Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 99 of 163
Found at i:27878671 original size:29 final size:29
Alignment explanation
Indices: 27878507--27878860 Score: 180
Period size: 29 Copynumber: 12.1 Consensus size: 29
27878497 AAAAATCATG
* *
27878507 TTTTAACCCCTAAACTTTCCAAAAATTATA
1 TTTT-ACCCTTAAACTTTCCAAAAATTACA
* *
27878537 TTTTAACCCTCAAAC-TTCATAAAAATTACA
1 TTTT-ACCCTTAAACTTTC-CAAAAATTACA
* ** * *
27878567 TTTTTGCCCCCAAACTTT-CAAAAAGTGCA
1 -TTTTACCCTTAAACTTTCCAAAAATTACA
*
27878596 TTTTTACCCTCT-AAC-TTCATAAAAATTACA
1 -TTTTACCCT-TAAACTTTC-CAAAAATTACA
* *** *
27878626 TTTCTTCCCCCGAACTTTCCAAAAATCACA
1 TTT-TACCCTTAAACTTTCCAAAAATTACA
*
27878656 TTTTACCCTTAAACTTT-TAAAAATTACCA
1 TTTTACCCTTAAACTTTCCAAAAATTA-CA
*
27878685 TTTTACCC-TAAACTTTCAAAAAAATTACA
1 TTTTACCCTTAAACTTTC-CAAAAATTACA
** **
27878714 TTTT-TTCTCGAAC-TTCCAAAAATTACCA
1 TTTTACCCTTAAACTTTCCAAAAATTA-CA
*
27878742 TTTTACCCTTGAAC-TTCC-AAAA-TATCA
1 TTTTACCCTTAAACTTTCCAAAAATTA-CA
* ***
27878769 TTTTTGACCC-TAAATTTTTTGAAAATTACCA
1 -TTTT-ACCCTTAAACTTTCCAAAAATTA-CA
**
27878800 TTTTACTCC-CGAAC-TTCCAAAAATTACCA
1 TTTTAC-CCTTAAACTTTCCAAAAATTA-CA
* *
27878829 TTTTACCCTTAAAC-TTCCAAAAGTCACA
1 TTTTACCCTTAAACTTTCCAAAAATTACA
27878857 TTTT
1 TTTT
27878861 TGCCCCTGAG
Statistics
Matches: 251, Mismatches: 51, Indels: 46
0.72 0.15 0.13
Matches are distributed among these distances:
27 12 0.05
28 46 0.18
29 103 0.41
30 77 0.31
31 13 0.05
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTTACCCTTAAACTTTCCAAAAATTACA
Found at i:27878715 original size:58 final size:57
Alignment explanation
Indices: 27878507--27878844 Score: 228
Period size: 59 Copynumber: 5.8 Consensus size: 57
27878497 AAAAATCATG
* *
27878507 TTTTAACCCCTAAACTTTCCAAAAATTATATTTTAACCCTCAAACTTCATAAAAATTA-CA
1 TTTT-ACCCC-AAACTTTCCAAAAATTACATTTT-ACCCTTAAACTT-ATAAAAATTACCA
* * *
27878567 TTTTTGCCCCCAAACTTT-CAAAAAGTGCATTTTTACCCTCT-AACTTCATAAAAATTA-CA
1 -TTTT-ACCCCAAACTTTCCAAAAATTACA-TTTTACCCT-TAAACTT-ATAAAAATTACCA
* * * *
27878626 TTTCTTCCCCCGAACTTTCCAAAAATCACATTTTACCCTTAAACTTTTAAAAATTACCA
1 -TT-TTACCCCAAACTTTCCAAAAATTACATTTTACCCTTAAACTTATAAAAATTACCA
* * ** ** **
27878685 TTTTACCCTAAACTTTCAAAAAAATTACATTTT-TTCTCGAACTTCCAAAAATTACCA
1 TTTTACCCCAAACTTTC-CAAAAATTACATTTTACCCTTAAACTTATAAAAATTACCA
** * * *
27878742 TTTTACCCTTGAAC-TTCC-AAAA-TATCATTTTTGACCC-TAAATTTTTTGAAAATTACCA
1 TTTTACCC-CAAACTTTCCAAAAATTA-CA-TTTT-ACCCTTAAA-CTTATAAAAATTACCA
*
27878800 TTTTACTCCCGAAC-TTCCAAAAATTACCATTTTACCCTTAAACTT
1 TTTTAC-CCCAAACTTTCCAAAAATTA-CATTTTACCCTTAAACTT
27878845 CCAAAAGTCA
Statistics
Matches: 225, Mismatches: 35, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
54 2 0.01
55 6 0.03
56 4 0.02
57 43 0.19
58 62 0.28
59 75 0.33
60 25 0.11
61 8 0.04
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (57 bp):
TTTTACCCCAAACTTTCCAAAAATTACATTTTACCCTTAAACTTATAAAAATTACCA
Found at i:27878745 original size:27 final size:28
Alignment explanation
Indices: 27878523--27878763 Score: 114
Period size: 30 Copynumber: 8.3 Consensus size: 28
27878513 CCCCTAAACT
* * *
27878523 TTCCAAAAATTATATTTTAACCCTCAAAC
1 TTCCAAAAATTACATTTTTA-CCTCGAAC
* * * *
27878552 TTCATAAAAATTACATTTTTGCCCCCAAAC
1 TTC-CAAAAATTACATTTTT-ACCTCGAAC
* * * *
27878582 TTTCAAAAAGTGCATTTTTACCCTCTAAC
1 TTCCAAAAATTACATTTTTA-CCTCGAAC
* * *
27878611 TTCATAAAAATTACATTTCTTCCCCCGAAC
1 TTC-CAAAAATTACATTT-TTACCTCGAAC
* **
27878641 TTTCCAAAAATCACA-TTTTACCCTTAAAC
1 -TTCCAAAAATTACATTTTTA-CCTCGAAC
** *
27878670 TTTTAAAAATTACCA-TTTTACC-CTAAAC
1 TTCCAAAAATTA-CATTTTTACCTC-GAAC
* *
27878698 TTTCAAAAAAATTACATTTTT-TCTCGAAC
1 -TTC-CAAAAATTACATTTTTACCTCGAAC
*
27878727 TTCCAAAAATTACCA-TTTTACCCTTGAAC
1 TTCCAAAAATTA-CATTTTTA-CCTCGAAC
27878756 TTCCAAAA
1 TTCCAAAA
27878764 TATCATTTTT
Statistics
Matches: 160, Mismatches: 36, Indels: 32
0.70 0.16 0.14
Matches are distributed among these distances:
27 12 0.08
28 22 0.14
29 60 0.38
30 61 0.38
31 5 0.03
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (28 bp):
TTCCAAAAATTACATTTTTACCTCGAAC
Found at i:27878878 original size:29 final size:29
Alignment explanation
Indices: 27878858--27878927 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
27878848 AAAGTCACAT
* *
27878858 TTTTGCCCCTGAGTGTTCAAAAATTACCA
1 TTTTGCCCCCGAGTGTTCAAAAATCACCA
* *
27878887 TTTTGCCCCCGAGTG-TCTAAAAATTACCG
1 TTTTGCCCCCGAGTGTTC-AAAAATCACCA
*
27878916 TTTTGCCTCCGA
1 TTTTGCCCCCGA
27878928 ACCTCTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 2 0.05
29 35 0.95
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (29 bp):
TTTTGCCCCCGAGTGTTCAAAAATCACCA
Found at i:27878914 original size:87 final size:87
Alignment explanation
Indices: 27878616--27878898 Score: 269
Period size: 87 Copynumber: 3.3 Consensus size: 87
27878606 CTAACTTCAT
* * **
27878616 AAAAATTA-CATTTCTTCCCCCGAACTTTCCAAAAATCA-CATTTTACCCTTAAACTTTTAAAAA
1 AAAAATTACCATTT-TACCCCCGAAC-TTCCAAAAATTACCATTTTACCCTTAAAC-TTCCAAAA
* *
27878679 TTACCA-TTTT-ACCCTAAACT-TTC
63 -TATCATTTTTGACCCTAAAGTGTTC
** * *
27878702 AAAAAAATTA-CATTTT-TTCTCGAACTTCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAT
1 --AAAAATTACCATTTTACCCCCGAACTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAT
* * *
27878765 ATCATTTTTGACCCTAAATTTTTT
64 ATCATTTTTGACCCTAAAGTGTTC
* *
27878789 GAAAATTACCATTTTACTCCCGAACTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAGTC
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAA-T-
* *
27878854 A-CATTTTTGCCCCT-GAGTGTTC
64 ATCATTTTTGACCCTAAAGTGTTC
*
27878876 AAAAATTACCATTTTGCCCCCGA
1 AAAAATTACCATTTTACCCCCGA
27878899 GTGTCTAAAA
Statistics
Matches: 165, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
84 4 0.02
85 28 0.17
86 36 0.22
87 70 0.42
88 26 0.16
89 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (87 bp):
AAAAATTACCATTTTACCCCCGAACTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAATAT
CATTTTTGACCCTAAAGTGTTC
Found at i:27878934 original size:29 final size:29
Alignment explanation
Indices: 27878876--27878948 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
27878866 CTGAGTGTTC
***
27878876 AAAAATTACCATTTTGCCCCCGAGTGTCT
1 AAAAATTACCATTTTGCCCCCGAACCTCT
* *
27878905 AAAAATTACCGTTTTGCCTCCGAACCTCT
1 AAAAATTACCATTTTGCCCCCGAACCTCT
* *
27878934 AAAAGTCACCATTTT
1 AAAAATTACCATTTT
27878949 ACTCCCGAGC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (29 bp):
AAAAATTACCATTTTGCCCCCGAACCTCT
Found at i:27879312 original size:81 final size:81
Alignment explanation
Indices: 27879210--27879376 Score: 325
Period size: 81 Copynumber: 2.1 Consensus size: 81
27879200 GGCAATGTCT
*
27879210 TTTTTGTGTGGAAACTTCGAGAAATCATGCCCTAACGTGTCGGGTGTGATTTTTCGTATAATTCA
1 TTTTCGTGTGGAAACTTCGAGAAATCATGCCCTAACGTGTCGGGTGTGATTTTTCGTATAATTCA
27879275 CACGAATCGAATATCC
66 CACGAATCGAATATCC
27879291 TTTTCGTGTGGAAACTTCGAGAAATCATGCCCTAACGTGTCGGGTGTGATTTTTCGTATAATTCA
1 TTTTCGTGTGGAAACTTCGAGAAATCATGCCCTAACGTGTCGGGTGTGATTTTTCGTATAATTCA
27879356 CACGAATCGAATATCC
66 CACGAATCGAATATCC
27879372 TTTTC
1 TTTTC
27879377 TAAGTTTTCT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (81 bp):
TTTTCGTGTGGAAACTTCGAGAAATCATGCCCTAACGTGTCGGGTGTGATTTTTCGTATAATTCA
CACGAATCGAATATCC
Found at i:27890698 original size:20 final size:21
Alignment explanation
Indices: 27890673--27890725 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
27890663 TAAAAATTCA
27890673 AAAAAGATATATTAAAAA-AT
1 AAAAAGATATATTAAAAATAT
27890693 AAAAAG-TAT-TTAAAAATTAT
1 AAAAAGATATATTAAAAA-TAT
27890713 AAAAAGATATATT
1 AAAAAGATATATT
27890726 TTTAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.24
19 3 0.10
20 14 0.48
21 3 0.10
22 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (21 bp):
AAAAAGATATATTAAAAATAT
Found at i:27890734 original size:8 final size:8
Alignment explanation
Indices: 27890723--27890753 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
27890713 AAAAAGATAT
27890723 ATTTTTAA
1 ATTTTTAA
27890731 ATTTTTAA
1 ATTTTTAA
27890739 ATATTTTAA
1 AT-TTTTAA
27890748 ATTTTT
1 ATTTTT
27890754 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
ATTTTTAA
Found at i:27890736 original size:9 final size:9
Alignment explanation
Indices: 27890724--27890757 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
27890714 AAAAGATATA
27890724 TTTTTAAA-
1 TTTTTAAAT
27890732 TTTTTAAAT
1 TTTTTAAAT
*
27890741 ATTTTAAAT
1 TTTTTAAAT
27890750 TTTTTAAA
1 TTTTTAAA
27890758 AAATAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:27900083 original size:43 final size:43
Alignment explanation
Indices: 27900035--27900134 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 43
27900025 AATTGCACAA
* * *
27900035 TTAATAACATGTGACGATATTGACA-AGAGTCAAGTAATATAAT
1 TTAATAACATGTCACAATATTAACACAGA-TCAAGTAATATAAT
* **
27900078 TTAATAACATGCCACAATATTAACACCTATCAAGTAATATAAT
1 TTAATAACATGTCACAATATTAACACAGATCAAGTAATATAAT
27900121 TTAATAACATGTCA
1 TTAATAACATGTCA
27900135 AGAAATAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
43 48 0.98
44 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (43 bp):
TTAATAACATGTCACAATATTAACACAGATCAAGTAATATAAT
Found at i:27901190 original size:6 final size:6
Alignment explanation
Indices: 27901169--27901243 Score: 73
Period size: 6 Copynumber: 12.8 Consensus size: 6
27901159 TTAGATTGGG
** * *
27901169 TTTAAA TTTATT TTTAAA TTTAAA TTTTAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
27901216 TTTAGA TTT-GT TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
27901244 CTAAATTTAA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
5 8 0.14
6 48 0.86
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:27901209 original size:17 final size:17
Alignment explanation
Indices: 27901187--27901219 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27901177 TATTTTTAAA
*
27901187 TTTAAATTTTAATTTAT
1 TTTAAATTTAAATTTAT
27901204 TTTAAATTTAAATTTA
1 TTTAAATTTAAATTTA
27901220 GATTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:27901236 original size:29 final size:29
Alignment explanation
Indices: 27901147--27901243 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 29
27901137 AAATTTTGAT
* * *
27901147 TTTAAA-TTAAGTTTAGATTGGGTTTAAA
1 TTTAAATTTAAATTTAGATTTGTTTTAAA
** * *
27901175 TTTATTTTTAAATTTAAATTT-TAATTT-AT
1 TTTAAATTTAAATTTAGATTTGT--TTTAAA
27901204 TTTAAATTTAAATTTAGATTTGTTTTAAA
1 TTTAAATTTAAATTTAGATTTGTTTTAAA
27901233 TTTAAATTTAA
1 TTTAAATTTAA
27901244 CTAAATTTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
28 7 0.13
29 42 0.79
30 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTAAATTTAAATTTAGATTTGTTTTAAA
Found at i:27901242 original size:23 final size:22
Alignment explanation
Indices: 27901173--27901243 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 22
27901163 ATTGGGTTTA
27901173 AATTTATTTTTAAATTTAAATTTT
1 AATTTA-TTTTAAATTTAAA-TTT
27901197 AATTTATTTTAAATTTAAATTT
1 AATTTATTTTAAATTTAAATTT
*
27901219 AGATTTGTTTTAAATTTAAATTT
1 A-ATTTATTTTAAATTTAAATTT
27901242 AA
1 AA
27901244 CTAAATTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
22 5 0.11
23 34 0.76
24 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (22 bp):
AATTTATTTTAAATTTAAATTT
Found at i:27903209 original size:30 final size:29
Alignment explanation
Indices: 27903144--27903335 Score: 147
Period size: 30 Copynumber: 6.6 Consensus size: 29
27903134 GAAGGTCCCT
* * *
27903144 AAACTGTCCAGAAATTATATATTTACCCCC
1 AAACT-TCCAAAAATTATATTTTTACCCCA
* **
27903174 GAACTTTTAAAAATTATATTTTTGACCCCA
1 AAACTTCCAAAAATTATATTTTT-ACCCCA
27903204 AAACTTCCAAAAATTATATTTTTACCCCCA
1 AAACTTCCAAAAATTATATTTTTA-CCCCA
** * **
27903234 AAA-TTCCAAAAATTCCATTTTTGATCTTA
1 AAACTTCCAAAAATTATATTTTT-ACCCCA
* *
27903263 AAACTTCCAAAATTTACATTTTTACCCCA
1 AAACTTCCAAAAATTATATTTTTACCCCA
* * * **
27903292 AAA-TTTCAAAAATCCA-ATTTTGACCTTA
1 AAACTTCCAAAAAT-TATATTTTTACCCCA
*
27903320 AAACTTTCAAAAATTA
1 AAACTTCCAAAAATTA
27903336 CCATTTTACC
Statistics
Matches: 130, Mismatches: 26, Indels: 14
0.76 0.15 0.08
Matches are distributed among these distances:
28 21 0.16
29 54 0.42
30 55 0.42
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTATATTTTTACCCCA
Found at i:27903247 original size:59 final size:58
Alignment explanation
Indices: 27903144--27903335 Score: 208
Period size: 59 Copynumber: 3.3 Consensus size: 58
27903134 GAAGGTCCCT
* * * * * **
27903144 AAACTGTCCAGAAATTATATATTTACCCCCGAACTTTTAAAAATTATATTTTTGACCCCA
1 AAACT-TCCAAAAATTATATTTTTACCCCCAAAATTTCAAAAATTA-ATTTTTGACCTTA
* * *
27903204 AAACTTCCAAAAATTATATTTTTACCCCCAAAATTCCAAAAATTCCATTTTTGATCTTA
1 AAACTTCCAAAAATTATATTTTTACCCCCAAAATTTCAAAAATT-AATTTTTGACCTTA
* * *
27903263 AAACTTCCAAAATTTACATTTTTA-CCCCAAAATTTCAAAAATCCAA-TTTTGACCTTA
1 AAACTTCCAAAAATTATATTTTTACCCCCAAAATTTCAAAAAT-TAATTTTTGACCTTA
*
27903320 AAACTTTCAAAAATTA
1 AAACTTCCAAAAATTA
27903336 CCATTTTACC
Statistics
Matches: 112, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
57 24 0.21
58 18 0.16
59 65 0.58
60 5 0.04
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.35
Consensus pattern (58 bp):
AAACTTCCAAAAATTATATTTTTACCCCCAAAATTTCAAAAATTAATTTTTGACCTTA
Found at i:27903361 original size:58 final size:58
Alignment explanation
Indices: 27903193--27903346 Score: 204
Period size: 57 Copynumber: 2.7 Consensus size: 58
27903183 AAAATTATAT
** * *
27903193 TTTTGACCCCAAAACTTCCAAAAATTATATTTTTACCCCCAAAATTCCAAAAATTCCAT
1 TTTTGACCTTAAAACTTCCAAAAATTACATTTTTA-CCCCAAAATTCCAAAAATTCCAA
* * *
27903252 TTTTGATCTTAAAACTTCCAAAATTTACATTTTTACCCCAAAATTTCAAAAA-TCCAA
1 TTTTGACCTTAAAACTTCCAAAAATTACATTTTTACCCCAAAATTCCAAAAATTCCAA
*
27903309 TTTTGACCTTAAAACTTTCAAAAATTACCA-TTTTACCC
1 TTTTGACCTTAAAACTTCCAAAAATTA-CATTTTTACCC
27903347 TCGAATGTCC
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
57 36 0.43
58 18 0.21
59 30 0.36
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (58 bp):
TTTTGACCTTAAAACTTCCAAAAATTACATTTTTACCCCAAAATTCCAAAAATTCCAA
Found at i:27916029 original size:207 final size:206
Alignment explanation
Indices: 27915721--27916238 Score: 829
Period size: 207 Copynumber: 2.5 Consensus size: 206
27915711 ACCAACTCAG
* * * * * *
27915721 CGCTCGATGCGAGCAAATCTTTGAACCTTCAGCTTCTTGATGAGGTACTGAGAAGCAAGTCAAAG
1 CGCTCGATGAGAGCAAATCTTCGAACC-CCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAG
*
27915786 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGA
65 CAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGA
*
27915851 TACAAAGAAGCGAATTGAAACAAGTGATGAGGTCATCTTCCTGATGAGATACTGAGAAGAAGACC
130 TACAAAGAAGCGAATTGAAACAAGTGATGAGGTCATCTTCCTGATGAGATACTAAGAAGAAGACC
27915916 AAATCAAACCCA
195 AAATCAAACCCA
* * * *
27915928 CTCTCGATGTGAGTAAATCTTCGAACTCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
1 CGCTCGATGAGAGCAAATCTTCGAAC-CCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAG
*
27915993 CAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGA
65 CAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGA
* * * *
27916058 TACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTAAGAAGAAGACC
130 TACAAAGAAGCGAATTGAAACAAGTGATGAGGTCATCTTCCTGATGAGATACTAAGAAGAAGACC
27916123 AAATCAAACCCA
195 AAATCAAACCCA
*
27916135 CGCTCGATGAGAGCAAATCTTCGAACCCCTAGCTTCCTAATGAGGTACTGAGAAGCAGGTCGAAG
1 CGCTCGATGAGAGCAAATCTTCGAACCCC-AGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAG
*
27916200 CAATAAAATGGTTAGCTTCTTTGATGAGATACAGAGAAG
65 CAATAAAATGGTTAGCTTC-TTGATGAGATACTGAGAAG
27916239 CGGATTGAAA
Statistics
Matches: 286, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
206 3 0.01
207 264 0.92
208 19 0.07
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (206 bp):
CGCTCGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGC
AATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGAT
ACAAAGAAGCGAATTGAAACAAGTGATGAGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCA
AATCAAACCCA
Found at i:27916668 original size:35 final size:36
Alignment explanation
Indices: 27916627--27916704 Score: 108
Period size: 35 Copynumber: 2.2 Consensus size: 36
27916617 TAGGTTTGAA
*
27916627 TTAAATTTTGA-TTTTAAAT-TAAGTTTAGATTGGTT
1 TTAAATTTT-ATTTTTAAATGTAAATTTAGATTGGTT
*
27916662 TTAAA-TTTATTTTTAAATGTAAATTTAGATTTGTT
1 TTAAATTTTATTTTTAAATGTAAATTTAGATTGGTT
27916697 TTAAATTT
1 TTAAATTT
27916705 AAATTTAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 1 0.03
34 11 0.29
35 24 0.63
36 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (36 bp):
TTAAATTTTATTTTTAAATGTAAATTTAGATTGGTT
Found at i:27916705 original size:35 final size:34
Alignment explanation
Indices: 27916638--27916705 Score: 109
Period size: 35 Copynumber: 2.0 Consensus size: 34
27916628 TAAATTTTGA
*
27916638 TTTTAAATTAAGTTTAGATTGGTTTTAAATTTAT
1 TTTTAAATTAAATTTAGATTGGTTTTAAATTTAT
*
27916672 TTTTAAATGTAAATTTAGATTTGTTTTAAATTTA
1 TTTTAAAT-TAAATTTAGATTGGTTTTAAATTTA
27916706 AATTTAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 8 0.26
35 23 0.74
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (34 bp):
TTTTAAATTAAATTTAGATTGGTTTTAAATTTAT
Found at i:27916712 original size:35 final size:34
Alignment explanation
Indices: 27916639--27916721 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 34
27916629 AAATTTTGAT
* **
27916639 TTTAAATTAAGTTTAGATTGGTTTTAAATTTATT
1 TTTAAATTAAATTTAGATTGGTTTTAAATTTAAA
*
27916673 TTTAAATGTAAATTTAGATTTGTTTTAAATTTAAA
1 TTTAAAT-TAAATTTAGATTGGTTTTAAATTTAAA
*
27916708 TTT-AACTAAATTTA
1 TTTAAATTAAATTTA
27916722 AGATAAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 8 0.19
34 9 0.21
35 26 0.60
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.53
Consensus pattern (34 bp):
TTTAAATTAAATTTAGATTGGTTTTAAATTTAAA
Found at i:27918700 original size:29 final size:29
Alignment explanation
Indices: 27918656--27918820 Score: 190
Period size: 29 Copynumber: 5.6 Consensus size: 29
27918646 CTCTAAATTA
27918656 TCCAAAAATTACATTTTTACCCTCAAACT
1 TCCAAAAATTACATTTTTACCCTCAAACT
* *
27918685 TTCAAAAATTACATTTTTGTCCC-CAAAACT
1 TCCAAAAATTACATTTTT-ACCCTC-AAACT
* *
27918715 TCCAAAAATTACATTTTTACCCTTAAAAT
1 TCCAAAAATTACATTTTTACCCTCAAACT
*
27918744 TCCAAAAAATT-CATTTTTGACCCTAAAACT
1 TCC-AAAAATTACATTTTT-ACCCTCAAACT
* * *
27918774 TCCAAAAAATACATTTTTACCCCCAAAAT
1 TCCAAAAATTACATTTTTACCCTCAAACT
* *
27918803 TGCAAAAATTCCATTTTT
1 TCCAAAAATTACATTTTT
27918821 GATCCTGATT
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
29 64 0.56
30 51 0.44
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCTCAAACT
Found at i:27918750 original size:59 final size:58
Alignment explanation
Indices: 27918656--27918822 Score: 235
Period size: 59 Copynumber: 2.8 Consensus size: 58
27918646 CTCTAAATTA
* * *
27918656 TCCAAAAATTACATTTTTACCCTCAAACTTTCAAAAATTACATTTTTGTCCCCAAAACT
1 TCCAAAAATTACATTTTTACCCTCAAAATTCCAAAAATT-CATTTTTGACCCCAAAACT
* *
27918715 TCCAAAAATTACATTTTTACCCTTAAAATTCCAAAAAATTCATTTTTGACCCTAAAACT
1 TCCAAAAATTACATTTTTACCCTCAAAATTCC-AAAAATTCATTTTTGACCCCAAAACT
* * *
27918774 TCCAAAAAATACATTTTTACCCCCAAAATTGCAAAAATTCCATTTTTGA
1 TCCAAAAATTACATTTTTACCCTCAAAATTCCAAAAATT-CATTTTTGA
27918823 TCCTGATTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
58 7 0.07
59 83 0.86
60 7 0.07
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTACCCTCAAAATTCCAAAAATTCATTTTTGACCCCAAAACT
Found at i:27918953 original size:28 final size:27
Alignment explanation
Indices: 27918895--27918968 Score: 130
Period size: 28 Copynumber: 2.7 Consensus size: 27
27918885 ATTTTTTTAC
27918895 AAAATTACCATTTTGCCCCGAAAGTCT
1 AAAATTACCATTTTGCCCCGAAAGTCT
*
27918922 AAAATTATCATTTTGCCCTCGAAAGTCT
1 AAAATTACCATTTTGCCC-CGAAAGTCT
27918950 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTGCCCC
27918969 CGGGCATCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 18 0.41
28 26 0.59
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (27 bp):
AAAATTACCATTTTGCCCCGAAAGTCT
Found at i:27921871 original size:21 final size:21
Alignment explanation
Indices: 27921842--27921895 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
27921832 GGAGTTTTTA
27921842 GTATCGGTAGAAGTAAT-ACTT
1 GTATCGGTAGAA-TAATCACTT
* *
27921863 GTTTCGGTAGAATTATCACTT
1 GTATCGGTAGAATAATCACTT
27921884 GTATCGGTAGAA
1 GTATCGGTAGAA
27921896 ATCTATAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAATAATCACTT
Found at i:27922745 original size:21 final size:21
Alignment explanation
Indices: 27922721--27922764 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
27922711 ACAAATTCAT
27922721 ATTACTTACTAACAAAATAAA
1 ATTACTTACTAACAAAATAAA
*
27922742 ATTACTTACTAATAAAATAAA
1 ATTACTTACTAACAAAATAAA
27922763 AT
1 AT
27922765 AAAATAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTACTTACTAACAAAATAAA
Found at i:27924593 original size:13 final size:13
Alignment explanation
Indices: 27924575--27924599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27924565 ATGTTTTGAT
27924575 TTATTTTGAATTC
1 TTATTTTGAATTC
27924588 TTATTTTGAATT
1 TTATTTTGAATT
27924600 TTTGTTAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
TTATTTTGAATTC
Found at i:27927080 original size:39 final size:37
Alignment explanation
Indices: 27927023--27927143 Score: 134
Period size: 39 Copynumber: 3.1 Consensus size: 37
27927013 ACCTATATCA
* *
27927023 TATATTACCCGAGAATCCGCGACAAATGTCGAATCTCAT
1 TATATTACCCGAGGATCCGC-ACAAATG-CAAATCTCAT
27927062 TATATTACCCGAGGATCCGCATCAAATGCTAAATCTCAT
1 TATATTACCCGAGGATCCGCA-CAAATGC-AAATCTCAT
* * * *
27927101 TATTTTACCTGAGGATCTGCAACAAATGCTAGATCTCAT
1 TATATTACCCGAGGATCCGC-ACAAATGC-AAATCTCAT
27927140 TATA
1 TATA
27927144 ATTTGGACAA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.03
39 69 0.96
40 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (37 bp):
TATATTACCCGAGGATCCGCACAAATGCAAATCTCAT
Found at i:27935235 original size:24 final size:24
Alignment explanation
Indices: 27935208--27935261 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
27935198 AAAAGATCCG
*
27935208 ATGAATAAGTGTCATCGTGAGTAA
1 ATGAATAAGTGTCATCATGAGTAA
***
27935232 ATGAATCCTTGTCATCATGAGTAA
1 ATGAATAAGTGTCATCATGAGTAA
27935256 ATGAAT
1 ATGAAT
27935262 CCTTTACAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (24 bp):
ATGAATAAGTGTCATCATGAGTAA
Found at i:27935262 original size:24 final size:24
Alignment explanation
Indices: 27935217--27935265 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
27935207 GATGAATAAG
*
27935217 TGTCATCGTGAGTAAATGAATCCT
1 TGTCATCATGAGTAAATGAATCCT
27935241 TGTCATCATGAGTAAATGAATCCT
1 TGTCATCATGAGTAAATGAATCCT
27935265 T
1 T
27935266 TACAGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (24 bp):
TGTCATCATGAGTAAATGAATCCT
Found at i:27942118 original size:28 final size:24
Alignment explanation
Indices: 27942088--27942137 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
27942078 GATTTTTCAG
27942088 GAAGGAAGATGTAATGGTTACCAT
1 GAAGGAAGATGTAATGGTTACCAT
27942112 GAAGGAAGATGTAATGGTTACCAT
1 GAAGGAAGATGTAATGGTTACCAT
27942136 GA
1 GA
27942138 GATAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.30, T:0.24
Consensus pattern (24 bp):
GAAGGAAGATGTAATGGTTACCAT
Found at i:27947559 original size:29 final size:29
Alignment explanation
Indices: 27947527--27947870 Score: 300
Period size: 30 Copynumber: 11.6 Consensus size: 29
27947517 TGGACATTCG
27947527 GGGGT-AAAATGGTAATTTTTGAAAGTTTT
1 GGGGTAAAAAT-GTAATTTTTGAAAGTTTT
* * *
27947556 GGGGTTAAAAATGGAGTTTTT-AGAAGTTTA
1 GGGG-TAAAAATGTAATTTTTGA-AAGTTTT
* * *
27947586 GGGGTAAAAATATAATTTTAGAAATTTTT
1 GGGGTAAAAATGTAATTTTTGAAAGTTTT
* * *
27947615 GGGGTCAAAAATGGAATTTTTGGAAGTTTG
1 GGGGT-AAAAATGTAATTTTTGAAAGTTTT
* * *
27947645 GGGGTAAAAATGTAATTTTTGGAAGCTTC
1 GGGGTAAAAATGTAATTTTTGAAAGTTTT
** * * *
27947674 GTAGTCAAAAATGGAATTTTTAAAAG-TTC
1 GGGGT-AAAAATGTAATTTTTGAAAGTTTT
27947703 GAGGGTAAAAAATGTAATTTTTGGAAA-TTTT
1 G-GGGT-AAAAATGTAATTTTT-GAAAGTTTT
* *
27947734 GGGGTTAAAATGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGTAATTTTTGAAAGTTTT
* *
27947763 GGGGTCAAAAATATAATTTTTGGAAGTTTT
1 GGGGT-AAAAATGTAATTTTTGAAAGTTTT
* *
27947793 AGGGTAAAAATGTAATTTTTGTAAGTTTT
1 GGGGTAAAAATGTAATTTTTGAAAGTTTT
* * * *
27947822 GGGGTTAAAAATATAATTCTGGAGAAGTTTA
1 GGGG-TAAAAATGTAATTTTTGA-AAGTTTT
* *
27947853 GGGGTCAAAATATAATTT
1 GGGGTAAAAATGTAATTT
27947871 CTAGACAGTT
Statistics
Matches: 258, Mismatches: 44, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.01
29 103 0.40
30 131 0.51
31 21 0.08
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGAAAGTTTT
Found at i:27947566 original size:59 final size:59
Alignment explanation
Indices: 27947503--27947862 Score: 334
Period size: 59 Copynumber: 6.1 Consensus size: 59
27947493 AATCAGGATC
* *
27947503 AAAAACGGAATTTTTGGACA-TTCGGGGGT-AAAATGGTAATTTTTGAAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAAT-GTAATTTTTGAAAGTTTTGGGGTT
* * * * * * *
27947562 AAAAATGGAGTTTTTAGAAGTTTAGGGGTAAAAATATAATTTTAGAAATTTTTGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAGTTTTGGGGTT
* * * ** *
27947621 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGCTTCGTAGTC
1 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAGTTTTGGGGTT
** * *
27947680 AAAAATGGAATTTTTAAAAGTTCGAGGGTAAAAAATGTAATTTTTGGAAA-TTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT-AAAAATGTAATTTTT-GAAAGTTTTGGGGTT
* * * * *
27947740 -AAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATATAATTTTTGGAAGTTTTAGGG-T
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT-AAAAATGTAATTTTTGAAAGTTTTGGGGTT
* * * * * * * *
27947798 AAAAATGTAATTTTTGTAAGTTTTGGGGTTAAAAATATAATTCTGGAGAAGTTTAGGGGTC
1 AAAAATGGAATTTTTGGAAG-TTTGGGGGTAAAAATGTAATTTTTGA-AAGTTTTGGGGTT
27947859 AAAA
1 AAAA
27947863 TATAATTTCT
Statistics
Matches: 243, Mismatches: 49, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
58 5 0.02
59 190 0.78
60 41 0.17
61 7 0.03
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAGTTTTGGGGTT
Found at i:27947883 original size:89 final size:89
Alignment explanation
Indices: 27947532--27947885 Score: 371
Period size: 89 Copynumber: 4.0 Consensus size: 89
27947522 ATTCGGGGGT
* * * * *
27947532 AAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATGGAGTTTTTAGAAGTTTAGGGGTAAAAAT
1 AAAAT-GTAATTTTTGGAAGTTTTGGGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTCAAAAT
* * *
27947597 ATAA-TTTTAGAAATTTTTGGGGTCA
65 ATAATTTTTAGAAA-GTTTAGGGTAA
* * * * **
27947622 AAAATGGAATTTTTGGAAG-TTTGGGGGTAAAAATGTAATTTTTGGAAGCTTCGTAGTCAAAA-A
1 AAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTCAAAATA
*
27947685 TGGAATTTTTA-AAAGTTCGAGGGTAA
66 T--AATTTTTAGAAAGTT-TAGGGTAA
* *
27947711 AAAATGTAATTTTTGGAAATTTTGGGGTT-AAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAAT
1 AAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTC-AAAAT
*
27947775 ATAATTTTT-GGAAGTTTTAGGGT-A
65 ATAATTTTTAGAAAG-TTTAGGGTAA
* * * *
27947799 AAAATGTAATTTTTGTAAGTTTTGGGGTTAAAAATATAATTCTGGAGAAGTTTAGGGGTCAAAAT
1 AAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATGTAATTTTTG-GAAGTTTAGGGGTCAAAAT
* *
27947864 ATAATTTCTAGACAGTTTAGGG
65 ATAATTTTTAGAAAGTTTAGGG
27947886 ACCTCCAAAG
Statistics
Matches: 219, Mismatches: 33, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
87 2 0.01
88 64 0.29
89 111 0.51
90 40 0.18
91 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (89 bp):
AAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTCAAAATA
TAATTTTTAGAAAGTTTAGGGTAA
Found at i:27948675 original size:17 final size:18
Alignment explanation
Indices: 27948646--27948679 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
27948636 TATTCCTTGT
27948646 TTTTAAGACCAGATCTGG
1 TTTTAAGACCAGATCTGG
27948664 TTTTAA-ACCAGATCTG
1 TTTTAAGACCAGATCTG
27948680 AAAGCTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (18 bp):
TTTTAAGACCAGATCTGG
Found at i:27949864 original size:16 final size:16
Alignment explanation
Indices: 27949843--27949886 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
27949833 TTACAATAAT
27949843 ATTAAAATTAAATTAA
1 ATTAAAATTAAATTAA
*
27949859 ATTAAAATTGAATTTAA
1 ATTAAAATT-AAATTAA
* *
27949876 AATAAATTTAA
1 ATTAAAATTAA
27949887 TTTCAAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTAAAATTAAATTAA
Found at i:27949875 original size:28 final size:29
Alignment explanation
Indices: 27949844--27949906 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
27949834 TACAATAATA
* *
27949844 TTAAAATTAAA-TTAAATTAAAATTGAAT
1 TTAAAATTAAATTTAAATTAAAAGTAAAT
* *
27949872 TTAAAA-TAAATTTAATTTCAAAGTAAAT
1 TTAAAATTAAATTTAAATTAAAAGTAAAT
27949900 TTAAAAT
1 TTAAAAT
27949907 GGTTTGGGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (29 bp):
TTAAAATTAAATTTAAATTAAAAGTAAAT
Found at i:27949898 original size:17 final size:16
Alignment explanation
Indices: 27949863--27949903 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
27949853 AATTAAATTA
*
27949863 AAATTGAATTTAAAAT
1 AAATTTAATTTAAAAT
*
27949879 AAATTTAATTTCAAAGT
1 AAATTTAATTT-AAAAT
27949896 AAATTTAA
1 AAATTTAA
27949904 AATGGTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (16 bp):
AAATTTAATTTAAAAT
Found at i:27950272 original size:92 final size:92
Alignment explanation
Indices: 27950157--27951121 Score: 1691
Period size: 92 Copynumber: 10.5 Consensus size: 92
27950147 GATGTCGAGG
27950157 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
27950222 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
*
27950249 CTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
* *
27950314 CAAGAGGATAGGGATTGATGTTAGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
*
27950341 CTTCATCTTGCTCTTACTACAACTTCAAAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
27950406 TAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
*
27950433 CTTCATCTT-CTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTGCAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
* *
27950497 CAAGAGGGTAGAAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
27950524 CTTCATATTGCTCTTACTACAACTTTAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
27950589 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
27950616 CTTTATCTTGCTCTTACTACAACTTCAGGGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
27950681 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
*
27950708 TTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
27950773 CAAGAGGATAGAAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* * * ** *
27950800 CTTCATCTTGCTCTTACTACAACTTTAGATAGATAAAGACTTGCTAGCCAACTTTTTTGCAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
* *
27950865 TAAGAGGATAAGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
27950892 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
27950957 CAAGAGGATAGGAA-TGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
27950983 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
27951048 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* * *
27951075 TTTCATCTTGCTCTTACTACAACTTTAGTGAGATAAAGACTTGCTAT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTAT
27951122 TTGATCTGAT
Statistics
Matches: 824, Mismatches: 47, Indels: 4
0.94 0.05 0.00
Matches are distributed among these distances:
91 176 0.21
92 648 0.79
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (92 bp):
CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
CAAGAGGATAGGAATTGATGTTTGAAA
Found at i:27950977 original size:367 final size:367
Alignment explanation
Indices: 27950157--27951121 Score: 1718
Period size: 367 Copynumber: 2.6 Consensus size: 367
27950147 GATGTCGAGG
27950157 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
27950222 CAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAAG
66 CAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAG
* * *
27950287 ACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGGATTGATGTTAGAAACTTCATCTTGC
131 ACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAATTTCATCTTGC
* *
27950352 TCTTACTACAACTTCAAAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTTAAGAGGATAG
196 TCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAG
* *
27950417 GAATTGATGTTTGAAACTTCATCTTCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCA
261 AAATTGATGTTTGAAACTTCATCTTCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTAGCCA
*
27950482 ACTTTACTGCAACTTCAAGAGGGTAGAAATTGATGTTTGAAA
326 ACTTTACTGCAACTTCAAGAGGATAGAAATTGATGTTTGAAA
* *
27950524 CTTCATATTGCTCTTACTACAACTTTAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
* *
27950589 CAAGAGGATAGGAATTGATGTTTGAAACTTTATCTTGCTCTTACTACAACTTCAGGGAGATAAAG
66 CAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAG
27950654 ACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAATTTCATCTTGC
131 ACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAATTTCATCTTGC
27950719 TCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAG
196 TCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAG
* *
27950784 AAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTTAGATAGATAAAGACTTGCTAGCC
261 AAATTGATGTTTGAAACTTCATCTT-CTCTTACTACAACTTCAGAGAGATAAAGACTTGCTAGCC
** *
27950849 AACTTTTTTGCAACTTTAAGAGGATA-AGAATTGATGTTTGAAA
325 AACTTTACTGCAACTTCAAGAGGATAGA-AATTGATGTTTGAAA
27950892 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
27950957 CAAGAGGATAGGAA-TGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAG
66 CAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAG
27951021 ACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAATTTCATCTTGC
131 ACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAATTTCATCTTGC
* *
27951086 TCTTACTACAACTTTAGTGAGATAAAGACTTGCTAT
196 TCTTACTACAACTTCAGAGAGATAAAGACTTGCTAT
27951122 TTGATCTGAT
Statistics
Matches: 572, Mismatches: 24, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
367 422 0.74
368 150 0.26
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (367 bp):
CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
CAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAG
ACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAATTTCATCTTGC
TCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAG
AAATTGATGTTTGAAACTTCATCTTCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTAGCCA
ACTTTACTGCAACTTCAAGAGGATAGAAATTGATGTTTGAAA
Found at i:27951286 original size:49 final size:49
Alignment explanation
Indices: 27951204--27951471 Score: 226
Period size: 49 Copynumber: 5.4 Consensus size: 49
27951194 ACCGAGTCAT
* * * *
27951204 CGTTGCGACTTAAACCTTTCCCTTCAAAT-CTTCT-TGGTACTGGATCCGC
1 CGTTGCGTCTTAGATCTTTCCCTTC--ATGCTTCTGAGGTACTGGATCCGC
* *
27951253 CGTTGCAGTCTTAGATCTTTCCCTTCATGCTTCTGAGGTACACGG-TTCGC
1 CGTTGC-GTCTTAGATCTTTCCCTTCATGCTTCTGAGGTAC-TGGATCCGC
* * * ** *
27951303 CGTTTCGACTTAGACCTTTCCCCTTTGTG-TT-TGCGGTACTGGATCCGC
1 CGTTGCGTCTTAGATCTTT-CCCTTCATGCTTCTGAGGTACTGGATCCGC
* * **
27951351 CATTGCGATCTTAGATCTTTCCCGTCATGCTTCTGAGGTACACGATCCGC
1 CGTTGCG-TCTTAGATCTTTCCCTTCATGCTTCTGAGGTACTGGATCCGC
* * * * *
27951401 CGTTGCGACTTAGACCTTTCCCTT-TTG-TGTTTGTGGTACTGGATCCGC
1 CGTTGCGTCTTAGATCTTTCCCTTCATGCT-TCTGAGGTACTGGATCCGC
27951449 CGTTGCGGTCTTAGATCTTTCCC
1 CGTTGC-GTCTTAGATCTTTCCC
27951472 GTTATATTTC
Statistics
Matches: 173, Mismatches: 35, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
47 3 0.02
48 47 0.27
49 64 0.37
50 57 0.33
51 2 0.01
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (49 bp):
CGTTGCGTCTTAGATCTTTCCCTTCATGCTTCTGAGGTACTGGATCCGC
Found at i:27951347 original size:98 final size:97
Alignment explanation
Indices: 27951239--27951473 Score: 380
Period size: 98 Copynumber: 2.4 Consensus size: 97
27951229 AAATCTTCTT
* * *
27951239 GGTACTGGATCCGCCGTTGCAGTCTTAGATCTTTCCCTTCATGCTTCTGAGGTACACGGTTCGCC
1 GGTACTGGATCCGCCGTTGC-GTCTTAGATCTTTCCCGTCATGCTTCTGAGGTACACGATCCGCC
*
27951304 GTTTCGACTTAGACCTTTCCCCTTTGTGTTTGC
65 GTTGCGACTTAGACCTTTCCCCTTTGTGTTTGC
*
27951337 GGTACTGGATCCGCCATTGCGATCTTAGATCTTTCCCGTCATGCTTCTGAGGTACACGATCCGCC
1 GGTACTGGATCCGCCGTTGCG-TCTTAGATCTTTCCCGTCATGCTTCTGAGGTACACGATCCGCC
* *
27951402 GTTGCGACTTAGACCTTTCCCTTTTGTGTTTGT
65 GTTGCGACTTAGACCTTTCCCCTTTGTGTTTGC
27951435 GGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGT
1 GGTACTGGATCCGCCGTTGC-GTCTTAGATCTTTCCCGT
27951474 TATATTTCAT
Statistics
Matches: 127, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
97 1 0.01
98 125 0.98
99 1 0.01
ACGTcount: A:0.13, C:0.28, G:0.23, T:0.36
Consensus pattern (97 bp):
GGTACTGGATCCGCCGTTGCGTCTTAGATCTTTCCCGTCATGCTTCTGAGGTACACGATCCGCCG
TTGCGACTTAGACCTTTCCCCTTTGTGTTTGC
Found at i:27963178 original size:58 final size:56
Alignment explanation
Indices: 27963047--27963185 Score: 147
Period size: 58 Copynumber: 2.4 Consensus size: 56
27963037 GGACTCTCGA
* ** *
27963047 GGGGTAAAATGGTAA-TTTTAGGAAAATTTGGGTTCAAAATGAAATTTTAGAAATTC
1 GGGGTAAAATGGTAATTTTTA-GAAAAATTAAGATCAAAATGAAATTTTAGAAATTC
*** * *
27963103 GAGGGTAAAACAATAATTTTTAGAAAAATTAAGATCAAAAATGGAATTTTTAGACATTC
1 G-GGGTAAAATGGTAATTTTTAGAAAAATTAAGATC-AAAAT-GAAATTTTAGAAATTC
27963162 GGGGTAAAATGGTAATTTTT-GAAA
1 GGGGTAAAATGGTAATTTTTAGAAA
27963186 GTTTTGGAGT
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
56 1 0.01
57 25 0.37
58 26 0.39
59 15 0.22
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.32
Consensus pattern (56 bp):
GGGGTAAAATGGTAATTTTTAGAAAAATTAAGATCAAAATGAAATTTTAGAAATTC
Found at i:27963199 original size:58 final size:56
Alignment explanation
Indices: 27963047--27963387 Score: 214
Period size: 59 Copynumber: 5.8 Consensus size: 56
27963037 GGACTCTCGA
* * *
27963047 GGGGTAAAATGGTAATTTTAGGAAAATTTGGGTTC-AAAAT-GAAATTTTAGAAA-TTC
1 GGGGTAAAAT-GTAATTTT-TGAAATTTTGGG-TCAAAAATGGAATTTTTAGAAAGTTC
** * ** * *
27963103 GAGGGTAAAACAATAATTTTTAGAAAAATTAAGATCAAAAATGGAATTTTTAGACA-TTC
1 G-GGGTAAAA-TGTAATTTTT-G-AAATTTTGGGTCAAAAATGGAATTTTTAGAAAGTTC
* *
27963162 GGGGTAAAATGGTAATTTTTGAAAGTTTTGGAGTCAAAAATGGAGTTTTT-GAAAGTTTA
1 GGGGTAAAAT-GTAATTTTTGAAA-TTTTGG-GTCAAAAATGGAATTTTTAGAAAG-TTC
* * *
27963221 GTGGTAAAAATGTAATTTTTGGAATTTTCGGGGTCAAAAATGGAATTTTT-GGAAGTTC
1 GGGGT-AAAATGTAATTTTTGAAATTTT--GGGTCAAAAATGGAATTTTTAGAAAGTTC
* * *
27963279 GAGGGTGAAAATGTAATTTCTGGAAATTTTGGGTC-AAAATGTAATTTTCTA-AAAGTGTT
1 G-GGGT-AAAATGTAATTT-TTGAAATTTTGGGTCAAAAATGGAATTTT-TAGAAAGT-TC
* * * *
27963338 GGGGTCAAAAATATAATTTTTGTAAGTTTTAAGGT-AAAAATGTAATTTTT
1 GGGGT--AAAATGTAATTTTTG-AAATTTT-GGGTCAAAAATGGAATTTTT
27963388 GTAAGTTTCA
Statistics
Matches: 228, Mismatches: 34, Indels: 43
0.75 0.11 0.14
Matches are distributed among these distances:
56 4 0.02
57 37 0.16
58 67 0.29
59 89 0.39
60 31 0.14
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.36
Consensus pattern (56 bp):
GGGGTAAAATGTAATTTTTGAAATTTTGGGTCAAAAATGGAATTTTTAGAAAGTTC
Found at i:27963213 original size:30 final size:29
Alignment explanation
Indices: 27963137--27963395 Score: 158
Period size: 29 Copynumber: 8.9 Consensus size: 29
27963127 AAAATTAAGA
* **
27963137 TCAAAAATGGAATTTTTAGACA-TTCGGGG
1 TCAAAAATGGAATTTTT-GAAAGTTTTGGG
27963166 T--AAAATGGTAATTTTTGAAAGTTTTGGAG
1 TCAAAAATGG-AATTTTTGAAAGTTTTGG-G
* *
27963195 TCAAAAATGGAGTTTTTGAAAGTTTAGTGG
1 TCAAAAATGGAATTTTTGAAAGTTTTG-GG
* *
27963225 T-AAAAATGTAATTTTTGGAA-TTTTCGGGG
1 TCAAAAATGGAATTTTTGAAAGTTTT--GGG
* **
27963254 TCAAAAATGGAATTTTTGGAAGTTCGAGGG
1 TCAAAAATGGAATTTTTGAAAGTT-TTGGG
* * *
27963284 T-GAAAATGTAATTTCTGGAAA-TTTTGGG
1 TCAAAAATGGAATTT-TTGAAAGTTTTGGG
* * *
27963312 TC-AAAATGTAATTTTCTAAAAGTGTTGGGG
1 TCAAAAATGGAATTTT-TGAAAGT-TTTGGG
** * *
27963342 TCAAAAATATAATTTTTGTAAGTTTTAAGG
1 TCAAAAATGGAATTTTTGAAAGTTTT-GGG
* *
27963372 T-AAAAATGTAATTTTTGTAAGTTT
1 TCAAAAATGGAATTTTTGAAAGTTT
27963396 CAGAGTCAAT
Statistics
Matches: 185, Mismatches: 27, Indels: 36
0.75 0.11 0.15
Matches are distributed among these distances:
27 11 0.06
28 33 0.18
29 60 0.32
30 59 0.32
31 22 0.12
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (29 bp):
TCAAAAATGGAATTTTTGAAAGTTTTGGG
Found at i:27963443 original size:30 final size:29
Alignment explanation
Indices: 27963162--27963457 Score: 203
Period size: 30 Copynumber: 10.1 Consensus size: 29
27963152 TTAGACATTC
* *
27963162 GGGGT-AAAATGGTAATTTTTGAAAGTTTT
1 GGGGTCAAAAT-GTAATTTTTGGAAGTTTA
* * * *
27963191 GGAGTCAAAAATGGAGTTTTTGAAAGTTTA
1 GGGGTC-AAAATGTAATTTTTGGAAGTTTA
* * * *
27963221 GTGGTAAAAATGTAATTTTTGGAATTTTC
1 GGGGTCAAAATGTAATTTTTGGAAGTTTA
* *
27963250 GGGGTCAAAAATGGAATTTTTGGAAG-TTC
1 GGGGTC-AAAATGTAATTTTTGGAAGTTTA
* * *
27963279 GAGGGTGAAAATGTAATTTCTGGAAATTT-
1 G-GGGTCAAAATGTAATTTTTGGAAGTTTA
* **
27963308 TGGGTCAAAATGTAATTTTCTAAAAGTGTT-
1 GGGGTCAAAATGTAATTTT-TGGAAGT-TTA
* *
27963338 GGGGTCAAAAATATAATTTTTGTAAGTTTTA
1 GGGGTC-AAAATGTAATTTTTGGAAG-TTTA
* * *
27963369 -AGGTAAAAATGTAATTTTTGTAAGTTTCA
1 GGGGTCAAAATGTAATTTTTGGAAGTTT-A
* *
27963398 -GAGTC--AATGTAATTTTGGAGAAGTTTA
1 GGGGTCAAAATGTAATTTTTG-GAAGTTTA
*
27963425 GGGGTCAAAATATAATTTTTGGACAGTTTA
1 GGGGTCAAAATGTAATTTTTGGA-AGTTTA
27963455 GGG
1 GGG
27963458 ACCTCAAAAG
Statistics
Matches: 210, Mismatches: 41, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
27 13 0.06
28 29 0.14
29 73 0.35
30 77 0.37
31 18 0.09
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTTGGAAGTTTA
Found at i:27965115 original size:11 final size:11
Alignment explanation
Indices: 27965099--27965151 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
27965089 TTACAATAAT
27965099 ATTAAATTGAA
1 ATTAAATTGAA
27965110 ATTAAATTGAA
1 ATTAAATTGAA
*
27965121 ATTGAAATTAAA
1 ATT-AAATTGAA
* *
27965133 ATTGAATTTAA
1 ATTAAATTGAA
*
27965144 AATAAATT
1 ATTAAATT
27965152 TAATTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 26 0.72
12 10 0.28
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
ATTAAATTGAA
Found at i:27965122 original size:6 final size:6
Alignment explanation
Indices: 27965102--27965138 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
27965092 CAATAATATT
*
27965102 AAATTG AAATT- AAATTG AAATTG AAATTA AAATTG AA
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AA
27965139 TTTAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (6 bp):
AAATTG
Found at i:27965122 original size:17 final size:17
Alignment explanation
Indices: 27965102--27965151 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
27965092 CAATAATATT
27965102 AAATTGAAATTAAATTG
1 AAATTGAAATTAAATTG
27965119 AAATTGAAATTAAAATTG
1 AAATTGAAATT-AAATTG
* *
27965137 -AATTTAAAATAAATT
1 AAATTGAAATTAAATT
27965152 TAATTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 5 0.17
17 19 0.63
18 6 0.20
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
AAATTGAAATTAAATTG
Found at i:27965134 original size:12 final size:12
Alignment explanation
Indices: 27965102--27965146 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
27965092 CAATAATATT
*
27965102 AAATTGAAATT-
1 AAATTAAAATTG
*
27965113 AAATTGAAATTG
1 AAATTAAAATTG
27965125 AAATTAAAATTG
1 AAATTAAAATTG
*
27965137 AATTTAAAAT
1 AAATTAAAAT
27965147 AAATTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (12 bp):
AAATTAAAATTG
Found at i:27965146 original size:18 final size:17
Alignment explanation
Indices: 27965099--27965154 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
27965089 TTACAATAAT
27965099 ATTAAATTGAAATT-AA
1 ATTAAATTGAAATTAAA
27965115 ATTGAAATTGAAATTAAA
1 ATT-AAATTGAAATTAAA
* * *
27965133 ATTGAATTTAAAATAAA
1 ATTAAATTGAAATTAAA
*
27965150 TTTAA
1 ATTAA
27965155 TTTCAAAGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 3 0.09
17 25 0.76
18 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (17 bp):
ATTAAATTGAAATTAAA
Found at i:27965166 original size:17 final size:16
Alignment explanation
Indices: 27965131--27965171 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
27965121 ATTGAAATTA
*
27965131 AAATTGAATTTAAAAT
1 AAATTTAATTTAAAAT
*
27965147 AAATTTAATTTCAAAGT
1 AAATTTAATTT-AAAAT
27965164 AAATTTAA
1 AAATTTAA
27965172 AATGGTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (16 bp):
AAATTTAATTTAAAAT
Found at i:27971073 original size:36 final size:35
Alignment explanation
Indices: 27971031--27971135 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 35
27971021 TGGATGTGTG
*
27971031 GGTATGTTATTCACGCCATGTGATAGTAAATATGT
1 GGTATGTTATTCATGCCATGTGATAGTAAATATGT
* * *
27971066 GGTTATGTTATTCATGCCATGAGACACTAAATATGT
1 GG-TATGTTATTCATGCCATGTGATAGTAAATATGT
* * *
27971102 GAGTATGTTATTCATGTCATATGATAGTGAATAT
1 G-GTATGTTATTCATGCCATGTGATAGTAAATAT
27971136 ATTTTGCTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
35 2 0.03
36 55 0.95
37 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (35 bp):
GGTATGTTATTCATGCCATGTGATAGTAAATATGT
Found at i:27971695 original size:10 final size:10
Alignment explanation
Indices: 27971680--27971855 Score: 79
Period size: 10 Copynumber: 17.8 Consensus size: 10
27971670 CTGAAATATT
27971680 AATGTGATTA
1 AATGTGATTA
*
27971690 AATGTGACTA
1 AATGTGATTA
27971700 AATGTGATTA
1 AATGTGATTA
27971710 ATATGTGATGTGA
1 A-ATGTGAT-T-A
** *
27971723 TAA-ACG-CTA
1 -AATGTGATTA
*
27971732 AA-AT-ATT-
1 AATGTGATTA
27971739 AATGTGATTA
1 AATGTGATTA
*
27971749 TATGTGATTA
1 AATGTGATTA
*
27971759 AATGTGACTA
1 AATGTGATTA
27971769 AATGTGATTA
1 AATGTGATTA
27971779 ATATGTGATGTGATA
1 A-ATGTGA--T--TA
27971794 AATGT--TTA
1 AATGTGATTA
27971802 AA--T-ATT-
1 AATGTGATTA
* *
27971808 CATGTGACT-
1 AATGTGATTA
*
27971817 AATATGATTA
1 AATGTGATTA
*
27971827 AATGTGACTA
1 AATGTGATTA
27971837 AATGTGATTA
1 AATGTGATTA
27971847 ATATGTGAT
1 A-ATGTGAT
27971856 GTGATAAATG
Statistics
Matches: 127, Mismatches: 20, Indels: 37
0.69 0.11 0.20
Matches are distributed among these distances:
6 2 0.02
7 4 0.03
8 10 0.08
9 12 0.09
10 66 0.52
11 20 0.16
12 2 0.02
13 3 0.02
14 5 0.04
15 3 0.02
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (10 bp):
AATGTGATTA
Found at i:27971695 original size:33 final size:33
Alignment explanation
Indices: 27971658--27971756 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 33
27971648 TGAATATGTG
27971658 ATGTGATAAACGCTGAAATATTAATGTGATTAA
1 ATGTGATAAACGCTGAAATATTAATGTGATTAA
* * *
27971691 ATGTGACTAAATG-TG----ATTAATATG--T-G
1 ATGTGA-TAAACGCTGAAATATTAATGTGATTAA
* *
27971717 ATGTGATAAACGCTAAAATATTAATGTGATTAT
1 ATGTGATAAACGCTGAAATATTAATGTGATTAA
27971750 ATGTGAT
1 ATGTGAT
27971757 TAAATGTGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
25 5 0.10
26 7 0.14
27 1 0.02
29 8 0.16
30 8 0.16
32 1 0.02
33 15 0.30
34 5 0.10
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.36
Consensus pattern (33 bp):
ATGTGATAAACGCTGAAATATTAATGTGATTAA
Found at i:27971704 original size:59 final size:59
Alignment explanation
Indices: 27971639--27971944 Score: 272
Period size: 68 Copynumber: 4.9 Consensus size: 59
27971629 TTCATATGAT
* *
27971639 TAAATGTGATGAATATGTGATGTGATAAACGCTGAAATATTAATGTGATTAAATGTGAC
1 TAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATGTGATTAAATGTGAC
* *
27971698 TAAATGTGATTAATATGTGATGTGATAAACGCTAAAATATTAATGTGATTATATGTGATTAAATG
1 TAAATGTGATTAATATGTGATGTGATAAATGCT----GA--AA--T-ATTA-ATGTGATTAAATG
27971763 TGAC
56 TGAC
* * *
27971767 TAAATGTGATTAATATGTGATGTGATAAATGTTTAAATATTCATGTGACTAATATGATTAAATGT
1 TAAATGTGATTAATATGTGATGTGATAAATG-CTGAA-A-T-A--T---TAATGTGATTAAATGT
27971832 GAC
57 GAC
* * * *
27971835 TAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACT-AATGTGAT
1 TAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATGTGATTAAATGTGAC
* * * * * * *
27971893 TATATGTGATTAATATGTGTTGTGTTAAATGCTTAAGTACTGATGTGATTAA
1 TAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATGTGATTAA
27971945 TATGATTAAT
Statistics
Matches: 207, Mismatches: 22, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
58 48 0.23
59 40 0.19
62 1 0.00
63 1 0.00
64 4 0.02
65 4 0.02
66 3 0.01
67 5 0.02
68 51 0.25
69 49 0.24
70 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (59 bp):
TAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATGTGATTAAATGTGAC
Found at i:27971812 original size:23 final size:23
Alignment explanation
Indices: 27971760--27971886 Score: 88
Period size: 25 Copynumber: 5.4 Consensus size: 23
27971750 ATGTGATTAA
*
27971760 ATGTGACTAAATGTGATTAATATGTG
1 ATGTGACTAAATGT--TTAATAT-TC
27971786 ATGTGA-TAAATGTTTAAATATTC
1 ATGTGACTAAATGTTT-AATATTC
*
27971809 ATGTGACTAATATGATT-A-A---
1 ATGTGACTAA-ATGTTTAATATTC
*
27971828 ATGTGACTAAATGTGATTAATATGTG
1 ATGTGACTAAATGT--TTAATAT-TC
*
27971854 ATGTGA-TAAATGTTGAAATATTC
1 ATGTGACTAAATGTT-TAATATTC
27971877 ATGTGACTAA
1 ATGTGACTAA
27971887 TGTGATTATA
Statistics
Matches: 83, Mismatches: 5, Indels: 28
0.72 0.04 0.24
Matches are distributed among these distances:
18 3 0.04
19 10 0.12
20 2 0.02
21 1 0.01
22 2 0.02
23 18 0.22
24 16 0.19
25 19 0.23
26 12 0.14
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.39
Consensus pattern (23 bp):
ATGTGACTAAATGTTTAATATTC
Found at i:27971862 original size:68 final size:68
Alignment explanation
Indices: 27971679--27971911 Score: 367
Period size: 68 Copynumber: 3.4 Consensus size: 68
27971669 GCTGAAATAT
* * *
27971679 TAATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAACGCTAAAATATTAATGT
1 TAATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGT
*
27971744 GAT
66 GAC
*
27971747 TATATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTTAAATATTCATG
1 TA-ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATG
27971812 TGAC
65 TGAC
* *
27971816 TAATATGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGT
1 TAATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGT
27971881 GAC
66 GAC
* *
27971884 TAATGTGATTATATGTGATTAATATGTG
1 TAATGTGATTAAATGTGACTAA-ATGTG
27971912 TTGTGTTAAA
Statistics
Matches: 153, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
68 85 0.56
69 68 0.44
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.39
Consensus pattern (68 bp):
TAATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGT
GAC
Found at i:27971897 original size:23 final size:25
Alignment explanation
Indices: 27971691--27971894 Score: 126
Period size: 23 Copynumber: 8.8 Consensus size: 25
27971681 ATGTGATTAA
*
27971691 ATGTGACTAAATGTGATTAATATGTG
1 ATGTGACTAAATGTGATTAATAT-TC
* * *
27971717 ATGTGA-TAAACGCT-A-AAATATTA
1 ATGTGACTAAATG-TGATTAATATTC
* *
27971740 ATGTGATTATATGTGATT-A-A---
1 ATGTGACTAAATGTGATTAATATTC
*
27971760 ATGTGACTAAATGTGATTAATATGTG
1 ATGTGACTAAATGTGATTAATAT-TC
27971786 ATGTGA-TAAATGT--TTAAATATTC
1 ATGTGACTAAATGTGATT-AATATTC
*
27971809 ATGTGACT-AATATGATT-A-A---
1 ATGTGACTAAATGTGATTAATATTC
*
27971828 ATGTGACTAAATGTGATTAATATGTG
1 ATGTGACTAAATGTGATTAATAT-TC
27971854 ATGTGA-TAAATGTTGA--AATATTC
1 ATGTGACTAAATG-TGATTAATATTC
27971877 ATGTGACT-AATGTGATTA
1 ATGTGACTAAATGTGATTA
27971895 TATGTGATTA
Statistics
Matches: 141, Mismatches: 12, Indels: 52
0.69 0.06 0.25
Matches are distributed among these distances:
19 8 0.06
20 24 0.17
21 2 0.01
22 6 0.04
23 34 0.24
24 24 0.17
25 21 0.15
26 22 0.16
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (25 bp):
ATGTGACTAAATGTGATTAATATTC
Found at i:27979545 original size:13 final size:13
Alignment explanation
Indices: 27979527--27979553 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27979517 AATATCAAGG
27979527 AGTGAAGAAATTA
1 AGTGAAGAAATTA
27979540 AGTGAAGAAATTA
1 AGTGAAGAAATTA
27979553 A
1 A
27979554 ATTCTGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (13 bp):
AGTGAAGAAATTA
Found at i:28004324 original size:77 final size:78
Alignment explanation
Indices: 28004239--28004383 Score: 256
Period size: 77 Copynumber: 1.9 Consensus size: 78
28004229 TTTTCCAAAA
28004239 TTTTGATAACTCTTAATATTAATTATAAATTAAA-TTTATAATTTATATTAATTATTATCAAAAG
1 TTTTGATAACTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATCAAAAG
28004303 TTTTCATTTAAGG
66 TTTTCATTTAAGG
* * *
28004316 TTTTGATAATTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAGTTATTATCAAGAG
1 TTTTGATAACTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATCAAAAG
28004381 TTT
66 TTT
28004384 GAGATTAGAT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
77 33 0.52
78 31 0.48
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (78 bp):
TTTTGATAACTCTTAATATTAATTATAAATTAAATTTTATAATTTATATTAATTATTATCAAAAG
TTTTCATTTAAGG
Found at i:28004925 original size:16 final size:16
Alignment explanation
Indices: 28004906--28004954 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
28004896 CGGCTGAGTT
*
28004906 ATGCTGCTGCTAAGTC
1 ATGCTGCTGCTAAGCC
* *
28004922 ATGCTGTTGCTGAGCC
1 ATGCTGCTGCTAAGCC
* *
28004938 GTGCTGCTGCCAAGCC
1 ATGCTGCTGCTAAGCC
28004954 A
1 A
28004955 CACCTAGGTC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (16 bp):
ATGCTGCTGCTAAGCC
Found at i:28006622 original size:32 final size:32
Alignment explanation
Indices: 28006582--28006645 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
28006572 TGCTTAAGTA
* *
28006582 CCAAGCTCTTCAATGTCCAATCTTATACATGT
1 CCAAGCTCTTCAATGTCCAATCCTAGACATGT
28006614 CCAAGCTCTTCAATGTCCAATCCTAGACATGT
1 CCAAGCTCTTCAATGTCCAATCCTAGACATGT
28006646 ACATATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.31
Consensus pattern (32 bp):
CCAAGCTCTTCAATGTCCAATCCTAGACATGT
Found at i:28006629 original size:16 final size:16
Alignment explanation
Indices: 28006582--28006633 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
28006572 TGCTTAAGTA
28006582 CCAAGCTCTTCAATGT
1 CCAAGCTCTTCAATGT
*
28006598 CCAA--TCTTATACATGT
1 CCAAGCTCTT-CA-ATGT
28006614 CCAAGCTCTTCAATGT
1 CCAAGCTCTTCAATGT
28006630 CCAA
1 CCAA
28006634 TCCTAGACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
15 1 0.03
16 20 0.67
17 1 0.03
18 4 0.13
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (16 bp):
CCAAGCTCTTCAATGT
Found at i:28009059 original size:24 final size:24
Alignment explanation
Indices: 28009023--28009073 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
28009013 GTATACTAGT
*
28009023 TAACCATTTTGGGATCGTAAGAGC
1 TAACCATTCTGGGATCGTAAGAGC
* **
28009047 TAACCATTCTGGGCTCGTGTGAGC
1 TAACCATTCTGGGATCGTAAGAGC
28009071 TAA
1 TAA
28009074 AGTTGTCTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (24 bp):
TAACCATTCTGGGATCGTAAGAGC
Found at i:28012027 original size:23 final size:25
Alignment explanation
Indices: 28012001--28012046 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28011991 CCAATTAGGG
28012001 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
28012024 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
28012047 TAGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:28013140 original size:19 final size:18
Alignment explanation
Indices: 28013094--28013157 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
28013084 TATTACTTTA
28013094 TCCATTTT--TTTATTATT
1 TCCATTTTAATTTATT-TT
*
28013111 TGCATTTTTAATTTAATTTT
1 TCCA-TTTTAATTT-ATTTT
*
28013131 TCTATTTTAATTTATTTT
1 TCCATTTTAATTTATTTT
28013149 TCCATTTTA
1 TCCATTTTA
28013158 TTTGCTTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.08
18 17 0.44
19 9 0.23
20 7 0.18
21 3 0.08
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (18 bp):
TCCATTTTAATTTATTTT
Found at i:28016988 original size:9 final size:9
Alignment explanation
Indices: 28016974--28017031 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 9
28016964 TTTATTGTTT
28016974 AGAAAAAAA
1 AGAAAAAAA
28016983 AGAAAAAAA
1 AGAAAAAAA
*
28016992 TTGAAAAAAAA
1 -AG-AAAAAAA
28017003 TTGAGAAAAAAA
1 ---AGAAAAAAA
28017015 AGAAAAAAA
1 AGAAAAAAA
28017024 AGACAAAA
1 AGA-AAAA
28017032 GTGTGTTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 21 0.51
10 5 0.12
11 7 0.17
12 7 0.17
13 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:28017010 original size:13 final size:11
Alignment explanation
Indices: 28016985--28017024 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
28016975 GAAAAAAAAG
28016985 AAAAAAATTGA
1 AAAAAAATTGA
28016996 AAAAAAATTGA
1 AAAAAAATTGA
*
28017007 GAAAAAAA-AGA
1 -AAAAAAATTGA
28017018 AAAAAAA
1 AAAAAAA
28017025 GACAAAAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 7 0.26
11 13 0.48
12 7 0.26
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:28017031 original size:11 final size:10
Alignment explanation
Indices: 28016976--28017024 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
28016966 TATTGTTTAG
28016976 AAAAAAAAGA
1 AAAAAAAAGA
**
28016986 AAAAAATTGA
1 AAAAAAAAGA
*
28016996 AAAAAAATTGA
1 AAAAAAA-AGA
28017007 GAAAAAAAAGA
1 -AAAAAAAAGA
28017018 AAAAAAA
1 AAAAAAA
28017025 GACAAAAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 21 0.64
11 5 0.15
12 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:28018005 original size:34 final size:33
Alignment explanation
Indices: 28017940--28018010 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
28017930 GACATAAGAC
* * **
28017940 TTTATTTTTTAGGATTATTATTATATTGTTTATA
1 TTTATCTTTTAGGATTATAATTATAGAGTTTA-A
28017974 TTTATCTTTTAGGATTTATAATT-TAGAGTTTAA
1 TTTATCTTTTAGGA-TTATAATTATAGAGTTTAA
28018007 TTTA
1 TTTA
28018011 GATCCAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 5 0.16
34 20 0.62
35 7 0.22
ACGTcount: A:0.28, C:0.01, G:0.10, T:0.61
Consensus pattern (33 bp):
TTTATCTTTTAGGATTATAATTATAGAGTTTAA
Found at i:28018065 original size:25 final size:23
Alignment explanation
Indices: 28018024--28018069 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
28018014 CCAATTAGGG
28018024 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
28018047 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
28018070 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Found at i:28021430 original size:78 final size:77
Alignment explanation
Indices: 28021342--28021493 Score: 268
Period size: 78 Copynumber: 2.0 Consensus size: 77
28021332 ATCTAATCTC
28021342 AAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATATTAAGAATTATCA
1 AAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATATTAAGAATTATCA
28021407 ACACTTTAAATGA
66 A-ACTTTAAATGA
* *
28021420 AAACTTTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATATTAAGAGTTATCA
1 AAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATATTAAGAATTATCA
*
28021485 AATTTTAAA
66 AACTTTAAA
28021494 AAAAATAAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 7 0.10
78 64 0.90
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (77 bp):
AAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATATTAAGAATTATCA
AACTTTAAATGA
Found at i:28021764 original size:26 final size:25
Alignment explanation
Indices: 28021725--28021773 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
28021715 TTACCAAAAT
28021725 TTTGAAAAAGTAAATAAAATAGATAA
1 TTTGAAAAAGTAAATAAAA-AGATAA
28021751 TTTGAATAAA-TAAATAAAAAGAT
1 TTTGAA-AAAGTAAATAAAAAGAT
28021774 TAGTTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 15 0.68
27 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (25 bp):
TTTGAAAAAGTAAATAAAAAGATAA
Found at i:28023046 original size:20 final size:19
Alignment explanation
Indices: 28023021--28023067 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28023011 TGATGTTCAG
28023021 AAAAAGAGAAATGAAAAAAA
1 AAAAAGAGAAA-GAAAAAAA
* *
28023041 AAAAAGAGAGAGAGAAAAA
1 AAAAAGAGAAAGAAAAAAA
*
28023060 AAAGAGAG
1 AAAAAGAG
28023068 CATATGTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (19 bp):
AAAAAGAGAAAGAAAAAAA
Found at i:28024686 original size:54 final size:54
Alignment explanation
Indices: 28024604--28024712 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
28024594 TTCAGGTACG
28024604 AAATTTCGAGGACGAAAGGGAAGAGAGTTGTAACATCTCGATTTTAGTGGTGTA
1 AAATTTCGAGGACGAAAGGGAAGAGAGTTGTAACATCTCGATTTTAGTGGTGTA
*
28024658 AAATTTCGAGGACGAAAGGGAGGAGAGTTGTAACATCTCGATTTTAGTGGTGTA
1 AAATTTCGAGGACGAAAGGGAAGAGAGTTGTAACATCTCGATTTTAGTGGTGTA
28024712 A
1 A
28024713 GGAACAATGG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (54 bp):
AAATTTCGAGGACGAAAGGGAAGAGAGTTGTAACATCTCGATTTTAGTGGTGTA
Found at i:28026427 original size:21 final size:19
Alignment explanation
Indices: 28026403--28026443 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
28026393 ATATCCTAAG
28026403 ATGATCTTTTGTAATTGTAGT
1 ATGATCTTTTG-AATTG-AGT
*
28026424 ATGATGTTTTGAATTGAGT
1 ATGATCTTTTGAATTGAGT
28026443 A
1 A
28026444 AATCTTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (19 bp):
ATGATCTTTTGAATTGAGT
Found at i:28027737 original size:8 final size:8
Alignment explanation
Indices: 28027724--28027753 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28027714 TTATGGGTGT
28027724 TTAATTGA
1 TTAATTGA
28027732 TTAATTGA
1 TTAATTGA
28027740 TTAATTGA
1 TTAATTGA
*
28027748 TCAATT
1 TTAATT
28027754 AATCGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.50
Consensus pattern (8 bp):
TTAATTGA
Found at i:28041670 original size:58 final size:58
Alignment explanation
Indices: 28041543--28041747 Score: 165
Period size: 58 Copynumber: 3.7 Consensus size: 58
28041533 TATACCTAGT
* * *
28041543 TGTCATAGCGTCTTTTATCTACGGTCTTACATCATGTACCTTACACCTTATACCGTGC
1 TGTCATAGCGTCTTTTATCTATGGTCTTACATCATATACCTTACACCTTATACCATGC
* * * ** * *
28041601 TGCCATAGCGTCTTTTATCTATGGTCTTACGTTATATACCTTTTATCTTGTACCATG-
1 TGTCATAGCGTCTTTTATCTATGGTCTTACATCATATACCTTACACCTTATACCATGC
* * * * * **
28041658 TAGTCATGGCGTCTTTCATCCATGGTCTT-C--CAT-TA-CGT--ACCTCATACCAAAC
1 T-GTCATAGCGTCTTTTATCTATGGTCTTACATCATATACCTTACACCTTATACCATGC
* * *
28041710 TGCCATAGCGTCTTTCATCTATGGTCTTACACCATATA
1 TGTCATAGCGTCTTTTATCTATGGTCTTACATCATATA
28041748 TCGTTGTTAC
Statistics
Matches: 117, Mismatches: 24, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
51 32 0.27
52 2 0.02
53 2 0.02
54 5 0.04
55 4 0.03
57 2 0.02
58 70 0.60
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (58 bp):
TGTCATAGCGTCTTTTATCTATGGTCTTACATCATATACCTTACACCTTATACCATGC
Found at i:28042751 original size:24 final size:24
Alignment explanation
Indices: 28042724--28042774 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
28042714 GGAAACATAT
28042724 ATATATATATTTAA-TTTTCAGAAC
1 ATATATATA-TTAATTTTTCAGAAC
* * *
28042748 ATATTTTTATTAATTTTTTAGAAC
1 ATATATATATTAATTTTTCAGAAC
28042772 ATA
1 ATA
28042775 CACTAACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (24 bp):
ATATATATATTAATTTTTCAGAAC
Found at i:28043087 original size:31 final size:30
Alignment explanation
Indices: 28043042--28043170 Score: 115
Period size: 31 Copynumber: 4.2 Consensus size: 30
28043032 AACTATACTA
*
28043042 TTAGTCATTGAACTATGAATAAATTTTCATT
1 TTAGTCATTGAACTAT-AAAAAATTTTCATT
*
28043073 TTAGTCACTT-AACTA-AAGAAAA-TTACAATT
1 TTAGTCA-TTGAACTATAA-AAAATTTTC-ATT
28043103 TTA-TCATTGAACTATTAAAAAATTTTCATT
1 TTAGTCATTGAACTA-TAAAAAATTTTCATT
* *
28043133 TAAGTCATTGAACTATTCAAAAAAATTT-ATT
1 TTAGTCATTGAACTA-T-AAAAAATTTTCATT
*
28043164 TAAGTCA
1 TTAGTCA
28043171 CTGGATTATT
Statistics
Matches: 84, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
28 2 0.02
29 13 0.15
30 18 0.21
31 40 0.48
32 11 0.13
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (30 bp):
TTAGTCATTGAACTATAAAAAATTTTCATT
Found at i:28043893 original size:18 final size:18
Alignment explanation
Indices: 28043870--28043924 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
28043860 ATTGCTTCTC
28043870 AAAAATATTTTTGAAATA
1 AAAAATATTTTTGAAATA
*
28043888 AAAAATACTTTTGAAAT-
1 AAAAATATTTTTGAAATA
*
28043905 AAAAATATTATT-AAATA
1 AAAAATATTTTTGAAATA
28043922 AAA
1 AAA
28043925 TATTTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.12
17 13 0.39
18 16 0.48
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (18 bp):
AAAAATATTTTTGAAATA
Found at i:28059379 original size:96 final size:96
Alignment explanation
Indices: 28059209--28059389 Score: 215
Period size: 96 Copynumber: 1.9 Consensus size: 96
28059199 AGGATATTTA
** * * * *
28059209 ATTATCTCGATTTGAAGAAAGGTTGCACCTAGTGAGTTAAGGTGCACATTTTCATAACCGAAGAT
1 ATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGCAAATTTTCATAACCGAAGAT
*
28059274 AAGGAAATATTACCTCGATTAAGGGTATTCG
66 AAAGAAATATTACCTCGATTAAGGGTATTCG
* * *
28059305 ATTATTTCGGTTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGCAAAATTTTGA-AACTCGAA-
1 ATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGC-AAATTTTCATAAC-CGAAG
*
28059368 ATAAA-AGAATATTGCCTCGATT
64 ATAAAGA-AATATTACCTCGATT
28059390 TTAAAGTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
95 1 0.01
96 59 0.83
97 11 0.15
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGCAAATTTTCATAACCGAAGAT
AAAGAAATATTACCTCGATTAAGGGTATTCG
Found at i:28059661 original size:29 final size:27
Alignment explanation
Indices: 28059616--28059839 Score: 95
Period size: 29 Copynumber: 7.8 Consensus size: 27
28059606 TGGATACCTA
*
28059616 GGGGT-AAAATGTTAATTTTGATGAAATT
1 GGGGTAAAAATG-GAATTTTG-TGAAATT
28059644 GGGGTCAAAAATGGAATTTTG-GAAAGTTT
1 GGGGT-AAAAATGGAATTTTGTGAAA--TT
* *
28059673 AGGGGT-AAAATGGTAATTTTTGGTAAAATC
1 -GGGGTAAAAATGG-AA-TTTT-GTGAAATT
*
28059703 GGGGTTAAAAATGGAATTTTG-GAAAAATC
1 GGGG-TAAAAATGGAATTTTGTG--AAATT
* * *
28059732 GAGGGT-GAAATGGCAATTTTGGTAAAATCA
1 G-GGGTAAAAATGG-AATTTT-GTGAAAT-T
* * *
28059762 GGGTTAAAAATAGAA-TTT-AGAAAGTT
1 GGGGTAAAAATGGAATTTTGTGAAA-TT
*
28059788 CAGGG-ATAAAATGGTAATTTTGGTGAAATT
1 -GGGGTA-AAAATGG-AATTTT-GTGAAATT
28059818 AGGGGTAAAAATGGAATTTTGT
1 -GGGGTAAAAATGGAATTTTGT
28059840 AAAAGTTTAA
Statistics
Matches: 150, Mismatches: 19, Indels: 54
0.67 0.09 0.24
Matches are distributed among these distances:
26 4 0.03
27 13 0.09
28 26 0.17
29 50 0.33
30 41 0.27
31 13 0.09
32 3 0.02
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.32
Consensus pattern (27 bp):
GGGGTAAAAATGGAATTTTGTGAAATT
Found at i:28059718 original size:59 final size:57
Alignment explanation
Indices: 28059614--28060047 Score: 294
Period size: 59 Copynumber: 7.4 Consensus size: 57
28059604 TTTGGATACC
* * *
28059614 TAGGGGTAAAATGTTAATTTTGATGAAATTGGGGTCAAAAATGGAATTTTGGAAAGTT
1 TAGGGGTAAAATG-TAATTTTGGTAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTT
* **
28059672 TAGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAA-AA
1 TAGGGGTAAAAT-GTAA-TTTTGGTAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTT
* * * ** * *
28059730 TCGAGGGTGAAATGGCAATTTTGGTAAAATCAGGGTTAAAAATAGAA-TTTAGAAAGTT
1 TAG-GGGTAAAAT-GTAATTTTGGTAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTT
* * * *
28059788 CAGGGATAAAATGGTAATTTTGGTGAAATTAGGGG-TAAAAATGGAATTTTGTAAAAGTT
1 TAGGGGTAAAAT-GTAATTTTGGTAAAATT-GGGGTTAAAAATGGAATTTTG-GAAAGTT
* * * * *
28059847 TAAGGGTCACAATGTAATTTT--TAGAAAGTTTTTGGGTCAAAATAT--AATTTTGAAGAAGTT
1 TAGGGGT-AAAATGTAATTTTGGTA-AAA---TTGGGGTTAAAA-ATGGAATTTTGGA-AAGTT
* * * *
28059907 TAGGGGTTAAATATAATTTTGG-AGAAGTTTAGGGGTT-AAAATGTAATTTTGGAAAAGTT
1 TAGGGGTAAAATGTAATTTTGGTA-AA-ATT-GGGGTTAAAAATGGAATTTTGG-AAAGTT
* * * * *
28059966 TAGGGGTCAAAATGTAATTTTGG-AAAAGTTTGGGGGTCATAATGTAATTTTGGAAAAGCT
1 TAGGGGT-AAAATGTAATTTTGGTAAAA--TTGGGGTTAAAAATGGAATTTTGG-AAAGTT
28060026 TAGAGGGTCAAAATGTAATTTT
1 TAG-GGGT-AAAATGTAATTTT
28060048 AGAAAAGTTT
Statistics
Matches: 303, Mismatches: 46, Indels: 51
0.76 0.12 0.13
Matches are distributed among these distances:
57 42 0.14
58 59 0.19
59 107 0.35
60 69 0.23
61 24 0.08
62 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (57 bp):
TAGGGGTAAAATGTAATTTTGGTAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:28059919 original size:29 final size:29
Alignment explanation
Indices: 28059614--28060059 Score: 271
Period size: 30 Copynumber: 15.1 Consensus size: 29
28059604 TTTGGATACC
28059614 TAGGGGTAAAATGTTAATTTT-GATGAAA--T
1 TAGGGGTAAAATG-TAATTTTGGA--AAAGTT
*
28059643 T-GGGGTCAAAAATGGAATTTTGG-AAAGTT
1 TAGGGGT--AAAATGTAATTTTGGAAAAGTT
28059672 TAGGGGTAAAATGGTAATTTTTGGTAAAA---
1 TAGGGGTAAAAT-GTAA-TTTTGG-AAAAGTT
* * * *
28059701 TCGGGGTTAAAAATGGAATTTTGGAAAAATC
1 TAGGGG-T-AAAATGTAATTTTGGAAAAGTT
* * *
28059732 GA-GGGTGAAATGGCAATTTTGGTAAAA--T
1 TAGGGGTAAAAT-GTAATTTTGG-AAAAGTT
* * *
28059760 CAGGGTTAAAAATAG-AA-TTTAG-AAAGTT
1 TAGGGGT-AAAAT-GTAATTTTGGAAAAGTT
* * *
28059788 CAGGGATAAAATGGTAATTTTGGTGAAA--T
1 TAGGGGTAAAAT-GTAATTTTGG-AAAAGTT
* *
28059817 TAGGGGTAAAAATGGAATTTTGTAAAAGTT
1 TAGGGGT-AAAATGTAATTTTGGAAAAGTT
* * *
28059847 TAAGGGTCACAATGTAATTTT-TAGAAAGTT
1 TAGGGGT-AAAATGTAATTTTGGA-AAAGTT
** *
28059877 TTTGGGTCAAAATATAATTTT-GAAGAAGTT
1 TAGGGGT-AAAATGTAATTTTGGAA-AAGTT
* * *
28059907 TAGGGGTTAAATATAATTTTGGAGAAGTT
1 TAGGGGTAAAATGTAATTTTGGAAAAGTT
28059936 TAGGGGTTAAAATGTAATTTTGGAAAAGTT
1 TAGGGG-TAAAATGTAATTTTGGAAAAGTT
28059966 TAGGGGTCAAAATGTAATTTTGGAAAAGTT
1 TAGGGGT-AAAATGTAATTTTGGAAAAGTT
* * *
28059996 TGGGGGTCATAATGTAATTTTGGAAAAGCT
1 TAGGGGT-AAAATGTAATTTTGGAAAAGTT
*
28060026 TAGAGGGTCAAAATGTAATTTTAGAAAAGTT
1 TAG-GGGT-AAAATGTAATTTTGGAAAAGTT
28060057 TAG
1 TAG
28060060 AGACCTCTAA
Statistics
Matches: 338, Mismatches: 45, Indels: 66
0.75 0.10 0.15
Matches are distributed among these distances:
26 3 0.01
27 9 0.03
28 35 0.10
29 83 0.25
30 170 0.50
31 35 0.10
32 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (29 bp):
TAGGGGTAAAATGTAATTTTGGAAAAGTT
Found at i:28059948 original size:119 final size:121
Alignment explanation
Indices: 28059802--28060059 Score: 310
Period size: 119 Copynumber: 2.2 Consensus size: 121
28059792 GATAAAATGG
* * * *
28059802 TAATTTTGGTGAA-ATTAGGGGTAAAAATGGAATTTTGTAAAAGTTTAAGGGTCACAATGTAATT
1 TAATTTTGGAGAAGTTTAGGGGTAAAAATGGAATTTTGGAAAAGTTTAAGGGTCAAAATGTAA-T
** * *
28059866 TTTAG-AAAGTTTTTGGGTCAAAATATAATTTT-GAAGAAGTTTAG-GGGT-TAAATA
65 TTTAGAAAAGTTTGGGGGTCAAAATATAATTTTGGAA-AAGCTTAGAGGGTCAAAATA
* * *
28059920 TAATTTTGGAGAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATT
1 TAATTTTGGAGAAGTTTAGGGGTAAAAATGGAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATT
* * * *
28059985 TTGGAAAAGTTTGGGGGTCATAATGTAATTTTGGAAAAGCTTAGAGGGTCAAAATG
66 TTAGAAAAGTTTGGGGGTCAAAATATAATTTTGGAAAAGCTTAGAGGGTCAAAATA
* *
28060041 TAATTTTAGAAAAGTTTAG
1 TAATTTTGGAGAAGTTTAG
28060060 AGACCTCTAA
Statistics
Matches: 118, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
118 17 0.14
119 73 0.62
120 7 0.06
121 21 0.18
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (121 bp):
TAATTTTGGAGAAGTTTAGGGGTAAAAATGGAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATT
TTAGAAAAGTTTGGGGGTCAAAATATAATTTTGGAAAAGCTTAGAGGGTCAAAATA
Found at i:28061353 original size:6 final size:6
Alignment explanation
Indices: 28061335--28061400 Score: 68
Period size: 6 Copynumber: 11.0 Consensus size: 6
28061325 TTAAATTGAT
28061335 TTTAAA TTT--A TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
28061382 TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TT-TAAA
28061401 ACAAATTTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
4 6 0.12
5 2 0.04
6 32 0.62
7 6 0.12
8 6 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:28061353 original size:17 final size:17
Alignment explanation
Indices: 28061335--28061377 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
28061325 TTAAATTGAT
28061335 TTTAAATTTAT-TTAAA
1 TTTAAATTTATCTTAAA
28061351 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
28061368 TTTAAATTTA
1 TTTAAATTTA
28061378 ATTATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:28061380 original size:11 final size:11
Alignment explanation
Indices: 28061325--28061380 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
28061315 AATTTAAAGG
* *
28061325 TTAAATTGATT
1 TTAAATTTAAT
28061336 TTAAATTT-AT
1 TTAAATTTAAT
28061346 TTAAATTTAAAT
1 TTAAATTT-AAT
** *
28061358 TTATCTTAAAT
1 TTAAATTTAAT
28061369 TTAAATTTAAT
1 TTAAATTTAAT
28061380 T
1 T
28061381 ATTTAAATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 9 0.26
11 19 0.54
12 7 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:28062145 original size:3 final size:3
Alignment explanation
Indices: 28062137--28062166 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28062127 TGAAAGACAT
*
28062137 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28062167 AAAAAAACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28063277 original size:30 final size:30
Alignment explanation
Indices: 28063243--28063460 Score: 296
Period size: 30 Copynumber: 7.3 Consensus size: 30
28063233 CCCTAAATTG
* * *
28063243 TCCAGAATTATCTTTTGACCCCGAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
* * * *
28063273 TCCAGAATTATGTTTTAACCCCGAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
28063303 TCC-AAATTATATTTTGACCCTAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
28063332 TCCAAAATTATATTTTGACCCCGAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
28063362 TCCAAAATTATATTTTGACCTCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
28063392 TCCAAAATCATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
* *
28063422 TCCAAAATTACATTTTGACCCCAAAA-TTA
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
28063451 TCAAAAATTA
1 TCCAAAATTA
28063461 CCTATTTCCC
Statistics
Matches: 170, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
29 35 0.21
30 135 0.79
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCAAAACTTT
Found at i:28063482 original size:90 final size:89
Alignment explanation
Indices: 28063255--28063469 Score: 243
Period size: 89 Copynumber: 2.4 Consensus size: 89
28063245 CAGAATTATC
* * * * * ** * * *
28063255 TTTTGACCCCGAAACTTTTCCAGAATTATGTTTTAACCCCGAAACTTTTCCAAATTATATTTTGA
1 TTTTGACCCCGAAAATTATCAAAAATTATATTTCCACCTCAAAACTTTTCCAAATCATATTTTGA
* *
28063320 CCCTAAAACTTTTCCAAAATTATA
66 CCCCAAAACTTTTCCAAAATTACA
* * * **
28063344 TTTTGACCCCGAAACTTTTCCAAAATTATATTTTGACCTCAAAACTTTTCCAAAATCATATTTTG
1 TTTTGACCCCGAAAATTATCAAAAATTATATTTCCACCTCAAAACTTTTCC-AAATCATATTTTG
28063409 ACCCCAAAACTTTTCCAAAATTACA
65 ACCCCAAAACTTTTCCAAAATTACA
28063434 TTTTGACCCC-AAAATTATCAAAAATTACCTATTTCC
1 TTTTGACCCCGAAAATTATCAAAAATTA--TATTTCC
28063470 CCCTTAATCT
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
89 60 0.55
90 45 0.41
91 5 0.05
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (89 bp):
TTTTGACCCCGAAAATTATCAAAAATTATATTTCCACCTCAAAACTTTTCCAAATCATATTTTGA
CCCCAAAACTTTTCCAAAATTACA
Found at i:28063515 original size:59 final size:58
Alignment explanation
Indices: 28063452--28063582 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 58
28063442 CCAAAATTAT
* * ** *
28063452 CAAAAATTACCTATTTCCCCCT-TAATCTTTTAAAATTCTGTTTTTAACCCCGATTTCAC
1 CAAAAATTACC-ATTTCACCCTCGAATCTTTTAAAATTC-CATTTTAACCCCGATTACAC
* *
28063511 CAAAAATTGCCATTTTACCCTCGAATCTTTTAAAATTCCATTTTAACCCCGATTACAC
1 CAAAAATTACCATTTCACCCTCGAATCTTTTAAAATTCCATTTTAACCCCGATTACAC
28063569 C-AAAATTACCATTT
1 CAAAAATTACCATTT
28063583 TGCCCCCGGG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 12 0.19
58 26 0.41
59 25 0.40
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (58 bp):
CAAAAATTACCATTTCACCCTCGAATCTTTTAAAATTCCATTTTAACCCCGATTACAC
Found at i:28063573 original size:28 final size:28
Alignment explanation
Indices: 28063493--28063583 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 28
28063483 AAAATTCTGT
*
28063493 TTTTAACCCCGATTTCACCAAAAATTGCCA
1 TTTTAACCCCGA-TTCACC-AAAATTACCA
* ***
28063523 TTTT-ACCCTCGAATCTTTTAAAATT-CCA
1 TTTTAACCC-CGATTC-ACCAAAATTACCA
28063551 TTTTAACCCCGATTACACCAAAATTACCA
1 TTTTAACCCCGATT-CACCAAAATTACCA
28063580 TTTT
1 TTTT
28063584 GCCCCCGGGT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
28 17 0.35
29 24 0.50
30 7 0.15
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.36
Consensus pattern (28 bp):
TTTTAACCCCGATTCACCAAAATTACCA
Found at i:28075585 original size:21 final size:21
Alignment explanation
Indices: 28075559--28075602 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
28075549 TGGATAGCAC
*
28075559 GTCTTCATCTCTGAAATTGAA
1 GTCTTCATCTCCGAAATTGAA
28075580 GTCTTCATCTCCGAAATTGAA
1 GTCTTCATCTCCGAAATTGAA
28075601 GT
1 GT
28075603 AAGAGCAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (21 bp):
GTCTTCATCTCCGAAATTGAA
Found at i:28075689 original size:68 final size:67
Alignment explanation
Indices: 28075580--28075806 Score: 350
Period size: 68 Copynumber: 3.4 Consensus size: 67
28075570 TGAAATTGAA
28075580 GTCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAA
1 GTCTTCATCTCCGAAATTGAAGTAAGAGCAA-GTCATCCCCTTGAAATTGAAGTAGAGTGGATAA
28075645 CAC
65 CAC
* * *
28075648 GTCTTCATCTCCGAAATTGAAGTAAGAGCAATGTCATCCCCTCGAAATTGATGTAGAGTGGATAG
1 GTCTTCATCTCCGAAATTGAAGTAAGAGCAA-GTCATCCCCTTGAAATTGAAGTAGAGTGGATAA
28075713 CAC
65 CAC
* *
28075716 GTCTTCATCTCTGAAATTGAAGTAAGAGCAA--CGTCCCCTTGAAATTGAAGTAGAGTGGATAAC
1 GTCTTCATCTCCGAAATTGAAGTAAGAGCAAGTCATCCCCTTGAAATTGAAGTAGAGTGGATAAC
28075779 AC
66 AC
*
28075781 GTCTTCATCCCCTTGAAATTGAAGTA
1 GTCTTCATCTCC--GAAATTGAAGTA
28075807 GAGTGGATAA
Statistics
Matches: 146, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
65 40 0.27
67 12 0.08
68 94 0.64
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (67 bp):
GTCTTCATCTCCGAAATTGAAGTAAGAGCAAGTCATCCCCTTGAAATTGAAGTAGAGTGGATAAC
AC
Found at i:28075866 original size:68 final size:68
Alignment explanation
Indices: 28075785--28076123 Score: 597
Period size: 68 Copynumber: 5.0 Consensus size: 68
28075775 TAACACGTCT
* *
28075785 TCATCCCCTTGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
*
28075850 ATG
66 ACG
* *
28075853 TCATCCCCCTGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
28075918 ACG
66 ACG
28075921 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
*
28075986 ATG
66 ACG
28075989 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
28076054 ACG
66 ACG
* *
28076057 TCATCCCCTTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGC
1 TCATCCCC-TTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGC
28076122 AA
65 AA
28076124 AACTACGCCT
Statistics
Matches: 261, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
68 205 0.79
69 56 0.21
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (68 bp):
TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
ACG
Found at i:28075906 original size:172 final size:173
Alignment explanation
Indices: 28075613--28075979 Score: 616
Period size: 172 Copynumber: 2.1 Consensus size: 173
28075603 AAGAGCAACG
*
28075613 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
* ** *
28075678 ATGTCATCCCCTCGAAATTGATGTAGAGTGGATAGCACGTCTTCATCTCTGAAATTGAAGTAAGA
66 ATGTCATCCCCTCGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCCGAAATTGAAGTAAGA
28075743 GCAACG-TCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
131 GCAACGATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
28075785 TCATCCCCTTGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
28075850 ATGTCATCCCC-CTGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCCGAAATTGAAGTAAG
66 ATGTCATCCCCTC-GAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCCGAAATTGAAGTAAG
28075914 AGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
130 AGCAACG--ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
28075960 TCATCTCC--GAAATTGAAGTA
1 TCATCCCCTTGAAATTGAAGTA
28075980 AGAGCAATGT
Statistics
Matches: 184, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
171 1 0.01
172 128 0.70
173 12 0.07
175 43 0.23
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (173 bp):
TCATCCCCTTGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCCGAAATTGAAGTAAGAGCA
ATGTCATCCCCTCGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCTCCGAAATTGAAGTAAGA
GCAACGATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
Found at i:28076415 original size:11 final size:11
Alignment explanation
Indices: 28076382--28076475 Score: 77
Period size: 11 Copynumber: 8.7 Consensus size: 11
28076372 AATTTAAAGG
* *
28076382 TTAAATTGATT
1 TTAAATTAAAT
*
28076393 TTAAATT-TAT
1 TTAAATTAAAT
28076403 TTAAATTAAAT
1 TTAAATTAAAT
**
28076414 TTATCTTAAAT
1 TTAAATTAAAT
*
28076425 TTAAATTTAA-
1 TTAAATTAAAT
*
28076435 TT-ATTTAAAT
1 TTAAATTAAAT
**
28076445 TTACCTTAAAT
1 TTAAATTAAAT
28076456 TTAAATTTAAAT
1 TTAAA-TTAAAT
28076468 TTAAATTA
1 TTAAATTA
28076476 TAAAACAAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
9 5 0.08
10 12 0.18
11 37 0.57
12 11 0.17
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:28076430 original size:6 final size:6
Alignment explanation
Indices: 28076392--28076479 Score: 80
Period size: 6 Copynumber: 15.0 Consensus size: 6
28076382 TTAAATTGAT
28076392 TTTAAA TTT--A TTTAAA -TTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* *
28076438 TTTAAA TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
28076480 ACAAATTTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
4 6 0.09
5 10 0.15
6 40 0.59
7 6 0.09
8 6 0.09
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:28076446 original size:31 final size:31
Alignment explanation
Indices: 28076392--28076474 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
28076382 TTAAATTGAT
* * *
28076392 TTTAAATTTATTTAAATTAAATTTATCTTAAA
1 TTTAAATTTAATT-ATTTAAATTTACCTTAAA
28076424 TTTAAATTTAATTATTTAAATTTACCTTAAA
1 TTTAAATTTAATTATTTAAATTTACCTTAAA
28076455 TTTAAATTTAA--ATTTAAATT
1 TTTAAATTTAATTATTTAAATT
28076475 ATAAAACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
29 9 0.19
31 27 0.56
32 12 0.25
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAAATTTAATTATTTAAATTTACCTTAAA
Found at i:28077220 original size:3 final size:3
Alignment explanation
Indices: 28077212--28077244 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
28077202 TGAAAGACAT
*
28077212 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28077245 AAAAAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28078357 original size:30 final size:30
Alignment explanation
Indices: 28078310--28078617 Score: 415
Period size: 30 Copynumber: 10.3 Consensus size: 30
28078300 CCCTAAATTG
* *
28078310 TCCAGAAATTATCTTTTAACCCCGAAACTTT
1 TCCA-AAATTATATTTTGACCCCGAAACTTT
* * * *
28078341 CCCATAATTATGTTTTAACCCCGAAAC-TT
1 TCCAAAATTATATTTTGACCCCGAAACTTT
*
28078370 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCGAAACTTT
*
28078400 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCGAAACTTT
28078430 TCCAAAATTATATTTTGACCCCGAAACTTT
1 TCCAAAATTATATTTTGACCCCGAAACTTT
* *
28078460 TCCAAAATTATATTTTAACCTCGAAAC-TT
1 TCCAAAATTATATTTTGACCCCGAAACTTT
28078489 TCCAAAATTATATTTTGACCCCGAAACTTT
1 TCCAAAATTATATTTTGACCCCGAAACTTT
* * *
28078519 TCCAAAATCATATTTTAACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCGAAACTTT
*
28078549 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCGAAACTTT
* * * *
28078579 TCCAAAATTACATTTTAAACCC-AAAATTT
1 TCCAAAATTATATTTTGACCCCGAAACTTT
*
28078608 TCAAAAATTA
1 TCCAAAATTA
28078618 CCATTTTACC
Statistics
Matches: 252, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
29 66 0.26
30 183 0.73
31 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCGAAACTTT
Found at i:28078491 original size:89 final size:90
Alignment explanation
Indices: 28078310--28078617 Score: 433
Period size: 89 Copynumber: 3.4 Consensus size: 90
28078300 CCCTAAATTG
* * * * *
28078310 TCCAGAAATTATCTTTTAACCCCGAAACTTTCCCATAATTATGTTTTAACCCCGAAAC-TTTCCA
1 TCCA-AAATTATATTTTAACCCCAAAACTTTTCCAAAATTATATTTTAACCCCGAAACTTTTCCA
28078374 AAATTATATTTTGACCCCAAAACTTT
65 AAATTATATTTTGACCCCAAAACTTT
* *
28078400 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCGAAACTTTTCCAA
1 TCCAAAATTATATTTTAACCCCAAAACTTTTCCAAAATTATATTTTAACCCCGAAACTTTTCCAA
* * *
28078465 AATTATATTTTAACCTCGAAAC-TT
66 AATTATATTTTGACCCCAAAACTTT
* * * *
28078489 TCCAAAATTATATTTTGACCCCGAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTTTCCAA
1 TCCAAAATTATATTTTAACCCCAAAACTTTTCCAAAATTATATTTTAACCCCGAAACTTTTCCAA
28078554 AATTATATTTTGACCCCAAAACTTT
66 AATTATATTTTGACCCCAAAACTTT
* * *
28078579 TCCAAAATTACATTTTAAACCCAAAA-TTTTCAAAAATTA
1 TCCAAAATTATATTTTAACCCCAAAACTTTTCCAAAATTA
28078618 CCATTTTACC
Statistics
Matches: 193, Mismatches: 23, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
89 139 0.72
90 54 0.28
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (90 bp):
TCCAAAATTATATTTTAACCCCAAAACTTTTCCAAAATTATATTTTAACCCCGAAACTTTTCCAA
AATTATATTTTGACCCCAAAACTTT
Found at i:28078526 original size:119 final size:119
Alignment explanation
Indices: 28078310--28078617 Score: 472
Period size: 119 Copynumber: 2.6 Consensus size: 119
28078300 CCCTAAATTG
* * * * *
28078310 TCCAGAAATTATCTTTTAACCCCGAAACTTTCCCATAATTATGTTTTAACCCCGAAACTTTCCAA
1 TCCA-AAATTATATTTTGACCCCGAAACTTTTCCAAAATTATATTTTAACCCCGAAACTTTCCAA
* *
28078375 AATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTT
65 AATTATATTTTGACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTT
*
28078430 TCCAAAATTATATTTTGACCCCGAAACTTTTCCAAAATTATATTTTAACCTCGAAACTTTCCAAA
1 TCCAAAATTATATTTTGACCCCGAAACTTTTCCAAAATTATATTTTAACCCCGAAACTTTCCAAA
*
28078495 ATTATATTTTGACCCCGAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTT
66 ATTATATTTTGACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTT
* * * * * *
28078549 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAAACCCAAAATTTTCAAAA
1 TCCAAAATTATATTTTGACCCCGAAACTTTTCCAAAATTATATTTTAACCCCGAAACTTTCCAAA
28078614 ATTA
66 ATTA
28078618 CCATTTTACC
Statistics
Matches: 172, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
119 168 0.98
120 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (119 bp):
TCCAAAATTATATTTTGACCCCGAAACTTTTCCAAAATTATATTTTAACCCCGAAACTTTCCAAA
ATTATATTTTGACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTT
Found at i:28078646 original size:60 final size:57
Alignment explanation
Indices: 28078582--28078743 Score: 150
Period size: 60 Copynumber: 2.7 Consensus size: 57
28078572 AAACTTTTCC
*
28078582 AAAATTACATTTTAAACCCAAAATTT-TCAAAAATTACCATTTTACCCCCCCGAATCTTTT
1 AAAATT-CATTTTAAACCC-AAATTTACCAAAAATTACCATTTTA--CCCCCGAATCTTTT
* ** *
28078642 AAAATTCTATTTTTTAACCCCGATTTCACCAAAAATTGCCATTTTACCCCCGAATCTTTT
1 AAAATTC-A-TTTTAAACCCAAATTT-ACCAAAAATTACCATTTTACCCCCGAATCTTTT
** *
28078702 AAAATTCCATTTT-AACCCCGA-TTACACCAAAATTACCATTTT
1 AAAATT-CATTTTAAACCCAAATTTAC-CAAAAATTACCATTTT
28078744 GCCCTCGGGT
Statistics
Matches: 89, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
56 2 0.02
57 16 0.18
58 8 0.09
59 5 0.06
60 32 0.36
61 10 0.11
62 16 0.18
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (57 bp):
AAAATTCATTTTAAACCCAAATTTACCAAAAATTACCATTTTACCCCCGAATCTTTT
Found at i:28078733 original size:28 final size:28
Alignment explanation
Indices: 28078653--28078743 Score: 85
Period size: 28 Copynumber: 3.1 Consensus size: 28
28078643 AAATTCTATT
*
28078653 TTTTAACCCCGATTTCACCAAAAATTGCCA
1 TTTTAACCCCGA-TTCACC-AAAATTACCA
* * ***
28078683 TTTTACCCCCGAATCTTTTAAAATT-CCA
1 TTTTAACCCCGATTC-ACCAAAATTACCA
28078711 TTTTAACCCCGATTACACCAAAATTACCA
1 TTTTAACCCCGATT-CACCAAAATTACCA
28078740 TTTT
1 TTTT
28078744 GCCCTCGGGT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
28 21 0.44
29 16 0.33
30 11 0.23
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (28 bp):
TTTTAACCCCGATTCACCAAAATTACCA
Found at i:28080510 original size:18 final size:18
Alignment explanation
Indices: 28080472--28080506 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28080462 GAATAATCTT
*
28080472 AAATTTACAAATAAATTC
1 AAATTTACAAATAAATCC
28080490 AAATTTA-AAATAAATCC
1 AAATTTACAAATAAATCC
28080507 CAAAATGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATTTACAAATAAATCC
Found at i:28082633 original size:18 final size:18
Alignment explanation
Indices: 28082591--28082638 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
28082581 ATTACATATT
*
28082591 TTATATTTTAAAAAAATTA
1 TTATATTAT-AAAAAATTA
*
28082610 AT-TATTATAAAAAATTA
1 TTATATTATAAAAAATTA
28082627 TTATATTGATAA
1 TTATATT-ATAA
28082639 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 10 0.42
18 9 0.38
19 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TTATATTATAAAAAATTA
Found at i:28083187 original size:24 final size:24
Alignment explanation
Indices: 28083157--28083205 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
28083147 CTTTTTTTCA
* *
28083157 CTCATTTTCTCTC-AATTTTCTCT
1 CTCAATTTCTCTCTAAATTTCTCT
28083180 CTCAATTTCTCTCTAAATTTCTCT
1 CTCAATTTCTCTCTAAATTTCTCT
28083204 CT
1 CT
28083206 AAAGCTCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (24 bp):
CTCAATTTCTCTCTAAATTTCTCT
Found at i:28083206 original size:12 final size:12
Alignment explanation
Indices: 28083162--28083208 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
28083152 TTTCACTCAT
*
28083162 TTTCTCTC-AAT
1 TTTCTCTCTAAA
*
28083173 TTTCTCTCTCAA
1 TTTCTCTCTAAA
28083185 TTTCTCTCTAAA
1 TTTCTCTCTAAA
28083197 TTTCTCTCTAAA
1 TTTCTCTCTAAA
28083209 GCTCTCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTCTCTCTAAA
Found at i:28083214 original size:24 final size:23
Alignment explanation
Indices: 28083164--28083214 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
28083154 TCACTCATTT
* * **
28083164 TCTCTCAATTTTCTCTCTCAATT
1 TCTCTCAAATTTCTCTCTAAAGC
28083187 TCTCTCTAAATTTCTCTCTAAAGC
1 TCTCTC-AAATTTCTCTCTAAAGC
28083211 TCTC
1 TCTC
28083215 AAAATTCTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.20, C:0.31, G:0.02, T:0.47
Consensus pattern (23 bp):
TCTCTCAAATTTCTCTCTAAAGC
Found at i:28083373 original size:26 final size:30
Alignment explanation
Indices: 28083344--28083403 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
28083334 TGAGAGTTAA
*
28083344 TTTTAATTT-TTTTTAT-A-TTATTTATTT
1 TTTTAATTTGTTTTTATAATTTAATTATTT
*
28083371 TTTTATTTTGTTTTTATAATTTAATTATTT
1 TTTTAATTTGTTTTTATAATTTAATTATTT
28083401 TTT
1 TTT
28083404 AATAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 7 0.25
29 1 0.04
30 12 0.43
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.77
Consensus pattern (30 bp):
TTTTAATTTGTTTTTATAATTTAATTATTT
Found at i:28083421 original size:29 final size:29
Alignment explanation
Indices: 28083389--28083464 Score: 75
Period size: 32 Copynumber: 2.6 Consensus size: 29
28083379 TGTTTTTATA
*
28083389 ATTTAATTATTTTTTAATA-ATATTTAATT
1 ATTTAATTATTTTTTAATATA-ATTAAATT
*
28083418 ATTTAATATTATTTTTATAATTTAATTAAATT
1 ATTT-A-ATTATTTTT-TAATATAATTAAATT
*
28083450 TTTTAA-TATTTTTTA
1 ATTTAATTATTTTTTA
28083465 TTTGAATAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.05
29 11 0.28
30 2 0.05
31 10 0.25
32 14 0.35
33 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
ATTTAATTATTTTTTAATATAATTAAATT
Found at i:28083434 original size:48 final size:47
Alignment explanation
Indices: 28083345--28083472 Score: 140
Period size: 48 Copynumber: 2.7 Consensus size: 47
28083335 GAGAGTTAAT
* * * * *
28083345 TTTAATT-TTTTTT-ATATTATTTATTTTTTTATTTTGTTTTTATAA
1 TTTAATTATTTTTTAATAATATTTATTATTTAATATTATTTTTATAA
28083390 TTTAATTATTTTTTAATAATATTTAATTATTTAATATTATTTTTATAA
1 TTTAATTATTTTTTAATAATATTT-ATTATTTAATATTATTTTTATAA
28083438 TTTAATTAAATTTTTTAAT-AT-TTT-TTATTTGAATA
1 TTTAATT--ATTTTTTAATAATATTTATTATTT-AATA
28083473 GCTGATCGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
45 7 0.10
46 12 0.17
47 12 0.17
48 29 0.40
49 2 0.03
50 10 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (47 bp):
TTTAATTATTTTTTAATAATATTTATTATTTAATATTATTTTTATAA
Found at i:28085462 original size:59 final size:59
Alignment explanation
Indices: 28085368--28085505 Score: 222
Period size: 59 Copynumber: 2.3 Consensus size: 59
28085358 GATTATTTTC
* * *
28085368 GAATATTTTTGTAAACATTATTTTTATATTATTTCATTTAATAAAAGCGAAGTTCATTT
1 GAATATTTTTGTACACATTATTTTTATATTATTTCATATAATAAAAGCGAAGTCCATTT
* * *
28085427 GAATATTTTTGTACACATTATTTTTATTTTGTTTCATATAATAAAGGCGAAGTCCATTT
1 GAATATTTTTGTACACATTATTTTTATATTATTTCATATAATAAAAGCGAAGTCCATTT
28085486 GAATATTTTTGTACACATTA
1 GAATATTTTTGTACACATTA
28085506 GTTTGGGTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 73 1.00
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (59 bp):
GAATATTTTTGTACACATTATTTTTATATTATTTCATATAATAAAAGCGAAGTCCATTT
Found at i:28085915 original size:21 final size:22
Alignment explanation
Indices: 28085891--28085936 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
28085881 ATAAATAATA
* *
28085891 AAACCTTAATTTTAAAAA-CCT
1 AAACCCTAATTTAAAAAACCCT
28085912 AAACCCTAATTTAAAAAACCCT
1 AAACCCTAATTTAAAAAACCCT
28085934 AAA
1 AAA
28085937 TCTAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (22 bp):
AAACCCTAATTTAAAAAACCCT
Found at i:28086271 original size:15 final size:15
Alignment explanation
Indices: 28086253--28086286 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28086243 TTTTAAATTT
28086253 AAAATTAAAAAGCCC
1 AAAATTAAAAAGCCC
*
28086268 AAAA-TAAAAAGTCC
1 AAAATTAAAAAGCCC
28086282 AAAAT
1 AAAAT
28086287 GTTTACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15
Consensus pattern (15 bp):
AAAATTAAAAAGCCC
Done.