Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chrUn_random
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: 10571689
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 1662808 characters in sequence are not A, C, G, or T
File 1 of 30
Found at i:6416 original size:16 final size:16
Alignment explanation
Indices: 6395--6429 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6385 ATAAAATATT
*
6395 ATGTTTTCTAATTAAA
1 ATGTTTTCTAATAAAA
*
6411 ATGTTTTTTAATAAAA
1 ATGTTTTCTAATAAAA
6427 ATG
1 ATG
6430 AGATTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (16 bp):
ATGTTTTCTAATAAAA
Found at i:10975 original size:2 final size:2
Alignment explanation
Indices: 10968--11008 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
10958 ACTAGTTTCA
*
10968 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11009 TCTTTACTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:13843 original size:44 final size:44
Alignment explanation
Indices: 13794--13924 Score: 235
Period size: 44 Copynumber: 3.0 Consensus size: 44
13784 AATAAGATAT
*
13794 AGTTTTAATTTTGTGTTCATATGGATGAATATATGTGGATGATC
1 AGTTTTAATTTTGTGTTCATATGGATGAATGTATGTGGATGATC
13838 AGTTTTAATTTTGTGTTCATATGGATGAATGTATGTGGATGATC
1 AGTTTTAATTTTGTGTTCATATGGATGAATGTATGTGGATGATC
* *
13882 AGTTTTAATTTTGTGTTTATATGGATGAATGTATATGGATGAT
1 AGTTTTAATTTTGTGTTCATATGGATGAATGTATGTGGATGAT
13925 TATGGACTAT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 84 1.00
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.47
Consensus pattern (44 bp):
AGTTTTAATTTTGTGTTCATATGGATGAATGTATGTGGATGATC
Found at i:16547 original size:34 final size:34
Alignment explanation
Indices: 16494--16570 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
16484 TTGGCTGCTG
* *
16494 AAAATTTGAGTTGTGTGCT-GTCAATTTGTGCAAA
1 AAAATTGGAGCTGTGTGCTGGT-AATTTGTGCAAA
* * *
16528 AAAATTGGAGCTGTTTGCTGGTAGTTTGTGCAGA
1 AAAATTGGAGCTGTGTGCTGGTAATTTGTGCAAA
16562 AAAATTGGA
1 AAAATTGGA
16571 CAGCTTTGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (34 bp):
AAAATTGGAGCTGTGTGCTGGTAATTTGTGCAAA
Found at i:16848 original size:25 final size:25
Alignment explanation
Indices: 16819--16878 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
16809 GAAAAAGAAA
*
16819 AGAAAATAAATGGGCATGACCTAAT
1 AGAAAATAAATGGGCATGACCCAAT
* *
16844 AGAAAATAAGTGGGCATGGCCCAAT
1 AGAAAATAAATGGGCATGACCCAAT
*
16869 AGGAAATAAA
1 AGAAAATAAA
16879 AATAAATAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.48, C:0.12, G:0.23, T:0.17
Consensus pattern (25 bp):
AGAAAATAAATGGGCATGACCCAAT
Found at i:17370 original size:2 final size:2
Alignment explanation
Indices: 17363--17393 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17353 ATCATTTGAA
17363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17394 GTAACGTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29141 original size:13 final size:13
Alignment explanation
Indices: 29123--29147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29113 TTTCAGAAAA
29123 TTTATAAAATCAT
1 TTTATAAAATCAT
29136 TTTATAAAATCA
1 TTTATAAAATCA
29148 CAATTTNNNN
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:31178 original size:21 final size:19
Alignment explanation
Indices: 31142--31182 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
31132 ACATGTTGAG
31142 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
31161 TAGTTCAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
31182 T
1 T
31183 GCTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:45332 original size:17 final size:17
Alignment explanation
Indices: 45310--45343 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45300 GCAAAATATA
45310 CACACACAAAGGGGGAG
1 CACACACAAAGGGGGAG
**
45327 CACACACTTAGGGGGAG
1 CACACACAAAGGGGGAG
45344 TAATCTCCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.24, G:0.35, T:0.06
Consensus pattern (17 bp):
CACACACAAAGGGGGAG
Found at i:55973 original size:40 final size:40
Alignment explanation
Indices: 55916--56023 Score: 121
Period size: 41 Copynumber: 2.7 Consensus size: 40
55906 ATAGTGCCCG
* * *
55916 TGTGCACGTTGTGGGGGGATGCACATGATGATGTC-ATTA
1 TGTGCACGATGTGGGGGGATGCACATGATGATGCCGACTA
* * *
55955 TTTGTGCACGATGTGGGGGGATGCACACGATGGTGCCGGCTA
1 --TGTGCACGATGTGGGGGGATGCACATGATGATGCCGACTA
*
55997 TGTGCACGATGT-GGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGCACATGA
56024 GCCGGGTGTG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 13 0.22
40 12 0.21
41 31 0.53
42 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.39, T:0.27
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACATGATGATGCCGACTA
Found at i:59092 original size:2 final size:2
Alignment explanation
Indices: 59085--59115 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
59075 ATTATGTTGG
*
59085 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59116 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:62527 original size:20 final size:20
Alignment explanation
Indices: 62504--62547 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
62494 TTTATAATAT
* *
62504 TTAAA-TATTATTTAATTAAA
1 TTAAATTATAATTAAATT-AA
62524 TTAAATTATAATTAAATTAA
1 TTAAATTATAATTAAATTAA
62544 TTAA
1 TTAA
62548 TTAAACTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATTATAATTAAATTAA
Found at i:73952 original size:23 final size:21
Alignment explanation
Indices: 73917--73964 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
73907 AACATGTTTT
* *
73917 TATTTAATTTTAATTGTAAAATA
1 TATTGAATATTAATT-TAAAA-A
73940 TATTGAATATTAATTTAAAAA
1 TATTGAATATTAATTTAAAAA
73961 TATT
1 TATT
73965 TTAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 5 0.22
23 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
TATTGAATATTAATTTAAAAA
Found at i:77863 original size:20 final size:19
Alignment explanation
Indices: 77835--77884 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
77825 AATATCCAAG
*
77835 TTTCTAGCAACTTCTTCAAA
1 TTTCCAGCAA-TTCTTCAAA
*
77855 TTTCCAGCAGATTCTTCAAG
1 TTTCCAGCA-ATTCTTCAAA
*
77875 CTTCCAGCAA
1 TTTCCAGCAA
77885 ATTTTTCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (19 bp):
TTTCCAGCAATTCTTCAAA
Found at i:80434 original size:11 final size:11
Alignment explanation
Indices: 80418--80442 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
80408 GTTATCAAGG
80418 AAAAAAAATTT
1 AAAAAAAATTT
80429 AAAAAAAATTT
1 AAAAAAAATTT
80440 AAA
1 AAA
80443 GACTATGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAAAAATTT
Found at i:85031 original size:20 final size:19
Alignment explanation
Indices: 85003--85052 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
84993 AATATCCAAG
*
85003 TTTCTAGCAACTTCTTCAAA
1 TTTCCAGCAA-TTCTTCAAA
*
85023 TTTCCAGCAGATTCTTCAAG
1 TTTCCAGCA-ATTCTTCAAA
*
85043 CTTCCAGCAA
1 TTTCCAGCAA
85053 ATTTTTCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (19 bp):
TTTCCAGCAATTCTTCAAA
Found at i:86098 original size:40 final size:38
Alignment explanation
Indices: 86005--86110 Score: 149
Period size: 38 Copynumber: 2.7 Consensus size: 38
85995 GATAATGTCG
* *
86005 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACCGAT
* *
86043 TGTGCACGATGTGGGGGGATGCACATGATGGCGCCGACT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACCGA-T
*
86082 ATGTGCACGATGTGGGGGTATGTACATGA
1 -TGTGCACGATGTGGGGGGATGTACATGA
86111 GCCGGGTATG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 33 0.55
39 1 0.02
40 26 0.43
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACCGAT
Found at i:91551 original size:21 final size:21
Alignment explanation
Indices: 91494--91552 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
91484 GAATTTCATC
*
91494 TTAGAGTTTAGGGTAT-AGGT
1 TTAGAGTTTAGGGTTTAAGGT
**
91514 TTCAGAGTTTAAAGTTTAAGGT
1 TT-AGAGTTTAGGGTTTAAGGT
*
91536 TTAGGGTTTAGGGTTTA
1 TTAGAGTTTAGGGTTTA
91553 CAATAATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.06
21 23 0.74
22 6 0.19
ACGTcount: A:0.25, C:0.02, G:0.31, T:0.42
Consensus pattern (21 bp):
TTAGAGTTTAGGGTTTAAGGT
Found at i:117444 original size:51 final size:51
Alignment explanation
Indices: 117383--117575 Score: 161
Period size: 51 Copynumber: 3.6 Consensus size: 51
117373 TTGTGAGATA
* * *
117383 GGTCGAGCCTAGATTAAGTCTAAAAATTTTAATTGAATTTGTTCTAATATG
1 GGTCAAGCCTAGATCAAGTCTAAAAATTTTAATCGAATTTGTTCTAATATG
** * * * *
117434 GGTCAAGCCTAGATCAAGTCTAGAAATTTCAATTTTGTTTAAATCGAACCTGTTGTGAGATA
1 GGTCAAGCCTAGATCAAGTCT--AAA----AA---T-TTT-AATCGAATTTGTTCTAATATG
* * *
117496 GGTCGAGCCTAGATTAAGTCTAGAAATTTTAATCGAATTTGTTCTAATATG
1 GGTCAAGCCTAGATCAAGTCTAAAAATTTTAATCGAATTTGTTCTAATATG
* *
117547 GGTCAAGCCTAGATCAAGTCGAGAAATTT
1 GGTCAAGCCTAGATCAAGTCTAAAAATTT
117576 CATTTTTGTT
Statistics
Matches: 110, Mismatches: 21, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
51 60 0.55
52 3 0.03
53 4 0.04
56 2 0.02
57 2 0.02
60 3 0.03
61 3 0.03
62 33 0.30
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (51 bp):
GGTCAAGCCTAGATCAAGTCTAAAAATTTTAATCGAATTTGTTCTAATATG
Found at i:117549 original size:113 final size:113
Alignment explanation
Indices: 117351--117622 Score: 463
Period size: 113 Copynumber: 2.4 Consensus size: 113
117341 NNNNNNNNNN
117351 AATTTTGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAAAATTTTAAT
1 AATTTTGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAAAATTTTAAT
* *
117416 TGAATTTGTTCTAATATGGGTCAAGCCTAGATCAAGTCTAGAAATTTC
66 CGAATTTGTTCTAATATGGGTCAAGCCTAGATCAAGTCGAGAAATTTC
*
117464 AATTTTGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTTAAT
1 AATTTTGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAAAATTTTAAT
117529 CGAATTTGTTCTAATATGGGTCAAGCCTAGATCAAGTCGAGAAATTTC
66 CGAATTTGTTCTAATATGGGTCAAGCCTAGATCAAGTCGAGAAATTTC
* * * * * *
117577 ATTTTTGTTTAATTCGAACTTATTTTGAGATAAGTCGAGCCTAGAT
1 AATTTTGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGAT
117623 CGATTTGATT
Statistics
Matches: 150, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 150 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (113 bp):
AATTTTGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAAAATTTTAAT
CGAATTTGTTCTAATATGGGTCAAGCCTAGATCAAGTCGAGAAATTTC
Found at i:118841 original size:8 final size:8
Alignment explanation
Indices: 118828--118853 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
118818 TAAATTACAT
118828 TTTTTTTG
1 TTTTTTTG
118836 TTTTTTTG
1 TTTTTTTG
118844 TTTTTTTG
1 TTTTTTTG
118852 TT
1 TT
118854 ATGATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:123273 original size:13 final size:13
Alignment explanation
Indices: 123255--123279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
123245 TTTCAAAAAA
123255 TTTATAAAATCAT
1 TTTATAAAATCAT
123268 TTTATAAAATCA
1 TTTATAAAATCA
123280 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:124535 original size:19 final size:19
Alignment explanation
Indices: 124511--124547 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
124501 CTTCTAAACT
124511 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
124530 TCAAATCATACTCCAATA
1 TCAAATCATACTCCAATA
124548 AGTCAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:128144 original size:28 final size:28
Alignment explanation
Indices: 128058--128144 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
128048 GGGTGATTCT
* *
128058 AGCTATGTGGGGTGTGGAAGTGCACATG
1 AGCTATGTGCGGTGTGGGAGTGCACATG
** * *
128086 AGCTGATGACCGGTG-GGTGA-TG-A-TTCC
1 AGCT-ATGTGCGGTGTGG-GAGTGCACAT-G
128113 AGCTATGTGCGGTGTGGGAGTGCACATG
1 AGCTATGTGCGGTGTGGGAGTGCACATG
128141 AGCT
1 AGCT
128145 GATGACCAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 11 0.26
27 9 0.21
28 13 0.31
29 9 0.21
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (28 bp):
AGCTATGTGCGGTGTGGGAGTGCACATG
Found at i:128244 original size:111 final size:110
Alignment explanation
Indices: 128051--128260 Score: 330
Period size: 111 Copynumber: 1.9 Consensus size: 110
128041 TGATGACGGG
* * * * *
128051 TGATTCTAGCTATGTGGGGTGTGGAAGTGCACATGAGCTGATGACCGGTGGGTGATGATTCCAGC
1 TGATTCCAGCTATATGCGGTGTGGAACTGCACATGAGCTGATGACCGGTGGATGATGATTCCAGC
** *
128116 TATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCAATGGATGA
66 TATGTGCAATGTGGGAGTGCACATCAGCTGATGACCAATGGATGA
*
128161 TGATTCCAGCTATATGCGGTGTGGGACTGCACATGAGCTGATGAGCCGGTGGATGATGATTCCAG
1 TGATTCCAGCTATATGCGGTGTGGAACTGCACATGAGCTGATGA-CCGGTGGATGATGATTCCAG
128226 CTATGTGCAATGTGGGAGTGCACATCAGCTGATGA
65 CTATGTGCAATGTGGGAGTGCACATCAGCTGATGA
128261 GCTGGTGGTT
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
110 39 0.43
111 51 0.57
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.26
Consensus pattern (110 bp):
TGATTCCAGCTATATGCGGTGTGGAACTGCACATGAGCTGATGACCGGTGGATGATGATTCCAGC
TATGTGCAATGTGGGAGTGCACATCAGCTGATGACCAATGGATGA
Found at i:128268 original size:56 final size:55
Alignment explanation
Indices: 128051--128260 Score: 312
Period size: 55 Copynumber: 3.8 Consensus size: 55
128041 TGATGACGGG
* * * *
128051 TGATTCTAGCTATGTGGGGTGTGGAAGTGCACATGAGCTGATGACCGGTGGGTGA
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
**
128106 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCAATGGATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
* *
128161 TGATTCCAGCTATATGCGGTGTGGGACTGCACATGAGCTGATGAGCCGGTGGATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGA-CCGGTGGATGA
** *
128217 TGATTCCAGCTATGTGCAATGTGGGAGTGCACATCAGCTGATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGA
128261 GCTGGTGGTT
Statistics
Matches: 139, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
55 91 0.65
56 48 0.35
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.26
Consensus pattern (55 bp):
TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
Found at i:138084 original size:30 final size:26
Alignment explanation
Indices: 138014--138082 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
138004 TTGCTTGTAG
138014 GCCTATTTTAATTAATTTTGGGTCTA
1 GCCTATTTTAATTAATTTTGGGTCTA
138040 GCCTATTTTAATTAATTTTGGGTCTA
1 GCCTATTTTAATTAATTTTGGGTCTA
* *
138066 GCCCATTTTACTTAATT
1 GCCTATTTTAATTAATT
138083 AAAATGTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.49
Consensus pattern (26 bp):
GCCTATTTTAATTAATTTTGGGTCTA
Found at i:148728 original size:40 final size:40
Alignment explanation
Indices: 148673--148753 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
148663 GATGAATCAA
148673 AAGTCAATGGCCTATTTTCATTAACAACGCAAGACCTTCC
1 AAGTCAATGGCCTATTTTCATTAACAACGCAAGACCTTCC
148713 AAGTCAATGGCCTATTTTCATTAACAACGCAAGACCTTCC
1 AAGTCAATGGCCTATTTTCATTAACAACGCAAGACCTTCC
148753 A
1 A
148754 CGAAGATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (40 bp):
AAGTCAATGGCCTATTTTCATTAACAACGCAAGACCTTCC
Found at i:156954 original size:17 final size:17
Alignment explanation
Indices: 156932--156964 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
156922 TCGTTTATAA
156932 ATTAAA-ATTTGTAAATC
1 ATTAAATATTT-TAAATC
156949 ATTAAATATTTTAAAT
1 ATTAAATATTTTAAAT
156965 TCGATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTAAATATTTTAAATC
Found at i:157208 original size:18 final size:17
Alignment explanation
Indices: 157185--157218 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
157175 TCGTTTATAA
157185 GTTAAAAATTTGTAAACC
1 GTTAAAAATTT-TAAACC
*
157203 GTTAAACATTTTAAAC
1 GTTAAAAATTTTAAAC
157219 ATGAGAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (17 bp):
GTTAAAAATTTTAAACC
Found at i:157343 original size:252 final size:251
Alignment explanation
Indices: 156771--157895 Score: 1135
Period size: 252 Copynumber: 4.5 Consensus size: 251
156761 TTTATTATCA
* * * * *
156771 TAACTTGTTACATTGAATCTCACAGGGTTACATCAATATTTTGATATTGCTTGTT-TAACCTTTA
1 TAACTTGTTACGTTAAATCTCACA-AGTTACGTCAATATTTTGATATTACTTGTTCT-ACCTTTA
* * * * * * *
156835 TAACTTTTCACGTTAATTCTTATAGGTTTAAATCAAGGTTTTTCAATTACCT-ATTTTCACTATA
64 TAAGTTTTTACGTTAATTCTTACAAGTTTAAGTCAAAGTTTTTCAACTA-CTAATTTTCACTATA
* *
156899 ATTATTTTTATAC-TTACTATTATTCGTTTATAAATTAAAATTTGTAAATCATTAAATATTTTAA
128 ATTATTTTTAT-CTTTACTATTATTCGTTTATAAATTAAAATTTGTAAACCATTAAACATTTTAA
* * * * *
156963 A-TTCGATATTTATAAATGTAAATATTTAATTTCTCAAAAAACTATGTTTATTTGACTTAAT
192 ACATCGAGA-ATATAAATTTAAATATTTAATTT-TCAAAAAATTATGTTTATTTGACTTAAT
* * * * * * *
157024 TAGCTTATTACATTAAAT-TC-CGTAGGTCTACATCAATATTTTGATATTGA-TTATTCTACTTT
1 TAACTTGTTACGTTAAATCTCAC--AAGT-TACGTCAATATTTTGATATT-ACTTGTTCTACCTT
** * *
157086 TATAAGTTTTTATATTAATTTTTACATGTTTAAGTCAAAGTTTTTCAACTACTAATTTTCACTAT
62 TATAAGTTTTTACGTTAATTCTTACAAGTTTAAGTCAAAGTTTTTCAACTACTAATTTTCACTAT
* * * * *
157151 AATTATTTTTGTCTTTACAACTATTCGTTTATAAGTTAAAAATTTGTAAACCGTTAAACATTTTA
127 AATTATTTTTATCTTTACTATTATTCGTTTATAAATT-AAAATTTGTAAACCATTAAACATTTTA
* *
157216 AACAT-GAGAATAT-AATTTAAATGTTTAATTTGTCTAAAAATTATGTTTATTTGACTTAAT
191 AACATCGAGAATATAAATTTAAATATTTAATTT-TCAAAAAATTATGTTTATTTGACTTAAT
* ** *
157276 TAACTTGTTATGTTAAATCTCACAAGTCTACGTCAATATTTTGACGTTACTTGTTCCACCTTTAT
1 TAACTTGTTACGTTAAATCTCACAAGT-TACGTCAATATTTTGATATTACTTGTTCTACCTTTAT
* * *
157341 AAGTTTTTACGTTAAATT-TTACAAGTTTATGT-TAAGATTTTTCAACTACTAATTTTCGCTATA
65 AAGTTTTTACGTT-AATTCTTACAAGTTTAAGTCAAAG-TTTTTCAACTACTAATTTTCACTATA
* * * * *
157404 ATTCTTTTTATATTTACTATTATTCGTTTAAAAATTAAAAATTTGTAAACCATAAAACACTTTAA
128 ATTATTTTTATCTTTACTATTATTCGTTTATAAATT-AAAATTTGTAAACCATTAAACATTTTAA
* * * * * **
157469 AC-TCAAGAATATAAATTTAAACATTTAATTTCCTAAAAA-CA----TA--T--CTTTGT
192 ACATCGAGAATATAAATTTAAATATTTAATTTTCAAAAAATTATGTTTATTTGACTTAAT
* ** *
157519 TGACTTGTTACGTTAAATCTCACAAGTTTTGGTCAATATTTTGATATTACTTATTCTACCTTTAT
1 TAACTTGTTACGTTAAATCTCACAAG-TTACGTCAATATTTTGATATTACTTGTTCTACCTTTAT
* * * *
157584 AAGATTTTACGTTAATTCTTATATGTTTACGTCAAAGTTTTTCAACTACTACTAATTTTCACTAT
65 AAGTTTTTACGTTAATTCTTACAAGTTTAAGTCAAAGTTTTTC-A--ACTACTAATTTTCACTAT
* * * * *
157649 AATTATCTTTATCTTTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTTAAATAGTTTAA
127 AATTATTTTTATCTTTACTATTATTCGTTTATAAATTAAAATTTGTAAACCATTAAACATTTTAA
* *
157714 A-TTCAAGAATATAAATTTAAATATTTAATTTTCAAAAAAATTATGTTTATTTGACTTAAT
192 ACATCGAGAATATAAATTTAAATATTTAATTTTC-AAAAAATTATGTTTATTTGACTTAAT
* * * * * * * * *
157774 TGATTTGTTAGGTTAAATCTCACATGTTTCTGT-AATATTTTAACATTGCTTGTTCTATCTTTAT
1 TAACTTGTTACGTTAAATCTCACAAGTTAC-GTCAATATTTTGATATTACTTGTTCTACCTTTAT
* * * *
157838 AAGTTTTTACTTTAATTCTTACAAGTTTATGTCAAGGTTTTTCACCTACTAATTTTCA
65 AAGTTTTTACGTTAATTCTTACAAGTTTAAGTCAAAGTTTTTCAACTACTAATTTTCA
157896 TTAGCACTTG
Statistics
Matches: 728, Mismatches: 110, Indels: 70
0.80 0.12 0.08
Matches are distributed among these distances:
242 4 0.01
243 88 0.12
244 5 0.01
245 55 0.08
246 54 0.07
247 3 0.00
251 22 0.03
252 216 0.30
253 154 0.21
254 97 0.13
255 30 0.04
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.47
Consensus pattern (251 bp):
TAACTTGTTACGTTAAATCTCACAAGTTACGTCAATATTTTGATATTACTTGTTCTACCTTTATA
AGTTTTTACGTTAATTCTTACAAGTTTAAGTCAAAGTTTTTCAACTACTAATTTTCACTATAATT
ATTTTTATCTTTACTATTATTCGTTTATAAATTAAAATTTGTAAACCATTAAACATTTTAAACAT
CGAGAATATAAATTTAAATATTTAATTTTCAAAAAATTATGTTTATTTGACTTAAT
Found at i:161688 original size:19 final size:20
Alignment explanation
Indices: 161644--161692 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
161634 CCTAGTGATT
* *
161644 TATATATTTTACTTTTATCA
1 TATATATTTTTCTATTATCA
*
161664 T-CATATTTTTCTATTA-CA
1 TATATATTTTTCTATTATCA
161682 TATATATTTTT
1 TATATATTTTT
161693 AACATCCTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.12
19 20 0.83
20 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATATTTTTCTATTATCA
Found at i:164711 original size:16 final size:17
Alignment explanation
Indices: 164679--164728 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
164669 GAGATGACAC
164679 AAGACATTACTAACAAA
1 AAGACATTACTAACAAA
*
164696 AAGACA-TACTAGCAAAA
1 AAGACATTACTAAC-AAA
164713 ATAGACATTACTAACA
1 A-AGACATTACTAACA
164729 TTAGCATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 10 0.36
18 6 0.21
19 6 0.21
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (17 bp):
AAGACATTACTAACAAA
Found at i:169247 original size:97 final size:97
Alignment explanation
Indices: 169096--169308 Score: 327
Period size: 97 Copynumber: 2.2 Consensus size: 97
169086 TTGAAAGTAG
* *
169096 AAAGGGTGAGACCGTGAGACGATGAGAGTGGAGATGGAAGACTAAAAGTGCTTGGAAAGGCAGTG
1 AAAGGGTGAGACCGTGAGACGATGAAAGTGGAGATGGAAGACTAAAAGTGCTTGGAAAGGCAATG
* * *
169161 ATCGATCGACAGTCGGCAGAAGCAAAAATCAA
66 ATCAATAGACAGTCGGCAAAAGCAAAAATCAA
*
169193 AAAGGGTGAGACCGTGAGACGATGAAAGTGGAGATGGAAGACTAAAAGTGCTTGGAAGGGCAATG
1 AAAGGGTGAGACCGTGAGACGATGAAAGTGGAGATGGAAGACTAAAAGTGCTTGGAAAGGCAATG
** *
169258 ATCAATAGGTATTCGGCAAAAGCAAAAATCAA
66 ATCAATAGACAGTCGGCAAAAGCAAAAATCAA
* *
169290 AAAGGGTGAAACGGTGAGA
1 AAAGGGTGAGACCGTGAGA
169309 ATGGAGATGG
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 105 1.00
ACGTcount: A:0.40, C:0.12, G:0.33, T:0.15
Consensus pattern (97 bp):
AAAGGGTGAGACCGTGAGACGATGAAAGTGGAGATGGAAGACTAAAAGTGCTTGGAAAGGCAATG
ATCAATAGACAGTCGGCAAAAGCAAAAATCAA
Found at i:169512 original size:14 final size:14
Alignment explanation
Indices: 169495--169555 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
169485 TAATTTCATT
*
169495 AACCGAATTAACCG
1 AACCGAACTAACCG
*
169509 AACCGAACTAATCG
1 AACCGAACTAACCG
169523 AACTCTGAACTAACCG
1 AAC-C-GAACTAACCG
** *
169539 AACTAAACTAACTG
1 AACCGAACTAACCG
169553 AAC
1 AAC
169556 TTAGTTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 26 0.67
15 1 0.03
16 12 0.31
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.16
Consensus pattern (14 bp):
AACCGAACTAACCG
Found at i:174069 original size:13 final size:13
Alignment explanation
Indices: 174051--174090 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
174041 TTAAACAGTA
174051 AGAATTATGTTTG
1 AGAATTATGTTTG
174064 AGAATTAATGTTT-
1 AGAATT-ATGTTTG
174077 AGAATTATTGTTTG
1 AGAATTA-TGTTTG
174091 GGTTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 17 0.71
14 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (13 bp):
AGAATTATGTTTG
Found at i:174143 original size:85 final size:85
Alignment explanation
Indices: 173990--174263 Score: 403
Period size: 85 Copynumber: 3.3 Consensus size: 85
173980 AAAGAGTTTT
* * *
173990 ATGTTTAGAATTATTGTTTGGATAATTACTTAAAATGATT--T--GATGCTAGAATTAAACAGTA
1 ATGTTTAGAATTATTGTTTGGATAATTAATTAAAATGATTGGTAATATGCTAGAATTAAACATTA
*
174051 AGAATTATGTTTGAGAATTA
66 AGAATTATGTTTGGGAATTA
* **
174071 ATGTTTAGAATTATTGTTTGGGTTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAACATTA
1 ATGTTTAGAATTATTGTTTGGATAATTAATTAAAATGATTGGTAATATGCTAGAATTAAACATTA
174136 AGAATTATGTTTGGGAATTA
66 AGAATTATGTTTGGGAATTA
** * *
174156 ATGTTTAGAATTACCGTTTGGATAATTAATTAAAATGATTGGTAATATGCTCGAATTAAATATTA
1 ATGTTTAGAATTATTGTTTGGATAATTAATTAAAATGATTGGTAATATGCTAGAATTAAACATTA
*
174221 AAAATTATGTTTGGGAATTA
66 AGAATTATGTTTGGGAATTA
*
174241 ATATTTAGAATTATTGTTTGGAT
1 ATGTTTAGAATTATTGTTTGGAT
174264 GTTAGAATTA
Statistics
Matches: 171, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
81 36 0.21
83 1 0.01
85 134 0.78
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (85 bp):
ATGTTTAGAATTATTGTTTGGATAATTAATTAAAATGATTGGTAATATGCTAGAATTAAACATTA
AGAATTATGTTTGGGAATTA
Found at i:174241 original size:27 final size:27
Alignment explanation
Indices: 174208--174261 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
174198 TAATATGCTC
174208 GAATTAAATATTAAAAATTA-TGTTTGG
1 GAATT-AATATTAAAAATTATTGTTTGG
* *
174235 GAATTAATATTTAGAATTATTGTTTGG
1 GAATTAATATTAAAAATTATTGTTTGG
174262 ATGTTAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (27 bp):
GAATTAATATTAAAAATTATTGTTTGG
Found at i:174301 original size:59 final size:60
Alignment explanation
Indices: 174208--174382 Score: 298
Period size: 59 Copynumber: 2.9 Consensus size: 60
174198 TAATATGCTC
* * * *
174208 GAATTAAATATTAAAAATTATGTTTGGGAATTAATATTTAGAATTATTGTTTGGATGTTA
1 GAATTAAACATTAAGAATTACGTTTGGGAATTAATGTTTAGAATTATTGTTTGGATGTTA
*
174268 GAATTAAACATCAAGAATTA-GTTTGGGAATTAATGTTTAGAATTATTGTTTGGATGTTA
1 GAATTAAACATTAAGAATTACGTTTGGGAATTAATGTTTAGAATTATTGTTTGGATGTTA
174327 GAATTAAACATTAAGAATTACGTTTGGGAATTAATGTTTAGAATTATTGTTTGGAT
1 GAATTAAACATTAAGAATTACGTTTGGGAATTAATGTTTAGAATTATTGTTTGGAT
174383 TTTTAATTAA
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
59 57 0.52
60 52 0.48
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (60 bp):
GAATTAAACATTAAGAATTACGTTTGGGAATTAATGTTTAGAATTATTGTTTGGATGTTA
Found at i:174536 original size:83 final size:85
Alignment explanation
Indices: 174325--174547 Score: 342
Period size: 85 Copynumber: 2.6 Consensus size: 85
174315 GTTTGGATGT
* * * *
174325 TAGAATTAAACATTAAGAATTACGTTTGGGAATTAATGTTTAGAATTATTGTTTGGATTTTTAAT
1 TAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAAAATTATTGTTTGGATTTTCAAT
*
174390 TAAAATGATTGGCAATATGC
66 TAAAATGATTGACAATATGC
* * *
174410 TAGAATTAAATAGTAAAAATTATGTTTGGGAATTAATGCTTAAAATTATTGTTTGGATTTTCAAT
1 TAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAAAATTATTGTTTGGATTTTCAAT
*
174475 TAAAATTATTGAC-A-ATGC
66 TAAAATGATTGACAATATGC
*
174493 TAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAAAATTATTATTTG
1 TAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAAAATTATTGTTTG
174548 AACTTTTAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
83 55 0.44
84 1 0.01
85 69 0.55
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.42
Consensus pattern (85 bp):
TAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAAAATTATTGTTTGGATTTTCAAT
TAAAATGATTGACAATATGC
Found at i:176897 original size:52 final size:52
Alignment explanation
Indices: 176820--176923 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
176810 TTATTTTATT
176820 TTTTAGATTTGACTAATATTGTGTTGGAGATAATAGCTGAATCTGAGCCTGA
1 TTTTAGATTTGACTAATATTGTGTTGGAGATAATAGCTGAATCTGAGCCTGA
176872 TTTTAGATTTGACTAATATTGTGTTGGAGATAATAGCTGAATCTGAGCCTGA
1 TTTTAGATTTGACTAATATTGTGTTGGAGATAATAGCTGAATCTGAGCCTGA
176924 GTTGGACTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (52 bp):
TTTTAGATTTGACTAATATTGTGTTGGAGATAATAGCTGAATCTGAGCCTGA
Found at i:177217 original size:25 final size:25
Alignment explanation
Indices: 177189--177310 Score: 70
Period size: 25 Copynumber: 4.8 Consensus size: 25
177179 TTATTTATTT
177189 ATTTATTATATGAAGATTAATGTTA
1 ATTTATTATATGAAGATTAATGTTA
* * **
177214 ATTTCTTTTATGACCA-TATAT-TTA
1 ATTTATTATATGAAGATTA-ATGTTA
** * * *
177238 ATTATAGAACTTTTGAA-ACTAATGTTT
1 ATT-TATTA--TATGAAGATTAATGTTA
* * *
177265 ATTTATTATATAAAGATTAATATTT
1 ATTTATTATATGAAGATTAATGTTA
*
177290 ATTTATTGTATGAAGATTAAT
1 ATTTATTATATGAAGATTAAT
177311 ATTATTAATT
Statistics
Matches: 71, Mismatches: 19, Indels: 14
0.68 0.18 0.13
Matches are distributed among these distances:
24 12 0.17
25 42 0.59
26 6 0.08
27 11 0.15
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (25 bp):
ATTTATTATATGAAGATTAATGTTA
Found at i:177311 original size:25 final size:25
Alignment explanation
Indices: 177257--177327 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
177247 CTTTTGAAAC
*
177257 TAATGTTTATTTATTATATAAAGAT
1 TAATATTTATTTATTATATAAAGAT
* *
177282 TAATATTTATTTATTGTATGAAGAT
1 TAATATTTATTTATTATATAAAGAT
* *
177307 TAATA-TTATTAATTATTTAAA
1 TAATATTTATTTATTATATAAA
177328 AAATAAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 12 0.31
25 27 0.69
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (25 bp):
TAATATTTATTTATTATATAAAGAT
Found at i:177815 original size:16 final size:16
Alignment explanation
Indices: 177791--177841 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
177781 ATATTCATAA
177791 AAAAT-AAATAAAAAT
1 AAAATGAAATAAAAAT
*
177806 AAAATGAAATAAAAGT
1 AAAATGAAATAAAAAT
*
177822 GAAA-GTAAATAAAAAT
1 AAAATG-AAATAAAAAT
177838 AAAA
1 AAAA
177842 AATAACAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 6 0.20
16 24 0.80
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.18
Consensus pattern (16 bp):
AAAATGAAATAAAAAT
Found at i:181373 original size:19 final size:19
Alignment explanation
Indices: 181349--181393 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
181339 TGACTACTTA
181349 CTTGCCAAAGGATTTTATT
1 CTTGCCAAAGGATTTTATT
** *
181368 CTTGCCACTGGATTTTGTT
1 CTTGCCAAAGGATTTTATT
181387 CTTGCCA
1 CTTGCCA
181394 TTCTTGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (19 bp):
CTTGCCAAAGGATTTTATT
Found at i:192975 original size:6 final size:7
Alignment explanation
Indices: 192958--192991 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
192948 TCAAAAAGGC
192958 AAAAAAT
1 AAAAAAT
192965 AAAAAAT
1 AAAAAAT
192972 AAAAAA-
1 AAAAAAT
192978 ATAAAAAT
1 A-AAAAAT
192986 AAAAAA
1 AAAAAA
192992 GGGAACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 23 0.92
8 1 0.04
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:192976 original size:15 final size:14
Alignment explanation
Indices: 192958--192991 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
192948 TCAAAAAGGC
192958 AAAAAATAAAAAATA
1 AAAAAAT-AAAAATA
192973 AAAAAATAAAAATA
1 AAAAAATAAAAATA
192987 AAAAA
1 AAAAA
192992 GGGAACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:196584 original size:48 final size:48
Alignment explanation
Indices: 196529--196680 Score: 209
Period size: 48 Copynumber: 3.1 Consensus size: 48
196519 AGCCAAATCC
*
196529 TCCAAATTGGTTTAAAAAGGAAAAAAGAGCAAAAAAAAAAAAAAGATA
1 TCCAAATTGGTTTAAAAAGGAAAAAAGAGCAAAAAAAAAAAAAAGAAA
196577 TCCAAATTGGTTTAAAAAGGAAAAAAGAGC-AAAAAAAAAAAAAGAAA
1 TCCAAATTGGTTTAAAAAGGAAAAAAGAGCAAAAAAAAAAAAAAGAAA
* * * *
196624 TCCAAATTGGTTTTAAAAATAAGGGAAAAAGAG-AAAAAAAGAAAAAATAAT
1 TCCAAATTGG-TTT--AAA-AAGGAAAAAAGAGCAAAAAAAAAAAAAAGAAA
196675 TCCAAA
1 TCCAAA
196681 AAGAGCAAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
47 26 0.28
48 33 0.35
50 3 0.03
51 32 0.34
ACGTcount: A:0.63, C:0.07, G:0.14, T:0.16
Consensus pattern (48 bp):
TCCAAATTGGTTTAAAAAGGAAAAAAGAGCAAAAAAAAAAAAAAGAAA
Found at i:196682 original size:29 final size:31
Alignment explanation
Indices: 196649--196711 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
196639 AAAATAAGGG
* * *
196649 AAAAAGAG-AAAAAAAGAA-AAAATAATTCC
1 AAAAAGAGCAAAAAAAAAAGAAAAGAAATCC
196678 AAAAAGAGCAAAAAAAAAAGAAAAGAAATCC
1 AAAAAGAGCAAAAAAAAAAGAAAAGAAATCC
196709 AAA
1 AAA
196712 TTGGTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.28
30 9 0.31
31 12 0.41
ACGTcount: A:0.75, C:0.08, G:0.11, T:0.06
Consensus pattern (31 bp):
AAAAAGAGCAAAAAAAAAAGAAAAGAAATCC
Found at i:196776 original size:42 final size:42
Alignment explanation
Indices: 196597--196788 Score: 148
Period size: 42 Copynumber: 4.7 Consensus size: 42
196587 TTTAAAAAGG
*
196597 AAAAAAG-AGCAAAAAAAAA-A-AAAGAAATCCAAATTGGTTT
1 AAAAAAGAAG-AAAAAAAAAGAGAAAAAAATCCAAATTGGTTT
* * ** *** * ** *
196637 TAAAAATAAG--GGAAAAAGAGAAAAAAAGAAAAAATAATTC
1 AAAAAAGAAGAAAAAAAAAGAGAAAAAAATCCAAATTGGTTT
*
196677 CAAAAAG-AGCAAAAAAAAA-AGAAAAGAAATCCAAATTGGTTT
1 AAAAAAGAAG-AAAAAAAAAGAGAAAA-AAATCCAAATTGGTTT
* *
196719 AAAAAAGAAG-GAAAAAAAGAGAAAAAAATCTAAATTGGTTT
1 AAAAAAGAAGAAAAAAAAAGAGAAAAAAATCCAAATTGGTTT
* *
196760 AAAAAAGAAGAAAAAAATAGGGAAAAAAA
1 AAAAAAGAAGAAAAAAAAAGAGAAAAAAA
196789 GAAAACAAAA
Statistics
Matches: 113, Mismatches: 29, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
38 5 0.04
39 3 0.03
40 22 0.19
41 40 0.35
42 41 0.36
43 2 0.02
ACGTcount: A:0.67, C:0.05, G:0.15, T:0.13
Consensus pattern (42 bp):
AAAAAAGAAGAAAAAAAAAGAGAAAAAAATCCAAATTGGTTT
Found at i:196776 original size:82 final size:80
Alignment explanation
Indices: 196597--196746 Score: 237
Period size: 82 Copynumber: 1.8 Consensus size: 80
196587 TTTAAAAAGG
* * *
196597 AAAAAAGAGCAAAAAAAAAAAAAGAAATCCAAATTGGTTTTAAAAATAAGGGAAAAAGAGAAAAA
1 AAAAAAGAGCAAAAAAAAAAAAAGAAATCCAAATTGGTTTAAAAAAGAAGGAAAAAAGAGAAAAA
196662 AAGAAAAAATAATTC
66 AAGAAAAAATAATTC
*
196677 CAAAAAGAGCAAAAAAAAAAGAAAAGAAATCCAAATTGGTTTAAAAAAGAAGGAAAAAAAGAGAA
1 AAAAAAGAGC-AAAAAAAAA-AAAAGAAATCCAAATTGGTTTAAAAAAGAAGG-AAAAAAGAGAA
196742 AAAAA
63 AAAAA
196747 TCTAAATTGG
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
80 9 0.14
81 9 0.14
82 30 0.48
83 15 0.24
ACGTcount: A:0.69, C:0.05, G:0.15, T:0.11
Consensus pattern (80 bp):
AAAAAAGAGCAAAAAAAAAAAAAGAAATCCAAATTGGTTTAAAAAAGAAGGAAAAAAGAGAAAAA
AAGAAAAAATAATTC
Found at i:196786 original size:41 final size:41
Alignment explanation
Indices: 196597--196788 Score: 160
Period size: 41 Copynumber: 4.7 Consensus size: 41
196587 TTTAAAAAGG
196597 AAAAAAG-AGCAAAAAAAA-A-AAAAGAAATCCAAATTGGTTT
1 AAAAAAGAAG-AAAAAAAAGAGAAAA-AAATCCAAATTGGTTT
* * ** *** * ** *
196637 TAAAAATAAG-GGAAAAAGAGAAAAAAAGAAAAAATAATTC
1 AAAAAAGAAGAAAAAAAAGAGAAAAAAATCCAAATTGGTTT
* *
196677 CAAAAAG-AGCAAAAAAAAAAGAAAAGAAATCCAAATTGGTTT
1 AAAAAAGAAG-AAAAAAAAGAGAAAA-AAATCCAAATTGGTTT
* *
196719 AAAAAAGAAGGAAAAAAAGAGAAAAAAATCTAAATTGGTTT
1 AAAAAAGAAGAAAAAAAAGAGAAAAAAATCCAAATTGGTTT
*
196760 AAAAAAGAAGAAAAAAATAGGGAAAAAAA
1 AAAAAAGAAGAAAAAAA-AGAGAAAAAAA
196789 GAAAACAAAA
Statistics
Matches: 115, Mismatches: 29, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
39 7 0.06
40 20 0.17
41 48 0.42
42 38 0.33
43 2 0.02
ACGTcount: A:0.67, C:0.05, G:0.15, T:0.13
Consensus pattern (41 bp):
AAAAAAGAAGAAAAAAAAGAGAAAAAAATCCAAATTGGTTT
Found at i:201719 original size:21 final size:21
Alignment explanation
Indices: 201695--201740 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
201685 GTTAGTGTAC
201695 TTTCAAAAT-AAAAGGTAGTCT
1 TTTCAAAATGAAAAGGTA-TCT
*
201716 TTTC-AAATGAAAAGTTATCT
1 TTTCAAAATGAAAAGGTATCT
201736 TTTCA
1 TTTCA
201741 TATTGTGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (21 bp):
TTTCAAAATGAAAAGGTATCT
Found at i:214657 original size:20 final size:20
Alignment explanation
Indices: 214632--214677 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
214622 ATTTGTCCCC
214632 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
214652 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
214672 ATTTGA
1 ATTTGA
214678 GGCTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:226028 original size:36 final size:35
Alignment explanation
Indices: 225988--226118 Score: 129
Period size: 36 Copynumber: 3.7 Consensus size: 35
225978 TCAACCCAGC
* *
225988 TCATGTACACTCCCACACCGCACATA-ACTAATGTCA
1 TCATGTGCACTCCCACACCGCACA-AGAC-AATATCA
*
226024 TCATGTGCACTCCCACACCGCACAAGGCAATATCA
1 TCATGTGCACTCCCACACCGCACAAGACAATATCA
* * *** *
226059 TCATGCGCACTCCCACATCGCACCTCACCATCATCA
1 TCATGTGCACTCCCACACCGCACAAGACAAT-ATCA
* *
226095 TCATGTGCATTCTCACACCGCACA
1 TCATGTGCACTCCCACACCGCACA
226119 CGCACAGTTG
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
35 31 0.40
36 47 0.60
ACGTcount: A:0.29, C:0.40, G:0.11, T:0.21
Consensus pattern (35 bp):
TCATGTGCACTCCCACACCGCACAAGACAATATCA
Found at i:229211 original size:61 final size:61
Alignment explanation
Indices: 229063--229245 Score: 307
Period size: 61 Copynumber: 3.0 Consensus size: 61
229053 AAACATCATC
229063 ACCTACTCGTGGGAACCT-CCCACGCCACCATATATAAATCGGGGCTTCAGGTCCCCC-TTT
1 ACCTACTCGTGGGAA-CTACCCACGCCACCATATATAAATCGGGGCTTCAGGTCCCCCTTTT
* *
229123 ACCTACTCGTGGGAACTATCCACGCCACCTTATATAAATCGGGGCTTCAGGTCCCCCTTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCATATATAAATCGGGGCTTCAGGTCCCCCTTTT
* *
229184 ACCTACTCGTGGGAACTACCCACGCCACCCTATATAAATCGGGGCTTTAGGTCCCCCTTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCATATATAAATCGGGGCTTCAGGTCCCCCTTTT
229245 A
1 A
229246 TAATCAAAAT
Statistics
Matches: 116, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
59 2 0.02
60 52 0.45
61 62 0.53
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (61 bp):
ACCTACTCGTGGGAACTACCCACGCCACCATATATAAATCGGGGCTTCAGGTCCCCCTTTT
Found at i:229859 original size:3 final size:3
Alignment explanation
Indices: 229851--229892 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
229841 AGTGAAACTC
229851 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
229893 TTCTTTCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:230166 original size:16 final size:16
Alignment explanation
Indices: 230145--230238 Score: 55
Period size: 16 Copynumber: 5.9 Consensus size: 16
230135 TCTTCCTTCT
230145 TCTTTCTTCTTCTCTC
1 TCTTTCTTCTTCTCTC
* *
230161 TCTTTCTTTTTCTCTA
1 TCTTTCTTCTTCTCTC
* * * ** *
230177 GCATGCCCCTACTCTC
1 TCTTTCTTCTTCTCTC
* * * *
230193 CCTCTCTT-TTCCTTTT
1 TCTTTCTTCTT-CTCTC
*
230209 TCTTTTTTCTTCTCTC
1 TCTTTCTTCTTCTCTC
230225 TCTTTCTTCTTCTC
1 TCTTTCTTCTTCTC
230239 CAACACGTTG
Statistics
Matches: 51, Mismatches: 25, Indels: 4
0.64 0.31 0.05
Matches are distributed among these distances:
15 1 0.02
16 48 0.94
17 2 0.04
ACGTcount: A:0.03, C:0.36, G:0.02, T:0.59
Consensus pattern (16 bp):
TCTTTCTTCTTCTCTC
Found at i:230275 original size:37 final size:37
Alignment explanation
Indices: 230221--230312 Score: 166
Period size: 37 Copynumber: 2.5 Consensus size: 37
230211 TTTTTTCTTC
* *
230221 TCTCTCTTTCTTCTTCTCCAACACGTTGCTCTCCCTT
1 TCTCTCTTTCTTTTTCTCCAACACGTCGCTCTCCCTT
230258 TCTCTCTTTCTTTTTCTCCAACACGTCGCTCTCCCTT
1 TCTCTCTTTCTTTTTCTCCAACACGTCGCTCTCCCTT
230295 TCTCTCTTTCTTTTTCTC
1 TCTCTCTTTCTTTTTCTC
230313 TTGGCCGGCC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.07, C:0.39, G:0.04, T:0.50
Consensus pattern (37 bp):
TCTCTCTTTCTTTTTCTCCAACACGTCGCTCTCCCTT
Found at i:233482 original size:14 final size:14
Alignment explanation
Indices: 233463--233492 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
233453 GTTCCTTCAA
233463 TATGTCATACATAT
1 TATGTCATACATAT
233477 TATGTCATACATAT
1 TATGTCATACATAT
233491 TA
1 TA
233493 AAATCATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (14 bp):
TATGTCATACATAT
Found at i:235024 original size:2 final size:2
Alignment explanation
Indices: 235019--235043 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
235009 CATATATCTC
235019 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
235044 CTGAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:239757 original size:14 final size:15
Alignment explanation
Indices: 239738--239769 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
239728 AAATAATATT
239738 TTAATTAAT-ATTAA
1 TTAATTAATCATTAA
239752 TTAATTAATCATTAA
1 TTAATTAATCATTAA
239767 TTA
1 TTA
239770 TAAATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTAATCATTAA
Found at i:244783 original size:25 final size:25
Alignment explanation
Indices: 244765--244815 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
244755 TATAAAATGA
244765 TAATGATATT-TTAATTATAAAAAAT
1 TAATGA-ATTATTAATTATAAAAAAT
*
244790 TAATTAATTATTAATTATAAAAAAT
1 TAATGAATTATTAATTATAAAAAAT
244815 T
1 T
244816 TATTTAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATGAATTATTAATTATAAAAAAT
Found at i:246175 original size:33 final size:33
Alignment explanation
Indices: 246131--246199 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
246121 TGCGTGACGT
* *
246131 TGATGTAACATGTTAAA-ATATCATAATTGATTA
1 TGATGTAACATG-CAAATATATCATAATTGATGA
*
246164 TGATGTGACATGCAAATATATCATAATTGATGA
1 TGATGTAACATGCAAATATATCATAATTGATGA
246197 TGA
1 TGA
246200 CATGGCGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (33 bp):
TGATGTAACATGCAAATATATCATAATTGATGA
Found at i:250562 original size:29 final size:28
Alignment explanation
Indices: 250495--250563 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
250485 TGCAGTAATG
** *
250495 AAATTAAAATTTTATGTTTGAGAGGCGA
1 AAATTAAAATTCAATGTTTGAGAGACGA
*
250523 AAATAAAAAATTCAATGTTTGTAGAGAC-A
1 AAAT-TAAAATTCAATGTTTG-AGAGACGA
250552 AAATTATAAATT
1 AAATTA-AAATT
250564 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 5 0.15
29 23 0.70
30 5 0.15
ACGTcount: A:0.48, C:0.04, G:0.14, T:0.33
Consensus pattern (28 bp):
AAATTAAAATTCAATGTTTGAGAGACGA
Found at i:250609 original size:28 final size:27
Alignment explanation
Indices: 250567--250631 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 27
250557 ATAAATTTTT
250567 TTTAAAAATAAAAAATAAAAATT-TAAAA
1 TTTAAAAA-AAAAAA-AAAAATTATAAAA
*
250595 TTTAAAAAAATAAAAAAAAATTATTAAA
1 TTTAAAAAAA-AAAAAAAAATTATAAAA
250623 TTTAAAAAA
1 TTTAAAAAA
250632 TTTAGGGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (27 bp):
TTTAAAAAAAAAAAAAAAATTATAAAA
Found at i:255109 original size:19 final size:18
Alignment explanation
Indices: 255069--255113 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
255059 GCCATTTATT
255069 TTTTTCCCAAAATATTTC
1 TTTTTCCCAAAATATTTC
255087 TTTTTCCCAAAATATTTC
1 TTTTTCCCAAAATATTTC
255105 TTTTTCCCA
1 TTTTTCCCA
255114 TAAGAAGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTCCCAAAATATTTC
Found at i:260306 original size:24 final size:25
Alignment explanation
Indices: 260268--260320 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
260258 GATTAAAGGC
*
260268 TTAACATGATATAATT-TTAACATGA
1 TTAACATGATATAATTAAT-ACATGA
*
260293 TTAACGTGAT-TAATTAATACATGA
1 TTAACATGATATAATTAATACATGA
260317 TTAA
1 TTAA
260321 ATTTAAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (25 bp):
TTAACATGATATAATTAATACATGA
Found at i:267936 original size:30 final size:30
Alignment explanation
Indices: 267900--267959 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
267890 TCTCCTGCTG
267900 GAATATGTGCAACTGGTCCCTCACACTCAA
1 GAATATGTGCAACTGGTCCCTCACACTCAA
267930 GAATATGTGCAACTGGTCCCTCACACTCAA
1 GAATATGTGCAACTGGTCCCTCACACTCAA
267960 AGGCACCTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (30 bp):
GAATATGTGCAACTGGTCCCTCACACTCAA
Found at i:268552 original size:22 final size:23
Alignment explanation
Indices: 268521--268564 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
268511 GGTAGCTAAA
* *
268521 GTCACGCAATGC-CTACAAATAG
1 GTCACACAATGCTCAACAAATAG
268543 GTCACACAATGCTCAACAAATA
1 GTCACACAATGCTCAACAAATA
268565 TTTAGTCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.18
Consensus pattern (23 bp):
GTCACACAATGCTCAACAAATAG
Found at i:268735 original size:55 final size:55
Alignment explanation
Indices: 268659--268832 Score: 152
Period size: 55 Copynumber: 3.3 Consensus size: 55
268649 TGCAATGTTC
* *
268659 AACAAATATTTAGTCAGGTAATATTCAGTCACGTATTAACTCTCACGCAACGCTT
1 AACAAATATTCAGTCAGGTAATATTCAGTCACGTATAAACTCTCACGCAACGCTT
* * ** *
268714 AACATATATTCAGTCACGT-A-A-T--G-C-C-TATAAAGAACT-AGCGCAATG-TT
1 AACAAATATTCAGTCAGGTAATATTCAGTCACGTATAAA-CTCTCA-CGCAACGCTT
* * *
268761 CAATAAATATTCAGTCAGGTAATATTCAGTCACGTATCAACTCTCACGCAACGCTC
1 -AACAAATATTCAGTCAGGTAATATTCAGTCACGTATAAACTCTCACGCAACGCTT
*
268817 AACATATATTCAGTCA
1 AACAAATATTCAGTCA
268833 TTTAATGCCT
Statistics
Matches: 89, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
47 8 0.09
48 25 0.28
49 2 0.02
50 2 0.02
51 1 0.01
52 1 0.01
53 2 0.02
54 2 0.02
55 39 0.44
56 7 0.08
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (55 bp):
AACAAATATTCAGTCAGGTAATATTCAGTCACGTATAAACTCTCACGCAACGCTT
Found at i:268757 original size:103 final size:103
Alignment explanation
Indices: 268520--268874 Score: 453
Period size: 103 Copynumber: 3.5 Consensus size: 103
268510 AGGTAGCTAA
* * * ** * * *
268520 AGTCACGCAATGCCTACAAATAGGTCACACAATGCTCAACAAATATTTAGTCACGTAATATTAAG
1 AGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTTAGTCAGGTAATATTCAG
* * ** * * *
268585 TCATGTAACGCCTATCACACAACG-TTAACAAATATTC
66 TCACGTATCAACTCTCACGCAACGCTTAACATATATTC
* * *
268622 AGTCACGTAATGCCTATAAAAAACTCATGCAATGTTCAACAAATATTTAGTCAGGTAATATTCAG
1 AGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTTAGTCAGGTAATATTCAG
*
268687 TCACGTATTAACTCTCACGCAACGCTTAACATATATTC
66 TCACGTATCAACTCTCACGCAACGCTTAACATATATTC
* * *
268725 AGTCACGTAATGCCTATAAAGAACT-AGCGCAATGTTCAATAAATATTCAGTCAGGTAATATTCA
1 AGTCACGTAATGCCTATAAAGAACTCA-CGCAATGCTCAACAAATATTTAGTCAGGTAATATTCA
*
268789 GTCACGTATCAACTCTCACGCAACGCTCAACATATATTC
65 GTCACGTATCAACTCTCACGCAACGCTTAACATATATTC
** *
268828 AGTCATTTAATGCCTATAAAGAACTCACGCCATGCTCAACAAATATT
1 AGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATT
268875 CAGGAACCTA
Statistics
Matches: 221, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
102 73 0.33
103 147 0.67
104 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (103 bp):
AGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTTAGTCAGGTAATATTCAG
TCACGTATCAACTCTCACGCAACGCTTAACATATATTC
Found at i:270369 original size:28 final size:29
Alignment explanation
Indices: 270328--270387 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
270318 GTCTATGGGC
*
270328 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCAGTTTTAGGGGGCAAAAATGT
* * *
270356 AATTTTTGATTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAGTTTTA-GGGGGCAAAAATGT
270386 AA
1 AA
270388 ATATCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (29 bp):
AATTTTTCAGTTTTAGGGGGCAAAAATGT
Found at i:273200 original size:30 final size:30
Alignment explanation
Indices: 273166--273225 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
273156 GACAAGCTTG
*
273166 GGGGAGTGATCATTCACACTTGGGAAGCAT
1 GGGGAGTGATAATTCACACTTGGGAAGCAT
273196 GGGGAGTGATAATTCACACTTGGGAAGCAT
1 GGGGAGTGATAATTCACACTTGGGAAGCAT
273226 TCTTTAGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.23
Consensus pattern (30 bp):
GGGGAGTGATAATTCACACTTGGGAAGCAT
Found at i:276738 original size:2 final size:2
Alignment explanation
Indices: 276733--276777 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
276723 TAAAAACAAT
276733 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
276775 GA G
1 GA G
276778 TTGAGAGCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:284525 original size:7 final size:7
Alignment explanation
Indices: 284513--284553 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
284503 GGTTATTTAA
284513 TTATTAT
1 TTATTAT
284520 TTATTAT
1 TTATTAT
284527 TTATTA-
1 TTATTAT
284533 TTATTTAT
1 TTA-TTAT
284541 TTATTAT
1 TTATTAT
284548 TT-TTAT
1 TTATTAT
284554 ATATACTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 7 0.22
7 22 0.69
8 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTAT
Found at i:284548 original size:17 final size:17
Alignment explanation
Indices: 284505--284541 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 17
284495 AAAATTTTGG
284505 TTATTTAATTATTATTTA
1 TTATTT-ATTATTATTTA
284523 TTATTTATTATTATTTA
1 TTATTTATTATTATTTA
284540 TT
1 TT
284542 TATTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTATTATTATTTA
Found at i:284553 original size:17 final size:17
Alignment explanation
Indices: 284505--284553 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 17
284495 AAAATTTTGG
284505 TTATTTAATTATTATTTA-
1 TTATTT-ATTATT-TTTAT
284523 TTATTTATTA---TTAT
1 TTATTTATTATTTTTAT
284537 TTATTTATTATTTTTAT
1 TTATTTATTATTTTTAT
284554 ATATACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.11
14 10 0.37
17 8 0.30
18 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTATTATTTTTAT
Found at i:309649 original size:19 final size:20
Alignment explanation
Indices: 309620--309659 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
309610 TCACTTCTAA
309620 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
309640 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
309659 A
1 A
309660 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:311493 original size:42 final size:42
Alignment explanation
Indices: 311447--311592 Score: 184
Period size: 42 Copynumber: 3.5 Consensus size: 42
311437 CAGCTCATAT
* * ** *
311447 GCACTCCCACTAGCACATGGTTGGGTCAGCATTGGCTTATGC
1 GCACTCCCACTCGCACATAGTAAGGTCAGCATCGGCTTATGC
* *
311489 GCACTCCTACTCGCACATAGCAAGGTCAGCATCGGCTTATGC
1 GCACTCCCACTCGCACATAGTAAGGTCAGCATCGGCTTATGC
* * *
311531 GCACTCCCATTCGCACATAGTCAGGTCAGCATCGGCTTATGT
1 GCACTCCCACTCGCACATAGTAAGGTCAGCATCGGCTTATGC
* *
311573 ACACTCCTACTCGCACATAG
1 GCACTCCCACTCGCACATAG
311593 CCGAGTCAAC
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (42 bp):
GCACTCCCACTCGCACATAGTAAGGTCAGCATCGGCTTATGC
Found at i:311631 original size:2 final size:2
Alignment explanation
Indices: 311624--311650 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
311614 ACATTATTCG
311624 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
311651 CAACATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:313421 original size:73 final size:73
Alignment explanation
Indices: 313341--313489 Score: 253
Period size: 73 Copynumber: 2.0 Consensus size: 73
313331 AAGGGTGAGA
* * *
313341 AAAAAAGAGCTGTTAGACGATTAATTGGGAAGGTGAATTTAGACATAGTCTATTTCTAAGAAACT
1 AAAAAAGAGCTGTTAGACAATTAATTGGGAAAGTGAATCTAGACATAGTCTATTTCTAAGAAACT
313406 AAGTCAAG
66 AAGTCAAG
*
313414 AAAAAAGAGCTGTTAGATAATTAATTGGGAAAGTGAATCTAGACATAGTCTATTTCTAAGAAACT
1 AAAAAAGAGCTGTTAGACAATTAATTGGGAAAGTGAATCTAGACATAGTCTATTTCTAAGAAACT
*
313479 AAGTTAAG
66 AAGTCAAG
313487 AAA
1 AAA
313490 TATTACGCGA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.28
Consensus pattern (73 bp):
AAAAAAGAGCTGTTAGACAATTAATTGGGAAAGTGAATCTAGACATAGTCTATTTCTAAGAAACT
AAGTCAAG
Found at i:317361 original size:36 final size:36
Alignment explanation
Indices: 317285--317382 Score: 119
Period size: 36 Copynumber: 2.7 Consensus size: 36
317275 CACACATGCA
* *
317285 GAAGTAACGGGGGAAAAACAAATCACGCATAGCATC
1 GAAGCAACGGGCGAAAAACAAATCACGCATAGCATC
** *
317321 GAAGCAATTGGCGAAAAATCAAATCACGCGTATGC-T-
1 GAAGCAACGGGCGAAAAA-CAAATCACGCATA-GCATC
317357 GAAGCAACGGGCGAAAAACAAATCAC
1 GAAGCAACGGGCGAAAAACAAATCAC
317383 ACACAACGCC
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
35 8 0.15
36 30 0.57
37 13 0.25
38 2 0.04
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (36 bp):
GAAGCAACGGGCGAAAAACAAATCACGCATAGCATC
Found at i:317912 original size:12 final size:12
Alignment explanation
Indices: 317897--317929 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
317887 ATAGTATACA
317897 TACATATATATG
1 TACATATATATG
317909 TAC--ATATATG
1 TACATATATATG
317919 TACATATATAT
1 TACATATATAT
317930 ATGTATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.53
12 9 0.47
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (12 bp):
TACATATATATG
Found at i:320708 original size:26 final size:26
Alignment explanation
Indices: 320679--320730 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
320669 TTTTAAAAGT
* * *
320679 AAAAATTAGATTAAATAAAATTTTTA
1 AAAAATAAGATTAAAAAAAAGTTTTA
*
320705 AAAAATAATATTAAAAAAAAGTTTTA
1 AAAAATAAGATTAAAAAAAAGTTTTA
320731 GAAAGGAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
AAAAATAAGATTAAAAAAAAGTTTTA
Found at i:321811 original size:21 final size:21
Alignment explanation
Indices: 321787--321834 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
321777 AAAAAATTAA
321787 TTTAATATTTAGGATTTAGGG
1 TTTAATATTTAGGATTTAGGG
* *
321808 TTTAGA-GTTTAGGGTTTAGGG
1 TTTA-ATATTTAGGATTTAGGG
*
321829 TCTAAT
1 TTTAAT
321835 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.05
21 20 0.91
22 1 0.05
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.46
Consensus pattern (21 bp):
TTTAATATTTAGGATTTAGGG
Found at i:321828 original size:7 final size:7
Alignment explanation
Indices: 321794--321829 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
321784 TAATTTAATA
*
321794 TTTAGGA
1 TTTAGGG
321801 TTTAGGG
1 TTTAGGG
*
321808 TTTAGAG
1 TTTAGGG
321815 TTTAGGG
1 TTTAGGG
321822 TTTAGGG
1 TTTAGGG
321829 T
1 T
321830 CTAATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:325450 original size:64 final size:64
Alignment explanation
Indices: 325349--325505 Score: 228
Period size: 64 Copynumber: 2.5 Consensus size: 64
325339 GTGACACGGT
* *
325349 TGTGACATGCCAGCATTCAGAGTTGGTGAAACACCATGGAGGGTGAGAC-GCCATGGAGGGAATC
1 TGTGACAAGCCAGCATTCAGAGTTGGTGAAACACCATGGAGGGTGACACAG-CATGGAGGGAATC
* * *
325413 TGTGACACGCCAGCATTCAGAGTTGGTGAGACTCCATGGAGGGTGACACAGCATGGAGGGAATC
1 TGTGACAAGCCAGCATTCAGAGTTGGTGAAACACCATGGAGGGTGACACAGCATGGAGGGAATC
*
325477 TGTGACAAGCCAG-AGTTAAGAGTTGGTGA
1 TGTGACAAGCCAGCA-TTCAGAGTTGGTGA
325506 CACGACAGCG
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
63 1 0.01
64 83 0.98
65 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (64 bp):
TGTGACAAGCCAGCATTCAGAGTTGGTGAAACACCATGGAGGGTGACACAGCATGGAGGGAATC
Found at i:325553 original size:47 final size:47
Alignment explanation
Indices: 325502--325726 Score: 265
Period size: 47 Copynumber: 4.8 Consensus size: 47
325492 TTAAGAGTTG
* * * * *
325502 GTGACACGAC-AGCGTTCAGAATTGGTGAGACACCATGGAGGGAATCT
1 GTGACACG-CTAGAGTTCAGAGTTGGTGACACGCCATGGAAGGAATCT
* *
325549 GTGACATGCTAGAGTTCAGAGTTGGTGACACGGCATGGAAGGAATCT
1 GTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATGGAAGGAATCT
* * * * *
325596 GTGACACGCCA-ACGTTCAGAGTTTGTGAGACGCCATGGAGGGAATTT
1 GTGACACGCTAGA-GTTCAGAGTTGGTGACACGCCATGGAAGGAATCT
*
325643 GTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATGGAAGGAAGCT
1 GTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATGGAAGGAATCT
* * * *
325690 GTGACAAGCCAAAGTTCAAAGTTGGTGACACGCCATG
1 GTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATG
325727 TTTAGAGTGT
Statistics
Matches: 151, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
46 2 0.01
47 148 0.98
48 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21
Consensus pattern (47 bp):
GTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATGGAAGGAATCT
Found at i:325613 original size:94 final size:94
Alignment explanation
Indices: 325502--325726 Score: 326
Period size: 94 Copynumber: 2.4 Consensus size: 94
325492 TTAAGAGTTG
* * * *
325502 GTGACACGACAGCGTTCAGAATTGGTGAGACACCATGGAGGGAATCTGTGACATGCTAGAGTTCA
1 GTGACACGCCAACGTTCAGAATTGGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTTCA
* *
325567 GAGTTGGTGACACGGCATGGAAGGAATCT
66 GAGTTGGTGACACGCCATGGAAGGAAGCT
* * *
325596 GTGACACGCCAACGTTCAGAGTTTGTGAGACGCCATGGAGGGAATTTGTGACACGCTAGAGTTCA
1 GTGACACGCCAACGTTCAGAATTGGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTTCA
325661 GAGTTGGTGACACGCCATGGAAGGAAGCT
66 GAGTTGGTGACACGCCATGGAAGGAAGCT
* * *
325690 GTGACAAGCCAAAGTTCA-AAGTTGGTGACACGCCATG
1 GTGACACGCCAACGTTCAGAA-TTGGTGAGACGCCATG
325727 TTTAGAGTGT
Statistics
Matches: 116, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
93 1 0.01
94 115 0.99
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21
Consensus pattern (94 bp):
GTGACACGCCAACGTTCAGAATTGGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTTCA
GAGTTGGTGACACGCCATGGAAGGAAGCT
Found at i:325743 original size:23 final size:23
Alignment explanation
Indices: 325714--325791 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
325704 TTCAAAGTTG
325714 GTGACACGCCATGTTTAGAGTGT
1 GTGACACGCCATGTTTAGAGTGT
* * **
325737 GTGACACGGCATTGCTT-GAAAAGT
1 GTGACACGCCA-TGTTTAG-AGTGT
*
325761 -TGACACTCCATGGTTTAGAGTGT
1 GTGACACGCCAT-GTTTAGAGTGT
325784 GTGACACG
1 GTGACACG
325792 GCATTGCTTG
Statistics
Matches: 40, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
22 1 0.03
23 25 0.62
24 14 0.35
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (23 bp):
GTGACACGCCATGTTTAGAGTGT
Found at i:325777 original size:47 final size:47
Alignment explanation
Indices: 325715--325870 Score: 217
Period size: 47 Copynumber: 3.3 Consensus size: 47
325705 TCAAAGTTGG
* *
325715 TGACACGCCAT-GTTTAGAGTGTGTGACACGGCATTGCTTGAAAAGT
1 TGACACTCCATGGTTTAGAGTGTGTGACACGGCATTGCTTGAAAAGC
325761 TGACACTCCATGGTTTAGAGTGTGTGACACGGCATTGCTTGAAAAGC
1 TGACACTCCATGGTTTAGAGTGTGTGACACGGCATTGCTTGAAAAGC
* * * * * *
325808 TGACACACCATGGTTTAGAATGTGTGGCGCGACATTGCTTGAACAGC
1 TGACACTCCATGGTTTAGAGTGTGTGACACGGCATTGCTTGAAAAGC
325855 TGACACAT-CATGGTTT
1 TGACAC-TCCATGGTTT
325871 GAAATAGAGA
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
46 10 0.10
47 89 0.90
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (47 bp):
TGACACTCCATGGTTTAGAGTGTGTGACACGGCATTGCTTGAAAAGC
Found at i:326422 original size:31 final size:31
Alignment explanation
Indices: 326336--326597 Score: 290
Period size: 31 Copynumber: 8.5 Consensus size: 31
326326 CAGCGTTAGT
* * * * * *
326336 GTGTGACAACATTTGACTCGATATACATAGT
1 GTGTCACAACATTTTACTTGATATGCATGGC
* *
326367 GTGTCACAACATTTGACTTGATATGCATGAC
1 GTGTCACAACATTTTACTTGATATGCATGGC
*
326398 GTGTCACAACGTTTTACTTGATATGCATGGC
1 GTGTCACAACATTTTACTTGATATGCATGGC
* * *
326429 ATGTCACAACGTTTTACTTGAGATGCATGGC
1 GTGTCACAACATTTTACTTGATATGCATGGC
* * * *
326460 GTGTCACAACGTTTTACTTGAGATGTATGAC
1 GTGTCACAACATTTTACTTGATATGCATGGC
** * *
326491 GTGTCACAACATTTTACTTCTTACGAATGGC
1 GTGTCACAACATTTTACTTGATATGCATGGC
* * *
326522 ATGTCACAACATTTTGCTTGCTATGCATGGC
1 GTGTCACAACATTTTACTTGATATGCATGGC
* *
326553 GTGTCACAACATTTTTCTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGATATGCATGGC
*
326584 GTTTCACAACATTT
1 GTGTCACAACATTT
326598 ATTCCTTATT
Statistics
Matches: 200, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 200 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (31 bp):
GTGTCACAACATTTTACTTGATATGCATGGC
Found at i:328831 original size:31 final size:31
Alignment explanation
Indices: 328782--329056 Score: 388
Period size: 31 Copynumber: 8.9 Consensus size: 31
328772 GTCAACGTTA
*
328782 GCGTGTGACAACATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
328813 GCGTGTCAGAACAATTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
328844 GCGTGTCACAACGTTTAACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * *
328875 GCGTGTCAGAATATTTTGCTTGTTATCCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
*
328906 GCGTGTCACAACGTTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
328937 GCGTGTCACAACGTTTTGCTTGTTATCCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
328968 GTGCGTCACAACATTTTGCTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
328999 GCGTGTCACAACATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
329030 GCATCTCACAACATTTTACTTGTTATG
1 GCGTGTCACAACATTTTACTTGTTATG
329057 GTTTATGGCA
Statistics
Matches: 215, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 215 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (31 bp):
GCGTGTCACAACATTTTACTTGTTATGCATG
Found at i:330608 original size:16 final size:17
Alignment explanation
Indices: 330582--330654 Score: 82
Period size: 17 Copynumber: 4.5 Consensus size: 17
330572 CTGTACATTT
*
330582 TTTTATATACATAATTA
1 TTTTATATACACAATTA
330599 TTTT-TAT--ACAATTA
1 TTTTATATACACAATTA
* *
330613 ATTT-TATACACAATTT
1 TTTTATATACACAATTA
330629 TTTTATATACACAATTTA
1 TTTTATATACACAA-TTA
330647 TTTTATAT
1 TTTTATAT
330655 TATTCATTGT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
14 12 0.26
16 12 0.26
17 13 0.28
18 10 0.21
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATATACACAATTA
Found at i:330611 original size:14 final size:14
Alignment explanation
Indices: 330594--330635 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
330584 TTATATACAT
330594 AATTATTTTTATAC
1 AATTATTTTTATAC
*
330608 AATTAATTTTATACAC
1 AATT-ATTTT-TATAC
330624 AATT-TTTTTATA
1 AATTATTTTTATA
330636 TACACAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 3 0.12
14 8 0.33
15 5 0.21
16 8 0.33
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTATTTTTATAC
Found at i:330651 original size:47 final size:47
Alignment explanation
Indices: 330578--330725 Score: 172
Period size: 47 Copynumber: 3.1 Consensus size: 47
330568 TTGTCTGTAC
330578 ATTTTTTTATATACATAA-TTATTTTTATACAATTAATTTTATACACA
1 ATTTTTTTATATACATAATTTA-TTTTATACAATTAATTTTATACACA
* ** * * *
330625 ATTTTTTTATATACACAATTTATTTTATATTATTCATTGTATATAGAATTA
1 ATTTTTTTATATACATAATTTATTTTATACAATTAATT-T-TATA-CA-CA
* *
330676 ATTTTTTTATATACATAATATATTTTATACAATTAAATTTATACACA
1 ATTTTTTTATATACATAATTTATTTTATACAATTAATTTTATACACA
330723 ATT
1 ATT
330726 AATTTTTTTG
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
47 34 0.41
48 5 0.06
49 8 0.10
50 2 0.02
51 33 0.40
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (47 bp):
ATTTTTTTATATACATAATTTATTTTATACAATTAATTTTATACACA
Found at i:330686 original size:51 final size:51
Alignment explanation
Indices: 330578--330758 Score: 185
Period size: 51 Copynumber: 3.6 Consensus size: 51
330568 TTGTCTGTAC
* *
330578 ATTTTTTTATATACATAA-TTATTTTTATACAATTAATTTTATACAC----A
1 ATTTTTTTATATACACAATTTA-TTTTATACAATTAAATTTATACACAATTA
** * * *
330625 ATTTTTTTATATACACAATTTATTTTATATTATT-CATTGTATATAGAATTA
1 ATTTTTTTATATACACAATTTATTTTATACAATTAAATT-TATACACAATTA
* *
330676 ATTTTTTTATATACATAATATATTTTATACAATTAAATTTATACACAATTA
1 ATTTTTTTATATACACAATTTATTTTATACAATTAAATTTATACACAATTA
* *
330727 ATTTTTTTGCGTATACACAATTCATTTTATAC
1 ATTTTTTT--ATATACACAATTTATTTTATAC
330759 TAAGAATTTT
Statistics
Matches: 107, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
46 2 0.02
47 32 0.30
48 3 0.03
51 49 0.46
52 3 0.03
53 18 0.17
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (51 bp):
ATTTTTTTATATACACAATTTATTTTATACAATTAAATTTATACACAATTA
Found at i:331789 original size:31 final size:31
Alignment explanation
Indices: 331751--332112 Score: 428
Period size: 31 Copynumber: 11.7 Consensus size: 31
331741 TCTTTTGATG
* *
331751 TGCATGGCATGTGACAACATTTGACTTGTTA
1 TGCATGGCGTGTCACAACATTTGACTTGTTA
* *
331782 TGGATGGCGTGT--CAACATTTGACTTATTA
1 TGCATGGCGTGTCACAACATTTGACTTGTTA
* * *
331811 TGCATGGCGTGTCAGAACGTTTTACTTGTTA
1 TGCATGGCGTGTCACAACATTTGACTTGTTA
** *
331842 TGCATGGCGTGTCACAATGTTTGACTTGATA
1 TGCATGGCGTGTCACAACATTTGACTTGTTA
* * * * * *
331873 TGCATGGTGTGTCACAGCGTTTTATTTGATA
1 TGCATGGCGTGTCACAACATTTGACTTGTTA
* * * *
331904 TGTATGGCGTGTCACAACGTTTTACTTGATA
1 TGCATGGCGTGTCACAACATTTGACTTGTTA
*
331935 TGCATGGCGTGTTACAACATTTGACTTGTTA
1 TGCATGGCGTGTCACAACATTTGACTTGTTA
* *
331966 TGCATGGTGTGTCACAACATTTTACTTGTTA
1 TGCATGGCGTGTCACAACATTTGACTTGTTA
*
331997 TGCATGGCGTGTCACAACATTTTACTTGTTA
1 TGCATGGCGTGTCACAACATTTGACTTGTTA
332028 TGCATGGCGTGTCACAACTGATTT-ACTTGTTA
1 TGCATGGCGTGTCACAAC--ATTTGACTTGTTA
332060 TGCATGGCGTGTC-CGAACATTTTG-CTTGTTA
1 TGCATGGCGTGTCAC-AACA-TTTGACTTGTTA
*
332091 TGCATGGCATGTCACAACATTT
1 TGCATGGCGTGTCACAACATTT
332113 ATTTCTTCAG
Statistics
Matches: 292, Mismatches: 31, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
29 27 0.09
30 4 0.01
31 232 0.79
32 25 0.09
33 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (31 bp):
TGCATGGCGTGTCACAACATTTGACTTGTTA
Found at i:333141 original size:31 final size:31
Alignment explanation
Indices: 333102--333188 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
333092 CTGTAAGAAG
*
333102 TCAATGTGTCACGCCATAAGTTTGCATTAAG
1 TCAATGTGTCACGCCATAAGTTTGCATTAAC
* * * * *
333133 TTAGTGTGTCATGCCATAAGTCTGAATTAAC
1 TCAATGTGTCACGCCATAAGTTTGCATTAAC
*
333164 TCAACGTGTCACGCCATAAGTTTGC
1 TCAATGTGTCACGCCATAAGTTTGC
333189 TTGCACTCAG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (31 bp):
TCAATGTGTCACGCCATAAGTTTGCATTAAC
Found at i:337163 original size:31 final size:31
Alignment explanation
Indices: 337099--337181 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
337089 TTTGTCAGTC
* *
337099 ATGTTGTTACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCAATGCATATAACGTAAA
* *
337130 ATGTTGTAATACGCAATGCATATCAA-GTCAA
1 ATGTTGTAACACGCAATGCATAT-AACGTAAA
* * *
337161 ATGTCGTGACACGCCATGCAT
1 ATGTTGTAACACGCAATGCAT
337182 CACTGTCGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 41 0.95
32 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (31 bp):
ATGTTGTAACACGCAATGCATATAACGTAAA
Found at i:337312 original size:55 final size:55
Alignment explanation
Indices: 337228--337468 Score: 243
Period size: 55 Copynumber: 4.4 Consensus size: 55
337218 TCATTACACC
* * * *
337228 AACAGTCGTGACACGCTAAAAACCCAAAAAACCAGTTTACCCACAACACGTTAGG
1 AACAGCCGTGACACGCCAAAAACCCAAAAAACCAGTTAACCCACAACACGTCAGG
* * * * *
337283 AACAGCCGTGACATGCCCAAAACCCAAAAAACCAATTAACCCACGACACGCCAGG
1 AACAGCCGTGACACGCCAAAAACCCAAAAAACCAGTTAACCCACAACACGTCAGG
* * * * * *
337338 AACAGTCGTGACACACCAAAAACGCATAAATCTAGTTAACCCACTATACAC-T-AGG
1 AACAGCCGTGACACGCCAAAAACCCAAAAAACCAGTTAACCCAC-A-ACACGTCAGG
* * * * *
337393 AACAACCGTGACACGCTAACAACTCAAAAAACTAGTTAACCCACAACACGTCAGG
1 AACAGCCGTGACACGCCAAAAACCCAAAAAACCAGTTAACCCACAACACGTCAGG
* * *
337448 AACAGTCATGACACGCTAAAA
1 AACAGCCGTGACACGCCAAAA
337469 TAACGCTAAC
Statistics
Matches: 150, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
53 4 0.03
54 2 0.01
55 140 0.93
57 4 0.03
ACGTcount: A:0.43, C:0.30, G:0.14, T:0.13
Consensus pattern (55 bp):
AACAGCCGTGACACGCCAAAAACCCAAAAAACCAGTTAACCCACAACACGTCAGG
Found at i:337421 original size:110 final size:109
Alignment explanation
Indices: 337228--337461 Score: 274
Period size: 110 Copynumber: 2.1 Consensus size: 109
337218 TCATTACACC
* * * *
337228 AACAGTCGTGACACGCTAAAAACCCAAAAAACCAGTTTACCCACAACACGTTAGGAACAGCCGTG
1 AACAGTCGTGACACACCAAAAACCCAAAAAACCAGTTAACCCACAACACG-TAGGAACAACCGTG
* *
337293 ACATGCCCAAAACCCAAAAAACCAATTAACCCACGACACGCCAGG
65 ACACGCCCAAAACCCAAAAAACCAATTAACCCACAACACGCCAGG
* * * *
337338 AACAGTCGTGACACACCAAAAACGCATAAATCTAGTTAACCCACTATACAC-TAGGAACAACCGT
1 AACAGTCGTGACACACCAAAAACCCAAAAAACCAGTTAACCCAC-A-ACACGTAGGAACAACCGT
* * * * *
337402 GACACG-CTAACAACTCAAAAAACTAGTTAACCCACAACACGTCAGG
64 GACACGCCCAA-AACCCAAAAAACCAATTAACCCACAACACGCCAGG
*
337448 AACAGTCATGACAC
1 AACAGTCGTGACAC
337462 GCTAAAATAA
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
109 3 0.03
110 97 0.92
111 1 0.01
112 4 0.04
ACGTcount: A:0.42, C:0.31, G:0.14, T:0.13
Consensus pattern (109 bp):
AACAGTCGTGACACACCAAAAACCCAAAAAACCAGTTAACCCACAACACGTAGGAACAACCGTGA
CACGCCCAAAACCCAAAAAACCAATTAACCCACAACACGCCAGG
Found at i:339224 original size:22 final size:23
Alignment explanation
Indices: 339198--339247 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
339188 ATAATTTTAA
*
339198 TTAATTTA-AT-AAATTTATATAT
1 TTAATTTATATAAAATTAATA-AT
339220 TTAA-TTATATAAAATTAATAAT
1 TTAATTTATATAAAATTAATAAT
339242 TTAATT
1 TTAATT
339248 ACCACTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.12
22 12 0.50
23 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATTTATATAAAATTAATAAT
Found at i:339248 original size:22 final size:23
Alignment explanation
Indices: 339180--339248 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 23
339170 CTATGGGTTA
* *
339180 AAAAATTCATAATTTTAATTAATTT
1 AAAAATTAATAA-TTTAATT-ATAT
*
339205 AATAAATTTATATATTTAATTATAT
1 AA-AAATTAATA-ATTTAATTATAT
339230 -AAAATTAATAATTTAATTA
1 AAAAATTAATAATTTAATTA
339249 CCACTAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 9 0.23
23 8 0.21
24 1 0.03
25 5 0.13
26 15 0.38
27 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAAATTAATAATTTAATTATAT
Found at i:344212 original size:21 final size:21
Alignment explanation
Indices: 344188--344242 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
344178 ACTTCTTTCG
344188 CCTAGGTGGTTTCTGGGGGGA
1 CCTAGGTGGTTTCTGGGGGGA
*
344209 CCTAGGTGGTTTCTGGGGGTA
1 CCTAGGTGGTTTCTGGGGGGA
344230 CCTAGGTGGTTTC
1 CCTAGGTGGTTTC
344243 CATGGGAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.09, C:0.16, G:0.42, T:0.33
Consensus pattern (21 bp):
CCTAGGTGGTTTCTGGGGGGA
Found at i:344256 original size:21 final size:21
Alignment explanation
Indices: 344232--344286 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
344222 TGGGGGTACC
344232 TAGGTGGTTTCCATGGGAACT
1 TAGGTGGTTTCCATGGGAACT
344253 TAGGTGGTTTCCATGGGAACT
1 TAGGTGGTTTCCATGGGAACT
*
344274 TAGGTGGTATCCA
1 TAGGTGGTTTCCA
344287 GGCGTGAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.33
Consensus pattern (21 bp):
TAGGTGGTTTCCATGGGAACT
Found at i:357419 original size:15 final size:15
Alignment explanation
Indices: 357399--357440 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
357389 TAAAACAGTC
357399 TTAAAATCAAAAACT
1 TTAAAATCAAAAACT
* *
357414 TTAAAATCCAAAGCT
1 TTAAAATCAAAAACT
357429 TTAAAATCAAAA
1 TTAAAATCAAAA
357441 TATCTAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.26
Consensus pattern (15 bp):
TTAAAATCAAAAACT
Found at i:367737 original size:40 final size:40
Alignment explanation
Indices: 367647--367723 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
367637 ATTTATTTTA
* * *
367647 TTAATAATTGATAATTTAAATATTAATATTTTATATATAAT
1 TTAAT-ATTAATATTTTAAATATTAATATTTAATATATAAT
*
367688 TTAATATTAATATTTTAAATATTAATGTTTAA-ATAT
1 TTAATATTAATATTTTAAATATTAATATTTAATATAT
367724 TAATATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.12
40 23 0.72
41 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (40 bp):
TTAATATTAATATTTTAAATATTAATATTTAATATATAAT
Found at i:368404 original size:23 final size:23
Alignment explanation
Indices: 368353--368404 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
368343 TTTTTGAAAT
* *
368353 GTGAACCTAGGTGGTTTCCGGAT
1 GTGAACCTAGGTGGTATCCGGAC
*
368376 GGGAACCTAGGTGGTATCCAGG-C
1 GTGAACCTAGGTGGTATCC-GGAC
368399 GTGAAC
1 GTGAAC
368405 GTAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (23 bp):
GTGAACCTAGGTGGTATCCGGAC
Found at i:370806 original size:22 final size:22
Alignment explanation
Indices: 370781--370822 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
370771 TGGCTTTAGG
*
370781 CATTACGTGACTAATTTTTATA
1 CATTACATGACTAATTTTTATA
* *
370803 CATTGCATGACTGATTTTTA
1 CATTACATGACTAATTTTTA
370823 AGCAATGCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (22 bp):
CATTACATGACTAATTTTTATA
Found at i:370867 original size:23 final size:23
Alignment explanation
Indices: 370834--370916 Score: 112
Period size: 23 Copynumber: 3.6 Consensus size: 23
370824 GCAATGCCTA
* *
370834 AGTCACACAATACCTTACGAATT
1 AGTCACGCAATACCTTACGAACT
*
370857 AGTCACGCAATGCCTTACGAACT
1 AGTCACGCAATACCTTACGAACT
* *
370880 AGTCACGCAATGCCTTACGAACA
1 AGTCACGCAATACCTTACGAACT
*
370903 AGTCATGCAATACC
1 AGTCACGCAATACC
370917 CTATCAACTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (23 bp):
AGTCACGCAATACCTTACGAACT
Found at i:370926 original size:46 final size:46
Alignment explanation
Indices: 370834--370942 Score: 112
Period size: 46 Copynumber: 2.4 Consensus size: 46
370824 GCAATGCCTA
* * ** * *
370834 AGTCACACAATACCTTACGAATTAGTCACGCAATGCCTTACGAACT
1 AGTCACGCAATGCCTTACGAACAAGTCACGCAATACCCTACGAACT
*
370880 AGTCACGCAATGCCTTACGAACAAGTCATGCAATACCCTATC-AACT
1 AGTCACGCAATGCCTTACGAACAAGTCACGCAATACCCTA-CGAACT
* * *
370926 AGTTATGCAATGTCTTA
1 AGTCACGCAATGCCTTA
370943 TCATAAACTA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 51 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.26
Consensus pattern (46 bp):
AGTCACGCAATGCCTTACGAACAAGTCACGCAATACCCTACGAACT
Found at i:370961 original size:26 final size:26
Alignment explanation
Indices: 370922--371050 Score: 115
Period size: 26 Copynumber: 5.1 Consensus size: 26
370912 ATACCCTATC
* * *
370922 AACTAGTTATGCAATGTCTTATCATA
1 AACTAGTCACGCAATGTCTTATCAAA
*
370948 AACTAGTCACGCAAT-ACTT-T-AAA
1 AACTAGTCACGCAATGTCTTATCAAA
* * *
370971 AACTAATCAC-CTAATGCCTTATAAAA
1 AACTAGTCACGC-AATGTCTTATCAAA
* *
370997 AACTAGTCACGCAATATCTTATCAGA
1 AACTAGTCACGCAATGTCTTATCAAA
*
371023 AACTAGTCACGTAATG-CTTTATCAAA
1 AACTAGTCACGCAATGTC-TTATCAAA
371049 AA
1 AA
371051 TCAATCACGT
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
22 1 0.01
23 14 0.17
24 4 0.05
25 5 0.06
26 58 0.70
27 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.29
Consensus pattern (26 bp):
AACTAGTCACGCAATGTCTTATCAAA
Found at i:371059 original size:52 final size:49
Alignment explanation
Indices: 370947--371066 Score: 125
Period size: 52 Copynumber: 2.4 Consensus size: 49
370937 GTCTTATCAT
*
370947 AAACTAGTCACGCAATACTTTAAAAACTAATCACCTAATGCCTTATAAA
1 AAACTAATCACGCAATACTTTAAAAACTAATCACCTAATGCCTTATAAA
* * * * * *
370996 AAACTAGTCACGCAATATCTTATCAGAAACTAGTCACGTAATGCTTTATCAA
1 AAACTAATCACGCAATA-CTT-T-AAAAACTAATCACCTAATGCCTTATAAA
*
371048 AAA-TCAATCACGTAATACT
1 AAACT-AATCACGCAATACT
371067 CAAAGTCAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
49 17 0.28
50 3 0.05
51 4 0.07
52 36 0.60
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (49 bp):
AAACTAATCACGCAATACTTTAAAAACTAATCACCTAATGCCTTATAAA
Found at i:377607 original size:28 final size:27
Alignment explanation
Indices: 377576--377634 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
377566 GGTTAATTAA
377576 AAAATTAT-ATTTAATTTCACTAAAAAAT
1 AAAATTATAATTTAATTT--CTAAAAAAT
* * *
377604 AAAATTTTAATTTACTTTTTAAAAAAT
1 AAAATTATAATTTAATTTCTAAAAAAT
377631 AAAA
1 AAAA
377635 AAGGCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.44
28 7 0.26
29 8 0.30
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAATTATAATTTAATTTCTAAAAAAT
Found at i:377806 original size:15 final size:15
Alignment explanation
Indices: 377782--377812 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
377772 CCTTCGAAAC
377782 AAACACTATAATAAA
1 AAACACTATAATAAA
*
377797 AAACATTATAATAAA
1 AAACACTATAATAAA
377812 A
1 A
377813 TATACTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACACTATAATAAA
Found at i:384073 original size:10 final size:10
Alignment explanation
Indices: 384058--384100 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
384048 AAAAATAAAA
384058 TTTTTAAATT
1 TTTTTAAATT
384068 TTTTTAAATT
1 TTTTTAAATT
*
384078 TTTTT--TTT
1 TTTTTAAATT
384086 TTTTTAAATT
1 TTTTTAAATT
384096 TTTTT
1 TTTTT
384101 TACAATCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.24
10 22 0.76
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:384078 original size:18 final size:18
Alignment explanation
Indices: 384055--384098 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
384045 TTAAAAAATA
384055 AAATTTTTAAATTTTTTT
1 AAATTTTTAAATTTTTTT
***
384073 AAATTTTTTTTTTTTTTT
1 AAATTTTTAAATTTTTTT
384091 AAATTTTT
1 AAATTTTT
384099 TTTACAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
AAATTTTTAAATTTTTTT
Found at i:384099 original size:18 final size:18
Alignment explanation
Indices: 384066--384101 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
384056 AATTTTTAAA
384066 TTTTTTTAAATTTTTTTT
1 TTTTTTTAAATTTTTTTT
384084 TTTTTTTAAATTTTTTTT
1 TTTTTTTAAATTTTTTTT
384102 ACAATCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTAAATTTTTTTT
Done.