Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015226.1 Kokia drynarioides strain JFW-HI SEQ_130270, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 713267
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:13565 original size:13 final size:13
Alignment explanation
Indices: 13549--13578 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13539 CAGCAATTTA
*
13549 TTCTTTTTTCTTT
1 TTCTTTCTTCTTT
13562 TTCTTTCTTCTTT
1 TTCTTTCTTCTTT
13575 TTCT
1 TTCT
13579 CATGTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTCTTCTTT
Found at i:26895 original size:20 final size:21
Alignment explanation
Indices: 26870--26910 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
26860 GATAGTTGAG
* *
26870 AAGG-TTCTACTGATACAAGT
1 AAGGTTTCTACCGAAACAAGT
26890 AAGGTTTCTACCGAAACAAGT
1 AAGGTTTCTACCGAAACAAGT
26911 CATACAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGGTTTCTACCGAAACAAGT
Found at i:27563 original size:35 final size:36
Alignment explanation
Indices: 27524--27618 Score: 122
Period size: 36 Copynumber: 2.6 Consensus size: 36
27514 TCAATGATCT
* *
27524 CTTCAAGTTTCCCAGTAATTTAGCTCATATGAGC-C
1 CTTCAAGTTTCCCAGTAATTTAACTCATACGAGCTC
*
27559 CTTCAAGTTTCCAAGTAATTTCAACTCATACGAGCTC
1 CTTCAAGTTTCCCAGTAATTT-AACTCATACGAGCTC
*
27596 C-TCAAGATTCCCAGTAAATTTAA
1 CTTCAAGTTTCCCAGT-AATTTAA
27619 GGCATAATTG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
35 20 0.38
36 25 0.48
37 7 0.13
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (36 bp):
CTTCAAGTTTCCCAGTAATTTAACTCATACGAGCTC
Found at i:32887 original size:40 final size:41
Alignment explanation
Indices: 32822--32953 Score: 137
Period size: 40 Copynumber: 3.3 Consensus size: 41
32812 ATCACCGACT
* * * * * * *
32822 AAAGCCTACCAAGTCATAACCTGAATCTTC-TCACCGGCTT
1 AAAGCCTGCTAAGTCATAGCTTGAATCTACATCACTGGCTC
*
32862 AAAGCCTGCTAAG-CAATAGCTTGAAT-TACATCACTAGCTC
1 AAAGCCTGCTAAGTC-ATAGCTTGAATCTACATCACTGGCTC
* *
32902 AAAACCTGCTAAGTCGTAGCTTGAATC-ACATCACTGGCTC
1 AAAGCCTGCTAAGTCATAGCTTGAATCTACATCACTGGCTC
32942 AAAGCCTGCTAA
1 AAAGCCTGCTAA
32954 TCTCTAGTAT
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
39 3 0.04
40 72 0.95
41 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAGCCTGCTAAGTCATAGCTTGAATCTACATCACTGGCTC
Found at i:35394 original size:62 final size:62
Alignment explanation
Indices: 35297--35438 Score: 155
Period size: 62 Copynumber: 2.3 Consensus size: 62
35287 GATTTAGGTT
* * ** * *
35297 TTTAAAAATTTAGGGATTTTTAGGATTTTTAGGGTTG-TGGGTTTTGGGGAA-TTTGATT-TAGG
1 TTTAAAAATTTGGGGATATCGA-GATTTTTAGGGTTGTTAGG-TTTGGGGAATTTTG-TTCAAGG
* *
35359 TTTAAGAAATTTGGGGATATCGAGATTTTTGGGGTTGTTAGGTTTGGGGAATTTTGTTCAAGT
1 TTTAA-AAATTTGGGGATATCGAGATTTTTAGGGTTGTTAGGTTTGGGGAATTTTGTTCAAGG
35422 TTTAAAAATTTGGGGAT
1 TTTAAAAATTTGGGGAT
35439 TTTCGGGACT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
62 41 0.60
63 27 0.40
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.44
Consensus pattern (62 bp):
TTTAAAAATTTGGGGATATCGAGATTTTTAGGGTTGTTAGGTTTGGGGAATTTTGTTCAAGG
Found at i:37017 original size:57 final size:57
Alignment explanation
Indices: 36929--37057 Score: 222
Period size: 57 Copynumber: 2.3 Consensus size: 57
36919 TTTCTAGAAA
* * *
36929 ATATATTTGACATGTTGATAATTTATTGAATCATATTGATTTCAAACTTGGTAATTT
1 ATATATTTGACATGTTGATAATTGATTGAATCATATTAATTTAAAACTTGGTAATTT
*
36986 ATATATTTGACATGTTGATAATTGATTGAATCGTATTAATTTAAAACTTGGTAATTT
1 ATATATTTGACATGTTGATAATTGATTGAATCATATTAATTTAAAACTTGGTAATTT
37043 ATATATTTGACATGT
1 ATATATTTGACATGT
37058 CTGCTGGTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 68 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (57 bp):
ATATATTTGACATGTTGATAATTGATTGAATCATATTAATTTAAAACTTGGTAATTT
Found at i:37728 original size:39 final size:39
Alignment explanation
Indices: 37653--37728 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
37643 TGGTAATAAA
* **
37653 GGTGGTGAGGGTGATGGTGGTGGTGAGGGTTCGGGTTCG
1 GGTGGTGAGGGTGATGGAGGTGGTGAGGGTGAGGGTTCG
*
37692 GGTGTTGAGGGTG-TGGGAGGTGGTGAGGGTGAGGGTT
1 GGTGGTGAGGGTGAT-GGAGGTGGTGAGGGTGAGGGTT
37729 TAGATGATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.09, C:0.03, G:0.61, T:0.28
Consensus pattern (39 bp):
GGTGGTGAGGGTGATGGAGGTGGTGAGGGTGAGGGTTCG
Found at i:37852 original size:63 final size:63
Alignment explanation
Indices: 37774--37985 Score: 217
Period size: 54 Copynumber: 3.7 Consensus size: 63
37764 GGTGGTGAGC
**
37774 GTGAGGGTAAGGGTAAAGGTGCTGTTAGTGAAGGTGTTGAGGGTGTTAAGGGTGAGGGAAGTG
1 GTGAGGGTTCGGGTAAAGGTGCTGTTAGTGAAGGTGTTGAGGGTGTTAAGGGTGAGGGAAGTG
* * *
37837 GTGAGGGTTCGGGTAAGGGTGCTG-T--T-AA-----TGAAGGTGTTAAGGGTGAGGGAGGTG
1 GTGAGGGTTCGGGTAAAGGTGCTGTTAGTGAAGGTGTTGAGGGTGTTAAGGGTGAGGGAAGTG
* * *
37891 GTGAGGGTTCGGGTAAGGGTGTTATTAGTGAAGGTGTTGAGGGTG--AA--G-GA--G-A-TG
1 GTGAGGGTTCGGGTAAAGGTGCTGTTAGTGAAGGTGTTGAGGGTGTTAAGGGTGAGGGAAGTG
*
37945 GTGAGGGTTCGGGTAAAGGTGTTGTTAGTGAAGGTGTTGAG
1 GTGAGGGTTCGGGTAAAGGTGCTGTTAGTGAAGGTGTTGAG
37986 TGTCAAGGTA
Statistics
Matches: 129, Mismatches: 11, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
54 87 0.67
55 1 0.01
56 1 0.01
57 1 0.01
58 4 0.03
59 3 0.02
60 1 0.01
61 2 0.02
62 1 0.01
63 28 0.22
ACGTcount: A:0.22, C:0.02, G:0.49, T:0.27
Consensus pattern (63 bp):
GTGAGGGTTCGGGTAAAGGTGCTGTTAGTGAAGGTGTTGAGGGTGTTAAGGGTGAGGGAAGTG
Found at i:37985 original size:54 final size:54
Alignment explanation
Indices: 37815--37982 Score: 257
Period size: 54 Copynumber: 3.1 Consensus size: 54
37805 AGGTGTTGAG
* *
37815 GGTGTTAAGGGTGAGGGA-AGTGGTGAGGGTTCGGGTAAGGGTGCTGTTAATGAA
1 GGTGTTAAGGGTGAGGGAGA-TGGTGAGGGTTCGGGTAAGGGTGTTGTTAGTGAA
* *
37869 GGTGTTAAGGGTGAGGGAGGTGGTGAGGGTTCGGGTAAGGGTGTTATTAGTGAA
1 GGTGTTAAGGGTGAGGGAGATGGTGAGGGTTCGGGTAAGGGTGTTGTTAGTGAA
* * *
37923 GGTGTTGAGGGTGAAGGAGATGGTGAGGGTTCGGGTAAAGGTGTTGTTAGTGAA
1 GGTGTTAAGGGTGAGGGAGATGGTGAGGGTTCGGGTAAGGGTGTTGTTAGTGAA
37977 GGTGTT
1 GGTGTT
37983 GAGTGTCAAG
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.21, C:0.02, G:0.49, T:0.28
Consensus pattern (54 bp):
GGTGTTAAGGGTGAGGGAGATGGTGAGGGTTCGGGTAAGGGTGTTGTTAGTGAA
Found at i:40414 original size:36 final size:35
Alignment explanation
Indices: 40363--40449 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 35
40353 TCTAGTGTTT
40363 TGTTTTTAATTTAAAATTGACAGCAAACATACTTA
1 TGTTTTTAATTTAAAATTGACAGCAAACATACTTA
* * *
40398 TGTTTTTAAATTTAAAATTGATAGCATACTTACTTA
1 TGTTTTT-AATTTAAAATTGACAGCAAACATACTTA
40434 TGTTTTTTAATTTAAA
1 TG-TTTTTAATTTAAA
40450 TTGTAGGGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
35 7 0.15
36 35 0.74
37 5 0.11
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (35 bp):
TGTTTTTAATTTAAAATTGACAGCAAACATACTTA
Found at i:41646 original size:160 final size:160
Alignment explanation
Indices: 41378--41754 Score: 612
Period size: 160 Copynumber: 2.4 Consensus size: 160
41368 CAAGATCTTG
41378 ACACAACGGGAACACAGGTATATTGTAAACACTTTCTCATTGTCAATTCCAAATTATAATAATCT
1 ACACAACGGGAACACAGGTATATTGTAAACACTTTCTCATTGTCAATTCCAAATTATAATAATCT
* * *
41443 AATTTCGGTTTTATTTTTTGTGTCTTAGTTTGGTACGAGTACGAGAACTACAACCCAAAAAAAGA
66 AATTTCGGTTTTATTTTTTGTGTCTTAATCTGGTACAAGTACGAGAACTACAACCCAAAAAAAGA
*
41508 ACGACAAAACACCACCATGCATTTAGCCTA
131 ACGACAAAACACCACCATGCATTCAGCCTA
* *
41538 ACATAACGGGAACACAGGTATATTGTAAACACTTTCTCATTGTCAATTCCAAATTATACTAATCT
1 ACACAACGGGAACACAGGTATATTGTAAACACTTTCTCATTGTCAATTCCAAATTATAATAATCT
* *
41603 AATTTCTGTTTTGA-TTTTTGTGTCTTAATCTGGTACAAGTACGAGAACTACAACCCAAAGAAAG
66 AATTTCGGTTTT-ATTTTTTGTGTCTTAATCTGGTACAAGTACGAGAACTACAACCCAAAAAAAG
*
41667 AACGACAAAACACCACCATGCATTCATCCTA
130 AACGACAAAACACCACCATGCATTCAGCCTA
** * * *
41698 ACACAACTAGATCACAGGTATCTCGTAAACACTTTCTCATTGTCAATTCCAAATTAT
1 ACACAACGGGAACACAGGTATATTGTAAACACTTTCTCATTGTCAATTCCAAATTAT
41755 TTAAATTTAA
Statistics
Matches: 201, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
160 200 1.00
161 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (160 bp):
ACACAACGGGAACACAGGTATATTGTAAACACTTTCTCATTGTCAATTCCAAATTATAATAATCT
AATTTCGGTTTTATTTTTTGTGTCTTAATCTGGTACAAGTACGAGAACTACAACCCAAAAAAAGA
ACGACAAAACACCACCATGCATTCAGCCTA
Found at i:43324 original size:22 final size:22
Alignment explanation
Indices: 43299--43343 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
43289 TACTCTCGAT
*
43299 AAAACAGCAACATCGATTAAAC
1 AAAACAACAACATCGATTAAAC
43321 AAAACAACAACATCGATTAAAC
1 AAAACAACAACATCGATTAAAC
43343 A
1 A
43344 TTATTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.22, G:0.07, T:0.13
Consensus pattern (22 bp):
AAAACAACAACATCGATTAAAC
Found at i:44578 original size:61 final size:62
Alignment explanation
Indices: 44491--44657 Score: 212
Period size: 61 Copynumber: 2.6 Consensus size: 62
44481 CTAAGGCCCG
* * * *
44491 AAAATACCCAAATTTTTAAACTTAAACCAATTTCCCCAAACCCAACAACCC-CAAAATCCT-
1 AAAATCCCCAAATTTTTAAACCTAAACCAAATTCCCAAAACCCAACAACCCTCAAAATCCTA
* *
44551 AAAATCCCCAAATTTCTTAAACCTAAACCAAATTCCCAAAACCCAACAACCCTGAAAATTCTA
1 AAAATCCCCAAATTT-TTAAACCTAAACCAAATTCCCAAAACCCAACAACCCTCAAAATCCTA
*
44614 AAAATCCCTAAATTTTTAAAACCTAAATCCCTAAATTCCCAAAA
1 AAAATCCCCAAATTTTT-AAACCTAAA--CC-AAATTCCCAAAA
44658 ATTTTGAAAT
Statistics
Matches: 93, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
60 14 0.15
61 33 0.35
62 9 0.10
63 23 0.25
65 2 0.02
66 12 0.13
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.23
Consensus pattern (62 bp):
AAAATCCCCAAATTTTTAAACCTAAACCAAATTCCCAAAACCCAACAACCCTCAAAATCCTA
Found at i:44703 original size:31 final size:30
Alignment explanation
Indices: 44615--44717 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 30
44605 AAAATTCTAA
* *
44615 AAATCCCTAAATTTTTAAAACCTAAATCCC
1 AAATCCCCAAATTTTTAAAACCTAAAACCC
* * * *
44645 TAAATTCCCAAAAATTTTGAAATCTAAAACCC
1 -AAA-TCCCCAAATTTTTAAAACCTAAAACCC
* * *
44677 AAATACCCCATATTTTTTAAACCT-AAACCA
1 AAAT-CCCCAAATTTTTAAAACCTAAAACCC
44707 AAATCCCCAAA
1 AAATCCCCAAA
44718 CCTAATAACC
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
29 6 0.10
30 10 0.17
31 20 0.34
32 22 0.38
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.27
Consensus pattern (30 bp):
AAATCCCCAAATTTTTAAAACCTAAAACCC
Found at i:44939 original size:17 final size:18
Alignment explanation
Indices: 44914--44947 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44904 AAATATTTTA
*
44914 TTATTTTTTAA-TTTAAT
1 TTATGTTTTAACTTTAAT
44931 TTATGTTTTAACTTTAA
1 TTATGTTTTAACTTTAA
44948 ATTTTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
TTATGTTTTAACTTTAAT
Found at i:51941 original size:19 final size:19
Alignment explanation
Indices: 51917--51959 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
51907 AAACATGAAT
51917 TAAATATAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
51936 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
51955 TAAAT
1 TAAAT
51960 CCTAAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:56812 original size:27 final size:27
Alignment explanation
Indices: 56774--56828 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
56764 TAATACATTT
56774 AAGATTAATGGTGTTACTGATGATGCC
1 AAGATTAATGGTGTTACTGATGATGCC
56801 AAGATTAATGGTGTTACTGATGATGCC
1 AAGATTAATGGTGTTACTGATGATGCC
56828 A
1 A
56829 TACATTTGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (27 bp):
AAGATTAATGGTGTTACTGATGATGCC
Found at i:59261 original size:20 final size:20
Alignment explanation
Indices: 59210--59264 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
59200 TTTATTACTT
* *
59210 AAAAAATCGTAAAAAATTAG
1 AAAAAATAGAAAAAAATTAG
*
59230 AAAAAAAAGAAAAAAATTCA-
1 AAAAAATAGAAAAAAATT-AG
*
59250 AAAAAATTGAAAAAA
1 AAAAAATAGAAAAAA
59265 GGTACCACAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAAAATAGAAAAAAATTAG
Found at i:61370 original size:25 final size:24
Alignment explanation
Indices: 61275--61363 Score: 92
Period size: 25 Copynumber: 3.7 Consensus size: 24
61265 CCGAAGTACT
* **
61275 TAACAGAGGGCACATAAGTGCTGGG
1 TAACAGAGGGCACACAAGTGCT-AA
*
61300 TAACAGAGGGCACATAAAGTGCTAA
1 TAACAGAGGGCACA-CAAGTGCTAA
*
61325 T--CAAAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACAC-AAGTGCTAA
61348 TAACAGAGGGCACACA
1 TAACAGAGGGCACACA
61364 CATTGCTGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
23 20 0.37
24 1 0.02
25 26 0.48
26 7 0.13
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.13
Consensus pattern (24 bp):
TAACAGAGGGCACACAAGTGCTAA
Found at i:61381 original size:48 final size:47
Alignment explanation
Indices: 61275--61382 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 47
61265 CCGAAGTACT
* ** *
61275 TAACAGAGGGCACATAAGTGCTGGGTAACAGAGGGCACATAAAGTGC
1 TAACAGAGGGCACAGAAGTGCTGAATAACAGAGGGCACACAAAGTGC
* * *
61322 TAATCAAAGGGCACACGAAGTGCT-AATAACAGAGGGCACACACATTGC
1 TAA-CAGAGGGCACA-GAAGTGCTGAATAACAGAGGGCACACAAAGTGC
61370 TGAACAGAGGGCA
1 T-AACAGAGGGCA
61383 TGAAACGTGC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
47 3 0.06
48 38 0.76
49 9 0.18
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (47 bp):
TAACAGAGGGCACAGAAGTGCTGAATAACAGAGGGCACACAAAGTGC
Found at i:68514 original size:25 final size:25
Alignment explanation
Indices: 68421--68550 Score: 96
Period size: 23 Copynumber: 5.4 Consensus size: 25
68411 CCGAAGTACT
* **
68421 TAACAGAGGGCACA-TAAGTGCTGGG
1 TAACAGAGGGCACACAAAGTGCT-AA
* *
68446 TAACAGAAGGCATACAAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
* *
68471 T--CAGAGGGTAGACAAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
*
68494 TAACAGAGGGCACACATAGTGCT--
1 TAACAGAGGGCACACAAAGTGCTAA
* *
68517 GAACAGAGGGCACGA-AACGTGCT-A
1 TAACAGAGGGCAC-ACAAAGTGCTAA
68541 -AACAGAGGGC
1 TAACAGAGGGC
68551 GCGCTAGTGT
Statistics
Matches: 86, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
23 48 0.56
24 1 0.01
25 30 0.35
26 7 0.08
ACGTcount: A:0.38, C:0.18, G:0.30, T:0.14
Consensus pattern (25 bp):
TAACAGAGGGCACACAAAGTGCTAA
Found at i:68539 original size:48 final size:47
Alignment explanation
Indices: 68446--68550 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 47
68436 AAGTGCTGGG
* * *
68446 TAACAGAAGGCATACAAAGTGCTAATCAGAGGGTAGACAAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAATCAGAGGGCAGACAAAGTGCT-A
* *
68494 TAACAGAGGGCACACATAGTGCTGAA-CAGAGGGCACGA-AACGTGCTA
1 TAACAGAGGGCACACAAAGTGCT-AATCAGAGGGCA-GACAAAGTGCTA
68541 -AACAGAGGGC
1 TAACAGAGGGC
68551 GCGCTAGTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
46 10 0.20
47 1 0.02
48 35 0.70
49 4 0.08
ACGTcount: A:0.40, C:0.18, G:0.29, T:0.13
Consensus pattern (47 bp):
TAACAGAGGGCACACAAAGTGCTAATCAGAGGGCAGACAAAGTGCTA
Found at i:71086 original size:3 final size:3
Alignment explanation
Indices: 71080--71126 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
71070 TTTTTTTTCT
* *
71080 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA GTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
71127 TTTGTGTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:73564 original size:47 final size:47
Alignment explanation
Indices: 73493--73615 Score: 151
Period size: 47 Copynumber: 2.6 Consensus size: 47
73483 TAATGTGACA
* *
73493 TTATTCACAA-TTTGATTATGTGGCATTTTATTTGCAAATGTGGTGGC
1 TTATCCACAATTTTGATTAT-TGGCAATTTATTTGCAAATGTGGTGGC
* * * * *
73540 TTATCCACGATTTTGGTTATTGGCAATATATTTGCAATTTTGGTGGC
1 TTATCCACAATTTTGATTATTGGCAATTTATTTGCAAATGTGGTGGC
*
73587 TTGTCCACAATTTTGATTA-TGGCAATTTA
1 TTATCCACAATTTTGATTATTGGCAATTTA
73616 CCTACGTTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 9 0.14
47 47 0.73
48 8 0.12
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.45
Consensus pattern (47 bp):
TTATCCACAATTTTGATTATTGGCAATTTATTTGCAAATGTGGTGGC
Found at i:75592 original size:13 final size:13
Alignment explanation
Indices: 75574--75598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75564 ACGTGTGAGG
75574 AAAGATTATTTAA
1 AAAGATTATTTAA
75587 AAAGATTATTTA
1 AAAGATTATTTA
75599 TTGTTTTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
AAAGATTATTTAA
Found at i:76181 original size:21 final size:20
Alignment explanation
Indices: 76157--76212 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
76147 AATATAAAAT
*
76157 AAATAAAATAAAATAAATAAG
1 AAATAAAATAAAA-AAATAAA
* *
76178 AAATAACATGAACAAAATAAA
1 AAATAAAAT-AAAAAAATAAA
76199 AAATAAAATAAAAA
1 AAATAAAATAAAAA
76213 TAATTATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 4 0.14
21 22 0.76
22 3 0.10
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.16
Consensus pattern (20 bp):
AAATAAAATAAAAAAATAAA
Found at i:76477 original size:11 final size:10
Alignment explanation
Indices: 76453--76524 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 10
76443 AATATATAAG
76453 TAAATAAAAA
1 TAAATAAAAA
76463 TAAATAAAGAA
1 TAAATAAA-AA
*
76474 TAAATAAATA
1 TAAATAAAAA
*
76484 -AAATAAACAC
1 TAAATAAA-AA
76494 TAATATAAACAAA
1 TAA-AT-AA-AAA
*
76507 TAAATACAAA
1 TAAATAAAAA
76517 T-AATAAAA
1 TAAATAAAA
76525 GTAACACAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
9 13 0.26
10 13 0.26
11 13 0.26
12 4 0.08
13 6 0.12
14 1 0.02
ACGTcount: A:0.72, C:0.06, G:0.01, T:0.21
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:76518 original size:20 final size:21
Alignment explanation
Indices: 76484--76523 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
76474 TAAATAAATA
*
76484 AAATAAACACTAAT-ATAAAC
1 AAATAAACACAAATAATAAAC
*
76504 AAATAAATACAAATAATAAA
1 AAATAAACACAAATAATAAA
76524 AGTAACACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATAAACACAAATAATAAAC
Found at i:79290 original size:20 final size:20
Alignment explanation
Indices: 79267--79304 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
79257 ATTACAAACA
79267 TTGGTAAAAAATAGCAAATG
1 TTGGTAAAAAATAGCAAATG
79287 TTGGTAAAAAATAGCAAA
1 TTGGTAAAAAATAGCAAA
79305 CATCAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.18, T:0.24
Consensus pattern (20 bp):
TTGGTAAAAAATAGCAAATG
Found at i:86988 original size:30 final size:30
Alignment explanation
Indices: 86954--87016 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
86944 GATCTGAAAG
86954 AAAGGACACCTGCACTTGGCAATGGTTGAT
1 AAAGGACACCTGCACTTGGCAATGGTTGAT
*
86984 AAAGGACACCTGCACTTGGTAATGGTTGAT
1 AAAGGACACCTGCACTTGGCAATGGTTGAT
87014 AAA
1 AAA
87017 TACTGATGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (30 bp):
AAAGGACACCTGCACTTGGCAATGGTTGAT
Found at i:94587 original size:78 final size:78
Alignment explanation
Indices: 94494--94649 Score: 285
Period size: 78 Copynumber: 2.0 Consensus size: 78
94484 TCCAAAGTAA
*
94494 GGTTTGGTTCCATTTCATAAACTGCCGTTTAATGCCTTCTACCCATAGTAACACAATTACCTTGG
1 GGTTTGGTTCCATTTCATAAACTGCCGTTTAATGCCTTCTACCCATAGCAACACAATTACCTTGG
94559 ATCGAATGTGTTT
66 ATCGAATGTGTTT
* *
94572 GGTTTGGTTCCATTTCATAAACTGTCGTTTAATGCCTTCTACCCGTAGCAACACAATTACCTTGG
1 GGTTTGGTTCCATTTCATAAACTGCCGTTTAATGCCTTCTACCCATAGCAACACAATTACCTTGG
94637 ATCGAATGTGTTT
66 ATCGAATGTGTTT
94650 AACTCATTCG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (78 bp):
GGTTTGGTTCCATTTCATAAACTGCCGTTTAATGCCTTCTACCCATAGCAACACAATTACCTTGG
ATCGAATGTGTTT
Found at i:104319 original size:27 final size:27
Alignment explanation
Indices: 104281--104376 Score: 138
Period size: 27 Copynumber: 3.5 Consensus size: 27
104271 AGGAGTAATC
* *
104281 GATTCTAGCTCGAAAGAGTGTTATTTT
1 GATTCTGGCTCGAAAGAGAGTTATTTT
* *
104308 GATTCTGGCTCGAAACAGCGTTATTTT
1 GATTCTGGCTCGAAAGAGAGTTATTTT
*
104335 GATTCTGGCTCGAAAGAGAGTTATTCT
1 GATTCTGGCTCGAAAGAGAGTTATTTT
104362 GATTCTGAGCTCGAA
1 GATTCTG-GCTCGAA
104377 TGAGCTTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
27 55 0.89
28 7 0.11
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (27 bp):
GATTCTGGCTCGAAAGAGAGTTATTTT
Found at i:104390 original size:28 final size:27
Alignment explanation
Indices: 104307--104413 Score: 87
Period size: 27 Copynumber: 4.0 Consensus size: 27
104297 AGTGTTATTT
** * *
104307 TGATTCTGGCTCGAAACAGCGTT-ATTT
1 TGATTCTGGCTCGAATGAGC-TTAAATC
* * *
104334 TGATTCTGGCTCGAAAGAGAGTT-ATTC
1 TGATTCTGGCTCGAATGAG-CTTAAATC
104361 TGATTCTGAGCTCGAATGAGCTTAAATC
1 TGATTCTG-GCTCGAATGAGCTTAAATC
104389 TG-TTCTGGGCTCGAATGAGC-TAAAT
1 TGATTCT-GGCTCGAATGAGCTTAAAT
104414 TCTATTCCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.07
27 49 0.70
28 16 0.23
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (27 bp):
TGATTCTGGCTCGAATGAGCTTAAATC
Found at i:104394 original size:27 final size:27
Alignment explanation
Indices: 104359--104439 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
104349 AGAGAGTTAT
104359 TCTGATTCTGAGCTCGAATGAGCTTAAA
1 TCTGATTCTGAGCTCGAATGAGC-TAAA
*
104387 TCTG-TTCTGGGCTCGAATGAGCTAAA
1 TCTGATTCTGAGCTCGAATGAGCTAAA
** * *
104413 TTCT-ATTCCAAGCTTGTATGAGCTAAA
1 -TCTGATTCTGAGCTCGAATGAGCTAAA
104440 AACTATTACG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.09
27 37 0.82
28 4 0.09
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (27 bp):
TCTGATTCTGAGCTCGAATGAGCTAAA
Found at i:104395 original size:54 final size:54
Alignment explanation
Indices: 104276--104403 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 54
104266 GCTTTAGGAG
* * *
104276 TAATC-GATTCTAGCTCGAAAGAGTGTTATTTTGATTCTGGCTCGAAACAGCGT
1 TAATCTGATTCTGGCTCGAAAGAGAGTTATTCTGATTCTGGCTCGAAACAGCGT
* * **
104329 TATTTTGATTCTGGCTCGAAAGAGAGTTATTCTGATTCTGAGCTCGAATGAGC-T
1 TAATCTGATTCTGGCTCGAAAGAGAGTTATTCTGATTCTG-GCTCGAAACAGCGT
104383 TAAATCTG-TTCTGGGCTCGAA
1 T-AATCTGATTCT-GGCTCGAA
104404 TGAGCTAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
53 3 0.05
54 37 0.60
55 22 0.35
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (54 bp):
TAATCTGATTCTGGCTCGAAAGAGAGTTATTCTGATTCTGGCTCGAAACAGCGT
Found at i:117467 original size:15 final size:14
Alignment explanation
Indices: 117424--117475 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 14
117414 GGAAAACCCT
117424 GAGGAAGAGA-AAG
1 GAGGAAGAGAGAAG
117437 GAGCTGAAGAGGAGAAG
1 GAG--GAAGA-GAGAAG
117454 GAGGAAGAGAAGAAG
1 GAGGAAGAG-AGAAG
*
117469 GATGAAG
1 GAGGAAG
117476 GGATGTAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 3 0.09
14 1 0.03
15 21 0.64
16 2 0.06
17 6 0.18
ACGTcount: A:0.48, C:0.02, G:0.46, T:0.04
Consensus pattern (14 bp):
GAGGAAGAGAGAAG
Found at i:117886 original size:17 final size:17
Alignment explanation
Indices: 117861--117930 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
117851 ATGCATCTCA
117861 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
* *
117878 TTTAGTTGTCGTTGCAT
1 TTTAATTGTCATTGCAT
* *
117895 TTTACTTGTTAGTT-CAT
1 TTTAATTGTCA-TTGCAT
** *
117912 TTGCATTGTCGTTGCAT
1 TTTAATTGTCATTGCAT
117929 TT
1 TT
117931 CCATTCTTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
16 2 0.05
17 37 0.90
18 2 0.05
ACGTcount: A:0.16, C:0.13, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:118528 original size:15 final size:15
Alignment explanation
Indices: 118496--118540 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
118486 AAAAGGGAAG
**
118496 AAGAAAAAGAAAGCA
1 AAGAAAAAGAAAAAA
118511 AAGAAAAAGAAAAAA
1 AAGAAAAAGAAAAAA
*
118526 AAG-AGAAGAAAAAA
1 AAGAAAAAGAAAAAA
118540 A
1 A
118541 TATATATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAAA
Found at i:118537 original size:14 final size:13
Alignment explanation
Indices: 118482--118540 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
118472 AATCACATAT
*
118482 AAAAAAAAGGGAAG
1 AAAAAAAA-GAAAG
*
118496 AAGAAAAAGAAAG
1 AAAAAAAAGAAAG
* *
118509 -CAAAGAA-AAAG
1 AAAAAAAAGAAAG
118520 AAAAAAAAGAGAAG
1 AAAAAAAAGA-AAG
118534 AAAAAAA
1 AAAAAAA
118541 TATATATTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 4 0.11
12 9 0.26
13 5 0.14
14 17 0.49
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:118539 original size:21 final size:21
Alignment explanation
Indices: 118496--118538 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
118486 AAAAGGGAAG
118496 AAGAAAAAGAAAGCAAAGAAA
1 AAGAAAAAGAAAGCAAAGAAA
118517 AAGAAAAA-AAAG-AGAAGAAA
1 AAGAAAAAGAAAGCA-AAGAAA
118537 AA
1 AA
118539 AATATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.05
20 12 0.57
21 8 0.38
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (21 bp):
AAGAAAAAGAAAGCAAAGAAA
Found at i:133816 original size:15 final size:14
Alignment explanation
Indices: 133784--133822 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
133774 ATATTCTTTA
133784 TTTTCTT-T-TTCC
1 TTTTCTTCTCTTCC
133796 TTTTCTTCTCTTCC
1 TTTTCTTCTCTTCC
133810 TTCTTCTTCTCTT
1 TT-TTCTTCTCTT
133823 TTCTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.29
13 1 0.04
14 6 0.25
15 10 0.42
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTCTCTTCC
Found at i:144768 original size:12 final size:12
Alignment explanation
Indices: 144751--144791 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
144741 TAGGTTCTTT
144751 TTCTTCCTTCTC
1 TTCTTCCTTCTC
144763 TTCTTCCTT-TCC
1 TTCTTCCTTCT-C
144775 TTCTT-CTTCTTC
1 TTCTTCCTTC-TC
144787 TTCTT
1 TTCTT
144792 AAACTTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.15
12 21 0.81
13 1 0.04
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTTCCTTCTC
Found at i:158006 original size:20 final size:20
Alignment explanation
Indices: 157983--158024 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
157973 AGAAACATAT
157983 TTACATGATTTGAGTGATAA
1 TTACATGATTTGAGTGATAA
158003 TTACATGATTTGAGTGATAA
1 TTACATGATTTGAGTGATAA
158023 TT
1 TT
158025 TCGATCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (20 bp):
TTACATGATTTGAGTGATAA
Found at i:164374 original size:28 final size:28
Alignment explanation
Indices: 164308--164374 Score: 100
Period size: 27 Copynumber: 2.4 Consensus size: 28
164298 ATCGACTCTA
*
164308 GCTCGAAAGAGCGTTATTCTGATTCT-G
1 GCTCGAAAGAGCGTTATTTTGATTCTGG
*
164335 GCTCAAAAGAGCGTTATTTTGATTCTGG
1 GCTCGAAAGAGCGTTATTTTGATTCTGG
*
164363 GCTCGAATGAGC
1 GCTCGAAAGAGC
164375 TAAAATTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 24 0.69
28 11 0.31
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (28 bp):
GCTCGAAAGAGCGTTATTTTGATTCTGG
Found at i:164387 original size:27 final size:28
Alignment explanation
Indices: 164352--164405 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
164342 AGAGCGTTAT
164352 TTTGATTCTGGGCTCGAATGAGCTAAAA
1 TTTGATTCTGGGCTCGAATGAGCTAAAA
*
164380 TTTG-TTCTGGGCTCGTATGAGCTAAA
1 TTTGATTCTGGGCTCGAATGAGCTAAA
164406 CACTATTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (28 bp):
TTTGATTCTGGGCTCGAATGAGCTAAAA
Found at i:168617 original size:21 final size:21
Alignment explanation
Indices: 168576--168618 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
168566 TAAATAAAAT
* *
168576 AAATAAGAAATAACACGAACA
1 AAATAAAAAATAACAAGAACA
*
168597 AAATAAAAAATAACAATAACA
1 AAATAAAAAATAACAAGAACA
168618 A
1 A
168619 TAATTATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.72, C:0.12, G:0.05, T:0.12
Consensus pattern (21 bp):
AAATAAAAAATAACAAGAACA
Found at i:168869 original size:14 final size:14
Alignment explanation
Indices: 168816--168923 Score: 53
Period size: 14 Copynumber: 7.5 Consensus size: 14
168806 AAAAGGCAAA
168816 AAATGAAATAAAAAT
1 AAAT-AAATAAAAAT
* *
168831 -CATAAAATAACAAT
1 AAAT-AAATAAAAAT
* *
168845 ATATAAGTAAATAA-
1 AAATAAATAAA-AAT
168859 AAATAAATAAACAAT
1 AAATAAATAAA-AAT
* *
168874 AAATAAATTAAATT
1 AAATAAATAAAAAT
*
168888 AAATACTAATATAAACT
1 AAATA--AATA-AAAAT
*
168905 -AATAAATACAAAT
1 AAATAAATAAAAAT
168918 -AATAAA
1 AAATAAA
168924 AGTAACAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
13 9 0.12
14 38 0.53
15 14 0.19
16 7 0.10
17 4 0.06
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.25
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:168876 original size:11 final size:10
Alignment explanation
Indices: 168852--168924 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 10
168842 AATATATAAG
168852 TAAATAAAAA
1 TAAATAAAAA
168862 TAAATAAACAA
1 TAAATAAA-AA
*
168873 TAAAT-AAAT
1 TAAATAAAAA
*
168882 TAAATTAAATAC
1 TAAA-TAAA-AA
168894 TAATATAAACTAA
1 TAA-ATAAA--AA
*
168907 TAAATACAAA
1 TAAATAAAAA
168917 T-AATAAAA
1 TAAATAAAA
168925 GTAACAGGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
9 11 0.21
10 14 0.27
11 9 0.17
12 12 0.23
13 6 0.12
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:173426 original size:15 final size:15
Alignment explanation
Indices: 173408--173445 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
173398 AGTAAGTTAC
173408 TGCATGAATAGTTTG
1 TGCATGAATAGTTTG
173423 TGCATGAATAGTTTG
1 TGCATGAATAGTTTG
173438 TGCATGAA
1 TGCATGAA
173446 GTTAAAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (15 bp):
TGCATGAATAGTTTG
Found at i:173903 original size:28 final size:28
Alignment explanation
Indices: 173837--173932 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 28
173827 CGAAAAGAGA
* * * * *
173837 GCCTTTGTGGCTACATCTATTTTAGGGT
1 GCCTTTGTGGCTACCTTTGTTTAAGGAT
* *
173865 GCATTTATGGCTACCTTTGTTTAAGGAT
1 GCCTTTGTGGCTACCTTTGTTTAAGGAT
*
173893 GCCTTTGTGGCTATCTTTGTTTAAGGAT
1 GCCTTTGTGGCTACCTTTGTTTAAGGAT
*
173921 GCCTATGTGGCT
1 GCCTTTGTGGCT
173933 TTCTATTATT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.43
Consensus pattern (28 bp):
GCCTTTGTGGCTACCTTTGTTTAAGGAT
Found at i:173953 original size:29 final size:28
Alignment explanation
Indices: 173872--173953 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 28
173862 GGTGCATTTA
* * * * *
173872 TGGCTACCTTTGTTTAAGGATGCCTTTG
1 TGGCTATCTTTATTCAAAGATGCCTATG
* * *
173900 TGGCTATCTTTGTTTAAGGATGCCTATG
1 TGGCTATCTTTATTCAAAGATGCCTATG
*
173928 TGGCTTTCTATTATTCAAAGATGCCT
1 TGGCTATCT-TTATTCAAAGATGCCT
173954 CTATGACTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 34 0.72
29 13 0.28
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (28 bp):
TGGCTATCTTTATTCAAAGATGCCTATG
Found at i:177739 original size:16 final size:16
Alignment explanation
Indices: 177699--177741 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
177689 TTAGGGAAAA
177699 AATAAAAAATTTTGAG
1 AATAAAAAATTTTGAG
**
177715 AATGTAAAATTTTGAG
1 AATAAAAAATTTTGAG
*
177731 AGAAAAAAAAT
1 A-ATAAAAAAT
177742 AAAAACAGTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (16 bp):
AATAAAAAATTTTGAG
Found at i:177776 original size:31 final size:31
Alignment explanation
Indices: 177718--177777 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
177708 TTTTGAGAAT
*
177718 GTAAAATTTTGAGAGAAAAAAAATAAAAACA
1 GTAAAATTTTGAAAGAAAAAAAATAAAAACA
* * *
177749 GTAAAATTTTGAAAGGAAAATATTAAAAA
1 GTAAAATTTTGAAAGAAAAAAAATAAAAA
177778 AAATTGAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (31 bp):
GTAAAATTTTGAAAGAAAAAAAATAAAAACA
Found at i:181138 original size:18 final size:18
Alignment explanation
Indices: 181115--181157 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
181105 GAATATGTTT
181115 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
181133 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
181151 TTAATTA
1 TTAATTA
181158 CATTTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:183406 original size:27 final size:26
Alignment explanation
Indices: 183376--183448 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
183366 TTAAGTTTAA
183376 GTATCAAATTAAAAAAAATAAATTCAG
1 GTATCAAATTAAAAAAAA-AAATTCAG
** * *
183403 GTATCAAATTGAATTAAAAAAGTTTAG
1 GTATCAAATT-AAAAAAAAAAATTCAG
* *
183430 GTATTAAATTAATAAAAAA
1 GTATCAAATTAAAAAAAAA
183449 GTTCAAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
26 8 0.21
27 25 0.64
28 6 0.15
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.30
Consensus pattern (26 bp):
GTATCAAATTAAAAAAAAAAATTCAG
Found at i:183483 original size:27 final size:27
Alignment explanation
Indices: 183330--183497 Score: 71
Period size: 27 Copynumber: 5.9 Consensus size: 27
183320 GATTTGAATT
183330 TAAAAA-AAAGTTTAGATACTAAATTAAA
1 TAAAAATAAA-TTTAGATA-TAAATTAAA
* *
183358 CAAAAGTATTAAGTTTA-AGTATCAAATTAAA
1 TAAAA--A-TAAATTTAGA-TAT-AAATTAAA
* * *
183389 -AAAAATAAATTCAGGTATCAAATTGAA
1 TAAAAATAAATTTAGATAT-AAATTAAA
* * *
183416 TTAAAA-AAGTTTAGGTATTAAATT-AA
1 TAAAAATAAATTTAGATA-TAAATTAAA
183442 TAAAAAAGTTCAAATTTAGATACTAAATTAAA
1 T-AAAAA--T-AAATTTAGATA-TAAATTAAA
*
183474 TAAAAA-AAA-TTAAATATCAAATTA
1 TAAAAATAAATTTAGATAT-AAATTA
183498 GAAAAAGTGT
Statistics
Matches: 110, Mismatches: 14, Indels: 34
0.70 0.09 0.22
Matches are distributed among these distances:
25 1 0.01
26 15 0.14
27 38 0.35
28 10 0.09
30 7 0.06
31 34 0.31
32 5 0.05
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.31
Consensus pattern (27 bp):
TAAAAATAAATTTAGATATAAATTAAA
Found at i:184815 original size:17 final size:16
Alignment explanation
Indices: 184795--184833 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
184785 ACAAAAGAAT
*
184795 TTAAACTTAAAAAATAA
1 TTAAAATTAAAAAA-AA
184812 TTAAAATTAAAAAAAA
1 TTAAAATTAAAAAAAA
184828 TTAAAA
1 TTAAAA
184834 CCCGTATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TTAAAATTAAAAAAAA
Found at i:187204 original size:158 final size:160
Alignment explanation
Indices: 186793--187217 Score: 425
Period size: 165 Copynumber: 2.6 Consensus size: 160
186783 ATTTTTCGAA
* *
186793 TTCTAGTTCTCATACTCATACCAAACT--GAAAACAAAAATTAGAACCCCAAATTAGATTTAAAT
1 TTCTAGTTCTCATACTCGTA-CAGACTAAGAAAA-AAAAATTAGAA-CCCAAATTAGATTTAAAT
* * **** * *
186856 AATTTGGAATTGACATTAAAAAATGTTTACGATATACCTGTGGTCCATTTGTGTTAGGCTGAATG
63 ATTTTGGAATTGACATTAAAAAGTGTTTACGATATACCTACAATCCAGTTGTATTAGGCTGAATG
* * *
186921 CATGATGTTCTATTGTTATTTTTTTTTTTTGGC
128 CATGATGTTCTATTGTTATGTTATTTTTTGGGC
* * * * * *
186954 TTCTAGTTCCCGTACTCGTACTAGACTAAGATAAAAAAAAATCAAAACCTCAAATTAGGTTAAAA
1 TTCTAGTTCTCATACTCGTAC-AGACTAAG--AAAAAAAAATTAGAACC-CAAATTAGATTTAAA
* * *
187019 TGCTTTT-GAATTGACATTAAAATAGTGTATACGATATACTTACAATCCAGTTGTATTAGGCTGA
62 T-ATTTTGGAATTGACATTAAAA-AGTGTTTACGATATACCTACAATCCAGTTGTATTAGGCTGA
* *
187083 ATGCGTGGTG-T-TA-TG-T-TGTTATTTTTTGGGC
125 ATGCATGATGTTCTATTGTTATGTTATTTTTTGGGC
* * **
187114 TTCTAGTTCTCATACTTGTATCAGACTAAGACAAAAAAAATTAGAACCAAAATTAGATTTTTATA
1 TTCTAGTTCTCATACTCGTA-CAGACTAAGA-AAAAAAAATTAGAACCCAAATTAGATTTAAATA
*
187179 TTTTGGAATTGACAATGAAAAAGTGTTTACGATATACCT
64 TTTTGGAATTGAC-ATTAAAAAGTGTTTACGATATACCT
187218 GTGTTCCTGT
Statistics
Matches: 214, Mismatches: 38, Indels: 27
0.77 0.14 0.10
Matches are distributed among these distances:
157 4 0.02
158 36 0.17
159 20 0.09
160 38 0.18
161 23 0.11
162 2 0.01
163 5 0.02
164 39 0.18
165 47 0.22
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (160 bp):
TTCTAGTTCTCATACTCGTACAGACTAAGAAAAAAAAATTAGAACCCAAATTAGATTTAAATATT
TTGGAATTGACATTAAAAAGTGTTTACGATATACCTACAATCCAGTTGTATTAGGCTGAATGCAT
GATGTTCTATTGTTATGTTATTTTTTGGGC
Found at i:187236 original size:158 final size:160
Alignment explanation
Indices: 186793--187249 Score: 446
Period size: 158 Copynumber: 2.8 Consensus size: 160
186783 ATTTTTCGAA
* *
186793 TTCTAGTTCTCATACTCATACCAAACT--GAAAACAAAAATTAGAACCCCAAATTAGATTTAAAT
1 TTCTAGTTCTCATACTCGTA-CAGACTAAGAAAA-AAAAATTAGAA-CCCAAATTAGATTTAAAT
* * *
186856 AATTTGGAATTGACATTAAAAAATGTTTACGATATACCTGTGGTCCAT-TTGTGTTAGGCTGAAT
63 ATTTTGGAATTGACATTAAAAAGTGTTTACGATATACCTGTGATCC-TGTTGTGTTAGGCTGAAT
* * *
186920 GCATGATGTTCTATTGTTATTTTTTTTTTTTGGC
127 GCATGATGTTCTATTGTTATGTTATTTTTTGGGC
* * * * * *
186954 TTCTAGTTCCCGTACTCGTACTAGACTAAGATAAAAAAAAATCAAAACCTCAAATTAGGTTAAAA
1 TTCTAGTTCTCATACTCGTAC-AGACTAAG--AAAAAAAAATTAGAACC-CAAATTAGATTTAAA
* * * *** * *
187019 TGCTTTT-GAATTGACATTAAAATAGTGTATACGATATACTTACAATCCAGTTGTATTAGGCTGA
62 T-ATTTTGGAATTGACATTAAAA-AGTGTTTACGATATACCTGTGATCCTGTTGTGTTAGGCTGA
* *
187083 ATGCGTGGTG-T-TA-TG-T-TGTTATTTTTTGGGC
125 ATGCATGATGTTCTATTGTTATGTTATTTTTTGGGC
* * **
187114 TTCTAGTTCTCATACTTGTATCAGACTAAGACAAAAAAAATTAGAACCAAAATTAGATTTTTATA
1 TTCTAGTTCTCATACTCGTA-CAGACTAAGA-AAAAAAAATTAGAACCCAAATTAGATTTAAATA
* * * *
187179 TTTTGGAATTGACAATGAAAAAGTGTTTACGATATACCTGTGTTCCTGTTATGTTAGGTTGAATG
64 TTTTGGAATTGAC-ATTAAAAAGTGTTTACGATATACCTGTGATCCTGTTGTGTTAGGCTGAATG
187244 CATGAT
128 CATGAT
187250 CTTTTGTTGT
Statistics
Matches: 235, Mismatches: 48, Indels: 29
0.75 0.15 0.09
Matches are distributed among these distances:
157 4 0.02
158 58 0.25
159 20 0.09
160 38 0.16
161 23 0.10
162 2 0.01
163 5 0.02
164 39 0.17
165 46 0.20
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (160 bp):
TTCTAGTTCTCATACTCGTACAGACTAAGAAAAAAAAATTAGAACCCAAATTAGATTTAAATATT
TTGGAATTGACATTAAAAAGTGTTTACGATATACCTGTGATCCTGTTGTGTTAGGCTGAATGCAT
GATGTTCTATTGTTATGTTATTTTTTGGGC
Found at i:189554 original size:26 final size:25
Alignment explanation
Indices: 189507--189589 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 25
189497 CAAGTCGTTC
* *
189507 CAGAAGTTTAGCTCATGCGAGCTCAGA
1 CAGAA-TTTAGCTCTTACGAGC-CAGA
* * *
189534 CATAATTTAGTTCTTATGAGCCTAGA
1 CAGAATTTAGCTCTTACGAGCC-AGA
189560 CAGAATTTAGCTCTTACGAGCCCAGA
1 CAGAATTTAGCTCTTACGAG-CCAGA
189586 CAGA
1 CAGA
189590 GTTACGCTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.02
26 39 0.85
27 6 0.13
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (25 bp):
CAGAATTTAGCTCTTACGAGCCAGA
Found at i:189598 original size:26 final size:26
Alignment explanation
Indices: 189507--189599 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
189497 CAAGTCGTTC
* * *
189507 CAGAAGTTTAGCTCATGCGAGCTCAGA
1 CAGAAG-TTAGCTCTTACGAGCCCAGA
* * * * *
189534 CATAATTTAGTTCTTATGAGCCTAGA
1 CAGAAGTTAGCTCTTACGAGCCCAGA
*
189560 CAGAATTTAGCTCTTACGAGCCCAGA
1 CAGAAGTTAGCTCTTACGAGCCCAGA
189586 CAG-AGTTACGCTCT
1 CAGAAGTTA-GCTCT
189600 AATCGAGTCA
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
25 4 0.08
26 44 0.85
27 4 0.08
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (26 bp):
CAGAAGTTAGCTCTTACGAGCCCAGA
Found at i:216176 original size:19 final size:20
Alignment explanation
Indices: 216154--216194 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
216144 ATTTATTATA
216154 TTATAT-ATATATTTC-TTCT
1 TTATATCATAT-TTTCTTTCT
216173 TTATATCATATTTTCTTTCT
1 TTATATCATATTTTCTTTCT
216193 TT
1 TT
216195 CTCTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATATCATATTTTCTTTCT
Found at i:217276 original size:15 final size:15
Alignment explanation
Indices: 217243--217287 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
217233 CTTAACAGTG
* *
217243 TCTTCCTCTTTCTCA
1 TCTTCTTCTTTCTCT
217258 TCTTC--CTTTCT-T
1 TCTTCTTCTTTCTCT
217270 TCTTCTTCTTTCTCT
1 TCTTCTTCTTTCTCT
217285 TCT
1 TCT
217288 GCCTTCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.19
13 6 0.23
14 6 0.23
15 9 0.35
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTCTTCTTTCTCT
Found at i:224325 original size:35 final size:35
Alignment explanation
Indices: 224275--224347 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
224265 TTCATTATAT
224275 TTATTATGCTAGCAAAACACTAACTGAAACACAGG
1 TTATTATGCTAGCAAAACACTAACTGAAACACAGG
*
224310 TTATTATGCTCGCAAAACACTAACTGAAACACAGG
1 TTATTATGCTAGCAAAACACTAACTGAAACACAGG
224345 TTA
1 TTA
224348 ATTACACCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (35 bp):
TTATTATGCTAGCAAAACACTAACTGAAACACAGG
Found at i:233093 original size:23 final size:22
Alignment explanation
Indices: 233063--233113 Score: 93
Period size: 23 Copynumber: 2.3 Consensus size: 22
233053 AGAGATACGA
233063 TGCCAAAGGACAATGCCTTCAG
1 TGCCAAAGGACAATGCCTTCAG
233085 TTGCCAAAGGACAATGCCTTCAG
1 -TGCCAAAGGACAATGCCTTCAG
233108 TGCCAA
1 TGCCAA
233114 TCACTTCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.21
23 22 0.79
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (22 bp):
TGCCAAAGGACAATGCCTTCAG
Found at i:242675 original size:19 final size:20
Alignment explanation
Indices: 242628--242675 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
242618 TTGATAATTC
242628 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
242646 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
242665 TTAATTATTAT
1 TTAATTATTAT
242676 CAAGAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:244157 original size:25 final size:26
Alignment explanation
Indices: 244129--244178 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
244119 TGACTTCCCT
244129 ATTTA-TCAAAGACCCAAACACTTAC
1 ATTTATTCAAAGACCCAAACACTTAC
244154 ATTTATTCAAAGACCCAAACACTTA
1 ATTTATTCAAAGACCCAAACACTTA
244179 TATTAACCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.44, C:0.26, G:0.04, T:0.26
Consensus pattern (26 bp):
ATTTATTCAAAGACCCAAACACTTAC
Found at i:245426 original size:17 final size:16
Alignment explanation
Indices: 245400--245438 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
245390 ATTCTATATA
245400 TTTTTTTCTTTTATCT
1 TTTTTTTCTTTTATCT
*
245416 TTTTCTTTCTTTTCTCT
1 TTTT-TTTCTTTTATCT
245433 TTTTTT
1 TTTTTT
245439 ATGCGACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTCTTTTATCT
Found at i:247250 original size:5 final size:5
Alignment explanation
Indices: 247228--247278 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
247218 ACACACTATA
* *
247228 AAAAA AAAAG AGATAAG AAAAG AGAAG AAGAAG AAAAG AAAAG -AAAG
1 AAAAG AAAAG A-A-AAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG
247275 AAAA
1 AAAA
247279 AGTCAAGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.10
5 24 0.62
6 7 0.18
7 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:247261 original size:16 final size:16
Alignment explanation
Indices: 247228--247272 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
247218 ACACACTATA
* *
247228 AAAAAAAAAGAGATAAG
1 AAAAGAAAAGA-AGAAG
*
247245 AAAAGAGAAGAAGAAG
1 AAAAGAAAAGAAGAAG
247261 AAAAGAAAAGAA
1 AAAAGAAAAGAA
247273 AGAAAAAGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAGAAGAAG
Found at i:247286 original size:20 final size:21
Alignment explanation
Indices: 247232--247280 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
247222 ACTATAAAAA
247232 AAAAAGAGATAAGAAAAGAGAAG
1 AAAAAGA-A-AAGAAAAGAGAAG
*
247255 AAGAAGAAAAGAAAAGA-AAG
1 AAAAAGAAAAGAAAAGAGAAG
247275 AAAAAG
1 AAAAAG
247281 TCAAGATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 9 0.38
22 1 0.04
23 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (21 bp):
AAAAAGAAAAGAAAAGAGAAG
Found at i:247315 original size:84 final size:84
Alignment explanation
Indices: 247226--247379 Score: 228
Period size: 84 Copynumber: 1.8 Consensus size: 84
247216 TAACACACTA
247226 TAAAAAAAAAAGAGATAAGAA-AAG-AGAAGAAGAAG-AAAA-GAAAAGAAAGAA-AAAGTCAAG
1 TAAAAAAAAAAGA-A-AAGAAGAAGAAGAAGAA-AAGAAAAAGGAAAA-AAA-AAGAAAGTCAAG
247286 ATGAAAACCCGCAAAGGGCACATT
61 ATGAAAACCCGCAAAGGGCACATT
247310 TAAAAAAAAAAGAAAAGAAGAAGAAGAAGAAAAGAAAAAGGAAAAAAAAAGAAAGTCAAGATGAA
1 TAAAAAAAAAAGAAAAGAAGAAGAAGAAGAAAAGAAAAAGGAAAAAAAAAGAAAGTCAAGATGAA
247375 AACCC
66 AACCC
247380 ACACCTCTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
82 5 0.08
83 9 0.14
84 46 0.71
85 5 0.08
ACGTcount: A:0.67, C:0.07, G:0.20, T:0.06
Consensus pattern (84 bp):
TAAAAAAAAAAGAAAAGAAGAAGAAGAAGAAAAGAAAAAGGAAAAAAAAAGAAAGTCAAGATGAA
AACCCGCAAAGGGCACATT
Found at i:247355 original size:7 final size:6
Alignment explanation
Indices: 247311--247363 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
247301 GGGCACATTT
* * *
247311 AAAAA- AAAAAG -AAAAG AAGAAG AAGAAG -AAAAG AAAAAG GAAAA-
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
247355 AAAAAG AAA
1 AAAAAG AAA
247364 GTCAAGATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
5 18 0.45
6 22 0.55
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:247359 original size:17 final size:16
Alignment explanation
Indices: 247311--247363 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
247301 GGGCACATTT
247311 AAAAA-AAAAAGAAAAG
1 AAAAAGAAAAA-AAAAG
* *
247327 AAGAAGAAGAAGAAAAG
1 AAAAAGAA-AAAAAAAG
247344 AAAAAGGAAAAAAAAAG
1 AAAAA-GAAAAAAAAAG
247361 AAA
1 AAA
247364 GTCAAGATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 4 0.13
17 21 0.70
18 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAG
Found at i:248207 original size:10 final size:10
Alignment explanation
Indices: 248166--248229 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
248156 AATTTCATCC
*
248166 AAAAAAAATA
1 AAAAAAAAGA
**
248176 AAAAAAGGGA
1 AAAAAAAAGA
*
248186 AGAGAAAAAGA
1 A-AAAAAAAGA
*
248197 AAAATAAAGA
1 AAAAAAAAGA
248207 AAAAAAAAGGA
1 AAAAAAAA-GA
248218 AAAAGAAAAGA
1 AAAA-AAAAGA
248229 A
1 A
248230 GAGGTCGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
10 22 0.52
11 16 0.38
12 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:249207 original size:99 final size:99
Alignment explanation
Indices: 249036--249492 Score: 517
Period size: 99 Copynumber: 4.6 Consensus size: 99
249026 ACCGAGGGAA
* * * * *
249036 CATGAAGATATGAAGGGAAAGGTTGA-GATCGCAATGGTGAACCC-AGTACCTTAGAATATCTGA
1 CATGAAGATATGAAGGGAAAGGTTGAGGCT-GCAACGGCGAACCCGA-TACCTTAGAAGATGTGA
* * **
249099 TTGGAAGGATTGAGGCCGCAATGATGAATCCGATAC
64 TGGGAAGGATTGAGGCCGCAACGGCGAATCCGATAC
249135 CATGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCGATACCTTAGAAGATGTGATG
1 CATGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCGATACCTTAGAAGATGTGATG
* * *
249200 GGAAGGATTGAGGCTGCAACGGCGAATCCGGTAT
66 GGAAGGATTGAGGCCGCAACGGCGAATCCGATAC
* * * *
249234 CATGAAGATATGAAGGGAAAGGTTGAGGCCGTAATGGCGAACCC-AGTACCTTAAAAGATGTGAT
1 CATGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCGA-TACCTTAGAAGATGTGAT
* * * *
249298 GGGAAGGATTGAGGCCACAATGGCGAATTCGATAG
65 GGGAAGGATTGAGGCCGCAACGGCGAATCCGATAC
* * * *
249333 CATGAAGATATGAAGGGAAAGGTTGAGG-TCGCAACGACGAACCTGGTACCTTAGAAAATGTGAT
1 CATGAAGATATGAAGGGAAAGGTTGAGGCT-GCAACGGCGAACCCGATACCTTAGAAGATGTGAT
* * * * * * *
249397 GGAAAAGATTAAGGTCGTAACGGTGAATCCGGTAC
65 GGGAAGGATTGAGGCCGCAACGGCGAATCCGATAC
* * ** * *
249432 CATAAAGATATGAAAGGAAAGGTTGAGGCCACAACGACGAACCCGATACCTTAAAAGATGT
1 CATGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCGATACCTTAGAAGATGT
249493 AAAGGGAAAG
Statistics
Matches: 303, Mismatches: 49, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
98 1 0.00
99 299 0.99
100 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.19
Consensus pattern (99 bp):
CATGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCGATACCTTAGAAGATGTGATG
GGAAGGATTGAGGCCGCAACGGCGAATCCGATAC
Found at i:249385 original size:198 final size:198
Alignment explanation
Indices: 249036--249531 Score: 622
Period size: 198 Copynumber: 2.5 Consensus size: 198
249026 ACCGAGGGAA
** * * * * *
249036 CATGAAGATATGAAGGGAAAGGTTGAGATCGCAATGGTGAACCCAGTACCTTAGAATATCTGATT
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCAGTACCTTAAAAGATGTGATG
* *
249101 GGAAGGATTGAGGCCGCAATGATGAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCTG
66 GGAAGGATTGAGGCCACAATGACGAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCTG
* * * * *
249166 CAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAGGATTGAGG-CTGCAACGGCGAATCCG
131 CAACGACGAACCCGATACCTTAGAAAATGTGATGGAAAAGATTAAGGTC-GCAACGGCGAATCCG
*
249230 GTAT
195 GTAC
*
249234 CATGAAGATATGAAGGGAAAGGTTGAGGCCGTAATGGCGAACCCAGTACCTTAAAAGATGTGATG
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCAGTACCTTAAAAGATGTGATG
* * *
249299 GGAAGGATTGAGGCCACAATGGCGAATTCGATAGCATGAAGATATGAAGGGAAAGGTTGAGG-TC
66 GGAAGGATTGAGGCCACAATGACGAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCT-
* * * *
249363 GCAACGACGAACCTGGTACCTTAGAAAATGTGATGGAAAAGATTAAGGTCGTAACGGTGAATCCG
130 GCAACGACGAACCCGATACCTTAGAAAATGTGATGGAAAAGATTAAGGTCGCAACGGCGAATCCG
249428 GTAC
195 GTAC
* * * * * * *
249432 CATAAAGATATGAAAGGAAAGGTTGAGGCCACAACGACGAACCC-GATACCTTAAAAGATGTAAA
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCAG-TACCTTAAAAGATGTGAT
* * * *
249496 GGGAAAGG-TTTAGGTCACAACGACGAACCCGATACC
65 GGG-AAGGATTGAGGCCACAATGACGAATCCGATACC
249532 TTAGAAAATG
Statistics
Matches: 256, Mismatches: 38, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
197 2 0.01
198 249 0.97
199 5 0.02
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (198 bp):
CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCAGTACCTTAAAAGATGTGATG
GGAAGGATTGAGGCCACAATGACGAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCTG
CAACGACGAACCCGATACCTTAGAAAATGTGATGGAAAAGATTAAGGTCGCAACGGCGAATCCGG
TAC
Found at i:249579 original size:149 final size:149
Alignment explanation
Indices: 249039--249639 Score: 568
Period size: 149 Copynumber: 4.0 Consensus size: 149
249029 GAGGGAACAT
* * * ** * * *
249039 GAAGATATGAAGGGAAAGGTTGAGATCGCAATGGTGAACCC-AGTACCTTAGAATATCTGATTGG
1 GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGACGAACCCGA-TACCTTAGAAAATGTGATGGG
* * * **
249103 AAGGATTGAGGCCGCAATGATGAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCTGCA
65 AAGGATTGAGGCCGCAATGGTGAATCCGGTACCATAAAGATATGAAGGGAAAGGTTGAGGCCACA
249168 ACGGCGAACCCGATACCTTA
130 ACGGCGAACCCGATACCTTA
* * * * * * * * *
249188 GAAGATGTGATGGG-AAGGATTGAGG-CTGCAACGGCGAATCCGGTATCAT-GAAGATATGAAGG
1 GAAGATGTGAAGGGAAAGG-TTGAGGTC-GCAACGACGAACCCGATACCTTAGAAAATGTGATGG
* * * * * * *
249250 GAAAGG-TTGAGGCCGTAATGGCGAACCCAGTACCTTAAAAGATGTGATGGG-AAGGATTGAGGC
64 G-AAGGATTGAGGCCGCAATGGTGAATCCGGTACCAT-AAAGATATGAAGGGAAAGG-TTGAGGC
* ** * *
249313 CACAATGGCGAATTCGATAGCAT-
126 CACAACGGCGAACCCGATACCTTA
* * * *
249336 GAAGATATGAAGGGAAAGGTTGAGGTCGCAACGACGAACCTGGTACCTTAGAAAATGTGATGGAA
1 GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGACGAACCCGATACCTTAGAAAATGTGATGGGA
* * * * * *
249401 AAGATTAAGGTCGTAACGGTGAATCCGGTACCATAAAGATATGAAAGGAAAGGTTGAGGCCACAA
66 AGGATTGAGGCCGCAATGGTGAATCCGGTACCATAAAGATATGAAGGGAAAGGTTGAGGCCACAA
*
249466 CGACGAACCCGATACCTTA
131 CGGCGAACCCGATACCTTA
* * * *
249485 AAAGATGTAAAGGGAAAGGTTTAGGTCACAACGACGAACCCGATACCTTAGAAAATGTGATGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGACGAACCCGATACCTTAGAAAATGTGATGGGA
** * * * * * *
249550 AGGATTGAGGCTACAATGGTAAATTCGGTACCATGAAGATAAGAAGGGAAAGGTGGAGGCCGCAA
66 AGGATTGAGGCCGCAATGGTGAATCCGGTACCATAAAGATATGAAGGGAAAGGTTGAGGCCACAA
* *
249615 TGGCAAACCCGATACCTTA
131 CGGCGAACCCGATACCTTA
249634 GAAGAT
1 GAAGAT
249640 ATGATTGAAA
Statistics
Matches: 356, Mismatches: 84, Indels: 24
0.77 0.18 0.05
Matches are distributed among these distances:
148 115 0.32
149 241 0.68
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.19
Consensus pattern (149 bp):
GAAGATGTGAAGGGAAAGGTTGAGGTCGCAACGACGAACCCGATACCTTAGAAAATGTGATGGGA
AGGATTGAGGCCGCAATGGTGAATCCGGTACCATAAAGATATGAAGGGAAAGGTTGAGGCCACAA
CGGCGAACCCGATACCTTA
Found at i:250002 original size:40 final size:40
Alignment explanation
Indices: 249909--250821 Score: 665
Period size: 40 Copynumber: 22.9 Consensus size: 40
249899 AGACATCATA
* * *
249909 CAATCTCCTACCCCAATCATG-GGGCAAATTGAAG-C-ATC
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAGACAATC
* *
249947 CAA--TCTTACCTTAATCAGAAGGCAGATTGAAGACAATC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACAATC
* *
249985 CAATCGCTTACTCTAATCAGAGGGCAGATTGAAGACACA-C
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACA-ATC
** *
250025 CAATCTCTTACCCCGATCATG-GGGCAAATTGAAG-C-ATC
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAGACAATC
* * *
250063 CAATCTCTTACCTTAATCAGAAGGCAGATTAAAGACACA-C
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACA-ATC
* * * *
250103 CAACCTCTTA-CCTCGATCATG-GAGTAGATTGAAG-C-ATC
1 CAATCTCTTACCCT-AATCA-GAGGGCAGATTGAAGACAATC
* * * *
250141 TAATCT-TT-TCTTAATCAGAAGGCAGATTGAAGACAATC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACAATC
* *
250179 CAATCACTTACCCTAATCAGAGGGCAAATTGAAGAC-ATAC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACAAT-C
* * ** *
250219 CAATCTCTTACCTTGATCATTGGGTAGATTGAAGACATCATC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACA--ATC
* * * *
250261 CAATCTCTTACCCCAATCATG-GGACAAATT-AA-AGAATC
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAGACAATC
* * * *
250299 CAATCGCTTACCTTAACCAGAGGGCAGACTGAAGAC-ATAC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACAAT-C
* * * *
250339 CAATCTCTTACCTTGATCATG-GAGCAGATTGAAGGCACA-C
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAGACA-ATC
*
250379 CAATCTCTTACCCTAATCATG-GGACAGATTGAAGAC-ATAC
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAGACAAT-C
** *
250419 CAATCTCTTACCCCGATCATG-GGGCATATTGAAGACATCATC
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAGACA--ATC
*
250461 CAATCTCTTACCCCAATCATGA-GGCAGATTGAAG--AATC
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAGACAATC
* *
250499 CAATCTCTTACCCTAATTAGAGGTCAGATTGAAGACAATC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACAATC
* ** * *
250539 AAATCTCTTACCCCGATCATAGGGCAAATTGAAG-C-ATC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACAATC
* * *
250577 CAATCTCTTACCTTAATCATAGGGCACATTGAAGAC-ATC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACAATC
* * *
250616 CAATCTCTTACCATAATCATAGGGCATATTGAAGAC-ATC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACAATC
*
250655 CAATCTCTTACCCCAATCATG-GGGCAGATTGAAGACATCATC
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAGACA--ATC
** *
250697 CAATCTCTTACCCCGATCATG-GGGCAGATTGAAGCCACCATC
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAG--ACAATC
* *
250739 CAATCT-TTACCCTTAAGTCAAGAGGGGAAAATTGAAGCCACAATC
1 CAATCTCTTACCC-TAA-TC-AGA-GGGCAGATTGAAG--ACAATC
* *
250784 CAATCTTTTACCCCTGAATCAAGAGGGGTAGATTGAAG
1 CAATCTCTTA-CCCT-AATC-AGA-GGGCAGATTGAAG
250822 TTACCATCTT
Statistics
Matches: 708, Mismatches: 110, Indels: 106
0.77 0.12 0.11
Matches are distributed among these distances:
35 2 0.00
36 36 0.05
37 12 0.02
38 136 0.19
39 86 0.12
40 260 0.37
41 13 0.02
42 102 0.14
43 7 0.01
44 3 0.00
45 24 0.03
46 22 0.03
47 5 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (40 bp):
CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACAATC
Found at i:250073 original size:78 final size:77
Alignment explanation
Indices: 249967--250730 Score: 661
Period size: 78 Copynumber: 9.6 Consensus size: 77
249957 TTAATCAGAA
*
249967 GGCAGATTGAAGACAATCCAATCGCTTACTCTAATCAGAGGGCAGATTGAAGACACACCAATCTC
1 GGCAGATTGAAGAC-ATCCAATCTCTTAC-CTAATCAGAGGGCAGATTGAAGACA-ACCAATCTC
*
250032 TTACCCCGATCATGG
63 TTACCCCAATCATGG
* * * *
250047 GGCAAATTGAAG-CATCCAATCTCTTACCTTAATCAGAAGGCAGATTAAAGACACACCAACCTCT
1 GGCAGATTGAAGACATCCAATCTCTTACC-TAATCAGAGGGCAGATTGAAGACA-ACCAATCTCT
* *
250111 TACCTCGATCATGG
64 TACCCCAATCATGG
* * * * * * *
250125 AGTAGATTGAAG-CATCTAATCT-TTTCTTAATCAGAAGGCAGATTGAAGACAATCCAATCACTT
1 GGCAGATTGAAGACATCCAATCTCTTACCTAATCAGAGGGCAGATTGAAGACAA-CCAATCTCTT
*
250188 ACCCTAATCA-GAG
65 ACCCCAATCATG-G
* * ** *
250201 GGCAAATTGAAGACATACCAATCTCTTACCTTGATCATTGGGTAGATTGAAGACATCATCCAATC
1 GGCAGATTGAAGACAT-CCAATCTCTTACC-TAATCAGAGGGCAGATTGAAGACA--A-CCAATC
250266 TCTTACCCCAATCATGG
61 TCTTACCCCAATCATGG
* * * * * *
250283 GACAAATTAAAGA-ATCCAATCGCTTACCTTAACCAGAGGGCAGACTGAAGACATACCAATCTCT
1 GGCAGATTGAAGACATCCAATCTCTTACC-TAATCAGAGGGCAGATTGAAGACA-ACCAATCTCT
***
250347 TACCTTGATCATGG
64 TACCCCAATCATGG
* *
250361 AGCAGATTGAAGGCACA-CCAATCTCTTACCCTAATCATG-GGACAGATTGAAGACATACCAATC
1 GGCAGATTGAA-G-ACATCCAATCTCTTA-CCTAATCA-GAGGGCAGATTGAAGACA-ACCAATC
*
250424 TCTTACCCCGATCATGG
61 TCTTACCCCAATCATGG
* * *
250441 GGCATATTGAAGACATCATCCAATCTCTTACCCCAATCATGA-GGCAGATTGAAGA-ATCCAATC
1 GGCAGATTGAAG--A-CATCCAATCTCTTA-CCTAATCA-GAGGGCAGATTGAAGACAACCAATC
* *
250504 TCTTACCCTAATTA-GAG
61 TCTTACCCCAATCATG-G
* * ** * * *
250521 GTCAGATTGAAGACAATCAAATCTCTTACCCCGATCATAGGGCAAATTGAAG-CATCCAATCTCT
1 GGCAGATTGAAGAC-ATCCAATCTCTTA-CCTAATCAGAGGGCAGATTGAAGACAACCAATCTCT
** *
250585 TACCTTAATCATAG
64 TACCCCAATCATGG
* * * *
250599 GGCACATTGAAGACATCCAATCTCTTACCATAATCATAGGGCATATTGAAGACATCCAATCTCTT
1 GGCAGATTGAAGACATCCAATCTCTTACC-TAATCAGAGGGCAGATTGAAGACAACCAATCTCTT
250664 ACCCCAATCATGG
65 ACCCCAATCATGG
**
250677 GGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG
1 GGCAGATTGAAG--A-CATCCAATCTCTTA-CCTAATCA-GAGGGCAGATTGAAG
250731 CCACCATCCA
Statistics
Matches: 568, Mismatches: 85, Indels: 61
0.80 0.12 0.09
Matches are distributed among these distances:
75 2 0.00
76 50 0.09
77 39 0.07
78 208 0.37
79 8 0.01
80 154 0.27
81 39 0.07
82 67 0.12
83 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (77 bp):
GGCAGATTGAAGACATCCAATCTCTTACCTAATCAGAGGGCAGATTGAAGACAACCAATCTCTTA
CCCCAATCATGG
Found at i:250332 original size:120 final size:116
Alignment explanation
Indices: 249909--250751 Score: 745
Period size: 120 Copynumber: 7.1 Consensus size: 116
249899 AGACATCATA
* * * * *
249909 CAATCTCCTACCCCAATCATGGGGCAAATTGAAGCATCCAA--TCTTACCTTAATCAGAAGGCAG
1 CAATCTCTTACCCTAATCAT-GGGCAAATTGAAGAATCCAATCTCTTACCCTAATCAGAGGGCAG
* * *
249972 ATTGAAGACA-ATCCAATCGCTTA-CTCTAATCAGAGGGCAGATTGAAGACACA-C
65 ATTGAAGACATA-CCAATCTCTTACCT-TGATCA-TGGGCAGATTGAAG-CACATC
** * * *
250025 CAATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAG
1 CAATCTCTTACCCTAATCAT-GGGCAAATTGAAGAATCCAATCTCTTACCCTAATCAGAGGGCAG
* * * * *
250090 ATTAAAGACACACCAACCTCTTACCTCGATCATGGAGTAGATTGAAG--CATC
65 ATTGAAGACATACCAATCTCTTACCTTGATCATGG-GCAGATTGAAGCACATC
* * * * *
250141 TAATCT-TT-TCTTAATCA-GAAGGCAGATTGAAGACAATCCAATCACTTACCCTAATCAGAGGG
1 CAATCTCTTACCCTAATCATG--GGCAAATTGAAG--AATCCAATCTCTTACCCTAATCAGAGGG
* *
250203 CAAATTGAAGACATACCAATCTCTTACCTTGATCATTGGGTAGATTGAAGACATCATC
62 CAGATTGAAGACATACCAATCTCTTACCTTGATCA-TGGGCAGATTGAAG-CA-CATC
* * * * *
250261 CAATCTCTTACCCCAATCATGGGACAAATTAAAGAATCCAATCGCTTACCTTAACCAGAGGGCAG
1 CAATCTCTTACCCTAATCATGGG-CAAATTGAAGAATCCAATCTCTTACCCTAATCAGAGGGCAG
*
250326 ACTGAAGACATACCAATCTCTTACCTTGATCATGGAGCAGATTGAAGGCACA-C
65 ATTGAAGACATACCAATCTCTTACCTTGATCATGG-GCAGATTGAA-GCACATC
* **
250379 CAATCTCTTACCCTAATCATGGGACAGATTGAAGACATACCAATCTCTTACCCCGATCATG-GGG
1 CAATCTCTTACCCTAATCATGGG-CAAATTGAAGA-AT-CCAATCTCTTACCCTAATCA-GAGGG
* ***
250443 CATATTGAAGACATCATCCAATCTCTTACCCCAATCATGAGGCAGATTGAAG-A-ATC
62 CAGATTGAAGACAT-A-CCAATCTCTTACCTTGATCATG-GGCAGATTGAAGCACATC
* * * ** *
250499 CAATCTCTTACCCTAATTA-GAGGTCAGATTGAAGACAATCAAATCTCTTACCCCGATCATAGGG
1 CAATCTCTTACCCTAATCATG-GG-CAAATTGAAG--AATCCAATCTCTTACCCTAATCAGAGGG
* * *
250563 CAAATTGAAG-CAT-CCAATCTCTTACCTTAATCATAGGGCACATTGAAG-ACATC
62 CAGATTGAAGACATACCAATCTCTTACCTTGATCAT-GGGCAGATTGAAGCACATC
* * *
250616 CAATCTCTTACCATAATCATAGGGCATATTGAAGACATCCAATCTCTTACCCCAATCATG-GGGC
1 CAATCTCTTACCCTAATCAT-GGGCAAATTGAAGA-ATCCAATCTCTTACCCTAATCA-GAGGGC
**
250680 AGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCCACCATC
63 AGATTGAAGACAT-A-CCAATCTCTTACCTTGATCAT-GGGCAGATTGAAG-CA-CATC
250739 CAATCT-TTACCCT
1 CAATCTCTTACCCT
250752 TAAGTCAAGA
Statistics
Matches: 612, Mismatches: 70, Indels: 84
0.80 0.09 0.11
Matches are distributed among these distances:
112 1 0.00
114 16 0.03
115 5 0.01
116 173 0.28
117 38 0.06
118 89 0.15
119 16 0.03
120 201 0.33
121 10 0.02
122 51 0.08
123 12 0.02
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (116 bp):
CAATCTCTTACCCTAATCATGGGCAAATTGAAGAATCCAATCTCTTACCCTAATCAGAGGGCAGA
TTGAAGACATACCAATCTCTTACCTTGATCATGGGCAGATTGAAGCACATC
Found at i:250774 original size:45 final size:46
Alignment explanation
Indices: 250724--250821 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 46
250714 CATGGGGCAG
* *
250724 ATTGAAGCCACCATCCAATC-TTTA-CCCTTAAGTCAAGAGGGGAAA
1 ATTGAAGCCACAATCCAATCTTTTACCCCTGAA-TCAAGAGGGGAAA
* *
250769 ATTGAAGCCACAATCCAATCTTTTACCCCTGAATCAAGAGGGGTAG
1 ATTGAAGCCACAATCCAATCTTTTACCCCTGAATCAAGAGGGGAAA
250815 ATTGAAG
1 ATTGAAG
250822 TTACCATCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
45 19 0.40
46 22 0.47
47 6 0.13
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (46 bp):
ATTGAAGCCACAATCCAATCTTTTACCCCTGAATCAAGAGGGGAAA
Found at i:252348 original size:33 final size:34
Alignment explanation
Indices: 252287--252352 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
252277 CTTCCGCATT
*
252287 TTTTTGTTTTTGTAATTTCATCCTTTAATTTTAC
1 TTTTTATTTTTGTAATTTCATCCTTTAATTTTAC
252321 TTTTTATTTTT-TAAATTT-ATCCTTTAATTTTA
1 TTTTTATTTTTGT-AATTTCATCCTTTAATTTTA
252353 TTTCATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.67
Consensus pattern (34 bp):
TTTTTATTTTTGTAATTTCATCCTTTAATTTTAC
Found at i:252540 original size:30 final size:30
Alignment explanation
Indices: 252497--252651 Score: 99
Period size: 30 Copynumber: 5.1 Consensus size: 30
252487 TTAAATTTGA
252497 CCCCTAA-ACTTTCTAAAAATTTCATTTTAGC
1 CCCCTAATA-TTTCTAAAAATTTCATTTTA-C
* *
252528 CCCCTAA-ATTTCT-TAAATTTCATTTTTAA
1 CCCCTAATATTTCTAAAAATTTCA-TTTTAC
* * * *
252557 ACCTTAATCTTTCTACAAATTTTCATTTTAAC
1 CCCCTAATATTTCTA-AAAATTTCATTTT-AC
* * *
252589 CCCCAAACATTT-TGAAAATTAT-ACTTTTA-
1 CCCCTAATATTTCTAAAAATT-TCA-TTTTAC
*
252618 CCCCTAATATTTCTAAAAATTAT-ATTTTAA
1 CCCCTAATATTTCTAAAAATT-TCATTTTAC
252648 CCCC
1 CCCC
252652 ATACTTTTCC
Statistics
Matches: 97, Mismatches: 18, Indels: 19
0.72 0.13 0.14
Matches are distributed among these distances:
29 28 0.29
30 36 0.37
31 18 0.19
32 15 0.15
ACGTcount: A:0.34, C:0.23, G:0.01, T:0.42
Consensus pattern (30 bp):
CCCCTAATATTTCTAAAAATTTCATTTTAC
Found at i:258716 original size:26 final size:26
Alignment explanation
Indices: 258686--258738 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
258676 CCTAGGAATA
*
258686 TCGCTGCATGAACATGTACAGAATTG
1 TCGCTGCATGAACATATACAGAATTG
* *
258712 TCGCTGCATGAACGTATCCAGAATTG
1 TCGCTGCATGAACATATACAGAATTG
258738 T
1 T
258739 GCCTAGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (26 bp):
TCGCTGCATGAACATATACAGAATTG
Found at i:259560 original size:16 final size:16
Alignment explanation
Indices: 259539--259569 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
259529 TTGTGTATCC
259539 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
259555 CATTTTATCTTTATT
1 CATTTTACCTTTATT
259570 TTCACATTAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:277885 original size:44 final size:44
Alignment explanation
Indices: 277835--277922 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
277825 ATAAGAGAGA
277835 ATGGAGTGAATTGGTGTTGAAAATGAGGTAGATGATGGTGGTAT
1 ATGGAGTGAATTGGTGTTGAAAATGAGGTAGATGATGGTGGTAT
* *
277879 ATGGAGTGAATTGGTGTTGAAAATGAGGTGGATGATGTTGGTAT
1 ATGGAGTGAATTGGTGTTGAAAATGAGGTAGATGATGGTGGTAT
277923 TTATAGGTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.28, C:0.00, G:0.39, T:0.33
Consensus pattern (44 bp):
ATGGAGTGAATTGGTGTTGAAAATGAGGTAGATGATGGTGGTAT
Found at i:280398 original size:18 final size:19
Alignment explanation
Indices: 280375--280412 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
280365 AGTATAAAAT
*
280375 ATTAAAAATT-TAAAATAA
1 ATTAAAAATTAGAAAATAA
280393 ATTAAAAATTAGAAAATAA
1 ATTAAAAATTAGAAAATAA
280412 A
1 A
280413 AATTTCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (19 bp):
ATTAAAAATTAGAAAATAA
Found at i:283787 original size:27 final size:27
Alignment explanation
Indices: 283749--283800 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
283739 GGGCATGTGA
283749 ATGTCATTTTGTGTTGATCTTTCTGGT
1 ATGTCATTTTGTGTTGATCTTTCTGGT
283776 ATGTCATTTTGTGTTGATCTTTCTG
1 ATGTCATTTTGTGTTGATCTTTCTG
283801 TGTGACTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.56
Consensus pattern (27 bp):
ATGTCATTTTGTGTTGATCTTTCTGGT
Found at i:291239 original size:20 final size:20
Alignment explanation
Indices: 291211--291250 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
291201 AAAAGACTCG
*
291211 AACTCCACTTCTACCGATAC
1 AACTACACTTCTACCGATAC
291231 AACTACACTTCTACCGATAC
1 AACTACACTTCTACCGATAC
291251 CTTGAAGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.25
Consensus pattern (20 bp):
AACTACACTTCTACCGATAC
Found at i:291490 original size:20 final size:20
Alignment explanation
Indices: 291467--291514 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
291457 CTTCTACTGG
291467 TACAACTACAATTCTACCGA
1 TACAACTACAATTCTACCGA
* ***
291487 TACAAGTATGCTTCTACCGA
1 TACAACTACAATTCTACCGA
*
291507 AACAACTA
1 TACAACTA
291515 AGTTGCAAAC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (20 bp):
TACAACTACAATTCTACCGA
Found at i:296395 original size:30 final size:30
Alignment explanation
Indices: 296359--296497 Score: 129
Period size: 30 Copynumber: 4.6 Consensus size: 30
296349 AAGTAAGTTA
* *
296359 GAAAGTTCAAGGGCCAAATTTAAATTTTTG
1 GAAAGTTTAAGGGTCAAATTTAAATTTTTG
* * *
296389 GAAAGTTT-GGAGGTCACATTCAAATTTTTG
1 GAAAGTTTAAG-GGTCAAATTTAAATTTTTG
* * *
296419 GAAAGTTTAGGGGTTAAATTTGAAA-TTTTA
1 GAAAGTTTAAGGGTCAAATTT-AAATTTTTG
* *
296449 GAAAGTTTAAGGGGTCAAATTTGATTTTTTG
1 GAAAGTTTAA-GGGTCAAATTTAAATTTTTG
* *
296480 GAAAATTTAGGGGTCAAA
1 GAAAGTTTAAGGGTCAAA
296498 AACATAATTT
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
29 1 0.01
30 60 0.68
31 27 0.31
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (30 bp):
GAAAGTTTAAGGGTCAAATTTAAATTTTTG
Found at i:296518 original size:31 final size:30
Alignment explanation
Indices: 296474--296538 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
296464 CAAATTTGAT
*
296474 TTTTTGGAAAA-TTTAGGGGTCAAAAACATAA
1 TTTTTAGAAAATTTTA-GGGTCAAAAA-ATAA
* *
296505 TTTTTAGATAATTTTAGGGTTAAAAAATAA
1 TTTTTAGAAAATTTTAGGGTCAAAAAATAA
296535 TTTT
1 TTTT
296539 AAAATAAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 8 0.27
31 18 0.60
32 4 0.13
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (30 bp):
TTTTTAGAAAATTTTAGGGTCAAAAAATAA
Found at i:298506 original size:39 final size:40
Alignment explanation
Indices: 298431--298533 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 40
298421 TGGTTGGGGG
* *
298431 AAGAGATCTGATGGTCTTCAATCTGTCCTTTAGTTAGCGT
1 AAGAGATCTGATGGTCTTCAATCTATCCTCTAGTTAGCGT
* * *
298471 AA-AGATCTGATGGTCTTCAATTTATCCTCTGGTTAGGGT
1 AAGAGATCTGATGGTCTTCAATCTATCCTCTAGTTAGCGT
*
298510 AAGAGAT-TGAATTG-CTTCAATCTA
1 AAGAGATCTG-ATGGTCTTCAATCTA
298534 CCCCATGGTC
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
39 45 0.83
40 9 0.17
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (40 bp):
AAGAGATCTGATGGTCTTCAATCTATCCTCTAGTTAGCGT
Found at i:298585 original size:78 final size:79
Alignment explanation
Indices: 298502--298657 Score: 192
Period size: 78 Copynumber: 2.0 Consensus size: 79
298492 TTATCCTCTG
* * * *
298502 GTTAGGGT-AAGAGATT-GAATTGCTTCAATCTACCCCATGGTCGGGGTAAGATATCGAATGA-T
1 GTTAGGGTGAA-AGATTAG-ATTGCCTCAATCTACCCCATGATCGGGGTAAGAGATCAAATGAGT
298564 CTTCAATCTGCCCTTT
64 CTTCAATCTGCCCTTT
** * *
298580 GTTAGGGTGAAAGATTAGATTGCCTCAATCTGTCCCATGATTGGGGTAAGAGATCAAATGATGTT
1 GTTAGGGTGAAAGATTAGATTGCCTCAATCTACCCCATGATCGGGGTAAGAGATCAAATGA-GTC
298645 TTCAATCTGCCCT
65 TTCAATCTGCCCT
298658 CTAATTAGGG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 49 0.74
79 3 0.05
80 14 0.21
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (79 bp):
GTTAGGGTGAAAGATTAGATTGCCTCAATCTACCCCATGATCGGGGTAAGAGATCAAATGAGTCT
TCAATCTGCCCTTT
Found at i:310177 original size:30 final size:30
Alignment explanation
Indices: 310040--310212 Score: 156
Period size: 30 Copynumber: 5.8 Consensus size: 30
310030 AAATTTGAAC
* *
310040 TTTTGGAAAATTTA-GGGTCAAA-TCAAAT
1 TTTTAGAAAATTTAGGGGTTAAATTCAAAT
310068 TTTTAAGAAAATTTAGGGGTTAAATTCAAAT
1 TTTT-AGAAAATTTAGGGGTTAAATTCAAAT
* * * *
310099 TTCTAGAAAGTTCAAGGGTTAAATTCAAAT
1 TTTTAGAAAATTTAGGGGTTAAATTCAAAT
* * **
310129 TTTTGGAAAGTTTAGGGGTTAAATTTGAAT
1 TTTTAGAAAATTTAGGGGTTAAATTCAAAT
* * *
310159 TTTTAGAAAATTTGGGGGTCAAA-ACATAAT
1 TTTTAGAAAATTTAGGGGTTAAATTCA-AAT
* *
310189 TTTT-GAACAATTTAGCGGTCAAAT
1 TTTTAGAA-AATTTAGGGGTTAAAT
310213 AATTTAAAAC
Statistics
Matches: 118, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
28 4 0.03
29 12 0.10
30 93 0.79
31 9 0.08
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (30 bp):
TTTTAGAAAATTTAGGGGTTAAATTCAAAT
Found at i:310190 original size:60 final size:58
Alignment explanation
Indices: 310025--310212 Score: 180
Period size: 60 Copynumber: 3.2 Consensus size: 58
310015 TAGTAAAATC
* * * *
310025 GGGTCAAATTTGAACTTTTGGAAAATTTAGGGTCAAATCAAATTTTTAAGAAAATTTAG
1 GGGTTAAATTTGAATTTTTAGAAAATTTAGGGTCAAATCAAATTTTT-GGAAAATTTAG
** * * * * *
310084 GGGTTAAATTCAAATTTCTAGAAAGTTCAAGGGTTAAATTCAAATTTTTGGAAAGTTTAG
1 GGGTTAAATTTGAATTTTTAGAAAATT-TAGGGTCAAA-TCAAATTTTTGGAAAATTTAG
* *
310144 GGGTTAAATTTGAATTTTTAGAAAATTTGGGGGTCAAAACATAATTTTT-GAACAATTTAG
1 GGGTTAAATTTGAATTTTTAGAAAATTT-AGGGTCAAATCA-AATTTTTGGAA-AATTTAG
* *
310204 CGGTCAAAT
1 GGGTTAAAT
310213 AATTTAAAAC
Statistics
Matches: 102, Mismatches: 22, Indels: 9
0.77 0.17 0.07
Matches are distributed among these distances:
59 25 0.25
60 67 0.66
61 10 0.10
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (58 bp):
GGGTTAAATTTGAATTTTTAGAAAATTTAGGGTCAAATCAAATTTTTGGAAAATTTAG
Found at i:311445 original size:14 final size:14
Alignment explanation
Indices: 311428--311469 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
311418 TATATTTATA
*
311428 AAATAATGATAAAT
1 AAATAATAATAAAT
311442 AAATAATAATAAAT
1 AAATAATAATAAAT
311456 -AATAATAATTAAAT
1 AAATAATAA-TAAAT
311470 TGGGTTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
AAATAATAATAAAT
Found at i:311452 original size:10 final size:10
Alignment explanation
Indices: 311439--311463 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
311429 AATAATGATA
311439 AATAAATAAT
1 AATAAATAAT
311449 AATAAATAAT
1 AATAAATAAT
311459 AATAA
1 AATAA
311464 TTAAATTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAAATAAT
Found at i:325556 original size:153 final size:153
Alignment explanation
Indices: 325278--325579 Score: 489
Period size: 153 Copynumber: 2.0 Consensus size: 153
325268 AATGCTAGCA
325278 TCATGCTTTAAATCCTAAATTCTTTCTACCAAAACAACATTTATTGTACAATAATATACATATAA
1 TCATGCTTTAAATCCTAAATTCTTTCTACCAAAACAACATTTATTGTACAATAATATACATATAA
*
325343 ATATCTTTTTCTTTTCTCTTTTTTTTTTATTTTTTTTATAAATGTGACTGAGGAATTTCGTTGTA
66 ATATCTTTTTCTTTTCTCTTTTTTTTTTATTTTTTTTATAAATGTGACTGAGGAATTTCGTTGCA
325408 TTACTATACTCTTGTTCCTAGAC
131 TTACTATACTCTTGTTCCTAGAC
* *** * **
325431 TCATGCTTTAAATCCTAAATTCTTTCTACCAAAACAACATTTATTGTATAATAATATTTTTTTTT
1 TCATGCTTTAAATCCTAAATTCTTTCTACCAAAACAACATTTATTGTACAATAATATACATATAA
* * *
325496 CT-TTTCTTTTCTTTTCTCTTTTTTTTTTATTTTTTTTATAAATGTGACTGAGGGATTTCGTTGC
66 ATATCT-TTTTCTTTTCTCTTTTTTTTTTATTTTTTTTATAAATGTGACTGAGGAATTTCGTTGC
325560 ATTACTATACTCTTGTTCCT
130 ATTACTATACTCTTGTTCCT
325580 GAGAAGTAAC
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
152 2 0.01
153 135 0.99
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (153 bp):
TCATGCTTTAAATCCTAAATTCTTTCTACCAAAACAACATTTATTGTACAATAATATACATATAA
ATATCTTTTTCTTTTCTCTTTTTTTTTTATTTTTTTTATAAATGTGACTGAGGAATTTCGTTGCA
TTACTATACTCTTGTTCCTAGAC
Found at i:326138 original size:17 final size:17
Alignment explanation
Indices: 326089--326150 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
326079 ATTAAATAAT
*
326089 AATGACAAATGGAAATGC
1 AATGAC-AATGAAAATGC
* *
326107 AACGACAATGCAAATGC
1 AATGACAATGAAAATGC
* *
326124 AATGACAATTAAAATGT
1 AATGACAATGAAAATGC
326141 AATGACAATG
1 AATGACAATG
326151 GGAATATGAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 32 0.86
18 5 0.14
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.19
Consensus pattern (17 bp):
AATGACAATGAAAATGC
Found at i:336823 original size:81 final size:81
Alignment explanation
Indices: 336684--336854 Score: 256
Period size: 81 Copynumber: 2.1 Consensus size: 81
336674 ATAGAGGCAG
* *
336684 TTAA-CAAGAATATCAAGAAGATCGAGACCTATAAAGATTGGCATAAGAATTTATCATTTGCTCT
1 TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGGCATAAGAAGTTATCATTTGCTCT
336748 CT-TCACTTATTGAACA
66 CTAT-ACTTATTGAACA
* *
336764 TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGGCATGAGAAGTTATCATTTTCTCT
1 TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGGCATAAGAAGTTATCATTTGCTCT
*
336829 CTATGCTTATTGAACA
66 CTATACTTATTGAACA
* *
336845 TCAATAAAGA
1 TTAATCAAGA
336855 TTTTGTTGGT
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
80 4 0.05
81 77 0.94
82 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (81 bp):
TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGGCATAAGAAGTTATCATTTGCTCT
CTATACTTATTGAACA
Found at i:337313 original size:7 final size:6
Alignment explanation
Indices: 337292--337361 Score: 72
Period size: 6 Copynumber: 11.7 Consensus size: 6
337282 AATAAAAATA
* * *
337292 AAAAAG GAAGAG AAAAAGG AAAAAG AAACAA- AAAAAG AAAAAG GAAAAG
1 AAAAAG AAAAAG AAAAA-G AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG
*
337341 AAAAA- AGAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAA
337362 GGAGAGGTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
5 6 0.12
6 38 0.73
7 8 0.15
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:337314 original size:19 final size:19
Alignment explanation
Indices: 337292--337350 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
337282 AATAAAAATA
* *
337292 AAAAAGGAAGAGAAAAAGG
1 AAAAAGGAAAAGAAAAAAG
337311 AAAAA-GAAACA-AAAAAAG
1 AAAAAGGAAA-AGAAAAAAG
337329 AAAAAGGAAAAGAAAAAAG
1 AAAAAGGAAAAGAAAAAAG
337348 AAA
1 AAA
337351 GAAAAAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 15 0.43
19 20 0.57
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAGGAAAAGAAAAAAG
Found at i:337340 original size:31 final size:31
Alignment explanation
Indices: 337291--337356 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
337281 AAATAAAAAT
* * *
337291 AAAAAAGGAAGAGAAAAAGGAAAAAGAAACA
1 AAAAAAGAAAAAGAAAAAGAAAAAAGAAACA
* *
337322 AAAAAAGAAAAAGGAAAAGAAAAAAGAAAGA
1 AAAAAAGAAAAAGAAAAAGAAAAAAGAAACA
337353 AAAA
1 AAAA
337357 GAAAAGGAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (31 bp):
AAAAAAGAAAAAGAAAAAGAAAAAAGAAACA
Found at i:337876 original size:112 final size:112
Alignment explanation
Indices: 337674--337890 Score: 344
Period size: 112 Copynumber: 1.9 Consensus size: 112
337664 AATGTGGGTC
*
337674 ATTTTTAATCTTTTCATTCATACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
1 ATTTTTAATCTTTTCATTCACACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
* ** *
337739 CTTTGTTCAAGCTTTTTTGCCTTGAAATAACGATTAGTGGACCAATG
66 CTCTGTTCAAGAATTTTTGCATTGAAATAACGATTAGTGGACCAATG
* * *
337786 ATTTTTATTCTTTTCATTCACACGAGCTTTGCCTCTAATAAAATTTAATTTTATCCACCTTACAA
1 ATTTTTAATCTTTTCATTCACACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
* *
337851 CTCTGTTCAAGAATTTTTGCATTGAAATGACGGTTAGTGG
66 CTCTGTTCAAGAATTTTTGCATTGAAATAACGATTAGTGG
337891 TCTAACAATA
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 95 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (112 bp):
ATTTTTAATCTTTTCATTCACACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
CTCTGTTCAAGAATTTTTGCATTGAAATAACGATTAGTGGACCAATG
Found at i:338575 original size:99 final size:98
Alignment explanation
Indices: 338315--338907 Score: 405
Period size: 99 Copynumber: 6.0 Consensus size: 98
338305 ACTAAGGAAA
* * *** * * * * *
338315 CATAGAGATATGAAGGGAAAGGTTAAGGCCGTAACAGCAAACCCGGTAACTTAGAAGACATGATA
1 CATA-AGATATAAAGGGAAAGGTTGAGGCTACAACGGCGAACCCGATACCTTAGAAGACATGATG
* * * *
338380 GGAAAGATCGAGGCCGTAACAGCGAATCTAGTAC
65 GGAAGGATTGAGGCCGTAACGGCGAATCCAGTAC
* * * * * ** * **
338414 CAT-GGAAATAAAAGGATAGGTTGAGGCTGCAATAGTGAACCCGATACCTTAGAAGATGTGATGG
1 CATAAGATATAAAGGGAAAGGTTGAGGCTACAACGGCGAACCCGATACCTTAGAAGACATGATGG
*
338478 GAAGGATTGACGCCGTAACGGCGAATCCAGTAC
66 GAAGGATTGAGGCCGTAACGGCGAATCCAGTAC
* * *
338511 CATAAGGATATAAAGGGAAAGGTTGAGGCTACAACGNCGAACCTTG-TACCTTAAAAGACATGAT
1 CATAA-GATATAAAGGGAAAGGTTGAGGCTACAACGGCGAACC-CGATACCTTAGAAGACATGAT
* * ** * **
338575 GGGAAGCATTGAAGCCACAATGGCGAATCTGGTAC
64 GGGAAGGATTGAGGCCGTAACGGCGAATCCAGTAC
* * * * *
338610 CATGAAGATATGAGGGGAAAGGTTGAGGCTGCAACGGTGAACCCTATACCTTAGAAGACATGATG
1 CAT-AAGATATAAAGGGAAAGGTTGAGGCTACAACGGCGAACCCGATACCTTAGAAGACATGATG
* * * * * *
338675 GGTAGGATTAAGGTCATAACAGCGAATCCGGTAC
65 GGAAGGATTGAGGCCGTAACGGCGAATCCAGTAC
* * * * *
338709 CATGAAGATATGAAGGGAAAGGTTGAGG-TCACAACGGCGAACCCGATACCTTAAAACATATGAA
1 CAT-AAGATATAAAGGGAAAGGTTGAGGCT-ACAACGGCGAACCCGATACCTTAGAAGACATGAT
* * *
338773 GGGAAAGG-TTGAGGCCGCAATGGCGAACTCGA-TAC
64 GGG-AAGGATTGAGGCCGTAACGGCGAA-TCCAGTAC
* ** * * * * *
338808 CATAAAAGATGTGATAA--GAAAGGTTGAGGCCGCAATGGCAAACTCGGTACCAT-GAAGACATG
1 CAT--AAGATAT-A-AAGGGAAAGGTTGAGGCTACAACGGCGAACCCGATACCTTAGAAGACATG
* * *
338870 AAGGGAAAGG-TTGATGCCGCAACGGCGAA-CCTAGTAC
62 ATGGG-AAGGATTGAGGCCGTAACGGCGAATCC-AGTAC
338907 C
1 C
338908 TTAGAAGCAT
Statistics
Matches: 389, Mismatches: 91, Indels: 28
0.77 0.18 0.06
Matches are distributed among these distances:
97 77 0.20
98 2 0.01
99 266 0.68
100 42 0.11
102 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (98 bp):
CATAAGATATAAAGGGAAAGGTTGAGGCTACAACGGCGAACCCGATACCTTAGAAGACATGATGG
GAAGGATTGAGGCCGTAACGGCGAATCCAGTAC
Found at i:338676 original size:198 final size:198
Alignment explanation
Indices: 338431--338799 Score: 485
Period size: 198 Copynumber: 1.9 Consensus size: 198
338421 ATAAAAGGAT
* ** * *
338431 AGGTTGAGGCTGCAATAGTGAACCCGATACCTTAGAAGATGTGATGGGAAGGATTGACGCCGTAA
1 AGGTTGAGGCTGCAACAGTGAACCCGATACCTTAGAAGACATGATGGGAAGGATTAACGCCATAA
* * *
338496 CGGCGAATCCAGTACCAT-AAGGATATAAAGGGAAAGGTTGAGG-CTACAACGNCGAACCTTG-T
66 CAGCGAATCCAGTACCATGAA-GATATAAAGGGAAAGGTTGAGGTC-ACAACGGCGAACC-CGAT
* *
338558 ACCTTAAAAGACATGATGGG-AAGCATTGAAGCCACAATGGCGAATCTGGTACCATGAAGATATG
128 ACCTTAAAACACATGAAGGGAAAG-ATTGAAGCCACAATGGCGAATCTGGTACCATGAAGATATG
338622 AGGGGAA
192 AGGGGAA
* * * * *
338629 AGGTTGAGGCTGCAACGGTGAACCCTATACCTTAGAAGACATGATGGGTAGGATTAAGGTCATAA
1 AGGTTGAGGCTGCAACAGTGAACCCGATACCTTAGAAGACATGATGGGAAGGATTAACGCCATAA
* *
338694 CAGCGAATCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGTCACAACGGCGAACCCGATACC
66 CAGCGAATCCAGTACCATGAAGATATAAAGGGAAAGGTTGAGGTCACAACGGCGAACCCGATACC
* * * *
338759 TTAAAACATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAA
131 TTAAAACACATGAAGGGAAAGATTGAAGCCACAATGGCGAA
338800 CTCGATACCA
Statistics
Matches: 146, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
197 1 0.01
198 139 0.95
199 6 0.04
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (198 bp):
AGGTTGAGGCTGCAACAGTGAACCCGATACCTTAGAAGACATGATGGGAAGGATTAACGCCATAA
CAGCGAATCCAGTACCATGAAGATATAAAGGGAAAGGTTGAGGTCACAACGGCGAACCCGATACC
TTAAAACACATGAAGGGAAAGATTGAAGCCACAATGGCGAATCTGGTACCATGAAGATATGAGGG
GAA
Found at i:338776 original size:50 final size:50
Alignment explanation
Indices: 338431--338900 Score: 267
Period size: 50 Copynumber: 9.5 Consensus size: 50
338421 ATAAAAGGAT
* ** * * * *
338431 AGGTTGAGGCTGCAATAGTGAACCCGATACCTTAGAAGATGTGATGGG-A
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATATGAAGGGAA
* * * * * *
338480 AGGATTGACGCCGTAACGGCGAATCC-AGTACCAT-AAGGATATAAAGGGAA
1 AGG-TTGAGGCCGCAACGGCGAACCCGA-TACCTTAAAAGATATGAAGGGAA
** * * * *
338530 AGGTTGAGGCTACAACGNCGAACCTTG-TACCTTAAAAGACATGATGGG-A
1 AGGTTGAGGCCGCAACGGCGAACC-CGATACCTTAAAAGATATGAAGGGAA
* * * * * * * * * *
338579 AGCATTGAAGCCACAATGGCGAATCTGGTACCAT-GAAGATATGAGGGGAA
1 AG-GTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATATGAAGGGAA
* * * * * * *
338629 AGGTTGAGGCTGCAACGGTGAACCCTATACCTTAGAAGACATGATGGG-T
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATATGAAGGGAA
* * ** * * * * *
338678 AGGATTAAGGTCATAACAGCGAATCCGGTACCAT-GAAGATATGAAGGGAA
1 AGG-TTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATATGAAGGGAA
* * *
338728 AGGTTGAGGTCACAACGGCGAACCCGATACCTTAAAACATATGAAGGGAA
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATATGAAGGGAA
* * * * *
338778 AGGTTGAGGCCGCAATGGCGAACTCGATACCATAAAAGATGTGATA-AGAA
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATATGA-AGGGAA
* * * * * * *
338828 AGGTTGAGGCCGCAATGGCAAACTCGGTACCAT-GAAGACATGAAGGGAA
1 AGGTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATATGAAGGGAA
*
338877 AGGTTGATGCCGCAACGGCGAACC
1 AGGTTGAGGCCGCAACGGCGAACC
338901 TAGTACCTTA
Statistics
Matches: 317, Mismatches: 89, Indels: 30
0.73 0.20 0.07
Matches are distributed among these distances:
48 1 0.00
49 138 0.44
50 177 0.56
51 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (50 bp):
AGGTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATATGAAGGGAA
Found at i:338867 original size:198 final size:198
Alignment explanation
Indices: 338451--338870 Score: 447
Period size: 198 Copynumber: 2.1 Consensus size: 198
338441 TGCAATAGTG
* ** * * * * * *
338451 AACCCGATACCTTAGAAGATGTGATGGGAAGGATTGACGCCGTAACGGCGAATCCAGTACCATAA
1 AACCCGATACCATAGAAGACATGATGGGTAGGATTAAGGTCATAACAGCGAATCCAGTACCATAA
* * * *
338516 GGATATAAAGGGAAAGGTTGAGGCTACAACGNCGAACCTTGTACCTTAAAAGACATGATGGGAAG
66 GGATATAAAGGGAAAGGTTGAGGCTACAACGGCGAACCTCGTACCTTAAAACACATGAAGGGAAG
* * ** *
338581 CATTGAAGCCACAATGGCGAATCTGGTACCATGAAGATATGAGGGGAAAGGTTGAGGCTGCAACG
131 CATTGAAGCCACAATGGCGAATCTGATACCATAAAGATATGAGAAGAAAGGTTGAGGCCGCAACG
**
338646 GTG
196 GCA
* * *
338649 AACCCTATACCTTAGAAGACATGATGGGTAGGATTAAGGTCATAACAGCGAATCCGGTACCATGA
1 AACCCGATACCATAGAAGACATGATGGGTAGGATTAAGGTCATAACAGCGAATCCAGTACCAT-A
* *
338714 A-GATATGAAGGGAAAGGTTGAGG-TCACAACGGCGAACC-CGATACCTTAAAACATATGAAGGG
65 AGGATATAAAGGGAAAGGTTGAGGCT-ACAACGGCGAACCTCG-TACCTTAAAACACATGAAGGG
* * * * *
338776 AAAG-GTTGAGGCCGCAATGGCGAA-CTCGATACCATAAAAGATGTGATAAGAAAGGTTGAGGCC
128 -AAGCATTGAAGCCACAATGGCGAATCT-GATACCAT-AAAGATATGAGAAGAAAGGTTGAGGCC
*
338839 GCAATGGCA
190 GCAACGGCA
* *
338848 AACTCGGTACCAT-GAAGACATGA
1 AACCCGATACCATAGAAGACATGA
338871 AGGGAAAGGT
Statistics
Matches: 183, Mismatches: 33, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
197 4 0.02
198 138 0.75
199 41 0.22
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.18
Consensus pattern (198 bp):
AACCCGATACCATAGAAGACATGATGGGTAGGATTAAGGTCATAACAGCGAATCCAGTACCATAA
GGATATAAAGGGAAAGGTTGAGGCTACAACGGCGAACCTCGTACCTTAAAACACATGAAGGGAAG
CATTGAAGCCACAATGGCGAATCTGATACCATAAAGATATGAGAAGAAAGGTTGAGGCCGCAACG
GCA
Found at i:339251 original size:42 final size:41
Alignment explanation
Indices: 339196--339860 Score: 570
Period size: 42 Copynumber: 16.4 Consensus size: 41
339186 GTTACATCAC
* *
339196 CATCCAATCTCTTACCTCGATCATGGGGCAGATTGCAGCCAT
1 CATCCAATCTCTTACC-CGATCATGGGGCAGATTGAAGACAT
* * * *
339238 CAACCAATCTCTTACCCTGATCATGGGGTAGATTGCAGCCAT
1 CATCCAATCTCTTACCC-GATCATGGGGCAGATTGAAGACAT
* * * *
339280 CAACCAATCTCTTACCCTGATCATGGGGTAGATTGCAGCCAT
1 CATCCAATCTCTTACCC-GATCATGGGGCAGATTGAAGACAT
*
339322 CATCCAATCTCTTACCTTGATCATGGGGCAGATTG-A-A-A-
1 CATCCAATCTCTTACC-CGATCATGGGGCAGATTGAAGACAT
* ** * * *
339360 CATCCAATCTTTTACCTTAGTTA-GATGGTAGATTGAAGACA-
1 CATCCAATCTCTTACCCGA-TCATG-GGGCAGATTGAAGACAT
* *
339401 CA-CCAATCTCTTACCCTGATCATGGGGTAGATT--A-A-AG
1 CATCCAATCTCTTACCC-GATCATGGGGCAGATTGAAGACAT
* * * ** *
339438 CATCCAATCTTTTA-CC-TTAATTAGGCAGATTAAAGACAT
1 CATCCAATCTCTTACCCGATCATGGGGCAGATTGAAGACAT
*
339477 CATCCAATCTCTTACCCCGATTATGGGGCAGATTGAAG-CAT
1 CATCCAATCTCTTA-CCCGATCATGGGGCAGATTGAAGACAT
* *
339518 --T-CAATCTTTTACCCCGATCATGGGGCAGATTGAAGGCAT
1 CATCCAATCTCTTA-CCCGATCATGGGGCAGATTGAAGACAT
*
339557 CATCCAATCTCCTACTCCGATCATGGGGCAGATTGAAG----
1 CATCCAATCTCTTAC-CCGATCATGGGGCAGATTGAAGACAT
* ** * *
339595 CATCCAATCTTTTACCTTAACCA-GAAGGCAGATTGAAGACAT
1 CATCCAATCTCTTACC-CGATCATG-GGGCAGATTGAAGACAT
* ** *
339637 CATCCAATCTTTTACCCTGATTGTGGGGCAAATTGAAGACAT
1 CATCCAATCTCTTACCC-GATCATGGGGCAGATTGAAGACAT
* **
339679 CATCCAATCTCTTACCACAATCATGGGAAAGATTGAAGACAT
1 CATCCAATCTCTTACC-CGATCATGGGGCAGATTGAAGACAT
* *
339721 CATCCAATCTCTTACCCTGATCATAGGGCAGATTGAAGGCAT
1 CATCCAATCTCTTACCC-GATCATGGGGCAGATTGAAGACAT
* * *
339763 CATTCAATCTCTTATCCCGATCATGGGCCAGATTG--CA-AT
1 CATCCAATCTCTTA-CCCGATCATGGGGCAGATTGAAGACAT
*
339802 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAC
1 CATCCAATCTCTTA-CCCGATCATGGGGCAGATTGAAGACAT
*
339844 CATTCAATCTCTTACCC
1 CATCCAATCTCTTACCC
339861 CGGTCATAAG
Statistics
Matches: 517, Mismatches: 69, Indels: 75
0.78 0.10 0.11
Matches are distributed among these distances:
35 10 0.02
36 1 0.00
37 11 0.02
38 97 0.19
39 54 0.10
40 23 0.04
41 19 0.04
42 297 0.57
43 5 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (41 bp):
CATCCAATCTCTTACCCGATCATGGGGCAGATTGAAGACAT
Found at i:363876 original size:15 final size:15
Alignment explanation
Indices: 363856--363907 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
363846 CATGCCGAGA
363856 AGGATGAAGAACAAG
1 AGGATGAAGAACAAG
*
363871 AGGATGAAG-A-GA-
1 AGGATGAAGAACAAG
363883 AGGATGAAGAACAAG
1 AGGATGAAGAACAAG
363898 AGGATGAAGA
1 AGGATGAAGA
363908 GAAGGACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 9 0.28
13 2 0.06
14 2 0.06
15 19 0.59
ACGTcount: A:0.52, C:0.04, G:0.37, T:0.08
Consensus pattern (15 bp):
AGGATGAAGAACAAG
Found at i:363888 original size:12 final size:12
Alignment explanation
Indices: 363852--363928 Score: 64
Period size: 12 Copynumber: 5.9 Consensus size: 12
363842 TGATCATGCC
363852 GAGAAGGATGAA
1 GAGAAGGATGAA
*
363864 GAACAAGAGGATGAA
1 G-A-GA-AGGATGAA
363879 GAGAAGGATGAA
1 GAGAAGGATGAA
*
363891 GAACAAGAGGATGAA
1 G-A-GA-AGGATGAA
*
363906 GAGAAGGACGAA
1 GAGAAGGATGAA
*
363918 GCGAAGGATGA
1 GAGAAGGATGA
363929 CGAACACATT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
12 26 0.50
13 4 0.08
14 4 0.08
15 18 0.35
ACGTcount: A:0.49, C:0.05, G:0.39, T:0.06
Consensus pattern (12 bp):
GAGAAGGATGAA
Found at i:363890 original size:27 final size:27
Alignment explanation
Indices: 363852--363918 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
363842 TGATCATGCC
363852 GAGAAGGATGAAGAACAAGAGGATGAA
1 GAGAAGGATGAAGAACAAGAGGATGAA
363879 GAGAAGGATGAAGAACAAGAGGATGAA
1 GAGAAGGATGAAGAACAAGAGGATGAA
*
363906 GAGAAGGACGAAG
1 GAGAAGGATGAAG
363919 CGAAGGATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.39, T:0.06
Consensus pattern (27 bp):
GAGAAGGATGAAGAACAAGAGGATGAA
Found at i:365005 original size:16 final size:16
Alignment explanation
Indices: 364993--365025 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
364983 AACAAAAATG
364993 AGAAAAAAAAAAAGAA
1 AGAAAAAAAAAAAGAA
365009 AGAAAAAAAAAAGAGAA
1 AGAAAAAAAAAA-AGAA
365026 TAAATTACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAAAGAA
Found at i:379491 original size:30 final size:30
Alignment explanation
Indices: 379430--379603 Score: 145
Period size: 30 Copynumber: 5.8 Consensus size: 30
379420 TTTTAGGGGC
* * * *
379430 AAAATGTAATTTTTGGAAAAATTTTAGGGTT
1 AAAATGTAA-TTTTAGAAAAGTTTAAAGGTT
379461 AAAATGTAATTTTAGAAAAGTTTAAAGGTT
1 AAAATGTAATTTTAGAAAAGTTTAAAGGTT
* **
379491 AAAATGTAATTTTAGGAAAGTTT-GGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAAAGGTT
* * *
379520 AAAATGTGATTTTAGGAAAGTTT-AAGGGT
1 AAAATGTAATTTTAGAAAAGTTTAAAGGTT
* * * * * *
379549 AAAATATAATTTTGGAGAAGTTCAATGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAAGGTT
* * * *
379579 AAAATATGATTTTTGAAAAATTTAA
1 AAAATGTAATTTTAGAAAAGTTTAA
379604 CGACCTCCTG
Statistics
Matches: 117, Mismatches: 25, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
29 46 0.39
30 62 0.53
31 9 0.08
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTAAAGGTT
Found at i:379531 original size:29 final size:30
Alignment explanation
Indices: 379430--379570 Score: 171
Period size: 29 Copynumber: 4.7 Consensus size: 30
379420 TTTTAGGGGC
* * *
379430 AAAATGTAATTTTTGGAAAAATTTTAGGGTT
1 AAAATGTAATTTTAGG-AAAGTTTAAGGGTT
* *
379461 AAAATGTAATTTTAGAAAAGTTTAAAGGTT
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTT
*
379491 AAAATGTAATTTTAGGAAAGTTT-GGGGTT
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTT
*
379520 AAAATGTGATTTTAGGAAAGTTTAAGGG-T
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTT
*
379549 AAAATATAATTTT-GGAGAAGTT
1 AAAATGTAATTTTAGGA-AAGTT
379571 CAATGGTCAA
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.03
29 43 0.45
30 36 0.38
31 14 0.15
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTAGGAAAGTTTAAGGGTT
Found at i:379533 original size:59 final size:57
Alignment explanation
Indices: 379421--379570 Score: 174
Period size: 59 Copynumber: 2.5 Consensus size: 57
379411 TTTTGAGACT
* * *
379421 TTTAGGGGCAAAATGTAATTTTTGGAAAAATTTTAGGGTTAAAATGTAATTTTAGAAAAG
1 TTTAAGGGTAAAATGTAA-TTTTGG--AAAGTTTAGGGTTAAAATGTAATTTTAGAAAAG
* * * *
379481 TTTAAAGGTTAAAATGTAATTTTAGGAAAGTTTGGGGTTAAAATGTGATTTTAGGAAAG
1 TTT-AAGGGTAAAATGTAATTTT-GGAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAG
*
379540 TTTAAGGGTAAAATATAATTTTGGAGAAGTT
1 TTTAAGGGTAAAATGTAATTTTGGA-AAGTT
379571 CAATGGTCAA
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
57 3 0.04
58 22 0.28
59 32 0.41
60 7 0.09
61 14 0.18
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (57 bp):
TTTAAGGGTAAAATGTAATTTTGGAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAG
Found at i:379583 original size:59 final size:59
Alignment explanation
Indices: 379455--379603 Score: 158
Period size: 59 Copynumber: 2.5 Consensus size: 59
379445 GAAAAATTTT
* * * * *
379455 AGGGTTAAAATGTAATTTTAGAAAAGTTTAAAGGTTAAAATGTAATTTTAGGAAAGTTT
1 AGGGTCAAAATGTGATTTTAGAAAAGTTTAAAGGGTAAAATATAATTTTAGGAAAGTTA
* * *
379514 GGGGTTAAAATGTGATTTTAGGAAAGTTT-AAGGGTAAAATATAATTTT-GGAGAAGTTCA
1 AGGGTCAAAATGTGATTTTAGAAAAGTTTAAAGGGTAAAATATAATTTTAGGA-AAGTT-A
* * * *
379573 ATGGTCAAAATATGATTTTTGAAAAATTTAA
1 AGGGTCAAAATGTGATTTTAGAAAAGTTTAA
379604 CGACCTCCTG
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
57 3 0.04
58 22 0.30
59 48 0.65
60 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.36
Consensus pattern (59 bp):
AGGGTCAAAATGTGATTTTAGAAAAGTTTAAAGGGTAAAATATAATTTTAGGAAAGTTA
Found at i:380217 original size:3 final size:3
Alignment explanation
Indices: 380209--380246 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
380199 AGTGTTCTTT
380209 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
380247 TAAAAGAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.