Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold755.1
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: 763931
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 3850 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:8008 original size:244 final size:244
Alignment explanation
Indices: 7579--8066 Score: 931
Period size: 244 Copynumber: 2.0 Consensus size: 244
7569 GTAAATAATT
*
7579 TCTTTCTACTTTATTTAATAAGCAGCCATAATCTAAAGAACATAATATACACGTGTTTGTTTATA
1 TCTTTCTACTTTATTTAATAAGCAGCCATAATCTAAAGAACATAATATACACGTGTTTGTATATA
* *
7644 TTTCAAAGTTCTAGATTTATAGGGATCTATTTACAAAAAGGAAGATAGGATTAACCAGTAGCTCA
66 TTTCAAAGTTCTAGATTTATAAGGATCTAATTACAAAAAGGAAGATAGGATTAACCAGTAGCTCA
*
7709 AAGCAAATTGTTATGTACTAAAAATCACAGTACTTAAACAAAGAGCGTCGCATAAAGAATCTTAA
131 AAGCAAACTGTTATGTACTAAAAATCACAGTACTTAAACAAAGAGCGTCGCATAAAGAATCTTAA
7774 ATCGGCGTTGAAGAACATATGTTGCAAAATGGATGTAGAATCGCTAAAA
196 ATCGGCGTTGAAGAACATATGTTGCAAAATGGATGTAGAATCGCTAAAA
7823 TCTTTCTACTTTATTTAATAAGCAGCCATAATCTAAAGAACATAATATACACGTGTTTGTATATA
1 TCTTTCTACTTTATTTAATAAGCAGCCATAATCTAAAGAACATAATATACACGTGTTTGTATATA
*
7888 TTTCTAAGTTCTAGATTTATAAGGATCTAATTACAAAAAGGAAGATAGGATTAACCAGTAGCTCA
66 TTTCAAAGTTCTAGATTTATAAGGATCTAATTACAAAAAGGAAGATAGGATTAACCAGTAGCTCA
7953 AAGCAAACTGTTATGTACTAAAAATCACAGTACTTAAACAAAGAGCGTCGCATAAAGAATCTTAA
131 AAGCAAACTGTTATGTACTAAAAATCACAGTACTTAAACAAAGAGCGTCGCATAAAGAATCTTAA
8018 ATCGGCGTTGAAGAACATATGTTGCAAAATGGATGTAGAATCGCTAAAA
196 ATCGGCGTTGAAGAACATATGTTGCAAAATGGATGTAGAATCGCTAAAA
8067 ACAAAAACAG
Statistics
Matches: 239, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
244 239 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (244 bp):
TCTTTCTACTTTATTTAATAAGCAGCCATAATCTAAAGAACATAATATACACGTGTTTGTATATA
TTTCAAAGTTCTAGATTTATAAGGATCTAATTACAAAAAGGAAGATAGGATTAACCAGTAGCTCA
AAGCAAACTGTTATGTACTAAAAATCACAGTACTTAAACAAAGAGCGTCGCATAAAGAATCTTAA
ATCGGCGTTGAAGAACATATGTTGCAAAATGGATGTAGAATCGCTAAAA
Found at i:11262 original size:15 final size:17
Alignment explanation
Indices: 11229--11271 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
11219 TTTAATTAAT
11229 AATATATTTAAAAAGTA
1 AATATATTTAAAAAGTA
*
11246 AATATA-TTATAAA-TA
1 AATATATTTAAAAAGTA
*
11261 AATAGATTTAA
1 AATATATTTAA
11272 TTAGTATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 7 0.32
16 9 0.41
17 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
AATATATTTAAAAAGTA
Found at i:14292 original size:21 final size:21
Alignment explanation
Indices: 14266--14306 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
14256 AGACGAGCAA
* *
14266 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
14287 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
14307 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:16245 original size:16 final size:16
Alignment explanation
Indices: 16212--16245 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16202 GGAAATTGTT
* *
16212 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
16228 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
16244 AA
1 AA
16246 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:19073 original size:21 final size:21
Alignment explanation
Indices: 19047--19087 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19037 AGACGAGCAA
* *
19047 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
19068 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
19088 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:22572 original size:2 final size:2
Alignment explanation
Indices: 22565--22589 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22555 TGACCTAAAA
22565 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
22590 AAAGAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27509 original size:28 final size:29
Alignment explanation
Indices: 27473--27534 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
27463 TCACTCAAGT
* *
27473 ATTAGGAAATA-TACACTTT-AGTCACTTA
1 ATTATGAAATATTACAATTTGA-TCACTTA
*
27501 ATTATGAAATATTATAATTTGATCACTTA
1 ATTATGAAATATTACAATTTGATCACTTA
27530 ATTAT
1 ATTAT
27535 TTGAAATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 10 0.34
29 18 0.62
30 1 0.03
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (29 bp):
ATTATGAAATATTACAATTTGATCACTTA
Found at i:27564 original size:21 final size:21
Alignment explanation
Indices: 27510--27569 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
27500 AATTATGAAA
* *
27510 TATTATAATTTGATCACTTAAT
1 TATT-TAAATTGATCATTTAAT
27532 TATTTGAAATTGATCATTTAAT
1 TATTT-AAATTGATCATTTAAT
*
27554 TATTTAAATTGCTCAT
1 TATTTAAATTGATCAT
27570 CTGGTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.32
22 23 0.68
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (21 bp):
TATTTAAATTGATCATTTAAT
Found at i:41171 original size:6 final size:6
Alignment explanation
Indices: 41150--41185 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
41140 TCCTCCACGC
* *
41150 CCTCTA CCCCTA CCTCTC CCTCTA CCTCTA CCTCTA
1 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA
41186 TTAGCTGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.14, C:0.56, G:0.00, T:0.31
Consensus pattern (6 bp):
CCTCTA
Found at i:41172 original size:18 final size:18
Alignment explanation
Indices: 41149--41184 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41139 TTCCTCCACG
41149 CCCTCTACCCCTACCTCT
1 CCCTCTACCCCTACCTCT
*
41167 CCCTCTACCTCTACCTCT
1 CCCTCTACCCCTACCTCT
41185 ATTAGCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.58, G:0.00, T:0.31
Consensus pattern (18 bp):
CCCTCTACCCCTACCTCT
Found at i:43360 original size:32 final size:32
Alignment explanation
Indices: 43324--43387 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
43314 ATTACATGAC
43324 AAGTATAAATATATGCTCGATCAAGGTAAAGG
1 AAGTATAAATATATGCTCGATCAAGGTAAAGG
* *
43356 AAGTATAAATATATGTTTGATCAAGGTAAAGG
1 AAGTATAAATATATGCTCGATCAAGGTAAAGG
43388 TTTTGTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (32 bp):
AAGTATAAATATATGCTCGATCAAGGTAAAGG
Found at i:44199 original size:19 final size:21
Alignment explanation
Indices: 44171--44213 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
44161 TTAAAACATG
*
44171 ACATGAGT-AATATATT-ATT
1 ACATGAGTAAACATATTGATT
*
44190 ACATGTGTAAACATATTGATT
1 ACATGAGTAAACATATTGATT
44211 ACA
1 ACA
44214 CACAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 7 0.35
21 6 0.30
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
ACATGAGTAAACATATTGATT
Found at i:47174 original size:7 final size:7
Alignment explanation
Indices: 47162--47204 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
47152 GTTAGCCAAC
47162 TAGCGAG
1 TAGCGAG
47169 TAGCGAG
1 TAGCGAG
47176 TAGCGAG
1 TAGCGAG
47183 TAGCGAG
1 TAGCGAG
47190 TAGCGAG
1 TAGCGAG
47197 TAGCGAG
1 TAGCGAG
47204 T
1 T
47205 CGCTAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.42, T:0.16
Consensus pattern (7 bp):
TAGCGAG
Found at i:47512 original size:30 final size:31
Alignment explanation
Indices: 47456--47514 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
47446 TCTTGGGACT
* *
47456 AAATTTTGGGAGGTTTAGTAATTTTTTTAAA
1 AAATTTTAGGAGGTTTAATAATTTTTTTAAA
47487 AAATTTTAGGA-GTTTAATGAATTTTTTT
1 AAATTTTAGGAGGTTTAAT-AATTTTTTT
47515 TTTAATTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (31 bp):
AAATTTTAGGAGGTTTAATAATTTTTTTAAA
Found at i:48227 original size:31 final size:31
Alignment explanation
Indices: 48192--48252 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
48182 GCTTAGTGAT
** *
48192 TTAAATAAAAACTTTTGAATAGTTCAATAAC
1 TTAAATAAAAACTTTCAAATAATTCAATAAC
*
48223 TTAAATGAAAACTTTCAAATAATTCAATAA
1 TTAAATAAAAACTTTCAAATAATTCAATAA
48253 TAATATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (31 bp):
TTAAATAAAAACTTTCAAATAATTCAATAAC
Found at i:50445 original size:31 final size:31
Alignment explanation
Indices: 50407--50465 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
50397 CAATCAAGTG
50407 ACTTAAATAAAAACTTTCTG-ATAATTCAATA
1 ACTTAAATAAAAA-TTTCTGAATAATTCAATA
* *
50438 ACTTAAATGAAAATTTTTGAATAATTCA
1 ACTTAAATAAAAATTTCTGAATAATTCA
50466 GTAATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.37
Consensus pattern (31 bp):
ACTTAAATAAAAATTTCTGAATAATTCAATA
Found at i:51951 original size:15 final size:15
Alignment explanation
Indices: 51933--51973 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
51923 CTTTTCTAGA
51933 TCTTCCTCTTCTTCC
1 TCTTCCTCTTCTTCC
* *
51948 TCTTTCTTTTCTTCC
1 TCTTCCTCTTCTTCC
*
51963 TCTTCTTCTTC
1 TCTTCCTCTTC
51974 ATTTTCTTCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
TCTTCCTCTTCTTCC
Found at i:51972 original size:21 final size:21
Alignment explanation
Indices: 51942--51982 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
51932 ATCTTCCTCT
51942 TCTTCCTCTTTC-TTTTCTTCC
1 TCTTCCTC-TTCATTTTCTTCC
*
51963 TCTTCTTCTTCATTTTCTTC
1 TCTTCCTCTTCATTTTCTTC
51983 GGGAGGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (21 bp):
TCTTCCTCTTCATTTTCTTCC
Found at i:56505 original size:12 final size:12
Alignment explanation
Indices: 56490--56520 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
56480 TTCTCTTTTA
56490 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
56502 TTTTTCTTTCTC
1 TTTTTCTTTCCC
56514 TTTTTCT
1 TTTTTCT
56521 CCCCTGCTTC
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:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:56621 original size:16 final size:16
Alignment explanation
Indices: 56600--56630 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56590 TTTATTATTT
56600 TATTAACATAATATAA
1 TATTAACATAATATAA
*
56616 TATTAATATAATATA
1 TATTAACATAATATA
56631 TTAAAATATC
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:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:63072 original size:38 final size:39
Alignment explanation
Indices: 62988--63122 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
62978 ACCAATATGG
*
62988 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
63027 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
63065 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
63106 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
63123 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:64704 original size:5 final size:5
Alignment explanation
Indices: 64686--64721 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
64676 TTTCTTTTAT
64686 ATATA ATAATA ATATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA
64722 CTTAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:70572 original size:31 final size:29
Alignment explanation
Indices: 70474--70573 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 29
70464 TTCATTTGAG
* *
70474 TACCAAATTAAATATTAAGATCAAATTTAA
1 TACCAAATT-AATATTAAAATAAAATTTAA
** *
70504 GTATTAAATTAA-AATAAAA-AAAATTTATA
1 -TACCAAATTAATATTAAAATAAAATTTA-A
* *
70533 TACAAAATTACATATTAAAATTAAATTTAGA
1 TACCAAATTA-ATATTAAAATAAAATTTA-A
70564 TACCAAATTA
1 TACCAAATTA
70574 TAAAGTTAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
28 15 0.28
29 7 0.13
30 8 0.15
31 24 0.44
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (29 bp):
TACCAAATTAATATTAAAATAAAATTTAA
Found at i:71021 original size:116 final size:116
Alignment explanation
Indices: 70799--71024 Score: 312
Period size: 116 Copynumber: 1.9 Consensus size: 116
70789 TATTTGTGAT
* ** *
70799 GCTATGGAATTTTTAAGAAGATTACTTGTTTAAAATTAGAAATTAAGGAAGTTAATTTCTCTTTG
1 GCTATGGAATTTTCAAGAAGATTACTTGTTTAAAATTAGAAACAAAGGAAGTTAATTGCTCTTTG
*
70864 CTTTGATTTCATGGAAAACCCAAATTGACTTCTTATATGAAAGCCGCAGTA
66 CTTTGATTTCATGGAAAACCCAAATTGACTTATTATATGAAAGCCGCAGTA
* * *
70915 GCTATGGCATTTTCAAG-AGATTTCTTGTTTAAAATTAGAGACAAAGGAAGTTAATTGCTCTTT-
1 GCTATGGAATTTTCAAGAAGATTACTTGTTTAAAATTAGAAACAAAGGAAGTTAATTGCTCTTTG
* ** *
70978 CTTTTAGCTTTCATGGAAAATTCAAATTGACTTATTATTTGAAAGCC
66 C-TTT-GATTTCATGGAAAACCCAAATTGACTTATTATATGAAAGCC
71025 TCGCTAACTC
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
114 1 0.01
115 44 0.46
116 51 0.53
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (116 bp):
GCTATGGAATTTTCAAGAAGATTACTTGTTTAAAATTAGAAACAAAGGAAGTTAATTGCTCTTTG
CTTTGATTTCATGGAAAACCCAAATTGACTTATTATATGAAAGCCGCAGTA
Found at i:72689 original size:24 final size:24
Alignment explanation
Indices: 72662--72711 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
72652 GAACTCTAAC
72662 ATAGATGTATTAACAATCTGAATT
1 ATAGATGTATTAACAATCTGAATT
72686 ATAGATGTATTAACAATCTGAATT
1 ATAGATGTATTAACAATCTGAATT
72710 AT
1 AT
72712 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (24 bp):
ATAGATGTATTAACAATCTGAATT
Found at i:77017 original size:18 final size:18
Alignment explanation
Indices: 76990--77064 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 18
76980 TTAAGATTGA
76990 ATTT-ATATTATTAAATT
1 ATTTGATATTATTAAATT
77007 ATTTGATATTACTT--ATT
1 ATTTGATATTA-TTAAATT
*
77024 -TTTG--A--A-TAAATGA
1 ATTTGATATTATTAAAT-T
77037 ATTT-ATATTATTAAATT
1 ATTTGATATTATTAAATT
77054 ATTTGATATTA
1 ATTTGATATTA
77065 CTTATTTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 23
0.64 0.03 0.33
Matches are distributed among these distances:
10 1 0.02
12 3 0.07
14 4 0.09
15 1 0.02
16 4 0.09
17 12 0.27
18 17 0.39
19 2 0.05
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTGATATTATTAAATT
Found at i:77367 original size:16 final size:17
Alignment explanation
Indices: 77346--77383 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
77336 AAATTATGAA
*
77346 TTTTATTCGTA-ATTTT
1 TTTTATTCATATATTTT
77362 TTTTATTCATATATTTT
1 TTTTATTCATATATTTT
77379 TTTTA
1 TTTTA
77384 ATTTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTATTCATATATTTT
Found at i:77710 original size:19 final size:19
Alignment explanation
Indices: 77686--77722 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
77676 TATAGGGATT
*
77686 AAAATTGACTAATTTAAAA
1 AAAATTGACTAAATTAAAA
77705 AAAATTGACTAAATTAAA
1 AAAATTGACTAAATTAAA
77723 GTATATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAATTGACTAAATTAAAA
Found at i:79027 original size:7 final size:7
Alignment explanation
Indices: 79012--79051 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
79002 TTTTTCTCGA
*
79012 ATTTCAG
1 ATTTAAG
79019 ATTTAAG
1 ATTTAAG
*
79026 ATTTAGG
1 ATTTAAG
*
79033 ATTTAGG
1 ATTTAAG
79040 ATTTAAG
1 ATTTAAG
79047 ATTTA
1 ATTTA
79052 TATTGAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (7 bp):
ATTTAAG
Found at i:81175 original size:18 final size:19
Alignment explanation
Indices: 81152--81188 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
81142 ATTATTAATT
*
81152 AATATATTA-TTTTTATTA
1 AATATAATATTTTTTATTA
81170 AATATAATATTTTTTATTA
1 AATATAATATTTTTTATTA
81189 TATGTGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATATAATATTTTTTATTA
Found at i:81198 original size:20 final size:20
Alignment explanation
Indices: 81161--81204 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
81151 TAATATATTA
81161 TTTTTATTAAATATAAT-AT
1 TTTTTATTAAATATAATAAT
* *
81180 TTTTTATTATATGTGAATAAT
1 TTTTTATTAAATAT-AATAAT
81201 TTTT
1 TTTT
81205 CAAAATGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 3 0.14
21 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTTATTAAATATAATAAT
Found at i:82534 original size:39 final size:39
Alignment explanation
Indices: 82481--82558 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
82471 GGTGGTCAAC
*
82481 ATAATAAAGGGCAACAAAATCCACCAGATTCAGAACCCA
1 ATAATAAAGGGCAACAAAATCCAACAGATTCAGAACCCA
*
82520 ATAATCAAGGGCAACAAAATCCAACAGATTCAGAACCCA
1 ATAATAAAGGGCAACAAAATCCAACAGATTCAGAACCCA
82559 TTCCTCCACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.49, C:0.26, G:0.13, T:0.13
Consensus pattern (39 bp):
ATAATAAAGGGCAACAAAATCCAACAGATTCAGAACCCA
Found at i:86217 original size:19 final size:19
Alignment explanation
Indices: 86193--86231 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
86183 ATGTAACAAA
86193 ACAGAACTATAAAAACTTT
1 ACAGAACTATAAAAACTTT
86212 ACAGAACTATAAAAACTTT
1 ACAGAACTATAAAAACTTT
86231 A
1 A
86232 TAAATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (19 bp):
ACAGAACTATAAAAACTTT
Found at i:92245 original size:22 final size:22
Alignment explanation
Indices: 92203--92245 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
92193 AAAATTATCG
* *
92203 AATTGAATTCAAGTTATTTTTA
1 AATTGAATTCAAGATACTTTTA
92225 AATTGAATTCAA-ATAGCTTTT
1 AATTGAATTCAAGATA-CTTTT
92246 GAGTGCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (22 bp):
AATTGAATTCAAGATACTTTTA
Found at i:94549 original size:12 final size:12
Alignment explanation
Indices: 94532--94563 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
94522 CGAACAAATC
*
94532 ATGATGATCATG
1 ATGATGATCACG
94544 ATGATGATCACG
1 ATGATGATCACG
94556 ATGATGAT
1 ATGATGAT
94564 GATCATAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.31
Consensus pattern (12 bp):
ATGATGATCACG
Found at i:101421 original size:31 final size:31
Alignment explanation
Indices: 101384--101444 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
101374 AATAGTCTAA
*
101384 TGACTTAAATAAAAACTTTCAAGTAGTTCAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAG
101415 TGACTTAAATAAAAACTTTCAAATAGTTCA
1 TGACTTAAATAAAAACTTTCAAATAGTTCA
101445 ATGATCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTCAG
Found at i:103089 original size:19 final size:18
Alignment explanation
Indices: 103044--103089 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
103034 ATTGAATAAC
103044 AGCAAAAAAAAAAAAAAG
1 AGCAAAAAAAAAAAAAAG
* *
103062 CGCAGAAAAAAAAAAGAAG
1 AGCA-AAAAAAAAAAAAAG
*
103081 AGCTAAAAA
1 AGCAAAAAA
103090 GAACGATGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.74, C:0.09, G:0.15, T:0.02
Consensus pattern (18 bp):
AGCAAAAAAAAAAAAAAG
Found at i:110304 original size:23 final size:22
Alignment explanation
Indices: 110265--110308 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
110255 TTTAAATATT
*
110265 GGTTTGGTTTGAGCTATTGAATG
1 GGTTTGGTTCGAGCTA-TGAATG
110288 GGTTTGTGTTCGA-CTATGAAT
1 GGTTTG-GTTCGAGCTATGAAT
110309 ATTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.18, C:0.07, G:0.32, T:0.43
Consensus pattern (22 bp):
GGTTTGGTTCGAGCTATGAATG
Found at i:116213 original size:25 final size:25
Alignment explanation
Indices: 116173--116223 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
116163 AAGAAGTAAT
*
116173 TGGTTCTTTGACACAAAACGGAACA
1 TGGTTCTTCGACACAAAACGGAACA
*
116198 TGGTTCTTCGATACAAAACGGAACA
1 TGGTTCTTCGACACAAAACGGAACA
116223 T
1 T
116224 ATTCGCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (25 bp):
TGGTTCTTCGACACAAAACGGAACA
Found at i:121459 original size:166 final size:166
Alignment explanation
Indices: 121197--121509 Score: 475
Period size: 166 Copynumber: 1.9 Consensus size: 166
121187 CACCACATTC
* * * *
121197 CAATACATAGATGACAATCAAAGATGGATATAGATAAAAATCCAAGAGCGAAAACAAGATTTTAA
1 CAATACATAGATGACAAACAAAAATGAATACAGATAAAAATCCAAGAGCGAAAACAAGATTTTAA
* * * *
121262 GCATTCAACACACCATATTTCAATGCATTGATCTAGTGTGCAAAAATTATAACACATAATTTAAT
66 ACATTCAACACACCATATTTCAATACATTGATCTAGTATGCAAAAATTAAAACACATAATTTAAT
* *
121327 AAGTCGACGAACAAAGACATTCAAGATGCTACAGTT
131 AAGTCAACAAACAAAGACATTCAAGATGCTACAGTT
* * *
121363 CAATACATAGATGACAAACAAAAATGAATGCAGATCAAAATCCAAGAGC-AAAGACACGATTTTA
1 CAATACATAGATGACAAACAAAAATGAATACAGATAAAAATCCAAGAGCGAAA-ACAAGATTTTA
* *
121427 AACATTCAACACACCATATTTCGATACATTGATCTAGTATGCAAAATTTAAAACACATAATTTAA
65 AACATTCAACACACCATATTTCAATACATTGATCTAGTATGCAAAAATTAAAACACATAATTTAA
121492 TAAGTCAACAAACAAAGA
130 TAAGTCAACAAACAAAGA
121510 TGAATATAAA
Statistics
Matches: 131, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
165 3 0.02
166 128 0.98
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (166 bp):
CAATACATAGATGACAAACAAAAATGAATACAGATAAAAATCCAAGAGCGAAAACAAGATTTTAA
ACATTCAACACACCATATTTCAATACATTGATCTAGTATGCAAAAATTAAAACACATAATTTAAT
AAGTCAACAAACAAAGACATTCAAGATGCTACAGTT
Found at i:126327 original size:3 final size:3
Alignment explanation
Indices: 126321--126369 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
126311 AAAGAGTAAA
* * * * *
126321 AAG AAG AAG AAA AAG AAG AAC AAG AAG AAT AAG AAG GAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
126369 A
1 A
126370 GCAAAAAAGA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:126335 original size:21 final size:20
Alignment explanation
Indices: 126309--126383 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
126299 CGATGATGAT
126309 AAAAAGAGTAAAAAGAAGAAG
1 AAAAAGAG-AAAAAGAAGAAG
* *
126330 AAAAAGAAGAACAAGAAGAAT
1 AAAAAG-AGAAAAAGAAGAAG
*
126351 AAGAAGGAGAAAAAGAAG-AG
1 AA-AAAGAGAAAAAGAAGAAG
126371 CAAAAA-AGAAAAA
1 -AAAAAGAGAAAAA
126384 AATACGATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 7 0.16
20 3 0.07
21 30 0.67
22 5 0.11
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (20 bp):
AAAAAGAGAAAAAGAAGAAG
Found at i:126336 original size:9 final size:9
Alignment explanation
Indices: 126324--126383 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 9
126314 GAGTAAAAAG
126324 AAGAAGAAA
1 AAGAAGAAA
*
126333 AAGAAGAAC
1 AAGAAGAAA
126342 AAGAAGAATAA
1 AAGAAG-A-AA
*
126353 GAAGGAGAAA
1 -AAGAAGAAA
126363 AAGAAGAGCAA
1 AAGAAGA--AA
126374 AA-AAGAAA
1 AAGAAGAAA
126382 AA
1 AA
126384 AATACGATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
8 4 0.10
9 20 0.48
10 7 0.17
11 6 0.14
12 5 0.12
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.02
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:130327 original size:12 final size:13
Alignment explanation
Indices: 130291--130327 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
130281 CGTTGGTAAA
*
130291 AATAAATAAATA-
1 AATATATAAATAT
130303 AATATATAAATAT
1 AATATATAAATAT
130316 AA-ATATAAATAT
1 AATATATAAATAT
130328 TTGATTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 21 0.91
13 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATATATAAATAT
Found at i:134414 original size:436 final size:433
Alignment explanation
Indices: 133303--134596 Score: 1783
Period size: 435 Copynumber: 3.0 Consensus size: 433
133293 TTTTTTCATT
* * * * * * * *
133303 AAAAGTTCTTACTGTTAGTGGTGTTCGCGATTCTCTAGTGGATT-GCCTCGCATTAATACCTACA
1 AAAAGTTCATAATGTTAGTAGCGTTC-CGATTCTCCAATGGATTGGCC-CACAATAATACCTACA
* * * *
133367 ACTTCTCCCAATTCAACTAGGTCACCATGAGTGGGGCT-TCGACAATATCATAATAGTGATATGT
64 ACTTCTCCCAATTCAACTAGATCACCTTGAGTGGGGCTCT-GACCATAACATAATAGTGATATGT
* * * * *
133431 CTAAATTGCAAGTTGATATAACATTAC-TAGTAATAATATGTTTGTAATATGATATTTTGGAAAT
128 -GAAATAGCAAGTTGATATAACATTACATA-TAATAATATGTTAGTAGTATCATATTTTGGAAAT
* * *
133495 ATTAGAATTGAACTTAATTAATTTATCATTTATTGTTTGATCATGATTAAAATTTTAAAATTCAC
191 AATAGAATTGAACTTAATGAATTTAACATTTATTGTTTGATCATGATTAAAATTTTAAAATTCAC
* * * *
133560 AAAGCATAAGACTAAAATTAAGGTGTG-GGACTAAATCCATAATTTAAATATAATATAGGGATTA
256 AAAGCATATGACTAAAATTAA-GTGTGAGGACTAAATCCATAATTTAAACATAATATAGGGACTG
* * * *
133624 ATAGCAAAATTTAACCTTTCATTAACTAATCTTCTTGTAAACACGGAGTGCTAATAAAAAAAACC
320 ATAGTAAAATTTAACCTTTTATTAACTAATCTTCTTGTAAACAAGGAGAGCTAATAAAAAAAACC
*
133689 CAAAATATTTTTATTAAGGTCAAATTCTACTAAATACTATATCGATATG
385 CAAAATATTTTTATTAAGGTCAAATTCTACTAAATACTATACCGATATG
* * * ** *
133738 AAAAGTTCATAATCTTAGTTGCGTTCCCAATTCTCCAACAGATTGCCCCACAATAATACCTACAA
1 AAAAGTTCATAATGTTAGTAGCGTT-CCGATTCTCCAATGGATTGGCCCACAATAATACCTACAA
* * *
133803 CTTCTCCCAATTCAATTACATCA-TTGTGAGTGGGGCTCTGACCATAACATAATAGTGATATGTG
65 CTTCTCCCAATTCAACTAGATCACCT-TGAGTGGGGCTCTGACCATAACATAATAGTGATATGTG
* * *
133867 AAAATAGCAAGTTGATATAACATTATACATAATAATATGTTAGTAGCATCATATTTTGGAAATAA
129 -AAATAGCAAGTTGATATAACATTACATATAATAATATGTTAGTAGTATCATATTTTGGAAATAA
* * *
133932 TAGAATTGACCTTAATGAATTTAACATTTATTCTTTGATCATGATTAAAATTTTAAAATTCATAA
193 TAGAATTGAACTTAATGAATTTAACATTTATTGTTTGATCATGATTAAAATTTTAAAATTCACAA
133997 AGCATATGACTAAAATTAGAGTGTGAGGACTAAATCCATAATTTAAACATAATATAGGGACTGAT
258 AGCATATGACTAAAATTA-AGTGTGAGGACTAAATCCATAATTTAAACATAATATAGGGACTGAT
* *
134062 AGTAAAATTTAACATTTTATTAACTAACCTTCTTGTAAACAAGGAGAGCTAATAAAAAAAACCCA
322 AGTAAAATTTAACCTTTTATTAACTAATCTTCTTGTAAACAAGGAGAGCTAATAAAAAAAACCCA
* *
134127 AAATAATTTTATTAAGGTCAAATTCTACTAAATACTCTACC-AGTATG
387 AAATATTTTTATTAAGGTCAAATTCTACTAAATACTATACCGA-TATG
* *
134174 AAAAGTTCCTAATGTTAGTAGCGTTCCGATTCTCCAATGGATTGGCCCACAGTAATACCTACAAC
1 AAAAGTTCATAATGTTAGTAGCGTTCCGATTCTCCAATGGATTGGCCCACAATAATACCTACAAC
*
134239 TTCTCCCAATTCAACTAGATCACCTTGAGTGGGGCTCTGACCATAACATAATACTGATATGTGAA
66 TTCTCCCAATTCAACTAGATCACCTTGAGTGGGGCTCTGACCATAACATAATAGTGATATGTGAA
*
134304 TATAACAAGTTGATATAACATTACATATAATAATATGTTAGTAGTATCATATTTTGGAAATAATA
131 -ATAGCAAGTTGATATAACATTACATATAATAATATGTTAGTAGTATCATATTTTGGAAATAATA
*
134369 GAATTGAACTTAATGAATTTAACATTTTTTTGTTTGATCATGATTAAAATTTTAAAATTCACAAA
195 GAATTGAACTTAATGAATTTAACA-TTTATTGTTTGATCATGATTAAAATTTTAAAATTCACAAA
* * *
134434 GTATATGACGTACTAAAATTAAAGTGTGAGGACTAAATCTATAATTTAAACATAGTATAGGGACT
259 GCATAT---G-ACTAAAATT-AAGTGTGAGGACTAAATCCATAATTTAAACATAATATAGGGACT
* ** * * * * *
134499 GATAATAAAATTGGACCTTTTATTAACTAATCTTCCTCTAAACAAGGA-ACTCTATTAGAAAAAA
319 GATAGTAAAATTTAACCTTTTATTAACTAATCTTCTTGTAAACAAGGAGA-GCTAATAAAAAAAA
*
134563 CCCAAAATATTTTTGTTAAGGTCAAATTCTACTA
383 CCCAAAATATTTTTATTAAGGTCAAATTCTACTA
134597 TTTGTTCATT
Statistics
Matches: 759, Mismatches: 82, Indels: 31
0.87 0.09 0.04
Matches are distributed among these distances:
434 2 0.00
435 412 0.54
436 208 0.27
439 2 0.00
440 134 0.18
441 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (433 bp):
AAAAGTTCATAATGTTAGTAGCGTTCCGATTCTCCAATGGATTGGCCCACAATAATACCTACAAC
TTCTCCCAATTCAACTAGATCACCTTGAGTGGGGCTCTGACCATAACATAATAGTGATATGTGAA
ATAGCAAGTTGATATAACATTACATATAATAATATGTTAGTAGTATCATATTTTGGAAATAATAG
AATTGAACTTAATGAATTTAACATTTATTGTTTGATCATGATTAAAATTTTAAAATTCACAAAGC
ATATGACTAAAATTAAGTGTGAGGACTAAATCCATAATTTAAACATAATATAGGGACTGATAGTA
AAATTTAACCTTTTATTAACTAATCTTCTTGTAAACAAGGAGAGCTAATAAAAAAAACCCAAAAT
ATTTTTATTAAGGTCAAATTCTACTAAATACTATACCGATATG
Found at i:134897 original size:63 final size:64
Alignment explanation
Indices: 134813--134934 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
134803 ATTTACACAT
* * * * *
134813 AATATAGGGACTAATAGC-AAA-ATTTAACCTTTTTATTAACTAAACTTCCTCTAAACAAGGAAC
1 AATAAAGGGACTAACAACAAAATATTTAA-CATTTTACTAACTAAACTTCCTCTAAACAAGGAAC
*
134876 AATAAAGGGACTAACAACAAAATATTTAACATTTTACTAACTAATCTTCCTCTAAACAA
1 AATAAAGGGACTAACAACAAAATATTTAACATTTTACTAACTAAACTTCCTCTAAACAA
134935 AGAGCAATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 15 0.29
64 30 0.59
65 6 0.12
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (64 bp):
AATAAAGGGACTAACAACAAAATATTTAACATTTTACTAACTAAACTTCCTCTAAACAAGGAAC
Found at i:138216 original size:30 final size:30
Alignment explanation
Indices: 138161--138222 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
138151 CTTAACAAGC
*
138161 AAATACCTCTAAAATAATAATAAAATTAAT
1 AAATACCTCTAAAATAATAACAAAATTAAT
* * *
138191 AAATGCCTTTAAAGTAATAACAAAATTAAT
1 AAATACCTCTAAAATAATAACAAAATTAAT
138221 AA
1 AA
138223 TAAAATAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATACCTCTAAAATAATAACAAAATTAAT
Found at i:143293 original size:42 final size:42
Alignment explanation
Indices: 143195--143324 Score: 158
Period size: 42 Copynumber: 3.1 Consensus size: 42
143185 TCATATAAAT
* *
143195 TTCAGTTTAACCCTA-AGGGTTTTCCGTTTAGCTCTTTTGGAGC
1 TTCAGTTTAACCCTATTGGGTTTT-CGTTCAGCTCTTTT-GAGC
*
143238 TTCGGTTTAACCCTATTGGG-TTTCAGTTCAGCTCTTTTGAGC
1 TTCAGTTTAACCCTATTGGGTTTTC-GTTCAGCTCTTTTGAGC
* *
143280 TTCAGTTTAACCCT-TCTGGGTTTTCGTTCAGGTCTTATGAGC
1 TTCAGTTTAACCCTAT-TGGGTTTTCGTTCAGCTCTTTTGAGC
143322 TTC
1 TTC
143325 CGATCTACCA
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
41 1 0.01
42 40 0.52
43 33 0.43
44 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (42 bp):
TTCAGTTTAACCCTATTGGGTTTTCGTTCAGCTCTTTTGAGC
Found at i:148749 original size:25 final size:24
Alignment explanation
Indices: 148708--148758 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
148698 ACATGATTTT
* * *
148708 ATTTATTTTCAAGATTAAATAGAA
1 ATTTATTTTAAAAATTAAATAAAA
*
148732 ATTTATTTTTAAAAATTATATAAAA
1 ATTTA-TTTTAAAAATTAAATAAAA
148757 AT
1 AT
148759 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTTATTTTAAAAATTAAATAAAA
Found at i:148869 original size:120 final size:119
Alignment explanation
Indices: 148644--148877 Score: 328
Period size: 120 Copynumber: 2.0 Consensus size: 119
148634 TTTCCAATTT
* * *
148644 AAATTTATTTAAAATTTTAATATTTAAATCTTGACTCATGAAAAAGGATATATTACATGATTTTA
1 AAATTTAATTAAAATATTAATATTTAAATCTTGACTCATGAAAAAGGAAATATTACATGATTTTA
**
148709 TTTATTTTCAAGATTAAATAGAAATTTATTTTTAAAAATTATATAAAAATAAAA
66 TTTATTTTCAAGATTAAATAGAAATGCATTTTTAAAAATTATATAAAAATAAAA
* * *
148763 AAATTATAATTAAAATATTAACTATTTAAATCTTGACTCGTGGAACAGGAAATATTACATGA-TT
1 AAATT-TAATTAAAATATTAA-TATTTAAATCTTGACTCATGAAAAAGGAAATATTACATGATTT
* **
148827 TGTTTATTTTCAAGATTAAATAGAAATGCATTTTCT-TGAATTATATAAAAA
64 TATTTATTTTCAAGATTAAATAGAAATGCATTTT-TAAAAATTATATAAAAA
148878 ATTATAATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
119 5 0.05
120 59 0.58
121 37 0.37
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (119 bp):
AAATTTAATTAAAATATTAATATTTAAATCTTGACTCATGAAAAAGGAAATATTACATGATTTTA
TTTATTTTCAAGATTAAATAGAAATGCATTTTTAAAAATTATATAAAAATAAAA
Found at i:152339 original size:32 final size:33
Alignment explanation
Indices: 152289--152354 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
152279 CTATGAAAGA
* *
152289 ATGTCGTATTTTTTTACCTAATCGAAGCCAATT
1 ATGTCATATTTTTTTACCTAACCGAAGCCAATT
152322 ATGTCATA-TTTTTTACCTAACCGAAGCCAATT
1 ATGTCATATTTTTTTACCTAACCGAAGCCAATT
152354 A
1 A
152355 GTTCTCGCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (33 bp):
ATGTCATATTTTTTTACCTAACCGAAGCCAATT
Found at i:159708 original size:7 final size:7
Alignment explanation
Indices: 159696--159724 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
159686 ATTATAGTAA
159696 TATTTTT
1 TATTTTT
159703 TATTTTT
1 TATTTTT
159710 TATTTTT
1 TATTTTT
159717 TATTTTT
1 TATTTTT
159724 T
1 T
159725 GTGTGATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TATTTTT
Found at i:159876 original size:23 final size:21
Alignment explanation
Indices: 159850--159902 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 21
159840 TATGTATAAA
159850 TAAAATATTTACTATAATATATT
1 TAAAATATTT--TATAATATATT
*
159873 TAAAAATGATTTTATATTATATT
1 T-AAAAT-ATTTTATAATATATT
159896 TAAAATA
1 TAAAATA
159903 AAAAGTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 1 0.04
22 5 0.19
23 12 0.44
24 5 0.19
25 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAAATATTTTATAATATATT
Found at i:160667 original size:4 final size:4
Alignment explanation
Indices: 160658--160686 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
160648 AGCAAACGTG
160658 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
160687 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:166131 original size:17 final size:15
Alignment explanation
Indices: 166084--166135 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
166074 ATTTAGTTTG
*
166084 ATTTGGGTTATTTTGA
1 ATTT-GGTTATTTTTA
* *
166100 ATTTGGTCATATTTA
1 ATTTGGTTATTTTTA
166115 GATTTGAGTTATTTTTA
1 -ATTTG-GTTATTTTTA
166132 ATTT
1 ATTT
166136 TAATTAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 8 0.28
16 13 0.45
17 8 0.28
ACGTcount: A:0.23, C:0.02, G:0.17, T:0.58
Consensus pattern (15 bp):
ATTTGGTTATTTTTA
Found at i:168545 original size:20 final size:20
Alignment explanation
Indices: 168517--168557 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
168507 AACATAATTC
168517 TCATAAAAAATAAAAAAAAA
1 TCATAAAAAATAAAAAAAAA
* * *
168537 TCATCAAAAATCATAAAAAA
1 TCATAAAAAATAAAAAAAAA
168557 T
1 T
168558 AGAAAAAAAT
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:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (20 bp):
TCATAAAAAATAAAAAAAAA
Found at i:176420 original size:22 final size:20
Alignment explanation
Indices: 176384--176423 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
176374 TTGATTATAT
176384 TTAAAATATTAAATATTTAA
1 TTAAAATATTAAATATTTAA
176404 TTAAAATAGTTTAAATATTT
1 TTAAAATA--TTAAATATTT
176424 TTTTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TTAAAATATTAAATATTTAA
Found at i:181264 original size:16 final size:16
Alignment explanation
Indices: 181243--181325 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
181233 TTAGATTGGT
* *
181243 AATTAAGATATATTTA
1 AATTAAAATAAATTTA
181259 AATTAAAATAAATTTA
1 AATTAAAATAAATTTA
* *
181275 AATTTAAACATTAA-TCA
1 AA-TTAAA-ATAAATTTA
* * ** *
181292 CATTCAACGAGATTTA
1 AATTAAAATAAATTTA
181308 AATTAAAATAAATTTA
1 AATTAAAATAAATTTA
181324 AA
1 AA
181326 AAATCATGAT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
15 1 0.02
16 35 0.73
17 8 0.17
18 4 0.08
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (16 bp):
AATTAAAATAAATTTA
Found at i:186677 original size:6 final size:6
Alignment explanation
Indices: 186668--186694 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
186658 AATATAAAAT
186668 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
186695 TAGCATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:191440 original size:14 final size:15
Alignment explanation
Indices: 191421--191449 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
191411 ATTTTTTATA
191421 TAAATTT-TATTTTT
1 TAAATTTATATTTTT
191435 TAAATTTATATTTTT
1 TAAATTTATATTTTT
191450 ATTCAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TAAATTTATATTTTT
Found at i:195090 original size:26 final size:26
Alignment explanation
Indices: 195060--195109 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
195050 GTCATTAAAG
195060 TTGATAGAAATATTCAATAAAAAAAA
1 TTGATAGAAATATTCAATAAAAAAAA
195086 TTGATAGAAATATTCAATAAAAAA
1 TTGATAGAAATATTCAATAAAAAA
195110 GTTGGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (26 bp):
TTGATAGAAATATTCAATAAAAAAAA
Found at i:196797 original size:14 final size:14
Alignment explanation
Indices: 196778--196807 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
196768 TAAAAATTAT
*
196778 AAATAATGGTAGTA
1 AAATAATAGTAGTA
196792 AAATAATAGTAGTA
1 AAATAATAGTAGTA
196806 AA
1 AA
196808 CGGTAGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.27
Consensus pattern (14 bp):
AAATAATAGTAGTA
Found at i:197142 original size:16 final size:16
Alignment explanation
Indices: 197121--197170 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
197111 CGAAAATGAT
197121 ATAATAAGTATAATAA
1 ATAATAAGTATAATAA
*
197137 ATAAT-AGTGTAA-AA
1 ATAATAAGTATAATAA
*
197151 A-AATAA-TACAATAA
1 ATAATAAGTATAATAA
197165 ATAATA
1 ATAATA
197171 GGAAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 6 0.21
14 7 0.25
15 10 0.36
16 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (16 bp):
ATAATAAGTATAATAA
Found at i:199659 original size:49 final size:49
Alignment explanation
Indices: 199587--199685 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
199577 GATAACATTG
199587 TAGGTAAACAATGAAGAATGCTAGAAGATTAGGAAATGTCATTAACCAA
1 TAGGTAAACAATGAAGAATGCTAGAAGATTAGGAAATGTCATTAACCAA
199636 TAGGTAAACAATGAAGAATGCTAGAAGATTAGGAAATGTCATTAACCAA
1 TAGGTAAACAATGAAGAATGCTAGAAGATTAGGAAATGTCATTAACCAA
199685 T
1 T
199686 CACTAATTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.23
Consensus pattern (49 bp):
TAGGTAAACAATGAAGAATGCTAGAAGATTAGGAAATGTCATTAACCAA
Found at i:201211 original size:23 final size:23
Alignment explanation
Indices: 201181--201224 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
201171 TTAATCTATG
201181 TATATTTAGTTTTAAAAATTTCA
1 TATATTTAGTTTTAAAAATTTCA
* *
201204 TATATTTATTTTTCAAAATTT
1 TATATTTAGTTTTAAAAATTT
201225 AAAATTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (23 bp):
TATATTTAGTTTTAAAAATTTCA
Found at i:212758 original size:27 final size:28
Alignment explanation
Indices: 212728--212787 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 28
212718 AATTAAATCT
*
212728 TTTTA-TAATTTTATACTTTTT-AAATAA
1 TTTTAGTAA-TTTATAATTTTTAAAATAA
*
212755 TTTTAGTGATTTATAATTTTTAAAAATAA
1 TTTTAGTAATTTATAATTTTT-AAAATAA
212784 TTTT
1 TTTT
212788 TTTGAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 16 0.57
28 2 0.07
29 10 0.36
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTTAGTAATTTATAATTTTTAAAATAA
Found at i:212952 original size:21 final size:20
Alignment explanation
Indices: 212910--212964 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
212900 ATTTTTAGGC
* *
212910 AATTTAATAAAAAAATTGAA
1 AATTTAATAAAAAAACTAAA
*
212930 AATTTAAGAAAAAGAACTAAA
1 AATTTAATAAAAA-AACTAAA
*
212951 AATTAAATAAAAAA
1 AATTTAATAAAAAA
212965 TTTTAATAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (20 bp):
AATTTAATAAAAAAACTAAA
Found at i:215461 original size:26 final size:25
Alignment explanation
Indices: 215403--215461 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
215393 ATAAAGTAAA
* *
215403 AATTT-ATTAATAAAATATTTTTAT
1 AATTTAATTAAAAAAATATATTTAT
*
215427 AATTAAATTAAAAAAATTATATTTAT
1 AATTTAATTAAAAAAA-TATATTTAT
*
215453 TATTTAATT
1 AATTTAATT
215462 TAAATTGGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 4 0.14
25 9 0.32
26 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AATTTAATTAAAAAAATATATTTAT
Found at i:227319 original size:13 final size:13
Alignment explanation
Indices: 227290--227321 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
227280 CTCTAATCAT
227290 TTTAATTTTTTTA
1 TTTAATTTTTTTA
227303 -TTAATTTTTTTA
1 TTTAATTTTTTTA
227315 TTTAATT
1 TTTAATT
227322 AAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTAATTTTTTTA
Found at i:230545 original size:24 final size:23
Alignment explanation
Indices: 230518--230566 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
230508 TTTGAGTGAG
230518 TTAAAAG-TAAAATTTTATAATTTT
1 TTAAAAGATAAAA--TTATAATTTT
* *
230542 TTAAGAGATGAAATTATAATTTT
1 TTAAAAGATAAAATTATAATTTT
230565 TT
1 TT
230567 TTTATTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 12 0.55
24 6 0.27
25 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (23 bp):
TTAAAAGATAAAATTATAATTTT
Found at i:235166 original size:24 final size:24
Alignment explanation
Indices: 235139--235204 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
235129 TTTGATATAT
*
235139 ATAGATTAATTTTTAATAATAGAA
1 ATAGATTAATTTTTAATAAAAGAA
* *
235163 ATAGATGGAATTTTTAACAAAAGAA
1 ATAGAT-TAATTTTTAATAAAAGAA
* * *
235188 TTAGATTACTCTTTAAT
1 ATAGATTAATTTTTAAT
235205 TTGACGTATA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (24 bp):
ATAGATTAATTTTTAATAAAAGAA
Found at i:236353 original size:100 final size:104
Alignment explanation
Indices: 236271--236463 Score: 217
Period size: 105 Copynumber: 1.9 Consensus size: 104
236261 AAAAAGGAAG
* ** *
236271 AGAAAAGAAGAAAGGAT-TTATCAATATCGATATTCTAATATTTGTTAAATCCACAATTACAATA
1 AGAAAAAAAGAAAGGATACCATCAATATCGATATTCTAATATATGTTAAATCCACAATTACAATA
* **
236335 TCCTTAACTAAGGTTATATGTAAAGCAAAAAAGAAAAGAA
66 CCCTTAACTAAGACTATATGTAAAGCAAAAAAGAAAAG-A
* ** * * **
236375 AGAAAAAAAGAGAGGATACCATCAATATTAATATCCTAATATATGTTAAATCCGCAATTATGATA
1 AGAAAAAAAGAAAGGATACCATCAATATCGATATTCTAATATATGTTAAATCCACAATTACAATA
* * *
236440 CACTTGACTAAGGCTATATGTAAA
66 CCCTTAACTAAGACTATATGTAAA
236464 AAAAGAAGAG
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
104 15 0.21
105 58 0.79
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (104 bp):
AGAAAAAAAGAAAGGATACCATCAATATCGATATTCTAATATATGTTAAATCCACAATTACAATA
CCCTTAACTAAGACTATATGTAAAGCAAAAAAGAAAAGA
Found at i:236469 original size:84 final size:86
Alignment explanation
Indices: 236377--236549 Score: 197
Period size: 86 Copynumber: 2.0 Consensus size: 86
236367 GAAAAGAAAG
* * *
236377 AAAAAAAG-AGA-GGATACCATCAATATTAATATCCTAATATATGTTAAATCCGCAATTATGATA
1 AAAAAAAGAAGAGGGATACCATCAATATTAATATCCTAATATATGTTAAATACGCAATCACGATA
* *
236440 CACTTGACTAAGGCTATATGT
66 CACTTCACTAAAGCTATATGT
* ** * * * * *
236461 AAAAAAAGAAGAGGGGTGTCATCAATATTGATGTTCTAATATTTGTTAAATATGCAATCACGATA
1 AAAAAAAGAAGAGGGATACCATCAATATTAATATCCTAATATATGTTAAATACGCAATCACGATA
* *
236526 CTCTTCATTAAAGCTATATGT
66 CACTTCACTAAAGCTATATGT
236547 AAA
1 AAA
236550 GCAAAAAAGA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
84 8 0.11
85 3 0.04
86 61 0.85
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (86 bp):
AAAAAAAGAAGAGGGATACCATCAATATTAATATCCTAATATATGTTAAATACGCAATCACGATA
CACTTCACTAAAGCTATATGT
Found at i:245892 original size:5 final size:5
Alignment explanation
Indices: 245882--245906 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
245872 AGGAGAGGGC
245882 GGGAA GGGAA GGGAA GGGAA GGGAA
1 GGGAA GGGAA GGGAA GGGAA GGGAA
245907 AAAGAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
GGGAA
Found at i:248900 original size:27 final size:27
Alignment explanation
Indices: 248870--248936 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
248860 ACCTATGCTA
*
248870 CCTATTAGATAGGGGTCATTGGTGCCG
1 CCTATTAGATAGGGGTCACTGGTGCCG
* *
248897 CCTATCAGATAAGGGTCACTGGTGCCG
1 CCTATTAGATAGGGGTCACTGGTGCCG
248924 CCTATTAGATAGG
1 CCTATTAGATAGG
248937 CACCACACCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (27 bp):
CCTATTAGATAGGGGTCACTGGTGCCG
Found at i:249552 original size:19 final size:19
Alignment explanation
Indices: 249528--249581 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
249518 ATAATTTTAA
249528 TAATATTAACAATTTAACT
1 TAATATTAACAATTTAACT
249547 TAATATTAACAATTTAACT
1 TAATATTAACAATTTAACT
*
249566 TAATTTTAA-AATTTAA
1 TAATATTAACAATTTAA
249582 AAAATAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 7 0.21
19 27 0.79
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTAACAATTTAACT
Found at i:249601 original size:29 final size:29
Alignment explanation
Indices: 249568--249656 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
249558 ATTTAACTTA
249568 ATTTTAAAATTTAAAAAATAGAAAATTTC
1 ATTTTAAAATTTAAAAAATAGAAAATTTC
249597 ATTTTAAAATTTAAAAAATAGAAAATTTC
1 ATTTTAAAATTTAAAAAATAGAAAATTTC
249626 ATTTTAAAATTTAAAAAATAGAAAATTTC
1 ATTTTAAAATTTAAAAAATAGAAAATTTC
249655 AT
1 AT
249657 GTAAATAAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTTTAAAATTTAAAAAATAGAAAATTTC
Found at i:250527 original size:25 final size:26
Alignment explanation
Indices: 250499--250583 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 26
250489 AAAATAAACA
*
250499 TTAAA-ATTAAACTCAAATATCAAAT
1 TTAAATATTAAAATCAAATATCAAAT
** *
250524 TTAAATAAAAAAATCAAATATTAAA-
1 TTAAATATTAAAATCAAATATCAAAT
* * *
250549 ATAAATATTAAATTCAAATACCAAAT
1 TTAAATATTAAAATCAAATATCAAAT
*
250575 ATTATATAT
1 -TTAAATAT
250584 CCCAAATAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
25 24 0.53
26 15 0.33
27 6 0.13
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (26 bp):
TTAAATATTAAAATCAAATATCAAAT
Found at i:250556 original size:12 final size:13
Alignment explanation
Indices: 250504--250568 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
250494 AAACATTAAA
*
250504 ATTAAACTCAAAT
1 ATTAAAATCAAAT
* * *
250517 ATCAAATTTAAAT
1 ATTAAAATCAAAT
**
250530 AAAAAAATCAAAT
1 ATTAAAATCAAAT
250543 ATTAAAAT-AAAT
1 ATTAAAATCAAAT
*
250555 ATTAAATTCAAAT
1 ATTAAAATCAAAT
250568 A
1 A
250569 CCAAATATTA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
12 11 0.27
13 30 0.73
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTAAAATCAAAT
Found at i:250561 original size:19 final size:19
Alignment explanation
Indices: 250479--250561 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
250469 TTTTAAAAAA
* *
250479 ATTAAATACTAAAATAAAC
1 ATTAAATATTAAAATAAAT
*
250498 ATTAAA-ATTAAACTCAAAT
1 ATTAAATATTAAAAT-AAAT
* * *
250517 ATCAAAT-TTAAATAAAAAA
1 ATTAAATATTAAA-ATAAAT
*
250536 ATCAAATATTAAAATAAAT
1 ATTAAATATTAAAATAAAT
250555 ATTAAAT
1 ATTAAAT
250562 TCAAATACCA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
18 6 0.12
19 39 0.78
20 5 0.10
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTAAATATTAAAATAAAT
Found at i:256666 original size:15 final size:18
Alignment explanation
Indices: 256632--256668 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
256622 TGCAATTTAA
256632 TTTTCTTTTTTGCACTTC
1 TTTTCTTTTTTGCACTTC
256650 TTTT-TTTTTTG-AC-TC
1 TTTTCTTTTTTGCACTTC
256665 TTTT
1 TTTT
256669 ACTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 2 0.11
17 7 0.37
18 4 0.21
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.73
Consensus pattern (18 bp):
TTTTCTTTTTTGCACTTC
Found at i:256821 original size:17 final size:17
Alignment explanation
Indices: 256799--256832 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
256789 CCTTAAATAT
*
256799 AAAAAAAGTAAAATTAC
1 AAAAAAAATAAAATTAC
*
256816 AAAAAAAATCAAATTAC
1 AAAAAAAATAAAATTAC
256833 TAAATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAAAAATAAAATTAC
Found at i:261035 original size:12 final size:13
Alignment explanation
Indices: 261020--261066 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
261010 TCTTTTGATG
261020 AGTAT-TTTTCAA
1 AGTATCTTTTCAA
* *
261032 AGTATGTTCTCAA
1 AGTATCTTTTCAA
*
261045 AATAT-TTTTCAA
1 AGTATCTTTTCAA
261057 AGTATCTTTT
1 AGTATCTTTT
261067 AAATCCATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 15 0.52
13 14 0.48
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (13 bp):
AGTATCTTTTCAA
Found at i:267329 original size:82 final size:81
Alignment explanation
Indices: 267229--267389 Score: 241
Period size: 82 Copynumber: 2.0 Consensus size: 81
267219 AAAACTACCA
** * ** * *
267229 TTATCTGTTTGTTGATTCAAGTTTGTTGTTCGGAATTTGGTTCCGGGACAAATCTTGCATGCCGA
1 TTATCTGTTTGTTGATTCAAGTTTGTCATTCAGAATCCGGTTCCGGGAC-AATCTTGCATACCAA
267294 GAAACTAATTCTTTTCG
65 GAAACTAATTCTTTTCG
267311 TTATCTGTTTGTTGATTCAAGTTTGTCATTCAGAATCCGGTTCCGGGACAATCTTGCATACCAAG
1 TTATCTGTTTGTTGATTCAAGTTTGTCATTCAGAATCCGGTTCCGGGACAATCTTGCATACCAAG
*
267376 AAACTAATTTTTTT
66 AAACTAATTCTTTT
267390 TATTATATTA
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 27 0.38
82 44 0.62
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (81 bp):
TTATCTGTTTGTTGATTCAAGTTTGTCATTCAGAATCCGGTTCCGGGACAATCTTGCATACCAAG
AAACTAATTCTTTTCG
Found at i:271096 original size:24 final size:24
Alignment explanation
Indices: 271046--271094 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
271036 CCAAAATATT
*
271046 TTCAAAATTAATTTCTTTTTTGAAA
1 TTCAAAATTAATTTATTTTTT-AAA
*
271071 TTCAAATTTAATTTATTTGTTTAA
1 TTCAAAATTAATTTATTT-TTTAA
271095 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (24 bp):
TTCAAAATTAATTTATTTTTTAAA
Found at i:271155 original size:18 final size:18
Alignment explanation
Indices: 271132--271166 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
271122 ATTAAGAGTG
*
271132 AGTTTTATTAATATTTTT
1 AGTTTTAATAATATTTTT
*
271150 AGTTTTAATATTATTTT
1 AGTTTTAATAATATTTT
271167 AATTTTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
AGTTTTAATAATATTTTT
Found at i:271173 original size:7 final size:7
Alignment explanation
Indices: 271172--271196 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
271162 ATTTTAATTT
271172 TTTTAAA
1 TTTTAAA
271179 TTTTAAA
1 TTTTAAA
271186 TTTTAAA
1 TTTTAAA
271193 TTTT
1 TTTT
271197 TTACTTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:276058 original size:23 final size:23
Alignment explanation
Indices: 276042--276087 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
276032 AACAAGTTAG
276042 ACTAATTGAACTAAACACACACA
1 ACTAATTGAACTAAACACACACA
276065 ACTAATTGAACTAAACACACACA
1 ACTAATTGAACTAAACACACACA
276088 TGGCAGCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.04, T:0.17
Consensus pattern (23 bp):
ACTAATTGAACTAAACACACACA
Found at i:286797 original size:142 final size:140
Alignment explanation
Indices: 286466--286817 Score: 372
Period size: 140 Copynumber: 2.5 Consensus size: 140
286456 AGTGAGCTCA
* * * * * * *
286466 ACCTGTCAAATGTTACCACTTTGAGCCAACTTAGCTAAT-TTCTGGTTTCGCTGCTACCTATATA
1 ACCTGTTAAACGTCACCACTTTGAACCAACTTAGCTAATGTTCTGGGTTCACTGCTACCCATATA
* *
286530 TAGATATGGATATCTTAGACATGATATTACCTGTGCATCATCACCACTGCCCTTTTTGTTTTCAG
66 TAGATATGGATATCTTACACATGATATTACCTGTGCATCATCACCACTG-CATTTTTGTTTTCAG
**
286595 GCTCTGGACTC
130 GCTCCAGACTC
* * * *** *
286606 ATCTGTTAAATGTCACCTCTTTGAACCAACTTAGCTAA-GTTCCACGTTCACTGCTTCCCATATA
1 ACCTGTTAAACGTCACCACTTTGAACCAACTTAGCTAATGTTCTGGGTTCACTGCTACCCATATA
* * * *
286670 TAGATGA-GGATATCTTACTCATGACTCTTATCTGTGCATCATCACGACTG-ATTGTATTGTTTT
66 TAGAT-ATGGATATCTTACACATGA-TATTACCTGTGCATCATCACCACTGCATT-T-TTGTTTT
* *
286733 CCGGCTCCAGACTTG
127 CAGGCTCCAGAC-TC
* **
286748 ACCTGTTACACGTCACCACTTTGAACCAACTTAGC-AATGTTCTGGGTTCACTGCTACCGGTATA
1 ACCTGTTAAACGTCACCACTTTGAACCAACTTAGCTAATGTTCTGGGTTCACTGCTACCCATATA
286812 TAGATA
66 TAGATA
286818 CAGATAAATA
Statistics
Matches: 173, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
139 2 0.01
140 72 0.42
141 42 0.24
142 57 0.33
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (140 bp):
ACCTGTTAAACGTCACCACTTTGAACCAACTTAGCTAATGTTCTGGGTTCACTGCTACCCATATA
TAGATATGGATATCTTACACATGATATTACCTGTGCATCATCACCACTGCATTTTTGTTTTCAGG
CTCCAGACTC
Found at i:289303 original size:116 final size:114
Alignment explanation
Indices: 289167--289398 Score: 353
Period size: 116 Copynumber: 2.0 Consensus size: 114
289157 AAAAAATAAA
* *
289167 AAAAAATAAACCAATTTAAATTGAATTATCATAAATAATTC-AAAAAATCCAATCT-AACTAACC
1 AAAAAATAAACCAATCTAAATCGAATTATCATAAATAATTCAAAAAAATCCAAT-TGAACTAACC
289230 AAAG-TTAACCCAAACATATACATTAATATTGGTGAACATTCATTATTTAAAAT
65 -AAGTTTAACCCAAACATAT--ATT-ATATTGGTGAACATTCATTATTTAAAAT
* *
289283 AAAAAATAAACCAATCTAAATCGAATTGTCATAAATAATTCAAAAAAATTCAATTGAACTAACCA
1 AAAAAATAAACCAATCTAAATCGAATTATCATAAATAATTCAAAAAAATCCAATTGAACTAACCA
*
289348 AGTTTATCCCAAACATATATTATATTGGTGAACATTCATTATTTAAAAT
66 AGTTTAACCCAAACATATATTATATTGGTGAACATTCATTATTTAAAAT
289397 AA
1 AA
289399 GGAAAGTTTT
Statistics
Matches: 108, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
114 30 0.28
115 3 0.03
116 42 0.39
117 33 0.31
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (114 bp):
AAAAAATAAACCAATCTAAATCGAATTATCATAAATAATTCAAAAAAATCCAATTGAACTAACCA
AGTTTAACCCAAACATATATTATATTGGTGAACATTCATTATTTAAAAT
Found at i:290151 original size:23 final size:24
Alignment explanation
Indices: 290116--290167 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
290106 TCTAGTGAAA
* *
290116 ACAATTT-TTTTTTTAATTTTCAC
1 ACAATTTCATTTTTAAATTTTCAC
290139 ACAATTTCATTTTTCAAATTTTCAC
1 ACAATTTCATTTTT-AAATTTTCAC
290164 ACAA
1 ACAA
290168 GAAAACGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 5 0.20
25 13 0.52
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (24 bp):
ACAATTTCATTTTTAAATTTTCAC
Found at i:304341 original size:21 final size:21
Alignment explanation
Indices: 304315--304355 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
304305 ATCTGCTCAA
* *
304315 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
304336 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
304356 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:309539 original size:16 final size:17
Alignment explanation
Indices: 309518--309549 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
309508 TTATAATCGA
309518 AATTTAATTT-TAATTT
1 AATTTAATTTATAATTT
309534 AATTTAATTTATAATT
1 AATTTAATTTATAATT
309550 ATTTTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTAATTTATAATTT
Found at i:311378 original size:18 final size:19
Alignment explanation
Indices: 311339--311378 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
311329 AATATCGAAG
311339 ATTATTTATTTAAAATATA
1 ATTATTTATTTAAAATATA
311358 ATTATTT-TTTAATAATA-A
1 ATTATTTATTTAA-AATATA
311376 ATT
1 ATT
311379 CTATTTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTATTTATTTAAAATATA
Found at i:311473 original size:6 final size:6
Alignment explanation
Indices: 311455--311485 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
311445 GAAAATTATT
*
311455 AAATTA AATTTA AAATTA AAATTA AAATTA A
1 AAATTA AAATTA AAATTA AAATTA AAATTA A
311486 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AAATTA
Found at i:311490 original size:29 final size:29
Alignment explanation
Indices: 311453--311510 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
311443 ATGAAAATTA
311453 TTAAATTAAATTTAAAATTA-AAATTAAAA
1 TTAAATT-AATTTAAAATTATAAATTAAAA
* *
311482 TTAATTTAATTTAAAATTATTAATTAAAA
1 TTAAATTAATTTAAAATTATAAATTAAAA
311511 AATTATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAAATTAATTTAAAATTATAAATTAAAA
Found at i:311493 original size:28 final size:29
Alignment explanation
Indices: 311456--311510 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
311446 AAAATTATTA
311456 AATTAAATTTAAAATTA-AAATTAAAATT
1 AATTAAATTTAAAATTATAAATTAAAATT
* *
311484 AATTTAATTTAAAATTATTAATTAAAA
1 AATTAAATTTAAAATTATAAATTAAAA
311511 AATTATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATTAAATTTAAAATTATAAATTAAAATT
Found at i:311499 original size:12 final size:12
Alignment explanation
Indices: 311455--311490 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
311445 GAAAATTATT
311455 AAATTAAATTTA
1 AAATTAAATTTA
*
311467 AAATTAAAATTA
1 AAATTAAATTTA
311479 AAATT-AATTTA
1 AAATTAAATTTA
311490 A
1 A
311491 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATTAAATTTA
Found at i:311506 original size:23 final size:24
Alignment explanation
Indices: 311446--311508 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 24
311436 AGAAAGTATG
311446 AAAATTATTAAATTAAATTTAAAATT
1 AAAATTATT-AATT-AATTTAAAATT
* *
311472 AAAATTA-AAATTAATTT-AATTT
1 AAAATTATTAATTAATTTAAAATT
311494 AAAATTATTAATTAA
1 AAAATTATTAATTAA
311509 AAAATTATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 11 0.33
23 11 0.33
24 4 0.12
26 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTATTAATTAATTTAAAATT
Found at i:311598 original size:12 final size:13
Alignment explanation
Indices: 311581--311612 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
311571 AAAATTTGTG
311581 ATAATTATAAT-T
1 ATAATTATAATAT
311593 ATAATT-TAATAT
1 ATAATTATAATAT
311605 ATAATTAT
1 ATAATTAT
311613 CAGTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 13 0.72
13 1 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATAATTATAATAT
Found at i:312845 original size:16 final size:16
Alignment explanation
Indices: 312826--312871 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
312816 TGTTTAATTG
312826 AAAATTTAAAAAATAAA
1 AAAATTTAAAAAAT-AA
312843 AAAATTT-AAAAAT-A
1 AAAATTTAAAAAATAA
* *
312857 GAAATTTATAAAATA
1 AAAATTTAAAAAATA
312872 TGGTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 7 0.28
15 5 0.20
16 6 0.24
17 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAATTTAAAAAATAA
Found at i:317393 original size:203 final size:203
Alignment explanation
Indices: 317044--317450 Score: 769
Period size: 203 Copynumber: 2.0 Consensus size: 203
317034 GGAAAGGCGA
* *
317044 CGGTTGTGAGTTTGCTCACGGCGTTTTCGAATGTTGGCTCCACCCAGCTCGTTATCGGACCGAAC
1 CGGTTGTGAGTTCGCTCACGGCGTTTTCGAATGTTGGCTCCACCCAGCTCGTTACCGGACCGAAC
*
317109 TATGTAAAGATGGACCAGGTTGTAAGCGTAAGGTTTGTTTCTTTGCTCATAGTCTAGACCAGCTT
66 TATGTAAAGATGGACCAGGCTGTAAGCGTAAGGTTTGTTTCTTTGCTCATAGTCTAGACCAGCTT
317174 AGGGTCGTGAGCTCCGCCAGTTCTGGCTCTCCTCTTATAAGCCCACGGACCGAGTCATCACCGCC
131 AGGGTCGTGAGCTCCGCCAGTTCTGGCTCTCCTCTTATAAGCCCACGGACCGAGTCATCACCGCC
317239 GGTTTCAC
196 GGTTTCAC
317247 CGGTTGTGAGTTCGCTCACGGCGTTTTCGAATGTTGGCTCCACCCAGCTCGTTACCGGACCGAAC
1 CGGTTGTGAGTTCGCTCACGGCGTTTTCGAATGTTGGCTCCACCCAGCTCGTTACCGGACCGAAC
*
317312 TGTGTAAAGATGGACCAGGCTGTAAGCGTAAGGTTTGTTTCTTTGCTCATAGTCTAGACCAGCTT
66 TATGTAAAGATGGACCAGGCTGTAAGCGTAAGGTTTGTTTCTTTGCTCATAGTCTAGACCAGCTT
*
317377 AGGGTCGTGAGCTCCGCCGGTTCTGGCTCTCCTCTTATAAGCCCACGGACCGAGTCATCACCGCC
131 AGGGTCGTGAGCTCCGCCAGTTCTGGCTCTCCTCTTATAAGCCCACGGACCGAGTCATCACCGCC
317442 GGTTTCAC
196 GGTTTCAC
317450 C
1 C
317451 TATATCCGAC
Statistics
Matches: 199, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
203 199 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (203 bp):
CGGTTGTGAGTTCGCTCACGGCGTTTTCGAATGTTGGCTCCACCCAGCTCGTTACCGGACCGAAC
TATGTAAAGATGGACCAGGCTGTAAGCGTAAGGTTTGTTTCTTTGCTCATAGTCTAGACCAGCTT
AGGGTCGTGAGCTCCGCCAGTTCTGGCTCTCCTCTTATAAGCCCACGGACCGAGTCATCACCGCC
GGTTTCAC
Found at i:318321 original size:13 final size:13
Alignment explanation
Indices: 318288--318328 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
318278 CCGAAACTTT
*
318288 AAAAAATTA-TGA
1 AAAAAATTATTCA
*
318300 AACAAATTATTCA
1 AAAAAATTATTCA
318313 AAAAAATTATTCA
1 AAAAAATTATTCA
318326 AAA
1 AAA
318329 TTTTTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (13 bp):
AAAAAATTATTCA
Found at i:319513 original size:116 final size:116
Alignment explanation
Indices: 319292--319878 Score: 811
Period size: 116 Copynumber: 5.0 Consensus size: 116
319282 ACTCAAATTG
* * * * * *
319292 TCTAAATTCTAAATAAAAAGACGAAAATTACGGAACTTTTCAAACAAGTTTTGACACAATATTGT
1 TCTAGATTTTAAAT-AAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACAC-A-A-TGT
** * * *
319357 CGCATTTTGAATATAACTA-AGCATAGTTGTATTCCATATATATAATAATAATTCA
62 CATACTTTGAATACAACTAGA-CACAGTTGTATTCCATATATATAATAATAATTCA
* *
319412 TCTAGATTTTAAATAAATGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCGTA
1 TCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCATA
* * *
319477 CTTTGAATACAACCAGACACAGTTGTATTCCATATATAT-GTAAATAATTGA
66 CTTTGAATACAACTAGACACAGTTGTATTCCATATATATAAT-AATAATTCA
319528 TCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCATA
1 TCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCATA
* *
319593 CTTTGAATATAACTA-AGCATAGTTGTATTCCATATATATAATAATAATTCA
66 CTTTGAATACAACTAGA-CACAGTTGTATTCCATATATATAATAATAATTCA
* * * *
319644 TTTAGATTTTAAATAAATGACGGAAGTCACGGAACTATTCAAACACGTTTTGACACAATGTCCTA
1 TCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCATA
* *
319709 CTTTGAATACAACCAGACACAGTTGTATTCCATATATATATATGTAAATAATTGA
66 CTTTGAATACAACTAGACACAGTTGTATTCCATATATATA-A--T-AATAATTCA
*
319764 TCTAGAATTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCATA
1 TCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCATA
*
319829 TTTTGAATACAACTAGACACAGTTGTATTCCATATATATATATAATAATT
66 CTTTGAATACAACTAGACACAGTTGTATTCCATATATATA-ATAATAATT
319879 TATGCGTATG
Statistics
Matches: 422, Mismatches: 36, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
115 2 0.00
116 248 0.59
117 12 0.03
118 2 0.00
119 38 0.09
120 120 0.28
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (116 bp):
TCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCATA
CTTTGAATACAACTAGACACAGTTGTATTCCATATATATAATAATAATTCA
Found at i:319716 original size:232 final size:233
Alignment explanation
Indices: 319287--319878 Score: 947
Period size: 232 Copynumber: 2.5 Consensus size: 233
319277 TTTAAACTCA
* * * * * *
319287 AATTG-TCTAAATTCTAAATAAAAAGACGAAAATTACGGAACTTTTCAAACAAGTTTTGACACAA
1 AATTGATCTAGATTTTAAAT-AAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACAC-A
**
319351 TATTGTCGCATTTTGAATATAACTAAGCATAGTTGTATTCCATATATATAATAATAATTCATCTA
64 -A-TGTCATATTTTGAATATAACTAAGCATAGTTGTATTCCATATATATAATAATAATTCATCTA
*
319416 GATTTTAAATAAATGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCGTACTTT
127 GATTTTAAATAAATGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCCTACTTT
319481 GAATACAACCAGACACAGTTGTATTCC-ATATATATGTAAAT
192 GAATACAACCAGACACAGTTGTATTCCAATATATATGTAAAT
319522 AATTGATCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAAT
1 AATTGATCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAAT
* *
319587 GTCATACTTTGAATATAACTAAGCATAGTTGTATTCCATATATATAATAATAATTCATTTAGATT
66 GTCATATTTTGAATATAACTAAGCATAGTTGTATTCCATATATATAATAATAATTCATCTAGATT
*
319652 TTAAATAAATGACGGAAGTCACGGAACTATTCAAACACGTTTTGACACAATGTCCTACTTTGAAT
131 TTAAATAAATGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCCTACTTTGAAT
319717 ACAACCAGACACAGTTGTATTCCATATATATATATGTAAAT
196 ACAACCAGACACAGTTGTATTCC--A-ATATATATGTAAAT
*
319758 AATTGATCTAGAATTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAAT
1 AATTGATCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAAT
* *
319823 GTCATATTTTGAATACAACT-AGACACAGTTGTATTCCATATATATATATAATAATT
66 GTCATATTTTGAATATAACTAAG-CATAGTTGTATTCCATATATATA-ATAATAATT
319879 TATGCGTATG
Statistics
Matches: 334, Mismatches: 16, Indels: 12
0.92 0.04 0.03
Matches are distributed among these distances:
232 148 0.44
233 1 0.00
234 1 0.00
235 45 0.13
236 130 0.39
237 9 0.03
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (233 bp):
AATTGATCTAGATTTTAAATAAAAGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAAT
GTCATATTTTGAATATAACTAAGCATAGTTGTATTCCATATATATAATAATAATTCATCTAGATT
TTAAATAAATGACGGAAGTCACGGAACTATTCAAACAAGTTTTGACACAATGTCCTACTTTGAAT
ACAACCAGACACAGTTGTATTCCAATATATATGTAAAT
Found at i:320108 original size:10 final size:10
Alignment explanation
Indices: 320078--320117 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
320068 AGAGAAGAGA
320078 TATTAATATT
1 TATTAATATT
320088 TAATTAA-ATT
1 T-ATTAATATT
320098 TATTAATATT
1 TATTAATATT
320108 TATTATATAT
1 TATTA-ATAT
320118 GAACGGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 5 0.19
10 13 0.48
11 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATTAATATT
Found at i:321358 original size:31 final size:31
Alignment explanation
Indices: 321322--321385 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
321312 AAAAGATCTT
321322 CAATTTATAGATAGGGAATATCAAAACTATA
1 CAATTTATAGATAGGGAATATCAAAACTATA
321353 CAATTTATAGATAGGGAATATCAAAACTATA
1 CAATTTATAGATAGGGAATATCAAAACTATA
321384 CA
1 CA
321386 TAAACTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.28
Consensus pattern (31 bp):
CAATTTATAGATAGGGAATATCAAAACTATA
Found at i:327010 original size:23 final size:22
Alignment explanation
Indices: 326966--327010 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
326956 ATTTAATTAA
* * *
326966 TATATTACTTTAATATTTTATT
1 TATATTAATTTAAAATTCTATT
326988 TATATTATATTTAAAATTCTATT
1 TATATTA-ATTTAAAATTCTATT
327011 CAAATTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTAATTTAAAATTCTATT
Found at i:334846 original size:33 final size:33
Alignment explanation
Indices: 334809--334872 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
334799 ATTTGTTGTG
*
334809 TATTAGCTGTAT-ATCACAGCCACGTTGCAAGCC
1 TATTAGCTGTATGAT-ACAGCCACGTCGCAAGCC
*
334842 TATTAGCTGTGTGATACAGCCACGTCGCAAG
1 TATTAGCTGTATGATACAGCCACGTCGCAAG
334873 TTTGCTGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (33 bp):
TATTAGCTGTATGATACAGCCACGTCGCAAGCC
Found at i:339948 original size:18 final size:19
Alignment explanation
Indices: 339927--339962 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
339917 ATTATTTATC
339927 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
339945 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
339963 TATACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:339971 original size:19 final size:18
Alignment explanation
Indices: 339931--339973 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
339921 TTTATCTAAT
*
339931 AAATATCTTTTAAATAAT
1 AAATATCTTTTAAATAAC
339949 AAATATCTATTT-AATATAC
1 AAATATCT-TTTAAATA-AC
339968 AAATAT
1 AAATAT
339974 AAATATTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATCTTTTAAATAAC
Found at i:342244 original size:139 final size:138
Alignment explanation
Indices: 342071--342330 Score: 400
Period size: 139 Copynumber: 1.9 Consensus size: 138
342061 ACCCGGACCC
* * *
342071 GGGATTTATTTCGATTGATTCATTCAGTTACCTTTAAAAGATGGCA-TCAGATATATATGGGGTT
1 GGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTC-GACATATATGGGGTT
342135 CGGAA-ACCAATATCTATACCAA-AAGGGAAACTTTTAATCATTTGGGGCGTATTGAAAAGTGTC
65 -GGAATACCAATATCTATA-CAATAAGGGAAACTTTTAATCATTT-GGGCGTATTGAAAAGTGTC
342198 GTGTGCTCAGAT
127 GTGTGCTCAGAT
*
342210 GGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTCGACATATATGGGGTTT
1 GGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTCGACATATATGGGGTTG
* * *
342275 GAATCCCAATATCTATACAATAAGGGAAAGTTTTAATCATTTGGGTGTATTGAAAA
66 GAATACCAATATCTATACAATAAGGGAAACTTTTAATCATTTGGGCGTATTGAAAA
342331 CTCAGAGAAT
Statistics
Matches: 111, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
138 19 0.17
139 90 0.81
140 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (138 bp):
GGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTCGACATATATGGGGTTG
GAATACCAATATCTATACAATAAGGGAAACTTTTAATCATTTGGGCGTATTGAAAAGTGTCGTGT
GCTCAGAT
Found at i:342497 original size:159 final size:158
Alignment explanation
Indices: 342202--342677 Score: 612
Period size: 160 Copynumber: 3.0 Consensus size: 158
342192 AGTGTCGTGT
* * * * * *
342202 GCTCAGATGGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTCGACATATA
1 GCTCGGATGGGACTTATTTCGATTGATTCATCCAGCCACCTTTAAAAGATGGCATCCAACATATT
* *
342267 TGGGGTTTGAATCCCAATATCTATA-CAATAAGGGAAAGTTTTAATCATTTGGGTGTATTGAAAA
66 TGGGG-TCGAATCCCAATATCTATACCAA-AAGGGAAACTTTTAATCATTTGGGTGTATTGAAAA
* *
342331 CTCAGAGAATGTGTCGTGGTGCTAAAAATGG
129 -TTAGAGAATGTGTCATGGTGCTAAAAATGG
* ** * * *
342362 GCTCGGATGGGACTTATTTCGAGTGATTCATTTAGCCACCTTTAAAAGATGACACCCAACAGATT
1 GCTCGGATGGGACTTATTTCGATTGATTCATCCAGCCACCTTTAAAAGATGGCATCCAACATATT
* * *
342427 TGGGGTCGAATCCCAATATCTGTACCAAAAGGGAAACTTTTAATCATTTGAGTGTACTGAAAATT
66 TGGGGTCGAATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTTGGGTGTATTGAAAATT
** * *
342492 GAGAGAATGTGTCACAGCGCTAAAAATGT
131 -AGAGAATGTGTCATGGTGCTAAAAATGG
* * * * *
342521 GCTCGAATGGGACTTCTTTCGATTGATTCATCCAACTATCTTTAAAAGATGGCATCCAACATATT
1 GCTCGGATGGGACTTATTTCGATTGATTCATCCAGCCACCTTTAAAAGATGGCATCCAACATATT
* *
342586 TGGGGTACGAATCCCAATATCTATACCAAAAGGGAAACTTCTAATCATTTGGGTGTATTGAAAGT
66 TGGGGT-CGAATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTTGGGTGTATTGAAAAT
*
342651 CTAGAGACTGTGTCATGGTGCTAAAAA
130 -TAGAGAATGTGTCATGGTGCTAAAAA
342678 AGTGCTTGGA
Statistics
Matches: 269, Mismatches: 43, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
158 1 0.00
159 132 0.49
160 135 0.50
161 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (158 bp):
GCTCGGATGGGACTTATTTCGATTGATTCATCCAGCCACCTTTAAAAGATGGCATCCAACATATT
TGGGGTCGAATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTTGGGTGTATTGAAAATT
AGAGAATGTGTCATGGTGCTAAAAATGG
Found at i:351979 original size:102 final size:101
Alignment explanation
Indices: 351710--352000 Score: 363
Period size: 102 Copynumber: 2.8 Consensus size: 101
351700 TATTAAAGAG
* * **
351710 TTGAAGTCAATTGCAAAAACTTTTTTTTTTAATTTGATGGTATAATTTTTCCCCAAGTCCCTGCA
1 TTGAAGTCAGTTGCAAAAAC---TTTTTTTAATTTGATGGTCTAATTTTT-CCCAAGTCCCTATA
351775 CTC-TTGAAAATTTGAAA-TTAATTTTTTTAAAAGAGAAC
62 CTCTTTGAAAATTTGAAATTTAATTTTTTTAAAAGAGAAC
* * *
351813 TTGAAGCCAGTTGCAAAAACTTTTTTTAATTTGATGGTCTAATTTTCACCCAAGTCTCTATACTC
1 TTGAAGTCAGTTGCAAAAACTTTTTTTAATTTGATGGTCTAATTTT-TCCCAAGTCCCTATACTC
* * * * *
351878 TTTGAAATTTTGAAATTTTA-TTTTTTATATGATAAC
65 TTTGAAAATTTGAAATTTAATTTTTTTAAAAGAGAAC
* * *
351914 TTGAAGTCAGTTGCAAAAACTTTTTTTAAATTTAATGATCTAATTTTGTCCCAAATCCCTATACT
1 TTGAAGTCAGTTGCAAAAACTTTTTTT-AATTTGATGGTCTAATTTT-TCCCAAGTCCCTATACT
351979 CTTTGAAAATTTGAAATTTAAT
64 CTTTGAAAATTTGAAATTTAAT
352001 CCTTCTTTTT
Statistics
Matches: 162, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
100 39 0.24
101 52 0.32
102 53 0.33
103 18 0.11
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (101 bp):
TTGAAGTCAGTTGCAAAAACTTTTTTTAATTTGATGGTCTAATTTTTCCCAAGTCCCTATACTCT
TTGAAAATTTGAAATTTAATTTTTTTAAAAGAGAAC
Found at i:354705 original size:12 final size:12
Alignment explanation
Indices: 354688--354712 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
354678 AAGACACACA
354688 TAATCAATAAAT
1 TAATCAATAAAT
354700 TAATCAATAAAT
1 TAATCAATAAAT
354712 T
1 T
354713 TCATCCAAAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATCAATAAAT
Found at i:366711 original size:2 final size:2
Alignment explanation
Indices: 366700--366734 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
366690 TATATCTGTT
* *
366700 TG TG TA TG TG TG TG TG TG TG TG TA TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
366735 TGAGGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.06, C:0.00, G:0.43, T:0.51
Consensus pattern (2 bp):
TG
Found at i:370098 original size:213 final size:213
Alignment explanation
Indices: 369731--370155 Score: 814
Period size: 213 Copynumber: 2.0 Consensus size: 213
369721 CCCGTACTGT
369731 CATTGTTCGAGTATCGCGGAGTAAAATCATTGCTGCTGCTGCGGCTGCCACTATAATTCAAGTGC
1 CATTGTTCGAGTATCGCGGAGTAAAATCATTGCTGCTGCTGCGGCTGCCACTATAATTCAAGTGC
*
369796 TGCCAACACCTTCCATTTACATTACCTGTTCTCTTGCAGGGAGTACCATTGCAGGTAGGTACTCC
66 TGCCAACACCTTCCATTTACATTACCTGTTCTCTTGCAGGGAATACCATTGCAGGTAGGTACTCC
369861 ACAAATGGGTGTACTACAATTGTTGCGATTACAGATGGAAATCGCCATCCCTGTACGATTTTCAT
131 ACAAATGGGTGTACTACAATTGTTGCGATTACAGATGGAAATCGCCATCCCTGTACGATTTTCAT
369926 AAAAATCTGAAGCTTCAC
196 AAAAATCTGAAGCTTCAC
* *
369944 CATTGTTCGAGTTTCGCGGAGTAAAATCATTGCTGCTGCTGCGGCTGCCACTATATTTCAAGTGC
1 CATTGTTCGAGTATCGCGGAGTAAAATCATTGCTGCTGCTGCGGCTGCCACTATAATTCAAGTGC
370009 TGCCAACACCTTCCATTTACATTACCTGTTCTCTTGCAGGGAATACCATTGCAGGTAGGTACTCC
66 TGCCAACACCTTCCATTTACATTACCTGTTCTCTTGCAGGGAATACCATTGCAGGTAGGTACTCC
*
370074 ACAAATGGGTGTACTACAATTGTTGCGATTATAGATGGAAATCGCCATCCCTGTACGATTTTCAT
131 ACAAATGGGTGTACTACAATTGTTGCGATTACAGATGGAAATCGCCATCCCTGTACGATTTTCAT
370139 AAAAATCTGAAGCTTCA
196 AAAAATCTGAAGCTTCA
370156 TCAGAATATG
Statistics
Matches: 208, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
213 208 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (213 bp):
CATTGTTCGAGTATCGCGGAGTAAAATCATTGCTGCTGCTGCGGCTGCCACTATAATTCAAGTGC
TGCCAACACCTTCCATTTACATTACCTGTTCTCTTGCAGGGAATACCATTGCAGGTAGGTACTCC
ACAAATGGGTGTACTACAATTGTTGCGATTACAGATGGAAATCGCCATCCCTGTACGATTTTCAT
AAAAATCTGAAGCTTCAC
Found at i:376148 original size:24 final size:24
Alignment explanation
Indices: 376116--376163 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
376106 AAACTGATTT
** *
376116 TTTTTCTTTCTCTCTTTCTCTCTG
1 TTTTTCTTTAGCTCTCTCTCTCTG
376140 TTTTTCTTTAGCTCTCTCTCTCTG
1 TTTTTCTTTAGCTCTCTCTCTCTG
376164 CCGAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.29, G:0.06, T:0.62
Consensus pattern (24 bp):
TTTTTCTTTAGCTCTCTCTCTCTG
Found at i:376872 original size:7 final size:7
Alignment explanation
Indices: 376860--376892 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
376850 AAATAAATCC
376860 AAAAAAT
1 AAAAAAT
376867 AAAAAAT
1 AAAAAAT
376874 -AAAAAT
1 AAAAAAT
376880 -AAAAAT
1 AAAAAAT
376886 AAAAAAT
1 AAAAAAT
376893 TAATATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:376877 original size:13 final size:12
Alignment explanation
Indices: 376861--376913 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
376851 AATAAATCCA
376861 AAAAATAAAAAAT
1 AAAAAT-AAAAAT
376874 AAAAATAAAAAT
1 AAAAATAAAAAT
* *
376886 AAAAAATTAATAT
1 -AAAAATAAAAAT
*
376899 GAAAA-AAAAAT
1 AAAAATAAAAAT
376910 AAAA
1 AAAA
376914 TCTAGTTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 7 0.21
12 10 0.30
13 16 0.48
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (12 bp):
AAAAATAAAAAT
Done.