Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2957
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: 77652
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:1724 original size:36 final size:37
Alignment explanation
Indices: 1677--1755 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 37
1667 TTATTACGAA
* *
1677 GTCTTACCCGGACATAA-TCTCCACA-GAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
1713 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
1750 GTCTTA
1 GTCTTA
1756 GAGCTGGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 21 0.55
37 17 0.45
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:2085 original size:48 final size:47
Alignment explanation
Indices: 1869--2157 Score: 390
Period size: 47 Copynumber: 6.2 Consensus size: 47
1859 CCCTTCGGGA
* * * * * * *
1869 CTTAT-ACATTTATGCACTTTCACATCCA-CACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1914 CCTGTCACATATATA-ACTTTCACATTCATCACAT-GGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1959 CTTACCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2006 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2053 CTTATCACAATATATACACTTTCACATTCATCACATCGGCTATTAGG-
1 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2100 CTTATCACATATATATACATTTCACATTCATCACATCGGCCATTATGC
1 CTTATCACATATATACAC-TTTCACATTCATCACATCGGCCATTAGGC
2148 CTTATCACAT
1 CTTATCACAT
2158 TCATCACATC
Statistics
Matches: 219, Mismatches: 18, Indels: 11
0.88 0.07 0.04
Matches are distributed among these distances:
45 36 0.16
46 39 0.18
47 96 0.44
48 48 0.22
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:2085 original size:95 final size:93
Alignment explanation
Indices: 1918--2156 Score: 383
Period size: 95 Copynumber: 2.5 Consensus size: 93
1908 CTCGGCCCTG
*
1918 TCACATATATAACTTTCACATTCATCACAT-GGCCATTAGGCCTTACCAC-ATATATACACTTTC
1 TCACATATATAACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTC
1981 ACATTCATCACATCGGCCATTAGGCCTTA
66 ACATTCATCACATCGGCCATTAGG-CTTA
* *
2010 TTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACAATATATACACTTT
1 TCACATATATA-ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTT
*
2075 CACATTCATCACATCGGCTATTAGGCTTA
65 CACATTCATCACATCGGCCATTAGGCTTA
*
2104 TCACATATATATACATTTCACATTCATCACATCGGCCATTATGCCTTATCACA
1 TCACATATATA-AC-TTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
2157 TTCATCACAT
Statistics
Matches: 135, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
92 10 0.07
93 19 0.14
94 33 0.24
95 73 0.54
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (93 bp):
TCACATATATAACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCTTA
Found at i:2159 original size:31 final size:31
Alignment explanation
Indices: 2121--2188 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
2111 TATATACATT
*
2121 TCACATTCATCACATCGGCCATTATGCCTTA
1 TCACATTCATCACATCGGCCATTAGGCCTTA
2152 TCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATTCATCACATCGGCCATTAGGCCTTA
2183 TCACAT
1 TCACAT
2189 ATATACACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.31
Consensus pattern (31 bp):
TCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:2167 original size:78 final size:78
Alignment explanation
Indices: 2074--2234 Score: 270
Period size: 78 Copynumber: 2.1 Consensus size: 78
2064 ATATACACTT
* *
2074 TCACATTCATCACATCGGCTATTAGG-CTTATCACATATATATACATTTCACATTCATCACATCG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC-TTTCACATTCATCACATCG
*
2138 GCCATTATGCCTTA
65 GCCATTAGGCCTTA
2152 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
*
2217 CTATTAGGCCTTA
66 CCATTAGGCCTTA
2230 TCACA
1 TCACA
2235 CATATACACT
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
78 61 0.78
79 17 0.22
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (78 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
CCATTAGGCCTTA
Found at i:2215 original size:125 final size:126
Alignment explanation
Indices: 2026--2282 Score: 455
Period size: 125 Copynumber: 2.0 Consensus size: 126
2016 ATATACACTT
*
2026 TCACATTCATCACATCGGCTATTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCG
* * *
2091 GCTATTAGG-CTTATCACATATATATACATTTCACATTCATCACATCGGCCATTATGCCTTA
66 GCTATTAGGCCTTATCACACATATACAC-TTTCACATTCATCACATCGGCCATTAGGCCTTA
2152 TCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATACACTTTCACATTCATCACATCG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCG
2216 GCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
66 GCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
2277 TCACAT
1 TCACAT
2283 ATATACACTC
Statistics
Matches: 126, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
125 76 0.60
126 50 0.40
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (126 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCG
GCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:2223 original size:47 final size:47
Alignment explanation
Indices: 2152--2336 Score: 329
Period size: 47 Copynumber: 4.0 Consensus size: 47
2142 TTATGCCTTA
2152 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
* *
2199 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
2246 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC--
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
*
2291 TCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
2337 GTCTTGGCTG
Statistics
Matches: 132, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
45 44 0.33
47 88 0.67
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (47 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
Found at i:2262 original size:94 final size:92
Alignment explanation
Indices: 2152--2336 Score: 343
Period size: 92 Copynumber: 2.0 Consensus size: 92
2142 TTATGCCTTA
2152 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC--TCACATTCATCACATCGG
2217 CTATTAGGCCTTATCACACATATACACTT
64 CTATTAGGCCTTATCACACATATACACTT
2246 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTCACATTCATCACATCGGCT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTCACATTCATCACATCGGCT
*
2311 ATTAGGCCTTATCACATATATACACT
66 ATTAGGCCTTATCACACATATACACT
2337 GTCTTGGCTG
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
92 45 0.50
94 45 0.50
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (92 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTCACATTCATCACATCGGCT
ATTAGGCCTTATCACACATATACACTT
Found at i:2279 original size:173 final size:170
Alignment explanation
Indices: 1979--2327 Score: 601
Period size: 173 Copynumber: 2.0 Consensus size: 170
1969 ATATACACTT
*
1979 TCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
* *
2044 CTATTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCGGCTATTAGGCTTATCACA
66 CTATTAGGCCTTATCACAACATATACACTTTCACATTCATCACATCGGCCATTAGGCTTATCAC-
* *
2109 TATATATACATTTCACATTCATCACATCGGCCATTATGCCTTA
130 -ATATATACA-CTCACATTCATCACATCGGCCATTAGGCCTTA
2152 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
2217 CTATTAGGCCTTATCAC-ACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
66 CTATTAGGCCTTATCACAACATATACACTTTCACATTCATCACATCGGCCATTAGG-CTTATCAC
*
2281 ATATATACACTCACATTCATCACATCGGCTATTAGGCCTTA
130 ATATATACACTCACATTCATCACATCGGCCATTAGGCCTTA
2322 TCACAT
1 TCACAT
2328 ATATACACTG
Statistics
Matches: 169, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
170 35 0.21
171 9 0.05
172 36 0.21
173 89 0.53
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (170 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
CTATTAGGCCTTATCACAACATATACACTTTCACATTCATCACATCGGCCATTAGGCTTATCACA
TATATACACTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:2376 original size:220 final size:218
Alignment explanation
Indices: 1933--2335 Score: 675
Period size: 220 Copynumber: 1.8 Consensus size: 218
1923 TATATAACTT
1933 TCACATTCATCACATGGCCATTAGGCCTTACCACATATATACACTTTCACATTCATCACATCGGC
1 TCACATTCATCACATGGCCATTAGGCCTTACCACATATATACACTTTCACATTCATCACATCGGC
* * *
1998 CATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACAA
66 CATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAA
* *
2063 TATATACACTTTCACATTCATCACATCGGCTATTAGGCTTATCACATATATATACATTTCACATT
131 TATATACAC-TTCACATTCATCACATCGGCTATTAGGCTTATCACATATATACACATTTCACATG
* * *
2128 CATCACATCGGCCATTATGCCTTA
195 AATCACATCGACCATTATGCCATA
*
2152 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACAT-GGCCATTAGGCCTTACCACATATATACACTTTCACATTCATCACATCGG
*
2217 CTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-
65 CCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
2281 ATATATACAC-TCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
130 ATATATACACTTCACATTCATCACATCGGCTATTAGG-CTTATCACATATATACAC
2336 TGTCTTGGCT
Statistics
Matches: 176, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
217 26 0.15
218 17 0.10
219 25 0.14
220 108 0.61
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (218 bp):
TCACATTCATCACATGGCCATTAGGCCTTACCACATATATACACTTTCACATTCATCACATCGGC
CATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAA
TATATACACTTCACATTCATCACATCGGCTATTAGGCTTATCACATATATACACATTTCACATGA
ATCACATCGACCATTATGCCATA
Found at i:5912 original size:40 final size:40
Alignment explanation
Indices: 5855--6014 Score: 171
Period size: 40 Copynumber: 4.0 Consensus size: 40
5845 AGAATACACG
* * *
5855 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATAT-
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
** *
5894 TACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 T-CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * * * *
5935 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCAGATACA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * *
5975 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGA-ATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
6014 T
1 T
6015 GTCACTTAGC
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 4 0.04
40 98 0.95
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
Found at i:6394 original size:29 final size:29
Alignment explanation
Indices: 6355--6433 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
6345 CTTAATAATC
*
6355 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
6385 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
6414 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
6434 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:6466 original size:43 final size:43
Alignment explanation
Indices: 6415--6517 Score: 188
Period size: 43 Copynumber: 2.4 Consensus size: 43
6405 TGCATTTCAA
6415 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
* *
6458 GCTCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
6501 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
6518 TGAAAACCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
Found at i:9102 original size:39 final size:39
Alignment explanation
Indices: 9045--9359 Score: 504
Period size: 39 Copynumber: 8.1 Consensus size: 39
9035 ATGCAAGACA
9045 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
9084 CTAGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
9123 CTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
9162 CTGGAAATGTATCTGGGCTAAAGTCCCGCAGGCTCCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
9201 CTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
9240 CTGGAAATGTATTCGGGCTAAAGTCCTGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
9279 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * * *
9318 CTGGAAATGTATCTGGGTTAAAGTCCCGCGGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
9357 CTG
1 CTG
9360 ATAATATAAT
Statistics
Matches: 252, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 252 1.00
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:15510 original size:46 final size:46
Alignment explanation
Indices: 15460--15585 Score: 225
Period size: 46 Copynumber: 2.7 Consensus size: 46
15450 TGGTTGAGCA
*
15460 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
15506 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
15552 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
15586 GGGGCGGGTT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:17230 original size:59 final size:59
Alignment explanation
Indices: 17167--17279 Score: 208
Period size: 59 Copynumber: 1.9 Consensus size: 59
17157 GCCTATATAC
17167 ATAATACAAGGTTCATTATTTCAAAATGTAATCCAACCTATACATGCCATAATTCAAGA
1 ATAATACAAGGTTCATTATTTCAAAATGTAATCCAACCTATACATGCCATAATTCAAGA
* *
17226 ATAATCCAAGGTTCATTATTTCAAAATGTAATCCAGCCTATACATGCCATAATT
1 ATAATACAAGGTTCATTATTTCAAAATGTAATCCAACCTATACATGCCATAATT
17280 AAAGTTCAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (59 bp):
ATAATACAAGGTTCATTATTTCAAAATGTAATCCAACCTATACATGCCATAATTCAAGA
Found at i:17258 original size:27 final size:27
Alignment explanation
Indices: 17168--17260 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 27
17158 CCTATATACA
*
17168 TAATACAAGGTTCATTATTTCAAAATG
1 TAATCCAAGGTTCATTATTTCAAAATG
** *
17195 TAATCCAACCTATACATGCCATAATTCAAGAA--
1 TAATCCAAGGT-T-CAT----TATTTCAA-AATG
17227 TAATCCAAGGTTCATTATTTCAAAATG
1 TAATCCAAGGTTCATTATTTCAAAATG
17254 TAATCCA
1 TAATCCA
17261 GCCTATACAT
Statistics
Matches: 50, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
25 2 0.04
26 7 0.14
27 15 0.30
28 1 0.02
29 3 0.06
30 3 0.06
31 1 0.02
32 9 0.18
33 7 0.14
34 2 0.04
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (27 bp):
TAATCCAAGGTTCATTATTTCAAAATG
Found at i:19544 original size:20 final size:22
Alignment explanation
Indices: 19519--19564 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
19509 TCATAATAAA
19519 ATATTT-T-GAATATGTACATC
1 ATATTTGTCGAATATGTACATC
19539 ATATTTGGTCGAATATGTACATC
1 ATATTT-GTCGAATATGTACATC
19562 ATA
1 ATA
19565 ATATGCATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
22 1 0.04
23 16 0.70
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (22 bp):
ATATTTGTCGAATATGTACATC
Found at i:23187 original size:53 final size:52
Alignment explanation
Indices: 23009--23263 Score: 205
Period size: 55 Copynumber: 4.8 Consensus size: 52
22999 ATTAGAGTTT
* * * *
23009 AAGGATAGCATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTCTAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-CATTGGTAA-G-TTCTAAGGC
* * * ** *
23064 AAGGAAATCATGTGAGACCATGTTAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C--TAAGGC
* * *
23119 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTC-TAAGGC
* * * *
23172 AAGGATACCATGTAAGGCCATGTCAAGACATGACAATGGTAAGTT-TCAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCT-AAGGC
* * * *
23221 AAGGATACCATGTAAGACCATGACAAGTCATGGAAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
23264 GTACCCGTGT
Statistics
Matches: 164, Mismatches: 30, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
49 38 0.23
51 1 0.01
52 8 0.05
53 42 0.26
54 8 0.05
55 63 0.38
56 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.22
Consensus pattern (52 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTAAGGC
Found at i:23215 original size:108 final size:110
Alignment explanation
Indices: 23017--23216 Score: 271
Period size: 108 Copynumber: 1.8 Consensus size: 110
23007 TTAAGGATAG
* *
23017 CATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTCTAAGGAAAGGAAATCATGTGAGAC
1 CATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTCTAAGGAAAGGAAACCATGTAAGAC
* * *
23082 CATGTTAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCC
66 CATGTCAAGACATGACAATGATAAGTTACTATAAGGCAAAGGTCC
* * * * *
23127 CATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGG
1 CATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTC-TAAGGAAAGGAAACCATGTAAGA
*
23189 CCATGTCAAGACATGACAATGGTAAGTT
65 CCATGTCAAGACATGACAATGATAAGTT
23217 TCAAAAGGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 3 0.04
108 43 0.55
109 7 0.09
110 25 0.32
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.23
Consensus pattern (110 bp):
CATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTCTAAGGAAAGGAAACCATGTAAGAC
CATGTCAAGACATGACAATGATAAGTTACTATAAGGCAAAGGTCC
Found at i:23358 original size:23 final size:24
Alignment explanation
Indices: 23332--23376 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
23322 AAGGTAAGGT
23332 AAGGTAAGACAAGTT-ATGCTAAA
1 AAGGTAAGACAAGTTCATGCTAAA
23355 AAGGTAAGACAAGTTCATGCTA
1 AAGGTAAGACAAGTTCATGCTA
23377 GAAGAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (24 bp):
AAGGTAAGACAAGTTCATGCTAAA
Found at i:23476 original size:16 final size:16
Alignment explanation
Indices: 23455--23485 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23445 ATAAATTTGA
23455 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
23471 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
23486 AGTGAAGAAG
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:30831 original size:55 final size:54
Alignment explanation
Indices: 30744--30998 Score: 235
Period size: 55 Copynumber: 4.8 Consensus size: 54
30734 ATTAGGGTTT
* * *
30744 AAGGATACAATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * ** *
30799 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGACAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* * * *
30854 AAAGG-TCCCATGGAAGACCATG-CTAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTC-AAGACATGGCAATTGGTAAGTTTC-TAAGGC
30907 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTTCTAAGGC
** * *
30956 AAGGATACCACATAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAG
30999 GTACCCGTGT
Statistics
Matches: 166, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
49 39 0.23
52 7 0.04
53 39 0.23
54 13 0.08
55 64 0.39
56 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:32599 original size:47 final size:47
Alignment explanation
Indices: 32530--32628 Score: 180
Period size: 47 Copynumber: 2.1 Consensus size: 47
32520 AGGCTCAAAG
32530 GGGTTCACTAAGGGTCAATTATGAAGGTAAGCTTTTGTGGAGTGAGT
1 GGGTTCACTAAGGGTCAATTATGAAGGTAAGCTTTTGTGGAGTGAGT
* *
32577 GGGTTCAGTAAGGGTCAATTATGAAGGTAGGCTTTTGTGGAGTGAGT
1 GGGTTCACTAAGGGTCAATTATGAAGGTAAGCTTTTGTGGAGTGAGT
32624 GGGTT
1 GGGTT
32629 AAACTTAAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.23, C:0.07, G:0.37, T:0.32
Consensus pattern (47 bp):
GGGTTCACTAAGGGTCAATTATGAAGGTAAGCTTTTGTGGAGTGAGT
Found at i:34626 original size:46 final size:46
Alignment explanation
Indices: 34559--34733 Score: 151
Period size: 46 Copynumber: 3.8 Consensus size: 46
34549 TGTAACCCGC
* * *
34559 CCATAAGCGAACTCGGCCTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
* *
34605 CCATAAGTGAACTCAAACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--G-C-A-TTCGCAT
* * * * ** *
34655 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
* *
34698 CCATAAGTGAACTCAGTCTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG
34734 ATGCTCAAAT
Statistics
Matches: 101, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 57 0.56
47 24 0.24
48 3 0.03
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
Found at i:34674 original size:93 final size:93
Alignment explanation
Indices: 34566--34737 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
34556 CGCCCATAAG
* **
34566 CGAACTCGGCCTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAAACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAAACTCAACTCA
34631 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* * **
34659 CGAACTCGGACTCAACTCAACGAGTTCGAACGTTCGCATCCATAAGTGAACTCAGTCTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAAACTCAACTCA
*
34724 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
34738 TCAAATATCC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAAACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:49743 original size:56 final size:56
Alignment explanation
Indices: 49652--49915 Score: 363
Period size: 56 Copynumber: 4.7 Consensus size: 56
49642 TGCCACTTGT
* * * *
49652 AATCACATATCGATGCC-ACGGT-TCTAGACAG-GGTCTTACTCGTACACTTATATCGG
1 AATCACATATCGATGCCAAC-GTAT-TAAAC-GTGGTCTTACTCGCACACATATATCAG
* * * **
49708 AGTCACATATCGATGCCAATGTATTAAATGTGGTCTTACTCCGCACACATATATTGG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACT-CGCACACATATATCAG
*
49765 AATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
*
49821 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCACACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
*
49877 AATCACATATCGATGCCAACGTATTAAACATGGTCTTAC
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTAC
49916 ACATAAACAC
Statistics
Matches: 190, Mismatches: 14, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
55 1 0.01
56 136 0.72
57 53 0.28
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (56 bp):
AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
Found at i:49854 original size:113 final size:112
Alignment explanation
Indices: 49652--49915 Score: 370
Period size: 113 Copynumber: 2.3 Consensus size: 112
49642 TGCCACTTGT
* * * * * *
49652 AATCACATATCGATGCC-ACGGT-TCTAGACAGGGTCTTACTCGTACACTTATATCGGAGTCACA
1 AATCACATATCGATGCCAAC-GTAT-TAAACATGGTCTTACTCGCACACATATATCAGAATCACA
* * * **
49715 TATCGATGCCAATGTATTAAATGTGGTCTTACTCCGCACACATATATTGG
64 TATCGATGCCAACGTATTAAACGTGGTCTTACT-CACACACATATATCAG
**
49765 AATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATATCAGAATCACATA
1 AATCACATATCGATGCCAACGTATTAAACATGGTCTTACTCGCACACATATATCAGAATCACATA
49830 TCGATGCCAACGTATTAAACGTGGTCTTACTCACACACATATATCAG
66 TCGATGCCAACGTATTAAACGTGGTCTTACTCACACACATATATCAG
49877 AATCACATATCGATGCCAACGTATTAAACATGGTCTTAC
1 AATCACATATCGATGCCAACGTATTAAACATGGTCTTAC
49916 ACATAAACAC
Statistics
Matches: 134, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
112 50 0.37
113 81 0.60
114 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (112 bp):
AATCACATATCGATGCCAACGTATTAAACATGGTCTTACTCGCACACATATATCAGAATCACATA
TCGATGCCAACGTATTAAACGTGGTCTTACTCACACACATATATCAG
Found at i:49942 original size:112 final size:114
Alignment explanation
Indices: 49708--49942 Score: 316
Period size: 112 Copynumber: 2.1 Consensus size: 114
49698 CTTATATCGG
* * * **
49708 AGTCACATATCGATGCCAATGTATTAAATGTGGTCTTACTCCGCACACATATATTGGAATCACAT
1 AGTCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCCACACACATATATCAGAATCACAT
** * * * *
49773 ATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATATCAGA
66 ATCGATGCCAACGTATTAAACATGGTCTTACACACAAACACATATCAGA
49822 A-TCACATATCGATGCCAACGTATTAAACGTGGTCTTACT-CACACACATATATCAGAATCACAT
1 AGTCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCCACACACATATATCAGAATCACAT
*
49885 ATCGATGCCAACGTATTAAACATGGTCTTACACATAAACACA-AGTC-GA
66 ATCGATGCCAACGTATTAAACATGGTCTTACACACAAACACATA-TCAGA
*
49933 AGTCTCATAT
1 AGTCACATAT
49943 ATACCCATAT
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
111 4 0.04
112 65 0.61
113 36 0.34
114 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (114 bp):
AGTCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCCACACACATATATCAGAATCACAT
ATCGATGCCAACGTATTAAACATGGTCTTACACACAAACACATATCAGA
Found at i:52144 original size:29 final size:29
Alignment explanation
Indices: 52109--52165 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
52099 AGGCCAACGG
* *
52109 GCCATATAAATGTGATTTTGGCCTAATGA
1 GCCATATAAAGGTGATTTGGGCCTAATGA
52138 GCCATATAAAGGTGATTTGGGCCTAATG
1 GCCATATAAAGGTGATTTGGGCCTAATG
52166 GGCATGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (29 bp):
GCCATATAAAGGTGATTTGGGCCTAATGA
Found at i:56765 original size:24 final size:24
Alignment explanation
Indices: 56738--56786 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
56728 AACTTGAATT
56738 ACTATCTATTTGGACTTTTTTTTA
1 ACTATCTATTTGGACTTTTTTTTA
56762 ACTATCTATTTGGACTTTTTTTTA
1 ACTATCTATTTGGACTTTTTTTTA
56786 A
1 A
56787 ACCTTAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.57
Consensus pattern (24 bp):
ACTATCTATTTGGACTTTTTTTTA
Found at i:62639 original size:30 final size:30
Alignment explanation
Indices: 62594--62653 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
62584 ATTTAATACG
*
62594 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
62624 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
62654 GGCTCGGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:71031 original size:47 final size:47
Alignment explanation
Indices: 70811--71245 Score: 557
Period size: 47 Copynumber: 9.3 Consensus size: 47
70801 CCCTTCGGGA
* * * * * *
70811 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
70858 CCTGTCACATATATACACTTTCACATTCA-CATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
70904 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
70950 CTTATCACATAAATATACACTTTCACACTCATCACATTTGGCCATTCGGC
1 CTTATCACAT--ATATACACTTTCACATTCATCACA-TCGGCCATTAGGC
71000 CTTATCACATATATAC-CTTTCACATTCATCACATCGGCCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGG-CCATTAGGC
*
71047 CTTATCACATAT-TATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
71093 CTAATAAACA-A-AAACACTTTC-CATTCTTACACATCGGCCATTA-GC
1 CTTAT-CACATATATACACTTTCACATTCAT-CACATCGGCCATTAGGC
* * *
71138 CTTATCACATATATACACTTTCACATTCATCAGATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
71185 CTTATCACATATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
71231 CTTATCGC-TATATAC
1 CTTATCACATATATAC
71246 TTCACATCAA
Statistics
Matches: 339, Mismatches: 35, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
44 3 0.01
45 20 0.06
46 125 0.37
47 142 0.42
48 29 0.09
49 10 0.03
50 10 0.03
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:71168 original size:92 final size:94
Alignment explanation
Indices: 70811--71245 Score: 557
Period size: 93 Copynumber: 4.7 Consensus size: 94
70801 CCCTTCGGGA
* * * * * * * *
70811 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
70876 TTTCACATTCA-CATATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
70904 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CTTATCACATAAATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT--ATATAC
* * *
70968 ACTTTCACACTCATCACATTTGGCCATTCGGC
64 ACTTTCACATTCATCACA-TCGGCCATTAGGC
*
71000 CTTATCACATATATAC-CTTTCACATTCATCACATCGGCCCATTAGGCCTTATCACATAT-TATA
1 CTTATCACATATATACACTTTCACATTCATCACATCGG-CCATTAGGCCTTATCACATATATACA
71063 CTTTCACATTCATCACATCGGCCATTAGGC
65 CTTTCACATTCATCACATCGGCCATTAGGC
* * * *
71093 CTAATAAACA-A-AAACACTTTC-CATTCTTACACATCGGCCATTA-GCCTTATCACATATATAC
1 CTTAT-CACATATATACACTTTCACATTCAT-CACATCGGCCATTAGGCCTTATCACATATATAC
* * *
71154 ACTTTCACATTCATCAGATTGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
71185 CTTATCACATATATACACTTTCACATTCATCACATC-GCCATTAGGCCTTATCGC-TATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
71246 TTCACATCAA
Statistics
Matches: 299, Mismatches: 29, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
91 17 0.06
92 72 0.24
93 93 0.31
94 46 0.15
95 26 0.09
96 35 0.12
97 10 0.03
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:74793 original size:78 final size:78
Alignment explanation
Indices: 74664--74934 Score: 412
Period size: 78 Copynumber: 3.5 Consensus size: 78
74654 CGAGTTTGCA
* * * *
74664 CGGATA-ATTACTAGCACGAATGCTCTTCGGAACTTAGCCGGATACAT-ACTAGCATGAATGCTC
1 CGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCGGGTACATCACTAGCACGAATGCTC
74727 TTCGGGACTTAGTC
66 TTCGGGACTTAG-C
74741 CGGATACATCACTAGCACGAATGC-CTTC-GGACTTAGCCCGGGTACATCACTAGCACGAATGCT
1 CGGATACATCACTAGCACGAATGCTCTTCGGGACTTAG-CCGGGTACATCACTAGCACGAATGCT
74804 CTTCGGGACTTAGCC
65 CTTCGGGACTTAG-C
74819 CGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCGGGT--ATCACTAGCACGAATGCT-
1 CGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCGGGTACATCACTAGCACGAATGCTC
74881 TTCGGGACTTAGC
66 TTCGGGACTTAGC
*
74894 CGGATTACATCACTAGCATGAATGCTCTTCGGGACTTAGCC
1 CGGA-TACATCACTAGCACGAATGCTCTTCGGGACTTAGCC
74935 CGGATCATCG
Statistics
Matches: 182, Mismatches: 6, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
75 5 0.03
76 54 0.30
77 37 0.20
78 68 0.37
79 10 0.05
80 8 0.04
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (78 bp):
CGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCGGGTACATCACTAGCACGAATGCTC
TTCGGGACTTAGC
Found at i:74827 original size:40 final size:40
Alignment explanation
Indices: 74610--74943 Score: 414
Period size: 40 Copynumber: 8.7 Consensus size: 40
74600 CCAGCATGAT
* * *
74610 TGCTCTTCGGGACCTAGCCCGGATATAAACAC-AGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATA-CATCACTAGCACGAA
* * * *
74650 ---TCTTC--GAGTTTGCACGGATA-ATTACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
74684 TGCTCTTCGGAACTTAG-CCGGATACAT-ACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
74722 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
74762 TGC-CTTC-GGACTTAGCCCGGGTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
74800 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
74840 TGCTCTTCGGGACTTAG-CCGGGT--ATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
74877 TGCT-TTCGGGACTTAG-CCGGATTACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGA-TACATCACTAGCACGAA
74916 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
74944 GTCGAGACCT
Statistics
Matches: 259, Mismatches: 19, Indels: 33
0.83 0.06 0.11
Matches are distributed among these distances:
33 3 0.01
34 8 0.03
35 11 0.04
36 16 0.06
37 29 0.11
38 64 0.25
39 50 0.19
40 73 0.28
41 5 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:74889 original size:116 final size:117
Alignment explanation
Indices: 74610--74943 Score: 422
Period size: 116 Copynumber: 2.9 Consensus size: 117
74600 CCAGCATGAT
* * * * *
74610 TGCTCTTCGGGACCTAGCCCGGATATAAACAC-AGCACGAAT--CTTC-GAGTTTGCACGGA-TA
1 TGCTCTTCGGGACTTAGTCCGG--ATAATCACTAGCACGAATGCCTTCGGACTTAGC-CGGAGTA
* * *
74670 -ATTACTAGCACGAATGCTCTTCGGAACTTAG-CCGGATACAT-ACTAGCATGAA
63 CATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
74722 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAATGCCTTCGGACTTAGCCCGG-GTAC
1 TGCTCTTCGGGACTTAGTCCGGATA-ATCACTAGCACGAATGCCTTCGGACTTAG-CCGGAGTAC
74786 ATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
64 ATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
74840 TGCTCTTCGGGACTTAG-CCGGGT-ATCACTAGCACGAATGCTTTCGGGACTTAGCCGGATTACA
1 TGCTCTTCGGGACTTAGTCCGGATAATCACTAGCACGAATGCCTTC-GGACTTAGCCGGAGTACA
*
74903 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT-CATC
65 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATC
74944 GTCGAGACCT
Statistics
Matches: 198, Mismatches: 12, Indels: 21
0.86 0.05 0.09
Matches are distributed among these distances:
110 3 0.02
111 4 0.02
112 29 0.15
114 4 0.02
115 38 0.19
116 78 0.39
117 15 0.08
118 27 0.14
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (117 bp):
TGCTCTTCGGGACTTAGTCCGGATAATCACTAGCACGAATGCCTTCGGACTTAGCCGGAGTACAT
CACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:77233 original size:24 final size:26
Alignment explanation
Indices: 77186--77241 Score: 98
Period size: 25 Copynumber: 2.2 Consensus size: 26
77176 ACTCGGCCTG
77186 TCACATATATACACATTTCACATTCA
1 TCACATATATACACATTTCACATTCA
77212 T-ACATATATACAC-TTTCACATTCA
1 TCACATATATACACATTTCACATTCA
77236 TCACAT
1 TCACAT
77242 CGGCTATTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 12 0.41
25 16 0.55
26 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.36
Consensus pattern (26 bp):
TCACATATATACACATTTCACATTCA
Found at i:77269 original size:50 final size:48
Alignment explanation
Indices: 77215--77635 Score: 523
Period size: 47 Copynumber: 8.8 Consensus size: 48
77205 ACATTCATAC
*
77215 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTTATCAC-
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCC-TTATCACT
77263 ATATATACACTTTCACATTCA-CACATCGGCCATTAGGCCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGG-CCTTATCAC-T
*
77312 ATATATACACTTTCACATTCATCACATCGGCTATTA-GCC-T-TCAC-
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACT
*
77356 ATATATACACTTTCACATTCATCAACAATCGGCCACTTAGG-CTTGTCAC-
1 ATATATACACTTTCACATTCATC-AC-ATCGGCCA-TTAGGCCTTATCACT
*
77405 ATATTAATAC-GTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
1 ATA-T-ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-T
* * *
77455 ATATATACCACTTTCACACTCATCACATTGGCCATTCGGCCTTATCAC-
1 ATATATA-CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACT
* *
77503 ATA-ATACACTTTCACATTCATAACATC-GCCATTAGGCCTTATCACC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACT
77549 ATATATACACTTTCACATTCATCACAT-GG-C-TTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-T
77595 AATATATACACATTTCACATTCATCACATTCGG-CATTAGGC
1 -ATATATACAC-TTTCACATTCATCACA-TCGGCCATTAGGC
77636 TTAACACACT
Statistics
Matches: 332, Mismatches: 15, Indels: 49
0.84 0.04 0.12
Matches are distributed among these distances:
44 23 0.07
45 33 0.10
46 33 0.10
47 68 0.20
48 64 0.19
49 34 0.10
50 67 0.20
51 10 0.03
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (48 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACT
Found at i:77307 original size:47 final size:47
Alignment explanation
Indices: 77213--77643 Score: 528
Period size: 50 Copynumber: 9.1 Consensus size: 47
77203 TCACATTCAT
*
77213 ACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC-TTATC
77261 ACATATATACACTTTCACATTCA-CACATCGGCCATTAGGCCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CCTTATC
*
77308 ACATATATATACACTTTCACATTCATCACATCGGCTATTA-GCC-T-TC
1 AC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
77354 ACATATATACACTTTCACATTCATCAACAATCGGCCACTTAGG-CTTGTC
1 ACATATATACACTTTCACATTCATC-AC-ATCGGCCA-TTAGGCCTTATC
*
77403 ACATATTAATAC-GTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACATA-T-ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
* * *
77451 ACATATATATACCACTTTCACACTCATCACATTGGCCATTCGGCCTTATC
1 AC--ATATATA-CACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
77501 ACATA-ATACACTTTCACATTCATAACATC-GCCATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
77546 ACCATATATACACTTTCACATTCATCACAT-GG-C-TTAGGCCTTATC
1 A-CATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
77591 ACATAATATATACACATTTCACATTCATCACATTCGG-CATTAGG-CTTAAC
1 AC---ATATATACAC-TTTCACATTCATCACA-TCGGCCATTAGGCCTTATC
77641 ACA
1 ACA
77644 CTAATAACG
Statistics
Matches: 341, Mismatches: 15, Indels: 55
0.83 0.04 0.13
Matches are distributed among these distances:
44 24 0.07
45 31 0.09
46 34 0.10
47 69 0.20
48 66 0.19
49 34 0.10
50 74 0.22
51 9 0.03
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.32
Consensus pattern (47 bp):
ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
Found at i:77450 original size:143 final size:142
Alignment explanation
Indices: 77213--77643 Score: 580
Period size: 143 Copynumber: 3.0 Consensus size: 142
77203 TCACATTCAT
*
77213 ACATATATACACTTTCACATTCATC-ACATCGGCTATTAGGCCTTTATCACATATATACACTTTC
1 ACATATATACACTTTCACATTCATCAACATCGGCCATTAGGCC-TTATCACATATATACACTTTC
77277 ACATTCA-CACATCGGCCATTAGGCCCTTATCACATATATATACACTTTCACATTCATCACATCG
65 ACATTCATCACATCGGCCATTAGG-CCTTATCACATATATATACACTTTCACATTCATCACATCG
77341 GCTATTAGCC-T-TC
129 GC-ATTAGCCTTATC
* *
77354 ACATATATACACTTTCACATTCATCAACAATCGGCCACTTAGG-CTTGTCACATATTAATAC-GT
1 ACATATATACACTTTCACATTCATCAAC-ATCGGCCA-TTAGGCCTTATCACATA-T-ATACACT
*
77417 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACCACTTTCACACTCATCACA
62 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA-CACTTTCACATTCATCACA
* *
77482 TTGGCCATTCGGCCTTATC
126 TCGG-CATT-AGCCTTATC
77501 ACATA-ATACACTTTCACATTCAT-AACATC-GCCATTAGGCCTTATCACCATATATACACTTTC
1 ACATATATACACTTTCACATTCATCAACATCGGCCATTAGGCCTTATCA-CATATATACACTTTC
77563 ACATTCATCACAT-GG-C-TTAGGCCTTATCACATAATATATACACATTTCACATTCATCACATT
65 ACATTCATCACATCGGCCATTAGGCCTTATCACAT-ATATATACAC-TTTCACATTCATCACA-T
* *
77625 CGGCATTAGGCTTAAC
127 CGGCATTAGCCTTATC
77641 ACA
1 ACA
77644 CTAATAACG
Statistics
Matches: 260, Mismatches: 13, Indels: 35
0.84 0.04 0.11
Matches are distributed among these distances:
140 28 0.11
141 52 0.20
142 25 0.10
143 66 0.25
144 56 0.22
145 7 0.03
146 19 0.07
147 7 0.03
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.32
Consensus pattern (142 bp):
ACATATATACACTTTCACATTCATCAACATCGGCCATTAGGCCTTATCACATATATACACTTTCA
CATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGC
ATTAGCCTTATC
Done.