Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015350.1 Kokia drynarioides strain JFW-HI SEQ_130397, 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: 324464
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 268 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:69 original size:2 final size:2
Alignment explanation
Indices: 62--86 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52 AAATTCTAAT
62 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 T
87 TTAGATTGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1039 original size:108 final size:108
Alignment explanation
Indices: 850--1065 Score: 432
Period size: 108 Copynumber: 2.0 Consensus size: 108
840 TTGATGCGAG
850 TTCCAGAGTCAAATCTCAGACTCATGGATGTTATTGGCTTACACTACCTCAAGGTCTAATAACGA
1 TTCCAGAGTCAAATCTCAGACTCATGGATGTTATTGGCTTACACTACCTCAAGGTCTAATAACGA
915 GGTTAAGGGCCAAACAAATAAAAGCAAGATTGAAAGAAACCAT
66 GGTTAAGGGCCAAACAAATAAAAGCAAGATTGAAAGAAACCAT
958 TTCCAGAGTCAAATCTCAGACTCATGGATGTTATTGGCTTACACTACCTCAAGGTCTAATAACGA
1 TTCCAGAGTCAAATCTCAGACTCATGGATGTTATTGGCTTACACTACCTCAAGGTCTAATAACGA
1023 GGTTAAGGGCCAAACAAATAAAAGCAAGATTGAAAGAAACCAT
66 GGTTAAGGGCCAAACAAATAAAAGCAAGATTGAAAGAAACCAT
1066 ACAAGACTTT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (108 bp):
TTCCAGAGTCAAATCTCAGACTCATGGATGTTATTGGCTTACACTACCTCAAGGTCTAATAACGA
GGTTAAGGGCCAAACAAATAAAAGCAAGATTGAAAGAAACCAT
Found at i:5394 original size:25 final size:25
Alignment explanation
Indices: 5352--5400 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5342 TATACTTCTA
*
5352 AAACTATAGATAGCAAAACTATAGG
1 AAACTATAGATAGCAAAACGATAGG
*
5377 AAACTATATATGAG-AAAACGATAG
1 AAACTATAGAT-AGCAAAACGATAG
5401 AGATTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.20
Consensus pattern (25 bp):
AAACTATAGATAGCAAAACGATAGG
Found at i:12477 original size:14 final size:15
Alignment explanation
Indices: 12460--12499 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
12450 TAGATACAAT
12460 TTTATTTTATTTTA-
1 TTTATTTTATTTTAC
12474 TTTA-TTTATTTTAC
1 TTTATTTTATTTTAC
*
12488 TTT-TTGTATTTT
1 TTTATTTTATTTT
12500 GTATCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTATTTTATTTTAC
Found at i:12497 original size:18 final size:18
Alignment explanation
Indices: 12460--12498 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12450 TAGATACAAT
*
12460 TTTATTTTATTTTATTTA
1 TTTATTTTATTTTATGTA
12478 TTTATTTTACTTTT-TGTA
1 TTTATTTTA-TTTTATGTA
12496 TTT
1 TTT
12499 TGTATCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTATTTTATTTTATGTA
Found at i:22749 original size:17 final size:17
Alignment explanation
Indices: 22729--22772 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
22719 ATTATCAGTA
*
22729 CATTTTAATTGTCATTG
1 CATTTCAATTGTCATTG
22746 CATTTGC-ATTGTCATTG
1 CATTT-CAATTGTCATTG
22763 CATTTCAATT
1 CATTTCAATT
22773 TATTAGTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (17 bp):
CATTTCAATTGTCATTG
Found at i:26877 original size:28 final size:28
Alignment explanation
Indices: 26837--27080 Score: 114
Period size: 28 Copynumber: 9.0 Consensus size: 28
26827 TTTACATGTG
*
26837 TGCACAAGTACAAGCTGGGGAGCGTAAA
1 TGCACAAGTACAAGCTGGCGAGCGTAAA
*
26865 TGCACAAGTACAAGTTGGCGAGCGTAAA
1 TGCACAAGTACAAGCTGGCGAGCGTAAA
* *
26893 --CACATATGTATAAGCTGACGAGCGT--A
1 TGCACA-A-GTACAAGCTGGCGAGCGTAAA
* * * *
26919 --CACATGTGCAAGCTGACGAGTGTAAA
1 TGCACAAGTACAAGCTGGCGAGCGTAAA
* * *
26945 TGCATAAGTACAAGCTGGTGAGGGTAAA
1 TGCACAAGTACAAGCTGGCGAGCGTAAA
* * * * * *
26973 CGCATATGTATAAG-AGGACAAGCGT-AA
1 TGCACAAGTACAAGCTGG-CGAGCGTAAA
** * * * *
27000 ---ACGTGTGCAAGTTGGTGCGCGTAAA
1 TGCACAAGTACAAGCTGGCGAGCGTAAA
* * *
27025 TGCAAAAGTACAAGCTGGCCAGCATAAA
1 TGCACAAGTACAAGCTGGCGAGCGTAAA
* * * *
27053 TGCATATGTATAAGCTGACGAGCGTAAA
1 TGCACAAGTACAAGCTGGCGAGCGTAAA
27081 CGTGTGCAAG
Statistics
Matches: 159, Mismatches: 45, Indels: 24
0.70 0.20 0.11
Matches are distributed among these distances:
24 26 0.16
25 4 0.03
26 10 0.06
27 5 0.03
28 114 0.72
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.20
Consensus pattern (28 bp):
TGCACAAGTACAAGCTGGCGAGCGTAAA
Found at i:26980 original size:80 final size:80
Alignment explanation
Indices: 26847--27092 Score: 303
Period size: 80 Copynumber: 3.1 Consensus size: 80
26837 TGCACAAGTA
** * * *
26847 CAAGCTGGGGAGCGTAAATGCACAAGTACAAGTTGGCGAGCGTAAACACATATGTATAAGCTGAC
1 CAAGCTGACGAGCGTAAATGCAAAAGTACAAGCTGGCGAGCGTAAACGCATATGTATAAGCTGAC
* *
26912 GAGCGTACACATGTG
66 GAGCGTAAACGTGTG
* * * * **
26927 CAAGCTGACGAGTGTAAATGCATAAGTACAAGCTGGTGAGGGTAAACGCATATGTATAAGAGGAC
1 CAAGCTGACGAGCGTAAATGCAAAAGTACAAGCTGGCGAGCGTAAACGCATATGTATAAGCTGAC
*
26992 AAGCGTAAACGTGTG
66 GAGCGTAAACGTGTG
* ** * * * *
27007 CAAGTTGGTGCGCGTAAATGCAAAAGTACAAGCTGGCCAGCATAAATGCATATGTATAAGCTGAC
1 CAAGCTGACGAGCGTAAATGCAAAAGTACAAGCTGGCGAGCGTAAACGCATATGTATAAGCTGAC
27072 GAGCGTAAACGTGTG
66 GAGCGTAAACGTGTG
27087 CAAGCT
1 CAAGCT
27093 AGTGAGCATA
Statistics
Matches: 138, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
80 138 1.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (80 bp):
CAAGCTGACGAGCGTAAATGCAAAAGTACAAGCTGGCGAGCGTAAACGCATATGTATAAGCTGAC
GAGCGTAAACGTGTG
Found at i:27830 original size:39 final size:39
Alignment explanation
Indices: 27745--27831 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
27735 ATTTTATGGT
* * * * *
27745 CATACACGGGTGTGGGATTTGGGCGTGCTTGCTGCAGGG
1 CATACACGGGCGTAGGACTTGGGCGTGCTTGCTACAAGG
* * * *
27784 CACACACGGGCGTAGGACTTGGGCGTGTTTGTTATAAGG
1 CATACACGGGCGTAGGACTTGGGCGTGCTTGCTACAAGG
27823 CATACACGG
1 CATACACGG
27832 CCTGGCACAC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.18, C:0.20, G:0.38, T:0.24
Consensus pattern (39 bp):
CATACACGGGCGTAGGACTTGGGCGTGCTTGCTACAAGG
Found at i:28371 original size:26 final size:26
Alignment explanation
Indices: 28342--28394 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
28332 CACCCAAGAA
*
28342 TGTCGCTGCATGAACGTGTCCAAAAT
1 TGTCGCTACATGAACGTGTCCAAAAT
* *
28368 TGTCGCTACATGAATGTGTCCAGAAT
1 TGTCGCTACATGAACGTGTCCAAAAT
28394 T
1 T
28395 ACACCCAAAA
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:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (26 bp):
TGTCGCTACATGAACGTGTCCAAAAT
Found at i:29207 original size:16 final size:16
Alignment explanation
Indices: 29186--29216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29176 TTGTGGATCC
29186 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
29202 CATTTTATCTTTATT
1 CATTTTACCTTTATT
29217 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:33713 original size:32 final size:33
Alignment explanation
Indices: 33654--33726 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
33644 CAAATTTTAA
* * * * *
33654 AAAAATAATAATTTAATTTAAT-TTTTTTAATT
1 AAAAATATTAAATAAATTAAATCTTTTTTAACT
33686 AAAAATATTAAATAAATTAAATCTTTTTTAACT
1 AAAAATATTAAATAAATTAAATCTTTTTTAACT
33719 AAAAATAT
1 AAAAATAT
33727 AGATGAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 18 0.51
33 17 0.49
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (33 bp):
AAAAATATTAAATAAATTAAATCTTTTTTAACT
Found at i:36714 original size:53 final size:53
Alignment explanation
Indices: 36634--36794 Score: 130
Period size: 55 Copynumber: 2.9 Consensus size: 53
36624 CGTTTACTAA
* * *
36634 TATTATTTGTGACGTTTTTATAAGTCACCAAAACTATTTTTCGTGATGTTTGTAT-
1 TATT-TTTGTGAC-ATTTTAAAAGTCACCAAAAATATTTTTCGTGATGTTT-TATG
** * * *
36689 T-TTTTTGTGACATTTTAAAATGTCACCCTAATTATTTTTTCGTGACGTTTTTTG
1 TATTTTTGTGACATTTTAAAA-GTCACCAAAAATA-TTTTTCGTGATGTTTTATG
* * *
36743 TATTTTTGTGATATTTTTAAACA-TCACAAAAAATAATTTTCCGTGATGTTTT
1 TATTTTTGTGACA-TTTTAAA-AGTCACCAAAAAT-ATTTTTCGTGATGTTTT
36795 TCATTGATCA
Statistics
Matches: 85, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
52 7 0.08
53 20 0.24
54 17 0.20
55 32 0.38
56 8 0.09
57 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.50
Consensus pattern (53 bp):
TATTTTTGTGACATTTTAAAAGTCACCAAAAATATTTTTCGTGATGTTTTATG
Found at i:39495 original size:54 final size:54
Alignment explanation
Indices: 39359--39471 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
39349 TGCAGGGTTC
* * * * *
39359 ACACAACCTGACACACGGGCTGAGACA-CAAGCGTGTGGCCCAAGTCAGTGAGTT
1 ACACGACCTGACACATGAGCAGAGACATGAA-CGTGTGGCCCAAGTCAGTGAGTT
*
39413 ACACGACCTGTCACATGAGCAGAGACATGAACGTGTGGCCCAAGTCAGTGAGTT
1 ACACGACCTGACACATGAGCAGAGACATGAACGTGTGGCCCAAGTCAGTGAGTT
39467 ACACG
1 ACACG
39472 GTTTGACACA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 50 0.96
55 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (54 bp):
ACACGACCTGACACATGAGCAGAGACATGAACGTGTGGCCCAAGTCAGTGAGTT
Found at i:39524 original size:21 final size:21
Alignment explanation
Indices: 39499--39538 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39489 GCACATGGGC
* *
39499 GTGTGGGAGGGCCATACGGGT
1 GTGTGGGAGAGCCAAACGGGT
39520 GTGTGGGAGAGCCAAACGG
1 GTGTGGGAGAGCCAAACGG
39539 CCATGTGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.15, G:0.50, T:0.15
Consensus pattern (21 bp):
GTGTGGGAGAGCCAAACGGGT
Found at i:45678 original size:8 final size:8
Alignment explanation
Indices: 45662--45727 Score: 55
Period size: 8 Copynumber: 8.4 Consensus size: 8
45652 TTGAAGTTAC
45662 ATAT-TAT
1 ATATCTAT
*
45669 ATATTTAT
1 ATATCTAT
*
45677 ATAT-TCGT
1 ATATCT-AT
45685 ATATCTAT
1 ATATCTAT
*
45693 CTATCTAT
1 ATATCTAT
*
45701 CTATCTAT
1 ATATCTAT
*
45709 CTATCTAT
1 ATATCTAT
*
45717 ATATATAT
1 ATATCTAT
45725 ATA
1 ATA
45728 GATATATATG
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
7 5 0.10
8 45 0.88
9 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.52
Consensus pattern (8 bp):
ATATCTAT
Found at i:45695 original size:4 final size:4
Alignment explanation
Indices: 45686--45716 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
45676 TATATTCGTA
45686 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
45717 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:46026 original size:22 final size:20
Alignment explanation
Indices: 45999--46042 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
45989 ATCAAATACT
*
45999 TTTATTTTAATAATACATTATA
1 TTTATTATAATAATA-ATT-TA
46021 TTTATTATAATAATAATTTA
1 TTTATTATAATAATAATTTA
46041 TT
1 TT
46043 ATATGATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 3 0.14
22 14 0.67
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATTATAATAATAATTTA
Found at i:46145 original size:40 final size:44
Alignment explanation
Indices: 46056--46149 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
46046 TGATTATTAA
* *
46056 ATATAAATATTTATTTTTAATAATATTGAAAATTATAATATTTG
1 ATATTAATATTTATTTTTAATAATATTGAAAATTATAAAATTTG
*
46100 ATATTAATATTTTTTTTTAA-AA-ATT-AAAATTA-AAAATTT-
1 ATATTAATATTTATTTTTAATAATATTGAAAATTATAAAATTTG
46139 ATTATTAATAT
1 A-TATTAATAT
46150 AATAATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
39 1 0.02
40 15 0.33
41 7 0.15
42 3 0.07
43 2 0.04
44 18 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (44 bp):
ATATTAATATTTATTTTTAATAATATTGAAAATTATAAAATTTG
Found at i:46593 original size:2 final size:2
Alignment explanation
Indices: 46586--46617 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46576 TTCCATAATT
46586 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46618 AGAACGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49983 original size:12 final size:12
Alignment explanation
Indices: 49966--49996 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
49956 TCCCTCATCA
49966 AATTATAAATAC
1 AATTATAAATAC
49978 AATTATAAATAC
1 AATTATAAATAC
49990 AACTTAT
1 AA-TTAT
49997 GGTATCTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (12 bp):
AATTATAAATAC
Found at i:50911 original size:374 final size:374
Alignment explanation
Indices: 50222--50969 Score: 1487
Period size: 374 Copynumber: 2.0 Consensus size: 374
50212 ATTCTATAAC
50222 AATCTTGTCCATCAACTATATCCATATAGGAACAAAGCAATCTTTGTCATATTAACCATGACTAA
1 AATCTTGTCCATCAACTATATCCATATAGGAACAAAGCAATCTTTGTCATATTAACCATGACTAA
50287 ACTCATCAATGGTCACATATACAAATATAGTCAAATGACATAGATCAATCATAGTGATGTCATGC
66 ACTCATCAATGGTCACATATACAAATATAGTCAAATGACATAGATCAATCATAGTGATGTCATGC
50352 TACTGTGTACATGGGTTGGGTTGTACGGTGGAAGACGTGGTTATCACCCCTTCAAACGGCGAATA
131 TACTGTGTACATGGGTTGGGTTGTACGGTGGAAGACGTGGTTATCACCCCTTCAAACGGCGAATA
50417 CTAAAACTACACTACAATTGGTGACAATTGGATGGGAAGGGGTTCTAGGAAACCTCTCCATTGTG
196 CTAAAACTACACTACAATTGGTGACAATTGGATGGGAAGGGGTTCTAGGAAACCTCTCCATTGTG
50482 TTGGTGTGCAGGTGATTGGGTGCATTGCATTGCATTGTGTTTGTGATTTTGTTGCTTTGAGTTGT
261 TTGGTGTGCAGGTGATTGGGTGCATTGCATTGCATTGTGTTTGTGATTTTGTTGCTTTGAGTTGT
50547 AACATGTTGTGTGCTTACTTAAAATGTTTTGAGAAATTACGGTTATATT
326 AACATGTTGTGTGCTTACTTAAAATGTTTTGAGAAATTACGGTTATATT
*
50596 AATCTTGTCCATCAACTATATCCATATAGGATCAAAGCAATCTTTGTCATATTAACCATGACTAA
1 AATCTTGTCCATCAACTATATCCATATAGGAACAAAGCAATCTTTGTCATATTAACCATGACTAA
50661 ACTCATCAATGGTCACATATACAAATATAGTCAAATGACATAGATCAATCATAGTGATGTCATGC
66 ACTCATCAATGGTCACATATACAAATATAGTCAAATGACATAGATCAATCATAGTGATGTCATGC
50726 TACTGTGTACATGGGTTGGGTTGTACGGTGGAAGACGTGGTTATCACCCCTTCAAACGGCGAATA
131 TACTGTGTACATGGGTTGGGTTGTACGGTGGAAGACGTGGTTATCACCCCTTCAAACGGCGAATA
50791 CTAAAACTACACTACAATTGGTGACAATTGGATGGGAAGGGGTTCTAGGAAACCTCTCCATTGTG
196 CTAAAACTACACTACAATTGGTGACAATTGGATGGGAAGGGGTTCTAGGAAACCTCTCCATTGTG
50856 TTGGTGTGCAGGTGATTGGGTGCATTGCATTGCATTGTGTTTGTGATTTTGTTGCTTTGAGTTGT
261 TTGGTGTGCAGGTGATTGGGTGCATTGCATTGCATTGTGTTTGTGATTTTGTTGCTTTGAGTTGT
50921 AACATGTTGTGTGCTTACTTAAAATGTTTTGAGAAATTACGGTTATATT
326 AACATGTTGTGTGCTTACTTAAAATGTTTTGAGAAATTACGGTTATATT
50970 GTGTTTGTGA
Statistics
Matches: 373, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
374 373 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (374 bp):
AATCTTGTCCATCAACTATATCCATATAGGAACAAAGCAATCTTTGTCATATTAACCATGACTAA
ACTCATCAATGGTCACATATACAAATATAGTCAAATGACATAGATCAATCATAGTGATGTCATGC
TACTGTGTACATGGGTTGGGTTGTACGGTGGAAGACGTGGTTATCACCCCTTCAAACGGCGAATA
CTAAAACTACACTACAATTGGTGACAATTGGATGGGAAGGGGTTCTAGGAAACCTCTCCATTGTG
TTGGTGTGCAGGTGATTGGGTGCATTGCATTGCATTGTGTTTGTGATTTTGTTGCTTTGAGTTGT
AACATGTTGTGTGCTTACTTAAAATGTTTTGAGAAATTACGGTTATATT
Found at i:54500 original size:12 final size:12
Alignment explanation
Indices: 54483--54543 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
54473 ATAACATCCG
54483 AACAACCAAAAT
1 AACAACCAAAAT
*
54495 AACAACCAAAAG
1 AACAACCAAAAT
* *
54507 AGCAGCCAAAAT
1 AACAACCAAAAT
**
54519 AACAATAAAAAT
1 AACAACCAAAAT
*
54531 AGC-ACCAAAAT
1 AACAACCAAAAT
54542 AA
1 AA
54544 TAATAAAAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
11 7 0.19
12 30 0.81
ACGTcount: A:0.64, C:0.21, G:0.07, T:0.08
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:54515 original size:24 final size:23
Alignment explanation
Indices: 54487--54630 Score: 97
Period size: 23 Copynumber: 6.6 Consensus size: 23
54477 CATCCGAACA
*
54487 ACCAAAATAACAACCAAAAGAGC
1 ACCAAAATAACAACAAAAAGAGC
* *
54510 AGCCAAAATAACAATAAAAATAGC
1 A-CCAAAATAACAACAAAAAGAGC
* * *
54534 ACCAAAATAATAATAAAAATAGC
1 ACCAAAATAACAACAAAAAGAGC
* **
54557 ACCAAAACAGTAA-AAAAAGA--
1 ACCAAAATAACAACAAAAAGAGC
* * *
54577 ATCAAAACAATAA-AAAAA-A-C
1 ACCAAAATAACAACAAAAAGAGC
*
54597 ACCAAAATAGCAA-AAAAA-AGC
1 ACCAAAATAACAACAAAAAGAGC
*
54618 ACCAAAACAACAA
1 ACCAAAATAACAA
54631 TATAATTTTT
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 31 0.30
21 12 0.12
22 6 0.06
23 33 0.32
24 20 0.19
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.08
Consensus pattern (23 bp):
ACCAAAATAACAACAAAAAGAGC
Found at i:54538 original size:23 final size:23
Alignment explanation
Indices: 54487--54632 Score: 119
Period size: 20 Copynumber: 6.7 Consensus size: 23
54477 CATCCGAACA
** *
54487 ACCAAAATAACAACCAAAAGAGC
1 ACCAAAATAACAATAAAAAAAGC
*
54510 AGCCAAAATAACAATAAAAATAGC
1 A-CCAAAATAACAATAAAAAAAGC
* *
54534 ACCAAAATAATAATAAAAATAGC
1 ACCAAAATAACAATAAAAAAAGC
* *
54557 ACC--AA-AACAGTAAAAAAAGA
1 ACCAAAATAACAATAAAAAAAGC
* *
54577 ATC--AA-AACAATAAAAAAAAC
1 ACCAAAATAACAATAAAAAAAGC
*
54597 ACCAAAATAGC-A-AAAAAAAGC
1 ACCAAAATAACAATAAAAAAAGC
*
54618 ACCAAAACAACAATA
1 ACCAAAATAACAATA
54633 TAATTTTTTT
Statistics
Matches: 100, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
20 29 0.29
21 19 0.19
22 4 0.04
23 28 0.28
24 20 0.20
ACGTcount: A:0.66, C:0.18, G:0.06, T:0.09
Consensus pattern (23 bp):
ACCAAAATAACAATAAAAAAAGC
Found at i:59184 original size:20 final size:20
Alignment explanation
Indices: 59159--59209 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
59149 TTTTAAGATG
* *
59159 ATTTTGACTTGGTTCAAATT
1 ATTTTGACTTGGTTAAAATC
*
59179 ATTTTGACTTGTTTAAAATC
1 ATTTTGACTTGGTTAAAATC
*
59199 ATTTTAACTTG
1 ATTTTGACTTG
59210 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (20 bp):
ATTTTGACTTGGTTAAAATC
Found at i:59194 original size:40 final size:40
Alignment explanation
Indices: 59119--59209 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 40
59109 GCCTGGAGCT
* * *
59119 ATTTTGACTTGTTTGAAAAATATTTTGAAGTTTTAAGATG
1 ATTTTGACTTGGTTGAAAAATATTTTGAAGTTTTAAAATC
* * **
59159 ATTTTGACTTGGTT-CAAATTATTTTGACTTGTTTAAAATC
1 ATTTTGACTTGGTTGAAAAATATTTTGAAGT-TTTAAAATC
*
59199 ATTTTAACTTG
1 ATTTTGACTTG
59210 ATTTTAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 12 0.29
40 30 0.71
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (40 bp):
ATTTTGACTTGGTTGAAAAATATTTTGAAGTTTTAAAATC
Found at i:59851 original size:18 final size:17
Alignment explanation
Indices: 59820--59853 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
59810 CCAAAATATT
59820 AATTAATTAAATTTTCC
1 AATTAATTAAATTTTCC
*
59837 AATTAAATTATATTTTC
1 AATT-AATTAAATTTTC
59854 AACACATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTAATTAAATTTTCC
Found at i:65438 original size:24 final size:24
Alignment explanation
Indices: 65410--65461 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
65400 TTTCTGGAAG
* *
65410 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
65434 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
65458 ATTT
1 ATTT
65462 GATATTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:66552 original size:26 final size:25
Alignment explanation
Indices: 66523--66571 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
66513 AAATTACTTG
66523 AAAAAAAAAAATGGGCAAAATGATCT
1 AAAAAAAAAAAT-GGCAAAATGATCT
** *
66549 AAAAAATTAAATGTCAAAATGAT
1 AAAAAAAAAAATGGCAAAATGAT
66572 AATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.20
Consensus pattern (25 bp):
AAAAAAAAAAATGGCAAAATGATCT
Found at i:66580 original size:2 final size:2
Alignment explanation
Indices: 66573--66600 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
66563 CAAAATGATA
66573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66601 TAAGTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83025 original size:22 final size:22
Alignment explanation
Indices: 83000--83049 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
82990 GGCGGCGCAT
* *
83000 GGTGGTGCTAGCAATGGCGGAA
1 GGTGGTGCTAGCAACGACGGAA
*
83022 GGTGGTGCTAGCAACGACGGAC
1 GGTGGTGCTAGCAACGACGGAA
83044 GGTGGT
1 GGTGGT
83050 TGGAGATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTGGTGCTAGCAACGACGGAA
Found at i:83163 original size:13 final size:13
Alignment explanation
Indices: 83145--83169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83135 GTTGATGATT
83145 AAATAAAAAAAAG
1 AAATAAAAAAAAG
83158 AAATAAAAAAAA
1 AAATAAAAAAAA
83170 TGAAGAGAAT
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:0.88, C:0.00, G:0.04, T:0.08
Consensus pattern (13 bp):
AAATAAAAAAAAG
Found at i:86205 original size:17 final size:17
Alignment explanation
Indices: 86139--86205 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
86129 TTTAATTTCG
86139 ATATAGTACTAAT-T-T
1 ATATAGTACTAATATAT
* *
86154 GTATAGTACTAATATAA
1 ATATAGTACTAATATAT
* *
86171 ATATA-TATTTATATTAT
1 ATATAGTACTAATA-TAT
86188 ATATAGTA-TAATACTAT
1 ATATAGTACTAATA-TAT
86205 A
1 A
86206 CAAATCCAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 12 0.30
16 7 0.17
17 19 0.47
18 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (17 bp):
ATATAGTACTAATATAT
Found at i:91499 original size:18 final size:17
Alignment explanation
Indices: 91473--91507 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
91463 TATATGCATG
*
91473 TAAATTAAATGAAGTAAA
1 TAAAGTAAATGAA-TAAA
91491 TAAAGTAAATGAATAAA
1 TAAAGTAAATGAATAAA
91508 CTTATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (17 bp):
TAAAGTAAATGAATAAA
Found at i:93778 original size:24 final size:25
Alignment explanation
Indices: 93751--93804 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
93741 ATCTTCTAGA
*
93751 TAAACTT-TATTTATTTGCTTCAAT
1 TAAACTTCTATTTATTTACTTCAAT
*
93775 TAAA-TTCTATTTATTTATTTCAAT
1 TAAACTTCTATTTATTTACTTCAAT
*
93799 CAAACT
1 TAAACT
93805 CTTGTTAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.08
24 22 0.88
25 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (25 bp):
TAAACTTCTATTTATTTACTTCAAT
Found at i:95894 original size:111 final size:111
Alignment explanation
Indices: 95720--95930 Score: 307
Period size: 111 Copynumber: 1.9 Consensus size: 111
95710 ATTCGAGCTA
* * *
95720 TGTGCCTAGTAGGCTTTATGCTAGTGTATTCAAGCTATGTGCCTAGCAAACTTTGTGTCGGTGTA
1 TGTGCCTAGCAGGCTTTATGCTAGTGCATTCAAGCTATGTGCCTAGCAAACTTCGTGTCGGTGTA
**
95785 TTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGTATTCAGACTG
66 TTCAGGCTATGTGCCTAGCAGGCTTCATGCCGGTGTATTCAGACTG
* * * ** *
95831 TGTGCCTAGCAGGCTTTGTGCT-GATGCATTCAGGCTATGTGCCTAGTAGGCTTCGTGTTGGTGT
1 TGTGCCTAGCAGGCTTTATGCTAG-TGCATTCAAGCTATGTGCCTAGCAAACTTCGTGTCGGTGT
95895 ATTCAGGCTATGTGCCTAGCAGGCTTCATGCCGGTG
65 ATTCAGGCTATGTGCCTAGCAGGCTTCATGCCGGTG
95931 ATCCAATAAC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
110 1 0.01
111 87 0.99
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (111 bp):
TGTGCCTAGCAGGCTTTATGCTAGTGCATTCAAGCTATGTGCCTAGCAAACTTCGTGTCGGTGTA
TTCAGGCTATGTGCCTAGCAGGCTTCATGCCGGTGTATTCAGACTG
Found at i:95921 original size:37 final size:37
Alignment explanation
Indices: 95716--95920 Score: 268
Period size: 37 Copynumber: 5.5 Consensus size: 37
95706 ACAAATTCGA
* * * *
95716 GCTATGTGCCTAGTAGGCTTTATGCTAGTGTATTCAA
1 GCTATGTGCCTAGCAGGCTTTGTGCTGGTGTATTCAG
**
95753 GCTATGTGCCTAGCAAACTTTGTG-TCGGTGTATTCAG
1 GCTATGTGCCTAGCAGGCTTTGTGCT-GGTGTATTCAG
*
95790 GCTATGTGCCTAGCAGGCTTTGTGCCGGTGTATTCAG
1 GCTATGTGCCTAGCAGGCTTTGTGCTGGTGTATTCAG
* * * *
95827 ACTGTGTGCCTAGCAGGCTTTGTGCTGATGCATTCAG
1 GCTATGTGCCTAGCAGGCTTTGTGCTGGTGTATTCAG
* * *
95864 GCTATGTGCCTAGTAGGCTTCGTGTTGGTGTATTCAG
1 GCTATGTGCCTAGCAGGCTTTGTGCTGGTGTATTCAG
95901 GCTATGTGCCTAGCAGGCTT
1 GCTATGTGCCTAGCAGGCTT
95921 CATGCCGGTG
Statistics
Matches: 144, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
36 1 0.01
37 143 0.99
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.35
Consensus pattern (37 bp):
GCTATGTGCCTAGCAGGCTTTGTGCTGGTGTATTCAG
Found at i:97255 original size:25 final size:25
Alignment explanation
Indices: 97221--97270 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
97211 ATAGCAAGGC
97221 AGATAAGCAAGCTTCCGTTTTGGTA
1 AGATAAGCAAGCTTCCGTTTTGGTA
97246 AGATAAGCAAGCTTCCGTTTTGGTA
1 AGATAAGCAAGCTTCCGTTTTGGTA
97271 GCATCAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (25 bp):
AGATAAGCAAGCTTCCGTTTTGGTA
Found at i:99148 original size:15 final size:15
Alignment explanation
Indices: 99128--99157 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
99118 TTATCAAAAA
*
99128 TTTCTTTCTTTTTCT
1 TTTCTTCCTTTTTCT
99143 TTTCTTCCTTTTTCT
1 TTTCTTCCTTTTTCT
99158 CATTTTGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTTCCTTTTTCT
Found at i:99926 original size:24 final size:24
Alignment explanation
Indices: 99898--99946 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
99888 CTCACCCTCT
* * *
99898 TCTTTGTGCTTCTTCTTCTTCTTA
1 TCTTTATGCCTCTTCCTCTTCTTA
*
99922 TCTTTATGCCTCTTCCTCTTTTTA
1 TCTTTATGCCTCTTCCTCTTCTTA
99946 T
1 T
99947 TCGTCGTACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.27, G:0.06, T:0.61
Consensus pattern (24 bp):
TCTTTATGCCTCTTCCTCTTCTTA
Found at i:100257 original size:12 final size:12
Alignment explanation
Indices: 100242--100277 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
100232 CTTCTCTTTA
100242 TTCTCTTCTTCC
1 TTCTCTTCTTCC
100254 TTCTCTTCTT-C
1 TTCTCTTCTTCC
100265 TTC-CTT-TTCC
1 TTCTCTTCTTCC
100275 TTC
1 TTC
100278 AGTTGGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 4 0.17
12 10 0.43
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTCTTCTTCC
Found at i:101907 original size:15 final size:16
Alignment explanation
Indices: 101876--101917 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
101866 ACAAGGAATT
101876 TGAAACAAAAAAAAAG
1 TGAAACAAAAAAAAAG
*
101892 TGAAAC-AAATAAAAG
1 TGAAACAAAAAAAAAG
*
101907 T-AAATAAAAAA
1 TGAAACAAAAAA
101918 TGCGTCGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 13 0.59
16 6 0.27
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.12
Consensus pattern (16 bp):
TGAAACAAAAAAAAAG
Found at i:109877 original size:21 final size:21
Alignment explanation
Indices: 109837--109877 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
109827 CTCACCCTCT
*
109837 TCTTTGTGCTTATTCTTCTTG
1 TCTTTGTGCTTATTCCTCTTG
109858 TCTTTGTGCCTT-TTCCTCTT
1 TCTTTGTG-CTTATTCCTCTT
109878 TTTATCTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.02, C:0.24, G:0.12, T:0.61
Consensus pattern (21 bp):
TCTTTGTGCTTATTCCTCTTG
Found at i:110480 original size:24 final size:25
Alignment explanation
Indices: 110448--110500 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
110438 TGTGAATCCG
* *
110448 TGTTTATTTTTTTCAATTAAACT-T
1 TGTTTATTTGTTTCAATCAAACTCT
*
110472 TGTTTATTTGTTTCAGTCAAACTCT
1 TGTTTATTTGTTTCAATCAAACTCT
110497 TGTT
1 TGTT
110501 AGTTTAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.58
Consensus pattern (25 bp):
TGTTTATTTGTTTCAATCAAACTCT
Found at i:110790 original size:8 final size:8
Alignment explanation
Indices: 110777--110817 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
110767 ATTTGTGTGT
110777 TCAATTTC
1 TCAATTTC
110785 TCAATTTC
1 TCAATTTC
110793 TCAATTTC
1 TCAATTTC
110801 TCAATTTC
1 TCAATTTC
110809 TCAATTTC
1 TCAATTTC
110817 T
1 T
110818 TTCGTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (8 bp):
TCAATTTC
Found at i:111913 original size:68 final size:67
Alignment explanation
Indices: 111828--111965 Score: 204
Period size: 68 Copynumber: 2.0 Consensus size: 67
111818 CAGTTGATAT
* * *
111828 CATTTAATCACATTTAATTACATTAGTCACATGAATATTTCAACATTTATGACATCACATATTAA
1 CATTTAATCAAATTTAATCACATTAGTCACATGAATATTTCAACATTTATCACATCACAT-TTAA
111893 TCA
65 TCA
* * **
111896 CATTTAGTCAAATTTAATCACATTAGTCACATGAATATTTTATTATTTATCACATCACATTTAAT
1 CATTTAATCAAATTTAATCACATTAGTCACATGAATATTTCAACATTTATCACATCACATTTAAT
111961 CA
66 CA
111963 CAT
1 CAT
111966 GAATATTTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
67 10 0.16
68 53 0.84
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (67 bp):
CATTTAATCAAATTTAATCACATTAGTCACATGAATATTTCAACATTTATCACATCACATTTAAT
CA
Found at i:111967 original size:38 final size:38
Alignment explanation
Indices: 111912--112004 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 38
111902 GTCAAATTTA
* * **
111912 ATCACA-TTAGTCACATGAATATTTTATTATTTATCAC
1 ATCACATTTAATCACATGAATATTTCAGCATTTATCAC
111949 ATCACATTTAATCACATGAATATTTCAGCATTTATCAC
1 ATCACATTTAATCACATGAATATTTCAGCATTTATCAC
*
111987 ATCAAATATTAATCACAT
1 ATCACAT-TTAATCACAT
112005 TTAGTCATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
37 6 0.12
38 33 0.67
39 10 0.20
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (38 bp):
ATCACATTTAATCACATGAATATTTCAGCATTTATCAC
Found at i:112019 original size:59 final size:59
Alignment explanation
Indices: 111954--112260 Score: 389
Period size: 59 Copynumber: 5.1 Consensus size: 59
111944 ATCACATCAC
*
111954 ATTTAATCACATGAATATTTCAGCATTTATCACATCAAATATTAATCACATTTAGTCAT
1 ATTTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCAT
* * *
112013 ATTTAATCACATGAATGTTTCAGCATTTATCACATCACATATTAATAATATTTAGTCACATT
1 ATTTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGT--CA-T
* * * *
112075 AACACATTTAATCACATGAATATTTTAACATTTATCACATCACATATTAATCATATTTAGTCAC
1 -----ATTTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCAT
* * * * *
112139 ATTTAATCACATGAATGTTTCAGCATTTATCACATCACATATTAATAACATCTAATCAC
1 ATTTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCAT
* * * *
112198 ATTTAATCACATGAATATTTCAACATTTATCATATCACATATTAATCACATATAATCAT
1 ATTTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCAT
112257 ATTT
1 ATTT
112261 TATGATAAAT
Statistics
Matches: 218, Mismatches: 22, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
59 161 0.74
61 2 0.01
62 1 0.00
65 2 0.01
67 52 0.24
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (59 bp):
ATTTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCAT
Found at i:112042 original size:165 final size:164
Alignment explanation
Indices: 111831--112127 Score: 436
Period size: 165 Copynumber: 1.8 Consensus size: 164
111821 TTGATATCAT
* * * *
111831 TTAATCACATTTAATTACATTAGTCACATGAATATTTCAACATTTATGACATCACATATTAATCA
1 TTAATCACATTTAATCACATTAATCACATGAATATTTCAACATTTATCACATCACATATTAATAA
* **
111896 CATTTAGTCAAATTTAATCACA-TTAGTCACATGAATATTTTATTATTTATCACATCACAT-TTA
66 CATTTAGTCAAA-TTAA-CACATTTAATCACATGAATATTTTAACATTTATCACATCACATATTA
111959 ATCACATGAATATTTCAGCATTTATCACATCAAATA
129 ATCACATGAATATTTCAGCATTTATCACATCAAATA
* * * *
111995 TTAATCACATTTAGTCATATTTAATCACATGAATGTTTCAGCATTTATCACATCACATATTAATA
1 TTAATCACATTTAATCACA-TTAATCACATGAATATTTCAACATTTATCACATCACATATTAATA
* *
112060 ATATTTAGTCACATTAACACATTTAATCACATGAATATTTTAACATTTATCACATCACATATTAA
65 ACATTTAGTCAAATTAACACATTTAATCACATGAATATTTTAACATTTATCACATCACATATTAA
112125 TCA
130 TCA
112128 TATTTAGTCA
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
163 4 0.03
164 55 0.47
165 58 0.50
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (164 bp):
TTAATCACATTTAATCACATTAATCACATGAATATTTCAACATTTATCACATCACATATTAATAA
CATTTAGTCAAATTAACACATTTAATCACATGAATATTTTAACATTTATCACATCACATATTAAT
CACATGAATATTTCAGCATTTATCACATCAAATA
Found at i:112090 original size:126 final size:118
Alignment explanation
Indices: 111949--112260 Score: 462
Period size: 126 Copynumber: 2.6 Consensus size: 118
111939 TATTTATCAC
* *
111949 ATCACATTTAATCACATGAATATTTCAGCATTTATCACATCAAATATTAATCACATTTAGTCATA
1 ATCACATTTAATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCATA
* *
112014 TTTAATCACATGAATGTTTCAGCATTTATCACATCACATATTAATAATATTTAGTCA
66 TTTAATCACATGAATGTTTCAGCATTTATCACATCACATATTAATAACA--T-CT-A
* *
112071 CATTAACACATTTAATCACATGAATATTTTAACATTTATCACATCACATATTAATCATATTTAGT
1 -A-T--CACATTTAATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGT
*
112136 CACATTTAATCACATGAATGTTTCAGCATTTATCACATCACATATTAATAACATCTA
62 CATATTTAATCACATGAATGTTTCAGCATTTATCACATCACATATTAATAACATCTA
* * *
112193 ATCACATTTAATCACATGAATATTTCAACATTTATCATATCACATATTAATCACATATAATCATA
1 ATCACATTTAATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCATA
112258 TTT
66 TTT
112261 TATGATAAAT
Statistics
Matches: 173, Mismatches: 13, Indels: 11
0.88 0.07 0.06
Matches are distributed among these distances:
118 60 0.35
120 1 0.01
121 1 0.01
122 1 0.01
123 2 0.01
124 2 0.01
126 106 0.61
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.38
Consensus pattern (118 bp):
ATCACATTTAATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCATA
TTTAATCACATGAATGTTTCAGCATTTATCACATCACATATTAATAACATCTA
Found at i:112442 original size:64 final size:65
Alignment explanation
Indices: 112332--112463 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 65
112322 TACATGGATA
* * * *
112332 TCCAAACACACTAAATGACTCATAAAGTCAAACGTATCCCATAAGTGAAGCATATAA-CTAACAC
1 TCCAAACACACCAAAAGACTCA-AAAGTCAAACATATCCCAAAAGTGAAGCATA-AAGCTAACAC
112396 TC
64 TC
* *
112398 TCCAAACACACCAAAAGACTC-AAAGTCAAACATGTCCCAAAAGTGAAGCATAAAGCTAATACTC
1 TCCAAACACACCAAAAGACTCAAAAGTCAAACATATCCCAAAAGTGAAGCATAAAGCTAACACTC
112462 TC
1 TC
112464 ATTATTTCCC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
63 2 0.03
64 38 0.64
66 19 0.32
ACGTcount: A:0.45, C:0.27, G:0.10, T:0.19
Consensus pattern (65 bp):
TCCAAACACACCAAAAGACTCAAAAGTCAAACATATCCCAAAAGTGAAGCATAAAGCTAACACTC
Found at i:112769 original size:36 final size:36
Alignment explanation
Indices: 112717--112905 Score: 252
Period size: 36 Copynumber: 5.2 Consensus size: 36
112707 TAATATAATC
* * *
112717 ACTATCACATGACATGAAAAACATACACACATATTT
1 ACTATCACATGGCATGAATAACATACCCACATATTT
* * *
112753 ACTGTCACACGGCATGAATAACACACCCACATATTT
1 ACTATCACATGGCATGAATAACATACCCACATATTT
* * *
112789 ACTATCACATGCCATGAAAAACATACCCACGTATTT
1 ACTATCACATGGCATGAATAACATACCCACATATTT
* * *
112825 ACTGTCTCATGGCATGAATAACATACACACATATTT
1 ACTATCACATGGCATGAATAACATACCCACATATTT
*
112861 ACTATCATATGGCATGAATAACATACCCACATATTT
1 ACTATCACATGGCATGAATAACATACCCACATATTT
*
112897 ACTTTCACA
1 ACTATCACA
112906 ACAGTCATCC
Statistics
Matches: 129, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 129 1.00
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.27
Consensus pattern (36 bp):
ACTATCACATGGCATGAATAACATACCCACATATTT
Found at i:112805 original size:72 final size:72
Alignment explanation
Indices: 112717--112905 Score: 279
Period size: 72 Copynumber: 2.6 Consensus size: 72
112707 TAATATAATC
* *
112717 ACTATCACATGACATGAAAAACATACACACATATTTACTGTCACACGGCATGAATAACACACCCA
1 ACTATCACATGACATGAAAAACATACCCACATATTTACTGTCACACGGCATGAATAACACACACA
112782 CATATTT
66 CATATTT
* * * * *
112789 ACTATCACATGCCATGAAAAACATACCCACGTATTTACTGTCTCATGGCATGAATAACATACACA
1 ACTATCACATGACATGAAAAACATACCCACATATTTACTGTCACACGGCATGAATAACACACACA
112854 CATATTT
66 CATATTT
* * * *
112861 ACTATCATATGGCATGAATAACATACCCACATATTTACTTTCACA
1 ACTATCACATGACATGAAAAACATACCCACATATTTACTGTCACA
112906 ACAGTCATCC
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 104 1.00
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.27
Consensus pattern (72 bp):
ACTATCACATGACATGAAAAACATACCCACATATTTACTGTCACACGGCATGAATAACACACACA
CATATTT
Found at i:129922 original size:13 final size:13
Alignment explanation
Indices: 129904--129933 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
129894 TTATGAGCAA
129904 AATCGAGGAACTG
1 AATCGAGGAACTG
*
129917 AATCGAGGAATTG
1 AATCGAGGAACTG
129930 AATC
1 AATC
129934 CTCTTACTAT
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:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (13 bp):
AATCGAGGAACTG
Found at i:138104 original size:2 final size:2
Alignment explanation
Indices: 138097--138137 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
138087 GTATTGTATA
*
138097 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
138138 AAAATAGAAA
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:0.02, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:143392 original size:23 final size:25
Alignment explanation
Indices: 143366--143412 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
143356 TTCAATTAGA
143366 AAATTA-TTGTTTAG-ATTTAATTC
1 AAATTATTTGTTTAGAATTTAATTC
*
143389 AAATTATTTTTTTAGAATTTAATT
1 AAATTATTTGTTTAGAATTTAATT
143413 TGGATTCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (25 bp):
AAATTATTTGTTTAGAATTTAATTC
Found at i:144512 original size:14 final size:14
Alignment explanation
Indices: 144495--144527 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
144485 ATTATTTGCA
144495 TTTTTAATTTAATT
1 TTTTTAATTTAATT
144509 TTTTTAATTTAATT
1 TTTTTAATTTAATT
144523 TTTTT
1 TTTTT
144528 CCTTTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTAATTTAATT
Found at i:162996 original size:32 final size:32
Alignment explanation
Indices: 162951--163022 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
162941 CTATTTACTA
* * *
162951 AAAATAAATAATTTAGTCAAAAGAAAATTAGG
1 AAAATAAATAATTTAATCAAAACAAAATTAAG
*
162983 AAAATAACA-AATTTAATCAAAACAAAATTAAT
1 AAAATAA-ATAATTTAATCAAAACAAAATTAAG
163015 AAAATAAA
1 AAAATAAA
163023 CAACTTTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.03
32 33 0.94
33 1 0.03
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (32 bp):
AAAATAAATAATTTAATCAAAACAAAATTAAG
Found at i:164625 original size:2 final size:2
Alignment explanation
Indices: 164618--164642 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
164608 AATAAGATAC
164618 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 T
164643 TAAATCTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:165908 original size:33 final size:34
Alignment explanation
Indices: 165871--165943 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
165861 TTTTTGAAAT
*
165871 AAAAATTATAAATAAAAAATTTAAAA-GTT-CAAA
1 AAAAATTATAAAT-AAAAATATAAAACGTTACAAA
* * *
165904 AAAAAATATATATAAAAATATAAAACTTTACAAA
1 AAAAATTATAAATAAAAATATAAAACGTTACAAA
165938 AAAAAT
1 AAAAAT
165944 CTTAAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
32 11 0.33
33 13 0.39
34 9 0.27
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.26
Consensus pattern (34 bp):
AAAAATTATAAATAAAAATATAAAACGTTACAAA
Found at i:167208 original size:21 final size:22
Alignment explanation
Indices: 167162--167209 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
167152 AAATTTTGTA
* *
167162 AATTTTTAACATAATTGTTACT
1 AATTTTTAACATAATTCTTAAT
*
167184 -ATTTTTAATAT-ATTCTTAAT
1 AATTTTTAACATAATTCTTAAT
167204 AATTTT
1 AATTTT
167210 ATTAATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (22 bp):
AATTTTTAACATAATTCTTAAT
Found at i:174751 original size:19 final size:20
Alignment explanation
Indices: 174729--174773 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
174719 TCATTTCTCA
*
174729 TTTTTTCCTTCCTT-TCCTT
1 TTTTTTCCTTCCTTATCATT
*
174748 TTTTTTCCTTTCTTATCATT
1 TTTTTTCCTTCCTTATCATT
174768 TTTTTT
1 TTTTTT
174774 ATTTTCCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTCCTTCCTTATCATT
Found at i:181933 original size:25 final size:24
Alignment explanation
Indices: 181886--181933 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
181876 AAACTTCACA
* **
181886 TTTTTTTTAATTTAGTATTTAAAT
1 TTTTTTTTAATTTAATACCTAAAT
181910 TTTTTTATTAATTTAATACCTAAA
1 TTTTTT-TTAATTTAATACCTAAA
181934 CTTATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTTTTAATTTAATACCTAAAT
Found at i:183420 original size:2 final size:2
Alignment explanation
Indices: 183413--183446 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
183403 TAAGCAGTTA
183413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
183447 TAATTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:190192 original size:16 final size:17
Alignment explanation
Indices: 190162--190199 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
190152 TTGTTTTTTG
190162 TTTTTAGTTTAATTTAA
1 TTTTTAGTTTAATTTAA
* *
190179 TTTTTA-TTTTATTTAG
1 TTTTTAGTTTAATTTAA
190195 TTTTT
1 TTTTT
190200 TAGATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTTAGTTTAATTTAA
Found at i:194266 original size:114 final size:115
Alignment explanation
Indices: 194117--194503 Score: 311
Period size: 114 Copynumber: 3.4 Consensus size: 115
194107 ATGGTGCTAC
* * * * *
194117 TACCATTCCAGTAGATACCAACTTAG-ACCATGTAAAAGATGAAGATATGTCCAGCAACCCCAAG
1 TACCATTCCAGTAGATACAAATTTAGAACCATGTAAAAGATAAAGATATATCCAACAACCCCAAG
* * * *
194181 AATCTTGTAACTTATCCCAA-GCGTGAAGTAGCATCCTCAGAGACAAGTGT
66 AATCCTGTAACTTATCCCAAGGC-TAAAGTAGAATCCGCAGAGACAAGTGT
* * * * *
194231 TACCATTCCGGTAGATACAAATTTAGAATC-TGTAAAAGATAAAGGTTTATCGAACAACCCCAAG
1 TACCATTCCAGTAGATACAAATTTAGAACCATGTAAAAGATAAAGATATATCCAACAACCCCAAG
* * * *
194295 AATCCTGTAAGTTATCCCATGGCTAAAGTTGAATCCGCAGAGACGAGTGT
66 AATCCTGTAACTTATCCCAAGGCTAAAGTAGAATCCGCAGAGACAAGTGT
* * * * * * * * * * * * *
194345 TACAATTCCAGTAGATGCGAATTTAG-ACTATGTAACAGATAACGGTTTGTCCGATAGCCCCAAC
1 TACCATTCCAGTAGATACAAATTTAGAACCATGTAAAAGATAAAGATATATCCAACAACCCCAAG
* * * * * * **
194409 AATCCTGTAACTTCTCCTATGGCTAAAGTTA-CATCCTCAGAGACGAGCAT
66 AATCCTGTAACTTATCCCAAGGCTAAAG-TAGAATCCGCAGAGACAAGTGT
* * * *
194459 TACCATTCCAGTAGGTATGAACTTT-G-ACCATGTAAAAGATGAAGA
1 TACCATTCCAGTAGATA-CAAATTTAGAACCATGTAAAAGATAAAGA
194504 CTCCCATGCC
Statistics
Matches: 217, Mismatches: 51, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
113 1 0.00
114 207 0.95
115 9 0.04
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (115 bp):
TACCATTCCAGTAGATACAAATTTAGAACCATGTAAAAGATAAAGATATATCCAACAACCCCAAG
AATCCTGTAACTTATCCCAAGGCTAAAGTAGAATCCGCAGAGACAAGTGT
Found at i:198294 original size:18 final size:18
Alignment explanation
Indices: 198271--198315 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
198261 ACCTATAAAA
*
198271 TAATATAAAAATTAATAT
1 TAATATAAAAATTAATAG
*
198289 TAATATGAAAATTAATAG
1 TAATATAAAAATTAATAG
198307 TAATA-AAAA
1 TAATATAAAA
198316 TTTCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
TAATATAAAAATTAATAG
Found at i:198715 original size:31 final size:30
Alignment explanation
Indices: 198646--198715 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
198636 AAAAAATCTG
* * *
198646 CAATTA-TATATATGAAATTTAATTTTATG
1 CAATTATTATATATAAAATTTAATTTAATC
* *
198675 TAATT-TTATATATAAAATTTTGATTTAATC
1 CAATTATTATATATAAAA-TTTAATTTAATC
198705 CAATTATTATA
1 CAATTATTATA
198716 AATTATTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 14 0.44
30 13 0.41
31 5 0.16
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (30 bp):
CAATTATTATATATAAAATTTAATTTAATC
Found at i:202663 original size:19 final size:20
Alignment explanation
Indices: 202627--202664 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
202617 AATAATGTTT
*
202627 AAATATTAATACTCAAATAA
1 AAATATTAATACTAAAATAA
*
202647 AAAT-TTAATATTAAAATA
1 AAATATTAATACTAAAATA
202665 TACTCAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATATTAATACTAAAATAA
Found at i:211575 original size:2 final size:2
Alignment explanation
Indices: 211568--211596 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
211558 GAATGAATAA
211568 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 A
211597 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:213806 original size:22 final size:23
Alignment explanation
Indices: 213758--213811 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
213748 TCTTTTATAT
213758 AATTT-AT-AAATTTTTATGTTA
1 AATTTGATAAAATTTTTATGTTA
* *
213779 AATTTGGTAAAATTTTTA-GTTT
1 AATTTGATAAAATTTTTATGTTA
*
213801 ATTTTGATAAA
1 AATTTGATAAA
213812 CTAATACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 13 0.48
23 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (23 bp):
AATTTGATAAAATTTTTATGTTA
Found at i:213898 original size:64 final size:61
Alignment explanation
Indices: 213813--213946 Score: 178
Period size: 64 Copynumber: 2.1 Consensus size: 61
213803 TTTGATAAAC
* *
213813 TAATACAAAATAGTATCTAAATATTAATTTGATAAAAAGATAACATTAAACAATTGCAACATA
1 TAATATAAAATAGTATCTAAATATTAATTTCATAAAAA-ATAAC-TTAAACAATTGCAACATA
* * * * *
213876 TAAATATAAAATAGTATTTAAATATTAATTTCATAAAAATTAACTTAAATAATTGTAACATC
1 T-AATATAAAATAGTATCTAAATATTAATTTCATAAAAAATAACTTAAACAATTGCAACATA
213938 TAATATAAA
1 TAATATAAA
213947 TTCAACATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
61 8 0.13
62 16 0.25
63 5 0.08
64 34 0.54
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.34
Consensus pattern (61 bp):
TAATATAAAATAGTATCTAAATATTAATTTCATAAAAAATAACTTAAACAATTGCAACATA
Found at i:213957 original size:62 final size:64
Alignment explanation
Indices: 213830--213958 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 64
213820 AAATAGTATC
* **
213830 TAAATATTAATTTGATAAAAAGATAACATTAAACAATTGCAACATATAAATATAAAATAGTATT
1 TAAATATTAATTTCATAAAAAGATAACATTAAACAATTGCAACATATAAATATAAAATAACATT
* * * * *
213894 TAAATATTAATTTCATAAAAA-TTAAC-TTAAATAATTGTAACATCT-AATATAAATTCAACATT
1 TAAATATTAATTTCATAAAAAGATAACATTAAACAATTGCAACATATAAATATAAAAT-AACATT
213956 TAA
1 TAA
213959 CCTATCTTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
61 9 0.16
62 23 0.41
63 4 0.07
64 20 0.36
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.36
Consensus pattern (64 bp):
TAAATATTAATTTCATAAAAAGATAACATTAAACAATTGCAACATATAAATATAAAATAACATT
Found at i:216064 original size:20 final size:20
Alignment explanation
Indices: 216039--216079 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
216029 TGAATTTTAT
*
216039 ATATTATAATCTAAAATTAA
1 ATATTATAATCTAAAAATAA
* *
216059 ATATTATTATTTAAAAATAA
1 ATATTATAATCTAAAAATAA
216079 A
1 A
216080 AAATAAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATTATAATCTAAAAATAA
Found at i:219063 original size:16 final size:16
Alignment explanation
Indices: 219034--219096 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
219024 AATTTCTAAT
219034 CATTTTTATAAATTTTA
1 CATTTTTAT-AATTTTA
219051 CATTTTTATAATTTTA
1 CATTTTTATAATTTTA
* **
219067 TAAATTT-TAATTTTA
1 CATTTTTATAATTTTA
219082 -ATTTTTTATAATTTT
1 CA-TTTTTATAATTTT
219097 TGTGTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 1 0.03
15 11 0.28
16 18 0.46
17 9 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
CATTTTTATAATTTTA
Found at i:219065 original size:8 final size:8
Alignment explanation
Indices: 219037--219096 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
219027 TTCTAATCAT
219037 TTTTATAAA
1 TTTTAT-AA
* *
219046 TTTTACAT
1 TTTTATAA
219054 TTTTATAA
1 TTTTATAA
219062 TTTTATAA
1 TTTTATAA
*
219070 ATTT-TAA
1 TTTTATAA
*
219077 TTTTA-ATT
1 TTTTATA-A
219085 TTTTATAA
1 TTTTATAA
219093 TTTT
1 TTTT
219097 TGTGTTATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
7 7 0.17
8 27 0.68
9 6 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTATAA
Found at i:223306 original size:22 final size:22
Alignment explanation
Indices: 223272--223318 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
223262 GTTGTAAAGG
*
223272 TTAATTTCCAGGTTGGTTGTTT
1 TTAACTTCCAGGTTGGTTGTTT
*
223294 TTAACTTCTAGGTTGGTTGTTT
1 TTAACTTCCAGGTTGGTTGTTT
223316 TTA
1 TTA
223319 CTTTATTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.09, G:0.21, T:0.55
Consensus pattern (22 bp):
TTAACTTCCAGGTTGGTTGTTT
Found at i:224258 original size:24 final size:24
Alignment explanation
Indices: 224211--224269 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
224201 TAAAGTAAGT
*
224211 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATTA
224234 TATATTATAATTTTTACTAAT-TTA
1 TATATTATAATTTTT-CTAATATTA
*
224258 TATTTTAATAAT
1 TATATT-ATAAT
224270 AATTATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 4 0.13
24 17 0.55
25 10 0.32
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATTA
Found at i:224488 original size:16 final size:15
Alignment explanation
Indices: 224466--224518 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
224456 TTACTGATTA
224466 CATTACAGCTCTATT
1 CATTACAGCTCTATT
*
224481 CTATTACAACTCTATT
1 C-ATTACAGCTCTATT
*
224497 GCATTACAGTTCTATT
1 -CATTACAGCTCTATT
224513 CCATTA
1 -CATTA
224519 TAACAAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (15 bp):
CATTACAGCTCTATT
Found at i:224660 original size:3 final size:3
Alignment explanation
Indices: 224652--224683 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
224642 TTATATTGTT
224652 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
224684 GACTTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:225786 original size:29 final size:30
Alignment explanation
Indices: 225756--225810 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
225746 ATGGACTGAT
*
225756 TTTTAATATA-TATTTTTATAA-TTTTCTA
1 TTTTAATAGAGTATTTTTATAAGTTTTCTA
*
225784 TTTTATTAGAGTATTTTTATAAGTTTT
1 TTTTAATAGAGTATTTTTATAAGTTTT
225811 TACAATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 8 0.35
29 11 0.48
30 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (30 bp):
TTTTAATAGAGTATTTTTATAAGTTTTCTA
Found at i:230850 original size:29 final size:30
Alignment explanation
Indices: 230799--230860 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
230789 GCATAAAAAT
*** *
230799 AAAAAATATTAATTTTTGAAAAAA-AATAA
1 AAAAAATATTAAAAATTGAAAAAAGAAGAA
*
230828 AAAAAATATTAAAAATTGTAAAAAGAAGAA
1 AAAAAATATTAAAAATTGAAAAAAGAAGAA
230858 AAA
1 AAA
230861 TGTTTGTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (30 bp):
AAAAAATATTAAAAATTGAAAAAAGAAGAA
Found at i:234249 original size:21 final size:22
Alignment explanation
Indices: 234208--234251 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
234198 TTACATATTA
*
234208 AAATTTTATATAAAATCAATTT
1 AAATTTTATATAAAATAAATTT
*
234230 AAATTTTTTA-AAAATAAATTT
1 AAATTTTATATAAAATAAATTT
234251 A
1 A
234252 TAATATCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATTTTATATAAAATAAATTT
Found at i:234920 original size:41 final size:43
Alignment explanation
Indices: 234875--234954 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 43
234865 TTTCGACATT
234875 TAAT-ATAACATCA-CTAAAAAA-AA-TTAAATTTTAAAAAATAA
1 TAATAATAA-ATCATCTAAAAAAGAAGTT-AATTTTAAAAAATAA
* *
234916 TAATAATAAATCATTTAAAAAAGAAGTTGATTTTAAAAA
1 TAATAATAAATCATCTAAAAAAGAAGTTAATTTTAAAAA
234955 GTGCTAGCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
41 8 0.24
42 11 0.33
43 12 0.36
44 2 0.06
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (43 bp):
TAATAATAAATCATCTAAAAAAGAAGTTAATTTTAAAAAATAA
Found at i:240346 original size:28 final size:28
Alignment explanation
Indices: 240313--240366 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
240303 AAATAATAAT
*
240313 AATAATAA-TAGAAAATGTATAAAAAACC
1 AATAATAAGTA-AAAATGTAAAAAAAACC
*
240341 AATAATAAGTAATAATGTAAAAAAAA
1 AATAATAAGTAAAAATGTAAAAAAAA
240367 AAAAGACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (28 bp):
AATAATAAGTAAAAATGTAAAAAAAACC
Found at i:240368 original size:31 final size:30
Alignment explanation
Indices: 240333--240395 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
240323 GAAAATGTAT
* *
240333 AAAAAACCAATAATAAGTAATAATGTAAAAA
1 AAAAAAACAATAATAAATAATAAT-TAAAAA
* * *
240364 AAAAAAAGACTAATAAATAGTAATTAAAAA
1 AAAAAAACAATAATAAATAATAATTAAAAA
240394 AA
1 AA
240396 GAGTTGACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.70, C:0.05, G:0.06, T:0.19
Consensus pattern (30 bp):
AAAAAAACAATAATAAATAATAATTAAAAA
Found at i:241426 original size:20 final size:19
Alignment explanation
Indices: 241392--241436 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
241382 CATTTATTTA
*
241392 AATTTTAAATTTTTTTTAAT
1 AATTTTAAA-TATTTTTAAT
*
241412 AATTTTAACTATTTTTAAT
1 AATTTTAAATATTTTTAAT
*
241431 TATTTT
1 AATTTT
241437 TTTTGTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTTTAAATATTTTTAAT
Found at i:241861 original size:1 final size:1
Alignment explanation
Indices: 241820--241844 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
241810 ATTTGTAAGC
241820 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
241845 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:242090 original size:23 final size:23
Alignment explanation
Indices: 242060--242108 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
242050 TATTTTCAAT
242060 ATCAGTGTAGTGGGTGTGATAAA
1 ATCAGTGTAGTGGGTGTGATAAA
242083 ATCAGTGTAGTGGGTGTGATAAA
1 ATCAGTGTAGTGGGTGTGATAAA
242106 ATC
1 ATC
242109 TATTAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.31
Consensus pattern (23 bp):
ATCAGTGTAGTGGGTGTGATAAA
Found at i:252802 original size:24 final size:24
Alignment explanation
Indices: 252772--252834 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
252762 ATTAAGAATG
*
252772 TTATTAAATTATATATTATTAT-TT
1 TTATTAAATTATAT-TTATGATCTT
*
252796 TTGTTAAA-T-TATTTATGATCTT
1 TTATTAAATTATATTTATGATCTT
252818 TTATTAAATTATATTTA
1 TTATTAAATTATATTTA
252835 ATAACAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 6 0.18
22 12 0.36
23 2 0.06
24 13 0.39
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (24 bp):
TTATTAAATTATATTTATGATCTT
Found at i:252824 original size:22 final size:22
Alignment explanation
Indices: 252772--252832 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
252762 ATTAAGAATG
*
252772 TTATTAAATTATATATTATTATTT
1 TTATTAAA-T-TATATTATGATTT
*
252796 TTGTTAAATTAT-TTATGATCTT
1 TTATTAAATTATATTATGAT-TT
252818 TTATTAAATTATATT
1 TTATTAAATTATATT
252833 TAATAACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 6 0.19
22 16 0.50
23 3 0.09
24 7 0.22
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (22 bp):
TTATTAAATTATATTATGATTT
Found at i:253021 original size:16 final size:16
Alignment explanation
Indices: 253000--253051 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
252990 TGAATTATTG
*
253000 ATTACAATTATATTCC
1 ATTACAACTATATTCC
* *
253016 ATTACAACTCTATTTC
1 ATTACAACTATATTCC
* *
253032 ATTACAGCTATATTCT
1 ATTACAACTATATTCC
253048 ATTA
1 ATTA
253052 TAGCTCTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTACAACTATATTCC
Found at i:253037 original size:32 final size:32
Alignment explanation
Indices: 253000--253061 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
252990 TGAATTATTG
*
253000 ATTACAATTATATTCCATTACAACTCTATTTC
1 ATTACAACTATATTCCATTACAACTCTATTTC
* * * *
253032 ATTACAGCTATATTCTATTATAGCTCTATT
1 ATTACAACTATATTCCATTACAACTCTATT
253062 CAAATTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.03, T:0.45
Consensus pattern (32 bp):
ATTACAACTATATTCCATTACAACTCTATTTC
Found at i:258307 original size:18 final size:17
Alignment explanation
Indices: 258280--258313 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
258270 AGTAAAATTT
258280 TAAATTTATTATTTAAC
1 TAAATTTATTATTTAAC
*
258297 TAAAGTTTATTTTTTAA
1 TAAA-TTTATTATTTAA
258314 GTTTCATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TAAATTTATTATTTAAC
Found at i:258634 original size:19 final size:20
Alignment explanation
Indices: 258610--258652 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
258600 AAAGCTTTAA
258610 TTTAA-TGTAATAT-CTATAT
1 TTTAATTGTAATATGC-ATAT
*
258629 TTTAATTGTATTATGCATAT
1 TTTAATTGTAATATGCATAT
258649 TTTA
1 TTTA
258653 TTGCATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 15 0.71
21 1 0.05
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTAATTGTAATATGCATAT
Found at i:258912 original size:246 final size:248
Alignment explanation
Indices: 258464--258920 Score: 550
Period size: 246 Copynumber: 1.9 Consensus size: 248
258454 AATATATTTT
* * * * *
258464 CGTAATTATATTAAGTTATATGATTTGATGATACTTTACTCTTATTATCTTAAAAAAAGGCAACA
1 CGTAATTAAATTAAGTTATATGATTGGATGACACTTTACTATTATTATCTTAAAAAAAGCCAACA
* *
258529 AAAAATTACATATGATGGGATCTAAACCAGTGCTATTGAAATTAATAAAACATTAATACTACCAC
66 AAAAATTACATATGATAGGATCTAAACCAGTGCTATTGAAATTAAAAAAACATTAATACTACCAC
* ** * * * *
258594 TAAATCAAAGCTTTAATTTAATGTAATATCTATATTTTAATTGTATTATGCATATTTTATTGCAT
131 TAAATCAAAGCTATAATTTAACATAATATCTACATTTTAATTGTATTATGCATACTTTACTACAT
*
258659 TCATCAATTGTATATTTATGACACCAACTCAATAAAAAAATTATAAAAACCTC
196 CCATCAATTGTATATTTATGACACCAACTCAATAAAAAAATTATAAAAACCTC
* * *
258712 CGTAATTAAATTAAGTTATATTATTGGAT-AGCACTTTAGTAATT-TTATCTTAAAAAATATCCA
1 CGTAATTAAATTAAGTTATATGATTGGATGA-CACTTTACT-ATTATTATCTTAAAAAA-AGCCA
* * * * * *
258775 ATAAAAAATTACATATGCTAGGATTTGAA-CA-TGTTATTGAAA-TAAAAAAACATTAATATTAC
63 ACAAAAAATTACATATGATAGGATCTAAACCAGTGCTATTGAAATTAAAAAAACATTAATACTAC
* * * * *
258837 CACTAAA-CTAAATCTAT-ATCTTAACATAATATTTACATTTTAATTGTATTGTTCGTACTTTAC
128 CACTAAATC-AAAGCTATAAT-TTAACATAATATCTACATTTTAATTGTATTATGCATACTTTAC
*
258900 TACCTCCATCAATTGTATATT
191 TACATCCATCAATTGTATATT
258921 AATTATGTTG
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
245 3 0.02
246 83 0.48
247 11 0.06
248 48 0.28
249 29 0.17
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (248 bp):
CGTAATTAAATTAAGTTATATGATTGGATGACACTTTACTATTATTATCTTAAAAAAAGCCAACA
AAAAATTACATATGATAGGATCTAAACCAGTGCTATTGAAATTAAAAAAACATTAATACTACCAC
TAAATCAAAGCTATAATTTAACATAATATCTACATTTTAATTGTATTATGCATACTTTACTACAT
CCATCAATTGTATATTTATGACACCAACTCAATAAAAAAATTATAAAAACCTC
Found at i:262136 original size:3 final size:3
Alignment explanation
Indices: 262128--262154 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
262118 TTGGTTATAT
262128 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
262155 GATGGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:262407 original size:5 final size:5
Alignment explanation
Indices: 262399--262425 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
262389 AAAAAAGGTT
262399 AAAGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AA
262426 TGGTAATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:262972 original size:17 final size:17
Alignment explanation
Indices: 262941--262974 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
262931 TATCTTTACT
**
262941 AATTTAAAATTTTAAAA
1 AATTTAAAAGGTTAAAA
262958 AATTTAAAAGGTTAAAA
1 AATTTAAAAGGTTAAAA
262975 TAGAAAAAAT
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:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
AATTTAAAAGGTTAAAA
Found at i:265159 original size:22 final size:22
Alignment explanation
Indices: 265100--265231 Score: 86
Period size: 22 Copynumber: 5.7 Consensus size: 22
265090 AACCAGCAGC
* * **
265100 AAAAATAACAGCAAAACAACAA
1 AAAAAAAACACCAAAACAGTAA
* *
265122 AAATAACAACATCAAAACAGTAA
1 AAA-AAAAACACCAAAACAGTAA
* **
265145 AAAAAAAGCACCAAAACAACCAAA
1 AAAAAAAACACCAAAAC-A-GTAA
*
265169 ATAGTAAAAAAAACCAAAACAGT-A
1 A-A--AAAAAACACCAAAACAGTAA
* *
265193 AAAAATAGCAACCAAAACAGTAA
1 AAAAAAAAC-ACCAAAACAGTAA
265216 AAAAAAAACACCAAAA
1 AAAAAAAACACCAAAA
265232 TAACAATATA
Statistics
Matches: 84, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
21 4 0.05
22 32 0.38
23 28 0.33
24 5 0.06
25 1 0.01
26 1 0.01
27 13 0.15
ACGTcount: A:0.70, C:0.18, G:0.05, T:0.07
Consensus pattern (22 bp):
AAAAAAAACACCAAAACAGTAA
Found at i:265166 original size:72 final size:69
Alignment explanation
Indices: 265096--265231 Score: 157
Period size: 71 Copynumber: 1.9 Consensus size: 69
265086 GCTAAACCAG
* *
265096 CAGCAAAAATAACAGCAAAACA-ACAAAAATAACAACATCAAAACAGTAAAAAAAAAGCACCAAA
1 CAGCAAAAA-AA-ACCAAAACAGA-AAAAATAACAAC--CAAAACAGTAAAAAAAAAACACCAAA
265160 ACAACCAAAA
61 ACAACC-AAA
* * *
265170 TAGTAAAAAAAACCAAAACAGTAAAAAATAGCAACCAAAACAGTAAAAAAAAAACACCAAAA
1 CAGCAAAAAAAACCAAAACAG-AAAAAATAACAACCAAAACAGTAAAAAAAAAACACCAAAA
265232 TAACAATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
71 26 0.47
72 8 0.15
73 13 0.24
74 8 0.15
ACGTcount: A:0.68, C:0.19, G:0.06, T:0.07
Consensus pattern (69 bp):
CAGCAAAAAAAACCAAAACAGAAAAAATAACAACCAAAACAGTAAAAAAAAAACACCAAAACAAC
CAAA
Found at i:265178 original size:18 final size:18
Alignment explanation
Indices: 265157--265221 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
265147 AAAAAGCACC
* *
265157 AAAACAACCAAAATAGTA
1 AAAAAAACCAAAACAGTA
265175 AAAAAAACCAAAACAGTAA
1 AAAAAAACCAAAACAGT-A
265194 AAAATAGCAACCAAAACAGTA
1 AAAA-A--AACCAAAACAGTA
265215 AAAAAAA
1 AAAAAAA
265222 AACACCAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 17 0.41
19 5 0.12
20 2 0.05
21 5 0.12
22 12 0.29
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (18 bp):
AAAAAAACCAAAACAGTA
Found at i:267338 original size:31 final size:31
Alignment explanation
Indices: 267283--267419 Score: 129
Period size: 31 Copynumber: 4.5 Consensus size: 31
267273 GGATCCCAAA
* * *
267283 AAGTTTAAGTACCAACTTAAAAAAAAATGAC
1 AAGTTTAGGTACCAAATTAGAAAAAAATGAC
* *
267314 AACTTTAGGTACCAAATTAGAAAAAAATGTC
1 AAGTTTAGGTACCAAATTAGAAAAAAATGAC
* * **
267345 AAGTTT-GAGTACCAAAATGGACCAAAA--A-
1 AAGTTTAG-GTACCAAATTAGAAAAAAATGAC
* *
267373 AAGTTTAGGCACCAAATTAGAAAAAAAATGTC
1 AAGTTTAGGTACCAAATTAG-AAAAAAATGAC
267405 AAGTTTAGGTACCAA
1 AAGTTTAGGTACCAA
267420 TTGTTATATT
Statistics
Matches: 82, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
28 15 0.18
29 6 0.07
30 1 0.01
31 46 0.56
32 14 0.17
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.23
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTAGAAAAAAATGAC
Found at i:267397 original size:90 final size:91
Alignment explanation
Indices: 267237--267419 Score: 221
Period size: 90 Copynumber: 2.0 Consensus size: 91
267227 ATTATATACA
* * * * *
267237 AAATTAAGAAAAAGAGTCAAGTTAAGGTACCAAATTGGATCCCAAAAAGTTTAAGTACCAACTT-
1 AAATTAAGAAAAAAAGTCAAGTTAAGGTACCAAAATGGATCCAAAAAAGTTTAAGCACCAAATTA
267301 AAAAAAAAATGACAACTTTAGGTACC
66 AAAAAAAAATGACAACTTTAGGTACC
* *
267327 AAATT-AGAAAAAAATGTCAAGTT-TGAGTACCAAAATGGA-CCAAAAAAAGTTTAGGCACCAAA
1 AAATTAAGAAAAAAA-GTCAAGTTAAG-GTACCAAAATGGATCC-AAAAAAGTTTAAGCACCAAA
* * *
267389 TTAGAAAAAAAATGTCAAGTTTAGGTACC
63 TTAAAAAAAAAATGACAACTTTAGGTACC
267418 AA
1 AA
267420 TTGTTATATT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
89 11 0.14
90 43 0.54
91 25 0.32
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (91 bp):
AAATTAAGAAAAAAAGTCAAGTTAAGGTACCAAAATGGATCCAAAAAAGTTTAAGCACCAAATTA
AAAAAAAAATGACAACTTTAGGTACC
Found at i:267614 original size:2 final size:2
Alignment explanation
Indices: 267582--267606 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
267572 AAGTTATTAC
267582 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
267607 GCATATATTC
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:268335 original size:35 final size:35
Alignment explanation
Indices: 268289--268359 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
268279 GTTATGACCT
268289 CTTCGTTGGAGAATTCTTAAACCATCCAAAATACC
1 CTTCGTTGGAGAATTCTTAAACCATCCAAAATACC
*
268324 CTTCGTTGGAGAATTCTTAGACCATCCAAAATACC
1 CTTCGTTGGAGAATTCTTAAACCATCCAAAATACC
268359 C
1 C
268360 CAAAGTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (35 bp):
CTTCGTTGGAGAATTCTTAAACCATCCAAAATACC
Found at i:271830 original size:22 final size:22
Alignment explanation
Indices: 271802--271844 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
271792 GGGGGAGAAA
271802 GAGGGAAAACGAAAAATACCAC
1 GAGGGAAAACGAAAAATACCAC
271824 GAGGGAAAACGAAAAATACCA
1 GAGGGAAAACGAAAAATACCA
271845 TGATGAGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.16, G:0.23, T:0.05
Consensus pattern (22 bp):
GAGGGAAAACGAAAAATACCAC
Found at i:272948 original size:2 final size:2
Alignment explanation
Indices: 272943--272967 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
272933 AAAAATTTAA
272943 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
272968 ACAAAATACG
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:274054 original size:105 final size:103
Alignment explanation
Indices: 273944--274181 Score: 306
Period size: 105 Copynumber: 2.3 Consensus size: 103
273934 GTGTCTCTTC
273944 CAATGGAGGCACCAAATTGCAATAAAAATGAT-TTTTTGGTTACAGGTTTATAAGTGGCAG-CAC
1 CAATGGAGGCACCAAATTGCAATAAAAA--ATCTTTTTGGTTACAGGTTTATAAGT-GCAGACAC
*
274007 CAAT-TAGGAATTTTTATTTTTATTTTTTGGTGTCGCCTCCTT
63 CAATGTAGGAA-TTTT-TTTTTATTTTTTGGTGTCGACTCCTT
* * *
274049 CAATGGAGGCACCAAA-TGTCAGTAACAAAATCTTTTTGGTTACAGGTTTATAAGTGCGGACATC
1 CAATGGAGGCACCAAATTG-CAATAA-AAAATCTTTTTGGTTACAGGTTTATAAGTGCAGACACC
*
274113 AGTGTAGGAATTTTTTTTTATTTTTTGGTGTCGACTCCTT
64 AATGTAGGAATTTTTTTTTATTTTTTGGTGTCGACTCCTT
* *
274153 CAATGGAGGTACCCAATT-CAATTAAAAAA
1 CAATGGAGGCACCAAATTGCAA-TAAAAAA
274182 AAGTATTCTC
Statistics
Matches: 118, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
103 6 0.05
104 49 0.42
105 54 0.46
106 9 0.08
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (103 bp):
CAATGGAGGCACCAAATTGCAATAAAAAATCTTTTTGGTTACAGGTTTATAAGTGCAGACACCAA
TGTAGGAATTTTTTTTTATTTTTTGGTGTCGACTCCTT
Found at i:276048 original size:11 final size:11
Alignment explanation
Indices: 276010--276063 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
276000 AACGAAAATT
*
276010 AAAGAAAAAAG
1 AAAGAAGAAAG
276021 AAAGAA-AAA-
1 AAAGAAGAAAG
*
276030 AAAAAAGAAAG
1 AAAGAAGAAAG
276041 AAAGAAG-AAG
1 AAAGAAGAAAG
* *
276051 GAAGAAGGAAG
1 AAAGAAGAAAG
276062 AA
1 AA
276064 GGAGAAGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 5 0.14
10 15 0.42
11 16 0.44
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAG
Found at i:276054 original size:7 final size:7
Alignment explanation
Indices: 276038--276070 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
276028 AAAAAAAAGA
*
276038 AAGAAAG
1 AAGAAGG
276045 AAGAAGG
1 AAGAAGG
276052 AAGAAGG
1 AAGAAGG
276059 AAGAAGG
1 AAGAAGG
276066 -AGAAG
1 AAGAAG
276071 AATGGGGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:276281 original size:12 final size:12
Alignment explanation
Indices: 276264--276289 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
276254 TTTAAGTATG
276264 ATTAATTTTAAA
1 ATTAATTTTAAA
276276 ATTAATTTTAAA
1 ATTAATTTTAAA
276288 AT
1 AT
276290 ATTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTAATTTTAAA
Found at i:276488 original size:20 final size:21
Alignment explanation
Indices: 276447--276489 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
276437 TAATTTACTT
276447 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
276468 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
276488 TA
1 TA
276490 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:276794 original size:16 final size:16
Alignment explanation
Indices: 276749--276798 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
276739 TAAACCTAAC
*
276749 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
276765 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
276779 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
276795 TAAT
1 TAAT
276799 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:278183 original size:43 final size:43
Alignment explanation
Indices: 278101--278185 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
278091 ATTAACATGT
* *
278101 TAAATTATATTACTTGACTTGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
*
278144 TAAATTATATTACTTTACTCT-TATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACT-TGTATTAATATGCTTG-CATGTTA
278186 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.08
43 33 0.89
44 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
Found at i:278820 original size:45 final size:45
Alignment explanation
Indices: 278756--278884 Score: 177
Period size: 45 Copynumber: 2.9 Consensus size: 45
278746 GCATAGCTCA
* *
278756 TCAAGCCAAGGATATCAGCCTCAGTTTGACGATCCATCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
*
278801 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * * **
278846 TCAAGGGAAGGATATCAGGCTGAGTTTGATAAGCCACCG
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCG
278885 TGATACTCTA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:279187 original size:13 final size:14
Alignment explanation
Indices: 279157--279203 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
279147 CATTAAACCC
*
279157 TAAAACCTAAATTA
1 TAAACCCTAAATTA
279171 TAAACCCTAAATT-
1 TAAACCCTAAATTA
*
279184 TAAAACCCTAAACTA
1 T-AAACCCTAAATTA
279199 TAAAC
1 TAAAC
279204 ACTAGACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAATTA
Found at i:279194 original size:28 final size:28
Alignment explanation
Indices: 279157--279224 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
279147 CATTAAACCC
* * *
279157 TAAAA-CCTAAATTATAAACCCTAAATT
1 TAAAACCCTAAACTATAAACACTAAACT
*
279184 TAAAACCCTAAACTATAAACACTAGACT
1 TAAAACCCTAAACTATAAACACTAAACT
*
279212 TAAAACTCTAAAC
1 TAAAACCCTAAAC
279225 CGTGAACACT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 5 0.14
28 30 0.86
ACGTcount: A:0.51, C:0.22, G:0.01, T:0.25
Consensus pattern (28 bp):
TAAAACCCTAAACTATAAACACTAAACT
Found at i:279232 original size:28 final size:28
Alignment explanation
Indices: 279157--279237 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 28
279147 CATTAAACCC
** * * *
279157 TAAAA-CCTAAATTATAAACCCTAAATT
1 TAAAACCCTAAACCATAAACACTAGACT
*
279184 TAAAACCCTAAACTATAAACACTAGACT
1 TAAAACCCTAAACCATAAACACTAGACT
* * *
279212 TAAAACTCTAAACCGTGAACACTAGA
1 TAAAACCCTAAACCATAAACACTAGA
279238 TTGATTAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 5 0.11
28 40 0.89
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.23
Consensus pattern (28 bp):
TAAAACCCTAAACCATAAACACTAGACT
Done.