Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012560.1 Kokia drynarioides strain JFW-HI SEQ_127569, whole genome shotgun sequence
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: 577970
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 376 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:134 original size:17 final size:16
Alignment explanation
Indices: 108--142 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
98 TTCTTCCTTC
108 TTCTTTTTTTCTTTCT
1 TTCTTTTTTTCTTTCT
124 TTCTCTTTTTTCTTTCT
1 TTCT-TTTTTTCTTTCT
141 TT
1 TT
143 TTTCCTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCTTTTTTTCTTTCT
Found at i:137 original size:13 final size:12
Alignment explanation
Indices: 108--145 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
98 TTCTTCCTTC
108 TTCTTT-TTTTCT
1 TTCTTTCTTTT-T
120 TTCTTTCTCTTTT
1 TTCTTTCT-TTTT
133 TTCTTTCTTTTT
1 TTCTTTCTTTTT
145 T
1 T
146 CCTTCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.46
13 10 0.42
14 3 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTTCTTTTT
Found at i:139 original size:21 final size:20
Alignment explanation
Indices: 106--156 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
96 CCTTCTTCCT
106 TCTTCTTTTTTTCTTTCTTTC
1 TCTTCTTTTTTTCTTT-TTTC
127 TCTT-TTTTCTTTCTTTTTTC
1 TCTTCTTTT-TTTCTTTTTTC
147 -CTTCATTTTT
1 TCTTC-TTTTT
157 CGTTGGTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.11
20 9 0.33
21 15 0.56
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTCTTTTTTTCTTTTTTC
Found at i:410 original size:12 final size:11
Alignment explanation
Indices: 380--409 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
370 TGGGTATCAG
*
380 GTATTTTTGTC
1 GTATTTTTCTC
391 GTATTTTTCTC
1 GTATTTTTCTC
402 GTATTTTT
1 GTATTTTT
410 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.10, G:0.13, T:0.67
Consensus pattern (11 bp):
GTATTTTTCTC
Found at i:8600 original size:36 final size:36
Alignment explanation
Indices: 8553--8640 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
8543 ACTGGTAACA
*
8553 ATCATGACCTTTGGGTCAATAGGGAGTAAAATGAGC
1 ATCATGACCTTTGGGTCAATAGGGAGTAAAATAAGC
8589 ATCATGACCTTTGGGTCAATAGGGAGTAAAATAAGC
1 ATCATGACCTTTGGGTCAATAGGGAGTAAAATAAGC
8625 ATCATGACCTTTGGGT
1 ATCATGACCTTTGGGT
8641 TAACAAGGTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (36 bp):
ATCATGACCTTTGGGTCAATAGGGAGTAAAATAAGC
Found at i:8681 original size:28 final size:28
Alignment explanation
Indices: 8627--8681 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
8617 AAATAAGCAT
* * *
8627 CATGACCTTTGGGTTAACAAGGTGTAAG
1 CATGACCTTTAGGTCAACAAGGAGTAAG
*
8655 CATGACCTTTAGGTCAACAGGGAGTAA
1 CATGACCTTTAGGTCAACAAGGAGTAA
8682 ATCAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (28 bp):
CATGACCTTTAGGTCAACAAGGAGTAAG
Found at i:14751 original size:21 final size:21
Alignment explanation
Indices: 14725--14772 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
14715 TTTAGTACCA
14725 GTAGAAGCATGATTTGT-TTCG
1 GTAGAAGCATGATTTGTATT-G
* *
14746 GTAGAAGCTTTATTTGTATTG
1 GTAGAAGCATGATTTGTATTG
14767 GTAGAA
1 GTAGAA
14773 CTGTCGTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.40
Consensus pattern (21 bp):
GTAGAAGCATGATTTGTATTG
Found at i:21076 original size:7 final size:6
Alignment explanation
Indices: 21055--21087 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
21045 CTAATATTGA
21055 AAAAAT -AAAAT AAAAAT AAAAAT AAAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAA
21088 TATTAATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:31646 original size:22 final size:24
Alignment explanation
Indices: 31619--31669 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
31609 AAGCTGATCA
31619 CTATGTCACAACAC-GGACT-GAT
1 CTATGTCACAACACAGGACTAGAT
*
31641 CTATGTCGCAACACAGGGACTAGAT
1 CTATGTCACAACACA-GGACTAGAT
31666 CTAT
1 CTAT
31670 AGAATTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 13 0.52
24 5 0.20
25 7 0.28
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (24 bp):
CTATGTCACAACACAGGACTAGAT
Found at i:40705 original size:50 final size:50
Alignment explanation
Indices: 40615--41139 Score: 282
Period size: 50 Copynumber: 11.0 Consensus size: 50
40605 TCGTGGCTAA
* **
40615 AGCTTTAGGGGTATAAAATTCGTCTT--TGCGACTTCAATCTGCCCCTCTAT
1 AGCTTTAGGGGTATAAGATTCACCTTCATG-G-CTTCAATCTGCCCCTCTAT
* *
40665 AGCTTTAGGGGTATAAGATTTACCTTCATGGCTTCTATCTGCCCCTC--T
1 AGCTTTAGGGGTATAAGATTCACCTTCATGGCTTCAATCTGCCCCTCTAT
* * * * *
40713 A-C---A--GCTATAAGATTCACCTT-TTCGACTTCAATATTCCCCTCTAT
1 AGCTTTAGGGGTATAAGATTCACCTTCAT-GGCTTCAATCTGCCCCTCTAT
* * * * * * *
40757 AGCTTTAGGGGTACAAGATTCACCTTTATAGCTTTAATCTGCCCTTTTAC
1 AGCTTTAGGGGTATAAGATTCACCTTCATGGCTTCAATCTGCCCCTCTAT
* ** * *
40807 ATCTTTAGGGGTATAAGATTTGCCTTCACGGCTTCAATCTACCCCTC--T
1 AGCTTTAGGGGTATAAGATTCACCTTCATGGCTTCAATCTGCCCCTCTAT
* * ** ** * * * *
40855 AG----A--GATTTAAGATTCGTCTTTGTGGCTTCAATTTTCTCCTCTAG
1 AGCTTTAGGGGTATAAGATTCACCTTCATGGCTTCAATCTGCCCCTCTAT
** * * *
40899 AGCTTTAATGGTATAAGATTCACCTTCGTCGCTTCAATCTTCCCCTCTAT
1 AGCTTTAGGGGTATAAGATTCACCTTCATGGCTTCAATCTGCCCCTCTAT
* * * * *
40949 AACTTTAGGGGTATAAGATTTACCTTCGTGGCTTCAATTTGCCCCTTTAT
1 AGCTTTAGGGGTATAAGATTCACCTTCATGGCTTCAATCTGCCCCTCTAT
* * ** * *
40999 AGCTTTAAGGATATAAGATTTGCCTTC-TCGACTTCAATCTACCCCTCTAT
1 AGCTTTAGGGGTATAAGATTCACCTTCAT-GGCTTCAATCTGCCCCTCTAT
** * *
41049 AGC--------TATAAGATTCGTCTT--TGCAGCTTCAATCTACCCCTCTAC
1 AGCTTTAGGGGTATAAGATTCACCTTCATG--GCTTCAATCTGCCCCTCTAT
* ***
41091 AGCTTTAGGGGTATAAGATTCATCTTTGCGGCTTCAATCTGCCCCTCTA
1 AGCTTTAGGGGTATAAGATTCACCTTCATGGCTTCAATCTGCCCCTCTA
41140 GAGAATGTTG
Statistics
Matches: 363, Mismatches: 79, Indels: 66
0.71 0.16 0.13
Matches are distributed among these distances:
40 1 0.00
41 2 0.01
42 91 0.25
44 6 0.02
45 1 0.00
47 1 0.00
48 5 0.01
49 1 0.00
50 250 0.69
51 2 0.01
52 3 0.01
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.37
Consensus pattern (50 bp):
AGCTTTAGGGGTATAAGATTCACCTTCATGGCTTCAATCTGCCCCTCTAT
Found at i:40925 original size:92 final size:91
Alignment explanation
Indices: 40816--41143 Score: 266
Period size: 92 Copynumber: 3.5 Consensus size: 91
40806 CATCTTTAGG
** *
40816 GGTATAAGATTTGCCTTCACGGCTTCAATCTACCCCTCTAGAGATTTAAGATTCGTCTTTGTGGC
1 GGTATAAGATTCACCTTCTCGGCTTCAATCTACCCCTCTAGAGATTTAAGATTCGTCTTTGTGGC
* * *
40881 TTCAATTTTCTCCTCTAGAGCTTTAA
66 TTCAATTTACCCCTCTACAGCTTTAA
* * *
40907 TGGTATAAGATTCACCTTCGTC-GCTTCAATCTTCCCCTCTATA-ACTTTAGGGGTATAAGATTT
1 -GGTATAAGATTCACCTTC-TCGGCTTCAATCTACCCCTCTAGAGA---T-----T-TAAGATTC
** * * * *
40970 ACCTTCGTGGCTTCAATTTGCCCCTTTATAGCTTTAA
55 GTCTTTGTGGCTTCAATTTACCCCTCTACAGCTTTAA
** * * * * **
41007 GGATATAAGATTTGCCTTCTCGACTTCAATCTACCCCTCTATAGCTATAAGATTCGTCTTTGCAG
1 GG-TATAAGATTCACCTTCTCGGCTTCAATCTACCCCTCTAGAGATTTAAGATTCGTCTTTGTGG
* *
41072 CTTCAATCTACCCCTCTACAGCTTTAGG
65 CTTCAATTTACCCCTCTACAGCTTTA-A
* *
41100 GGTATAAGATTCATCTT-TGCGGCTTCAATCTGCCCCTCTAGAGA
1 GGTATAAGATTCACCTTCT-CGGCTTCAATCTACCCCTCTAGAGA
41144 ATGTTGATAT
Statistics
Matches: 184, Mismatches: 37, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
91 2 0.01
92 102 0.55
93 3 0.02
94 1 0.01
98 1 0.01
99 5 0.03
100 70 0.38
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (91 bp):
GGTATAAGATTCACCTTCTCGGCTTCAATCTACCCCTCTAGAGATTTAAGATTCGTCTTTGTGGC
TTCAATTTACCCCTCTACAGCTTTAA
Found at i:40944 original size:192 final size:191
Alignment explanation
Indices: 40718--41139 Score: 531
Period size: 192 Copynumber: 2.2 Consensus size: 191
40708 CCTCTACAGC
* * *
40718 TATAAGATTCACCTTTTCGACTTCAATATTCCCCTCTATAGCTTTAGGGGTACAAGATTCACCTT
1 TATAAGATTCACCTTGTCG-CTTCAATCTTCCCCTCTATAACTTTAGGGGTACAAGATTCACCTT
* * * * * * *
40783 TATAGCTTTAATCTGCCCTTTTACATCTTTAGGGGTATAAGATTTGCCTTCACGGCTTCAATCTA
65 CATAGCTTCAATCTGCCCCTTTACAGCTTTAAGGATATAAGATTTGCCTTCACGACTTCAATCTA
* ** * * * * *
40848 CCCCTCTAGAGATTTAAGATTCGTCTTTGTGGCTTCAATTTTCTCCTCTAGAGCTTTAATGG
130 CCCCTCTAGAGATATAAGATTCGTCTTTGCAGCTTCAATCTACCCCTCTACAGCTTTAAGGG
* *
40910 TATAAGATTCACCTTCGTCGCTTCAATCTTCCCCTCTATAACTTTAGGGGTATAAGATTTACCTT
1 TATAAGATTCACCTT-GTCGCTTCAATCTTCCCCTCTATAACTTTAGGGGTACAAGATTCACCTT
* * * * *
40975 CGTGGCTTCAATTTGCCCCTTTATAGCTTTAAGGATATAAGATTTGCCTTCTCGACTTCAATCTA
65 CATAGCTTCAATCTGCCCCTTTACAGCTTTAAGGATATAAGATTTGCCTTCACGACTTCAATCTA
* * *
41040 CCCCTCTATAGCTATAAGATTCGTCTTTGCAGCTTCAATCTACCCCTCTACAGCTTTAGGGG
130 CCCCTCTAGAGATATAAGATTCGTCTTTGCAGCTTCAATCTACCCCTCTACAGCTTTAAGGG
* *
41102 TATAAGATTCATCTT-TGCGGCTTCAATCTGCCCCTCTA
1 TATAAGATTCACCTTGT-C-GCTTCAATCTTCCCCTCTA
41140 GAGAATGTTG
Statistics
Matches: 197, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
190 1 0.01
191 1 0.01
192 192 0.97
193 3 0.02
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (191 bp):
TATAAGATTCACCTTGTCGCTTCAATCTTCCCCTCTATAACTTTAGGGGTACAAGATTCACCTTC
ATAGCTTCAATCTGCCCCTTTACAGCTTTAAGGATATAAGATTTGCCTTCACGACTTCAATCTAC
CCCTCTAGAGATATAAGATTCGTCTTTGCAGCTTCAATCTACCCCTCTACAGCTTTAAGGG
Found at i:41006 original size:142 final size:142
Alignment explanation
Indices: 40646--41007 Score: 438
Period size: 142 Copynumber: 2.5 Consensus size: 142
40636 GTCTTTGCGA
* *
40646 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTTACCTTCATGGCTTCTATCTGCCCCT
1 CTTCAATCTGCCCCTCTATAACTTTAGGGGTATAAGATTTACCTTCATGGCTTCAATCTGCCCCT
* * *
40711 CTACAGCTATAAGATTCACCTTTTCGACTTCAATATTCCCCTCTATAGCTTTAGGGGTACAAGAT
66 CTACAGCTTTAAGATTCACCTTTTCGACTTCAATATTCCCCTCTAGAGCTTTAAGGGTACAAGAT
*
40776 TCACCTTTATAG
131 TCACCTTCATAG
* * * * * * * *
40788 CTTTAATCTGCCCTTTTACATCTTTAGGGGTATAAGATTTGCCTTCACGGCTTCAATCTACCCCT
1 CTTCAATCTGCCCCTCTATAACTTTAGGGGTATAAGATTTACCTTCATGGCTTCAATCTGCCCCT
* * ** * * * * *
40853 CTAGAGATTTAAGATTCGTCTTTGT-GGCTTCAATTTTCTCCTCTAGAGCTTTAATGGTATAAGA
66 CTACAGCTTTAAGATTCACCTTT-TCGACTTCAATATTCCCCTCTAGAGCTTTAAGGGTACAAGA
* *
40917 TTCACCTTCGTCG
130 TTCACCTTCATAG
* * *
40930 CTTCAATCTTCCCCTCTATAACTTTAGGGGTATAAGATTTACCTTCGTGGCTTCAATTTGCCCCT
1 CTTCAATCTGCCCCTCTATAACTTTAGGGGTATAAGATTTACCTTCATGGCTTCAATCTGCCCCT
* *
40995 TTATAGCTTTAAG
66 CTACAGCTTTAAG
41008 GATATAAGAT
Statistics
Matches: 181, Mismatches: 38, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
142 180 0.99
143 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (142 bp):
CTTCAATCTGCCCCTCTATAACTTTAGGGGTATAAGATTTACCTTCATGGCTTCAATCTGCCCCT
CTACAGCTTTAAGATTCACCTTTTCGACTTCAATATTCCCCTCTAGAGCTTTAAGGGTACAAGAT
TCACCTTCATAG
Found at i:44848 original size:27 final size:28
Alignment explanation
Indices: 44817--44871 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
44807 TGTGACAACA
*
44817 TCTTCCTATTTCTCGTCTTCCTT-TCTT
1 TCTTCCTATTTCTCGTCTGCCTTCTCTT
* * *
44844 TCTTCTTCTTTCTCTTCTGCCTTCTCTT
1 TCTTCCTATTTCTCGTCTGCCTTCTCTT
44872 CCTTAATACC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.02, C:0.35, G:0.04, T:0.60
Consensus pattern (28 bp):
TCTTCCTATTTCTCGTCTGCCTTCTCTT
Found at i:66320 original size:30 final size:30
Alignment explanation
Indices: 66286--66346 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
66276 GCTTGGAAGA
* * * *
66286 TGTGAGCACTGGTGTTGCGAGCACTCATGT
1 TGTGAACACTGGAGTTGAGAACACTCATGT
66316 TGTGAACACTGGAGTTGAGAACACTCATGT
1 TGTGAACACTGGAGTTGAGAACACTCATGT
66346 T
1 T
66347 ACGAACAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (30 bp):
TGTGAACACTGGAGTTGAGAACACTCATGT
Found at i:66353 original size:30 final size:30
Alignment explanation
Indices: 66292--66353 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
66282 AAGATGTGAG
* * * **
66292 CACTGGTGTTGCGAGCACTCATGTTGTGAA
1 CACTGGAGTTGAGAACACTCATGTTACGAA
66322 CACTGGAGTTGAGAACACTCATGTTACGAA
1 CACTGGAGTTGAGAACACTCATGTTACGAA
66352 CA
1 CA
66354 AACACAATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (30 bp):
CACTGGAGTTGAGAACACTCATGTTACGAA
Found at i:66406 original size:30 final size:30
Alignment explanation
Indices: 66334--66406 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
66324 CTGGAGTTGA
66334 GAACACTCATGTTACGAACAAACACAATAC
1 GAACACTCATGTTACGAACAAACACAATAC
** * **
66364 GAATGCTCATGTTACGAACACACACAATGT
1 GAACACTCATGTTACGAACAAACACAATAC
*
66394 GAACACTAATGTT
1 GAACACTCATGTT
66407 GTGAGCATGG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (30 bp):
GAACACTCATGTTACGAACAAACACAATAC
Found at i:75065 original size:24 final size:24
Alignment explanation
Indices: 75037--75098 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
75027 CAAGTCTTCC
*
75037 AAATAGGTTAACTCTTACGAGCCT
1 AAATAGGTTAACTCTTACAAGCCT
* * *
75061 AAATAGAATTAGCTCTTACAAGCGT
1 AAATAG-GTTAACTCTTACAAGCCT
* *
75086 AGATAAGTTAACT
1 AAATAGGTTAACT
75099 AGTATATGAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
AAATAGGTTAACTCTTACAAGCCT
Found at i:80243 original size:24 final size:24
Alignment explanation
Indices: 80213--80287 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
80203 CTAGACAGAA
80213 TTAGCTCTTATGAGCCCAGATAGG
1 TTAGCTCTTATGAGCCCAGATAGG
* *
80237 TTAGCTCTTATGAGCCCAAAGAGG
1 TTAGCTCTTATGAGCCCAGATAGG
* * *
80261 TTAGCTTTTACGAGCCCAGATGGG
1 TTAGCTCTTATGAGCCCAGATAGG
80285 TTA
1 TTA
80288 ACCAATACAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (24 bp):
TTAGCTCTTATGAGCCCAGATAGG
Found at i:85164 original size:23 final size:23
Alignment explanation
Indices: 85132--85175 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
85122 ACTACCATTT
85132 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
85155 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
85176 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:85168 original size:13 final size:11
Alignment explanation
Indices: 85136--85178 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
85126 CCATTTTCTA
*
85136 AATAAAATAAT
1 AATAAAATATT
85147 AAT-AAATATCT
1 AATAAAATAT-T
85158 AAGTAAAATATT
1 AA-TAAAATATT
85170 AATAAAATA
1 AATAAAATA
85179 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:92024 original size:20 final size:20
Alignment explanation
Indices: 91999--92044 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
91989 TTTTTTTATT
91999 TATATAGAT-AAAATAATAAA
1 TATATA-ATGAAAATAATAAA
* *
92019 TATATAATGCAAATAATATA
1 TATATAATGAAAATAATAAA
92039 TATATA
1 TATATA
92045 TATATCACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
TATATAATGAAAATAATAAA
Found at i:102033 original size:319 final size:319
Alignment explanation
Indices: 101454--102094 Score: 1264
Period size: 319 Copynumber: 2.0 Consensus size: 319
101444 CACTTGTAAG
101454 TTATACATGCGTCATTAAGGGAAGTACTTTGTTTTACTTTCTATTGTATTTATGCTGAAGGCATT
1 TTATACATGCGTCATTAAGGGAAGTACTTTGTTTTACTTTCTATTGTATTTATGCTGAAGGCATT
101519 CATTTGATGTAGTCTCGTTGTTGCCTGCTATCAGTTTTACTTATTCATTGGTAATAGATTACACA
66 CATTTGATGTAGTCTCGTTGTTGCCTGCTATCAGTTTTACTTATTCATTGGTAATAGATTACACA
101584 GTGGAATTATGGGATTTGCTGATATATGCATTATTTTCATAATGGAAGTGCTTGATTCTTTGTTA
131 GTGGAATTATGGGATTTGCTGATATATGCATTATTTTCATAATGGAAGTGCTTGATTCTTTGTTA
101649 AGCTACTAGAGGTGGCATGATTCTTATCAGTGGTTCCAGAAGATCTGGATGTCACTTTTTACAGG
196 AGCTACTAGAGGTGGCATGATTCTTATCAGTGGTTCCAGAAGATCTGGATGTCACTTTTTACAGG
101714 CTCTGTTTCATGGAAAATACTTTTCCATGGGAAAATGTATTTCATAGAAGGCATTTTCC
261 CTCTGTTTCATGGAAAATACTTTTCCATGGGAAAATGTATTTCATAGAAGGCATTTTCC
*
101773 TTATACATGCGTCATTAAGGGAAGTTCTTTGTTTTACTTTCTATTGTATTTATGCTGAAGGCATT
1 TTATACATGCGTCATTAAGGGAAGTACTTTGTTTTACTTTCTATTGTATTTATGCTGAAGGCATT
101838 CATTTGATGTAGTCTCGTTGTTGCCTGCTATCAGTTTTACTTATTCATTGGTAATAGATTACACA
66 CATTTGATGTAGTCTCGTTGTTGCCTGCTATCAGTTTTACTTATTCATTGGTAATAGATTACACA
101903 GTGGAATTATGGGATTTGCTGATATATGCATTATTTTCATAATGGAAGTGCTTGATTCTTTGTTA
131 GTGGAATTATGGGATTTGCTGATATATGCATTATTTTCATAATGGAAGTGCTTGATTCTTTGTTA
*
101968 AGCTATTAGAGGTGGCATGATTCTTATCAGTGGTTCCAGAAGATCTGGATGTCACTTTTTACAGG
196 AGCTACTAGAGGTGGCATGATTCTTATCAGTGGTTCCAGAAGATCTGGATGTCACTTTTTACAGG
102033 CTCTGTTTCATGGAAAATACTTTTCCATGGGAAAATGTATTTCATAGAAGGCATTTTCC
261 CTCTGTTTCATGGAAAATACTTTTCCATGGGAAAATGTATTTCATAGAAGGCATTTTCC
102092 TTA
1 TTA
102095 ACAGATTATT
Statistics
Matches: 320, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
319 320 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (319 bp):
TTATACATGCGTCATTAAGGGAAGTACTTTGTTTTACTTTCTATTGTATTTATGCTGAAGGCATT
CATTTGATGTAGTCTCGTTGTTGCCTGCTATCAGTTTTACTTATTCATTGGTAATAGATTACACA
GTGGAATTATGGGATTTGCTGATATATGCATTATTTTCATAATGGAAGTGCTTGATTCTTTGTTA
AGCTACTAGAGGTGGCATGATTCTTATCAGTGGTTCCAGAAGATCTGGATGTCACTTTTTACAGG
CTCTGTTTCATGGAAAATACTTTTCCATGGGAAAATGTATTTCATAGAAGGCATTTTCC
Found at i:110330 original size:12 final size:12
Alignment explanation
Indices: 110313--110337 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
110303 ACAAGTCTCT
110313 TTTATTTATTTG
1 TTTATTTATTTG
110325 TTTATTTATTTG
1 TTTATTTATTTG
110337 T
1 T
110338 CACTCCAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:110581 original size:56 final size:55
Alignment explanation
Indices: 110515--110625 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 55
110505 ATATGCAGAT
**
110515 TAGGACTTACCTGATTATTTTAGAAATATGGTACAGTAGAAATGGGACTAAGGAC
1 TAGGACTTACCTGATTATTTTAGAAATACAGTACAGTAGAAATGGGACTAAGGAC
110570 TAGGACATTACCTGATTATTTTAGAAATACAGTACAGTAGAAATGGGACTAAGGAC
1 TAGGAC-TTACCTGATTATTTTAGAAATACAGTACAGTAGAAATGGGACTAAGGAC
110626 GTTTGGATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 6 0.11
56 47 0.89
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (55 bp):
TAGGACTTACCTGATTATTTTAGAAATACAGTACAGTAGAAATGGGACTAAGGAC
Found at i:129193 original size:24 final size:24
Alignment explanation
Indices: 129159--129230 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
129149 CAAAAATATG
129159 AAAGGTTGAGGAAGATGGAAGGTT
1 AAAGGTTGAGGAAGATGGAAGGTT
* *
129183 AAAGGTCGAGGAAGATAGAAGGTT
1 AAAGGTTGAGGAAGATGGAAGGTT
* * *
129207 AAAAGTTAAGGAAGATGAAAGGTT
1 AAAGGTTGAGGAAGATGGAAGGTT
129231 GAACATTCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.43, C:0.01, G:0.36, T:0.19
Consensus pattern (24 bp):
AAAGGTTGAGGAAGATGGAAGGTT
Found at i:129462 original size:43 final size:44
Alignment explanation
Indices: 129370--129493 Score: 214
Period size: 43 Copynumber: 2.8 Consensus size: 44
129360 AATACTTAAG
*
129370 CATTCTATCAATTTAATCCTAATCTTAAATAATCCAATAATAAA
1 CATTCTATCAATTTAATCCTAATCCTAAATAATCCAATAATAAA
129414 CATTCTATCAATTTAATCCTAATCCTAAAT-ATCCAATAATAAA
1 CATTCTATCAATTTAATCCTAATCCTAAATAATCCAATAATAAA
* *
129457 CATTCTATCAATTTAATCTTAATTCTAAATAATCCAA
1 CATTCTATCAATTTAATCCTAATCCTAAATAATCCAA
129494 CAAACACAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
43 41 0.54
44 35 0.46
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (44 bp):
CATTCTATCAATTTAATCCTAATCCTAAATAATCCAATAATAAA
Found at i:129832 original size:28 final size:26
Alignment explanation
Indices: 129792--129844 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
129782 CAAGTTGAAG
*
129792 GATGATGTGGCAAAAATAAATTAAATAA
1 GATGATATGGC-AAAA-AAATTAAATAA
129820 GATGATATGGCAAAAAAATTAAATA
1 GATGATATGGCAAAAAAATTAAATA
129845 CAATAAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.42
27 4 0.17
28 10 0.42
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.25
Consensus pattern (26 bp):
GATGATATGGCAAAAAAATTAAATAA
Found at i:129932 original size:16 final size:16
Alignment explanation
Indices: 129908--129938 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
129898 CTCAAATTTG
*
129908 AAAATCCTAATTTCTC
1 AAAACCCTAATTTCTC
129924 AAAACCCTAATTTCT
1 AAAACCCTAATTTCT
129939 GAAATCCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAACCCTAATTTCTC
Found at i:130355 original size:17 final size:16
Alignment explanation
Indices: 130329--130380 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
130319 AAATGCAAAT
130329 ATGCGAGCTCACCAAG
1 ATGCGAGCTCACCAAG
*
130345 ATTGTGAGCTCACCAAAAG
1 A-TGCGAGCTCACC--AAG
130364 ATGCGAGCTCACCAAG
1 ATGCGAGCTCACCAAG
130380 A
1 A
130381 CTAACGTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 5 0.16
17 11 0.35
18 11 0.35
19 4 0.13
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (16 bp):
ATGCGAGCTCACCAAG
Found at i:130373 original size:18 final size:18
Alignment explanation
Indices: 130329--130378 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
130319 AAATGCAAAT
130329 ATGCGAGCTCACC--AAG
1 ATGCGAGCTCACCAAAAG
*
130345 ATTGTGAGCTCACCAAAAG
1 A-TGCGAGCTCACCAAAAG
130364 ATGCGAGCTCACCAA
1 ATGCGAGCTCACCAA
130379 GACTAACGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 11 0.38
18 13 0.45
19 4 0.14
ACGTcount: A:0.34, C:0.28, G:0.22, T:0.16
Consensus pattern (18 bp):
ATGCGAGCTCACCAAAAG
Found at i:130568 original size:16 final size:16
Alignment explanation
Indices: 130525--130561 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
130515 TGAAATTCTC
130525 AATTTCTCAAAA-CCCT
1 AATTTCT-AAAATCCCT
130541 AATTTCTAAAATCCCT
1 AATTTCTAAAATCCCT
130557 AATTT
1 AATTT
130562 GTGAAATACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTTCTAAAATCCCT
Found at i:132956 original size:19 final size:18
Alignment explanation
Indices: 132910--132956 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
132900 TTTACTAGAA
*
132910 AATAT-TGATAAATAAAG
1 AATATATGAAAAATAAAG
*
132927 CATATAGTGAAAAATACAAG
1 AATATA-TGAAAAATA-AAG
132947 AATATATGAA
1 AATATATGAA
132957 TTTTGTAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 4 0.17
19 12 0.50
20 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (18 bp):
AATATATGAAAAATAAAG
Found at i:133216 original size:20 final size:20
Alignment explanation
Indices: 133187--133272 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 20
133177 AAATTGAGTT
* *
133187 AAAATGATTTTAAACATGTC
1 AAAATAATTTTAAACAAGTC
* **
133207 AAAATAATTTGAATTAAGTC
1 AAAATAATTTTAAACAAGTC
* **
133227 AAAATTATTTT-AACACTTC
1 AAAATAATTTTAAACAAGTC
**
133246 AAAATGTTTTTCAAACAAGTC
1 AAAATAATTTT-AAACAAGTC
133267 AAAATA
1 AAAATA
133273 GCTCTAGGCC
Statistics
Matches: 48, Mismatches: 16, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
19 13 0.27
20 24 0.50
21 11 0.23
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAATAATTTTAAACAAGTC
Found at i:140146 original size:19 final size:20
Alignment explanation
Indices: 140109--140146 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
140099 ATACTTTTAT
140109 AAAAATATCAATACTCATGA
1 AAAAATATCAATACTCATGA
*
140129 AAAAATATCGATAC-CATG
1 AAAAATATCAATACTCATG
140147 GGCCTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (20 bp):
AAAAATATCAATACTCATGA
Found at i:142309 original size:20 final size:20
Alignment explanation
Indices: 142263--142365 Score: 66
Period size: 20 Copynumber: 5.0 Consensus size: 20
142253 AGTTTGAAAC
*
142263 AATTTTAAAATCAAGTTAAAAT
1 AATTTT-AAA-CAAGTCAAAAT
* *
142285 GATTTTAAACATGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
* *
142305 AA-TTTAAATTAAGTTAAAAT
1 AATTTTAAA-CAAGTCAAAAT
* **
142325 CATTTT-AACACTTCAAAAT
1 AATTTTAAACAAGTCAAAAT
**
142344 GTTTTTCAAACAAGTCAAAAT
1 AATTTT-AAACAAGTCAAAAT
142365 A
1 A
142366 GCTCCAGGCT
Statistics
Matches: 60, Mismatches: 17, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
19 17 0.28
20 21 0.35
21 17 0.28
22 5 0.08
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.36
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:146263 original size:18 final size:18
Alignment explanation
Indices: 146236--146276 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
146226 AAGGACTTCC
* *
146236 TCCTCTCTAACATCAACT
1 TCCTCCCTAACAGCAACT
*
146254 TCCTCCCTAACAGCAAGT
1 TCCTCCCTAACAGCAACT
146272 TCCTC
1 TCCTC
146277 TTGACCAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.41, G:0.05, T:0.29
Consensus pattern (18 bp):
TCCTCCCTAACAGCAACT
Found at i:154822 original size:28 final size:29
Alignment explanation
Indices: 154786--154856 Score: 117
Period size: 28 Copynumber: 2.4 Consensus size: 29
154776 GTGATTTACA
154786 TGTATTTAGCACTTTGTGTGCTCTTTGTTC
1 TGTA-TTAGCACTTTGTGTGCTCTTTGTTC
154816 TG-ATTAGCACTTTGTGTGCTCTTTGTTC
1 TGTATTAGCACTTTGTGTGCTCTTTGTTC
*
154844 TGTAATAGCACTT
1 TGTATTAGCACTT
154857 CGGTGCTTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 27 0.69
29 10 0.26
30 2 0.05
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.49
Consensus pattern (29 bp):
TGTATTAGCACTTTGTGTGCTCTTTGTTC
Found at i:155920 original size:33 final size:33
Alignment explanation
Indices: 155878--155956 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
155868 ACATGACTTT
*
155878 TGGGGAGGGTGATGTTGAAGGGGTACAAGTTGA
1 TGGGGAGGGTGATGTTGAAGGGGTAAAAGTTGA
* *
155911 TGGGGAGGGTGATGTTTAAGGGGTAAAAGTTGT
1 TGGGGAGGGTGATGTTGAAGGGGTAAAAGTTGA
155944 TGGGGAGGGTGAT
1 TGGGGAGGGTGAT
155957 CGGCCTGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.23, C:0.01, G:0.49, T:0.27
Consensus pattern (33 bp):
TGGGGAGGGTGATGTTGAAGGGGTAAAAGTTGA
Found at i:158944 original size:18 final size:16
Alignment explanation
Indices: 158911--158956 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
158901 CAACAAATTA
158911 TTTCTTTTTTCATTCT
1 TTTCTTTTTTCATTCT
*
158927 TTTCTCTTTTTCTTTTCT
1 TTTCT-TTTTTC-ATTCT
*
158945 TTCCTTTTTTCA
1 TTTCTTTTTTCA
158957 CTTTTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 5 0.20
17 12 0.48
18 8 0.32
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTTTTCATTCT
Found at i:161905 original size:57 final size:57
Alignment explanation
Indices: 161817--161933 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
161807 ACGCGATTCT
161817 TGCTGAAAAAGCTTTGCTGAGTCATCACAGAATGTGCCCACAAGTTGTGCTTTGCGA
1 TGCTGAAAAAGCTTTGCTGAGTCATCACAGAATGTGCCCACAAGTTGTGCTTTGCGA
161874 TGCTGAAAAAGCTTTGCTGAGTCATCACAGAATGTGCCCACAAGTTGTGCTTTGCGA
1 TGCTGAAAAAGCTTTGCTGAGTCATCACAGAATGTGCCCACAAGTTGTGCTTTGCGA
161931 TGC
1 TGC
161934 ATTGACAAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (57 bp):
TGCTGAAAAAGCTTTGCTGAGTCATCACAGAATGTGCCCACAAGTTGTGCTTTGCGA
Found at i:168340 original size:18 final size:18
Alignment explanation
Indices: 168319--168389 Score: 51
Period size: 19 Copynumber: 4.1 Consensus size: 18
168309 GTGAATGTGT
168319 TGTTGAAGGGGTAGAATC
1 TGTTGAAGGGGTAGAATC
* *
168337 TGTT---GGGGAAG-GTC
1 TGTTGAAGGGGTAGAATC
* *
168351 ATTTTGAAGGGGTAGAAGC
1 -TGTTGAAGGGGTAGAATC
*
168370 TGTTGGAGGGGGTAGAATC
1 TGTT-GAAGGGGTAGAATC
168389 T
1 T
168390 TATGGGAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 11
0.66 0.16 0.19
Matches are distributed among these distances:
14 2 0.05
15 9 0.24
18 13 0.34
19 14 0.37
ACGTcount: A:0.24, C:0.06, G:0.42, T:0.28
Consensus pattern (18 bp):
TGTTGAAGGGGTAGAATC
Found at i:171478 original size:3 final size:3
Alignment explanation
Indices: 171470--171510 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
171460 AATATTTAAG
171470 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
171511 ATTGTTTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:171552 original size:21 final size:20
Alignment explanation
Indices: 171515--171553 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
171505 TATTATATTG
**
171515 TTTATATTTATCTTTTAAGC
1 TTTATATTTATAGTTTAAGC
171535 TTTATAATTTATAGTTTAA
1 TTTAT-ATTTATAGTTTAA
171554 TTTGGATCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTATATTTATAGTTTAAGC
Found at i:172715 original size:21 final size:20
Alignment explanation
Indices: 172685--172741 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
172675 AATTTAGCCA
* *
172685 TTTTTATTTTTATTTTCATAT
1 TTTTTATTTTTAATTTAAT-T
*
172706 TTTTTGTTTTTAATTTAATT
1 TTTTTATTTTTAATTTAATT
**
172726 TTTTTACATTTAATTT
1 TTTTTATTTTTAATTT
172742 TTTATTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTATTTTTAATTTAATT
Found at i:172730 original size:15 final size:15
Alignment explanation
Indices: 172712--172744 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
172702 ATATTTTTTG
172712 TTTTTA-ATTTAATT
1 TTTTTACATTTAATT
172726 TTTTTACATTTAATT
1 TTTTTACATTTAATT
172741 TTTT
1 TTTT
172745 ATTTTATAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTACATTTAATT
Found at i:174866 original size:10 final size:9
Alignment explanation
Indices: 174843--174894 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
174833 TAAGTTTTTA
*
174843 AAAAAAGATG
1 AAAAAA-ATT
174853 AAAAAAATT
1 AAAAAAATT
174862 CAAAAAAATT
1 -AAAAAAATT
* *
174872 AAAAAACTG
1 AAAAAAATT
174881 AAAAAAATT
1 AAAAAAATT
*
174890 GAAAA
1 AAAAA
174895 TTTCAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
9 20 0.57
10 15 0.43
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (9 bp):
AAAAAAATT
Found at i:174875 original size:18 final size:18
Alignment explanation
Indices: 174854--174905 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
174844 AAAAAGATGA
174854 AAAAAATTCAAAAAAATT
1 AAAAAATTCAAAAAAATT
* *
174872 AAAAAACTGAAAAAAATT
1 AAAAAATTCAAAAAAATT
* *
174890 GAAAATTTCAAAAAAA
1 AAAAAATTCAAAAAAA
174906 ATTAGTATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (18 bp):
AAAAAATTCAAAAAAATT
Found at i:174938 original size:6 final size:6
Alignment explanation
Indices: 174915--174981 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
174905 AATTAGTATA
* * * * *
174915 TTTATT TTCATA TTTATT TTTATT TTTATT TTTAGT TTCAAT TTTA-T
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* *
174962 TTAATT TTTAAT TTTATT TT
1 TTTATT TTTATT TTTATT TT
174982 AATTATGCAC
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
5 4 0.08
6 44 0.92
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTATT
Found at i:178362 original size:17 final size:17
Alignment explanation
Indices: 178297--178374 Score: 86
Period size: 17 Copynumber: 4.6 Consensus size: 17
178287 AGAGCTCGCA
178297 GGTGAGCTC-TAATGTTT
1 GGTGAGCTCGTAAT-TTT
*
178314 GGTGAGCTCGTAATCTT
1 GGTGAGCTCGTAATTTT
** *
178331 GGTGAGCTCACAGTTTT
1 GGTGAGCTCGTAATTTT
*
178348 GGTGAGCTCGTAGTTTT
1 GGTGAGCTCGTAATTTT
*
178365 AGTGAGCTCG
1 GGTGAGCTCG
178375 CATCTTTGCA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 48 0.92
18 4 0.08
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.36
Consensus pattern (17 bp):
GGTGAGCTCGTAATTTT
Found at i:178667 original size:15 final size:15
Alignment explanation
Indices: 178649--178697 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
178639 GGGATTTAAC
178649 GATTTGGGAATAAGG
1 GATTTGGGAATAAGG
* * *
178664 GATTTGGGATTTCA-C
1 GATTTGGGA-ATAAGG
178679 GATTTGGGAATAAGG
1 GATTTGGGAATAAGG
178694 GATT
1 GATT
178698 AAGGATGTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (15 bp):
GATTTGGGAATAAGG
Found at i:178674 original size:30 final size:30
Alignment explanation
Indices: 178638--178697 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
178628 CCGGAAATTA
178638 TGGGATTTAACGATTTGGGAATAAGGGATT
1 TGGGATTTAACGATTTGGGAATAAGGGATT
*
178668 TGGGATTTCACGATTTGGGAATAAGGGATT
1 TGGGATTTAACGATTTGGGAATAAGGGATT
178698 AAGGATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.33
Consensus pattern (30 bp):
TGGGATTTAACGATTTGGGAATAAGGGATT
Found at i:179404 original size:23 final size:22
Alignment explanation
Indices: 179374--179429 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
179364 AAAAGTACAT
*
179374 AAAT-TATAAATAAAAAACCAA
1 AAATATATAAATAAAAAAACAA
* *
179395 AACATATAT-ATTAAAAAAAGAA
1 AA-ATATATAAATAAAAAAACAA
179417 AAATATATCAAAT
1 AAATATAT-AAAT
179430 GATTCAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
21 8 0.30
22 14 0.52
23 5 0.19
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATATATAAATAAAAAAACAA
Found at i:179422 original size:21 final size:22
Alignment explanation
Indices: 179384--179424 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
179374 AAATTATAAA
*
179384 TAAAAAACCAAAACATATATAT
1 TAAAAAAACAAAACATATATAT
*
179406 TAAAAAAAGAAAA-ATATAT
1 TAAAAAAACAAAACATATAT
179425 CAAATGATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (22 bp):
TAAAAAAACAAAACATATATAT
Found at i:180151 original size:60 final size:59
Alignment explanation
Indices: 180026--180151 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 59
180016 CTTTTTTCTA
* * *** *
180026 AATTTTTAGAATTTAAACTAAATTGAATTTTTTTTAAATGTTGAAGGTTAAATTTATTG
1 AATTTTTAGAATTCAAACTAAAATGAATTTTTTTTAAACAATGAAGGCTAAATTTATTG
* *
180085 AATTTTTAGAATTCAAACTAAAAT-AATTAATTTTTTAAACAATGAGGGCTAAATTTGTTG
1 AATTTTTAGAATTCAAACTAAAATGAATT--TTTTTTAAACAATGAAGGCTAAATTTATTG
*
180145 ATTTTTT
1 AATTTTT
180152 TAGATTTAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
58 4 0.07
59 22 0.39
60 30 0.54
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (59 bp):
AATTTTTAGAATTCAAACTAAAATGAATTTTTTTTAAACAATGAAGGCTAAATTTATTG
Found at i:185347 original size:26 final size:26
Alignment explanation
Indices: 185318--185397 Score: 115
Period size: 26 Copynumber: 3.1 Consensus size: 26
185308 CCAATTAGGG
185318 TATCGCTCTTACAAGCCAGTTCAATA
1 TATCGCTCTTACAAGCCAGTTCAATA
* * *
185344 TATCGCTCTTATAAGCCAATTCAGTA
1 TATCGCTCTTACAAGCCAGTTCAATA
* *
185370 TATCGCTTTTACAAGCTAGTTCAATA
1 TATCGCTCTTACAAGCCAGTTCAATA
185396 TA
1 TA
185398 ATTCTTCAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (26 bp):
TATCGCTCTTACAAGCCAGTTCAATA
Found at i:189285 original size:26 final size:26
Alignment explanation
Indices: 189240--189297 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
189230 ATTTAGCTCA
*
189240 TACGAGCCTAGTCAGGATATCGTTCT
1 TACGAGCCTAGTCAGGATATCGATCT
* * * *
189266 TACGAGCCTATTTAGTATATTGATCT
1 TACGAGCCTAGTCAGGATATCGATCT
189292 TACGAG
1 TACGAG
189298 GCAGTTCAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (26 bp):
TACGAGCCTAGTCAGGATATCGATCT
Found at i:207765 original size:77 final size:76
Alignment explanation
Indices: 207626--208128 Score: 585
Period size: 77 Copynumber: 6.5 Consensus size: 76
207616 ATTTTATAGG
* * * * * *
207626 TCTCTTACCCCGATCATAGGGCAGATCGAAGCATCCAAATCTCTTACCCTAATTAGAGGGTAGAT
1 TCTCTTACCCCGATCAT-GGGCAGATTGAAGAATCC-AATCTCTTACCTTAATCAGAAGGCAGA-
*
207691 TTGAAGACAAACAA
63 TTGAAGACAACCAA
* * *
207705 TCTCTTACCCCGATCGA-GGGCAGATTAAAGAATCCAATCTCTTACCTTAATCAAAAGGTAGATT
1 TCTCTTACCCCGATC-ATGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGATT
* ** *
207769 GAATACATGCGA
65 GAAGACAACCAA
* * * *
207781 TCTCTTACCCTGATCATGAGGTAGATTGAAGAATCCAAACTCTTGCCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCATG-GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGATT
*
207846 GAAGACACACCGA
65 GAAGACA-ACCAA
207859 TCTCTTACCCCGATCATGGAGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCATGG-GCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGATT
207924 GAAGACACACCAA
65 GAAGACA-ACCAA
* * * * *
207937 TCTCTTACCTCGATCATGGGGCAGATTAAAGAATTCAATCTCTTACCTTAATCAGAATGCACATT
1 TCTCTTACCCCGATCAT-GGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGATT
* * ** *
208002 AAAGATATTCAG
65 GAAGACAACCAA
* * *
208014 TCTCTTACCTCAATCATGGGGCAAATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCAT-GGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGATT
** *
208079 GAAGACATGCAG
65 GAAGACAACCAA
208091 TCTCTTACCCCGATCATGAGGCAGATTGAAGAATCCAA
1 TCTCTTACCCCGATCATG-GGCAGATTGAAGAATCCAA
208129 ATCAGAAGAC
Statistics
Matches: 369, Mismatches: 48, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
75 1 0.00
76 26 0.07
77 173 0.47
78 151 0.41
79 17 0.05
80 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (76 bp):
TCTCTTACCCCGATCATGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGATTG
AAGACAACCAA
Found at i:207787 original size:39 final size:39
Alignment explanation
Indices: 207726--208099 Score: 188
Period size: 38 Copynumber: 9.7 Consensus size: 39
207716 GATCGAGGGC
* *
207726 AGATTAAAGA-ATCCAATCTCTTACCTTAATCAAAAGGT
1 AGATTGAAGACATCCGATCTCTTACCTTAATCAAAAGGT
* * * * **
207764 AGATTGAATACATGCGATCTCTTACCCTGATCATGAGGT
1 AGATTGAAGACATCCGATCTCTTACCTTAATCAAAAGGT
* * * * *
207803 AGATTGAAGA-ATCCAAACTCTTGCCTTAATCAGAAGGC
1 AGATTGAAGACATCCGATCTCTTACCTTAATCAAAAGGT
* *** ** *
207841 AGATTGAAGACACACCGATCTCTTACCCCGATC-ATGGAGC
1 AGATTGAAGACA-TCCGATCTCTTACCTTAATCAAAAG-GT
* * *
207881 AGATTGAAGA-ATCCAATCTCTTACCTTAATCAGAAGGC
1 AGATTGAAGACATCCGATCTCTTACCTTAATCAAAAGGT
* * ** *** *
207919 AGATTGAAGACACACCAATCTCTTACCTCGATCATGGGGC
1 AGATTGAAGACA-TCCGATCTCTTACCTTAATCAAAAGGT
* * * * * *
207959 AGATTAAAGA-ATTCAATCTCTTACCTTAATCAGAATGC
1 AGATTGAAGACATCCGATCTCTTACCTTAATCAAAAGGT
* * * * * *** *
207997 ACATTAAAGATATTC-AGTCTCTTACCTCAATCATGGGGC
1 AGATTGAAGACATCCGA-TCTCTTACCTTAATCAAAAGGT
* * * *
208036 AAATTGAAGA-ATCCAATCTCTTACCTTAATCAGAAGGC
1 AGATTGAAGACATCCGATCTCTTACCTTAATCAAAAGGT
*
208074 AGATTGAAGACATGC-AGTCTCTTACC
1 AGATTGAAGACATCCGA-TCTCTTACC
208100 CCGATCATGA
Statistics
Matches: 258, Mismatches: 66, Indels: 23
0.74 0.19 0.07
Matches are distributed among these distances:
38 124 0.48
39 79 0.31
40 55 0.21
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (39 bp):
AGATTGAAGACATCCGATCTCTTACCTTAATCAAAAGGT
Found at i:207883 original size:155 final size:152
Alignment explanation
Indices: 207626--208129 Score: 600
Period size: 155 Copynumber: 3.3 Consensus size: 152
207616 ATTTTATAGG
* * * * * *
207626 TCTCTTACCCCGATCAT-AGGGCAGATCGAAGCATCCAAATCTCTTACCCTAATTAGAGGGTAGA
1 TCTCTTACCCCGATCATGA-GGCAGATTGAAGAATCCAAA-CTCTTACCTTAATCAGAAGGCAGA
* * *
207690 TTTGAAGACAAACAATCTCTTACCCCGATCGA-GGGCAGATTAAAGAATCCAATCTCTTACCTTA
64 -TTGAAGACAACCGATCTCTTACCCCGATC-ATGGGCAGATTGAAGAATCCAATCTCTTACCTTA
* * *
207754 ATCAAAAGGTAGATTGAATACATGCGA
127 ATCAGAAGGCAGATTGAAGACATGC-A
* * *
207781 TCTCTTACCCTGATCATGAGGTAGATTGAAGAATCCAAACTCTTGCCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCATGAGGCAGATTGAAGAATCCAAACTCTTACCTTAATCAGAAGGCAGATT
207846 GAAGACACACCGATCTCTTACCCCGATCATGGAGCAGATTGAAGAATCCAATCTCTTACCTTAAT
66 GAAGACA-ACCGATCTCTTACCCCGATCATGG-GCAGATTGAAGAATCCAATCTCTTACCTTAAT
**
207911 CAGAAGGCAGATTGAAGACACACCAA
129 CAGAAGGCAGATTGAAGACA-TGC-A
* * * * * * *
207937 TCTCTTACCTCGATCATGGGGCAGATTAAAGAATTCAATCTCTTACCTTAATCAGAATGCACATT
1 TCTCTTACCCCGATCATGAGGCAGATTGAAGAATCCAAACTCTTACCTTAATCAGAAGGCAGATT
* * ** * * *
208002 AAAGATATTC-AGTCTCTTACCTCAATCATGGGGCAAATTGAAGAATCCAATCTCTTACCTTAAT
66 GAAGACAACCGA-TCTCTTACCCCGATCAT-GGGCAGATTGAAGAATCCAATCTCTTACCTTAAT
208066 CAGAAGGCAGATTGAAGACATGCA
129 CAGAAGGCAGATTGAAGACATGCA
208090 GTCTCTTACCCCGATCATGAGGCAGATTGAAGAATCCAAA
1 -TCTCTTACCCCGATCATGAGGCAGATTGAAGAATCCAAA
208130 TCAGAAGACA
Statistics
Matches: 299, Mismatches: 42, Indels: 17
0.84 0.12 0.05
Matches are distributed among these distances:
153 11 0.04
154 75 0.25
155 148 0.49
156 65 0.22
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (152 bp):
TCTCTTACCCCGATCATGAGGCAGATTGAAGAATCCAAACTCTTACCTTAATCAGAAGGCAGATT
GAAGACAACCGATCTCTTACCCCGATCATGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCA
GAAGGCAGATTGAAGACATGCA
Found at i:208191 original size:64 final size:65
Alignment explanation
Indices: 208063--208192 Score: 181
Period size: 64 Copynumber: 2.0 Consensus size: 65
208053 CTCTTACCTT
* * * * *
208063 AATCAGAAGGCAGATTGAAGACATGCAGTCTCTTACCCCGATCATGAGGCAGATTGAAGAATCCA
1 AATCAGAAGACAGATTGAAGACATGCAATCTCTTACCCCGATCAAGACGCAGAATGAAGAATCCA
* * *
208128 AATCAGAAGACAGATTGAAGACAT-CAATCTCTTACCTCGATCAAGACGTAGAATGAAGCATCCA
1 AATCAGAAGACAGATTGAAGACATGCAATCTCTTACCCCGATCAAGACGCAGAATGAAGAATCCA
208192 A
1 A
208193 TCTTTTACCC
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 34 0.60
65 23 0.40
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (65 bp):
AATCAGAAGACAGATTGAAGACATGCAATCTCTTACCCCGATCAAGACGCAGAATGAAGAATCCA
Found at i:219308 original size:43 final size:42
Alignment explanation
Indices: 219218--219348 Score: 108
Period size: 42 Copynumber: 3.1 Consensus size: 42
219208 ATTAGCGGCG
* * * * *
219218 TTTTCCTCATAAATGTCGCTAATGCTCTTTACTTTTTACG-GT
1 TTTTCCT-ATAAATGCCGCTATTGCTCTTTACCTTTTGCGCAT
*
219260 GTTTTCCTATAAATGCCGCTATTGCTCCTTACCTTTTGCAGCAT
1 -TTTTCCTATAAATGCCGCTATTGCTCTTTACCTTTTGC-GCAT
* * *
219304 TTTTCCCATAAA-CCTCACTATTG-T-TTTACCTTTTGCGGCAT
1 TTTTCCTATAAATGC-CGCTATTGCTCTTTACCTTTTGC-GCAT
219345 TTTT
1 TTTT
219349 TGTCCAAACG
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
41 19 0.26
42 28 0.38
43 26 0.35
44 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.11, T:0.46
Consensus pattern (42 bp):
TTTTCCTATAAATGCCGCTATTGCTCTTTACCTTTTGCGCAT
Found at i:234991 original size:29 final size:32
Alignment explanation
Indices: 234939--235006 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 32
234929 GCTCTCTATT
** *
234939 TTCTTTTGTTTTTTTTGCTCTTTC-C-T-CTC
1 TTCTTTTGCATTTTTTGATCTTTCTCATACTC
*
234968 TTCTTTTGCATTTTTTGATTTTTCTCATACTC
1 TTCTTTTGCATTTTTTGATCTTTCTCATACTC
235000 TTCTTTT
1 TTCTTTT
235007 TCTTTTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 20 0.62
30 1 0.03
31 1 0.03
32 10 0.31
ACGTcount: A:0.06, C:0.21, G:0.06, T:0.68
Consensus pattern (32 bp):
TTCTTTTGCATTTTTTGATCTTTCTCATACTC
Found at i:238499 original size:30 final size:30
Alignment explanation
Indices: 238465--238521 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
238455 TGTGTCCGCA
*
238465 ACATGAGTG-TTCGCACCTCTAGTGCTCACT
1 ACATGAGTGCTT-GCACCACTAGTGCTCACT
*
238495 ACATGAGTGCTTGCAGCACTAGTGCTC
1 ACATGAGTGCTTGCACCACTAGTGCTC
238522 GCATTGTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (30 bp):
ACATGAGTGCTTGCACCACTAGTGCTCACT
Found at i:238536 original size:15 final size:15
Alignment explanation
Indices: 238518--238556 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
238508 CAGCACTAGT
238518 GCTCGCATTGTCTAA
1 GCTCGCATTGTCTAA
** *
238533 GCTCGCAAGGTCTAT
1 GCTCGCATTGTCTAA
238548 GCTCGCATT
1 GCTCGCATT
238557 ATTAGAGCTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (15 bp):
GCTCGCATTGTCTAA
Found at i:242366 original size:78 final size:78
Alignment explanation
Indices: 242237--242392 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
242227 AGTATTTATG
242237 GCTACCTTTACCAAATTTCCATCTGACTTCCCTACAAAACTCTTCACAAAAACTCCACTAAGGAA
1 GCTACCTTTACCAAATTTCCATCTGACTTCCCTACAAAACTCTTCACAAAAACTCCACTAAGGAA
242302 CAATTTCCCCTAA
66 CAATTTCCCCTAA
242315 GCTACCTTTACCAAATTTCCATCTGACTTCCCTACAAAACTCTTCACAAAAACTCCACTAAGGAA
1 GCTACCTTTACCAAATTTCCATCTGACTTCCCTACAAAACTCTTCACAAAAACTCCACTAAGGAA
242380 CAATTTCCCCTAA
66 CAATTTCCCCTAA
242393 AAGACACCAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.27
Consensus pattern (78 bp):
GCTACCTTTACCAAATTTCCATCTGACTTCCCTACAAAACTCTTCACAAAAACTCCACTAAGGAA
CAATTTCCCCTAA
Found at i:246470 original size:21 final size:21
Alignment explanation
Indices: 246446--246485 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
246436 TTTGAATTTT
*
246446 ATCAAGAGGAAAAAGCTGAAA
1 ATCAAGAGAAAAAAGCTGAAA
* *
246467 ATCAGGAGAAAAAATCTGA
1 ATCAAGAGAAAAAAGCTGA
246486 TTTGTCATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.10, G:0.23, T:0.12
Consensus pattern (21 bp):
ATCAAGAGAAAAAAGCTGAAA
Found at i:258140 original size:36 final size:36
Alignment explanation
Indices: 258068--258141 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
258058 TTCTCCAATC
**
258068 ACCCATCACAATTTTAAGCATAATCCATATTATATG
1 ACCCATCACAATTTTAAGCATAATCCATACCATATG
*
258104 ACCCATCACAATTTT-AGTCATAATCCATACCGTATG
1 ACCCATCACAATTTTAAG-CATAATCCATACCATATG
258140 AC
1 AC
258142 ATACACATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 2 0.06
36 32 0.94
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (36 bp):
ACCCATCACAATTTTAAGCATAATCCATACCATATG
Found at i:267461 original size:18 final size:18
Alignment explanation
Indices: 267431--267478 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
267421 TCAAAAGCAC
267431 TTTTGTGAT-AAAAACAA
1 TTTTGTGATAAAAAACAA
*
267448 TTTTGTGATAAAAAACAT
1 TTTTGTGATAAAAAACAA
*
267466 TTTTGGGATAAAA
1 TTTTGTGATAAAA
267479 GCATTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (18 bp):
TTTTGTGATAAAAAACAA
Found at i:267483 original size:17 final size:17
Alignment explanation
Indices: 267431--267483 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
267421 TCAAAAGCAC
*
267431 TTTTGTGATAAAAACAA
1 TTTTGTGATAAAAACAT
267448 TTTTGTGATAAAAAACAT
1 TTTTGTGAT-AAAAACAT
* *
267466 TTTTGGGATAAAAGCAT
1 TTTTGTGATAAAAACAT
267483 T
1 T
267484 ATTAAACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TTTTGTGATAAAAACAT
Found at i:269310 original size:151 final size:148
Alignment explanation
Indices: 268934--269750 Score: 1090
Period size: 151 Copynumber: 5.4 Consensus size: 148
268924 TTTGGGAAAT
* * * * * *
268934 GTTTTGGTTTTTTTTAAACAATTTTGAAATAAAAGCTTTGATTTTTTTAAGTAAAATAGTTATTT
1 GTTTTGATTTTTTTT-AACTATTTCGAAATAAAA-ATTTGA-ATTTTTAAGTAAAATAGTGATTT
*
268999 TCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAA
63 TCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAA
** *
269064 AAAAATTAAATTTTTAATAAA
128 AAAGTTTAAATTTTTAACAAA
* * * *
269085 -TTTTTAATTTTTTTAATTATTTCGAAATAAAAATTTGAATTTTTAGGTAAAATAGTGATTTTCT
1 GTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTTC-
* *
269149 TTTAAAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTTAGTTATTTTAAAGA
65 TTT--AAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTG-TTTTTTAGTTATTTTAAAGA
*
269214 AAAATTTTAAATTTTTAACAAA
127 AAAAGTTTAAATTTTTAACAAA
* * *
269236 ATTTTGATTTTTTTTTAACTATTTAGAAATAAAAAAATTTGAATTTTTAAGCAAAATAGTGATTT
1 GTTTTGA-TTTTTTTTAACTATTTCGAAAT--AAAAATTTGAATTTTTAAGTAAAATAGTGATTT
269301 TCTTTAAAAAAGAGAAAGTTTAGATTTTT-AAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAA
63 TCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAA
*
269365 AAAGTTTAAATTTTTAATAAA
128 AAAGTTTAAATTTTTAACAAA
* * *
269386 GTTTT-AATTTTTTTAATTATTTCGAAATAAAAATTTGGATTTTTAAGTAAAAATAGTGATTTTC
1 GTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTGAATTTTTAAGT-AAAATAGTGATTTTC
* * *
269450 TTTAAAAAAAGAGAAAATTTATATTTTTAAAAA-ATAAAATCTATTTTTTTTAGTTATTTTAAAG
65 TTT-AAAAAAGAGAAAGTTTAGATTTTTAAAAATA-AAAATC--TGTTTTTTAGTTATTTTAAAG
*
269514 AAAAATTTTAAATTTTTAACAAA
126 AAAAAGTTTAAATTTTTAACAAA
*
269537 GTTTTGATTTTTTTTTCTAACTATTTCGAAATAAAAATTTGGATTTTTAAGT--AA-AGTGATTT
1 GTTTTGA--TTTTTTT-TAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTT
*
269599 TCTTTAAAAAAAGAAAAAGTTTAGATTTTTAAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAA
63 TCTTT-AAAAAAGAGAAAGTTTAGATTTTT--AAAAATAAAAATCTGTTTTTTAGTTATTTTAAA
*
269664 TAAAAAGTTTAAATTTTTAACAAA
125 GAAAAAGTTTAAATTTTTAACAAA
** *
269688 GTTCAGATTTTTTTTAACTATTTCGAAATAAAAATTTGGATTTTTAAGTAAAATAGTGATTTT
1 GTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTT
269751 TGTTTAATCA
Statistics
Matches: 595, Mismatches: 47, Indels: 48
0.86 0.07 0.07
Matches are distributed among these distances:
146 18 0.03
147 40 0.07
148 85 0.14
149 33 0.06
150 93 0.16
151 189 0.32
152 30 0.05
153 30 0.05
154 10 0.02
155 67 0.11
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (148 bp):
GTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTTCT
TTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAA
GTTTAAATTTTTAACAAA
Found at i:269481 original size:22 final size:22
Alignment explanation
Indices: 269455--269499 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
269445 TTTTCTTTAA
*
269455 AAAAAGAGAAAATTTATATTTTT
1 AAAAA-AGAAAATCTATATTTTT
* *
269478 AAAAAATAAAATCTATTTTTTT
1 AAAAAAGAAAATCTATATTTTT
269500 TAGTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAAAAGAAAATCTATATTTTT
Found at i:269485 original size:301 final size:300
Alignment explanation
Indices: 268935--269750 Score: 1216
Period size: 301 Copynumber: 2.7 Consensus size: 300
268925 TTGGGAAATG
* * * * ** * *
268935 TTTTGGTTTTTTTTAAACAATTTTGAAATAAAAGCTTTGATTTTTTTAAGTAAAATAGTTATTTT
1 TTTTGATTTTTTTTTAACTATTTAGAAATAAAAAATTTGA-ATTTTTAAG-AAAATAGTGATTTT
*
269000 CTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAA
64 CTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAA
** * *
269065 AAAATTAAATTTTTAATAAATTTTTAATTTTTTTAATTATTTCGAAATAAAAATTTGAATTTTTA
129 AAGTTTAAATTTTTAATAAAGTTTTAATTTTTTTAATTATTTCGAAATAAAAATTTGGATTTTTA
* *
269130 GGTAAAATAGTGATTTTCTTTTAAAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAATCT-GT
194 AGTAAAATAGTGATTTTCTTTTAAAAAAAAAAGAAAATTTATATTTTTAAAAAT-AAAATCTAGT
269194 TTTTTTAGTTATTTTAAAGAAAAATTTTAAATTTTTAACAAAA
258 TTTTTTAGTTATTTTAAAGAAAAATTTTAAATTTTTAACAAAA
269237 TTTTGATTTTTTTTTAACTATTTAGAAATAAAAAAATTTGAATTTTTAAGCAAAATAGTGATTTT
1 TTTTGATTTTTTTTTAACTATTTAGAAAT-AAAAAATTTGAATTTTTAAG-AAAATAGTGATTTT
269302 CTTTAAAAAAGAGAAAGTTTAGATTTTT-AAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAA
64 CTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAA
269366 AAGTTTAAATTTTTAATAAAGTTTTAATTTTTTTAATTATTTCGAAATAAAAATTTGGATTTTTA
129 AAGTTTAAATTTTTAATAAAGTTTTAATTTTTTTAATTATTTCGAAATAAAAATTTGGATTTTTA
* *
269431 AGTAAAAATAGTGATTTTC-TTT-AAAAAAAGAGAAAATTTATATTTTTAAAAAATAAAATCTAT
194 AGT-AAAATAGTGATTTTCTTTTAAAAAAAAAAGAAAATTTATATTTTT-AAAAATAAAATCTAG
*
269494 TTTTTTTAGTTATTTTAAAGAAAAATTTTAAATTTTTAACAAAG
257 TTTTTTTAGTTATTTTAAAGAAAAATTTTAAATTTTTAACAAAA
* * *
269538 TTTTGATTTTTTTTTCTAACTATTTCGAAAT-AAAAATTTGGATTTTTAAG-TAA-AGTGATTTT
1 TTTTGA-TTTTTTTT-TAACTATTTAGAAATAAAAAATTTGAATTTTTAAGAAAATAGTGATTTT
* *
269600 CTTTAAAAAAAGAAAAAGTTTAGATTTTTAAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAT
64 CTTT-AAAAAAGAGAAAGTTTAGATTTTT--AAAAATAAAAATCTGTTTTTTAGTTATTTTAAAG
* * *
269665 AAAAAGTTTAAATTTTTAACAAAG-TTCAGATTTTTTTTAACTATTTCGAAATAAAAATTTGGAT
126 AAAAAGTTTAAATTTTTAATAAAGTTTTA-A-TTTTTTTAATTATTTCGAAATAAAAATTTGGAT
269729 TTTTAAGTAAAATAGTGATTTT
189 TTTTAAGTAAAATAGTGATTTT
269751 TGTTTAATCA
Statistics
Matches: 475, Mismatches: 27, Indels: 24
0.90 0.05 0.05
Matches are distributed among these distances:
298 13 0.03
299 25 0.05
300 30 0.06
301 177 0.37
302 167 0.35
303 63 0.13
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (300 bp):
TTTTGATTTTTTTTTAACTATTTAGAAATAAAAAATTTGAATTTTTAAGAAAATAGTGATTTTCT
TTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAA
GTTTAAATTTTTAATAAAGTTTTAATTTTTTTAATTATTTCGAAATAAAAATTTGGATTTTTAAG
TAAAATAGTGATTTTCTTTTAAAAAAAAAAGAAAATTTATATTTTTAAAAATAAAATCTAGTTTT
TTTAGTTATTTTAAAGAAAAATTTTAAATTTTTAACAAAA
Found at i:271202 original size:239 final size:237
Alignment explanation
Indices: 270785--271260 Score: 670
Period size: 239 Copynumber: 2.0 Consensus size: 237
270775 AAAATCATAA
* ** * *
270785 TAATGATAAAAGATCCAATAAATTGTAGATGAATTTTAATGTTTCTCTTAATTCATTAGTAACTT
1 TAATGATAAAAAATAAAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGAAACTT
*
270850 TTAGGCTTTTTTTAGGATTCTAAAATAGAATAATTTTAAGAATTGAATATATTTTACTAGAATTA
66 TTAGGCTTTTTTTAGGATTCTAAAATAGAATAATTTTAAAAATTGAATATATTTTACTAGAATTA
270915 TTTAGATATCCTTTAGGATTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAA
131 TTTAGATATCCTTTAGGATTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAA
** * * * *
270980 GTTTGGTGAACACGTTTTAGTCAAGTTATAAGTAAATCGGAG
196 GTTTGGAAAACACATCTTAGTCAAATTACAAGTAAATCGGAG
* ** *
271022 TAATGATAAAAAATAAAATAAGTTGTTTATGAATTTTAATATTTCTCTTAATTCATTAGAAATTT
1 TAATGATAAAAAATAAAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGAAA-CT
* *
271087 TTTAGG-TCTTTTTTAGGATTCTAAAGTTGAATTAATTTTAAAAATTGAA-AGTATTTTACTAGA
65 TTTAGGCT-TTTTTTAGGATTCTAAAATAGAA-TAATTTTAAAAATTGAATA-TATTTTACTAGA
* * * *
271150 ATTATTTA-AGTATTCTTTAGGGTTCTTATTAGGAGTAAAAATCTTTAATTTAAGTTTTAAATTC
127 ATTATTTAGA-TATCCTTTAGGATTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTA
* *
271214 GATAAGTTTGGAAAACATATCTTAGTCAAATTACAAGTAAATTGGAG
191 GATAAGTTTGGAAAACACATCTTAGTCAAATTACAAGTAAATCGGAG
271261 GCATTTTTTA
Statistics
Matches: 210, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
237 55 0.26
238 30 0.14
239 125 0.60
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (237 bp):
TAATGATAAAAAATAAAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGAAACTT
TTAGGCTTTTTTTAGGATTCTAAAATAGAATAATTTTAAAAATTGAATATATTTTACTAGAATTA
TTTAGATATCCTTTAGGATTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAA
GTTTGGAAAACACATCTTAGTCAAATTACAAGTAAATCGGAG
Found at i:280010 original size:18 final size:18
Alignment explanation
Indices: 279989--280032 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
279979 AATTTTTTTT
279989 TATTTTTTC-TTTTTCTC
1 TATTTTTTCTTTTTTCTC
280006 GTA-TTTTTCTTTTTTCTC
1 -TATTTTTTCTTTTTTCTC
280024 TACTTTTTT
1 TA-TTTTTT
280033 GATCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (18 bp):
TATTTTTTCTTTTTTCTC
Found at i:280030 original size:17 final size:17
Alignment explanation
Indices: 279993--280030 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
279983 TTTTTTTATT
*
279993 TTTTCTTTTTCTCGTAT
1 TTTTCTTTTTCTCGTAC
280010 TTTTCTTTTTTCTC-TAC
1 TTTTC-TTTTTCTCGTAC
280027 TTTT
1 TTTT
280031 TTGATCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTCTTTTTCTCGTAC
Found at i:285127 original size:109 final size:106
Alignment explanation
Indices: 284994--285195 Score: 273
Period size: 106 Copynumber: 1.9 Consensus size: 106
284984 AACAAAGAAC
* * *
284994 ATTTATTGATTTTAAATAGAATATTCAATTATTTAGGTTCAAGGAAAAATCATACCCA-ACACCT
1 ATTTATCGATTTTAAATAGAATATTCAATTATTTAGGTT-AA--AAAAACCATACCCACA-ACAT
* *
285058 CT-GGGCACAATTTCTCGAGTTCCCTAAAATAACAAAACATTAAGT
62 -TAGGGCACAATTTCTCGAATTCCCGAAAATAACAAAACATTAAGT
* * *
285103 ATTTATCGATTTTGAATAGGATATTCAATTATTTAGGTTAAAAATACCATACCCACAACATTAGG
1 ATTTATCGATTTTAAATAGAATATTCAATTATTTAGGTTAAAAAAACCATACCCACAACATTAGG
285168 GCACAATTTCTCGAATTCCCGAAAATAA
66 GCACAATTTCTCGAATTCCCGAAAATAA
285196 AAGAAAATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
105 1 0.01
106 43 0.52
107 1 0.01
108 2 0.02
109 36 0.43
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.32
Consensus pattern (106 bp):
ATTTATCGATTTTAAATAGAATATTCAATTATTTAGGTTAAAAAAACCATACCCACAACATTAGG
GCACAATTTCTCGAATTCCCGAAAATAACAAAACATTAAGT
Found at i:287713 original size:30 final size:30
Alignment explanation
Indices: 287679--287743 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
287669 ACTTATTTTA
*
287679 TTGTTAATTTTGTTATTATTTAAGAGGCAT
1 TTGTTAATTTTGTTATTATTTAAGAGACAT
*
287709 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTAAGAGACAT
287739 TTGTT
1 TTGTT
287744 TTTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTAAGAGACAT
Found at i:291419 original size:16 final size:16
Alignment explanation
Indices: 291398--291429 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
291388 GAATTGTTGC
291398 GTTTCATATACACATA
1 GTTTCATATACACATA
291414 GTTTCATATACACATA
1 GTTTCATATACACATA
291430 TATTCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
GTTTCATATACACATA
Found at i:294233 original size:120 final size:120
Alignment explanation
Indices: 294017--294253 Score: 359
Period size: 120 Copynumber: 2.0 Consensus size: 120
294007 AGTGGGTTCC
* *
294017 TTGATAAGGTAGAAGACAACGTGGCCATGCGTATGTGGTCAAAGAAAAAACAACGCAAAAAAGTA
1 TTGATAAGGTAGAAGACAACATGGCCATGCGCATGTGGTCAAAGAAAAAACAACGCAAAAAAGTA
294082 AGAGCCTACCGGAAGGGCACATATCAAAGTTTTGGGTTTACACTCAAATAAACGT
66 AGAGCCTACCGGAAGGGCACATATCAAAGTTTTGGGTTTACACTCAAATAAACGT
* * * * *
294137 TTGATAAGGTAGAAGACAACATGGTCGTGCGCATGTGGTCAAAGGAAAAATAACGCGAAAAAGTA
1 TTGATAAGGTAGAAGACAACATGGCCATGCGCATGTGGTCAAAGAAAAAACAACGCAAAAAAGTA
* * * *
294202 GGAGCTTACC-GATAGGGCACATATTAGAGTTTTGGGTTTACACTCAAATAAA
66 AGAGCCTACCGGA-AGGGCACATATCAAAGTTTTGGGTTTACACTCAAATAAA
294254 TGTAATCCAT
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
119 2 0.02
120 103 0.98
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (120 bp):
TTGATAAGGTAGAAGACAACATGGCCATGCGCATGTGGTCAAAGAAAAAACAACGCAAAAAAGTA
AGAGCCTACCGGAAGGGCACATATCAAAGTTTTGGGTTTACACTCAAATAAACGT
Found at i:298378 original size:7 final size:7
Alignment explanation
Indices: 298335--298407 Score: 77
Period size: 7 Copynumber: 11.1 Consensus size: 7
298325 TTTCACCCAA
298335 AAAGAA-
1 AAAGAAG
298341 AAAG-AG
1 AAAGAAG
298347 AAAGAA-
1 AAAGAAG
298353 AAAG-A-
1 AAAGAAG
*
298358 AAACAAG
1 AAAGAAG
298365 AAAAGAAG
1 -AAAGAAG
298373 AAAGAAG
1 AAAGAAG
*
298380 AAAAAAG
1 AAAGAAG
298387 AAAGAAG
1 AAAGAAG
298394 AAAGAA-
1 AAAGAAG
298400 AAAGAAG
1 AAAGAAG
298407 A
1 A
298408 GGTCGAGATG
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
5 5 0.09
6 19 0.33
7 27 0.47
8 6 0.11
ACGTcount: A:0.77, C:0.01, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:299329 original size:49 final size:49
Alignment explanation
Indices: 299271--299414 Score: 189
Period size: 49 Copynumber: 2.9 Consensus size: 49
299261 TAGGAATGTT
*
299271 GAGGAAAAGATTGAAGCCGTAATGACGAATCTTGTACCTTAGAGATATG
1 GAGGGAAAGATTGAAGCCGTAATGACGAATCTTGTACCTTAGAGATATG
* * * *
299320 GAGGGAAAGATTGAAACCGTAATGACGAATCTTGTACCCTAGAAATGTG
1 GAGGGAAAGATTGAAGCCGTAATGACGAATCTTGTACCTTAGAGATATG
*** * * *
299369 GAGGGAAAGATTGAAGTTTTAATGACAAATCTTATACCTTAAAGAT
1 GAGGGAAAGATTGAAGCCGTAATGACGAATCTTGTACCTTAGAGAT
299415 TGTAGAGGGC
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 81 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (49 bp):
GAGGGAAAGATTGAAGCCGTAATGACGAATCTTGTACCTTAGAGATATG
Found at i:299967 original size:45 final size:44
Alignment explanation
Indices: 299834--300310 Score: 464
Period size: 42 Copynumber: 11.0 Consensus size: 44
299824 TTACATCAGA
*
299834 CACCATCCAATCTTTTA-CCCTAA-CCAGA-GGGCAGATTGAAG
1 CACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAG
* *
299875 -ACCATCCAATCTTTTA-CCCTAA-CCAAAGGGACAGATCGAAG
1 CACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAG
* * *
299916 CTACCATCCAATCTTTTACCCCTAATTCAAAGGGGAAAATTGAAG
1 C-ACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAG
* * *
299961 CCACCATCCGATCTTTTACCCCTAATCCAGAGGGGCAGTTTGAAG
1 -CACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAG
* *
300006 CA--ATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAG
1 CACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAG
* * * * * *
300048 --TCATCCAATCTTTTACCCCTGATCTAAAGAGGTAGATTAAAG
1 CACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAG
* * *
300090 --CCATCTAATCTATTACCCCTAATCCAAAGGGGCAAATT-ATAG
1 CACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGA-AG
* *
300132 --CCATCCGATCTTTTACCCCTAATCCAGAGGGGCAGATTGAAG
1 CACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAG
* *
300174 CCACCATCCAATCTTTTACCTCTAATCCAAAGAGGCAGATTGAAG
1 -CACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAG
* * * * *
300219 CCATCATCCAATCATTTAGCCCTAAATCCAGAGGGGCAGATTGAAAT
1 -CACCATCCAATCTTTTACCCCT-AATCCAAAGGGGCAGATTG-AAG
* * * * *
300266 CAACATCCATTATTTTACTCCTAATCCAGAA-GGGTAGATTGAAG
1 CACCATCCAATCTTTTACCCCTAATCCA-AAGGGGCAGATTGAAG
300310 C
1 C
300311 CACACACATA
Statistics
Matches: 365, Mismatches: 55, Indels: 29
0.81 0.12 0.06
Matches are distributed among these distances:
40 26 0.07
41 12 0.03
42 139 0.38
43 17 0.05
44 11 0.03
45 123 0.34
46 35 0.10
47 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (44 bp):
CACCATCCAATCTTTTACCCCTAATCCAAAGGGGCAGATTGAAG
Found at i:300520 original size:17 final size:17
Alignment explanation
Indices: 300498--300532 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
300488 TGAAGTGAAA
300498 AAGTTGATCAACCAATG
1 AAGTTGATCAACCAATG
300515 AAGTTGATCAACCAATG
1 AAGTTGATCAACCAATG
300532 A
1 A
300533 CGCGAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (17 bp):
AAGTTGATCAACCAATG
Found at i:303501 original size:12 final size:13
Alignment explanation
Indices: 303479--303511 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
303469 ATCTGGGCCC
303479 AACACAAAAAT-AA
1 AACA-AAAAATAAA
303492 AACAAAAAATAAA
1 AACAAAAAATAAA
303505 AACAAAA
1 AACAAAA
303512 GTCCATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (13 bp):
AACAAAAAATAAA
Found at i:305205 original size:17 final size:16
Alignment explanation
Indices: 305185--305226 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
305175 CCTTTTATTA
305185 TTTTTTAAATTAAATC
1 TTTTTTAAATTAAATC
* * *
305201 CTTTTAAAATTTAATC
1 TTTTTTAAATTAAATC
305217 TTTTTTAAAT
1 TTTTTTAAAT
305227 CACCCCTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTTTAAATTAAATC
Found at i:309626 original size:37 final size:37
Alignment explanation
Indices: 309585--309659 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
309575 AGAGAAAGAT
309585 AGTACTTCACAGCTAGAGAGCATGGAACTTACTTTTC
1 AGTACTTCACAGCTAGAGAGCATGGAACTTACTTTTC
*
309622 AGTACTTCACAGCTAGAGAGCATGGAACTTCCTTTTC
1 AGTACTTCACAGCTAGAGAGCATGGAACTTACTTTTC
309659 A
1 A
309660 TTCCCTACCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (37 bp):
AGTACTTCACAGCTAGAGAGCATGGAACTTACTTTTC
Found at i:329075 original size:57 final size:57
Alignment explanation
Indices: 329004--329118 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
328994 TGTGATTGTT
* * *
329004 GAGTAGAAATGGTTAATTAAATTATGGTGATTTTAAGTAAAGTGTTGAATTACTCAA
1 GAGTAGAAAAGGTTAATTAAATTATGGTGATTTAAAGTAAAGTGTTGAATTACACAA
*
329061 GAGTAGAAAAGGTTAATTAAATTGTGGTGATTTAAAGTAAAGTGTTGAATTACACAA
1 GAGTAGAAAAGGTTAATTAAATTATGGTGATTTAAAGTAAAGTGTTGAATTACACAA
329118 G
1 G
329119 CTAGTAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (57 bp):
GAGTAGAAAAGGTTAATTAAATTATGGTGATTTAAAGTAAAGTGTTGAATTACACAA
Found at i:329814 original size:6 final size:6
Alignment explanation
Indices: 329803--329842 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
329793 GAGCATAAAC
*
329803 GAAAAG GAAAAG GAAAAG GAAAAA GAAAAG GAAAAG GAAA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAA
329843 TATGTATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:337328 original size:42 final size:42
Alignment explanation
Indices: 337264--337346 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
337254 GCTCATATGA
* *
337264 GCAGCATCGTGTAGCTACTATCCTG-CCCTACATCTTGTGTGG
1 GCAGCATCGTGTAGCTACTATCCCGACCC-ACAGCTTGTGTGG
*
337306 GCAGTATCGTGTAGCTACTATCCCGACCCACAGCTTGTGTG
1 GCAGCATCGTGTAGCTACTATCCCGACCCACAGCTTGTGTG
337347 AGGAAGCCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 34 0.92
43 3 0.08
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (42 bp):
GCAGCATCGTGTAGCTACTATCCCGACCCACAGCTTGTGTGG
Found at i:354534 original size:10 final size:10
Alignment explanation
Indices: 354519--354543 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
354509 TAATTAAGAA
354519 ATTTATTTAG
1 ATTTATTTAG
354529 ATTTATTTAG
1 ATTTATTTAG
354539 ATTTA
1 ATTTA
354544 ATTATTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (10 bp):
ATTTATTTAG
Found at i:365602 original size:214 final size:214
Alignment explanation
Indices: 364113--366031 Score: 2042
Period size: 214 Copynumber: 9.0 Consensus size: 214
364103 CTCGCATCAT
* ** *
364113 ATGGAATGTTC-GAAAAATTGCTCGAAGGAGTGGATTTTCCTGAATACTTTAAGGAACCGAAGTT
1 ATGGAATGTTCAG-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTT
* * * * * *
364177 GTAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCAAAGAACCAAGGGAGAACAATCC
65 ATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGA-AACAATTC
* * *
364242 TCACGTAAATAAGTGTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGAGC
129 TCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACC
* *
364307 AAATGATGAGATTTCCCAAGC
194 AAATGATGCGATTTCCCGAGC
* * *
364328 ATGGAATGTTCGGAAAATTGCTCG-AGAGAAAGGATCGTCTTGAATACTGTAAGGAACC-AAGTT
1 ATGGAATGTTCAGAAAATTGCTCGAAG-GAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTT
* * * * * * * * * *
364391 ATAAAAAAACTAGTAAAACTTTAAAAAGTTCGGAAGTTCATCCAATAGCTAAGAGAAACAATTCT
65 ATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAAACAATTCT
*** * * *
364456 CACGTAAATAAGTTTTCGTTTTAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACTA
130 CACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCA
364521 AATGATGCGATTTCCCGAG-
195 AATGATGCGATTTCCCGAGC
* * *
364540 AGTGGAGTGTTCA-AAATTTGCTC-AATGGAATGGATTGTCTTGAATACTTTAAGGAACCGAAGT
1 A-TGGAATGTTCAGAAAATTGCTCGAA-GGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGT
* * *
364603 TATAAAAGAACTCCTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAAT
64 TATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC-A-AGAGAAACAAT
* * * * *
364668 TCTCACGTAAATAAGTATTTAATTCAAAGACCAAAACTTTGTTTACAAAACGATAGACAATTTAG
127 TCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC-TTGTTTACAAAATGACAAACTATTTAG
* * * *
364733 A-AAAAGGATGCAATTT-TCGAGC
191 ACCAAATGATGCGATTTCCCGAGC
* * * * * ** * *
364755 ATAGAATGTTTAGAAAGTTGCTCGAGGGAATGTATCGTCTTGAATACAATAAGGAATCAAAGTTA
1 ATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTA
* * * ** *
364820 TAAAAGAACTCATAAATGTTTGATAAGTTCGAAAGTTTATCCAAGAACCAAGAGAAATAATTCTC
66 TAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAAACAATTCTC
* * * * *
364885 ACGTAAATAATTTTTTTATTCAAAGACCATAACTTGTTTCCAAAATGACAAACAATTTAGACCAA
131 ACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAA
* * ** *
364950 ATGCTGCTATTTCCATAGA
196 ATGATGCGATTTCCCGAGC
* * * *
364969 ATGGAATATTCAGAAAATAGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTA
1 ATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTA
* * * * *
365034 TGAAAGAACTCGTAAAAGTTTGACCAGTTCAAAAGTTCGTCCAATATCCTAGAGAGAAACAATTC
66 TAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC-A-AGAGAAACAATTC
* * * ** * *
365099 TAATGTAAATAAGTTTGTAATTCAAAGAATAAAACTTGTTTACAAAATGACAAACTTTTTAGGCC
129 TCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACC
* * *
365164 AAATGACGTGATTTCCCAAGC
194 AAATGATGCGATTTCCCGAGC
* ** * * * *
365185 AAGGAATGTTTGGAAAATTGCTCG-ATGACATGGATTGCCTTGAATACCTTAAGGAACCGAAGTT
1 ATGGAATGTTCAGAAAATTGCTCGAAGGA-ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTT
** * * * * * * *
365249 ATGCAAGAACTCGAAAAAGTTTTACATGGTCGGATGTTCGTCCAATAACCAAGTGAGAAACAATT
65 ATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAA--GAGAAACAATT
* * * *
365314 CTCATGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAGAATGACTAACTATTTAGAC
128 CTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGAC
365379 CAAATGATGCGATTTCCCGAGC
193 CAAATGATGCGATTTCCCGAGC
* * * * **
365401 ATGGAATGTTCAGAAAATTGGTCGAAGGAATGGATCATCTTGTATACTGTAAGGAACTAAAGTTA
1 ATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTA
* * * *
365466 TAAGAGAATTCGTAAAAGTTTGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAAACAACTCTC
66 TAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAAACAATTCTC
* * * *
365531 ACGTAAATAAGTTTTTTATTTAAAGACCAAAACTTGTTTACAAAATAACAAACTATTTAAACCAA
131 ACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAA
** *
365596 ATGATGCGATTTTTCGAGA
196 ATGATGCGATTTCCCGAGC
* * * *
365615 ATGGAATGTT-TGAAATATCGCTAGAAGGAATGGAT-GATCTTGAATACATTAAGGAACCGAAGT
1 ATGGAATGTTCAGAAA-ATTGCTCGAAGGAATGGATCG-TCTTGAATACTTTAAGGAACCGAAGT
** *
365678 TATAAAAGAACT-GT-AAAGTATT-ATGAGTTCGGATA-TTCGTCCAAGAACCAAGAGAGAAACA
64 TATAAAAGAACTCGTAAAAGT-TTGACAAGTTC-GAAAGTTCGTCCAAGAACC-A-AGAGAAACA
* *
365739 ATTCTCACAG-AAATAAGTATTTAATTCAAAGACCAAAAGTT-TTTGACAAAATGACAAACTATT
125 ATTCTCAC-GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTT-ACAAAATGACAAACTATT
365802 TAGACCAAATGATGCGATTTCCCGAGC
188 TAGACCAAATGATGCGATTTCCCGAGC
* *
365829 ATAGAATGTTC-GAAAAATTGCTCGAAGGAAAGG-TCCGTCTTGAATACTTTAAGGAACCGAAGT
1 ATGGAATGTTCAG-AAAATTGCTCGAAGGAATGGAT-CGTCTTGAATACTTTAAGGAACCGAAGT
* * * * *
365892 TATAAAAGAACTCGTAACTA-TTTGA-AAGTTC----G-TC-TACGAATAGA--GAGAGAAATAA
64 TATAAAAGAACTCGTAA-AAGTTTGACAAGTTCGAAAGTTCGT-CCAAGA-ACCAAGAGAAACAA
* * * *
365947 TTCTCACGTAAATAAGTTTGTAATTTAAAGAACAAAACTTGTTTACAAAATGACAAACTATTGAG
126 TTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAG
*
366012 ACCAAATGATGTGATTTCCC
191 ACCAAATGATGCGATTTCCC
366032 AAGTAACGTT
Statistics
Matches: 1412, Mismatches: 251, Indels: 90
0.81 0.14 0.05
Matches are distributed among these distances:
206 1 0.00
207 81 0.06
208 3 0.00
209 1 0.00
210 6 0.00
211 1 0.00
212 88 0.06
213 204 0.14
214 447 0.32
215 206 0.15
216 370 0.26
217 4 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (214 bp):
ATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTA
TAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAAACAATTCTC
ACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAA
ATGATGCGATTTCCCGAGC
Found at i:367371 original size:21 final size:22
Alignment explanation
Indices: 367331--367385 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
367321 CCAAAAAGAG
367331 AGAAAAA-GAG-AAAAATCAAA
1 AGAAAAATGAGTAAAAATCAAA
*
367351 AGAAAAATGAGTAGAAA-CAAA
1 AGAAAAATGAGTAAAAATCAAA
**
367372 AGAATCATGAGTAA
1 AGAAAAATGAGTAA
367386 GGAAAATGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 7 0.24
21 18 0.62
22 4 0.14
ACGTcount: A:0.65, C:0.05, G:0.18, T:0.11
Consensus pattern (22 bp):
AGAAAAATGAGTAAAAATCAAA
Found at i:372788 original size:3 final size:3
Alignment explanation
Indices: 372780--372808 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
372770 CTCATCACCT
372780 GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
372809 TGTAGCTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.34, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:388436 original size:18 final size:18
Alignment explanation
Indices: 388413--388450 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
388403 GAAATCCTTG
388413 TTCATTTGTAATTT-CATT
1 TTCATTT-TAATTTCCATT
*
388431 TTCATTTTTATTTCCATT
1 TTCATTTTAATTTCCATT
388449 TT
1 TT
388451 GAAAAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.18, C:0.13, G:0.03, T:0.66
Consensus pattern (18 bp):
TTCATTTTAATTTCCATT
Found at i:393629 original size:26 final size:27
Alignment explanation
Indices: 393598--393661 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
393588 GTATAGCTCA
393598 TACGAGCTCAGT-CAGTAAATTGCCCT
1 TACGAGCTCAGTACAGTAAATTGCCCT
* * *
393624 TTCGAG-TCAGTACAGTATATTGCTCT
1 TACGAGCTCAGTACAGTAAATTGCCCT
393650 TACGAGC-CAGTA
1 TACGAGCTCAGTA
393662 TTATCTATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 5 0.16
26 27 0.84
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (27 bp):
TACGAGCTCAGTACAGTAAATTGCCCT
Found at i:395006 original size:17 final size:17
Alignment explanation
Indices: 394992--395025 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
394982 TATGAACATG
394992 AATTAAATATAAACAAC
1 AATTAAATATAAACAAC
* *
395009 AATTAAACATAATCAAC
1 AATTAAATATAAACAAC
395026 CCAACACTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
AATTAAATATAAACAAC
Found at i:395082 original size:12 final size:12
Alignment explanation
Indices: 395065--395089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
395055 ATTAAATAAG
395065 TAATAGCATTCA
1 TAATAGCATTCA
395077 TAATAGCATTCA
1 TAATAGCATTCA
395089 T
1 T
395090 CATGATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:401817 original size:56 final size:56
Alignment explanation
Indices: 401731--401845 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
401721 CCGAAACAGG
* *
401731 TATGCAGATTACTAAATTACACATAATTCTTCAAAGTTTAGTGGATATATATTCAT
1 TATGCAGATTACCAAATTACACATAATTCTTCAAAGTTTAGTGGACATATATTCAT
401787 TATGCAGATTACCAAATTACACATAATTCTTCAAAGTTTAGTGGACATATATTCAT
1 TATGCAGATTACCAAATTACACATAATTCTTCAAAGTTTAGTGGACATATATTCAT
401843 TAT
1 TAT
401846 ATGTTATGCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (56 bp):
TATGCAGATTACCAAATTACACATAATTCTTCAAAGTTTAGTGGACATATATTCAT
Found at i:410920 original size:14 final size:14
Alignment explanation
Indices: 410901--410927 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
410891 CTTTTAAAGA
410901 AATAAAAGAAAATC
1 AATAAAAGAAAATC
410915 AATAAAAGAAAAT
1 AATAAAAGAAAAT
410928 TAGACGGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (14 bp):
AATAAAAGAAAATC
Found at i:412557 original size:19 final size:19
Alignment explanation
Indices: 412533--412672 Score: 172
Period size: 19 Copynumber: 7.4 Consensus size: 19
412523 ATCAACAGTA
*
412533 TATTGCTCTTACGAGCTAG
1 TATTGCTCTTACGAGCCAG
*
412552 TATTGCTCTCACGAGCCAG
1 TATTGCTCTTACGAGCCAG
*
412571 TATTGCTCTTACGAGCTAG
1 TATTGCTCTTACGAGCCAG
** * *
412590 TATCACTCTCATGAGCCAG
1 TATTGCTCTTACGAGCCAG
412609 TATTGCTCTTACGAGCCAG
1 TATTGCTCTTACGAGCCAG
* * *
412628 TATCGCTCTCACGAGTCAG
1 TATTGCTCTTACGAGCCAG
**
412647 TATCACTCTTACGAGCCAG
1 TATTGCTCTTACGAGCCAG
412666 TATTGCT
1 TATTGCT
412673 GATTCCTTCT
Statistics
Matches: 100, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 100 1.00
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.31
Consensus pattern (19 bp):
TATTGCTCTTACGAGCCAG
Found at i:412581 original size:38 final size:38
Alignment explanation
Indices: 412533--412668 Score: 200
Period size: 38 Copynumber: 3.6 Consensus size: 38
412523 ATCAACAGTA
* *
412533 TATTGCTCTTACGAGCTAGTATTGCTCTCACGAGCCAG
1 TATTGCTCTTACGAGCCAGTATCGCTCTCACGAGCCAG
* * *
412571 TATTGCTCTTACGAGCTAGTATCACTCTCATGAGCCAG
1 TATTGCTCTTACGAGCCAGTATCGCTCTCACGAGCCAG
*
412609 TATTGCTCTTACGAGCCAGTATCGCTCTCACGAGTCAG
1 TATTGCTCTTACGAGCCAGTATCGCTCTCACGAGCCAG
**
412647 TATCACTCTTACGAGCCAGTAT
1 TATTGCTCTTACGAGCCAGTAT
412669 TGCTGATTCC
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 89 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
TATTGCTCTTACGAGCCAGTATCGCTCTCACGAGCCAG
Found at i:412623 original size:57 final size:57
Alignment explanation
Indices: 412538--412672 Score: 191
Period size: 57 Copynumber: 2.4 Consensus size: 57
412528 CAGTATATTG
* * * *
412538 CTCTTACGAGCTAGTATTGCTCTCACGAGCCAGTATTGCTCTTACGAG-CTAGTATCA
1 CTCTCACGAGCCAGTATTGCTCTCACGAGCCAGTATCGCTCTCACGAGTC-AGTATCA
* *
412595 CTCTCATGAGCCAGTATTGCTCTTACGAGCCAGTATCGCTCTCACGAGTCAGTATCA
1 CTCTCACGAGCCAGTATTGCTCTCACGAGCCAGTATCGCTCTCACGAGTCAGTATCA
*
412652 CTCTTACGAGCCAGTATTGCT
1 CTCTCACGAGCCAGTATTGCT
412673 GATTCCTTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 68 0.99
58 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.30
Consensus pattern (57 bp):
CTCTCACGAGCCAGTATTGCTCTCACGAGCCAGTATCGCTCTCACGAGTCAGTATCA
Found at i:415070 original size:11 final size:11
Alignment explanation
Indices: 415054--415080 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
415044 GATATCTTTG
415054 TTTTTCTTTTC
1 TTTTTCTTTTC
415065 TTTTTCTTTTC
1 TTTTTCTTTTC
415076 TTTTT
1 TTTTT
415081 GGGCTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:415762 original size:54 final size:53
Alignment explanation
Indices: 415658--415763 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 53
415648 TAGAAATATG
** **
415658 TTTTTTAGTTATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTC
1 TTTTTTAACTATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTAATGATTTC
* ** *
415711 TTTTTTAACTATTTTGAAATAAAAGTTTGGATTTTTAAGTAAAGTAATGATTT
1 TTTTTTAACTATTTT-AAAGAAAAGTTTAAATTTTTAAATAAAGTAATGATTT
415764 TCATTAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
53 13 0.30
54 31 0.70
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (53 bp):
TTTTTTAACTATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTAATGATTTC
Found at i:415815 original size:156 final size:154
Alignment explanation
Indices: 415541--415917 Score: 476
Period size: 156 Copynumber: 2.4 Consensus size: 154
415531 GTCTAAGGGA
* * * * *
415541 AAAGTTTTGATTTTTGTAAATAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTT
1 AAAGTTTTGATTTTTTTAACT-ATTTTGAAATAAAAG-TTTGATTTTTAAGTAAAATAATGATTT
* * *
415606 TCTTTAAAAAAAAAAATAAGAGAAAGTTTATATTTTTAAAAATAGAAATATGTTTTTTAGTTATT
64 TCATTAAAAAAAAAAATAAGAGAAAGTTTATATTTTTAAAAATAAAAATATG-TTTTTAGTGATT
415671 TTAAAG-AAAAGTTTAAATTTTTAAAT
128 TTAAAGAAAAAGTTTAAATTTTTAAAT
*
415697 AAAGTTTTGATTTCTTTTTTAACTATTTTGAAATAAAAGTTTGGATTTTTAAGTAAAGTAATGAT
1 AAAGTTTTGA--T-TTTTTTAACTATTTTGAAATAAAAGTTT-GATTTTTAAGTAAAATAATGAT
***
415762 TTTCATTAAAAAAAAAAGA-AAG-TTTAGATTT-T-TTTTTAAAAATAAAAATATGTTTTTAGTG
62 TTTCATTAAAAAAAAAA-ATAAGAGAAAG-TTTATATTTTTAAAAATAAAAATATGTTTTTAGTG
* *
415823 ATTTTAAAGAAAAATTTTTAATTTTTAAAT
125 ATTTTAAAGAAAAAGTTTAAATTTTTAAAT
* * *
415853 AAAGTTTTGATTTTTTTAACTATTTTAAAATAAAAGTTCTGATTTTGAAGTAAAATAATAATTTT
1 AAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTT-TGATTTTTAAGTAAAATAATGATTTT
415918 GTTTTAATCA
Statistics
Matches: 195, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
153 48 0.25
154 2 0.01
155 17 0.09
156 57 0.29
157 6 0.03
158 56 0.29
159 9 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (154 bp):
AAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTGATTTTTAAGTAAAATAATGATTTTC
ATTAAAAAAAAAAATAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTAGTGATTTTA
AAGAAAAAGTTTAAATTTTTAAAT
Found at i:415959 original size:156 final size:155
Alignment explanation
Indices: 415643--415956 Score: 361
Period size: 153 Copynumber: 2.0 Consensus size: 155
415633 TTATATTTTT
* *
415643 AAAAATAGAAATATGTTTTTTAGTTATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGAT
1 AAAAATAAAAATATGTTTTTTAGTGATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGA-
* * * *
415708 TTCTTTTTTAACTATTTTGAAATAAAAGTTTGGATTTTTAAGTAAAGTAATGATTTTCATTAAAA
65 TTCTTTTTTAACTATTTTAAAATAAAAGTTTGGATTTTGAAGTAAAATAATAATTTTCATTAAAA
* ******
415773 AAAAAAGAAAGTTTAGATTTTTTTTT
130 AAAAAAGAAACTTTAGATTTAAAAAA
* *
415799 AAAAATAAAAATATG-TTTTTAGTGATTTTAAAGAAAAATTTTTAATTTTTAAATAAAGTTTTGA
1 AAAAATAAAAATATGTTTTTTAGTGATTTTAAAG-AAAAGTTTAAATTTTTAAATAAAGTTTTGA
* **
415863 -T-TTTTTTAACTATTTTAAAATAAAAGTTCT-GATTTTGAAGTAAAATAATAATTTT-GTTTTA
65 TTCTTTTTTAACTATTTTAAAATAAAAGTT-TGGATTTTGAAGTAAAATAATAATTTTCATTAAA
**
415924 ATCAAAAGAAAACTTT-GATTTCAAAAAA
129 AAAAAAAG-AAACTTTAGATTT-AAAAAA
415952 AAAAA
1 AAAAA
415957 AAAGAAGAAA
Statistics
Matches: 134, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
152 14 0.10
153 59 0.44
154 2 0.01
155 17 0.13
156 42 0.31
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (155 bp):
AAAAATAAAAATATGTTTTTTAGTGATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGAT
TCTTTTTTAACTATTTTAAAATAAAAGTTTGGATTTTGAAGTAAAATAATAATTTTCATTAAAAA
AAAAAGAAACTTTAGATTTAAAAAA
Found at i:449625 original size:4 final size:4
Alignment explanation
Indices: 449616--449649 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
449606 TGCCCCCAAT
* *
449616 TTCA TTCA TTTA TTCA TTCA TTCA TTCA CTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
449650 TATTTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (4 bp):
TTCA
Found at i:449633 original size:12 final size:12
Alignment explanation
Indices: 449616--449653 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
449606 TGCCCCCAAT
449616 TTCATTCATTTA
1 TTCATTCATTTA
*
449628 TTCATTCATTCA
1 TTCATTCATTTA
*
449640 TTCACTCATTTA
1 TTCATTCATTTA
449652 TT
1 TT
449654 TATTTAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (12 bp):
TTCATTCATTTA
Found at i:450957 original size:17 final size:18
Alignment explanation
Indices: 450923--450973 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
450913 TTAAATAAAG
450923 AAACAAAAAAAGAGAAAA
1 AAACAAAAAAAGAGAAAA
*
450941 AAACAACAAAA-AGAAAA
1 AAACAAAAAAAGAGAAAA
* *
450958 GAAGAAAAAATAGAGA
1 AAACAAAAAA-AGAGA
450974 GAGCAAGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 13 0.48
18 11 0.41
19 3 0.11
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (18 bp):
AAACAAAAAAAGAGAAAA
Found at i:451426 original size:42 final size:42
Alignment explanation
Indices: 451367--451766 Score: 548
Period size: 42 Copynumber: 9.5 Consensus size: 42
451357 AAGGAAAGCA
* *
451367 TTCATTGCATTTAGAGGTCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
451409 TTCATTGCATTTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
451451 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
451493 TTCCATAGCATTTAGAGGCCCAAGTGTGGAGGTTCATTTACTT
1 TT-CATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
451536 TTCATCGCATTTAAAGACCCAGATGTGGAGGTCCACTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** *
451578 TTCATTGCATTTAGAGGCCCAGGAATGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
451620 TTCATTGCATTTAGAGACCCAAGTGTGGAGGTCCCTTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * ** *
451662 TTCGTCGCATTTAGAGGCAAATGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
451704 TTCATTGCATTTAGAGGCTCAGGTGTAGAAGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
451746 TTCATTGCATTTAGAGACCCA
1 TTCATTGCATTTAGAGGCCCA
451767 AATGTGAGGT
Statistics
Matches: 315, Mismatches: 42, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
42 275 0.87
43 40 0.13
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:452190 original size:3 final size:3
Alignment explanation
Indices: 452182--452233 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
452172 AAGAGCCCAA
* * * * * *
452182 ATT ATT ATT GTT GTT GTT GTT ATT GTT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
452230 ATT A
1 ATT A
452234 GGGTTTCATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:453028 original size:146 final size:145
Alignment explanation
Indices: 452570--453079 Score: 614
Period size: 146 Copynumber: 3.4 Consensus size: 145
452560 GATTTTGGGA
* * * * *
452570 AAAGTTTTGATTTTTTAAAATAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTT
1 AAAGTTTTAATTTTTTTAACT-ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTT
* * *
452635 T-TTTAAAAAAGAGAAAATTTAGA-TTCTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGA
65 TCTTT-AAAAA-A-AAAATTTAGATTTTTTAAAAATAAAAATCTGTTTTTTAGTCATTTTAAAGA
* *
452698 AAAGTTTAAATTGTTAAAC
127 AAAGTTTAAATTTTTAAAT
* * * *
452717 AAAATTTTGATTTTTTTTTACTATTTCGAAATAAAAGTTTGGATTTTTTAAGTAAAATAGTGTTT
1 AAAGTTTT-AATTTTTTTAACTATTTCGAAATAAAAGTTTGGA-TTTTTAAGTAAAATAGTGATT
*** *
452782 TTCTTTAAAAAAAAAAGAAAGTTTAGATTTTTTTTTTAA-AAAAATCTGTTTTTTAGTCATTTTT
64 TTCTTT---AAAAAAA-AAA-TTTAGA-TTTTTTAAAAATAAAAATCTGTTTTTTAGTCATTTTA
452846 AAGAAAAGTTTAAATTTTTAAAT
123 AAGAAAAGTTTAAATTTTTAAAT
* *
452869 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTT
1 AAAGTTTTAATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
* * * *
452934 CATT-AAAAAAATATTTTGATTTTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAGAA
66 CTTTAAAAAAAAAATTTAGATTTTTT-AAAAATAAAAATCTGTTTTTTAGTCATTTTAAAGA-AA
*
452998 AATTTAAATTTTTAAAT
129 AGTTTAAATTTTTAAAT
* * *
453015 AAAGTTTTAATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTGAAGTAAAATAGTGATTTT
1 AAAGTTTTAATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
453080 ATTTTATTTT
Statistics
Matches: 313, Mismatches: 38, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
143 6 0.02
144 7 0.02
145 29 0.09
146 84 0.27
147 27 0.09
148 29 0.09
149 4 0.01
150 28 0.09
151 43 0.14
152 50 0.16
153 6 0.02
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.46
Consensus pattern (145 bp):
AAAGTTTTAATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
CTTTAAAAAAAAAATTTAGATTTTTTAAAAATAAAAATCTGTTTTTTAGTCATTTTAAAGAAAAG
TTTAAATTTTTAAAT
Found at i:454756 original size:14 final size:14
Alignment explanation
Indices: 454737--454764 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
454727 ATTAATATGC
454737 TTAAATAAAAAAAA
1 TTAAATAAAAAAAA
454751 TTAAATAAAAAAAA
1 TTAAATAAAAAAAA
454765 AAACTAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TTAAATAAAAAAAA
Found at i:481418 original size:22 final size:20
Alignment explanation
Indices: 481381--481421 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
481371 GTCACTTGTT
*
481381 AAAAAAAAGAAGAAGAAAAG
1 AAAAAAAAGAAAAAGAAAAG
481401 AAAAGAAAAGAAAAAAGAAAA
1 AAAA-AAAAG-AAAAAGAAAA
481422 TATTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAAAGAAAAG
Found at i:481421 original size:5 final size:5
Alignment explanation
Indices: 481381--481414 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
481371 GTCACTTGTT
481381 AAAA- AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
481415 AAGAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:482572 original size:19 final size:18
Alignment explanation
Indices: 482548--482595 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
482538 ATATTTTTTT
482548 TATTTTTTTCTTTTTATC
1 TATTTTTTTCTTTTTATC
* *
482566 ATATTTTTCTTTTTTTTCTC
1 -TATTTTT-TTCTTTTTATC
482586 TACTTTTTTT
1 TA-TTTTTTT
482596 ATCACTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTTTTCTTTTTATC
Found at i:495737 original size:17 final size:17
Alignment explanation
Indices: 495697--495741 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
495687 AGAGAAAAGA
495697 AAAAGAAAGAAAAATGTT
1 AAAAGAAA-AAAAATGTT
*
495715 AAAAGAAAAAAATTG-T
1 AAAAGAAAAAAAATGTT
495731 AAGAAGAAAAA
1 AA-AAGAAAAA
495742 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 14 0.56
18 8 0.32
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (17 bp):
AAAAGAAAAAAAATGTT
Found at i:501245 original size:21 final size:22
Alignment explanation
Indices: 501190--501247 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
501180 ATTCAAGAAT
*
501190 AAGTGCAGACTTCTACCGATACC
1 AAGTGAAG-CTTCTACCGATACC
*
501213 TA-TGATAG-TTCTACCGATA-C
1 AAGTGA-AGCTTCTACCGATACC
501233 AAGTGAAGCTTCTAC
1 AAGTGAAGCTTCTAC
501248 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
20 4 0.14
21 20 0.69
22 2 0.07
23 3 0.10
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (22 bp):
AAGTGAAGCTTCTACCGATACC
Found at i:514584 original size:26 final size:27
Alignment explanation
Indices: 514548--514601 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
514538 TATTTTTATA
* *
514548 ATATTTAAATTAT-TTAATAAGTTAAT
1 ATATTTAAATTATATTAAAAAATTAAT
*
514574 ATATTTTAATTATATTAAAAAATTAAT
1 ATATTTAAATTATATTAAAAAATTAAT
514601 A
1 A
514602 AGATTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATTTAAATTATATTAAAAAATTAAT
Done.