Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 1 of 143
Found at i:1303 original size:68 final size:68
Alignment explanation
Indices: 1169--1615 Score: 732
Period size: 68 Copynumber: 6.5 Consensus size: 68
1159 TGCAGGTCAC
* * * * *
1169 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTTTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1234 AGAG
65 AGAG
* * *
1238 TAATGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1303 GAG
66 GAG
* *
1306 CAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1371 GAG
66 GAG
1374 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTG-AAATTGAAGTA
1439 AGAG
65 AGAG
*
1443 CAACATCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1508 GAG
66 GAG
* *
1511 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTACCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1576 GAG
66 GAG
* *
1579 CAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATA
1616 GCAAAGTCTT
Statistics
Matches: 358, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
68 258 0.72
69 100 0.28
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (68 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
GAG
Found at i:1498 original size:137 final size:137
Alignment explanation
Indices: 1169--1631 Score: 741
Period size: 137 Copynumber: 3.4 Consensus size: 137
1159 TGCAGGTCAC
* * * *
1169 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTTTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
* * *
1234 AGAGTAATGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAA
66 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
1299 GTAAGAG
131 GTAAGAG
* *
1306 CAACGTCATCCCCTTGAAATTGAAATAGAG-TGGATAACATGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
1370 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAAATTGA
66 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTG-AAATTGA
1435 AGTAAGAG
130 AGTAAGAG
* *
1443 CAACATCATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
* *
1507 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTACCTCTGAAATTGAA
66 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
1572 GTAAGAG
131 GTAAGAG
* * * *
1579 CAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAAGTCTTTATCTC
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAAC-AAGTCTTCATCTC
1632 CCTGAAGAGC
Statistics
Matches: 303, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
136 126 0.42
137 166 0.55
138 11 0.04
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (137 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
GTAAGAG
Found at i:1521 original size:205 final size:205
Alignment explanation
Indices: 1169--1631 Score: 757
Period size: 205 Copynumber: 2.3 Consensus size: 205
1159 TGCAGGTCAC
* * *
1169 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTTTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
* ** *
1234 AGAGTAATGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAA
66 AGAGCAACATCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
* *
1299 GTAAGAGCAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACATGTCTTCATCTCTGAAATT
131 GTAAGAGCAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACACGTCTTCACCTCTGAAATT
1364 GAAGTAAGAG
196 GAAGTAAGAG
* *
1374 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAAATTGAAGT
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTG-AAATTGAAGT
1438 AAGAGCAACATCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
65 AAGAGCAACATCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
* *
1503 AGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTACCTCTGAAAT
130 AGTAAGAGCAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACACGTCTTCACCTCTGAAAT
1568 TGAAGTAAGAG
195 TGAAGTAAGAG
* * *
1579 CAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAAGTCTTTATCTC
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAAC-AAGTCTTCATCTC
1632 CCTGAAGAGC
Statistics
Matches: 237, Mismatches: 18, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
204 19 0.08
205 200 0.84
206 7 0.03
207 11 0.05
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (205 bp):
CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
AGAGCAACATCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
GTAAGAGCAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACACGTCTTCACCTCTGAAATT
GAAGTAAGAG
Found at i:1953 original size:6 final size:6
Alignment explanation
Indices: 1944--2020 Score: 63
Period size: 6 Copynumber: 13.2 Consensus size: 6
1934 AAATTCATGG
* * **
1944 TTAAAT TTAAAT TT-ATT TTAAA- TTAAAT GTAAAAAT TTAAAT TT-GCT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -T-TAAAT TTAAAT TTAAAT
*
1991 TTAAAT TTAAAT TT-AAT TAAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
2021 AATAAAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
5 16 0.29
6 33 0.60
7 2 0.04
8 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:1966 original size:17 final size:17
Alignment explanation
Indices: 1928--2020 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 17
1918 GTTTTGAACA
* *
1928 AAATTTAAATTCATGGTT
1 AAATTTAAATTTAT-TTT
1946 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
1963 AAA-TTAAATGTA---A
1 AAATTTAAATTTATTTT
**
1976 AAATTTAAATTTGCTTT
1 AAATTTAAATTTATTTT
* *
1993 AAATTTAAATTTAATTA
1 AAATTTAAATTTATTTT
2010 AAATTTAAATT
1 AAATTTAAATT
2021 AATAAAAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
13 3 0.05
14 7 0.11
16 8 0.13
17 30 0.49
18 13 0.21
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:2002 original size:47 final size:48
Alignment explanation
Indices: 1927--2019 Score: 127
Period size: 47 Copynumber: 1.9 Consensus size: 48
1917 GGTTTTGAAC
* *
1927 AAAATTTAAATTCATGGTTAAATTTAAATTTATTTTAAA-TTAAATGTA
1 AAAATTTAAATT-ATGGTTAAATTTAAATTTAATTAAAATTTAAATGTA
*
1975 AAAATTTAAATT-TGCTTTAAATTTAAATTTAATTAAAATTTAAAT
1 AAAATTTAAATTATG-GTTAAATTTAAATTTAATTAAAATTTAAAT
2020 TAATAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 2 0.05
47 20 0.50
48 18 0.45
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (48 bp):
AAAATTTAAATTATGGTTAAATTTAAATTTAATTAAAATTTAAATGTA
Found at i:2029 original size:17 final size:17
Alignment explanation
Indices: 1973--2028 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
1963 AAATTAAATG
**
1973 TAAAAATTTAAATTTGC
1 TAAAAATTTAAATTTAA
**
1990 TTTAAATTTAAATTTAA
1 TAAAAATTTAAATTTAA
*
2007 TTAAAATTTAAA-TTAA
1 TAAAAATTTAAATTTAA
2023 TAAAAA
1 TAAAAA
2029 AACCAAATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 9 0.27
17 24 0.73
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAAAATTTAAATTTAA
Found at i:2731 original size:24 final size:24
Alignment explanation
Indices: 2701--2756 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
2691 TAAGGATGGT
*
2701 TAATAATAGT-ATCATTAATAACAA
1 TAATAATAGTGAT-AATAATAACAA
*
2725 TAATAATAGTGATAATAATAACAG
1 TAATAATAGTGATAATAATAACAA
2749 TAATAATA
1 TAATAATA
2757 ATAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (24 bp):
TAATAATAGTGATAATAATAACAA
Found at i:2743 original size:15 final size:15
Alignment explanation
Indices: 2723--2760 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2713 CATTAATAAC
* *
2723 AATAATAATAGTGAT
1 AATAATAACAGTAAT
2738 AATAATAACAGTAAT
1 AATAATAACAGTAAT
2753 AATAATAA
1 AATAATAA
2761 ATATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (15 bp):
AATAATAACAGTAAT
Found at i:3905 original size:30 final size:30
Alignment explanation
Indices: 3869--4097 Score: 386
Period size: 30 Copynumber: 7.6 Consensus size: 30
3859 AAATTATCTA
*
3869 AAAATTATATTTCGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
3899 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* * *
3929 GAAATTACATTTTGACCCCAAAACTTTTAC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
*
3959 AAAATTATATTTTGACCCTAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* *
3989 AGAATTATATTTTGACCCTAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
4019 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
*
4049 AAAATTATATTTTGACCCTAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
4079 AAAATTATATTTTGACCCC
1 AAAATTATATTTTGACCCC
4098 CGAAACTTCT
Statistics
Matches: 186, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 186 1.00
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCAAAACTTTTCC
Found at i:4156 original size:59 final size:59
Alignment explanation
Indices: 4079--4393 Score: 447
Period size: 59 Copynumber: 5.3 Consensus size: 59
4069 AAACTTTTCC
* * * *
4079 AAAATTA-TATTTTGACCCCCGAAACTTCTAAAATTCCATTTTTAATCCC-GATTTCTCTG
1 AAAATTACCATTTT-ACCCCCGAAGCTTCTAAAATTCCATTTTTAA-CCCTGATTTCACCG
*
4138 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTTAACCCTGATTTCACCA
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCA-TTTTTAACCCTGATTTCACCG
* *
4198 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTGATTTTATCG
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTGATTTCACCG
*
4257 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTAATTTCACCG
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTGATTTCACCG
* * * * * *
4316 AAGATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACC-
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTGATTTCACCG
*
4374 AAAATTACCATTTTGCCCCC
1 AAAATTACCATTTTACCCCC
4394 CGGGTATCCA
Statistics
Matches: 232, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
58 17 0.07
59 158 0.68
60 57 0.25
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTGATTTCACCG
Found at i:4216 original size:119 final size:117
Alignment explanation
Indices: 4079--4393 Score: 438
Period size: 119 Copynumber: 2.7 Consensus size: 117
4069 AAACTTTTCC
*
4079 AAAATTA-TATTTTGACCCCCGAAACTTCTAAAATTCCATTTTTAATCCCGATTTCTCTGAAAAT
1 AAAATTACCATTTT-ACCCCCGAAACTTCTAAAATTCCATTTTTAA-CCCGATTTCTCTGAAAAT
*
4143 TACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTTAACCCTGATTTCACCA
64 TACCATTTTACCCCCGAAGCTTCTAAAATTCCA-TTTTTAACCCTAATTTCACCA
* *
4198 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTGATTT-TATCGAAAAT
1 AAAATTACCATTTTACCCCCGAAACTTCTAAAATTCCATTTTTAACCC-GATTTCTCT-GAAAAT
*
4262 TACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTAATTTCACCG
64 TACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTAATTTCACCA
* * * * * * *
4316 AAGATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACAC-CAAAATT
1 AAAATTACCATTTTACCCCCGAAACTTCTAAAATTCCATTTTTAA-CCCGATTTCTCTGAAAATT
*
4380 ACCATTTTGCCCCC
65 ACCATTTTACCCCC
4394 CGGGTATCCA
Statistics
Matches: 177, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
117 19 0.11
118 69 0.39
119 84 0.47
120 5 0.03
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCCGAAACTTCTAAAATTCCATTTTTAACCCGATTTCTCTGAAAATTA
CCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCTAATTTCACCA
Found at i:4377 original size:29 final size:30
Alignment explanation
Indices: 4108--4387 Score: 79
Period size: 30 Copynumber: 9.5 Consensus size: 30
4098 CGAAACTTCT
* * * *
4108 AAAATT-CCATTTTTAATCCCGATTTCTCTG
1 AAAATTACCATTTTTAACCCCGATTACAC-C
* * *
4138 AAAATTACCA-TTTTACCCCCGA--AGCTTCT
1 AAAATTACCATTTTTAACCCCGATTA-C-ACC
* *
4167 AAAATT-CCATTTTTTAACCCTGATTTCACC
1 AAAATTACCA-TTTTTAACCCCGATTACACC
* * *
4197 AAAAATTACCA-TTTTACCCCCGA--AGCTTCT
1 -AAAATTACCATTTTTAACCCCGATTA-C-ACC
* ** *
4227 AAAATT-CCATTTTTAACCCTGATTTTATCG
1 AAAATTACCATTTTTAACCCCGATTACA-CC
* * *
4257 AAAATTACCA-TTTTACCCCCGA--AGCTTCT
1 AAAATTACCATTTTTAACCCCGATTA-C-ACC
** *
4286 AAAATT-CCATTTTTAACCCTAATTTCACC
1 AAAATTACCATTTTTAACCCCGATTACACC
* * * * ***
4315 GAAGATTGCCA-TTTTACCCCCGAAT-CTTTT
1 -AAAATTACCATTTTTAACCCCGATTAC-ACC
4345 AAAATT-CCATTTTTAACCCCGATTACACC
1 AAAATTACCATTTTTAACCCCGATTACACC
4374 AAAATTACCATTTT
1 AAAATTACCATTTT
4388 GCCCCCCGGG
Statistics
Matches: 177, Mismatches: 46, Indels: 54
0.64 0.17 0.19
Matches are distributed among these distances:
28 12 0.07
29 65 0.37
30 81 0.46
31 16 0.09
32 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTTAACCCCGATTACACC
Found at i:12381 original size:19 final size:19
Alignment explanation
Indices: 12345--12381 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12335 TCGATGTCAA
*
12345 CATGTCTCGAGGCAAGGTT
1 CATGTCTCGAGACAAGGTT
*
12364 CATGTCTCGAGACTAGGT
1 CATGTCTCGAGACAAGGT
12382 CTAGAGACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (19 bp):
CATGTCTCGAGACAAGGTT
Found at i:14818 original size:18 final size:18
Alignment explanation
Indices: 14795--14835 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
14785 TTTTTTAATT
* *
14795 AAAAAAATTATAATTATG
1 AAAAAAATTAAAATTAAG
14813 AAAAAAATTAAAATTAAG
1 AAAAAAATTAAAATTAAG
14831 AAAAA
1 AAAAA
14836 GGAAGAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAAAAAATTAAAATTAAG
Found at i:21895 original size:25 final size:26
Alignment explanation
Indices: 21841--21897 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
21831 AATTTAAAAT
* * * *
21841 AAAATATATAAAAATTATATATTTTT
1 AAAATATATAAAAAGTATAAATTATA
21867 AAAATATA-AAAAAGTATAAATTATA
1 AAAATATATAAAAAGTATAAATTATA
21892 AAAATA
1 AAAATA
21898 AATGTATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AAAATATATAAAAAGTATAAATTATA
Found at i:39285 original size:7 final size:7
Alignment explanation
Indices: 39257--39306 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
39247 AAATACAAGG
39257 ATTAAAT
1 ATTAAAT
*
39264 TTCTAAAT
1 AT-TAAAT
39272 A-TAAAT
1 ATTAAAT
39278 ATTAAAT
1 ATTAAAT
39285 ATTAAAT
1 ATTAAAT
39292 ATTAAAT
1 ATTAAAT
39299 ATATAAAT
1 AT-TAAAT
39307 GAAGACCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 6 0.16
7 22 0.58
8 10 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTAAAT
Found at i:41737 original size:31 final size:32
Alignment explanation
Indices: 41689--41759 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
41679 TTTGTGTGAT
41689 TATACATATTAAACTTTGACTTTAG-TTCAAATG
1 TATACATA-TAAACTTTGA-TTTAGATTCAAATG
* *
41722 TATACATA-AAACTTTGATTTTGATTCAATTG
1 TATACATATAAACTTTGATTTAGATTCAAATG
41753 TATACAT
1 TATACAT
41760 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 4 0.11
31 23 0.66
33 8 0.23
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (32 bp):
TATACATATAAACTTTGATTTAGATTCAAATG
Found at i:47455 original size:22 final size:23
Alignment explanation
Indices: 47422--47471 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
47412 AACATATAAA
47422 AAAAAAATTTAAAGGACCCATTC
1 AAAAAAATTTAAAGGACCCATTC
*
47445 AAAAAAA-TTAAAGGACTCATTC
1 AAAAAAATTTAAAGGACCCATTC
47467 AAAAA
1 AAAAA
47472 TGTAACTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.20
Consensus pattern (23 bp):
AAAAAAATTTAAAGGACCCATTC
Found at i:50218 original size:20 final size:20
Alignment explanation
Indices: 50193--50233 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
50183 CTCAAATGCT
50193 TGGCATGTGTTATTTTTTTG
1 TGGCATGTGTTATTTTTTTG
* * *
50213 TGGCATTTTTTGTTTTTTTG
1 TGGCATGTGTTATTTTTTTG
50233 T
1 T
50234 TGCTCTTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.05, G:0.22, T:0.66
Consensus pattern (20 bp):
TGGCATGTGTTATTTTTTTG
Found at i:50725 original size:21 final size:20
Alignment explanation
Indices: 50701--50761 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 20
50691 AAAGAAAAGC
*
50701 AAAAGAAAAAAAAAGATGTAA
1 AAAAGAAAAAAAAAGAT-AAA
*
50722 AAAAGAAAAGGAAAAGTATAAA
1 AAAAGAAAA-AAAAAG-ATAAA
50744 AAAAGAAAGAAAGAAAGA
1 AAAAGAAA-AAA-AAAGA
50762 AGAGGAAGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 9 0.27
22 17 0.52
23 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAAAAAAGATAAA
Found at i:53349 original size:2 final size:2
Alignment explanation
Indices: 53342--53380 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
53332 AGTATTAGAA
53342 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
53381 AAGATAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54876 original size:22 final size:21
Alignment explanation
Indices: 54830--54876 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
54820 ATCAAGGTTC
* *
54830 GTTT-CTTTTCTCCCAACATG
1 GTTTGCTTTTCTCCAAACAGG
*
54850 CTTTGCTTTTCTACCAAACAGG
1 GTTTGCTTTTCT-CCAAACAGG
54872 GTTTG
1 GTTTG
54877 TTCTTATACT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 3 0.14
21 7 0.33
22 11 0.52
ACGTcount: A:0.17, C:0.26, G:0.15, T:0.43
Consensus pattern (21 bp):
GTTTGCTTTTCTCCAAACAGG
Found at i:56850 original size:44 final size:44
Alignment explanation
Indices: 56787--56875 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
56777 CAATACTAGG
56787 TCTGCCCATGACTTGATCCTCAGCCCATTTTAAGTGCCCAAAAA
1 TCTGCCCATGACTTGATCCTCAGCCCATTTTAAGTGCCCAAAAA
56831 TCTGCCCATGACTTGATCCTCAGCCCATTTTAAGTGCCCAAAAA
1 TCTGCCCATGACTTGATCCTCAGCCCATTTTAAGTGCCCAAAAA
56875 T
1 T
56876 TGTCTTTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.28
Consensus pattern (44 bp):
TCTGCCCATGACTTGATCCTCAGCCCATTTTAAGTGCCCAAAAA
Found at i:69303 original size:22 final size:25
Alignment explanation
Indices: 69273--69320 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
69263 ATGCCACATC
69273 ACATGTCAT-A-TCATTCG-TCACT
1 ACATGTCATAATTCATTCGCTCACT
*
69295 ACATTTCATAATTCATTCGCTCACT
1 ACATGTCATAATTCATTCGCTCACT
69320 A
1 A
69321 GTATTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 1 0.05
24 7 0.32
25 6 0.27
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (25 bp):
ACATGTCATAATTCATTCGCTCACT
Found at i:74918 original size:18 final size:18
Alignment explanation
Indices: 74878--74920 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
74868 GTTCAATGTG
*
74878 TAATTAATTTAATATTTT
1 TAATTAATTCAATATTTT
*
74896 CAATTAATTCAAT-TTATT
1 TAATTAATTCAATATT-TT
74914 TAATTAA
1 TAATTAA
74921 AAACCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTCAATATTTT
Found at i:79393 original size:18 final size:20
Alignment explanation
Indices: 79370--79406 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
79360 TACAGCAGTG
79370 AATATTT-TAA-AACTAAAA
1 AATATTTATAATAACTAAAA
79388 AATATTTATAATAACTAAA
1 AATATTTATAATAACTAAA
79407 TGTCTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 3 0.18
20 7 0.41
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AATATTTATAATAACTAAAA
Found at i:91790 original size:2 final size:2
Alignment explanation
Indices: 91778--91807 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
91768 TAAATATGCT
*
91778 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91808 ATTTTTAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:118891 original size:13 final size:13
Alignment explanation
Indices: 118875--118926 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
118865 CACAAGCAAT
118875 TTTTTTTCATTAA
1 TTTTTTTCATTAA
* *
118888 TTTTTTTAATCAAA
1 TTTTTTTCAT-TAA
*
118902 TTTTTATCCATTAA
1 TTTTT-TTCATTAA
*
118916 TTTTATTCATT
1 TTTTTTTCATT
118927 TTTGTTTAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 14 0.47
14 13 0.43
15 3 0.10
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTTTCATTAA
Found at i:123304 original size:18 final size:17
Alignment explanation
Indices: 123281--123314 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
123271 TCCACTCATT
123281 ATTAATTATAAAAAAATA
1 ATTAATT-TAAAAAAATA
123299 ATTAATTTAAAAAAAT
1 ATTAATTTAAAAAAAT
123315 CAAGGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTAATTTAAAAAAATA
Found at i:124422 original size:14 final size:13
Alignment explanation
Indices: 124398--124434 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
124388 ATTTATTTTA
124398 AAATTATTAAATC
1 AAATTATTAAATC
124411 AAATTAATTAAATC
1 AAATT-ATTAAATC
124425 AAATTTATTA
1 AAA-TTATTA
124435 TAAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 15 0.68
15 2 0.09
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTATTAAATC
Found at i:128132 original size:6 final size:6
Alignment explanation
Indices: 128112--128149 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
128102 TGTTGATACT
*
128112 TGGCAG TGG-AA TGGCAA TGGCAA TGGCAA TGGCAA TGG
1 TGGCAA TGGCAA TGGCAA TGGCAA TGGCAA TGGCAA TGG
128150 GGGTTTCACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (6 bp):
TGGCAA
Found at i:135910 original size:25 final size:27
Alignment explanation
Indices: 135864--135915 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
135854 TTTCTCGATT
**
135864 CAATTTTAGTTTTGTTAAAATC-ATGA
1 CAATTTTAGTTTTACTAAAATCTATGA
*
135890 CAATTTTA-TTTTACTAGAATCTATGA
1 CAATTTTAGTTTTACTAAAATCTATGA
135916 GTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (27 bp):
CAATTTTAGTTTTACTAAAATCTATGA
Found at i:141621 original size:11 final size:11
Alignment explanation
Indices: 141526--141621 Score: 77
Period size: 11 Copynumber: 8.4 Consensus size: 11
141516 TTATTACTGA
*
141526 TTTGCTATTAT
1 TTTGTTATTAT
141537 TTT-TTATTAT
1 TTTGTTATTAT
*
141547 GTTAGTTATTAT
1 -TTTGTTATTAT
*
141559 TTTGTTACTATT
1 TTTGTTATTA-T
*
141571 ATTTGAATATTAT
1 -TTTG-TTATTAT
* *
141584 ATTATTATTAT
1 TTTGTTATTAT
*
141595 TTTATTATTAAT
1 TTTGTTATT-AT
141607 TTTGTTATTAT
1 TTTGTTATTAT
141618 TTTG
1 TTTG
141622 AATGTATTTG
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
10 6 0.09
11 33 0.49
12 20 0.29
13 5 0.07
14 4 0.06
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (11 bp):
TTTGTTATTAT
Found at i:142624 original size:21 final size:22
Alignment explanation
Indices: 142587--142627 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
142577 AAATAGGGAG
142587 AAAACAACAAGAAAATAACATT
1 AAAACAACAAGAAAATAACATT
142609 AAAACAACAA-AAAATAACA
1 AAAACAACAAGAAAATAACA
142628 AATTTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.73, C:0.15, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAACAACAAGAAAATAACATT
Found at i:143555 original size:6 final size:6
Alignment explanation
Indices: 143546--143576 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
143536 TACTTGGAAG
*
143546 TGGCAG TGGCAA TGGCAA TGGCAA TGGCAA T
1 TGGCAA TGGCAA TGGCAA TGGCAA TGGCAA T
143577 AGGGGTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.19
Consensus pattern (6 bp):
TGGCAA
Found at i:144030 original size:33 final size:33
Alignment explanation
Indices: 143993--144064 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
143983 TTAAAATAAC
* *
143993 TTAAATTAATTTAAATTATGAATGAAAAGAAAT
1 TTAAATTAATTTAAATTATAAATAAAAAGAAAT
*
144026 TTAAAATAATTTAAATTATAAATAAAAAGAAAT
1 TTAAATTAATTTAAATTATAAATAAAAAGAAAT
144059 TTAAAT
1 TTAAAT
144065 AGGTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (33 bp):
TTAAATTAATTTAAATTATAAATAAAAAGAAAT
Found at i:147627 original size:11 final size:11
Alignment explanation
Indices: 147613--147695 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 11
147603 TTTACCACTG
*
147613 TTTTGTTATTA
1 TTTTATTATTA
*
147624 TTTT-TCTATCA
1 TTTTAT-TATTA
* *
147635 TGTTGTTATTA
1 TTTTATTATTA
* *
147646 TTTGAATATTA
1 TTTTATTATTA
*
147657 TATTATTATTA
1 TTTTATTATTA
*
147668 TTTTAATATTAA
1 TTTTATTATT-A
*
147680 TTTTATTACTA
1 TTTTATTATTA
147691 TTTTA
1 TTTTA
147696 AGGGTATTTA
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
10 1 0.02
11 44 0.80
12 10 0.18
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.64
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:147665 original size:22 final size:20
Alignment explanation
Indices: 147640--147687 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 20
147630 TATCATGTTG
147640 TTATTATTTGAATATTATATT
1 TTATTATTTGAATATTA-ATT
*
147661 ATTATTATTTTAATATTAATT
1 -TTATTATTTGAATATTAATT
147682 TTATTA
1 TTATTA
147688 CTATTTTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 3 0.12
22 16 0.64
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATTATTTGAATATTAATT
Found at i:147692 original size:23 final size:22
Alignment explanation
Indices: 147644--147696 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
147634 ATGTTGTTAT
* *
147644 TATTTGAATATTATATTATTAT
1 TATTTTAATATTATATTATTAC
*
147666 TATTTTAATATTAATTTTATTAC
1 TATTTTAATATT-ATATTATTAC
147689 TATTTTAA
1 TATTTTAA
147697 GGGTATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTTTAATATTATATTATTAC
Found at i:148787 original size:23 final size:23
Alignment explanation
Indices: 148682--148869 Score: 163
Period size: 23 Copynumber: 8.1 Consensus size: 23
148672 GGAAACAGTA
*
148682 AGCACACACAGTGC-AACCCAGTAG
1 AGCACACACAGTGCTAA-TCAG-AG
*
148706 -GCACATACAGTGC-AATCAGTAG
1 AGCACACACAGTGCTAATCAG-AG
* * * *
148728 -GCGCACATAGCGCAAATCAGTAG
1 AGCACACACAGTGCTAATCAG-AG
*
148751 -GCACACAAAGTGCTAATCAGAG
1 AGCACACACAGTGCTAATCAGAG
*
148773 AGCACACACAGTGCTAATAACAAAG
1 AGCACACACAGTGCTAAT--CAGAG
* *
148798 AGCACGAGAC-GTGCTAAACAGAG
1 AGCAC-ACACAGTGCTAATCAGAG
*
148821 AGCACACACAGTGCTAAACAGAG
1 AGCACACACAGTGCTAATCAGAG
*
148844 AGCACACACAGTGCTAAACAGAG
1 AGCACACACAGTGCTAATCAGAG
148867 AGC
1 AGC
148870 GCACTAGTGT
Statistics
Matches: 142, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
22 20 0.14
23 103 0.73
25 16 0.11
26 3 0.02
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (23 bp):
AGCACACACAGTGCTAATCAGAG
Found at i:148848 original size:46 final size:48
Alignment explanation
Indices: 148751--148869 Score: 172
Period size: 48 Copynumber: 2.5 Consensus size: 48
148741 AAATCAGTAG
* *
148751 GCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAATAACAAAGA
1 GCACACACAGTGCTAAACAGAGAGCACACACAGTGCTAATAACAAAGA
* *
148799 GCACGAGAC-GTGCTAAACAGAGAGCACACACAGTGCT-A-AACAGAGA
1 GCAC-ACACAGTGCTAAACAGAGAGCACACACAGTGCTAATAACAAAGA
148845 GCACACACAGTGCTAAACAGAGAGC
1 GCACACACAGTGCTAAACAGAGAGC
148870 GCACTAGTGT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
45 3 0.05
46 27 0.42
47 1 0.02
48 31 0.48
49 2 0.03
ACGTcount: A:0.43, C:0.24, G:0.23, T:0.10
Consensus pattern (48 bp):
GCACACACAGTGCTAAACAGAGAGCACACACAGTGCTAATAACAAAGA
Found at i:152357 original size:14 final size:15
Alignment explanation
Indices: 152338--152370 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
152328 CTATTCGATT
*
152338 AAATAAATA-ATTAA
1 AAATAAAAATATTAA
152352 AAATAAAAATATTAA
1 AAATAAAAATATTAA
152367 AAAT
1 AAAT
152371 TCCTATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAAAATATTAA
Found at i:158383 original size:18 final size:18
Alignment explanation
Indices: 158326--158385 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
158316 AGATGTTTGA
158326 CTTGGATTTCTCCGAAAC
1 CTTGGATTTCTCCGAAAC
* *
158344 CATGGATTTC-CCAGAGAC
1 CTTGGATTTCTCC-GAAAC
*
158362 CTTGGATTTCTCCGAAAT
1 CTTGGATTTCTCCGAAAC
158380 CTTGGA
1 CTTGGA
158386 GAACCTCCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 2 0.06
18 31 0.89
19 2 0.06
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (18 bp):
CTTGGATTTCTCCGAAAC
Found at i:158511 original size:72 final size:72
Alignment explanation
Indices: 158394--158538 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
158384 GAGAACCTCC
*
158394 TCGCAATGCGGCAACATCATGTTTGTTCCGTTTATTTGGTTTATGAAATGGTCTTGTTGGTTCAT
1 TCGCAAGGCGGCAACATCATGTTTGTTCCGTTTATTTGGTTTATGAAATGGTCTTGTTGGTTCAT
158459 GAGCTCA
66 GAGCTCA
158466 TCGCAAGGCGGCAACATCATGTTTGTTCCGTTTATTTGGTTTATGAAATGGTCTTGTTGGTTCAT
1 TCGCAAGGCGGCAACATCATGTTTGTTCCGTTTATTTGGTTTATGAAATGGTCTTGTTGGTTCAT
158531 GAGCTCA
66 GAGCTCA
158538 T
1 T
158539 GCCAATCCCT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (72 bp):
TCGCAAGGCGGCAACATCATGTTTGTTCCGTTTATTTGGTTTATGAAATGGTCTTGTTGGTTCAT
GAGCTCA
Found at i:167768 original size:27 final size:27
Alignment explanation
Indices: 167717--167768 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
167707 ATGGAAAACA
* ** *
167717 AATTTAGGAACCAACTAGGTCCAAAAT
1 AATTTAAGAACCAACTAAATACAAAAT
167744 AATTTAAGAACCAACTAAATACAAA
1 AATTTAAGAACCAACTAAATACAAA
167769 TTAACAAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (27 bp):
AATTTAAGAACCAACTAAATACAAAAT
Found at i:168610 original size:18 final size:18
Alignment explanation
Indices: 168584--168656 Score: 65
Period size: 18 Copynumber: 4.1 Consensus size: 18
168574 ATGATGATCC
* *
168584 TAACGAAAATAATATTAG
1 TAACAAAAATAATAATAG
* *
168602 TAACAAAAATCATAATAT
1 TAACAAAAATAATAATAG
* * * *
168620 TAATATAAATAATCATAT
1 TAACAAAAATAATAATAG
*
168638 TAATAAAAATAATAATAG
1 TAACAAAAATAATAATAG
168656 T
1 T
168657 GGAAACGAGA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (18 bp):
TAACAAAAATAATAATAG
Found at i:173145 original size:21 final size:22
Alignment explanation
Indices: 173121--173164 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
173111 TTTTGAAGGC
*
173121 TTGAAAATG-TTTTATGAGATT
1 TTGAAAATGATTTTATGACATT
*
173142 TTGAAATTGATTTTATGACATT
1 TTGAAAATGATTTTATGACATT
173164 T
1 T
173165 ATGGTACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (22 bp):
TTGAAAATGATTTTATGACATT
Found at i:181248 original size:31 final size:31
Alignment explanation
Indices: 181210--181271 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
181200 TCAATATACA
*
181210 AAACTTTGATTGTGATTTAAATATACACATT
1 AAACTTTGATTGTGATTCAAATATACACATT
* * *
181241 AAACTTTGATTTTGATTCAATTTTACACATT
1 AAACTTTGATTGTGATTCAAATATACACATT
181272 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.45
Consensus pattern (31 bp):
AAACTTTGATTGTGATTCAAATATACACATT
Found at i:183519 original size:38 final size:37
Alignment explanation
Indices: 183469--183541 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 37
183459 CCAAAGGGTT
183469 AAAAAAGCTTAAAATTTATACTTAATTGGTAAAAATA
1 AAAAAAGCTTAAAATTTATACTTAATTGGTAAAAATA
183506 AAAAAAGGCTTAAAATTTATACTTAATTGGTAAAAA
1 AAAAAA-GCTTAAAATTTATACTTAATTGGTAAAAA
183542 GGGTTAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 6 0.17
38 29 0.83
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (37 bp):
AAAAAAGCTTAAAATTTATACTTAATTGGTAAAAATA
Found at i:190616 original size:10 final size:10
Alignment explanation
Indices: 190601--190637 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
190591 TTTTTTTACT
190601 ATTGTTTTTC
1 ATTGTTTTTC
*
190611 ATTGTTTTGC
1 ATTGTTTTTC
190621 ATT-TTTTTC
1 ATTGTTTTTC
190630 ATTGTTTT
1 ATTGTTTT
190638 GTTGTGCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.11, C:0.08, G:0.11, T:0.70
Consensus pattern (10 bp):
ATTGTTTTTC
Found at i:210300 original size:6 final size:6
Alignment explanation
Indices: 210266--210299 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
210256 CAATCTTCAA
*
210266 GAAAAT GAAAAC GAAAAC GAAAAC GAAAAC -AAAA
1 GAAAAC GAAAAC GAAAAC GAAAAC GAAAAC GAAAA
210300 ATGATCTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.71, C:0.12, G:0.15, T:0.03
Consensus pattern (6 bp):
GAAAAC
Found at i:218777 original size:51 final size:50
Alignment explanation
Indices: 218721--218838 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 50
218711 TGTGTAAATG
* ** * * *
218721 TTGACATAATATGTAAATGTTGTAGG-TTAAATTTGTTAAATTATGACCAAA
1 TTGACATAATATGTAAATATTGT-GGACAAAATTTATTAAATCAAGACC-AA
* * *
218772 TTGACAGAATATATAAATATTGTGGACAAAATTTATTAAATCAAGATCAA
1 TTGACATAATATGTAAATATTGTGGACAAAATTTATTAAATCAAGACCAA
*
218822 TTGACATAATGTGTAAA
1 TTGACATAATATGTAAA
218839 CTTTGAGAGC
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
50 18 0.33
51 36 0.67
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (50 bp):
TTGACATAATATGTAAATATTGTGGACAAAATTTATTAAATCAAGACCAA
Found at i:219014 original size:17 final size:16
Alignment explanation
Indices: 218992--219034 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
218982 ATTCATTTGG
218992 AAAATAAAATAAAACTA
1 AAAATAAAA-AAAACTA
*
219009 AAAATAAACAAAAAGTA
1 AAAATAAA-AAAAACTA
219026 AAAA-AAAAA
1 AAAATAAAAA
219035 CATTTATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 3 0.12
17 18 0.75
18 1 0.04
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (16 bp):
AAAATAAAAAAAACTA
Found at i:223054 original size:29 final size:31
Alignment explanation
Indices: 223020--223093 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 31
223010 AATCCCTCTA
*
223020 AAAAATTACAAAA-ATTCA-AAATA-ATCTTC
1 AAAAATTA-AAAATATTCATAAATATATATTC
*
223049 AAAAATTAAAAATATTTATAAATATATATTC
1 AAAAATTAAAAATATTCATAAATATATATTC
*
223080 AAAAAATGAAAAAT
1 -AAAAATTAAAAAT
223094 TATTAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 4 0.11
29 12 0.32
30 5 0.13
31 5 0.13
32 12 0.32
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.30
Consensus pattern (31 bp):
AAAAATTAAAAATATTCATAAATATATATTC
Found at i:224765 original size:2 final size:2
Alignment explanation
Indices: 224758--224794 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
224748 AATGCTAAGT
224758 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
224795 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:224799 original size:2 final size:2
Alignment explanation
Indices: 224794--224840 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
224784 TCTCTCTCTC
*
224794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
224836 TA TA T
1 TA TA T
224841 TGTCATCTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:246600 original size:3 final size:3
Alignment explanation
Indices: 246592--246635 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
246582 TACAAGCTTG
246592 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
246636 TAAGCATCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:248663 original size:23 final size:23
Alignment explanation
Indices: 248637--248695 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
248627 CACTAGCGCA
248637 CTTACTGTTTTGCA-CTTCGTGTG
1 CTTACTGTTTTGCATC-TCGTGTG
*
248660 CTTACTGTTTCGCATCTCGTGTG
1 CTTACTGTTTTGCATCTCGTGTG
* *
248683 CCTACTGATTTGC
1 CTTACTGTTTTGC
248696 GTTATGTGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.44
Consensus pattern (23 bp):
CTTACTGTTTTGCATCTCGTGTG
Found at i:248708 original size:23 final size:23
Alignment explanation
Indices: 248682--248742 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
248672 CATCTCGTGT
**
248682 GCCTACTGATTTGCGTTATGTGC
1 GCCTACTGATTTGCACTATGTGC
* * *
248705 GCCTATTGA-TTGCACTGTGTGT
1 GCCTACTGATTTGCACTATGTGC
248727 GCCTACTGA-TTGCACT
1 GCCTACTGATTTGCACT
248743 GTGTACCTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (23 bp):
GCCTACTGATTTGCACTATGTGC
Found at i:248725 original size:22 final size:21
Alignment explanation
Indices: 248700--248768 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
248690 ATTTGCGTTA
248700 TGTGCGCCTATTGATTGCACTG
1 TGTG-GCCTATTGATTGCACTG
*
248722 TGTGTGCCTACTGATTGCACTG
1 TGTG-GCCTATTGATTGCACTG
* *
248744 TGT-ACCTATTGGATTGCGCTG
1 TGTGGCCTATT-GATTGCACTG
248765 TGTG
1 TGTG
248769 TGCTTACTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 5 0.12
21 12 0.30
22 23 0.57
ACGTcount: A:0.13, C:0.20, G:0.29, T:0.38
Consensus pattern (21 bp):
TGTGGCCTATTGATTGCACTG
Found at i:249545 original size:16 final size:16
Alignment explanation
Indices: 249521--249563 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
249511 AAAAGGTACA
* * *
249521 ATTTTAATTTATTTCT
1 ATTTAAATTTAATCCT
249537 ATTTAAATTTAATCCT
1 ATTTAAATTTAATCCT
*
249553 ATTCAAATTTA
1 ATTTAAATTTA
249564 CTTTAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTAAATTTAATCCT
Found at i:259303 original size:9 final size:10
Alignment explanation
Indices: 259290--259322 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
259280 TCTCTTTCAA
259290 CATTTTCTTT
1 CATTTTCTTT
259300 -ATTTTCTTT
1 CATTTTCTTT
259309 CATTTTTCTTT
1 CA-TTTTCTTT
259320 CAT
1 CAT
259323 GTAAAACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.43
10 2 0.10
11 10 0.48
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (10 bp):
CATTTTCTTT
Found at i:286769 original size:23 final size:23
Alignment explanation
Indices: 286739--286797 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
286729 AAAAATGATG
*
286739 AAATTATAAATTAATTCATAATA
1 AAATTATAAATTAATTCATAAAA
* ** *
286762 AATTTATATTTTAATTTATAAAA
1 AAATTATAAATTAATTCATAAAA
286785 AAATTAT-AATTAA
1 AAATTATAAATTAA
286798 ATTTCCACCA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTATAAATTAATTCATAAAA
Found at i:293485 original size:160 final size:157
Alignment explanation
Indices: 293161--293485 Score: 371
Period size: 160 Copynumber: 2.1 Consensus size: 157
293151 ATATTATCGA
* * * * * * *
293161 TAAAATGTCATAGATTAATGAGAATATTTCGCATCGATTGAAAATACACATTTTAGTAATAAGTA
1 TAAATTGTCATAGATTAATGAGAATATTCCGCATCAACTGAAAACACACACTTTAGCAATAAGTA
* * * * * * *
293226 ACCAGTAAGAGTTCATATGTAGCTGTTTCAGCCTCTTTACATAGATTGATCTGTCAAGGCTTCTC
66 ACCAATAAGAGTTCATATGTAACTATCTCAGCCTCCTCACATAGATTGATCTGTCAAGACTTCTC
** *
293291 CTTCACATCATTAATAGCAAGATTTGC
131 CTTCACATCATTAATAGCAAGACATAC
* * *
293318 TAAATTGTCATAGATTGATGAGAGTATTCCGCATCAACTGAAAACGCACACTTTAGCAATAAGTA
1 TAAATTGTCATAGATTAATGAGAATATTCCGCATCAACTGAAAACACACACTTTAGCAATAAGTA
* * * *
293383 ACCAATAAGACTTGTTCATATGTAACTATCTCAGCCTCCTCACGTAGATTGATTTGTTAAGATTT
66 ACCAATAAGA---GTTCATATGTAACTATCTCAGCCTCCTCACATAGATTGATCTGTCAAGACTT
* * * *
293448 TTCTTTCACATCATTAATGGCTAGACATAC
128 CTCCTTCACATCATTAATAGCAAGACATAC
293478 TAAATTGT
1 TAAATTGT
293486 TTTTCACTTT
Statistics
Matches: 137, Mismatches: 28, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
157 64 0.47
160 73 0.53
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (157 bp):
TAAATTGTCATAGATTAATGAGAATATTCCGCATCAACTGAAAACACACACTTTAGCAATAAGTA
ACCAATAAGAGTTCATATGTAACTATCTCAGCCTCCTCACATAGATTGATCTGTCAAGACTTCTC
CTTCACATCATTAATAGCAAGACATAC
Found at i:299884 original size:12 final size:12
Alignment explanation
Indices: 299867--299897 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
299857 AACAGGGTTA
*
299867 TAAATTGATTTT
1 TAAATTGATGTT
299879 TAAATTGATGTT
1 TAAATTGATGTT
299891 TAAATTG
1 TAAATTG
299898 TTGCAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (12 bp):
TAAATTGATGTT
Found at i:319124 original size:31 final size:30
Alignment explanation
Indices: 319088--319161 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
319078 CACTATCAAC
* *
319088 TTAATTTAATTACATTATATAACATTTTAAT
1 TTAATTTAATTACATTACATAACA-TTAAAT
* *
319119 TTAATTTAATCACATTACATAATATTAAAT
1 TTAATTTAATTACATTACATAACATTAAAT
319149 TTAATTTAATTAC
1 TTAATTTAATTAC
319162 CATATTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 17 0.45
31 21 0.55
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAATTTAATTACATTACATAACATTAAAT
Found at i:340266 original size:16 final size:17
Alignment explanation
Indices: 340245--340287 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
340235 TTCTAAAAAA
340245 AATTTAATAATCT-AAT
1 AATTTAATAATCTAAAT
*
340261 AATTTAAAAATCTCAAAT
1 AATTTAATAATCT-AAAT
*
340279 AATTCAATA
1 AATTTAATA
340288 TACTTTCCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 12 0.55
18 10 0.45
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTTAATAATCTAAAT
Found at i:341781 original size:24 final size:23
Alignment explanation
Indices: 341734--341777 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
341724 AGTCACTATA
341734 TTTTTATTTTCAAGAATTTAATT
1 TTTTTATTTTCAAGAATTTAATT
*
341757 TTTTTACTTTTC-AGATTTTAA
1 TTTTTA-TTTTCAAGAATTTAA
341778 ATTTAGGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTTTATTTTCAAGAATTTAATT
Found at i:343831 original size:31 final size:31
Alignment explanation
Indices: 343796--343854 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
343786 GATCAATGAC
343796 TTAAATAAAAATTTTCGAATAATTTAATAAT
1 TTAAATAAAAATTTTCGAATAATTTAATAAT
*
343827 TTAAATGAAAATTTTCGAATAATTTAAT
1 TTAAATAAAAATTTTCGAATAATTTAAT
343855 TATTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (31 bp):
TTAAATAAAAATTTTCGAATAATTTAATAAT
Found at i:346283 original size:30 final size:29
Alignment explanation
Indices: 346202--346286 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 29
346192 ATGGAATAAT
*
346202 AATATGTAAATGTGAATGATTAAATTTATGG
1 AATATGTAAAT-TGAA-GATTAAATTTATAG
* *
346233 AATCATTTAGAATT-AGGATTAAATTTATAG
1 AAT-ATGTA-AATTGAAGATTAAATTTATAG
346263 AATATGTAATATTGAAGATTAAAT
1 AATATGTAA-ATTGAAGATTAAAT
346287 GTGTTATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 7 0.16
30 25 0.56
31 4 0.09
32 5 0.11
33 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.15, T:0.39
Consensus pattern (29 bp):
AATATGTAAATTGAAGATTAAATTTATAG
Found at i:347524 original size:17 final size:17
Alignment explanation
Indices: 347502--347542 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
347492 AGGCAACCAA
347502 AACAAAAGGAGAGAA-AG
1 AACAAAA-GAGAGAAGAG
347519 AACAAAA-AGAGAAGAG
1 AACAAAAGAGAGAAGAG
347535 AA-AAAAGA
1 AACAAAAGA
347543 AAAAAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 10 0.45
16 5 0.23
17 7 0.32
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (17 bp):
AACAAAAGAGAGAAGAG
Found at i:347550 original size:19 final size:19
Alignment explanation
Indices: 347505--347552 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
347495 CAACCAAAAC
* *
347505 AAAAGGAGAGAAAGAACAA
1 AAAAGAAGAGAAAAAACAA
*
347524 AAAGAGAAGAGAAAAAAGAA
1 AAA-AGAAGAGAAAAAACAA
347544 AAAAGAAGA
1 AAAAGAAGA
347553 CAAGAATCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAGAAAAAACAA
Found at i:375184 original size:61 final size:61
Alignment explanation
Indices: 375074--375212 Score: 147
Period size: 61 Copynumber: 2.3 Consensus size: 61
375064 TTTGGAGAAT
* * * * * * *
375074 AACATTAAATTTCAACTTAAAACTTAATAGAGCAATAACTCACCTATATAGCT-TAGACAGC
1 AACATTAAATTTAAAATTAAAACCTAATAGAGCAACAACTCACCCATATAG-TACAGACAAC
* * *
375135 AACATTAAATTTAAAATTAAAGCCTAATAGAGCAACATCTTC-CCCATATAGTACAGAGAAC
1 AACATTAAATTTAAAATTAAAACCTAATAGAGCAACAAC-TCACCCATATAGTACAGACAAC
*
375196 AACATTAAAATTAAAAT
1 AACATTAAATTTAAAAT
375213 AAATTAAACA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 1 0.02
61 62 0.95
62 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (61 bp):
AACATTAAATTTAAAATTAAAACCTAATAGAGCAACAACTCACCCATATAGTACAGACAAC
Found at i:375979 original size:18 final size:18
Alignment explanation
Indices: 375956--376002 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
375946 GCTTAATTTC
*
375956 AGAGATTTTAGTGAGATA
1 AGAGATTTCAGTGAGATA
* *
375974 AGAGATTTCAGTGATATC
1 AGAGATTTCAGTGAGATA
375992 AGAGATTTCAG
1 AGAGATTTCAG
376003 AGGCCATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (18 bp):
AGAGATTTCAGTGAGATA
Found at i:377435 original size:3 final size:3
Alignment explanation
Indices: 377429--377464 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
377419 AACAAGTAGG
377429 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
377465 CAGGGGTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:379848 original size:27 final size:27
Alignment explanation
Indices: 379810--379898 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
379800 CTCTCGCTTA
379810 ATTTCAGATATTTCAGTGATATCAGAG
1 ATTTCAGATATTTCAGTGATATCAGAG
*
379837 ATTTCAGATATTTCAGTGATATCAGAA
1 ATTTCAGATATTTCAGTGATATCAGAG
*
379864 ATTTCAG-TGATTTCAGTGATATCAAAG
1 ATTTCAGAT-ATTTCAGTGATATCAGAG
379891 ATTTCAGA
1 ATTTCAGA
379899 GGCCATTGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 1 0.02
27 56 0.98
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (27 bp):
ATTTCAGATATTTCAGTGATATCAGAG
Found at i:379880 original size:9 final size:9
Alignment explanation
Indices: 379810--379897 Score: 72
Period size: 9 Copynumber: 9.8 Consensus size: 9
379800 CTCTCGCTTA
379810 ATTTCAGAT-
1 ATTTCAG-TG
379819 ATTTCAGTG
1 ATTTCAGTG
* *
379828 ATATCAGAG
1 ATTTCAGTG
379837 ATTTCAGAT-
1 ATTTCAG-TG
379846 ATTTCAGTG
1 ATTTCAGTG
* **
379855 ATATCAGAA
1 ATTTCAGTG
379864 ATTTCAGTG
1 ATTTCAGTG
379873 ATTTCAGTG
1 ATTTCAGTG
* **
379882 ATATCAAAG
1 ATTTCAGTG
379891 ATTTCAG
1 ATTTCAG
379898 AGGCCATTGA
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
8 2 0.03
9 59 0.97
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (9 bp):
ATTTCAGTG
Found at i:380020 original size:3 final size:3
Alignment explanation
Indices: 380012--380053 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
380002 AATGGGTAGG
380012 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
380054 GGGTTGGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:381235 original size:27 final size:27
Alignment explanation
Indices: 381196--381282 Score: 122
Period size: 27 Copynumber: 3.2 Consensus size: 27
381186 CTCTCACTTA
* *
381196 ATTTCAGATATTTCAGTGATATCGAAA-
1 ATTTCAAAGATTTCAGTGATATC-AAAG
*
381223 ATTTTAAAGATTTCAGTGATATCAAAG
1 ATTTCAAAGATTTCAGTGATATCAAAG
*
381250 ATTTCAAAGATTTCAGTGATATCAGAG
1 ATTTCAAAGATTTCAGTGATATCAAAG
381277 ATTTCA
1 ATTTCA
381283 GAGGCCATTG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 3 0.06
27 51 0.94
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (27 bp):
ATTTCAAAGATTTCAGTGATATCAAAG
Found at i:381283 original size:9 final size:9
Alignment explanation
Indices: 381230--381285 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
381220 AAAATTTTAA
381230 AGATTTCAG
1 AGATTTCAG
* * *
381239 TGATATCAA
1 AGATTTCAG
*
381248 AGATTTCAA
1 AGATTTCAG
381257 AGATTTCAG
1 AGATTTCAG
* *
381266 TGATATCAG
1 AGATTTCAG
381275 AGATTTCAG
1 AGATTTCAG
381284 AG
1 AG
381286 GCCATTGATT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (9 bp):
AGATTTCAG
Found at i:381406 original size:3 final size:3
Alignment explanation
Indices: 381398--381439 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
381388 AATGGGTAGG
381398 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
381440 GGGTTGGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:384965 original size:9 final size:9
Alignment explanation
Indices: 384953--384979 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
384943 AGATATTTCT
384953 GTGATATCA
1 GTGATATCA
384962 GTGATATCA
1 GTGATATCA
384971 GTGATATCA
1 GTGATATCA
384980 AAGACCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (9 bp):
GTGATATCA
Found at i:385103 original size:3 final size:3
Alignment explanation
Indices: 385095--385141 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
385085 AACGGGTTGG
385095 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
385142 GGGGTTGGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:386774 original size:6 final size:6
Alignment explanation
Indices: 386746--386807 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
386736 TAAAATTCAT
* * *
386746 AAAATA AAATAAA AAACACA AAAATA AAAATA AAAAT- AAAATA ATAATA
1 AAAATA AAA-ATA AAA-ATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
386795 ATAATA ATAATA A
1 AAAATA AAAATA A
386808 GAGCAGCTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 5 0.10
6 34 0.69
7 10 0.20
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:386793 original size:3 final size:3
Alignment explanation
Indices: 386768--386807 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
386758 AAAACACAAA
* *
386768 AAT AAA AAT AAA AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
386808 GAGCAGCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:387157 original size:61 final size:59
Alignment explanation
Indices: 387050--387186 Score: 157
Period size: 61 Copynumber: 2.3 Consensus size: 59
387040 TTTGAAAAAT
* * * * *
387050 AACATTAAATTTCAACTTAAAACTTAATAGAGCAATAACTCACCTATATAGCTTGGACAAC
1 AACATTAAAATTAAAATTAAAACCTAATAGAGCAACAACTCACC--TATAGCTTGGACAAC
* * * ** *
387111 AACATTAAACTTAAAATTAAAGCCTAATAGAGCAACATCTTGCCTATAGTTTGGACAAC
1 AACATTAAAATTAAAATTAAAACCTAATAGAGCAACAACTCACCTATAGCTTGGACAAC
387170 AACATTAAAATTAAAAT
1 AACATTAAAATTAAAAT
387187 AAACTAAACA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 30 0.46
61 35 0.54
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.28
Consensus pattern (59 bp):
AACATTAAAATTAAAATTAAAACCTAATAGAGCAACAACTCACCTATAGCTTGGACAAC
Found at i:387948 original size:9 final size:9
Alignment explanation
Indices: 387934--388023 Score: 69
Period size: 9 Copynumber: 10.0 Consensus size: 9
387924 CTCTCGCTTA
387934 ATTTCAGAG
1 ATTTCAGAG
*
387943 ATTTCAGTG
1 ATTTCAGAG
*
387952 ATATC-GAAG
1 ATTTCAG-AG
387961 ATTTCA-ATG
1 ATTTCAGA-G
*
387970 ATATCAGAG
1 ATTTCAGAG
*
387979 ATTTCAGTG
1 ATTTCAGAG
* *
387988 ATATCGGAG
1 ATTTCAGAG
387997 ATTTCA-ATG
1 ATTTCAGA-G
*
388006 ATATCAGAG
1 ATTTCAGAG
388015 ATTTCAGAG
1 ATTTCAGAG
388024 GCTATTGATT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
8 3 0.05
9 56 0.92
10 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (9 bp):
ATTTCAGAG
Found at i:387964 original size:18 final size:18
Alignment explanation
Indices: 387937--388021 Score: 127
Period size: 18 Copynumber: 4.7 Consensus size: 18
387927 TCGCTTAATT
387937 TCAGAGATTTCAGTGATA
1 TCAGAGATTTCAGTGATA
*
387955 TC-GAAGATTTCAATGATA
1 TCAG-AGATTTCAGTGATA
387973 TCAGAGATTTCAGTGATA
1 TCAGAGATTTCAGTGATA
* *
387991 TCGGAGATTTCAATGATA
1 TCAGAGATTTCAGTGATA
388009 TCAGAGATTTCAG
1 TCAGAGATTTCAG
388022 AGGCTATTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
17 1 0.02
18 57 0.97
19 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (18 bp):
TCAGAGATTTCAGTGATA
Found at i:387984 original size:36 final size:36
Alignment explanation
Indices: 387937--388021 Score: 161
Period size: 36 Copynumber: 2.4 Consensus size: 36
387927 TCGCTTAATT
387937 TCAGAGATTTCAGTGATATCGAAGATTTCAATGATA
1 TCAGAGATTTCAGTGATATCGAAGATTTCAATGATA
*
387973 TCAGAGATTTCAGTGATATCGGAGATTTCAATGATA
1 TCAGAGATTTCAGTGATATCGAAGATTTCAATGATA
388009 TCAGAGATTTCAG
1 TCAGAGATTTCAG
388022 AGGCTATTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (36 bp):
TCAGAGATTTCAGTGATATCGAAGATTTCAATGATA
Found at i:388149 original size:3 final size:3
Alignment explanation
Indices: 388135--388183 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
388125 TAACGGGTAG
* * *
388135 ATA ATG ATA ATA ATA ATA ATA GTA ATA GTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
388183 A
1 A
388184 GGGTTGGTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:390134 original size:429 final size:429
Alignment explanation
Indices: 389335--390187 Score: 1670
Period size: 429 Copynumber: 2.0 Consensus size: 429
389325 AAGGTTCCAG
389335 TTTTATGATGGGGATGGGGGACAGCCAAGGGTTAATGTAGTGCCTATGCATGCCAAATCATTAAC
1 TTTTATGATGGGGATGGGGGACAGCCAAGGGTTAATGTAGTGCCTATGCATGCCAAATCATTAAC
389400 CGATCAACATTTAACGTAGCACATTTGAATTATTGATCAGAAGAATGCTTGTCAACATAATATTC
66 CGATCAACATTTAACGTAGCACATTTGAATTATTGATCAGAAGAATGCTTGTCAACATAATATTC
*
389465 ATCTGAATACTTAATTTAATGTCCTTATGTGACTAATCATTTTAAATCATCGAATTTTGAAATTT
131 ATCTGAATACTTAATTTAATGCCCTTATGTGACTAATCATTTTAAATCATCGAATTTTGAAATTT
*
389530 TAATTTATTAGATTTGGAGTTTTCTGTTATTAGATGCATGTTAATTAGAAGGCTCATGAGCATCT
196 TAATTTATTAGATTTGGAGTTTTCTGTTATTAGATGCATGTAAATTAGAAGGCTCATGAGCATCT
389595 TCTAATGTTATAGTTGTTTCACTACATGGGAGATGAAACATATGGTTTTTGGGTCTTCACCGTTT
261 TCTAATGTTATAGTTGTTTCACTACATGGGAGATGAAACATATGGTTTTTGGGTCTTCACCGTTT
389660 AATCAGAGTGAATATGATGTTGGATAAATGATATTTTTGGGTAACTTTGAGACATATTCTTGATA
326 AATCAGAGTGAATATGATGTTGGATAAATGATATTTTTGGGTAACTTTGAGACATATTCTTGATA
389725 GGTAAAGGTGGAGGGTTAAGTCATAAAATTATGGGTAAC
391 GGTAAAGGTGGAGGGTTAAGTCATAAAATTATGGGTAAC
389764 TTTTATGATGGGGATGGGGGACAGCCAAGGGTTAATGTAGTGCCTATGCATGCCAAATCATTAAC
1 TTTTATGATGGGGATGGGGGACAGCCAAGGGTTAATGTAGTGCCTATGCATGCCAAATCATTAAC
389829 CGATCAACATTTAACGTAGCACATTTGAATTATTGATCAGAAGAATGCTTGTCAACATAATATTC
66 CGATCAACATTTAACGTAGCACATTTGAATTATTGATCAGAAGAATGCTTGTCAACATAATATTC
389894 ATCTGAATACTTAATTTAATGCCCTTATGTGACTAATCATTTTAAATCATCGAATTTTGAAATTT
131 ATCTGAATACTTAATTTAATGCCCTTATGTGACTAATCATTTTAAATCATCGAATTTTGAAATTT
389959 TAATTTATTAGATTTGGAGTTTTCTGTTATTAGATGCATGTAAATTAGAAGGCTCATGAGCATCT
196 TAATTTATTAGATTTGGAGTTTTCTGTTATTAGATGCATGTAAATTAGAAGGCTCATGAGCATCT
*
390024 TCTAATGTTATAGTTGTTTCACTACATGGGAGATGAAACATATGGTTTTTGGGTCTTCATCGTTT
261 TCTAATGTTATAGTTGTTTCACTACATGGGAGATGAAACATATGGTTTTTGGGTCTTCACCGTTT
390089 AATCAGAGTGAATATGATGTTGGATAAATGATATTTTTGGGTAACTTTGAGACATATTCTTGATA
326 AATCAGAGTGAATATGATGTTGGATAAATGATATTTTTGGGTAACTTTGAGACATATTCTTGATA
*
390154 GGTAAAGGTGGAGGGTTGAGTCATAAAATTATGG
391 GGTAAAGGTGGAGGGTTAAGTCATAAAATTATGG
390188 TTTTATATTC
Statistics
Matches: 420, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
429 420 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.37
Consensus pattern (429 bp):
TTTTATGATGGGGATGGGGGACAGCCAAGGGTTAATGTAGTGCCTATGCATGCCAAATCATTAAC
CGATCAACATTTAACGTAGCACATTTGAATTATTGATCAGAAGAATGCTTGTCAACATAATATTC
ATCTGAATACTTAATTTAATGCCCTTATGTGACTAATCATTTTAAATCATCGAATTTTGAAATTT
TAATTTATTAGATTTGGAGTTTTCTGTTATTAGATGCATGTAAATTAGAAGGCTCATGAGCATCT
TCTAATGTTATAGTTGTTTCACTACATGGGAGATGAAACATATGGTTTTTGGGTCTTCACCGTTT
AATCAGAGTGAATATGATGTTGGATAAATGATATTTTTGGGTAACTTTGAGACATATTCTTGATA
GGTAAAGGTGGAGGGTTAAGTCATAAAATTATGGGTAAC
Found at i:391746 original size:18 final size:18
Alignment explanation
Indices: 391723--391785 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
391713 TTAATTTCAG
391723 ATATTTCAGTGATATCAT
1 ATATTTCAGTGATATCAT
* *
391741 ATATTTCAGAGATTTCAGT
1 ATATTTCAGTGATATCA-T
* *
391760 A-ATTTTAGTGATATCAG
1 ATATTTCAGTGATATCAT
*
391777 AGATTTCAG
1 ATATTTCAG
391786 AAGCCATTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
17 1 0.03
18 33 0.92
19 2 0.06
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (18 bp):
ATATTTCAGTGATATCAT
Found at i:393437 original size:31 final size:31
Alignment explanation
Indices: 393374--393442 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
393364 CTCAACAGCC
* * **
393374 CAGTGACTTAAATTAAAGCTTCTTAATAGTT
1 CAGTGACTTAAATGAAAACTTCCGAATAGTT
*
393405 CAGTGACTTAAATGAAAACTTCCGAATGGTT
1 CAGTGACTTAAATGAAAACTTCCGAATAGTT
*
393436 CATTGAC
1 CAGTGAC
393443 CAAATTGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (31 bp):
CAGTGACTTAAATGAAAACTTCCGAATAGTT
Found at i:395679 original size:21 final size:21
Alignment explanation
Indices: 395653--395694 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
395643 ATAATGCTAC
395653 TTAAAG-TCATTTTTAAAACAA
1 TTAAAGCT-ATTTTTAAAACAA
395674 TTAAAGCTATTTTTAAAACAA
1 TTAAAGCTATTTTTAAAACAA
395695 AAATAGGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (21 bp):
TTAAAGCTATTTTTAAAACAA
Found at i:396364 original size:10 final size:9
Alignment explanation
Indices: 396349--396393 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
396339 ACTGCATTTC
396349 TTCTTTTCTT
1 TTCTTTT-TT
396359 TTCTTTTTT
1 TTCTTTTTT
396368 CTT-TTTTTT
1 -TTCTTTTTT
396377 TTCTTTTTT
1 TTCTTTTTT
*
396386 TTATTTTT
1 TTCTTTTT
396394 ATTACATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 2 0.06
9 21 0.66
10 9 0.28
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:396376 original size:11 final size:11
Alignment explanation
Indices: 396352--396387 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
396342 GCATTTCTTC
396352 TTTTCTTTTCTT
1 TTTTCTTTT-TT
396364 TTTTCTTTTTT
1 TTTTCTTTTTT
396375 TTTTCTTTTTT
1 TTTTCTTTTTT
396386 TT
1 TT
396388 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:396378 original size:18 final size:20
Alignment explanation
Indices: 396345--396385 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
396335 ATGCACTGCA
396345 TTTCTTCTTTTCTTTTCTTT
1 TTTCTTCTTTTCTTTTCTTT
396365 TTTCTT-TTTT-TTTTCTTT
1 TTTCTTCTTTTCTTTTCTTT
396383 TTT
1 TTT
396386 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.52
19 4 0.19
20 6 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTCTTCTTTTCTTTTCTTT
Found at i:398813 original size:29 final size:29
Alignment explanation
Indices: 398754--398820 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
398744 TTAAATTAGT
*
398754 AATGATAAAATTATATTTTGATCTTTCAA
1 AATGATAAAATTATATTTTAATCTTTCAA
* * *
398783 AATGATAAAATTTTGA-TTTAATTTTTTAA
1 AATGATAAAATTAT-ATTTTAATCTTTCAA
*
398812 AATTATAAA
1 AATGATAAA
398821 GATATAAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (29 bp):
AATGATAAAATTATATTTTAATCTTTCAA
Found at i:398947 original size:125 final size:125
Alignment explanation
Indices: 398749--399001 Score: 384
Period size: 125 Copynumber: 2.0 Consensus size: 125
398739 AAATTTTAAA
* * * *
398749 TTAGTAATGATAAAATTATATTTTGATCTTTCAAAATGATAAAATTTTGATTTAATTTTTTAAAA
1 TTAGTAATGATAAAATTACACTTTGACCTTTCAAAATGATAAAATTTTGATTTAATTCTTTAAAA
* **
398814 TTATAAAGATATAAGCTATTATGGTGAAATTGTATTTTTA-TGAT-AGTAAAAATATACAAT
66 TTATAAAGATATAAGCTATTATGATGAAATTACATTTTTACT-ATCA-TAAAAATATACAAT
*
398874 TTAGTAATGGTAAAATTACACTTTGACCTTTCAAAATGATAAAATTTTGATTTAATTCTTTAAAA
1 TTAGTAATGATAAAATTACACTTTGACCTTTCAAAATGATAAAATTTTGATTTAATTCTTTAAAA
* *
398939 TTATAAAGATATAAGCTATTATGATGAATTTACATTTTTACTATCATAAAAATATATAAT
66 TTATAAAGATATAAGCTATTATGATGAAATTACATTTTTACTATCATAAAAATATACAAT
398999 TTA
1 TTA
399002 ATTCCACCTC
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
125 114 0.98
126 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (125 bp):
TTAGTAATGATAAAATTACACTTTGACCTTTCAAAATGATAAAATTTTGATTTAATTCTTTAAAA
TTATAAAGATATAAGCTATTATGATGAAATTACATTTTTACTATCATAAAAATATACAAT
Found at i:402193 original size:9 final size:9
Alignment explanation
Indices: 402179--402214 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
402169 CTCTTGCTTA
402179 ATTTCAGAG
1 ATTTCAGAG
*
402188 ATTTCAGTG
1 ATTTCAGAG
*
402197 ATATCAGAG
1 ATTTCAGAG
402206 ATTTCAGAG
1 ATTTCAGAG
402215 GCCATTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (9 bp):
ATTTCAGAG
Found at i:406058 original size:25 final size:23
Alignment explanation
Indices: 406004--406060 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
405994 AAGTTTAAGA
406004 AAATATTTTTTATATAAGATTAT
1 AAATATTTTTTATATAAGATTAT
*
406027 AAA-ATTTATTTTTATACA-ATTAT
1 AAATATTT-TTTATATA-AGATTAT
406050 GAAATATTTTT
1 -AAATATTTTT
406061 GATACCAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 4 0.14
23 15 0.52
24 6 0.21
25 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
AAATATTTTTTATATAAGATTAT
Found at i:408179 original size:20 final size:21
Alignment explanation
Indices: 408142--408180 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
408132 ATACATTTTT
*
408142 AAAAAAATTATGAAATATTGG
1 AAAAAAATTATCAAATATTGG
*
408163 AAAAAAATTA-CATATATT
1 AAAAAAATTATCAAATATT
408181 TTGGATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (21 bp):
AAAAAAATTATCAAATATTGG
Found at i:408359 original size:31 final size:31
Alignment explanation
Indices: 408323--408393 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
408313 ACTTGACTCG
* **
408323 AACTCAAAAAATTAAATTATT-TGTTTGAATT
1 AACTCAAAAAATTAAATAATTCAATTTG-ATT
408354 AACTCAAAAAATTAAATAATTCAATTTGATT
1 AACTCAAAAAATTAAATAATTCAATTTGATT
408385 AACTCAAAA
1 AACTCAAAA
408394 TTCAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 32 0.89
32 4 0.11
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (31 bp):
AACTCAAAAAATTAAATAATTCAATTTGATT
Found at i:409943 original size:21 final size:21
Alignment explanation
Indices: 409912--409964 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
409902 CTTTAAACTA
409912 TTTATAAATTTATATC-TATATT
1 TTTA-AAATTTA-ATCTTATATT
*
409934 TTTAAAATTTAATCTTTTATT
1 TTTAAAATTTAATCTTATATT
409955 TTTAAAATTT
1 TTTAAAATTT
409965 TAAAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 3 0.10
21 22 0.76
22 4 0.14
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAAAATTTAATCTTATATT
Found at i:409973 original size:21 final size:21
Alignment explanation
Indices: 409930--409973 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
409920 TTTATATCTA
**
409930 TATTTTTAAAATTTAATCTTT
1 TATTTTTAAAATTTAATAATT
409951 TATTTTTAAAATTTTAA-AATT
1 TATTTTTAAAA-TTTAATAATT
409972 TA
1 TA
409974 AATTCAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTTAAAATTTAATAATT
Found at i:413119 original size:16 final size:17
Alignment explanation
Indices: 413093--413137 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
413083 ATTTATTAAA
413093 TTAATTTAAATTATTTTC
1 TTAA-TTAAATTATTTTC
*
413111 -TAATTAAATAATTTTC
1 TTAATTAAATTATTTTC
*
413127 TTAATTCAATT
1 TTAATTAAATT
413138 CTAATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTAAATTATTTTC
Found at i:414104 original size:43 final size:45
Alignment explanation
Indices: 414055--414159 Score: 124
Period size: 46 Copynumber: 2.3 Consensus size: 45
414045 AACTTACATT
* *
414055 AACATTAAAAT-AAACCAAA-CATTACATATATAGTTTGGAGAAC
1 AACATTAAAATAAAACCAAAGCATAACATATATAGTTAGGAGAAC
* * * *
414098 AACATTAAACTTAAAATCAAAGCCTAACCTATATAGTTAGGAGAAC
1 AACATTAAA-ATAAAACCAAAGCATAACATATATAGTTAGGAGAAC
414144 AACATTAAAATTAAAA
1 AACATTAAAA-TAAAA
414160 TAAACTAAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
43 9 0.18
44 1 0.02
45 7 0.14
46 34 0.67
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (45 bp):
AACATTAAAATAAAACCAAAGCATAACATATATAGTTAGGAGAAC
Found at i:415062 original size:3 final size:3
Alignment explanation
Indices: 415054--415088 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
415044 AAAAGTGGTG
415054 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
415089 TTAGAACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:415809 original size:3 final size:3
Alignment explanation
Indices: 415801--415835 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
415791 TACCTATCAT
415801 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
415836 GAGCAAACCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:416303 original size:18 final size:19
Alignment explanation
Indices: 416270--416305 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
416260 TTTGAAAATT
*
416270 AAAATATTTAAAATTTAAG
1 AAAATAATTAAAATTTAAG
416289 AAAATAATT-AAATTTAA
1 AAAATAATTAAAATTTAA
416306 ATGTATCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAATAATTAAAATTTAAG
Found at i:417358 original size:28 final size:27
Alignment explanation
Indices: 417326--417386 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
417316 AGTTTTATAG
417326 TTTTTTAAATAATTTTAATAATGTTT-AA
1 TTTTTTAAAT-ATTTTAATAAT-TTTAAA
* * *
417354 TTTTTAAAATATTTTTATACTTTTAAA
1 TTTTTTAAATATTTTAATAATTTTAAA
417381 TTTTTT
1 TTTTTT
417387 TAATTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.11
27 16 0.57
28 9 0.32
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTTTAAATATTTTAATAATTTTAAA
Found at i:417399 original size:18 final size:18
Alignment explanation
Indices: 417349--417400 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 18
417339 TTTAATAATG
417349 TTTAATTTTTAAAATATTTT
1 TTTAA-TTTTAAAA-ATTTT
* *
417369 TATACTTTT--AAATTTT
1 TTTAATTTTAAAAATTTT
417385 TTTAATTTTAAAAATT
1 TTTAATTTTAAAAATT
417401 AATTAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
16 12 0.46
17 2 0.08
18 5 0.19
19 4 0.15
20 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATTTTAAAAATTTT
Found at i:423477 original size:3 final size:3
Alignment explanation
Indices: 423471--423518 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
423461 ATCATCATCG
* * * * *
423471 GAA GAA GAA GAA GAG GAG GAG GAA GAA GAA GAG GAA GAA GAA GGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
423519 CCTGGAGTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:423495 original size:15 final size:15
Alignment explanation
Indices: 423474--423513 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
423464 ATCATCGGAA
*
423474 GAAGAAGAAGAGGAG
1 GAAGAAGAAGAAGAG
*
423489 GAGGAAGAAGAAGAG
1 GAAGAAGAAGAAGAG
423504 GAAGAAGAAG
1 GAAGAAGAAG
423514 GAGAACCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAGAG
Found at i:423504 original size:12 final size:12
Alignment explanation
Indices: 423471--423513 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
423461 ATCATCATCG
*
423471 GAAGAAGAAGAA
1 GAAGAAGAGGAA
* *
423483 GAGGAGGAGGAA
1 GAAGAAGAGGAA
423495 GAAGAAGAGGAA
1 GAAGAAGAGGAA
423507 GAAGAAG
1 GAAGAAG
423514 GAGAACCTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
GAAGAAGAGGAA
Found at i:423513 original size:18 final size:18
Alignment explanation
Indices: 423471--423518 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
423461 ATCATCATCG
*
423471 GAAGAAGAAGAAGAGGAG
1 GAAGAAGAAGAAGAGGAA
*
423489 GAGGAAGAAGAAGAGGAA
1 GAAGAAGAAGAAGAGGAA
*
423507 GAAGAAGGAGAA
1 GAAGAAGAAGAA
423519 CCTGGAGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAAGAGGAA
Found at i:424114 original size:12 final size:12
Alignment explanation
Indices: 424097--424121 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
424087 TGTATATACC
424097 AAATTTACATAT
1 AAATTTACATAT
424109 AAATTTACATAT
1 AAATTTACATAT
424121 A
1 A
424122 TACTAAATTT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTTACATAT
Found at i:448684 original size:2 final size:2
Alignment explanation
Indices: 448677--448741 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
448667 TTCTACAAGC
448677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
448719 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
448742 AAAGGTATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:464330 original size:17 final size:17
Alignment explanation
Indices: 464308--464342 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
464298 ATCATTTCCT
464308 CTTAAATTTTAATGTGA
1 CTTAAATTTTAATGTGA
464325 CTTAAATTTTAATGTGA
1 CTTAAATTTTAATGTGA
464342 C
1 C
464343 ATTTCGAATG
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:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (17 bp):
CTTAAATTTTAATGTGA
Done.