA-GTATTTA
1 AAATTAG-GGTTTAGGTATTTA
27738940 TTTTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (21 bp):
AAATTAGGGTTTAGGTATTTA
Found at i:27740941 original size:17 final size:17
Alignment explanation
Indices: 27740919--27740962 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
27740909 CAAGGAGGTA
27740919 ATGCTTTAGTGATTTTT
1 ATGCTTTAGTGATTTTT
27740936 ATGCTTTAGTGATTTTT
1 ATGCTTTAGTGATTTTT
*
27740953 ATTCTTTAGT
1 ATGCTTTAGT
27740963 AGAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.18, C:0.07, G:0.16, T:0.59
Consensus pattern (17 bp):
ATGCTTTAGTGATTTTT
Found at i:27744085 original size:12 final size:12
Alignment explanation
Indices: 27744070--27744094 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27744060 ATTAAAGAAT
27744070 TAATAGCATTCA
1 TAATAGCATTCA
27744082 TAATAGCATTCA
1 TAATAGCATTCA
27744094 T
1 T
27744095 CATATAACAA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:27745933 original size:22 final size:23
Alignment explanation
Indices: 27745904--27745948 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
27745894 TCTTTCATGA
27745904 TTAGTTTAATTAA-TC-ACTTAT
1 TTAGTTTAATTAATTCTACTTAT
27745925 TTAGCTTTAATTAATTCTACTTAT
1 TTAG-TTTAATTAATTCTACTTAT
27745949 GATCAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 9 0.43
23 2 0.10
24 6 0.29
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.53
Consensus pattern (23 bp):
TTAGTTTAATTAATTCTACTTAT
Found at i:27748697 original size:17 final size:17
Alignment explanation
Indices: 27748675--27748713 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
27748665 AGGTGGAGAA
* *
27748675 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
27748692 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
27748709 CTTGT
1 CTTGT
27748714 CAAGGTGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:27752484 original size:21 final size:21
Alignment explanation
Indices: 27752438--27752484 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
27752428 GACTTAAAGA
27752438 GAATTACAAAATCTCACATAC
1 GAATTACAAAATCTCACATAC
*
27752459 CAATT-CAAAATGCTCTA-ATAC
1 GAATTACAAAAT-CTC-ACATAC
27752480 GAATT
1 GAATT
27752485 GATGTCCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.27
21 15 0.68
22 1 0.05
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (21 bp):
GAATTACAAAATCTCACATAC
Found at i:27757891 original size:16 final size:16
Alignment explanation
Indices: 27757870--27757909 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
27757860 CGTTTGGTTC
*
27757870 GCTGTAATGGAATAGA
1 GCTGTAATGGAATACA
27757886 GCTGTAATGGAATACA
1 GCTGTAATGGAATACA
27757902 GCTGTAAT
1 GCTGTAAT
27757910 CACTATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATACA
Found at i:27758109 original size:26 final size:26
Alignment explanation
Indices: 27758079--27758167 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
27758069 GTTATTAAAT
27758079 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAGATTATTATTAAATATAA
* * * * *
27758105 TTTAATAAAAAAATATAATTTAATCATAT
1 TTTAAT--AAGATTATTATTAAAT-ATAA
***
27758134 TTTAACGTGATTATTATTAAATATAA
1 TTTAATAAGATTATTATTAAATATAA
27758160 TTTAATAA
1 TTTAATAA
27758168 AATAGTATTT
Statistics
Matches: 44, Mismatches: 16, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
26 14 0.32
27 10 0.23
28 12 0.27
29 8 0.18
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (26 bp):
TTTAATAAGATTATTATTAAATATAA
Found at i:27758161 original size:55 final size:57
Alignment explanation
Indices: 27758087--27758228 Score: 173
Period size: 55 Copynumber: 2.5 Consensus size: 57
27758077 ATTTTAATAA
* * * *
27758087 GATTATTATTAAATATAATTTAATAAAAA-AATATAATTTAATCATATT-TTAACGT
1 GATTATTATTAAATATAATTTAATAAAAAGAATATAATTTAATAACATTCCTAACAT
* * *
27758142 GATTATTATTAAATATAATTTAATAAAATAGTATTTAATTTAATAACATTCCTAATAT
1 GATTATTATTAAATATAATTTAATAAAA-AGAATATAATTTAATAACATTCCTAACAT
*
27758200 AATTATTATTAAATATGAA-TTAATAAAAA
1 GATTATTATTAAATAT-AATTTAATAAAAA
27758229 TCATAATATA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 28 0.37
56 1 0.01
57 16 0.21
58 28 0.37
59 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (57 bp):
GATTATTATTAAATATAATTTAATAAAAAGAATATAATTTAATAACATTCCTAACAT
Found at i:27758224 original size:58 final size:55
Alignment explanation
Indices: 27758088--27758228 Score: 167
Period size: 58 Copynumber: 2.5 Consensus size: 55
27758078 TTTTAATAAG
* * * * *
27758088 ATTATTATTAAATATAATTTAATAAAAAAATATAATTTAATCATATTTTAACGTG
1 ATTATTATTAAATATAATTTAATAAAAAAATATAATTTAATAACATTCTAACATA
* * *
27758143 ATTATTATTAAATATAATTTAATAAAATAGTATTTAATTTAATAACATTCCTAATATA
1 ATTATTATTAAATATAATTTAATAAAA-A-AATATAATTTAATAACATT-CTAACATA
27758201 ATTATTATTAAATATGAA-TTAATAAAAA
1 ATTATTATTAAATAT-AATTTAATAAAAA
27758229 TCATAATATA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 27 0.36
56 1 0.01
57 16 0.22
58 28 0.38
59 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (55 bp):
ATTATTATTAAATATAATTTAATAAAAAAATATAATTTAATAACATTCTAACATA
Found at i:27766714 original size:26 final size:26
Alignment explanation
Indices: 27766677--27766732 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
27766667 GATTAAACAT
* *
27766677 AATTTTTGATGACTAAAATATGAATC
1 AATTTTTAATGACCAAAATATGAATC
27766703 AATTTTTAATGACCAAAATATGAATC
1 AATTTTTAATGACCAAAATATGAATC
27766729 AATT
1 AATT
27766733 AATATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (26 bp):
AATTTTTAATGACCAAAATATGAATC
Found at i:27778237 original size:17 final size:17
Alignment explanation
Indices: 27778196--27778245 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
27778186 TTTGTTAATA
27778196 AAAGAAAAGAAAAAAAG
1 AAAGAAAAGAAAAAAAG
*
27778213 AAACAAAAGAAAAAAA-
1 AAAGAAAAGAAAAAAAG
*
27778229 AAGGGAAAAGAAAAAAA
1 AA-AGAAAAGAAAAAAA
27778246 TAAGAATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 2 0.07
17 27 0.93
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAAAAAAG
Found at i:27779664 original size:5 final size:5
Alignment explanation
Indices: 27779654--27779685 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
27779644 GACTAAGATT
27779654 TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TA
27779686 TTTCTCCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:27782256 original size:15 final size:15
Alignment explanation
Indices: 27782214--27782244 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27782204 ACCAATGCTA
27782214 ATAATATCTATTTTT
1 ATAATATCTATTTTT
27782229 ATAATATCTATTTTT
1 ATAATATCTATTTTT
27782244 A
1 A
27782245 GTGATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAATATCTATTTTT
Found at i:27790211 original size:21 final size:21
Alignment explanation
Indices: 27790170--27790236 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
27790160 GGTGTTTTTA
** *
27790170 GTATCGGTAGAAGCAAGACTT
1 GTATCGGTAGAAGTGACACTT
*
27790191 GTTTCGGTAGAAGTGACACTT
1 GTATCGGTAGAAGTGACACTT
* *
27790212 GTATCAGTAAAAGTGACACTT
1 GTATCGGTAGAAGTGACACTT
27790233 GTAT
1 GTAT
27790237 TGTTAGAACT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGTGACACTT
Found at i:27796299 original size:18 final size:18
Alignment explanation
Indices: 27796276--27796329 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
27796266 AAGGAATAGT
27796276 ATACTGGCTCGTTTGAGC
1 ATACTGGCTCGTTTGAGC
**
27796294 ATACTGGCTCGTAAGAGC
1 ATACTGGCTCGTTTGAGC
* *
27796312 ATTACTGGATCGCTTGAG
1 A-TACTGGCTCGTTTGAG
27796330 ATATTTCCAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (18 bp):
ATACTGGCTCGTTTGAGC
Found at i:27797031 original size:21 final size:21
Alignment explanation
Indices: 27796999--27797052 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
27796989 AGAGTTTTTA
* *
27796999 GTATCAGTAGAAGCAAGACTT
1 GTATCGGTAGAAGCAACACTT
* **
27797020 GTTTCGGTAGAAGTGACACTT
1 GTATCGGTAGAAGCAACACTT
27797041 GTATCGGTAGAA
1 GTATCGGTAGAA
27797053 CTATCACAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (21 bp):
GTATCGGTAGAAGCAACACTT
Found at i:27797869 original size:21 final size:21
Alignment explanation
Indices: 27797843--27797884 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27797833 GCCATTCCAA
*
27797843 TATAGTATTCTTGTGAATGTC
1 TATAGTATTCTTATGAATGTC
27797864 TATAGTATTCTTATGAATGTC
1 TATAGTATTCTTATGAATGTC
27797885 AGGATTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.48
Consensus pattern (21 bp):
TATAGTATTCTTATGAATGTC
Found at i:27800454 original size:78 final size:78
Alignment explanation
Indices: 27800300--27800457 Score: 190
Period size: 78 Copynumber: 2.0 Consensus size: 78
27800290 TTCCAAATAG
* * * * * *
27800300 AAATCAAATGAATTCTATTGAATAACATGAATAGAATCTTGAAACAGAATTGTTCAATTGATTTA
1 AAATCAAATAAATTCTATTGAACAACAGGAATAAAATCTTGAAACAGAATTATTCAATTAATTTA
**
27800365 TATTTGGAAACAA
66 TATTTACAAACAA
* * * * *
27800378 AAATCAAATAAATTCTGTTGAACGACAGGAATAAAATCTTGAAATATAATTATTCAATTAATTTC
1 AAATCAAATAAATTCTATTGAACAACAGGAATAAAATCTTGAAACAGAATTATTCAATTAATTTA
*
27800443 TGTTTACAAACAA
66 TATTTACAAACAA
27800456 AA
1 AA
27800458 TACAATTTCG
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (78 bp):
AAATCAAATAAATTCTATTGAACAACAGGAATAAAATCTTGAAACAGAATTATTCAATTAATTTA
TATTTACAAACAA
Found at i:27805817 original size:38 final size:38
Alignment explanation
Indices: 27805759--27805858 Score: 130
Period size: 38 Copynumber: 2.7 Consensus size: 38
27805749 ATTCTTGCGG
* * * *
27805759 CGACAGTTTTGGGTGC-AATTTGGAAGTGCTCATGCGA
1 CGACAGTTGTGGGCGCAAATTTGGAAGTACTCATACGA
*
27805796 CGATAGTTGTGGGCGCAAATTTGGAAGTACTCATACGA
1 CGACAGTTGTGGGCGCAAATTTGGAAGTACTCATACGA
* *
27805834 CGACAGTTTTGGGCTCAAATTTGGA
1 CGACAGTTGTGGGCGCAAATTTGGA
27805859 TGTTATTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
37 13 0.24
38 41 0.76
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (38 bp):
CGACAGTTGTGGGCGCAAATTTGGAAGTACTCATACGA
Found at i:27813024 original size:17 final size:18
Alignment explanation
Indices: 27812981--27813025 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
27812971 TGGCAATATA
*
27812981 TTTCTTTTCTTTTTTCTCT
1 TTTC-TTTCTTCTTTCTCT
27813000 TTTC-TTCTTCTTTCT-T
1 TTTCTTTCTTCTTTCTCT
27813016 TTTCTTTCTT
1 TTTCTTTCTT
27813026 TTTTTGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 5 0.21
17 15 0.62
19 4 0.17
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCTTTCTTCTTTCTCT
Found at i:27813026 original size:10 final size:10
Alignment explanation
Indices: 27812981--27813028 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
27812971 TGGCAATATA
27812981 TTTC-TTTTC
1 TTTCTTTTTC
*
27812990 TTT-TTTCTC
1 TTTCTTTTTC
*
27812999 TTTTCTTCTTC
1 -TTTCTTTTTC
27813010 TTTCTTTTTC
1 TTTCTTTTTC
27813020 TTTCTTTTT
1 TTTCTTTTT
27813029 TTGAGTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 7 0.22
10 21 0.66
11 4 0.12
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:27814449 original size:42 final size:42
Alignment explanation
Indices: 27814391--27814699 Score: 411
Period size: 42 Copynumber: 7.3 Consensus size: 42
27814381 TTATGAGGAA
* * * *
27814391 AAACGCCGCTATAGAACCTGATCTTTAGCGGCGCTTTCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
* *
27814433 AAACGCCGCTAAAGAACATGGTCTTTAACGGCGCTTATCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TCCCAC
* *
27814476 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
* * **
27814518 AAACGCCGCTATAGAGCATGGTCTTTAGCGGCGCTTTTTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
* * *
27814560 AAACGCCGCTACAGAGCATGGTCTTTAGCGGCGCTTATCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TCCCAC
* **
27814603 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
* *
27814645 AAACGCCGCTAAAGAACATAGTCTTTAGCGGCACTTATCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TCCCAC
27814688 AAACGCCGCTAA
1 AAACGCCGCTAA
27814700 TATTAACAAA
Statistics
Matches: 238, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
42 146 0.61
43 92 0.39
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
Found at i:27814492 original size:85 final size:84
Alignment explanation
Indices: 27814391--27814699 Score: 417
Period size: 85 Copynumber: 3.7 Consensus size: 84
27814381 TTATGAGGAA
* * *
27814391 AAACGCCGCTATAGAACCTGATCTTTAGCGGCGCTT-TCCCAAAAACGCCGCTAAAGAACATGGT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGAACATGGT
*
27814455 CTTTAACGGCGCTTATCTCAC
66 CTTTAGCGGCGCTT-T-TCAC
* * * * *
27814476 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTT-TTCCACAAACGCCGCTATAGAGCATGGT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGAACATGGT
27814540 CTTTAGCGGCGCTTTTTCAC
66 CTTTAGCGGCGC-TTTTCAC
* * * * *
27814560 AAACGCCGCTACAGAGCATGGTCTTTAGCGGCGCTTATCTCACAAACGCCGCTAAAGAACATGAT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGAACATGGT
27814625 CTTTAGCGGCGCTTTTACAC
66 CTTTAGCGGCGCTTTT-CAC
*
27814645 AAACGCCGCTAAAGAACAT-AGTCTTTAGCGGCACTTATCCCACAAACGCCGCTAA
1 AAACGCCGCTAAAGAACATGA-TCTTTAGCGGCGCTTATCCCACAAACGCCGCTAA
27814700 TATTAACAAA
Statistics
Matches: 198, Mismatches: 22, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
84 41 0.21
85 155 0.78
86 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (84 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGAACATGGT
CTTTAGCGGCGCTTTTCAC
Found at i:27814547 original size:127 final size:127
Alignment explanation
Indices: 27814391--27814699 Score: 474
Period size: 127 Copynumber: 2.4 Consensus size: 127
27814381 TTATGAGGAA
* * *
27814391 AAACGCCGCTATAGAACCTGATCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACATGGTC
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGAACATGGTC
* * *
27814456 TTTAACGGCGCTTATCTCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCAC
66 TTTAACGGCGCTTATCTCACAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACAC
* ** * *
27814518 AAACGCCGCTATAGAGCATGGTCTTTAGCGGCGCTTTTTCACAAACGCCGCTACAGAGCATGGTC
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGAACATGGTC
*
27814583 TTTAGCGGCGCTTATCTCACAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACAC
66 TTTAACGGCGCTTATCTCACAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACAC
* * *
27814645 AAACGCCGCTAAAGAACATAGTCTTTAGCGGCACTTATCCCACAAACGCCGCTAA
1 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGCTT-TCCCACAAACGCCGCTAA
27814700 TATTAACAAA
Statistics
Matches: 162, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
127 147 0.91
128 15 0.09
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (127 bp):
AAACGCCGCTATAGAACATGGTCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGAACATGGTC
TTTAACGGCGCTTATCTCACAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACAC
Found at i:27815266 original size:91 final size:91
Alignment explanation
Indices: 27815135--27815320 Score: 363
Period size: 91 Copynumber: 2.0 Consensus size: 91
27815125 GTTCGAGAGA
27815135 AAACATTTCATTGAACTATTTCCTAATAAATAAGATAATGCAAAATCAAGCTCAAATCTGACATG
1 AAACATTTCATTGAACTATTTCCTAATAAATAAGATAATGCAAAATCAAGCTCAAATCTGACATG
27815200 CAAATAAGTCTTGAGTCTTGAATCTT
66 CAAATAAGTCTTGAGTCTTGAATCTT
*
27815226 AAACATTTCATTGAACTATTTCCTAATAAATAAGATAATGCAAAATCATGCTCAAATCTGACATG
1 AAACATTTCATTGAACTATTTCCTAATAAATAAGATAATGCAAAATCAAGCTCAAATCTGACATG
27815291 CAAATAAGTCTTGAGTCTTGAATCTT
66 CAAATAAGTCTTGAGTCTTGAATCTT
27815317 AAAC
1 AAAC
27815321 TCTAAACTTC
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.32
Consensus pattern (91 bp):
AAACATTTCATTGAACTATTTCCTAATAAATAAGATAATGCAAAATCAAGCTCAAATCTGACATG
CAAATAAGTCTTGAGTCTTGAATCTT
Found at i:27815974 original size:17 final size:18
Alignment explanation
Indices: 27815941--27815979 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
27815931 CAGAGAAGCT
*
27815941 AAAAGAGAAAAGCAAAA-
1 AAAAGAGAAAAACAAAAC
*
27815958 AAAAGAGAAAAATAAAAC
1 AAAAGAGAAAAACAAAAC
27815976 AAAA
1 AAAA
27815980 AATAAAACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (18 bp):
AAAAGAGAAAAACAAAAC
Found at i:27818295 original size:41 final size:41
Alignment explanation
Indices: 27818238--27818587 Score: 447
Period size: 41 Copynumber: 8.6 Consensus size: 41
27818228 GACCTTGGAA
* *
27818238 AAGCGTCGCTATTGCTCTGACCTTTAGCGGTGCTTTTCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCAT
* * *
27818279 AAGCGCCGCTATTGCTCTGATCTTTAGCGGTGCTTTTCCAC
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCAT
27818320 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCAT
*
27818361 AAACGCCGCTATTGCTCTGACCTTTAGCGGCGC--TTCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCAT
* * ***
27818400 AAGCGTCGCTATTGCTCTGACCTTTAGCGGTGCTTGGACAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCAT
* * * ***
27818441 AAGTGCCACTATTGCTCCGACCTTTAGCGGCGCTTATGGGA-
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTT-TTCCAT
* ** *
27818482 AAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTTGGCTAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCAT
* **
27818523 AAGCGCCGCTATTGCTCCGACCTTTAGCGGCGCTTGACCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCAT
27818564 AAGCGCCGCTATTGCTCT-ACCTTT
1 AAGCGCCGCTATTGCTCTGACCTTT
27818588 TGTGGCGTTT
Statistics
Matches: 272, Mismatches: 33, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
39 36 0.13
40 8 0.03
41 226 0.83
42 2 0.01
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.31
Consensus pattern (41 bp):
AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCAT
Found at i:27818507 original size:162 final size:163
Alignment explanation
Indices: 27818238--27818587 Score: 499
Period size: 162 Copynumber: 2.2 Consensus size: 163
27818228 GACCTTGGAA
*** * * *
27818238 AAGCGTCGCTATTGCTCTGACCTTTAGCGGTGCTTTTCCATAAGCGCCGCTATTGCTCTGATCTT
1 AAGCGTCGCTATTGCTCTGACCTTTAGCGGTGCTTGGACATAAGCGCCACTATTGCTCCGACCTT
* * * **
27818303 TAGCGGTGCTTTTCCACAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCATAAACGCC
66 TAGCGGCGCTTTGCCACAAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTTGGCCATAAACGCC
*
27818368 GCTATTGCTCTGACCTTTAGCGGCGCTT-CCAT
131 GCTATTGCTCCGACCTTTAGCGGCGCTTACCAT
*
27818400 AAGCGTCGCTATTGCTCTGACCTTTAGCGGTGCTTGGACATAAGTGCCACTATTGCTCCGACCTT
1 AAGCGTCGCTATTGCTCTGACCTTTAGCGGTGCTTGGACATAAGCGCCACTATTGCTCCGACCTT
** * *
27818465 TAGCGGCGCTTATGGGA-AAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTTGGCTATAAGCGC
66 TAGCGGCGCTT-TGCCACAAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTTGGCCATAAACGC
27818529 CGCTATTGCTCCGACCTTTAGCGGCGCTTGACCAT
130 CGCTATTGCTCCGACCTTTAGCGGCGCTT-ACCAT
*
27818564 AAGCGCCGCTATTGCTCT-ACCTTT
1 AAGCGTCGCTATTGCTCTGACCTTT
27818588 TGTGGCGTTT
Statistics
Matches: 167, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
162 138 0.83
163 8 0.05
164 21 0.13
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.31
Consensus pattern (163 bp):
AAGCGTCGCTATTGCTCTGACCTTTAGCGGTGCTTGGACATAAGCGCCACTATTGCTCCGACCTT
TAGCGGCGCTTTGCCACAAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTTGGCCATAAACGCC
GCTATTGCTCCGACCTTTAGCGGCGCTTACCAT
Found at i:27827722 original size:92 final size:92
Alignment explanation
Indices: 27827564--27827755 Score: 251
Period size: 92 Copynumber: 2.1 Consensus size: 92
27827554 TTGGATTATG
* * *
27827564 TGCATCTGGCATGTTAACGGTCGGAATAGCTCTTATGAGCAATATGGCGTGGTATCGAGGGTGAA
1 TGCATCTGGCATGTTAACGGTCGGAATAACTCTTATGAGCAATATGGCGTGGTATAGAGGGAGAA
27827629 TATTTAGCCTACGGGCTTTACACTATA
66 TATTTAGCCTACGGGCTTTACACTATA
** * * * * *
27827656 TGCATCTGGTGTGTTATCGGTTGGAATAACTCTTATGAGCAATCTGGTGTGTTAATAG-GGGAGA
1 TGCATCTGGCATGTTAACGGTCGGAATAACTCTTATGAGCAATATGGCGTGGT-ATAGAGGGAGA
* * *
27827720 ATATTTAGCTTACGGGCTTTGCACTATG
65 ATATTTAGCCTACGGGCTTTACACTATA
27827748 TGCATCTG
1 TGCATCTG
27827756 TCATTGATCT
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
92 83 0.97
93 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (92 bp):
TGCATCTGGCATGTTAACGGTCGGAATAACTCTTATGAGCAATATGGCGTGGTATAGAGGGAGAA
TATTTAGCCTACGGGCTTTACACTATA
Found at i:27831453 original size:110 final size:110
Alignment explanation
Indices: 27831339--27831544 Score: 322
Period size: 110 Copynumber: 1.9 Consensus size: 110
27831329 TGACTAGCCA
*
27831339 TGTGAACATGCAAAAATACCCCACACACTCGTGTGTCAAACCGTGGGCTAGACCGTGTGTCAACT
1 TGTGAACATGCAAAAATACCCCACACACTCGTGTGTCAAACCATGGGCTAGACCGTGTGTCAACT
*
27831404 CGAAATAGGGTCACACAACCGTGTCCTAGCCTGTGTCACTAGCTG
66 CGAAATAGGGTCACACAACCGTGTCCCAGCCTGTGTCACTAGCTG
* ** * * *
27831449 TGTGAACATGTAAAAATACCCCACATGCTCGTGTGTCAAATCATGGGCTAGATCGTTTGTCAACT
1 TGTGAACATGCAAAAATACCCCACACACTCGTGTGTCAAACCATGGGCTAGACCGTGTGTCAACT
* *
27831514 TGAAATAGGGTCACACGACCGTGTCCCAGCC
66 CGAAATAGGGTCACACAACCGTGTCCCAGCC
27831545 CATGTGATCC
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (110 bp):
TGTGAACATGCAAAAATACCCCACACACTCGTGTGTCAAACCATGGGCTAGACCGTGTGTCAACT
CGAAATAGGGTCACACAACCGTGTCCCAGCCTGTGTCACTAGCTG
Found at i:27834963 original size:31 final size:35
Alignment explanation
Indices: 27834925--27835002 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
27834915 TTATAACTAT
* *
27834925 TTAATTTAATAATTA-TTT-TA-AT-AATATTTTG
1 TTAATTTAATAATTATTTTGTAGATAAATATTCTA
**
27834956 TTAATTTAATGTTTATTTTGTAGATAAATATTCTA
1 TTAATTTAATAATTATTTTGTAGATAAATATTCTA
27834991 TTAATTTAATAA
1 TTAATTTAATAA
27835003 GATTTAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
31 13 0.35
32 3 0.08
33 2 0.05
34 2 0.05
35 17 0.46
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (35 bp):
TTAATTTAATAATTATTTTGTAGATAAATATTCTA
Found at i:27846192 original size:37 final size:37
Alignment explanation
Indices: 27846124--27846206 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
27846114 ATTTCTAGAA
* *
27846124 TGCACCCAAGACTGTCGCTGCATAAGTATTCTTAAAT
1 TGCACCCAGGACTATCGCTGCATAAGTATTCTTAAAT
* * *
27846161 TGCATCCAGGACTATCGTTGCATAAGTATTCTTCAAT
1 TGCACCCAGGACTATCGCTGCATAAGTATTCTTAAAT
27846198 TGCACCCAG
1 TGCACCCAG
27846207 TAATGTTGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (37 bp):
TGCACCCAGGACTATCGCTGCATAAGTATTCTTAAAT
Found at i:27846220 original size:37 final size:37
Alignment explanation
Indices: 27846124--27846220 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 37
27846114 ATTTCTAGAA
* * *
27846124 TGCACCCAAGACTGTCGCTGCATAAGTATTCTTAAAT
1 TGCACCCAGGAATATCGCTGCATAAGTATTCTTAAAT
* * * *
27846161 TGCATCCAGGACTATCGTTGCATAAGTATTCTTCAAT
1 TGCACCCAGGAATATCGCTGCATAAGTATTCTTAAAT
* * *
27846198 TGCACCCAGTAATGTTGCTGCAT
1 TGCACCCAGGAATATCGCTGCAT
27846221 GAACATGTCT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (37 bp):
TGCACCCAGGAATATCGCTGCATAAGTATTCTTAAAT
Found at i:27846246 original size:26 final size:26
Alignment explanation
Indices: 27846210--27846263 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
27846200 CACCCAGTAA
*
27846210 TGTTGCTGCATGAACATGTCTAGAAT
1 TGTTGCTGCATGAACATGTCCAGAAT
* *
27846236 TGTTGTTGCATGAACGTGTCCAGAAT
1 TGTTGCTGCATGAACATGTCCAGAAT
27846262 TG
1 TG
27846264 CACCTAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (26 bp):
TGTTGCTGCATGAACATGTCCAGAAT
Found at i:27850981 original size:41 final size:41
Alignment explanation
Indices: 27850901--27850981 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
27850891 GTTTATTGTA
* *
27850901 TCTAATGAATCTCAATGCATGTTGAAAACATGACCACTATT
1 TCTAATAAATCTCAATGCATATTGAAAACATGACCACTATT
27850942 TCTAATAAATCT-AATCGCATATT-AAAATCATG-CCTACTAT
1 TCTAATAAATCTCAAT-GCATATTGAAAA-CATGACC-ACTAT
27850982 ACTAATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 9 0.26
41 26 0.74
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (41 bp):
TCTAATAAATCTCAATGCATATTGAAAACATGACCACTATT
Found at i:27854716 original size:52 final size:51
Alignment explanation
Indices: 27854497--27854784 Score: 432
Period size: 51 Copynumber: 5.6 Consensus size: 51
27854487 TAAATGAAAA
* * * *
27854497 AGGTTCGATGACTATGTATCATAGTGAGTATATGAATCCTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTACGGATTATG
*
27854548 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTACGGATTATG
*
27854599 AGTTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTACGGATTATG
* *
27854650 AGGTCCGATAACTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTACGGATTATG
* * * *
27854702 AGGTCCGATGACTATGTGTCATTGTGAGTGTATGATTCCTTTACGGATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTACGGATTATG
* *
27854754 AGGTCCGATAACTATGTGTCATCATGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
27854785 TAAATGAAAT
Statistics
Matches: 216, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
51 131 0.61
52 85 0.39
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (51 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTACGGATTATG
Found at i:27857195 original size:15 final size:16
Alignment explanation
Indices: 27857163--27857196 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27857153 TATTCATCTT
*
27857163 ATTTGCATTTAGGTTA
1 ATTTGCATCTAGGTTA
27857179 ATTTGCATCTA-GTTA
1 ATTTGCATCTAGGTTA
27857194 ATT
1 ATT
27857197 AATTTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (16 bp):
ATTTGCATCTAGGTTA
Found at i:27858623 original size:13 final size:13
Alignment explanation
Indices: 27858605--27858636 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
27858595 TAAAAGTCCA
27858605 AATTACAAAACCC
1 AATTACAAAACCC
*
27858618 AATTACAAAGCCC
1 AATTACAAAACCC
27858631 AATTAC
1 AATTAC
27858637 TTAAACAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.19
Consensus pattern (13 bp):
AATTACAAAACCC
Found at i:27859298 original size:18 final size:18
Alignment explanation
Indices: 27859275--27859353 Score: 65
Period size: 18 Copynumber: 4.2 Consensus size: 18
27859265 TTTACTTTGC
27859275 AATATT-TAATAAGTAATA
1 AATATTATAATAA-TAATA
27859293 AATATTATAATAATAAT-
1 AATATTATAATAATAATA
*
27859310 AATAATGATAATGATATTAATA
1 AAT-ATTATAAT-A-A-TAATA
*
27859332 AATATTAATAAAAATAA-A
1 AATATT-ATAATAATAATA
27859350 AATA
1 AATA
27859354 AAAATGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
17 3 0.06
18 22 0.43
19 10 0.20
20 2 0.04
21 7 0.14
22 7 0.14
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AATATTATAATAATAATA
Found at i:27859307 original size:3 final size:3
Alignment explanation
Indices: 27859281--27859354 Score: 51
Period size: 3 Copynumber: 24.0 Consensus size: 3
27859271 TTGCAATATT
* * * *
27859281 TAA TAA GTAA TAA -ATA TTA TAA TAA TAA TAA TAA TGA TAA TGA TAT
1 TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
27859327 TAA TAAA TAT TAA TAA AAA TAA AAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA
27859355 AAATGAAAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
2 1 0.02
3 46 0.87
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27860509 original size:28 final size:28
Alignment explanation
Indices: 27860478--27860638 Score: 123
Period size: 29 Copynumber: 5.6 Consensus size: 28
27860468 CACGTTTTAA
27860478 CCCCTAAACTTCAAAAATTACAATTTTG
1 CCCCTAAACTTCAAAAATTACAATTTTG
*
27860506 CCCCCAAACTTTCAAAAAATTAC-ATTTTG
1 CCCCTAAAC-TTC-AAAAATTACAATTTTG
*
27860535 CCCC-AAACTTCCAAAAA-TATCATTTTTG
1 CCCCTAAACTT-CAAAAATTA-CAATTTTG
* ** **
27860563 ACCCC-AAATTTTTTGAAAATTACCGTTTTG
1 -CCCCTAAA--CTTCAAAAATTACAATTTTG
* * *
27860593 CTCCTAAACTTCCAAAAATTACCATTTTA
1 CCCCTAAACTT-CAAAAATTACAATTTTG
*
27860622 CCCCTAAACTTCCAAAA
1 CCCCTAAACTTCAAAAA
27860639 GTCGCATTTT
Statistics
Matches: 107, Mismatches: 15, Indels: 22
0.74 0.10 0.15
Matches are distributed among these distances:
26 2 0.02
27 8 0.07
28 25 0.23
29 46 0.43
30 22 0.21
31 4 0.04
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (28 bp):
CCCCTAAACTTCAAAAATTACAATTTTG
Found at i:27860668 original size:87 final size:87
Alignment explanation
Indices: 27860491--27860677 Score: 216
Period size: 87 Copynumber: 2.1 Consensus size: 87
27860481 CTAAACTTCA
* * *
27860491 AAAATTACAATTTTGCCCCCAAACTTTCAAAAAATTACATTTTGCCCCAAACTTCCAAAAATATC
1 AAAATTACCATTTTGCCCCCAAACTTTCAAAAAATTACATTTTACCCCAAACTTCCAAAAATAGC
* * *
27860556 ATTTTTGACCCCAAATTTTTTG
66 ATTTTTGACCCCAAAGTGTTCG
* * * * * *
27860578 AAAATTACCGTTTTGCTCCTAAAC-TTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAGTC
1 AAAATTACCATTTTGCCCCCAAACTTTCAAAAAATTA-CATTTTACCCC-AAACTTCCAAAAATA
**
27860642 GCATTTTTG-CCCCCGAGTGTTCG
64 GCATTTTTGACCCCAAAGTGTTCG
27860665 AAAATTACCATTT
1 AAAATTACCATTT
27860678 ACACCCCCGA
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
86 11 0.13
87 51 0.61
88 21 0.25
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.34
Consensus pattern (87 bp):
AAAATTACCATTTTGCCCCCAAACTTTCAAAAAATTACATTTTACCCCAAACTTCCAAAAATAGC
ATTTTTGACCCCAAAGTGTTCG
Found at i:27860685 original size:30 final size:30
Alignment explanation
Indices: 27860651--27860707 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
27860641 CGCATTTTTG
* * *
27860651 CCCCCGAGTGTTCGAAAATTACCATTTACA
1 CCCCCGAGTATCCAAAAATTACCATTTACA
*
27860681 CCCCCGAGTATCCAAAAATTACTATTT
1 CCCCCGAGTATCCAAAAATTACCATTT
27860708 TGCCTCCGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.28
Consensus pattern (30 bp):
CCCCCGAGTATCCAAAAATTACCATTTACA
Found at i:27876126 original size:209 final size:209
Alignment explanation
Indices: 27875577--27876264 Score: 959
Period size: 209 Copynumber: 3.3 Consensus size: 209
27875567 AGAGGAGCAA
* * * * * * * *
27875577 ATCAAAATAAGTAAGGCGCTCATCTTCCTGATGAGATA-TAGAGAAGTATATCAACTCAATGAAA
1 ATCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACT-GAGAAGTAGACCAAATCAATGAAA
* * * *
27875641 CCAAAGCTCGATGTAAGCGAAA-CTTCGAACCCCAGCTTCCTGATGAGATACTGAAAAGCAGGTC
65 CC-AGGCTCAAAGTAAGC-AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTC
* * *
27875705 GAAGCAATAAAATGGTTACCTTCCTAATGAGATACAGAGAAATGAACCAAATCCGTCTTCCTGAT
128 GAAGCAATAAAGTGGTTACCTTCCTAATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGAT
27875770 GAGACACAGAGAAATGG
193 GAGACACAGAGAAATGG
*
27875787 ATCAAAAACAAGAGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAA
1 ATC-AAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAA
* *
27875852 CCAGGCTCAAAGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTAAGAAGCAGGTCGA
65 CCAGGCTCAAAGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGA
* * * * *
27875917 AGCAATAAAGCGGTTACCTTCTTGATGAGATACAGAGAAGTGGACCAGATCCGTCTTCTTGATGA
130 AGCAATAAAGTGGTTACCTTCCTAATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGA
*
27875982 GACACAGAGAATTGG
195 GACACAGAGAAATGG
*
27875997 ATC-AAACTATGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAA
1 ATCAAAAC-AAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAA
* * * **
27876061 CCAGGCTCAAAGTGAGCAAATCTTCGAACCCTAACTTCCTGATGAGATACTGAGAAGTGGGTCGA
65 CCAGGCTCAAAGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGA
* **
27876126 AGCAATAAAGTTGTTACCTTCCTAATGAGATACAGAGAAGTGAACCAGATTTGTCTTCCTGATGA
130 AGCAATAAAGTGGTTACCTTCCTAATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGA
* *
27876191 GACATAGAGAAGTGG
195 GACACAGAGAAATGG
* * *
27876206 ATCAAAAACAAGTGATGCGGCCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATCA
1 ATC-AAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCA
27876265 GTAACACCAA
Statistics
Matches: 425, Mismatches: 47, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
208 4 0.01
209 188 0.44
210 176 0.41
211 56 0.13
212 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (209 bp):
ATCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAAC
CAGGCTCAAAGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
GCAATAAAGTGGTTACCTTCCTAATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAG
ACACAGAGAAATGG
Found at i:27876569 original size:6 final size:6
Alignment explanation
Indices: 27876558--27876634 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
27876548 GGCCCAATAG
* *
27876558 AATTTA AATTT- ATTTTA AGTTTA AATTT- -ATTTAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
*
27876603 -ATTATA AATTTA AGTTTA AATTT- -ATTTA AATT
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATT
27876635 AATAATGTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
4 11 0.19
5 5 0.09
6 34 0.60
7 7 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
AATTTA
Found at i:27876582 original size:17 final size:17
Alignment explanation
Indices: 27876558--27876620 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
27876548 GGCCCAATAG
27876558 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
27876575 AGTTTAAATTTATTTAA
1 AATTTAAATTTATTTTA
*
27876592 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
*
27876609 AATTTAAGTTTA
1 AATTTAAATTTA
27876621 AATTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:27876597 original size:23 final size:23
Alignment explanation
Indices: 27876571--27876632 Score: 73
Period size: 17 Copynumber: 3.0 Consensus size: 23
27876561 TTAAATTTAT
27876571 TTTAAGTTTAAATTTATTTAAAA
1 TTTAAGTTTAAATTTATTTAAAA
*
27876594 TTTAAATTT--A-TTA--T-AAA
1 TTTAAGTTTAAATTTATTTAAAA
27876611 TTTAAGTTTAAATTTATTTAAA
1 TTTAAGTTTAAATTTATTTAAA
27876633 TTAATAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
17 11 0.35
18 1 0.03
19 1 0.03
20 6 0.19
21 1 0.03
22 1 0.03
23 10 0.32
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
TTTAAGTTTAAATTTATTTAAAA
Found at i:27877349 original size:3 final size:3
Alignment explanation
Indices: 27877334--27877386 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
27877324 TTGCAATATT
* * *
27877334 TAA TAA GTAA TAA TAA TAA TAA TAA TGA TAT TAA TAAA TAT TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
27877381 AAA TAA
1 TAA TAA
27877387 AAAAGAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27878520 original size:30 final size:30
Alignment explanation
Indices: 27878484--27878707 Score: 96
Period size: 30 Copynumber: 7.6 Consensus size: 30
27878474 CCCAGAAGGT
*
27878484 CCCTAAACTATT-CAAAAATCATGTTTTAAC
1 CCCTAAACT-TTCCAAAAATCATATTTTAAC
*
27878514 CCCTAAACTTTCCAAAAATTATATTTTAA-
1 CCCTAAACTTTCCAAAAATCATATTTTAAC
* * * **
27878543 CCCTCAAAC-TTCATAAAAATTACATTTTTGC
1 CCCT-AAACTTTC-CAAAAATCATATTTTAAC
*
27878574 CCCCAAACTTT-CAAAAAGTGCAT-TTTT-AC
1 CCCTAAACTTTCCAAAAA-T-CATATTTTAAC
* * * *
27878603 CCTCT-AAC-TTCATAAAAATTACATTTCT-TC
1 CC-CTAAACTTTC-CAAAAATCATATTT-TAAC
** *
27878633 CCCCGAACTTTCCAAAAATCACATTTT-AC
1 CCCTAAACTTTCCAAAAATCATATTTTAAC
* * * *
27878662 CCTTAAACTTT-TAAAAATTACCATTTT-A-
1 CCCTAAACTTTCCAAAAATCA-TATTTTAAC
*
27878690 CCCTAAACTTTCAAAAAA
1 CCCTAAACTTTCCAAAAA
27878708 ATTACATTTT
Statistics
Matches: 151, Mismatches: 27, Indels: 33
0.72 0.13 0.16
Matches are distributed among these distances:
28 20 0.13
29 47 0.31
30 75 0.50
31 9 0.06
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.34
Consensus pattern (30 bp):
CCCTAAACTTTCCAAAAATCATATTTTAAC
Done.