Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 59 of 132
Found at i:16393325 original size:11 final size:10
Alignment explanation
Indices: 16393307--16393335 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
16393297 AAAATGTACT
16393307 AATTTTTTTG
1 AATTTTTTTG
16393317 AATTTTTTTG
1 AATTTTTTTG
16393327 AATTTTTTT
1 AATTTTTTT
16393336 AAAATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (10 bp):
AATTTTTTTG
Found at i:16396184 original size:41 final size:41
Alignment explanation
Indices: 16396060--16396372 Score: 371
Period size: 41 Copynumber: 7.6 Consensus size: 41
16396050 TTTCCATAAA
* * * * *
16396060 CGCCGCAAAAGGT-AAAGCAATAGTGGCGTTTAT-AGTAAAAA
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAG--AAAG
* * *
16396101 CGCCGCTAAAGGTTAGAGCATTTAGTGGCGCTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCA-TTAGCGGCGTTTATGAGAAAG
* * *
16396143 CACCGCTAAAGGTCAAAGCATTAGCGGCGCTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* * *
16396184 CGCCGCTAAAGGTCAGAGCATTACCGACGTTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* *
16396225 TGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* * *
16396266 CGCAGCTAAAGGTCAAAGCATTAGCGGCGTTTATG-GGAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
* * * *
16396306 CGCCGCTAAAGGTCAGAGCATTAGCTGCATTTCTGTGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
16396347 CGCCGCTAAAGGTCAGAGCATTAGCG
1 CGCCGCTAAAGGTCAGAGCATTAGCG
16396373 ACGCTTTCTC
Statistics
Matches: 239, Mismatches: 29, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
40 34 0.14
41 166 0.69
42 25 0.10
43 12 0.05
44 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.20
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
Found at i:16396400 original size:122 final size:123
Alignment explanation
Indices: 16396101--16396375 Score: 365
Period size: 122 Copynumber: 2.2 Consensus size: 123
16396091 ATAGTAAAAA
* * * * * * *
16396101 CGCCGCTAAAGGTTAGAGCATTTAGTGGCGCTTATGAGAAAGCACCGCTAAAGGTCAAAGCATTA
1 CGCCGCTAAAGGTCAGAGCA-TTAGCGACGTTTATCAGAAAGCGCAGCTAAAGGTCAAAGCATTA
*
16396166 GCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTACCGACGTTTATGGGAAAG
65 GCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTACCGACATTTATGGGAAAG
* * **
16396225 TGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAGCGCAGCTAAAGGTCAAAGCATTAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGACGTTTATCAGAAAGCGCAGCTAAAGGTCAAAGCATTAG
* * * * *
16396290 CGGCGTTTATG-GGAAGCGCCGCTAAAGGTCAGAGCATTAGCTG-CATTTCTGTGAAAG
66 CGGCGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTA-CCGACATTTATGGGAAAG
16396347 CGCCGCTAAAGGTCAGAGCATTAGCGACG
1 CGCCGCTAAAGGTCAGAGCATTAGCGACG
16396376 CTTTCTCATA
Statistics
Matches: 135, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
122 65 0.48
123 52 0.39
124 18 0.13
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.20
Consensus pattern (123 bp):
CGCCGCTAAAGGTCAGAGCATTAGCGACGTTTATCAGAAAGCGCAGCTAAAGGTCAAAGCATTAG
CGGCGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTACCGACATTTATGGGAAAG
Found at i:16397692 original size:17 final size:17
Alignment explanation
Indices: 16397670--16397733 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
16397660 AAGCCCAACA
16397670 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
*
16397687 AAATTTCAATTTATTTT
1 AAATTTAAATTTATTTT
** *
16397704 AGGTTTAAATTTATTAT
1 AAATTTAAATTTATTTT
*
16397721 AAATTTAAGTTTA
1 AAATTTAAATTTA
16397734 AATTTATTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:16397716 original size:12 final size:11
Alignment explanation
Indices: 16397673--16397746 Score: 64
Period size: 11 Copynumber: 6.6 Consensus size: 11
16397663 CCCAACAAAA
*
16397673 TTTAAATTTAT
1 TTTAAATTTAG
*
16397684 TTTAAATTTCAA
1 TTTAAATTT-AG
*
16397696 TTT-ATTTTAGG
1 TTTAAATTTA-G
16397707 TTTAAATTTA-
1 TTTAAATTTAG
16397717 TTATAAATTTAAG
1 TT-TAAATTT-AG
16397730 TTTAAATTTA-
1 TTTAAATTTAG
16397740 TTTAAAT
1 TTTAAAT
16397747 AAAAAAATCC
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
10 10 0.19
11 24 0.45
12 17 0.32
13 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAG
Found at i:16397727 original size:23 final size:22
Alignment explanation
Indices: 16397672--16397746 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
16397662 GCCCAACAAA
*
16397672 ATTTAAATTT-ATTTTAAATTT
1 ATTTAAATTTAAGTTTAAATTT
* *
16397693 CAATTT-ATTTTAGGTTTAAATTT
1 --ATTTAAATTTAAGTTTAAATTT
16397716 ATTATAAATTTAAGTTTAAATTT
1 ATT-TAAATTTAAGTTTAAATTT
16397739 ATTTAAAT
1 ATTTAAAT
16397747 AAAAAAATCC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.07
22 10 0.23
23 31 0.70
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (22 bp):
ATTTAAATTTAAGTTTAAATTT
Found at i:16399667 original size:57 final size:58
Alignment explanation
Indices: 16399592--16399757 Score: 182
Period size: 57 Copynumber: 2.9 Consensus size: 58
16399582 TAACCCCCCG
*
16399592 AACTTCACAAAAATTACATTTTTACCCTAAACTTCTAAAAATTA-CATTTTTACCCTTA
1 AACTTC-CAAAAATTACATTTTTACCCTAAACTTCTAAAAATTACCATTTTTACCCCTA
* * *
16399650 AACTTCCAAAAATTACATTTTTAACCCCAAACTT-TCAAAATTACCA-TTTTACCCCTG
1 AACTTCCAAAAATTACATTTTT-ACCCTAAACTTCTAAAAATTACCATTTTTACCCCTA
* *
16399707 AA-TGTCCAAAAA-TACCATTTTTA-CCTCAAACTTTCCAAAAACTACCATTTT
1 AACT-TCCAAAAATTA-CATTTTTACCCT-AAAC-TTCTAAAAATTACCATTTT
16399758 ACCATCGGAT
Statistics
Matches: 92, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
55 2 0.02
56 8 0.09
57 52 0.57
58 27 0.29
59 3 0.03
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.35
Consensus pattern (58 bp):
AACTTCCAAAAATTACATTTTTACCCTAAACTTCTAAAAATTACCATTTTTACCCCTA
Found at i:16399917 original size:60 final size:58
Alignment explanation
Indices: 16399783--16399933 Score: 164
Period size: 60 Copynumber: 2.6 Consensus size: 58
16399773 AAAATTACAT
* * *
16399783 TTTTACCCCCGAGTGTCCAAAAATTACCA--TTTTACCCTCGAAGTGTCAAAAATTACCA
1 TTTTA-CCCCGAATGTCCAAAAATT-CCATTTTTTACCCTCGAAATGTCAAAAAATACCA
* *
16399841 TTTTACCCCTAGATGTCCAAAAATTCCATTTTTTGACCC-CGAAATTTCCAAAAAATACCA
1 TTTTACCCCGA-ATGTCCAAAAATTCCATTTTTT-ACCCTCGAAATGT-CAAAAAATACCA
* *
16399901 TTTTATCCCCGAATGTCTAAAAATTACATTTTT
1 TTTTA-CCCCGAATGTCCAAAAATTCCATTTTT
16399934 GCCTCTGAGT
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
57 8 0.10
58 17 0.22
59 10 0.13
60 39 0.49
61 5 0.06
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (58 bp):
TTTTACCCCGAATGTCCAAAAATTCCATTTTTTACCCTCGAAATGTCAAAAAATACCA
Found at i:16399933 original size:29 final size:29
Alignment explanation
Indices: 16399599--16399956 Score: 237
Period size: 29 Copynumber: 12.3 Consensus size: 29
16399589 CCGAACTTCA
**
16399599 CAAAAATTA-CATTTTTACCCTAAACT-TC
1 CAAAAATTACCATTTTTACCCCGAA-TGTC
* **
16399627 TAAAAATTA-CATTTTTACCCTTAAACT-TC
1 CAAAAATTACCATTTTTACCC-CGAA-TGTC
* *
16399656 CAAAAATTA-CATTTTTAACCCCAAACT-TT
1 CAAAAATTACCATTTTT-ACCCCGAA-TGTC
16399685 C-AAAATTACCA-TTTTACCCCTGAATGTC
1 CAAAAATTACCATTTTTACCCC-GAATGTC
* * *
16399713 CAAAAA-TACCATTTTTACCTCAAACTTTC
1 CAAAAATTACCATTTTTACCCCGAA-TGTC
* * *
16399742 CAAAAACTACCA-TTTTACCATCGGATGTC
1 CAAAAATTACCATTTTTACC-CCGAATGTC
** *
16399771 TGAAAATTA-CATTTTTACCCCCGAGTGTC
1 CAAAAATTACCATTTTTA-CCCCGAATGTC
16399800 CAAAAATTACCA-TTTTACCCTCGAAGTGT-
1 CAAAAATTACCATTTTTACCC-CGAA-TGTC
*
16399829 CAAAAATTACCA-TTTTACCCCTAGATGTC
1 CAAAAATTACCATTTTTACCCCGA-ATGTC
*
16399858 CAAAAATT-CCATTTTTTGACCCCGAAATTTC
1 CAAAAATTACCA-TTTTT-ACCCCG-AATGTC
*
16399889 CAAAAAATACCA-TTTTATCCCCGAATGTC
1 CAAAAATTACCATTTTTA-CCCCGAATGTC
* * * *
16399918 TAAAAATTA-CATTTTTGCCTCTGAGTGTC
1 CAAAAATTACCATTTTTACC-CCGAATGTC
16399947 CAAAAATTAC
1 CAAAAATTAC
16399957 TGTTTCGCCC
Statistics
Matches: 272, Mismatches: 32, Indels: 50
0.77 0.09 0.14
Matches are distributed among these distances:
27 6 0.02
28 58 0.21
29 156 0.57
30 32 0.12
31 16 0.06
32 4 0.01
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (29 bp):
CAAAAATTACCATTTTTACCCCGAATGTC
Found at i:16399974 original size:147 final size:145
Alignment explanation
Indices: 16399625--16399994 Score: 392
Period size: 147 Copynumber: 2.5 Consensus size: 145
16399615 ACCCTAAACT
*** * * * * * *
16399625 TCTAAAAATTACATTTTTACCCTTAAACT-TCCAAAAATTA-CATTTTTAACCCCAAACTTTC-A
1 TCTAAAAATTACATTTTTACCC-CCGAGTGTCCAAAAATTACCA-TTTCACCCCCGAAGTGTCAA
* *
16399687 AAATTACCATTTTACCCCTGAATGTCCAAAAATACCATTTTTACCTCAAACTTTCCAAAAACTAC
64 AAATTACCATTTTACCCCTGAATGTCCAAAAATACCATTTTTACCCCAAACTTTCCAAAAAATAC
* *
16399752 CATTTTACCATCGGATG
129 CATTTTACCACCGAATG
* * *
16399769 TCTGAAAATTACATTTTTACCCCCGAGTGTCCAAAAATTACCATTTTACCCTCGAAGTGTCAAAA
1 TCTAAAAATTACATTTTTACCCCCGAGTGTCCAAAAATTACCATTTCACCCCCGAAGTGTCAAAA
*
16399834 ATTACCATTTTACCCCT-AGATGTCCAAAAATTCCATTTTTTGACCCCGAAA-TTTCCAAAAAAT
66 ATTACCATTTTACCCCTGA-ATGTCCAAAAATACCA-TTTTT-ACCCC-AAACTTTCCAAAAAAT
16399897 ACCATTTTATCC-CCGAATG
127 ACCATTTTA-CCACCGAATG
* * * ** * * *
16399916 TCTAAAAATTACATTTTTGCCTCTGAGTGTCCAAAAATTACTGTTTCGCCCCCTAAGTGTCCAAA
1 TCTAAAAATTACATTTTTACCCCCGAGTGTCCAAAAATTACCATTTCACCCCCGAAGTGTCAAAA
* *
16399981 ATTATCGTTTTACC
66 ATTACCATTTTACC
16399995 TTCGGGCATC
Statistics
Matches: 190, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
143 2 0.01
144 46 0.24
145 37 0.19
146 5 0.03
147 95 0.50
148 5 0.03
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (145 bp):
TCTAAAAATTACATTTTTACCCCCGAGTGTCCAAAAATTACCATTTCACCCCCGAAGTGTCAAAA
ATTACCATTTTACCCCTGAATGTCCAAAAATACCATTTTTACCCCAAACTTTCCAAAAAATACCA
TTTTACCACCGAATG
Found at i:16407724 original size:13 final size:13
Alignment explanation
Indices: 16407706--16407737 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
16407696 ATAATCATTC
16407706 TTTTGTACATTTA
1 TTTTGTACATTTA
16407719 TTTTGTACATTTA
1 TTTTGTACATTTA
16407732 TTTTGT
1 TTTTGT
16407738 TCTTTGGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.66
Consensus pattern (13 bp):
TTTTGTACATTTA
Found at i:16412634 original size:123 final size:123
Alignment explanation
Indices: 16412359--16412636 Score: 358
Period size: 123 Copynumber: 2.3 Consensus size: 123
16412349 TGTGGTCATC
* * * * *
16412359 TTCCTGATGGGGTACTGAGAAGAAGACCAAATCAATGAAGCCAGGCTCAAAGTGAGCGAATCTTC
1 TTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAAATCTTC
* * *
16412424 GAACCCCAGCTTCCTAATGAGGTACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
66 GAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGATCGAAGCAATAAAATGGTTAGA
* * * * * * * *
16412482 TTCCTGATGAGATACAGAGAGGTATACCAACTCGATGAAATCAAGCTCCAAGTGAGCAAATCTTC
1 TTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAAATCTTC
* * * *
16412547 GAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGATCGAAGCAATAAAATGGTTGGA
66 GAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGATCGAAGCAATAAAATGGTTAGA
**
16412605 TTCCTGATGAGATACTGAGAAGCGGACCAAAT
1 TTCCTGATGAGATACTGAGAAGAAGACCAAAT
16412637 TCGTCTTCCT
Statistics
Matches: 129, Mismatches: 26, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
123 129 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (123 bp):
TTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAAATCTTC
GAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGATCGAAGCAATAAAATGGTTAGA
Found at i:16412760 original size:332 final size:332
Alignment explanation
Indices: 16412149--16412833 Score: 1181
Period size: 332 Copynumber: 2.1 Consensus size: 332
16412139 AGTTGGTCGT
*
16412149 CTTCTTGATGAGATACAGAGAGGTATACCAACTCGATGAAATCAAGCTCCAAGTGAGCAAATCTT
1 CTTCCTGATGAGATACAGAGAGGTATACCAACTCGATGAAATCAAGCTCCAAGTGAGCAAATCTT
* *
16412214 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGATCGAAGTAATAAAATGGTTAGCTTCCTG
66 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGATCGAAGCAATAAAATGGTTAGATTCCTG
* *
16412279 ATGAGATACTAAGAAGCGAACCAAATTCATCTTCTTGATGAGATACAGAGAAGCGGATTGAAACA
131 ATGAGATACTAAGAAGCGAACCAAATTCATCTTCCTGATGAGATACAAAGAAGCGGATTGAAACA
* * *
16412344 AGTGATGTGGTCATCTTCCTGATGGGGTACTGAGAAGAAGACCAAATCAATGAAGCCAGGCTCAA
196 AGTGATGCGATCATCTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAGGCTCAA
* * *
16412409 AGTGAGCGAATCTTCGAACCCCAGCTTCCTAATGAGGTACTAAGAAGCAGGTCGAAGCAATAAAA
261 AGTGAGCGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAACAAGTCGAAGCAATAAAA
16412474 TGGTTAG
326 TGGTTAG
16412481 CTTCCTGATGAGATACAGAGAGGTATACCAACTCGATGAAATCAAGCTCCAAGTGAGCAAATCTT
1 CTTCCTGATGAGATACAGAGAGGTATACCAACTCGATGAAATCAAGCTCCAAGTGAGCAAATCTT
* *
16412546 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGATCGAAGCAATAAAATGGTTGGATTCCTG
66 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGATCGAAGCAATAAAATGGTTAGATTCCTG
* * * *
16412611 ATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTGGTGAGATACAAAGAAGCGGATTGAAACA
131 ATGAGATACTAAGAAGCGAACCAAATTCATCTTCCTGATGAGATACAAAGAAGCGGATTGAAACA
16412676 AGTGATGCGATCATCTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAGGCTCAA
196 AGTGATGCGATCATCTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAGGCTCAA
* * *
16412741 AGTGAGCGAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAACAAGTCGAAGCAATAAAA
261 AGTGAGCGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAACAAGTCGAAGCAATAAAA
16412806 TGGTTAG
326 TGGTTAG
*
16412813 CTTCCTGATGAGATACTGAGA
1 CTTCCTGATGAGATACAGAGA
16412834 AGTGGACCAA
Statistics
Matches: 332, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
332 332 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (332 bp):
CTTCCTGATGAGATACAGAGAGGTATACCAACTCGATGAAATCAAGCTCCAAGTGAGCAAATCTT
CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGATCGAAGCAATAAAATGGTTAGATTCCTG
ATGAGATACTAAGAAGCGAACCAAATTCATCTTCCTGATGAGATACAAAGAAGCGGATTGAAACA
AGTGATGCGATCATCTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAGGCTCAA
AGTGAGCGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAACAAGTCGAAGCAATAAAA
TGGTTAG
Found at i:16413214 original size:208 final size:209
Alignment explanation
Indices: 16412481--16413557 Score: 1547
Period size: 209 Copynumber: 5.2 Consensus size: 209
16412471 AAATGGTTAG
* * * * * * * ** *
16412481 CTTCCTGATGAGATACAGAGAGGTATACCAACTCGATGAAATCAAGCTCCAAGTGAGCAAATCTT
1 CTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTT
* * * *
16412546 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGATCGAAGCAATAAAATGGTTGGATTCCTG
66 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
* * *
16412611 ATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTGGTGAGATACAAAGAAGCGGATTGAAACA
131 ATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACA
*
16412676 AGTGATGCGATCAT
196 AGTGATGCGGTCAT
* *
16412690 CTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAGGCTCAAAGTGAGCGAATCTT
1 CTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTT
* * *
16412755 CGAACCCTAGCTTCCTGATGAGATACTGAGAAACAAGTCGAAGCAATAAAATGGTTAGCTTCCTG
66 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
* * * *
16412820 ATGAGATACTGAGAAGTGGACCAAATTCTTCTTCCTGATAAGATACAGAGAAGC-GAATTGAAAT
131 ATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAG-ATTGAAAC
16412884 AAGTGATGCGGTCAT
195 AAGTGATGCGGTCAT
*
16412899 CTTCC---TG-GGTACTGAGAAGAAGACCAAATCAATGAAGCCAGGCTCAAAGTGAG-AGAATCT
1 CTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCA-AATCT
* *
16412959 TCGAACCCCAGCTTCCTGATGAGATATTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTCCT
65 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
* *
16413024 GATGAGATATTGAGAAGCGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCAGATTGAAAC
130 GATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAAC
*
16413089 AAGTGATGCAGTCAT
195 AAGTGATGCGGTCAT
*
16413104 CTTCCTGATGAGGT-CTGAGAAGAAGACCAAATCAATGAAGCTAAGCTCAAAGTGAGCAAATCTT
1 CTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTT
* * *
16413168 CGAACCCCAGCTTCTTGATGAGATACTGAGAAACAGGTCAAAGCAATAAAATGGTTAGCTTCCTG
66 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
*
16413233 ATGAGATAGTGAGAAGCGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACA
131 ATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACA
*
16413298 AGTGATACGGTCAT
196 AGTGATGCGGTCAT
* * *
16413312 CTTTCTGATGAGGTACTGAGAATAAGACTAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTT
1 CTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTT
* * **
16413377 CGAAGCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTTTTG
66 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
* * * * * * * ** **
16413442 ATGAGATACAGAGAAGTGAACCAGATCCGTCTTCTTGATGAGACACAGAGAAGTGGATCAAAAAC
131 ATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGAT-TGAAAC
16413507 AAGTGATGCGGTCAT
195 AAGTGATGCGGTCAT
* *
16413522 CTTCCTGATGAGATACTGAGAAGAGGACCAAATCAA
1 CTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAA
16413558 ATGACACCAA
Statistics
Matches: 779, Mismatches: 79, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
205 187 0.24
206 3 0.00
208 197 0.25
209 343 0.44
210 49 0.06
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (209 bp):
CTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTT
CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
ATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACA
AGTGATGCGGTCAT
Found at i:16413851 original size:6 final size:6
Alignment explanation
Indices: 16413840--16413898 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
16413830 AGTTACAACA
*
16413840 AAATTT AAATTT --ATTAT AAATTT AAGTTT AAATTT --ATTAT AAATTT
1 AAATTT AAATTT AAATT-T AAATTT AAATTT AAATTT AAATT-T AAATTT
*
16413886 AAGTTT AAATTT A
1 AAATTT AAATTT A
16413899 TTTAAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
4 6 0.14
5 2 0.05
6 29 0.67
7 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:16413861 original size:11 final size:10
Alignment explanation
Indices: 16413842--16413905 Score: 74
Period size: 11 Copynumber: 5.8 Consensus size: 10
16413832 TTACAACAAA
16413842 ATTTAAATTT
1 ATTTAAATTT
16413852 ATTATAAATTT
1 ATT-TAAATTT
16413863 AAGTTTAAATTT
1 -A-TTTAAATTT
16413875 ATTATAAATTT
1 ATT-TAAATTT
16413886 AAGTTTAAATTT
1 -A-TTTAAATTT
16413898 ATTTAAAT
1 ATTTAAAT
16413906 AAAAAAATCT
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 12 0.25
11 16 0.33
12 16 0.33
13 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:16413872 original size:23 final size:23
Alignment explanation
Indices: 16413843--16413905 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
16413833 TACAACAAAA
16413843 TTTAAATTTATTATAAATTTAAG
1 TTTAAATTTATTATAAATTTAAG
16413866 TTTAAATTTATTATAAATTTAAG
1 TTTAAATTTATTATAAATTTAAG
16413889 TTTAAATTTATT-TAAAT
1 TTTAAATTTATTATAAAT
16413906 AAAAAAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 5 0.12
23 35 0.88
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (23 bp):
TTTAAATTTATTATAAATTTAAG
Found at i:16415780 original size:30 final size:29
Alignment explanation
Indices: 16415755--16415954 Score: 214
Period size: 29 Copynumber: 6.9 Consensus size: 29
16415745 TTAAAAAATG
*
16415755 CATTTTAACCCTCAAACTTCATAAAAATTA
1 CATTTTAACCCTCAAACTTC-CAAAAATTA
** *
16415785 CATTTTTGCCCTTAAACTTCCAAAAATTA
1 CATTTTAACCCTCAAACTTCCAAAAATTA
*
16415814 CATTTTTGACCCT-AAACTTTCCAAAAATTA
1 CA-TTTTAACCCTCAAAC-TTCCAAAAATTA
16415844 CATTTTAACCCT-AAACTTTCCAAAAATTA
1 CATTTTAACCCTCAAAC-TTCCAAAAATTA
* * *
16415873 TATTTTTACCCCCAAACTTCCAAAAATTA
1 CATTTTAACCCTCAAACTTCCAAAAATTA
16415902 CATTTTTAACCC-CAAACTTCC-AAAATTA
1 CA-TTTTAACCCTCAAACTTCCAAAAATTA
*
16415930 CCATTTT-ACCCCCAAA-TGTCCAAAA
1 -CATTTTAACCCTCAAACT-TCCAAAA
16415955 TACCATTTTT
Statistics
Matches: 150, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.03
28 18 0.12
29 76 0.51
30 51 0.34
ACGTcount: A:0.39, C:0.27, G:0.01, T:0.34
Consensus pattern (29 bp):
CATTTTAACCCTCAAACTTCCAAAAATTA
Found at i:16415799 original size:59 final size:58
Alignment explanation
Indices: 16415715--16415954 Score: 204
Period size: 59 Copynumber: 4.1 Consensus size: 58
16415705 CCCTGAATTA
* * * * * * * *
16415715 TCCAAAAATCATATTATAACCCTTAAAGTTTTAAAAAATGCATTTTAACCCTCAAACT
1 TCCAAAAATTACATTTTTACCCTTAAACTTTCAAAAATTACATTTTAACCCTCAAACT
* * * *
16415773 TCATAAAAATTACATTTTTGCCCTTAAACTTCCAAAAATTACATTTTTGACCCT-AAACTT
1 TC-CAAAAATTACATTTTTACCCTTAAACTTTCAAAAATTACA-TTTTAACCCTCAAAC-T
* * * *
16415833 TCCAAAAATTACATTTTAACCC-TAAACTTTCCAAAAATTATATTTTTACCCCCAAACT
1 TCCAAAAATTACATTTTTACCCTTAAACTTT-CAAAAATTACATTTTAACCCTCAAACT
* * *
16415891 TCCAAAAATTACATTTTTAACCC-CAAAC-TTCCAAAATTACCATTTT-ACCCCCAAA-T
1 TCCAAAAATTACATTTTT-ACCCTTAAACTTTCAAAAATTA-CATTTTAACCCTCAAACT
16415947 GTCCAAAA
1 -TCCAAAA
16415955 TACCATTTTT
Statistics
Matches: 151, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
56 1 0.01
57 24 0.16
58 42 0.28
59 72 0.48
60 12 0.08
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTACCCTTAAACTTTCAAAAATTACATTTTAACCCTCAAACT
Found at i:16416027 original size:28 final size:29
Alignment explanation
Indices: 16415923--16416234 Score: 164
Period size: 29 Copynumber: 10.7 Consensus size: 29
16415913 CCAAACTTCC
* * *
16415923 AAAATTACCATTTTACCCCCAAATGTCC-
1 AAAATTACCATTTTACCCTCGAGTGTCCA
* *
16415951 AAAA-TACCATTTTTGA-CCTCGAACTTTCCA
1 AAAATTACCA-TTTT-ACCCTCG-AGTGTCCA
* * **
16415981 AAAACTACCCTTTTACCCTCG-GATGTCTG
1 AAAATTACCATTTTACCCTCGAG-TGTCCA
*
16416010 AAAATTA-CATTTTGCCCTCGAGTGTCCA
1 AAAATTACCATTTTACCCTCGAGTGTCCA
*
16416038 AAAATTACCATTTTACCC-CTGAAGTATCC-
1 AAAATTACCATTTTACCCTC-G-AGTGTCCA
* *
16416067 AAAATTACCATTTTACCCCCG-GATGCCCA
1 AAAATTACCATTTTACCCTCGAG-TGTCCA
* * *
16416096 AAAATT-CCATTTTTTTA-CCTCAAAATTTCCA
1 AAAATTACCA---TTTTACCCTC-GAGTGTCCA
* * * *
16416127 AAAAATACCATTTTATCGTCGAATGTCCA
1 AAAATTACCATTTTACCCTCGAGTGTCCA
16416156 AAAATTA-CATTTTTA-CCTCCGAGTGTCCA
1 AAAATTACCA-TTTTACCCT-CGAGTGTCCA
*** ** *
16416185 AAAATTACTGCTTCGCCCCCGAAGTGTCC-
1 AAAATTACCATTTTACCCTCG-AGTGTCCA
*
16416214 AAAATTATCATTTTACCCTCG
1 AAAATTACCATTTTACCCTCG
16416235 GGCATCCAAA
Statistics
Matches: 215, Mismatches: 43, Indels: 51
0.70 0.14 0.17
Matches are distributed among these distances:
27 6 0.03
28 44 0.20
29 109 0.51
30 35 0.16
31 18 0.08
32 3 0.01
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAGTGTCCA
Found at i:16416244 original size:147 final size:145
Alignment explanation
Indices: 16415920--16416256 Score: 367
Period size: 147 Copynumber: 2.3 Consensus size: 145
16415910 ACCCCAAACT
** * * * *
16415920 TCCAAAATTACCATTTTACCCCCAAATGTCC-AAAATACCA-TTTTTGACCTCGAACTTTCCAAA
1 TCCAAAATTACCATTTTACCCCCGGAT-CCCAAAAATTCCATTTTTTGACCTCAAAATTTCCAAA
* * * ** *
16415983 AACTACCCTTTTACCCTCGGATGTCTGAAAATTACATTTTGCCCTCGAGTGTCCAAAAATTACCA
65 AAATACCATTTTACCCTCGAATGTCCAAAAATTACATTTTGACCTCGAGTGTCCAAAAATTACCA
* * *
16416048 TTTTACCCCTGAAGTA
130 CTTCACCCCCGAAGTA
*
16416064 TCCAAAATTACCATTTTACCCCCGGATGCCCAAAAATTCCATTTTTTTACCTCAAAATTTCCAAA
1 TCCAAAATTACCATTTTACCCCCGGAT-CCCAAAAATTCCATTTTTTGACCTCAAAATTTCCAAA
* * * *
16416129 AAATACCATTTTATCGTCGAATGTCCAAAAATTACATTTTTACCTCCGAGTGTCCAAAAATTACT
65 AAATACCATTTTACCCTCGAATGTCCAAAAATTACATTTTGACCT-CGAGTGTCCAAAAATTACC
* * *
16416194 GCTTCGCCCCCGAAGTG
129 ACTTCACCCCCGAAGTA
* *
16416211 TCCAAAATTATCATTTTACCCTCGGGCAT-CCAAAAA-TCGCATTTTT
1 TCCAAAATTACCATTTTACCC-CCGG-ATCCCAAAAATTC-CATTTTT
16416257 GACTCCGTTT
Statistics
Matches: 162, Mismatches: 25, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
144 28 0.17
145 8 0.05
146 58 0.36
147 63 0.39
148 3 0.02
149 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (145 bp):
TCCAAAATTACCATTTTACCCCCGGATCCCAAAAATTCCATTTTTTGACCTCAAAATTTCCAAAA
AATACCATTTTACCCTCGAATGTCCAAAAATTACATTTTGACCTCGAGTGTCCAAAAATTACCAC
TTCACCCCCGAAGTA
Found at i:16420905 original size:43 final size:43
Alignment explanation
Indices: 16420787--16421072 Score: 333
Period size: 43 Copynumber: 6.7 Consensus size: 43
16420777 TTTGTTAATG
* * * ** *
16420787 TTAGTGGCATTTGTAGGAAAAGCGCCATTAAAGGCCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
16420830 TTAGCGGCGTTTGT-GGAAAAGCGCCACTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
16420872 TTAGCTGCGTTTGTGGGAAAAGTGCCGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
16420915 TTAGTGGCGTTTGTGGGATAAGCGCCGCTAAAGACCATGATCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
16420958 TTAGCGGTGTTTGT-GGAAAAGCACTGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * * *
16421000 TTAGTGGCGTTTATGGGATAAGCTCCACTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
16421043 TTAGCGGTGTTTGTGAGATAAGCGCCGCTA
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTA
16421073 TAGGCCCAAA
Statistics
Matches: 208, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 73 0.35
43 135 0.65
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:16420976 original size:85 final size:85
Alignment explanation
Indices: 16420796--16421072 Score: 367
Period size: 85 Copynumber: 3.2 Consensus size: 85
16420786 GTTAGTGGCA
** * * *
16420796 TTTGTAGGAAAAGCGCCATTAAAGGCCATGTTCTTTAGCGGCGTTTGT-GGAAAAGCGCCACTAA
1 TTTGT-GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGGATAAGCGCCACTAA
* * *
16420860 AGATCATGTTCTTTAGCTGCG
65 AGACCATGTTCTTTAGCGGTG
* * *
16420881 TTTGTGGGAAAAGTGCCGCTAAAGATCATGTTCTTTAGTGGCGTTTGTGGGATAAGCGCCGCTAA
1 TTTGT-GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGGATAAGCGCCACTAA
*
16420946 AGACCATGATCTTTAGCGGTG
65 AGACCATGTTCTTTAGCGGTG
* * * *
16420967 TTTGTGGAAAAGCACTGCTAAAGACCATGTTCTTTAGTGGCGTTTATGGGATAAGCTCCACTAAA
1 TTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGGATAAGCGCCACTAAA
16421032 GACCATGTTCTTTAGCGGTG
66 GACCATGTTCTTTAGCGGTG
*
16421052 TTTGTGAGATAAGCGCCGCTA
1 TTTGTG-GAAAAGCGCCGCTA
16421073 TAGGCCCAAA
Statistics
Matches: 166, Mismatches: 24, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
85 119 0.72
86 47 0.28
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (85 bp):
TTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGGATAAGCGCCACTAAA
GACCATGTTCTTTAGCGGTG
Found at i:16421017 original size:128 final size:128
Alignment explanation
Indices: 16420787--16421072 Score: 369
Period size: 128 Copynumber: 2.2 Consensus size: 128
16420777 TTTGTTAATG
* * * ** * *
16420787 TTAGTGGCATTTGTAGGAAAAGCGCCATTAAAGGCCATGTTCTTTAGCGGCGTTTGTGGAAAAGC
1 TTAGTGGCGTTTGTGGGATAAGCGCCGCTAAAGACCATGATCTTTAGCGGCGTTTGTGGAAAAGC
* * * * *
16420852 GCCACTAAAGATCATGTTCTTTAGCTGCGTTTGTGGGAAAAG-TGCCGCTAAAGATCATGTTCT
66 ACCACTAAAGACCATGTTCTTTAGCTGCGTTTATGGGAAAAGCT-CCACTAAAGACCATGTTCT
*
16420915 TTAGTGGCGTTTGTGGGATAAGCGCCGCTAAAGACCATGATCTTTAGCGGTGTTTGTGGAAAAGC
1 TTAGTGGCGTTTGTGGGATAAGCGCCGCTAAAGACCATGATCTTTAGCGGCGTTTGTGGAAAAGC
** *
16420980 ACTGCTAAAGACCATGTTCTTTAG-TGGCGTTTATGGGATAAGCTCCACTAAAGACCATGTTCT
66 ACCACTAAAGACCATGTTCTTTAGCT-GCGTTTATGGGAAAAGCTCCACTAAAGACCATGTTCT
* * *
16421043 TTAGCGGTGTTTGTGAGATAAGCGCCGCTA
1 TTAGTGGCGTTTGTGGGATAAGCGCCGCTA
16421073 TAGGCCCAAA
Statistics
Matches: 137, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
127 1 0.01
128 135 0.99
129 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (128 bp):
TTAGTGGCGTTTGTGGGATAAGCGCCGCTAAAGACCATGATCTTTAGCGGCGTTTGTGGAAAAGC
ACCACTAAAGACCATGTTCTTTAGCTGCGTTTATGGGAAAAGCTCCACTAAAGACCATGTTCT
Found at i:16423836 original size:80 final size:80
Alignment explanation
Indices: 16423703--16423865 Score: 326
Period size: 80 Copynumber: 2.0 Consensus size: 80
16423693 GGGAAAGTGA
16423703 TACCTATTTTTAGGAAAATGTCTTACCCTTTCTTTTTCGGTAAGATATTTTAGGGTCCATTTGTT
1 TACCTATTTTTAGGAAAATGTCTTACCCTTTCTTTTTCGGTAAGATATTTTAGGGTCCATTTGTT
16423768 TGACTGAAAATGGTT
66 TGACTGAAAATGGTT
16423783 TACCTATTTTTAGGAAAATGTCTTACCCTTTCTTTTTCGGTAAGATATTTTAGGGTCCATTTGTT
1 TACCTATTTTTAGGAAAATGTCTTACCCTTTCTTTTTCGGTAAGATATTTTAGGGTCCATTTGTT
16423848 TGACTGAAAATGGTT
66 TGACTGAAAATGGTT
16423863 TAC
1 TAC
16423866 TTAAAATGAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 83 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (80 bp):
TACCTATTTTTAGGAAAATGTCTTACCCTTTCTTTTTCGGTAAGATATTTTAGGGTCCATTTGTT
TGACTGAAAATGGTT
Found at i:16423954 original size:33 final size:33
Alignment explanation
Indices: 16423908--16423981 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
16423898 CCGGAAAGTT
* * *
16423908 AATATTTTTTGATGTTTAGATGAATCTGTGTAA
1 AATATTTTCTGATGTTTAGATAAATATGTGTAA
* * *
16423941 ATTATTTTCTGATGTTTTGATAAATATTTGTAA
1 AATATTTTCTGATGTTTAGATAAATATGTGTAA
16423974 AATATTTT
1 AATATTTT
16423982 TTGGTATTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (33 bp):
AATATTTTCTGATGTTTAGATAAATATGTGTAA
Found at i:16446082 original size:23 final size:23
Alignment explanation
Indices: 16446019--16446082 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
16446009 ACATTGTTAT
*
16446019 TGAAGATGTTCAATTATATGTTCA
1 TGAACATGTTCAATTA-ATGTTCA
** **
16446043 TGAACATGTTCGTTTAATGTTTG
1 TGAACATGTTCAATTAATGTTCA
16446066 TGAACATGTTCAATTAA
1 TGAACATGTTCAATTAA
16446083 GTTAAATGAC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 20 0.61
24 13 0.39
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.42
Consensus pattern (23 bp):
TGAACATGTTCAATTAATGTTCA
Found at i:16454876 original size:20 final size:20
Alignment explanation
Indices: 16454851--16454890 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16454841 ATTTCACAAA
16454851 AATTACCAGTGGGGTAATTT
1 AATTACCAGTGGGGTAATTT
16454871 AATTACCAGTGGGGTAATTT
1 AATTACCAGTGGGGTAATTT
16454891 TACAATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (20 bp):
AATTACCAGTGGGGTAATTT
Found at i:16474149 original size:12 final size:12
Alignment explanation
Indices: 16474132--16474156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16474122 ATTTTGTCGA
16474132 TCTTCTTTTTTT
1 TCTTCTTTTTTT
16474144 TCTTCTTTTTTT
1 TCTTCTTTTTTT
16474156 T
1 T
16474157 TTTGCTTAAG
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTCTTTTTTT
Found at i:16478568 original size:12 final size:13
Alignment explanation
Indices: 16478531--16478561 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
16478521 TTTCTTGGAC
16478531 ATATAATAAATAA
1 ATATAATAAATAA
16478544 ATA-AATAAATAA
1 ATATAATAAATAA
16478556 ATATAA
1 ATATAA
16478562 AAGTAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATATAATAAATAA
Found at i:16486364 original size:9 final size:8
Alignment explanation
Indices: 16486346--16486387 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
16486336 AAAAGTACTG
*
16486346 AAAATTAA
1 AAAAATAA
16486354 AAAAATAA
1 AAAAATAA
16486362 AAAAATAA
1 AAAAATAA
*
16486370 CAAAATAA
1 AAAAATAA
16486378 AATAAATAA
1 AA-AAATAA
16486387 A
1 A
16486388 CAAAGGCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:16486500 original size:15 final size:13
Alignment explanation
Indices: 16486463--16486506 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
16486453 TGTTAGAAAT
16486463 AAATAAATAA-ACA
1 AAATAAATAATA-A
16486476 AAATAAATAAGTAA
1 AAATAAATAA-TAA
16486490 AAATAAAATAATAA
1 AAAT-AAATAATAA
16486504 AAA
1 AAA
16486507 ATAATTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.36
14 11 0.39
15 7 0.25
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (13 bp):
AAATAAATAATAA
Found at i:16488555 original size:201 final size:199
Alignment explanation
Indices: 16488199--16488684 Score: 539
Period size: 201 Copynumber: 2.4 Consensus size: 199
16488189 ATGCTAATGC
* *
16488199 AGCTTTAATCCGATTCACTGCAACTTT-AGTGATATAGGATTTGATGTCGTAACTTCATGTTGCT
1 AGCTTTAATCCGATTC-CT-CAACTTTAAG-GATATAGGATTTGATGTTGTAACTTCATCTTGCT
* * * * * * * ** *
16488263 CTACTGTATCTTCAAGGAGATAAGATTTGTTTCTCTAGCTTCAATCCGACCCATTGTAACTTCAG
63 CCACTGCAACTTCAAGGAGATAAAATTTGGTTCTATAGCTTCAATCCGACCCACTACAACTTCAA
* * * * *
16488328 GGGTATAGGATTTGATGTGGTAGCTTCATCTTGCTCTATTGTAACTTCAGAGAGATAAAGATTTG
128 GGGTATAGGATTTGATGTGCTAGCTTCATCTTGCTCTACTGCAACTTCAAAGAGATAAAAATTTG
* *
16488393 CTATTGT
193 CTACTAT
* * *
16488400 AGTTTTAATCCGATTCCTACAACTTTAAGGATATAGGATTTGATTTTGTAGCTTCATCTTGCTCC
1 AGCTTTAATCCGATTCCT-CAACTTTAAGGATATAGGATTTGATGTTGTAACTTCATCTTGCTCC
* * *
16488465 ACTGCAACTTCAGGGAGATAAAAATTTGGTTCTATAG-TTTAATTCTGACCCACTACAACTTCAA
65 ACTGCAACTTCAAGGAGAT-AAAATTTGGTTCTATAGCTTCAA-TCCGACCCACTACAACTTCAA
* * * *
16488529 GGGTATATGATTTGGTTTTCTAGCTTCATCTTGCTCTACTGCAACTTCAAAGAGATAAAAATTTG
128 GGGTATAGGATTTGATGTGCTAGCTTCATCTTGCTCTACTGCAACTTCAAAGAGATAAAAATTTG
16488594 CTACTAT
193 CTACTAT
** * * * *
16488601 AGCTTTAATTTGATCCCTCTAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCA-C-TCCATT
1 AGCTTTAATCCGATTCCTC-AACTTTAAGGATATAGGATTTGATGTTGTAACTTCATCTTGC--T
*
16488664 CCACTACAACTTCAAGGAGAT
63 CCACTGCAACTTCAAGGAGAT
16488685 TAAGATCCAC
Statistics
Matches: 238, Mismatches: 41, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
199 2 0.01
200 62 0.26
201 174 0.73
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (199 bp):
AGCTTTAATCCGATTCCTCAACTTTAAGGATATAGGATTTGATGTTGTAACTTCATCTTGCTCCA
CTGCAACTTCAAGGAGATAAAATTTGGTTCTATAGCTTCAATCCGACCCACTACAACTTCAAGGG
TATAGGATTTGATGTGCTAGCTTCATCTTGCTCTACTGCAACTTCAAAGAGATAAAAATTTGCTA
CTAT
Found at i:16488563 original size:101 final size:101
Alignment explanation
Indices: 16488229--16488656 Score: 397
Period size: 100 Copynumber: 4.3 Consensus size: 101
16488219 CAACTTTAGT
* * * * * * *
16488229 GATATAGGATTTGATGTCGTAACTTCATGTTGCTCTACTGTATCTTCA-AGGAGAT-AAGATTTG
1 GATATAGGATTTGATTTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGA-GAGATAAAAATTTG
* * * * ** *
16488292 TTTCTCTAGCTTCAA-TCCGA-CCCATTGTAACTTCAGG
65 CTTCTATAGCTTTAATTCTGATCCC--TACAACTTCAAG
* * * * * *
16488329 GGTATAGGATTTGATGTGGTAGCTTCATCTTGCTCTATTGTAACTTCAGAGAGATAAAGATTTGC
1 GATATAGGATTTGATTTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAAAATTTGC
* * * * *
16488394 TAT-TGTAGTTTTAA-TCCGATTCCTACAACTTTAAG
66 T-TCTATAGCTTTAATTCTGATCCCTACAACTTCAAG
* * *
16488429 GATATAGGATTTGATTTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAAAATTTGG
1 GATATAGGATTTGATTTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAAAATTTGC
*
16488494 TTCTATAG-TTTAATTCTGACCCACTACAACTTCAAG
66 TTCTATAGCTTTAATTCTGATCC-CTACAACTTCAAG
* * * * *
16488530 GGTATATGATTTGGTTTTCTAGCTTCATCTTGCTCTACTGCAACTTCAAAGAGATAAAAATTTGC
1 GATATAGGATTTGATTTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAAAATTTGC
*
16488595 TACTATAGCTTTAATT-TGATCCCT-CTAACTTCAAG
66 TTCTATAGCTTTAATTCTGATCCCTAC-AACTTCAAG
* * *
16488630 GATATAGGATTTGGTGTTGTAACTTCA
1 GATATAGGATTTGATTTTGTAGCTTCA
16488657 CTCCATTCCA
Statistics
Matches: 275, Mismatches: 44, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
99 7 0.03
100 154 0.56
101 104 0.38
102 10 0.04
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (101 bp):
GATATAGGATTTGATTTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAAAATTTGC
TTCTATAGCTTTAATTCTGATCCCTACAACTTCAAG
Found at i:16488574 original size:50 final size:50
Alignment explanation
Indices: 16488419--16488578 Score: 137
Period size: 50 Copynumber: 3.2 Consensus size: 50
16488409 CCGATTCCTA
* * * * *
16488419 CAACTTTAAGGATATAGGATTTGATTTTGTAGCTTCATCTTGCTCCACTG
1 CAACTTCAAGGGTATAAGATTTGGTTTTATAGCTTCATCTTGCTCCACTG
* * * * * *
16488469 CAACTTC-AGGGAGATAAAAATTTGGTTCTATAGTTTAAT-TCTGAC-CCACTA
1 CAACTTCAAGGG-TAT-AAGATTTGGTTTTATAGCTTCATCT-TG-CTCCACTG
* * *
16488520 CAACTTCAAGGGTATATGATTTGGTTTTCTAGCTTCATCTTGCTCTACTG
1 CAACTTCAAGGGTATAAGATTTGGTTTTATAGCTTCATCTTGCTCCACTG
16488570 CAACTTCAA
1 CAACTTCAA
16488579 AGAGATAAAA
Statistics
Matches: 83, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
49 4 0.05
50 41 0.49
51 33 0.40
52 5 0.06
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (50 bp):
CAACTTCAAGGGTATAAGATTTGGTTTTATAGCTTCATCTTGCTCCACTG
Found at i:16488604 original size:51 final size:51
Alignment explanation
Indices: 16488448--16488605 Score: 144
Period size: 51 Copynumber: 3.1 Consensus size: 51
16488438 TTTGATTTTG
**
16488448 TAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAAAATTTGGTTCTA
1 TAGCTTCATCTTGCTCCACTGCAACTTCAAAGAGATAAAAATTTGGTTCTA
* * * * ** * *
16488499 TAGTTTAAT-TCTGAC-CCACTACAACTTC-AAG-GGTATATGATTTGGTTTTC
1 TAGCTTCATCT-TG-CTCCACTGCAACTTCAAAGAGATA-AAAATTTGGTTCTA
* * *
16488549 TAGCTTCATCTTGCTCTACTGCAACTTCAAAGAGATAAAAATTTGCTACTA
1 TAGCTTCATCTTGCTCCACTGCAACTTCAAAGAGATAAAAATTTGGTTCTA
16488600 TAGCTT
1 TAGCTT
16488606 TAATTTGATC
Statistics
Matches: 79, Mismatches: 21, Indels: 14
0.69 0.18 0.12
Matches are distributed among these distances:
49 4 0.05
50 32 0.41
51 39 0.49
52 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (51 bp):
TAGCTTCATCTTGCTCCACTGCAACTTCAAAGAGATAAAAATTTGGTTCTA
Found at i:16491319 original size:28 final size:28
Alignment explanation
Indices: 16491285--16491341 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
16491275 TCTCTATGCC
16491285 AATTCAACCGACTAAATCAATTCTAATA
1 AATTCAACCGACTAAATCAATTCTAATA
16491313 AATTCAACCGACTAAATCAATTCTAATA
1 AATTCAACCGACTAAATCAATTCTAATA
16491341 A
1 A
16491342 GTAAATGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (28 bp):
AATTCAACCGACTAAATCAATTCTAATA
Found at i:16491823 original size:12 final size:12
Alignment explanation
Indices: 16491806--16491830 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16491796 ATTAAATAAT
16491806 TAATAGCATTCA
1 TAATAGCATTCA
16491818 TAATAGCATTCA
1 TAATAGCATTCA
16491830 T
1 T
16491831 CATAATGACA
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:16496482 original size:42 final size:42
Alignment explanation
Indices: 16496421--16496687 Score: 374
Period size: 42 Copynumber: 6.4 Consensus size: 42
16496411 TCAAAATGCG
* * **
16496421 ATGAAAAGTAAATGAGCCTCCACACCTAGGCCTCTAAATATG
1 ATGAAAAGTAAATGGGCCTCCACACCTCGGCCTCTAAATACA
* *
16496463 ATGAAAAGTAAATGGGCCTCCACACCT-GAGCCTGTAAATGCA
1 ATGAAAAGTAAATGGGCCTCCACACCTCG-GCCTCTAAATACA
* * * *
16496505 ATGAAAAGTAAATAGGCCTCCACACCTGGGCCTATAAATGCA
1 ATGAAAAGTAAATGGGCCTCCACACCTCGGCCTCTAAATACA
**
16496547 ATGAAAAGTAAATGGGCCTCCACACCTCGGCCTCTAAATGTA
1 ATGAAAAGTAAATGGGCCTCCACACCTCGGCCTCTAAATACA
*
16496589 ATGAAAAGTAAATGGGTCTCCACACCTCGGCCTCTAAATACA
1 ATGAAAAGTAAATGGGCCTCCACACCTCGGCCTCTAAATACA
* *
16496631 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCA
1 ATGAAAAGTAAATGGGCCTCCACACCTCGGCCTCTAAATACA
*
16496673 GTGAAAAGTAAATGG
1 ATGAAAAGTAAATGG
16496688 ACCTGATGGC
Statistics
Matches: 205, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
41 1 0.00
42 203 0.99
43 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
ATGAAAAGTAAATGGGCCTCCACACCTCGGCCTCTAAATACA
Found at i:16496639 original size:126 final size:126
Alignment explanation
Indices: 16496414--16496687 Score: 433
Period size: 126 Copynumber: 2.2 Consensus size: 126
16496404 AGCCACCTCA
* * *
16496414 AAATGCGATGAAAAGTAAATGAGCCTCCACACCTAGGCCTCTAAATATGATGAAAAGTAAATGGG
1 AAATGCAATGAAAAGTAAATGGGCCTCCACACCTAGGCCTCTAAATATAATGAAAAGTAAATGGG
* *
16496479 CCTCCACACCTGAGCCTGTAAATGCAATGAAAAGTAAATAGGCCTCCACACCTGGGCCTAT
66 CCTCCACACCTGAGCCTCTAAATACAATGAAAAGTAAATAGGCCTCCACACCTGGGCCTAT
* *
16496540 AAATGCAATGAAAAGTAAATGGGCCTCCACACCTCGGCCTCTAAATGTAATGAAAAGTAAATGGG
1 AAATGCAATGAAAAGTAAATGGGCCTCCACACCTAGGCCTCTAAATATAATGAAAAGTAAATGGG
* * *
16496605 TCTCCACACCTCG-GCCTCTAAATACAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCT
66 CCTCCACACCT-GAGCCTCTAAATACAATGAAAAGTAAATAGGCCTCCACACCTGGGCCTAT
*
16496666 AAATGCAGTGAAAAGTAAATGG
1 AAATGCAATGAAAAGTAAATGG
16496688 ACCTGATGGC
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
126 135 0.99
127 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (126 bp):
AAATGCAATGAAAAGTAAATGGGCCTCCACACCTAGGCCTCTAAATATAATGAAAAGTAAATGGG
CCTCCACACCTGAGCCTCTAAATACAATGAAAAGTAAATAGGCCTCCACACCTGGGCCTAT
Found at i:16506336 original size:19 final size:17
Alignment explanation
Indices: 16506298--16506350 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
16506288 TTTACTTACT
*
16506298 TAATT-TTTAATTTTTAC
1 TAATTGTTTTATTTTT-C
16506315 TAATCTGTTATTATTTTTC
1 TAAT-TGTT-TTATTTTTC
*
16506334 TAATTGTTTTCTTTTTC
1 TAATTGTTTTATTTTTC
16506351 AGATTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 12 0.39
18 5 0.16
19 7 0.23
20 7 0.23
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.66
Consensus pattern (17 bp):
TAATTGTTTTATTTTTC
Found at i:16513866 original size:24 final size:24
Alignment explanation
Indices: 16513846--16513907 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
16513836 GAGAAGGATA
16513846 AAGAAAAAGAAGAAGGAAAGGAAT
1 AAGAAAAAGAAGAAGGAAAGGAAT
16513870 AAGAAAAAGAAGAAGGAAAGGAAT
1 AAGAAAAAGAAGAAGGAAAGGAAT
*
16513894 AAGAGAAAGAAGAA
1 AAGAAAAAGAAGAA
16513908 ACAGAACTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (24 bp):
AAGAAAAAGAAGAAGGAAAGGAAT
Found at i:16513878 original size:13 final size:13
Alignment explanation
Indices: 16513861--16513902 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
16513851 AAAGAAGAAG
16513861 GAAAGGAATAAGA
1 GAAAGGAATAAGA
* *
16513874 -AAAAGAAGAAG-
1 GAAAGGAATAAGA
16513885 GAAAGGAATAAGA
1 GAAAGGAATAAGA
16513898 GAAAG
1 GAAAG
16513903 AAGAAACAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.05
Consensus pattern (13 bp):
GAAAGGAATAAGA
Found at i:16518363 original size:22 final size:22
Alignment explanation
Indices: 16518338--16518380 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
16518328 AATCTAGGGT
16518338 CAAAAATATCAAAAAAA-CTAAC
1 CAAAAAT-TCAAAAAAATCTAAC
**
16518360 CAAAGGTTCAAAAAAATCTAA
1 CAAAAATTCAAAAAAATCTAA
16518381 GAAACCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.63, C:0.16, G:0.05, T:0.16
Consensus pattern (22 bp):
CAAAAATTCAAAAAAATCTAAC
Found at i:16529447 original size:21 final size:20
Alignment explanation
Indices: 16529346--16529447 Score: 82
Period size: 20 Copynumber: 5.0 Consensus size: 20
16529336 TTTTGAAACA
16529346 ATTTTAAAATCAAGTTAAAATT
1 ATTTT-AAA-CAAGTTAAAATT
* *
16529368 ATTTTAAACAAGTCAAAATG
1 ATTTTAAACAAGTTAAAATT
* * * * *
16529388 ATTTCAACCTAGTCAAAATC
1 ATTTTAAACAAGTTAAAATT
16529408 ATTTT-AACACA-TTAAAATT
1 ATTTTAAACA-AGTTAAAATT
*
16529427 ATTTTCAAACAAGTTAGAATT
1 ATTTT-AAACAAGTTAAAATT
16529448 GCTCCAAGCC
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 13 0.20
20 32 0.50
21 14 0.22
22 5 0.08
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (20 bp):
ATTTTAAACAAGTTAAAATT
Found at i:16534873 original size:20 final size:20
Alignment explanation
Indices: 16534850--16534904 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
16534840 GATGCCGATT
**
16534850 TAAAATTATCGATACTTTTA
1 TAAAATTATCGATACTCATA
* *
16534870 TAAAAATATCGATACTCATG
1 TAAAATTATCGATACTCATA
16534890 TAAAATTATCGATAC
1 TAAAATTATCGATAC
16534905 CACGGGGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (20 bp):
TAAAATTATCGATACTCATA
Found at i:16536985 original size:20 final size:20
Alignment explanation
Indices: 16536941--16537034 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
16536931 GAAAATTTTG
* *
16536941 AAATAATTTTAAAATCAAGTTA
1 AAATGATTTT-AAA-CAAGTCA
*
16536963 AAATTATTTTAAACAAGTCA
1 AAATGATTTTAAACAAGTCA
** **
16536983 AAATGATTCCAATTAAGTCA
1 AAATGATTTTAAACAAGTCA
*
16537003 AAATCATTTT-AACACA-TCA
1 AAATGATTTTAAACA-AGTCA
16537022 AAATGATTTTAAA
1 AAATGATTTTAAA
16537035 ATGATTTTCA
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 14 0.25
20 31 0.54
21 3 0.05
22 9 0.16
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
AAATGATTTTAAACAAGTCA
Found at i:16541253 original size:19 final size:19
Alignment explanation
Indices: 16541222--16541280 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
16541212 TCATACCATT
16541222 AAATAATTT-AAAATTATAA
1 AAAT-ATTTAAAAATTATAA
*
16541241 AAATATTTAAAAA--GTAA
1 AAATATTTAAAAATTATAA
16541258 AAATAGTTTATAAAATTA-AA
1 AAATA-TTTA-AAAATTATAA
16541278 AAA
1 AAA
16541281 GAATTACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
17 8 0.24
18 8 0.24
19 12 0.36
20 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATATTTAAAAATTATAA
Found at i:16541260 original size:18 final size:19
Alignment explanation
Indices: 16541238--16541279 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
16541228 TTTAAAATTA
16541238 TAAAAATA-TTTA-AAAAG
1 TAAAAATAGTTTATAAAAG
*
16541255 TAAAAATAGTTTATAAAAT
1 TAAAAATAGTTTATAAAAG
16541274 TAAAAA
1 TAAAAA
16541280 AGAATTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
TAAAAATAGTTTATAAAAG
Found at i:16547387 original size:21 final size:21
Alignment explanation
Indices: 16547358--16547410 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
16547348 TGGGTAGCCT
* *
16547358 TTGAATGTTGTGTTTGGAGGG
1 TTGATTGTTGTGTTTGCAGGG
*
16547379 TTGATTGTTGTTTTTGCAGGG
1 TTGATTGTTGTGTTTGCAGGG
16547400 TTGATTGTTGT
1 TTGATTGTTGT
16547411 CTGTGGGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.11, C:0.02, G:0.36, T:0.51
Consensus pattern (21 bp):
TTGATTGTTGTGTTTGCAGGG
Found at i:16552210 original size:36 final size:36
Alignment explanation
Indices: 16552162--16552372 Score: 341
Period size: 36 Copynumber: 5.9 Consensus size: 36
16552152 AGCTATTCAT
*
16552162 GCATTACGCTCTAACCGAGATGTAAGCAATCACATA
1 GCATTACGCTCTAACCGAGACGTAAGCAATCACATA
*
16552198 GCATTACACTCTAACCGAGACGTAAGCAATCACATA
1 GCATTACGCTCTAACCGAGACGTAAGCAATCACATA
* *
16552234 CCATTAAGCTCTAACCGAGACGTAAGCAATCACATA
1 GCATTACGCTCTAACCGAGACGTAAGCAATCACATA
* *
16552270 GCATTACGCTCTAACCAAGACGTAAGCAATCATATA
1 GCATTACGCTCTAACCGAGACGTAAGCAATCACATA
* *
16552306 TCATTACGCTCTAACCGAGACGTAAACAATCACATA
1 GCATTACGCTCTAACCGAGACGTAAGCAATCACATA
*
16552342 GCATTACGCTCTAACTGAGACGTAAGCAATC
1 GCATTACGCTCTAACCGAGACGTAAGCAATC
16552373 CATCGAAGTA
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 159 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (36 bp):
GCATTACGCTCTAACCGAGACGTAAGCAATCACATA
Found at i:16554915 original size:3 final size:3
Alignment explanation
Indices: 16554907--16554936 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16554897 AGTTGACAGA
16554907 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16554937 TTCGGTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16561268 original size:16 final size:17
Alignment explanation
Indices: 16561241--16561282 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
16561231 ATCTCGTTCC
16561241 AAACTGAAAAAC-AAAAT
1 AAACT-AAAAACTAAAAT
*
16561258 AAACTAAAAACTAAGAT
1 AAACTAAAAACTAAAAT
*
16561275 ATACTAAA
1 AAACTAAA
16561283 TGGTGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.67, C:0.12, G:0.05, T:0.17
Consensus pattern (17 bp):
AAACTAAAAACTAAAAT
Found at i:16577072 original size:22 final size:22
Alignment explanation
Indices: 16577047--16577091 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
16577037 ATGAAAAGTG
16577047 ACCAAGTCACAAAAACACAAAA
1 ACCAAGTCACAAAAACACAAAA
*
16577069 ACCAAGTCATAAAAACACAAAA
1 ACCAAGTCACAAAAACACAAAA
16577091 A
1 A
16577092 AGAGAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.24, G:0.04, T:0.07
Consensus pattern (22 bp):
ACCAAGTCACAAAAACACAAAA
Found at i:16580497 original size:13 final size:13
Alignment explanation
Indices: 16580481--16580514 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16580471 GGGGATAAAA
16580481 ATAAATAACTAAG
1 ATAAATAACTAAG
*
16580494 ATAAATAACTATG
1 ATAAATAACTAAG
*
16580507 AAAAATAA
1 ATAAATAA
16580515 ACAAACGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (13 bp):
ATAAATAACTAAG
Found at i:16581613 original size:31 final size:31
Alignment explanation
Indices: 16581575--16581661 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
16581565 TATAAGGGTA
*
16581575 AATGACAAAACAGTTACTCAACTTTGATCTC
1 AATGACAAAACAGTCACTCAACTTTGATCTC
*
16581606 AATGACAAAGA-AATCACTCAACTTTGATCTC
1 AATGACAAA-ACAGTCACTCAACTTTGATCTC
* *
16581637 CATGACAAAGCAGTCACTCAACTTT
1 AATGACAAAACAGTCACTCAACTTT
16581662 CAATTCAGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 48 0.98
32 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.26
Consensus pattern (31 bp):
AATGACAAAACAGTCACTCAACTTTGATCTC
Found at i:16581672 original size:20 final size:20
Alignment explanation
Indices: 16581647--16581684 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16581637 CATGACAAAG
16581647 CAGTCACTCAACTTTCAATT
1 CAGTCACTCAACTTTCAATT
16581667 CAGTCACTCAACTTTCAA
1 CAGTCACTCAACTTTCAA
16581685 ACAATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (20 bp):
CAGTCACTCAACTTTCAATT
Found at i:16582601 original size:29 final size:29
Alignment explanation
Indices: 16582559--16582617 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
16582549 AAGAAGAAGT
* * *
16582559 ATAAACATATTGAGTCATTTACTCAAAAA
1 ATAAAAATATTGAGCCATTTACTAAAAAA
*
16582588 ATAAAAATATTGAGCCATTTATTAAAAAA
1 ATAAAAATATTGAGCCATTTACTAAAAAA
16582617 A
1 A
16582618 GGGAAAAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.31
Consensus pattern (29 bp):
ATAAAAATATTGAGCCATTTACTAAAAAA
Found at i:16597096 original size:28 final size:28
Alignment explanation
Indices: 16597064--16597120 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
16597054 ATTTTCTTAG
*
16597064 AGGTAAAAAATAGCCCACATCTTTTATT
1 AGGTAAAAAACAGCCCACATCTTTTATT
16597092 AGGTAAAAAACAGCCCACATCTTTTATT
1 AGGTAAAAAACAGCCCACATCTTTTATT
16597120 A
1 A
16597121 ATTCACACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (28 bp):
AGGTAAAAAACAGCCCACATCTTTTATT
Found at i:16601484 original size:18 final size:19
Alignment explanation
Indices: 16601461--16601498 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
16601451 GTAACTAAAT
16601461 TAACAAAA-AGAAATGCAA
1 TAACAAAATAGAAATGCAA
16601479 TAACAAAATAGAAATGCAA
1 TAACAAAATAGAAATGCAA
16601498 T
1 T
16601499 GACAGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (19 bp):
TAACAAAATAGAAATGCAA
Found at i:16615057 original size:7 final size:7
Alignment explanation
Indices: 16615045--16615083 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
16615035 TAATTGTGTT
*
16615045 ATAAAAA
1 ATAAATA
16615052 ATAAA-A
1 ATAAATA
16615058 A-AAATA
1 ATAAATA
16615064 ATAAATA
1 ATAAATA
16615071 ATAAATA
1 ATAAATA
16615078 ATAAAT
1 ATAAAT
16615084 TAACTTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 3 0.10
6 4 0.13
7 23 0.77
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
ATAAATA
Found at i:16631817 original size:35 final size:37
Alignment explanation
Indices: 16631778--16631848 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
16631768 TCAAACGATC
* *
16631778 TCTTCGAGTTTCCCAGT-AA-TTTAGCTCATACGAGT
1 TCTTCAAGTCTCCCAGTAAATTTTAGCTCATACGAGT
*
16631813 TCTTCAAGTCTCCTAGTAAATTTTAGCTCATACGAG
1 TCTTCAAGTCTCCCAGTAAATTTTAGCTCATACGAG
16631849 CCCAGTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 14 0.45
36 2 0.06
37 15 0.48
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (37 bp):
TCTTCAAGTCTCCCAGTAAATTTTAGCTCATACGAGT
Found at i:16634810 original size:33 final size:33
Alignment explanation
Indices: 16634772--16634834 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
16634762 ATTTTGACAA
*
16634772 GTACTAACTCAATTTTAATTTATAGTCACTAAC
1 GTACTAACTCAAATTTAATTTATAGTCACTAAC
16634805 GTACTAACTCAAATTTAATTTATAGTCACT
1 GTACTAACTCAAATTTAATTTATAGTCACT
16634835 CTTGTCTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (33 bp):
GTACTAACTCAAATTTAATTTATAGTCACTAAC
Found at i:16635151 original size:21 final size:21
Alignment explanation
Indices: 16635125--16635201 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 21
16635115 AATAGTGCAG
*
16635125 ACTTCTATCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* * *
16635146 AGTTCTACCAATACAAATGAC
1 ACTTCTACCGATACAAGTGAC
* * ***
16635167 TCTTCTACCGAAACAAGTCTT
1 ACTTCTACCGATACAAGTGAC
16635188 ACTTCTACCGATAC
1 ACTTCTACCGATAC
16635202 TAAAAACTTC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:16637044 original size:21 final size:23
Alignment explanation
Indices: 16637020--16637061 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
16637010 CATAATTAAG
*
16637020 CTTACTTAATCA-CTC-TTAATC
1 CTTAATTAATCATCTCATTAATC
16637041 CTTAATTAATCATCTCATTAA
1 CTTAATTAATCATCTCATTAA
16637062 CACCTAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 3 0.17
23 4 0.22
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (23 bp):
CTTAATTAATCATCTCATTAATC
Found at i:16641766 original size:18 final size:18
Alignment explanation
Indices: 16641743--16641785 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16641733 TATCACAAGA
* *
16641743 GGAGGTGGAGGCCTTGTG
1 GGAGGTGGAGGCCTTATC
*
16641761 GGAGGTGTAGGCCTTATC
1 GGAGGTGGAGGCCTTATC
16641779 GGAGGTG
1 GGAGGTG
16641786 CCATAGGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.12, G:0.51, T:0.23
Consensus pattern (18 bp):
GGAGGTGGAGGCCTTATC
Found at i:16642448 original size:21 final size:21
Alignment explanation
Indices: 16642422--16642498 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
16642412 AATAGTGCAG
16642422 ACTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* *
16642443 AGTTCTATCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* * * **
16642464 TCTTCTACCAAAACAAGTGTT
1 ACTTCTACCGATACAAGTGAC
*
16642485 ACTTTTACCGATAC
1 ACTTCTACCGATAC
16642499 TAAAAACTCC
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:16643636 original size:26 final size:26
Alignment explanation
Indices: 16643599--16643701 Score: 118
Period size: 26 Copynumber: 4.0 Consensus size: 26
16643589 TTCTGGGCGC
* *
16643599 AATTCTGAACATGCTCATACAGCAAT
1 AATTCTGGACATGCTCATGCAGCAAT
* * *
16643625 AACTCTGGACATGTTCATGCAACAAT
1 AATTCTGGACATGCTCATGCAGCAAT
* * *
16643651 AATTCTGGACAAGTTTC-TGCAGCGAT
1 AATTCTGGACATG-CTCATGCAGCAAT
16643677 AATTCTGGACATGCTCATGCAGCAA
1 AATTCTGGACATGCTCATGCAGCAA
16643702 CATTAGTAGT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
25 2 0.03
26 58 0.92
27 3 0.05
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (26 bp):
AATTCTGGACATGCTCATGCAGCAAT
Found at i:16658629 original size:30 final size:30
Alignment explanation
Indices: 16658595--16658672 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 30
16658585 ATTAGTAATG
* *
16658595 ATAAAATTATATTTTGAT-CTTTCAAAAATA
1 ATAAAATTATAATTTAATCCTTT-AAAAATA
*
16658625 ATAAAAATT-TAATTTAATCCTTTAAAAATT
1 AT-AAAATTATAATTTAATCCTTTAAAAATA
*
16658655 AT-AAATTATTAAATTAAT
1 ATAAAATTA-TAATTTAAT
16658673 GAAATTACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 5 0.12
30 25 0.62
31 10 0.25
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (30 bp):
ATAAAATTATAATTTAATCCTTTAAAAATA
Found at i:16660106 original size:28 final size:27
Alignment explanation
Indices: 16660071--16660160 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
16660061 AAGATGACTA
16660071 TATAAAAAATTTTAATAAATAAAAAAT
1 TATAAAAAATTTTAATAAATAAAAAAT
* * *
16660098 GTAT-AAAAATATTAATTATTAAAATAA-
1 -TATAAAAAATTTTAATAAATAAAA-AAT
*
16660125 TATAATATAAATATTT-TTAAA-AAAAAAT
1 TATAA-A-AAAT-TTTAATAAATAAAAAAT
16660153 TATAAAAA
1 TATAAAAA
16660161 TAATATGAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
26 5 0.10
27 21 0.43
28 15 0.31
29 6 0.12
30 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (27 bp):
TATAAAAAATTTTAATAAATAAAAAAT
Found at i:16660161 original size:25 final size:25
Alignment explanation
Indices: 16660071--16660162 Score: 69
Period size: 25 Copynumber: 3.4 Consensus size: 25
16660061 AAGATGACTA
16660071 TATAAAAA-ATTTTAATAAATAAAAAAT
1 TATAAAAATATTTT--TAAA-AAAAAAT
* *
16660098 GTATAAAAATATTAATTATTAAAATAATAT
1 -TATAAAAATA-T--TT-TTAAAAAAAAAT
* *
16660128 AATATAAATATTTTTAAAAAAAAAT
1 TATAAAAATATTTTTAAAAAAAAAT
16660153 TATAAAAATA
1 TATAAAAATA
16660163 ATATGAACTA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
25 18 0.35
26 2 0.04
28 9 0.18
29 9 0.18
30 6 0.12
31 4 0.08
32 2 0.04
33 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (25 bp):
TATAAAAATATTTTTAAAAAAAAAT
Found at i:16663667 original size:11 final size:12
Alignment explanation
Indices: 16663641--16663665 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16663631 TTTTTTAATA
16663641 TTATTTCATTTT
1 TTATTTCATTTT
16663653 TTATTTCATTTT
1 TTATTTCATTTT
16663665 T
1 T
16663666 ATAATTTAAT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTCATTTT
Found at i:16666492 original size:20 final size:20
Alignment explanation
Indices: 16666462--16666511 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
16666452 ATTAGCATGA
*
16666462 TTTATATTAAGTTTAAATAG-G
1 TTTA-ATTAAGATTAAA-AGTG
16666483 TTTAATTAAGATTAAAAGTG
1 TTTAATTAAGATTAAAAGTG
*
16666503 GTTAATTAA
1 TTTAATTAA
16666512 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (20 bp):
TTTAATTAAGATTAAAAGTG
Found at i:16668253 original size:21 final size:21
Alignment explanation
Indices: 16668227--16668303 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 21
16668217 TGACTTGGAT
16668227 TGTATCGGTAGTTGTATAGTA
1 TGTATCGGTAGTTGTATAGTA
16668248 TGTATCGGTAGTTCTGTACTTAG-A
1 TGTATCGGTAG-T-TGTA--TAGTA
* * *
16668272 AGTATCGGTAGTTCGTGTACT-
1 TGTATCGGTAGTT-GTATAGTA
16668293 TGTATCGGTAG
1 TGTATCGGTAG
16668304 AAATTACAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
21 23 0.50
22 2 0.04
23 7 0.15
24 11 0.24
25 3 0.07
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (21 bp):
TGTATCGGTAGTTGTATAGTA
Found at i:16670806 original size:80 final size:81
Alignment explanation
Indices: 16670716--16670868 Score: 236
Period size: 80 Copynumber: 1.9 Consensus size: 81
16670706 AACCAATTCC
* * * *
16670716 GTCAATTCATGGCACTCGGTGCCTAACAGATAAACCGCAA-TAAGTGAGCCCAGCTTTAGTCGGA
1 GTCAATTCATGGCACCCAGTGCCTAACAGATAAACCACAATTAAGTGAGCCCAGCTCTAGTCGGA
16670780 TTAACCAACAAAGTCT
66 TTAACCAACAAAGTCT
* * *
16670796 GTCAATTCATGGCACCCAGTGCCTAGCTGATAAACCACAATTAAGTGAGCCCAGCTCTAGTTGGA
1 GTCAATTCATGGCACCCAGTGCCTAACAGATAAACCACAATTAAGTGAGCCCAGCTCTAGTCGGA
16670861 TTAACCAA
66 TTAACCAA
16670869 TGGTTTGTGC
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 35 0.54
81 30 0.46
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (81 bp):
GTCAATTCATGGCACCCAGTGCCTAACAGATAAACCACAATTAAGTGAGCCCAGCTCTAGTCGGA
TTAACCAACAAAGTCT
Found at i:16674903 original size:153 final size:155
Alignment explanation
Indices: 16674621--16674939 Score: 498
Period size: 153 Copynumber: 2.1 Consensus size: 155
16674611 TCCCGAGTTA
16674621 TTTTTCAGAACCATCTTCTCAAATTTATTTTTTCAAAATCATCAATACGAAAAAAGCATCCAACT
1 TTTTTCAGAACCATCTTCTCAAATTTATTTTTTCAAAATCATCAATACGAAAAAAGCATCCAACT
* * ** *
16674686 GGAAGCTTTTTCTGTACTTCCTCCAACATGGAATCCTACTTAGAGCGTGTTTTCAAAAATAAAAA
66 GGAAGCTTTTTCTGTACTACCTCCAACATGGAATCCTACTAAGAGAATGTTTTCAAAAAAAAAAA
16674751 -CAAAATTCATCTCGTCAAAATAAT
131 TCAAAATTCATCTCGTCAAAATAAT
* * * *
16674775 TTTTTCAGAACCATCTTCTCAAATTTA-TTTTTCAGAATCATCAGTACGAAAAAAGCATTCAGCT
1 TTTTTCAGAACCATCTTCTCAAATTTATTTTTTCAAAATCATCAATACGAAAAAAGCATCCAACT
* * * *
16674839 GGAAGCTTTTTTTGTACTACCTCCAACATGGCATCTTACTAAGAGAATTTTTTCAAAAAAAAAAA
66 GGAAGCTTTTTCTGTACTACCTCCAACATGGAATCCTACTAAGAGAATGTTTTCAAAAAAAAAAA
16674904 TCAAAATTCATCTCGTCAAAATAAT
131 TCAAAATTCATCTCGTCAAAATAAT
*
16674929 TTTTTTAGAAC
1 TTTTTCAGAAC
16674940 AAATCACATC
Statistics
Matches: 150, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
153 89 0.59
154 61 0.41
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (155 bp):
TTTTTCAGAACCATCTTCTCAAATTTATTTTTTCAAAATCATCAATACGAAAAAAGCATCCAACT
GGAAGCTTTTTCTGTACTACCTCCAACATGGAATCCTACTAAGAGAATGTTTTCAAAAAAAAAAA
TCAAAATTCATCTCGTCAAAATAAT
Found at i:16676431 original size:22 final size:22
Alignment explanation
Indices: 16676403--16676459 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
16676393 TTTCTGTTAA
16676403 TACATGCGAACTTGAATTATAT
1 TACATGCGAACTTGAATTATAT
16676425 TACATGCGAACTTGAATTATAT
1 TACATGCGAACTTGAATTATAT
*
16676447 TACATGCAAACTT
1 TACATGCGAACTT
16676460 ATATACGTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (22 bp):
TACATGCGAACTTGAATTATAT
Found at i:16680747 original size:18 final size:19
Alignment explanation
Indices: 16680712--16680753 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
16680702 TAACATTCTA
*
16680712 ATATTTTCATATTTTTTT-
1 ATATTTTAATATTTTTTTC
16680730 ATATTTTAAT-TTTATTTTC
1 ATATTTTAATATTT-TTTTC
16680749 ATATT
1 ATATT
16680754 ATGTTACCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 13 0.62
19 5 0.24
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (19 bp):
ATATTTTAATATTTTTTTC
Found at i:16685390 original size:11 final size:11
Alignment explanation
Indices: 16685368--16685405 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16685358 TAAACCAATC
16685368 AAAAAT-AAAA
1 AAAAATGAAAA
**
16685378 AAAAATGCCAA
1 AAAAATGAAAA
16685389 AAAAATGAAAA
1 AAAAATGAAAA
16685400 AAAAAT
1 AAAAAT
16685406 TCTAGTACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (11 bp):
AAAAATGAAAA
Found at i:16687943 original size:16 final size:15
Alignment explanation
Indices: 16687918--16687950 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
16687908 CATGTATTCC
16687918 TTTTTCTTTTTCTTT
1 TTTTTCTTTTTCTTT
16687933 TTTTATCTTTTTCTTT
1 TTTT-TCTTTTTCTTT
16687949 TT
1 TT
16687951 CAGATGAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:16693380 original size:22 final size:22
Alignment explanation
Indices: 16693355--16693441 Score: 147
Period size: 22 Copynumber: 4.0 Consensus size: 22
16693345 TAGCGCGCTC
* *
16693355 TCTGCTCAGCACTGTGTGTGCT
1 TCTGTTCAGCACTATGTGTGCT
16693377 TCTGTTCAGCACTATGTGTGCT
1 TCTGTTCAGCACTATGTGTGCT
16693399 TCTGTTCAGCACTATGTGTGCT
1 TCTGTTCAGCACTATGTGTGCT
*
16693421 TCTGTTCAGCACTGTGTGTGC
1 TCTGTTCAGCACTATGTGTGC
16693442 CTACTGTTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.39
Consensus pattern (22 bp):
TCTGTTCAGCACTATGTGTGCT
Found at i:16693479 original size:25 final size:24
Alignment explanation
Indices: 16693445--16693498 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
16693435 TGTGTGCCTA
* * *
16693445 CTGTTTCCCAATACTTATGTGTTT
1 CTGTTTCCCAACACTTATGCGCTT
*
16693469 CTGTTTCCCCAGCACTTATGCGCTT
1 CTGTTT-CCCAACACTTATGCGCTT
16693494 CTGTT
1 CTGTT
16693499 AAGTACTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.13, C:0.28, G:0.15, T:0.44
Consensus pattern (24 bp):
CTGTTTCCCAACACTTATGCGCTT
Found at i:16705179 original size:34 final size:35
Alignment explanation
Indices: 16705141--16705323 Score: 109
Period size: 34 Copynumber: 5.3 Consensus size: 35
16705131 AAGCAGATTG
16705141 AAATTGTATTTATTTCAAATAAATT-T-TTTACTTT
1 AAATT-TATTTATTTCAAATAAATTCTATTTACTTT
* *
16705175 AAATTTTATTT-TTT-AATTAAATTCTATTTATTTT
1 AAA-TTTATTTATTTCAAATAAATTCTATTTACTTT
* * * *
16705209 AAATTTATTTATATTCAATTAATTTCT-TTTTC-TA
1 AAATTTATTTAT-TTCAAATAAATTCTATTTACTTT
* * ** *
16705243 AAATTTTATTT-TTTAAAATTAATT-TATATTTGTTG
1 AAA-TTTATTTATTTCAAATAAATTCTAT-TTACTTT
*
16705278 AAATTGTATTT-TTT-AATTAAATTCTATTT-CTTTT
1 AAATT-TATTTATTTCAAATAAATTCTATTTAC-TTT
16705312 AAATTTAATTTA
1 AAATTT-ATTTA
16705324 ATTTTTTAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
32 9 0.08
33 21 0.18
34 49 0.42
35 29 0.25
36 10 0.08
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (35 bp):
AAATTTATTTATTTCAAATAAATTCTATTTACTTT
Found at i:16705187 original size:19 final size:18
Alignment explanation
Indices: 16705163--16705306 Score: 67
Period size: 18 Copynumber: 8.2 Consensus size: 18
16705153 TTTCAAATAA
* *
16705163 ATTTTTTACTTTAAATTTT
1 ATTTTTTA-ATTAAATTCT
16705182 ATTTTTTAATTAAATTCT
1 ATTTTTTAATTAAATTCT
*
16705200 ATTTATT--TTAAATT-T
1 ATTTTTTAATTAAATTCT
*
16705215 ATTTATATTCAATTAATTTCT
1 ATTT-T-TT-AATTAAATTCT
* *
16705236 -TTTTCT-A--AAATTTT
1 ATTTTTTAATTAAATTCT
16705250 ATTTTTTAAAATT-AATT-T
1 ATTTTTT--AATTAAATTCT
* * *
16705268 ATATTTGT--TGAAATTGT
1 AT-TTTTTAATTAAATTCT
16705285 ATTTTTTAATTAAATTCT
1 ATTTTTTAATTAAATTCT
16705303 ATTT
1 ATTT
16705307 CTTTTAAATT
Statistics
Matches: 94, Mismatches: 14, Indels: 35
0.66 0.10 0.24
Matches are distributed among these distances:
14 5 0.05
15 11 0.12
16 16 0.17
17 5 0.05
18 30 0.32
19 17 0.18
20 9 0.10
21 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTTTAATTAAATTCT
Found at i:16705228 original size:15 final size:15
Alignment explanation
Indices: 16705182--16705233 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
16705172 TTTAAATTTT
16705182 ATTT-TTTA-ATTAA
1 ATTTATTTATATTAA
*
16705195 ATTCTATTTATTTTAA
1 ATT-TATTTATATTAA
*
16705211 ATTTATTTATATTCA
1 ATTTATTTATATTAA
*
16705226 ATTAATTT
1 ATTTATTT
16705234 CTTTTTCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 3 0.09
14 1 0.03
15 21 0.66
16 7 0.22
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTATTTATATTAA
Found at i:16705316 original size:21 final size:20
Alignment explanation
Indices: 16705286--16705347 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
16705276 TGAAATTGTA
16705286 TTTTTT-AATTAAATTCT-AT
1 TTTTTTAAATTAAATT-TAAT
*
16705305 TTCTTTTAAATTTAATTTAAT
1 TT-TTTTAAATTAAATTTAAT
*
16705326 TTTTTAAAATT-AA-TTAAT
1 TTTTTTAAATTAAATTTAAT
16705344 TTTT
1 TTTT
16705348 AATAATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.24
19 4 0.11
20 13 0.34
21 12 0.32
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTTAAATTAAATTTAAT
Found at i:16705354 original size:18 final size:19
Alignment explanation
Indices: 16705244--16705347 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 19
16705234 CTTTTTCTAA
*
16705244 AATTTTATTTTTTAAAATT
1 AATTTAATTTTTTAAAATT
* *
16705263 AATTTATATTTGTTGAAA-T
1 AATTTA-ATTTTTTAAAATT
*
16705282 --TGT-ATTTTTT--AATT
1 AATTTAATTTTTTAAAATT
* *
16705296 AAATTCTATTTCTTTTAAATTT
1 -AATT-TAATT-TTTTAAAATT
16705318 AATTTAATTTTTTAAAATT
1 AATTTAATTTTTTAAAATT
16705337 AA-TTAATTTTT
1 AATTTAATTTTT
16705348 AATAATTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
13 2 0.03
14 1 0.02
15 6 0.09
17 3 0.05
18 10 0.15
19 19 0.29
20 17 0.26
21 4 0.06
22 3 0.05
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (19 bp):
AATTTAATTTTTTAAAATT
Found at i:16705362 original size:18 final size:18
Alignment explanation
Indices: 16705308--16705362 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
16705298 ATTCTATTTC
* *
16705308 TTTTAAATTTAATTTAATT
1 TTTTAAAATT-ATTTAAAT
*
16705327 TTTTAAAATTAATT-AAT
1 TTTTAAAATTATTTAAAT
16705344 TTTTAATAATT-TTTAAAT
1 TTTTAA-AATTATTTAAAT
16705362 T
1 T
16705363 AAAAATACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 10 0.33
18 11 0.37
19 9 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAAAATTATTTAAAT
Found at i:16705400 original size:21 final size:21
Alignment explanation
Indices: 16705362--16705429 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
16705352 ATTTTTAAAT
*
16705362 TAAAAATACAATTT-AAAGAAA
1 TAAAATTA-AATTTAAAAGAAA
16705383 TAAAATTAAATTTAAAAGAAA
1 TAAAATTAAATTTAAAAGAAA
* *
16705404 TAGAATTTAA-TTAAAA-AAA
1 TAAAATTAAATTTAAAAGAAA
*
16705423 TACAATT
1 TAAAATT
16705430 TCAACAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.21
20 11 0.26
21 22 0.52
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAAATTAAATTTAAAAGAAA
Found at i:16705416 original size:53 final size:54
Alignment explanation
Indices: 16705359--16705546 Score: 224
Period size: 53 Copynumber: 3.5 Consensus size: 54
16705349 ATAATTTTTA
*
16705359 AATTAAAAATACAATTTAAAGAAATA-AAATTAAATTTAAAAGAAATAGAATTT
1 AATTAAAAATACAATTTAAAGAAATATAAATTAAATTTAAAATAAATAGAATTT
* *
16705412 AATTAAAAAAATACAATTTCAACAAATATAAATT-AATTTAAAATAAATAGAATTT
1 AATT--AAAAATACAATTTAAAGAAATATAAATTAAATTTAAAATAAATAGAATTT
* * * *
16705467 AATAAAAAAT-CGAAATTAATTG-AATATAAA-TAGATTTAAAATAAATAGAATTT
1 AATTAAAAATAC-AATTTAA-AGAAATATAAATTAAATTTAAAATAAATAGAATTT
* *
16705520 AATTAAAAATAAAATTTAAAAAAATAT
1 AATTAAAAATACAATTTAAAGAAATAT
16705547 TTAAAATAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
52 2 0.02
53 63 0.56
55 43 0.38
56 5 0.04
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (54 bp):
AATTAAAAATACAATTTAAAGAAATATAAATTAAATTTAAAATAAATAGAATTT
Found at i:16705439 original size:55 final size:55
Alignment explanation
Indices: 16705363--16705528 Score: 200
Period size: 55 Copynumber: 3.1 Consensus size: 55
16705353 TTTTTAAATT
* *
16705363 AAAAATACAATTTAAAGAAATA-AAATTAAATTTAAAAGAAATAGAATTTAATTAA
1 AAAAATACAATTT-AACAAATATAAATTAAATTTAAAATAAATAGAATTTAATTAA
16705418 AAAAATACAATTTCAACAAATATAAATT-AATTTAAAATAAATAGAATTTAA-T-A
1 AAAAATACAATTT-AACAAATATAAATTAAATTTAAAATAAATAGAATTTAATTAA
* ** *
16705471 AAAAAT-CGAAATTAATTGAATATAAA-TAGATTTAAAATAAATAGAATTTAATTAA
1 AAAAATAC-AATTTAA-CAAATATAAATTAAATTTAAAATAAATAGAATTTAATTAA
16705526 AAA
1 AAA
16705529 TAAAATTTAA
Statistics
Matches: 98, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
52 4 0.04
53 41 0.42
54 2 0.02
55 46 0.47
56 5 0.05
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (55 bp):
AAAAATACAATTTAACAAATATAAATTAAATTTAAAATAAATAGAATTTAATTAA
Found at i:16705510 original size:15 final size:15
Alignment explanation
Indices: 16705492--16705558 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
16705482 TTAATTGAAT
16705492 ATAAATAGATTTAAA
1 ATAAATAGATTTAAA
16705507 ATAAATAGAATTTAATTA
1 ATAAATAG-ATTTAA--A
*
16705525 A-AAATAAAATTTAAA
1 ATAAAT-AGATTTAAA
16705540 A-AAAT--ATTTAAA
1 ATAAATAGATTTAAA
16705552 ATAAATA
1 ATAAATA
16705559 CAATTTCAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
12 8 0.18
13 4 0.09
15 14 0.31
16 6 0.13
17 10 0.22
18 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
ATAAATAGATTTAAA
Found at i:16705528 original size:21 final size:20
Alignment explanation
Indices: 16705380--16705532 Score: 84
Period size: 21 Copynumber: 8.2 Consensus size: 20
16705370 CAATTTAAAG
* * *
16705380 AAATAAAATTAAATTTAAAAG
1 AAATAGAATTTAA-TTAAAAT
16705401 AAATAGAATTTAATTAAAA-
1 AAATAGAATTTAATTAAAAT
* *
16705420 AAATACAATTTCAA--CAAAT
1 AAATAGAATTT-AATTAAAAT
16705439 --ATA-AA-TTAATTTAAAAT
1 AAATAGAATTTAA-TTAAAAT
16705456 AAATAGAATTTAA-T-AAA-
1 AAATAGAATTTAATTAAAAT
* * *
16705473 AAATCGAAATTAATTGAATAT
1 AAATAGAATTTAATT-AAAAT
16705494 AAATAG-A--T--TTAAAAT
1 AAATAGAATTTAATTAAAAT
16705509 AAATAGAATTTAATTAAAAAT
1 AAATAGAATTTAATT-AAAAT
16705530 AAA
1 AAA
16705533 ATTTAAAAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 38
0.68 0.07 0.25
Matches are distributed among these distances:
14 2 0.02
15 12 0.12
16 5 0.05
17 18 0.17
18 9 0.09
19 14 0.14
20 15 0.15
21 28 0.27
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (20 bp):
AAATAGAATTTAATTAAAAT
Found at i:16706503 original size:13 final size:15
Alignment explanation
Indices: 16706483--16706523 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
16706473 TACTATTTAT
*
16706483 ATTATTAAATATT-T
1 ATTATTAAATATTGA
16706497 A-TATTAAA-ATTGA
1 ATTATTAAATATTGA
16706510 ATTATTAAATATTG
1 ATTATTAAATATTG
16706524 CATAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 8 0.35
15 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
ATTATTAAATATTGA
Found at i:16707573 original size:14 final size:14
Alignment explanation
Indices: 16707550--16707582 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16707540 TTTTCCCAAA
*
16707550 TTCTTTCCTCTTTC
1 TTCTTCCCTCTTTC
16707564 TTCTTCCCTCTTTC
1 TTCTTCCCTCTTTC
16707578 -TCTTC
1 TTCTTC
16707583 TCCCCCCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
TTCTTCCCTCTTTC
Found at i:16709359 original size:21 final size:20
Alignment explanation
Indices: 16709324--16709363 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16709314 GTCAATAACT
*
16709324 AAATTTATCATTATATCTATA
1 AAATTTATCAGTATA-CTATA
*
16709345 AAATTTATGAGTATACTAT
1 AAATTTATCAGTATACTAT
16709364 TATCTTGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTTATCAGTATACTATA
Found at i:16712513 original size:24 final size:24
Alignment explanation
Indices: 16712462--16712514 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
16712452 TCTTTTAGTT
* *
16712462 AAACTCTGTTTATTTGTTTCAATT
1 AAACTATGTTTATTTGTTTCAATC
* *
16712486 AAACTATGTTTATTTGTTTGAGTC
1 AAACTATGTTTATTTGTTTCAATC
16712510 AAACT
1 AAACT
16712515 CTTATTAGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTATGTTTATTTGTTTCAATC
Found at i:16714486 original size:24 final size:24
Alignment explanation
Indices: 16714435--16714489 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
16714425 TCTTTTAGTT
* *
16714435 AAACTATGTTTATTTGTTTAAATT
1 AAACTCTGTTTATTTGTTTAAATC
* *
16714459 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTAAATC
16714483 AAACTCT
1 AAACTCT
16714490 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTAAATC
Found at i:16716320 original size:16 final size:16
Alignment explanation
Indices: 16716299--16716358 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
16716289 AACAGAGAGT
* *
16716299 ACACAAAGTACGGAGC
1 ACACAAAGTGCTGAGC
16716315 ACACAAAGTGCTGAGC
1 ACACAAAGTGCTGAGC
*
16716331 ATACAAAGTGCTGAGC
1 ACACAAAGTGCTGAGC
*
16716347 ATACAAAGTGCT
1 ACACAAAGTGCT
16716359 AATTAGAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.15
Consensus pattern (16 bp):
ACACAAAGTGCTGAGC
Found at i:16716375 original size:23 final size:23
Alignment explanation
Indices: 16716343--16716465 Score: 95
Period size: 23 Copynumber: 5.3 Consensus size: 23
16716333 ACAAAGTGCT
* *
16716343 GAGCATACAAAGTGCTAATTAGA
1 GAGCACACAAAGTGCTAATCAGA
16716366 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* * * *
16716389 GAGTACACGAAGTTCTAATAATGGA
1 GAGCACACAAAGTGCTAATCA--GA
* * * * *
16716414 GAGCACGA-GACGTGCTAAACGGG
1 GAGCAC-ACAAAGTGCTAATCAGA
* *
16716437 GAGCACACACAGTGCTAAACAGA
1 GAGCACACAAAGTGCTAATCAGA
16716460 GAGCAC
1 GAGCAC
16716466 GCTAAAGTTC
Statistics
Matches: 78, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
22 1 0.01
23 61 0.78
25 15 0.19
26 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.15
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:16720486 original size:17 final size:17
Alignment explanation
Indices: 16720464--16720560 Score: 58
Period size: 17 Copynumber: 5.7 Consensus size: 17
16720454 TAATTAATAG
16720464 ATTTAATATTTAATTTA
1 ATTTAATATTTAATTTA
*
16720481 ATTTAATACTT-ATCTTA
1 ATTTAATATTTAAT-TTA
* *
16720498 A--TAGTATTTTA-TTA
1 ATTTAATATTTAATTTA
* * *
16720512 ATTTGATATTAAAGTTATT
1 ATTTAATATTTAA-TT-TA
* *
16720531 GTCTTAATATTAAATTTA
1 AT-TTAATATTTAATTTA
16720549 ATTTAATATTTA
1 ATTTAATATTTA
16720561 TCTTGATAAG
Statistics
Matches: 59, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
14 4 0.07
15 6 0.10
16 9 0.15
17 23 0.39
18 3 0.05
19 4 0.07
20 10 0.17
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTTAATATTTAATTTA
Found at i:16720549 original size:68 final size:69
Alignment explanation
Indices: 16720466--16720593 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 69
16720456 ATTAATAGAT
* * *
16720466 TTAATATTTAATTTAATTTAATACTTATCTTAAT-AGTATTTTATTAATTTGATATTAAAGTTAT
1 TTAATATTAAATTTAATTTAATACTTATCTTAATAAGTATTATATTAATTTAATATTAAAGTTAT
16720530 TGTC
66 TGTC
* *
16720534 TTAATATTAAATTTAATTTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAA
1 TTAATATTAAATTTAATTTAATACTTATCTTAATAAGTATTATATTAATTTAATATTAAA
16720594 ATGATTAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
68 31 0.57
69 23 0.43
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (69 bp):
TTAATATTAAATTTAATTTAATACTTATCTTAATAAGTATTATATTAATTTAATATTAAAGTTAT
TGTC
Found at i:16724205 original size:18 final size:18
Alignment explanation
Indices: 16724182--16724216 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16724172 AACTCAACTC
16724182 AACAATGGAAAATTTTAT
1 AACAATGGAAAATTTTAT
* *
16724200 AACAATTGATAATTTTA
1 AACAATGGAAAATTTTA
16724217 CAAATTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (18 bp):
AACAATGGAAAATTTTAT
Found at i:16727381 original size:29 final size:28
Alignment explanation
Indices: 16727335--16727451 Score: 89
Period size: 29 Copynumber: 4.0 Consensus size: 28
16727325 TTTCTCCCTA
**
16727335 TTAAATTTTACCCATTTATTGTGTA-TTTT
1 TTAAATTAAACCC-TTTATT-TGTATTTTT
*
16727364 TTAAATTAAATCCCTTTATTTTTATTTTT
1 TTAAATTAAA-CCCTTTATTTGTATTTTT
* *
16727393 TTAAATTTAACCCTTTTATTTTTATTTCTT
1 TTAAATTAAACCC-TTTATTTGTATTT-TT
16727423 TTAAAATT--ACCCTTTGATTCTGT-TTTTT
1 TT-AAATTAAACCCTTT-ATT-TGTATTTTT
16727451 T
1 T
16727452 ATTTTGTAAT
Statistics
Matches: 76, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
28 12 0.16
29 50 0.66
30 9 0.12
31 5 0.07
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.61
Consensus pattern (28 bp):
TTAAATTAAACCCTTTATTTGTATTTTT
Found at i:16727495 original size:17 final size:18
Alignment explanation
Indices: 16727473--16727508 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16727463 CTTTTATATC
16727473 TTTTT-AATTAAATCCTT
1 TTTTTAAATTAAATCCTT
*
16727490 TTTTTAAATTTAATCCTT
1 TTTTTAAATTAAATCCTT
16727508 T
1 T
16727509 CATCACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTAAATTAAATCCTT
Found at i:16744973 original size:2 final size:2
Alignment explanation
Indices: 16744966--16745030 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
16744956 AATACTAATA
16744966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16745008 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
16745031 AAATAGAAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16746048 original size:5 final size:5
Alignment explanation
Indices: 16746038--16746063 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16746028 TTTGAAATAG
16746038 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
16746064 TATAGAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:16747093 original size:101 final size:101
Alignment explanation
Indices: 16746914--16747095 Score: 231
Period size: 101 Copynumber: 1.8 Consensus size: 101
16746904 ATGTAATCTC
* * * * * *
16746914 AATCCAATCCATTGCAACTTTAGGGATATAGGATTTGATGTTGTAGCTTCATCTTGCCCTACTGT
1 AATCCAACCCACTGCAACTTCAGGGATATAAGATTTGATGTTGTAACTTCATCCTGCCCTACTGT
* *
16746979 AGCTTGAGGGAGATAAAGATTTGCTTTCATGACTTT
66 AACTTGAGAGAGATAAAGATTTGCTTTCATGACTTT
* * * * *
16747015 AATCCAACCCACTGCAACTTCAGGGGTATAAGATTTGGTTTTGTAACTTGATCCTGCTCTACTGT
1 AATCCAACCCACTGCAACTTCAGGGATATAAGATTTGATGTTGTAACTTCATCCTGCCCTACTGT
16747080 AAC-TGTAGAGAGATAA
66 AACTTG-AGAGAGATAA
16747096 GAATTCCCCT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
100 2 0.03
101 65 0.97
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (101 bp):
AATCCAACCCACTGCAACTTCAGGGATATAAGATTTGATGTTGTAACTTCATCCTGCCCTACTGT
AACTTGAGAGAGATAAAGATTTGCTTTCATGACTTT
Found at i:16747336 original size:50 final size:50
Alignment explanation
Indices: 16747242--16747386 Score: 146
Period size: 50 Copynumber: 2.9 Consensus size: 50
16747232 AACTTTAGGG
* * * * * * **
16747242 GTATAGGATTTGCTCTTGTAGCTTCAATTTGCCCTTTTCCAGCTTCAAGA
1 GTATAAGATTCGCCCTTGTAGCTTCAATATGCCCCTCTATAGCTTCAAGA
* *** *
16747292 GTATAATATTCGCCCTTGTAGCTTCAATATGCCCCTCTATAGCTTTGGGT
1 GTATAAGATTCGCCCTTGTAGCTTCAATATGCCCCTCTATAGCTTCAAGA
* * *
16747342 GTATGAGATTTGCCCTTGCAGCTTCAATATGCCCCTCTATAGCTT
1 GTATAAGATTCGCCCTTGTAGCTTCAATATGCCCCTCTATAGCTT
16747387 TGGGTGTATG
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (50 bp):
GTATAAGATTCGCCCTTGTAGCTTCAATATGCCCCTCTATAGCTTCAAGA
Found at i:16747387 original size:50 final size:50
Alignment explanation
Indices: 16747299--16747603 Score: 326
Period size: 50 Copynumber: 6.1 Consensus size: 50
16747289 AGAGTATAAT
* * * *
16747299 ATTCGCCCTTGTAGCTTCAATATGCCCCTCTATAGCTTTGGGTGTATGAG
1 ATTCGCCATTGCAGCTTCAATCTGCCCCTCTATAGCTTTAGGTGTATGAG
* * * *
16747349 ATTTGCCCTTGCAGCTTCAATATGCCCCTCTATAGCTTTGGGTGTATGAG
1 ATTCGCCATTGCAGCTTCAATCTGCCCCTCTATAGCTTTAGGTGTATGAG
* * * *
16747399 ATTCGCCATTGC-GATTTCAATCTACCCCTCTACAACTTTAGGTGTATGAG
1 ATTCGCCATTGCAG-CTTCAATCTGCCCCTCTATAGCTTTAGGTGTATGAG
* * * * *
16747449 ATTCGCCATTGCGGGTTCAATCTACCCCTCTACAACTTTAGGTGTATGAG
1 ATTCGCCATTGCAGCTTCAATCTGCCCCTCTATAGCTTTAGGTGTATGAG
* * *
16747499 ATTTGCCATTGCAGTTTCAATCTGCCCCTTTATAGCTTTAGGTGTATGAG
1 ATTCGCCATTGCAGCTTCAATCTGCCCCTCTATAGCTTTAGGTGTATGAG
** * ** * * *
16747549 ATTCATCGTTGCAGCTTCAATCTGTTCCTCTACAG-TTCTAGGGGTATAAG
1 ATTCGCCATTGCAGCTTCAATCTGCCCCTCTATAGCTT-TAGGTGTATGAG
16747599 ATTCG
1 ATTCG
16747604 TTGTTTTGTC
Statistics
Matches: 222, Mismatches: 30, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
49 3 0.01
50 218 0.98
51 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (50 bp):
ATTCGCCATTGCAGCTTCAATCTGCCCCTCTATAGCTTTAGGTGTATGAG
Found at i:16747601 original size:150 final size:150
Alignment explanation
Indices: 16747314--16747603 Score: 368
Period size: 150 Copynumber: 1.9 Consensus size: 150
16747304 CCCTTGTAGC
* * * * *
16747314 TTCAATATGCCCCTCTATAGCTTTGGGTGTATGAGATTTGCCCTTGCAGCTTCAATATGCCCCTC
1 TTCAATATACCCCTCTACAACTTTAGGTGTATGAGATTTGCCATTGCAGCTTCAATATGCCCCTC
* * * *
16747379 TATAGCTTTGGGTGTATGAGATTCGCCATTGCGATTTCAATCTACCCCTCTACAACTTTAGGTGT
66 TATAGCTTTAGGTGTATGAGATTCACCATTGCGACTTCAATCTACCCCTCTACAACTTTAGGGGT
*
16747444 ATGAGATTCGCCATTGCGGG
131 ATAAGATTCGCCATTGCGGG
* * * *
16747464 TTCAATCTACCCCTCTACAACTTTAGGTGTATGAGATTTGCCATTGCAGTTTCAATCTGCCCCTT
1 TTCAATATACCCCTCTACAACTTTAGGTGTATGAGATTTGCCATTGCAGCTTCAATATGCCCCTC
* * *** *
16747529 TATAGCTTTAGGTGTATGAGATTCATCGTTGC-AGCTTCAATCTGTTCCTCTAC-AGTTCTAGGG
66 TATAGCTTTAGGTGTATGAGATTCACCATTGCGA-CTTCAATCTACCCCTCTACAACTT-TAGGG
16747592 GTATAAGATTCG
129 GTATAAGATTCG
16747604 TTGTTTTGTC
Statistics
Matches: 118, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
149 4 0.03
150 114 0.97
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (150 bp):
TTCAATATACCCCTCTACAACTTTAGGTGTATGAGATTTGCCATTGCAGCTTCAATATGCCCCTC
TATAGCTTTAGGTGTATGAGATTCACCATTGCGACTTCAATCTACCCCTCTACAACTTTAGGGGT
ATAAGATTCGCCATTGCGGG
Found at i:16759257 original size:4 final size:4
Alignment explanation
Indices: 16759248--16759284 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
16759238 AGATAATACT
16759248 AATA AATA AATA AATA AATA AATA AATA AATA TAATA
1 AATA AATA AATA AATA AATA AATA AATA AATA -AATA
16759285 GAAATGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:16760317 original size:14 final size:16
Alignment explanation
Indices: 16760298--16760330 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
16760288 AGAAAATAAA
16760298 ATAAAATA-A-AATAT
1 ATAAAATATAGAATAT
16760312 ATAAAATATAGAATAT
1 ATAAAATATAGAATAT
16760328 ATA
1 ATA
16760331 TATAAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAAAATATAGAATAT
Found at i:16761080 original size:14 final size:14
Alignment explanation
Indices: 16761061--16761093 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16761051 AATGTGTGAA
16761061 ATTTGTATGAAATG
1 ATTTGTATGAAATG
*
16761075 ATTTGTATGTAATG
1 ATTTGTATGAAATG
16761089 ATTTG
1 ATTTG
16761094 GTTTTTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTATGAAATG
Found at i:16763546 original size:18 final size:18
Alignment explanation
Indices: 16763525--16763559 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16763515 ATTATGATTA
*
16763525 TATTATATTAAATTATTT
1 TATTATATTAAAATATTT
*
16763543 TATTTTATTAAAATATT
1 TATTATATTAAAATATT
16763560 AGAGATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATATTAAAATATTT
Found at i:16770058 original size:40 final size:39
Alignment explanation
Indices: 16770003--16770120 Score: 148
Period size: 40 Copynumber: 2.9 Consensus size: 39
16769993 GATGCAAGAT
**
16770003 AGGGGCATCGAAGTGCAAAT-AGAGGCACCGAAGTGTTAAC
1 AGGGGCATCGAAGTGC-AATCAG-GGCACCGAAGTGCGAAC
*
16770043 AGGGGCATCGAAGTGCAATCAGGGACATCGAAGTGCGAAC
1 AGGGGCATCGAAGTGCAATCAGGG-CACCGAAGTGCGAAC
* *
16770083 AGGGGCACCGAAGTGCGATCAGGGGCACCGAAGTGCGA
1 AGGGGCATCGAAGTGCAATCA-GGGCACCGAAGTGCGA
16770121 TCATTTCCGT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
39 5 0.07
40 61 0.88
41 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.36, T:0.12
Consensus pattern (39 bp):
AGGGGCATCGAAGTGCAATCAGGGCACCGAAGTGCGAAC
Found at i:16770076 original size:60 final size:60
Alignment explanation
Indices: 16770003--16770123 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
16769993 GATGCAAGAT
* * ** *
16770003 AGGGGCATCGAAGTGCAAATAGAGGCACCGAAGTGTTAACAGGGGCATCGAAGTGCAATC
1 AGGGACATCGAAGTGCAAACAGAGGCACCGAAGTGCGAACAGGGGCACCGAAGTGCAATC
* * * *
16770063 AGGGACATCGAAGTGCGAACAGGGGCACCGAAGTGCGATCAGGGGCACCGAAGTGCGATC
1 AGGGACATCGAAGTGCAAACAGAGGCACCGAAGTGCGAACAGGGGCACCGAAGTGCAATC
16770123 A
1 A
16770124 TTTCCGTAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.31, C:0.21, G:0.36, T:0.12
Consensus pattern (60 bp):
AGGGACATCGAAGTGCAAACAGAGGCACCGAAGTGCGAACAGGGGCACCGAAGTGCAATC
Found at i:16770119 original size:20 final size:20
Alignment explanation
Indices: 16770003--16770123 Score: 127
Period size: 20 Copynumber: 6.0 Consensus size: 20
16769993 GATGCAAGAT
* *
16770003 AGGGGCATCGAAGTGCAAAT-
1 AGGGGCACCGAAGTGC-GATC
* ** *
16770023 AGAGGCACCGAAGTGTTAAC
1 AGGGGCACCGAAGTGCGATC
* *
16770043 AGGGGCATCGAAGTGCAATC
1 AGGGGCACCGAAGTGCGATC
* * *
16770063 AGGGACATCGAAGTGCGAAC
1 AGGGGCACCGAAGTGCGATC
16770083 AGGGGCACCGAAGTGCGATC
1 AGGGGCACCGAAGTGCGATC
16770103 AGGGGCACCGAAGTGCGATC
1 AGGGGCACCGAAGTGCGATC
16770123 A
1 A
16770124 TTTCCGTAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
19 1 0.01
20 83 0.99
ACGTcount: A:0.31, C:0.21, G:0.36, T:0.12
Consensus pattern (20 bp):
AGGGGCACCGAAGTGCGATC
Found at i:16772197 original size:13 final size:13
Alignment explanation
Indices: 16772178--16772240 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
16772168 TTAAACTAAG
16772178 CTTTTCAAAAGTA
1 CTTTTCAAAAGTA
*
16772191 ATTTTCAAAA-TCA
1 CTTTTCAAAAGT-A
* *
16772204 CTTTTCCAAAGCA
1 CTTTTCAAAAGTA
* *
16772217 TTTTTTAAAAGTA
1 CTTTTCAAAAGTA
*
16772230 CTTCTCAAAAG
1 CTTTTCAAAAG
16772241 CAATGCTAAA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
12 1 0.03
13 36 0.97
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (13 bp):
CTTTTCAAAAGTA
Found at i:16773282 original size:24 final size:24
Alignment explanation
Indices: 16773250--16773306 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
16773240 AATCTTCCAG
*
16773250 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
*
16773274 TTAAACTCTATTTATTTGTTTCAG
1 TTAAACTCTATTTATTTGTTTCAA
*
16773298 TCAAACTCT
1 TTAAACTCT
16773307 TATTAGTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (24 bp):
TTAAACTCTATTTATTTGTTTCAA
Done.