Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 1 of 311
Found at i:3264 original size:46 final size:46
Alignment explanation
Indices: 3097--3273 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
3087 GGTTGAGCAT
*
3097 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG--C
* * * *
3145 CAGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
3190 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
3238 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3274 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
44 2 0.02
45 5 0.05
46 35 0.32
47 30 0.27
48 31 0.28
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:4849 original size:30 final size:32
Alignment explanation
Indices: 4789--4852 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
4779 CACTTATTTT
4789 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
4822 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
4853 ACATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:5112 original size:41 final size:41
Alignment explanation
Indices: 5067--5258 Score: 375
Period size: 41 Copynumber: 4.7 Consensus size: 41
5057 ACCGGCTCTT
*
5067 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
5108 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
5149 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
5190 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
5231 AGCCTGCTAGACTTATAGTCTGAAATGT
1 AGCCTGCTAGACTTATAGTCTGAAATGT
5259 CTGCATTAAC
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 150 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:12519 original size:32 final size:31
Alignment explanation
Indices: 12481--12544 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
12471 ACACTTATTT
12481 TCACCTATGCCGAATGCATACACATAAATATA
1 TCACCTATGCCGAATGCA-ACACATAAATATA
* *
12513 TCACCTATGCCGAATGCAACATATATATATA
1 TCACCTATGCCGAATGCAACACATAAATATA
12544 T
1 T
12545 ACATATCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (31 bp):
TCACCTATGCCGAATGCAACACATAAATATA
Found at i:12804 original size:41 final size:41
Alignment explanation
Indices: 12759--13035 Score: 477
Period size: 41 Copynumber: 6.8 Consensus size: 41
12749 ACCGGCTCTT
*
12759 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
*
12800 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACTGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
12841 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
*
12882 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCAGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
*
12923 AGTCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
12964 AGCCTGCTAGACTTATAGTCTGAAATGT-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
* * *
13004 AGCCTGCTAGACGTA-AGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
13036 TAACGATAAA
Statistics
Matches: 225, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
39 10 0.04
40 30 0.13
41 185 0.82
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:17628 original size:38 final size:38
Alignment explanation
Indices: 17586--17689 Score: 93
Period size: 38 Copynumber: 2.7 Consensus size: 38
17576 AAATAGGGTA
*
17586 TTATTCAGGCTTAGTGCCTAGCAAGCTTAGTGCCGGTG
1 TTATTCAGGCTTAGTGCCTAGCAAGCTTAATGCCGGTG
* * ** ** * *
17624 TTATTTAGGCTTACTTTCTAATAGGCTTAATGTCGGTG
1 TTATTCAGGCTTAGTGCCTAGCAAGCTTAATGCCGGTG
* *
17662 TTGA-TCAAGCTTAGTGCTTAGCAAGCTT
1 TT-ATTCAGGCTTAGTGCCTAGCAAGCTT
17690 TAAGTCGGTG
Statistics
Matches: 47, Mismatches: 18, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
38 46 0.98
39 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (38 bp):
TTATTCAGGCTTAGTGCCTAGCAAGCTTAATGCCGGTG
Found at i:18653 original size:29 final size:30
Alignment explanation
Indices: 18611--18678 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
18601 TTGCACAAGA
* *
18611 GTAAATACTAAAAATTTG-AGGGCTAA-AGT
1 GTAAATA-TAAAAAGTTGAAGGACTAATAGT
18640 GTAAATATAAAAAAGTTGAAGGACTAATAGT
1 GTAAATAT-AAAAAGTTGAAGGACTAATAGT
*
18671 GAAAATAT
1 GTAAATAT
18679 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 15 0.45
30 7 0.21
31 10 0.30
ACGTcount: A:0.50, C:0.04, G:0.19, T:0.26
Consensus pattern (30 bp):
GTAAATATAAAAAGTTGAAGGACTAATAGT
Found at i:21200 original size:49 final size:48
Alignment explanation
Indices: 21071--21207 Score: 168
Period size: 48 Copynumber: 2.8 Consensus size: 48
21061 CGACCAAATT
* * *
21071 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
1 ATGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGAG
* * * *
21119 ACGAGT-GCCAGTGTAAGACCATGTCTGGGACATGACATTGGCCTCGTTG
1 ATGA-TAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCG-AG
* *
21168 ATGATAGCTAGTGTAAGACCATGTTTGGGACATGGCATTG
1 ATGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATTG
21208 ACACACTTAC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
48 40 0.53
49 35 0.47
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (48 bp):
ATGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGAG
Found at i:36420 original size:18 final size:17
Alignment explanation
Indices: 36384--36432 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
36374 AAATAGATAG
*
36384 AATAAAAATTAATAAAAA
1 AATAAAAATT-ATATAAA
36402 AATAAGAAATTATATAAA
1 AATAA-AAATTATATAAA
36420 AATATAAAATTAT
1 AATA-AAAATTAT
36433 TAATAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AATAAAAATTATATAAA
Found at i:36449 original size:19 final size:18
Alignment explanation
Indices: 36384--36449 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
36374 AAATAGATAG
*
36384 AATA-AAAATTAATAAAAA
1 AATAGAAAATT-ATATAAA
36402 AATA-AGAAATTATATAAA
1 AATAGA-AAATTATATAAA
*
36420 AATATAAAATTAT-TAATA
1 AATAGAAAATTATATAA-A
36438 AATTAGAAAATT
1 AA-TAGAAAATT
36450 GTAACAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.07
18 25 0.60
19 14 0.33
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
AATAGAAAATTATATAAA
Found at i:36847 original size:64 final size:64
Alignment explanation
Indices: 36778--36902 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 64
36768 TAAAGGGAGT
* * * *
36778 ATACAAATTCAAATATTAGAGTAGACATTGTTGAGAGAGATAACCATGAACTTCGAAGGGGAAG
1 ATACAAATTCAAATATTAGAGTAAACATTGATGAGAGAGACAACCATGAACTCCGAAGGGGAAG
36842 ATACAAATTCAAATATTAGAGTAAACATTGATGAGAGAGACAACCATGAACTCCGAAGGGG
1 ATACAAATTCAAATATTAGAGTAAACATTGATGAGAGAGACAACCATGAACTCCGAAGGGG
36903 TTAAGTAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (64 bp):
ATACAAATTCAAATATTAGAGTAAACATTGATGAGAGAGACAACCATGAACTCCGAAGGGGAAG
Found at i:37832 original size:3 final size:3
Alignment explanation
Indices: 37824--37849 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
37814 TTATATTTTA
37824 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
37850 AAGAAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:39344 original size:25 final size:25
Alignment explanation
Indices: 39316--39377 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
39306 ACCTTAGCGC
39316 GCTATCTGATTATTAGCACGTCAGT
1 GCTATCTGATTATTAGCACGTCAGT
39341 GCTATCTGATTATTAGCACGTCAGT
1 GCTATCTGATTATTAGCACGTCAGT
*
39366 GCTCTCTGATTA
1 GCTATCTGATTA
39378 GCACATCTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (25 bp):
GCTATCTGATTATTAGCACGTCAGT
Found at i:39380 original size:22 final size:23
Alignment explanation
Indices: 39326--39394 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 23
39316 GCTATCTGAT
*
39326 TATTAGCACGTCAGTGCTATCTG
1 TATTAGCACGTCAGTGCTCTCTG
39349 ATTATTAGCACGTCAGTGCTCTCTG
1 --TATTAGCACGTCAGTGCTCTCTG
* *
39374 -ATTAGCACATCTGTGCTCTCT
1 TATTAGCACGTCAGTGCTCTCT
39395 ATTCATTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
22 19 0.46
25 22 0.54
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (23 bp):
TATTAGCACGTCAGTGCTCTCTG
Found at i:40086 original size:12 final size:12
Alignment explanation
Indices: 40069--40094 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40059 AAAATAAAAA
40069 ATTATAAAATAC
1 ATTATAAAATAC
40081 ATTATAAAATAC
1 ATTATAAAATAC
40093 AT
1 AT
40095 AAAATAAAAA
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:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
ATTATAAAATAC
Found at i:49135 original size:39 final size:42
Alignment explanation
Indices: 49081--49178 Score: 162
Period size: 44 Copynumber: 2.3 Consensus size: 42
49071 TTTCTGCATT
*
49081 TATTTA-TTTTAATAAAATAAGATATCATATTTTAATGATAA
1 TATTTAGTTATAATAAAATAAGATATCATATTTTAATGATAA
49122 TATTTAGTTATAAAATAAAATAAGATATCATATTTTAATGATAA
1 TATTTAGTTAT--AATAAAATAAGATATCATATTTTAATGATAA
49166 TATTTAGTTATAA
1 TATTTAGTTATAA
49179 AATTATTAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
41 6 0.11
42 5 0.09
44 42 0.79
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (42 bp):
TATTTAGTTATAATAAAATAAGATATCATATTTTAATGATAA
Found at i:49139 original size:44 final size:44
Alignment explanation
Indices: 49091--49181 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
49081 TATTTATTTT
49091 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
1 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
49135 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
1 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
49179 AAT
1 AAT
49182 TATTAGTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (44 bp):
AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
Found at i:49324 original size:19 final size:19
Alignment explanation
Indices: 49284--49329 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
49274 TTTTTCAAAA
*
49284 TTTAGAGAAATAAGCTATT
1 TTTAGAGAAATAAGCGATT
*
49303 TTTAGAGAAATACATCGA-T
1 TTTAGAGAAATA-AGCGATT
49322 TTTAGAGA
1 TTTAGAGA
49330 TAGAGTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (19 bp):
TTTAGAGAAATAAGCGATT
Found at i:49495 original size:18 final size:19
Alignment explanation
Indices: 49449--49495 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
49439 TCTTAAATTT
*
49449 AACTCTCTCTATTCTCTCTA
1 AACT-TCTCAATTCTCTCTA
49469 AACTT-TCAATTCTCTC-A
1 AACTTCTCAATTCTCTCTA
*
49486 AATTTCTCAA
1 AACTTCTCAA
49496 GATTTATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 1 0.04
20 4 0.17
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (19 bp):
AACTTCTCAATTCTCTCTA
Found at i:53037 original size:14 final size:14
Alignment explanation
Indices: 53018--53044 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53008 TCAGAAAAAT
53018 AAAAATATTTTTAG
1 AAAAATATTTTTAG
53032 AAAAATATTTTTA
1 AAAAATATTTTTA
53045 ACGTAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
AAAAATATTTTTAG
Found at i:55019 original size:18 final size:18
Alignment explanation
Indices: 54996--55036 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
54986 TACTTTTCTC
54996 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
55014 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
55032 TTTCT
1 TTTCT
55037 TTTTCTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:56469 original size:23 final size:24
Alignment explanation
Indices: 56413--56471 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
56403 AAATTAATTA
* *
56413 TTTTATTACGAGTGTACATATATC
1 TTTTATTACAAATGTACATATATC
56437 TATTTATTACAAATGTACCA-ATAT-
1 T-TTTATTACAAATGTA-CATATATC
56461 TTTTATTACAA
1 TTTTATTACAA
56472 TTGTCATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 10 0.32
24 2 0.06
25 17 0.55
26 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.46
Consensus pattern (24 bp):
TTTTATTACAAATGTACATATATC
Found at i:56569 original size:19 final size:19
Alignment explanation
Indices: 56545--56609 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 19
56535 ATCTTTAACT
56545 TAATTTTAAAAAATAATAA
1 TAATTTTAAAAAATAATAA
*
56564 TAATTTAATAAAAAA-ACATAC
1 TAATTT--TAAAAAATA-ATAA
*
56585 TAATAATTAATAATAATAATAA
1 TAAT-TTTAA-AA-AATAATAA
56607 TAA
1 TAA
56610 AATCTTAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
19 6 0.17
20 4 0.11
21 16 0.44
22 9 0.25
23 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATTTTAAAAAATAATAA
Found at i:56579 original size:24 final size:23
Alignment explanation
Indices: 56552--56597 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
56542 ACTTAATTTT
56552 AAAAAATAATAATAATTTAATAAA
1 AAAAAATAATAATAA-TTAATAAA
* *
56576 AAAACATACTAATAATTAATAA
1 AAAAAATAATAATAATTAATAA
56598 TAATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAAATAATAATAATTAATAAA
Found at i:62195 original size:94 final size:94
Alignment explanation
Indices: 62034--62238 Score: 365
Period size: 94 Copynumber: 2.2 Consensus size: 94
62024 TGGAAGCTTA
*
62034 GCACACGCCCATGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCTATTTGGT
1 GCACACGCCCATGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCCATTTGGT
*
62099 CATGAGCAAGTTAGGGTCACATGGCCAAG
66 CATGAACAAGTTAGGGTCACATGGCCAAG
* * *
62128 GCACACGCCCGTGTGCTAAGGACACGCCTGTGTCCCGTGCCCATAGAGCTCTTTGTCCATTTGGT
1 GCACACGCCCATGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCCATTTGGT
62193 CATGAACAAGTTAGGGTCACATGGCCAAG
66 CATGAACAAGTTAGGGTCACATGGCCAAG
62222 GCACACGCCCATGTGCT
1 GCACACGCCCATGTGCT
62239 TAAGCCATAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 105 1.00
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.22
Consensus pattern (94 bp):
GCACACGCCCATGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCCATTTGGT
CATGAACAAGTTAGGGTCACATGGCCAAG
Found at i:63718 original size:15 final size:15
Alignment explanation
Indices: 63698--63727 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
63688 TGTATTGTTA
63698 ATTGATAACACAATG
1 ATTGATAACACAATG
63713 ATTGATAACACAATG
1 ATTGATAACACAATG
63728 TGTGAAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
ATTGATAACACAATG
Found at i:64062 original size:22 final size:22
Alignment explanation
Indices: 64034--64107 Score: 121
Period size: 22 Copynumber: 3.4 Consensus size: 22
64024 TGTACCTGTC
*
64034 CACACGGGCCTATTAGGGGTTG
1 CACACGGGCCTATGAGGGGTTG
64056 CACACGGGCCTATGAGGGGTTG
1 CACACGGGCCTATGAGGGGTTG
*
64078 CACACGGGCCTGTGAGGGGTTG
1 CACACGGGCCTATGAGGGGTTG
*
64100 TACACGGG
1 CACACGGG
64108 TGTGTGGGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.18, C:0.23, G:0.41, T:0.19
Consensus pattern (22 bp):
CACACGGGCCTATGAGGGGTTG
Found at i:64156 original size:30 final size:30
Alignment explanation
Indices: 64122--64186 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
64112 TGGGTAAGTA
* *
64122 ACACGGGCATGTGGAAACTAGAGCTATCAC
1 ACACGGGCATATGAAAACTAGAGCTATCAC
** * *
64152 ACACGGGTGTATGAAAATTGGAGCTATCAC
1 ACACGGGCATATGAAAACTAGAGCTATCAC
64182 ACACG
1 ACACG
64187 AGTGTATGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (30 bp):
ACACGGGCATATGAAAACTAGAGCTATCAC
Found at i:66465 original size:18 final size:18
Alignment explanation
Indices: 66442--66498 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
66432 ACACTAAGAT
66442 AAATGCAACTTAACAAGC
1 AAATGCAACTTAACAAGC
** *
66460 AAATGCTTC-TAA-AA-T
1 AAATGCAACTTAACAAGC
66475 AAATGCAACTTAACAAGC
1 AAATGCAACTTAACAAGC
66493 AAATGC
1 AAATGC
66499 TTCTAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 5 0.17
18 13 0.43
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (18 bp):
AAATGCAACTTAACAAGC
Found at i:66480 original size:33 final size:33
Alignment explanation
Indices: 66435--66509 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
66425 TTAAATAACA
*
66435 CTAAGATAAATGCAACTTAACAAGCAAATGCTT
1 CTAAAATAAATGCAACTTAACAAGCAAATGCTT
66468 CTAAAATAAATGCAACTTAACAAGCAAATGCTT
1 CTAAAATAAATGCAACTTAACAAGCAAATGCTT
66501 CTAAAATAA
1 CTAAAATAA
66510 TAAAAAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.24
Consensus pattern (33 bp):
CTAAAATAAATGCAACTTAACAAGCAAATGCTT
Found at i:66551 original size:30 final size:31
Alignment explanation
Indices: 66492--66552 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
66482 ACTTAACAAG
66492 CAAATGCTTCTAAAATAATAAAAAAAATTAA
1 CAAATGCTTCTAAAATAATAAAAAAAATTAA
*
66523 CAAATGCCTT-TAAAATAAT-AAGAAAATTAA
1 CAAATG-CTTCTAAAATAATAAAAAAAATTAA
66553 TAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 10 0.36
31 15 0.54
32 3 0.11
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (31 bp):
CAAATGCTTCTAAAATAATAAAAAAAATTAA
Found at i:67454 original size:19 final size:19
Alignment explanation
Indices: 67430--67477 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
67420 TTCTCTTTTT
67430 TTTCTATTCATTCTATCCA
1 TTTCTATTCATTCTATCCA
*
67449 TTTCTATTCATTCTATTCA
1 TTTCTATTCATTCTATCCA
67468 TTTCTATTCA
1 TTTCTATTCA
67478 AACACACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTCTATTCATTCTATCCA
Found at i:67455 original size:10 final size:10
Alignment explanation
Indices: 67430--67477 Score: 73
Period size: 9 Copynumber: 5.0 Consensus size: 10
67420 TTCTCTTTTT
67430 TTTCTATTCA
1 TTTCTATTCA
*
67440 -TTCTATCCA
1 TTTCTATTCA
67449 TTTCTATTCA
1 TTTCTATTCA
67459 -TTCTATTCA
1 TTTCTATTCA
67468 TTTCTATTCA
1 TTTCTATTCA
67478 AACACACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 17 0.50
10 17 0.50
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:70219 original size:21 final size:20
Alignment explanation
Indices: 70195--70337 Score: 74
Period size: 20 Copynumber: 7.2 Consensus size: 20
70185 TAGCCTTCGG
70195 GCTTCCGTTTAGTACTTGTGT
1 GCTTCCGTTTAG-ACTTGTGT
* *
70216 GCTTCAG-TTAGCCTTCG-G-
1 GCTTCCGTTTAGACTT-GTGT
70234 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCGTTTAG-ACTTGTGT
*
70255 GCTTCAC--TTAGCCTTCG-G-
1 GCTTC-CGTTTAGACTT-GTGT
*
70273 GCTTCCGTTTAACACTTGTGT
1 GCTTCCGTTT-AGACTTGTGT
*
70294 GCTTCAC--TTAGCCTTCG-G-
1 GCTTC-CGTTTAGACTT-GTGT
*
70312 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAG-ACTTGTGT
70333 GCTTC
1 GCTTC
70338 AGCTAGACTT
Statistics
Matches: 92, Mismatches: 11, Indels: 38
0.65 0.08 0.27
Matches are distributed among these distances:
17 2 0.02
18 16 0.17
19 25 0.27
20 26 0.28
21 21 0.23
22 2 0.02
ACGTcount: A:0.11, C:0.27, G:0.22, T:0.40
Consensus pattern (20 bp):
GCTTCCGTTTAGACTTGTGT
Found at i:70223 original size:39 final size:39
Alignment explanation
Indices: 70177--70355 Score: 295
Period size: 39 Copynumber: 4.6 Consensus size: 39
70167 GCTCTGATGA
*
70177 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGTACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
70216 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
70255 GCTTCACTTAGCCTTCGGGCTTCCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
70294 GCTTCACTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
70333 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
70356 AGATCACGAT
Statistics
Matches: 132, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 132 1.00
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:88103 original size:21 final size:21
Alignment explanation
Indices: 88077--88119 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
88067 TATCATTATC
88077 TAAATCCTCAAAGAAAGTAAT
1 TAAATCCTCAAAGAAAGTAAT
*
88098 TAAATCCTCAGAGAAAGTAAT
1 TAAATCCTCAAAGAAAGTAAT
88119 T
1 T
88120 TGAACCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (21 bp):
TAAATCCTCAAAGAAAGTAAT
Found at i:90269 original size:20 final size:20
Alignment explanation
Indices: 90244--90285 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
90234 TTCTGCTGCC
90244 AACTTTTATAATATTTTGCA
1 AACTTTTATAATATTTTGCA
*
90264 AACTTTTCTAATATTTTGCA
1 AACTTTTATAATATTTTGCA
90284 AA
1 AA
90286 TTCTTGGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (20 bp):
AACTTTTATAATATTTTGCA
Found at i:97105 original size:51 final size:51
Alignment explanation
Indices: 97029--97130 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
97019 TTGGAGATAG
97029 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
1 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
97080 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
1 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
97131 ACCATATACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (51 bp):
GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
Found at i:97389 original size:25 final size:25
Alignment explanation
Indices: 97355--97405 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
97345 AGTTTCCAGC
97355 ATGCTGATCTGGGTTCTTTGTTCTT
1 ATGCTGATCTGGGTTCTTTGTTCTT
*
97380 ATGCTGATCTGGGTTGTTTGTTCTT
1 ATGCTGATCTGGGTTCTTTGTTCTT
97405 A
1 A
97406 GTCCCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.10, C:0.14, G:0.25, T:0.51
Consensus pattern (25 bp):
ATGCTGATCTGGGTTCTTTGTTCTT
Found at i:99992 original size:6 final size:7
Alignment explanation
Indices: 99975--99999 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
99965 CTTGTAATTG
99975 CCCCCCA
1 CCCCCCA
99982 CCCCCCA
1 CCCCCCA
99989 CCCCCCA
1 CCCCCCA
99996 CCCC
1 CCCC
100000 TCACAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.88, G:0.00, T:0.00
Consensus pattern (7 bp):
CCCCCCA
Found at i:108651 original size:23 final size:23
Alignment explanation
Indices: 108602--108651 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
108592 GATTTTTTCT
* *
108602 AAATATTATTACTAAATATTCCT
1 AAATATTATCACTAAATATTCCA
*
108625 AAATGTTATCACTAAATAATT-CA
1 AAATATTATCACTAAAT-ATTCCA
108648 AAAT
1 AAAT
108652 TTAAAAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATATTATCACTAAATATTCCA
Found at i:110364 original size:33 final size:33
Alignment explanation
Indices: 110327--110400 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
110317 GAGTCAAATC
*
110327 TAATAGGAAAATTCATAAATCGAGTTAATGTGA
1 TAATAGGAAAATCCATAAATCGAGTTAATGTGA
110360 TAATAGGAAAATCCATAAATCGAGTTAATGTGA
1 TAATAGGAAAATCCATAAATCGAGTTAATGTGA
110393 TAATAGGA
1 TAATAGGA
110401 GTTTTAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (33 bp):
TAATAGGAAAATCCATAAATCGAGTTAATGTGA
Found at i:111209 original size:23 final size:23
Alignment explanation
Indices: 111182--111226 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
111172 ATTTTATGAT
111182 TAAAATGTCAAAATTTTCTGACA
1 TAAAATGTCAAAATTTTCTGACA
111205 TAAAATGTCAAAATTTTCTGAC
1 TAAAATGTCAAAATTTTCTGAC
111227 TTTTCTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (23 bp):
TAAAATGTCAAAATTTTCTGACA
Found at i:111698 original size:15 final size:15
Alignment explanation
Indices: 111675--111709 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
111665 CATTATCCTA
* *
111675 AATATATTATAATTT
1 AATAAATTATAATAT
111690 AATAAATTATAATAT
1 AATAAATTATAATAT
111705 AATAA
1 AATAA
111710 TTAATCAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATTATAATAT
Found at i:112617 original size:14 final size:14
Alignment explanation
Indices: 112594--112635 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
112584 AATTCTTAAA
112594 TATAAAATATTTAT
1 TATAAAATATTTAT
*
112608 TA-ATAAATATTTAA
1 TATA-AAATATTTAT
112622 TATAAAATATTTAT
1 TATAAAATATTTAT
112636 CAGTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAAAATATTTAT
Found at i:116142 original size:26 final size:27
Alignment explanation
Indices: 116112--116177 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
116102 TTTTTAATGG
*
116112 TGCTCACACGAGCTA-TGAAATGGGTC
1 TGCTCACACGAGCTAGTGAAATGGGCC
*
116138 TGCTCATACGAGC-AGTGAAATGGGCC
1 TGCTCACACGAGCTAGTGAAATGGGCC
116164 TGCTCACACGAGCT
1 TGCTCACACGAGCT
116178 GTAGGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (27 bp):
TGCTCACACGAGCTAGTGAAATGGGCC
Found at i:124957 original size:56 final size:56
Alignment explanation
Indices: 124891--125003 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
124881 GCATTATGAA
124891 TAGATTGGAGCAGTTGGGATAAATTATGCAATCCGAAATGCGCTGGTGGGTTAGGT
1 TAGATTGGAGCAGTTGGGATAAATTATGCAATCCGAAATGCGCTGGTGGGTTAGGT
124947 TAGATTGGAGCAGTTGGGATAAATTATGCAATCCGAAATGCGCTGGTGGGTTAGGT
1 TAGATTGGAGCAGTTGGGATAAATTATGCAATCCGAAATGCGCTGGTGGGTTAGGT
125003 T
1 T
125004 TTAAAAACTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.11, G:0.34, T:0.29
Consensus pattern (56 bp):
TAGATTGGAGCAGTTGGGATAAATTATGCAATCCGAAATGCGCTGGTGGGTTAGGT
Found at i:126961 original size:18 final size:17
Alignment explanation
Indices: 126930--126965 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
126920 AGGCCTTCCT
126930 TTTATATAATAGTAGTA
1 TTTATATAATAGTAGTA
126947 TTTATATATATAGTAGTA
1 TTTATATA-ATAGTAGTA
126965 T
1 T
126966 AGATACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTATATAATAGTAGTA
Found at i:127159 original size:28 final size:28
Alignment explanation
Indices: 127097--127161 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
127087 TCATATACAT
*
127097 AAGTAAATTATATAAAATATTCAAAAAA
1 AAGTAAATTATATAAAAAATTCAAAAAA
* *
127125 AAGTAAATTATATAAAAGAATTCACATAA
1 AAGTAAATTATATAAAA-AATTCAAAAAA
127154 AA-TAAATT
1 AAGTAAATT
127162 CAACAATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 23 0.70
29 10 0.30
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (28 bp):
AAGTAAATTATATAAAAAATTCAAAAAA
Found at i:127847 original size:165 final size:169
Alignment explanation
Indices: 127575--127908 Score: 577
Period size: 165 Copynumber: 2.0 Consensus size: 169
127565 ATACTCTACC
* *
127575 ATCAATCTCTTTTGTCTCCTCTATCTTCTAATCTCTTCCCATCCAGATTCTGTCATGCCAAAATT
1 ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
*
127640 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTGCCATTGTTGTGTCG-C-CA-AA-TTTCAA
66 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCCACACAACTTTCAA
127701 TCTTATGTCGCCAAAACTAAAAACACATATTGCAACATA
131 TCTTATGTCGCCAAAACTAAAAACACATATTGCAACATA
127740 ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
1 ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
127805 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCCAAATCACAACTTT
66 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCC--A-CACAACTTT
*
127870 CAATCTTATGTCGCCAAAACTAGAAACACATATTGCAAC
128 CAATCTTATGTCGCCAAAACTAAAAACACATATTGCAAC
127909 CTAACTGCTT
Statistics
Matches: 158, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
165 112 0.71
166 1 0.01
170 2 0.01
171 2 0.01
172 41 0.26
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (169 bp):
ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCCACACAACTTTCAA
TCTTATGTCGCCAAAACTAAAAACACATATTGCAACATA
Found at i:128303 original size:9 final size:9
Alignment explanation
Indices: 128281--128321 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
128271 ACTCTAGAAG
128281 TTTT-TTCT
1 TTTTCTTCT
128289 TTTTCTTCT
1 TTTTCTTCT
*
128298 TCTTCTTC-
1 TTTTCTTCT
*
128306 TTTGCTTCT
1 TTTTCTTCT
128315 TTTTCTT
1 TTTTCTT
128322 TTACTGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 10 0.37
9 17 0.63
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:128701 original size:22 final size:22
Alignment explanation
Indices: 128657--128702 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
128647 ACCGTGGGAC
** * *
128657 AATCCAAAAAATCAAGAATGAA
1 AATCCAAAAAAGAAAAAAAGAA
128679 AATCCAAAAAAGAAAAAAAGAA
1 AATCCAAAAAAGAAAAAAAGAA
128701 AA
1 AA
128703 GAAAAGAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.72, C:0.11, G:0.09, T:0.09
Consensus pattern (22 bp):
AATCCAAAAAAGAAAAAAAGAA
Found at i:132844 original size:28 final size:28
Alignment explanation
Indices: 132804--132861 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
132794 AGGCCAACAG
132804 ATAACACTTCTATTGCAGCATGATTCTT
1 ATAACACTTCTATTGCAGCATGATTCTT
*
132832 ATAACCCTTCTATTGCAGCATGATTCTT
1 ATAACACTTCTATTGCAGCATGATTCTT
132860 AT
1 AT
132862 CCAAAAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (28 bp):
ATAACACTTCTATTGCAGCATGATTCTT
Found at i:144044 original size:134 final size:133
Alignment explanation
Indices: 143787--144110 Score: 461
Period size: 134 Copynumber: 2.4 Consensus size: 133
143777 CATTCTAACA
* * * *
143787 GCTCATTGATTTACGATCACAACCTAAGTTTATTGATTTATGATCATGAATAATTTCTTTAAGTT
1 GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTCTTTAAGTT
* *
143852 AGCTGATTTACGATTGCAACTCCATTTTAACAACTCACTGATTTACGATCACGATTGATATTATT
66 AGCTGATTTACGATTGCAACTCCATTCTAACAACTCACTGATTTACAATCACGATTGATATTATT
143917 AAG
131 AAG
* * * * *
143920 GCTTATTGATTTATGATCATAGCCTAAGTTCATTGATTTACGATCACGAACAATTTCTTTTGAGT
1 GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTC-TTTAAGT
* *** *
143985 TAGCTGATTTATGATTGCAACTCCATTCTAATTGCTTACTGATTTACAATCAC-ATTTGATATTA
65 TAGCTGATTTACGATTGCAACTCCATTCTAACAACTCACTGATTTACAATCACGA-TTGATATTA
144049 TTAAG
129 TTAAG
* *
144054 GCTCACTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACGATTTC
1 GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTC
144111 ATCTGTTAAA
Statistics
Matches: 167, Mismatches: 22, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
133 50 0.30
134 117 0.70
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (133 bp):
GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTCTTTAAGTT
AGCTGATTTACGATTGCAACTCCATTCTAACAACTCACTGATTTACAATCACGATTGATATTATT
AAG
Found at i:144265 original size:19 final size:20
Alignment explanation
Indices: 144229--144271 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
144219 AATTAAAATT
*
144229 TTTTCAATTGAGTTAAAC-A
1 TTTTCAATTCAGTTAAACTA
144248 TTTTCAA-TCAGTTAAAACTA
1 TTTTCAATTCAGTT-AAACTA
144268 TTTT
1 TTTT
144272 TAAACAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTTCAATTCAGTTAAACTA
Found at i:144424 original size:21 final size:21
Alignment explanation
Indices: 144398--144437 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
144388 CAATCAACAT
*
144398 AAAAAGTATTGATACCTTTCC
1 AAAAAGTATCGATACCTTTCC
*
144419 AAAAAGTCTCGATACCTTT
1 AAAAAGTATCGATACCTTT
144438 TAGCAGGTAT
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:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGTATCGATACCTTTCC
Found at i:145642 original size:134 final size:133
Alignment explanation
Indices: 145388--145841 Score: 349
Period size: 134 Copynumber: 3.4 Consensus size: 133
145378 TAAGGTTTGC
* * * * * * * * *
145388 TGATTTATGATCATGAACGATTTCATCTGATTTAGCTAATTTACGATCGCAACGCCATTCAAACA
1 TGATTTACGATCATGAA-AATTTCATCAGAGTTAGCTGATTTATGATTGCAACTCTATTCAAACA
* * * * * * * * * *
145453 GCTC-ATGGATTTATGGTCACAATTGATATT-TTCAAGGCTCGCTGATTT-CTTATCACACCCTA
65 ACTCGCT-AACTTACGATCACAACTGATATTATT-AAGGCTCGTTAATTTAC-AATCACACCCTA
145515 AGTTCAT
127 AGTTCAT
* * *
145522 TAATTTACGATCATGAAAATTTTCTTCAGAGTTAGCTGATTTATGATCGCAACTCTATTCAAACA
1 TGATTTACGATCATGAAAA-TTTCATCAGAGTTAGCTGATTTATGATTGCAACTCTATTCAAACA
* *** * * * *
145587 ACTTGCTGGTTTACGATTACAGCTGATATTATTGAGGCTCGTTAATTTACAATCACATCCTAAGT
65 ACTCGCTAACTTACGATCACAACTGATATTATTAAGGCTCGTTAATTTACAATCACACCCTAAGT
145652 TCAT
130 TCAT
* * * * * * *
145656 TGATTTATGATCATTAACAGTTTCAT-ATGAGTTAGCAGATTTACGATTGCAACTCTATTCTAAT
1 TGATTTACGATCATGAA-AATTTCATCA-GAGTTAGCTGATTTATGATTGCAACTCTATTCAAAC
* * ** * *** **
145720 AGCTCGCTAACTTACTATCACAACTGATATTATTAAGGCTTTTTGATTTATGGTCACAGACTAAG
64 AACTCGCTAACTTACGATCACAACTGATATTATTAAGGCTCGTTAATTTACAATCACACCCTAAG
145785 TTCAT
129 TTCAT
* * * *
145790 TGATTTACAATCATGAACGATTTCATCTGAGTTAGCTTATTTATGATTGCAA
1 TGATTTACGATCATGAA-AATTTCATCAGAGTTAGCTGATTTATGATTGCAA
145842 ATCCAGTCAA
Statistics
Matches: 253, Mismatches: 60, Indels: 14
0.77 0.18 0.04
Matches are distributed among these distances:
133 2 0.01
134 246 0.97
135 5 0.02
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (133 bp):
TGATTTACGATCATGAAAATTTCATCAGAGTTAGCTGATTTATGATTGCAACTCTATTCAAACAA
CTCGCTAACTTACGATCACAACTGATATTATTAAGGCTCGTTAATTTACAATCACACCCTAAGTT
CAT
Found at i:148880 original size:9 final size:9
Alignment explanation
Indices: 148866--148900 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
148856 TATTTGAATA
148866 GAAATGAAC
1 GAAATGAAC
148875 GAAATGAAC
1 GAAATGAAC
148884 GAAATGAAC
1 GAAATGAAC
148893 GAAATGAA
1 GAAATGAA
148901 TAGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.57, C:0.09, G:0.23, T:0.11
Consensus pattern (9 bp):
GAAATGAAC
Found at i:149220 original size:26 final size:26
Alignment explanation
Indices: 149158--149220 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
149148 ACGAATTTTC
*
149158 TCGAAATTTTAACGAAGGTAAAATTG
1 TCGAAATTTTAACAAAGGTAAAATTG
* * *
149184 TCAAAAATTTATCAAAGGTAAAATTTG
1 TCGAAATTTTAACAAAGGTAAAA-TTG
149211 T-GAAATTTTA
1 TCGAAATTTTA
149221 CTAGGGTAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.35
Consensus pattern (26 bp):
TCGAAATTTTAACAAAGGTAAAATTG
Found at i:151599 original size:29 final size:29
Alignment explanation
Indices: 151566--151634 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
151556 TGTGTGTACC
151566 ATGTGAAAAGGGATAGCTTCGACTATCGA
1 ATGTGAAAAGGGATAGCTTCGACTATCGA
*
151595 ATGTGAAAAGGGATAGCTTCGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGACTATCGA
151624 ATGTGAAAAGG
1 ATGTGAAAAGG
151635 AAAGAGATAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (29 bp):
ATGTGAAAAGGGATAGCTTCGACTATCGA
Found at i:151736 original size:33 final size:33
Alignment explanation
Indices: 151695--151763 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
151685 GTACACTTAA
*
151695 AAAGGTATACTCTGTGTGTACCATTTGAAAAGG
1 AAAGGTATACTCTGTATGTACCATTTGAAAAGG
* *
151728 AAAGGTATACTTTGTATTTACCATTTGAAAAGG
1 AAAGGTATACTCTGTATGTACCATTTGAAAAGG
151761 AAA
1 AAA
151764 TGTACAACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (33 bp):
AAAGGTATACTCTGTATGTACCATTTGAAAAGG
Found at i:163894 original size:48 final size:48
Alignment explanation
Indices: 163839--163940 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
163829 TTCAAGAGGG
* *
163839 GATAAATAGTGATAATAGTATAGACAGTGGAAAACCAAATTTAACAAT
1 GATAAATAGTGATAAGAGTATAGACAGTGGAAAACCAAATTTAAAAAT
* * * *
163887 GATAAATAGTGATGAGAGTGTAGACAGTGGAAGACCAAGTTTAAAAAT
1 GATAAATAGTGATAAGAGTATAGACAGTGGAAAACCAAATTTAAAAAT
163935 GCATAA
1 G-ATAA
163941 CATAATTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 43 0.91
49 4 0.09
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.24
Consensus pattern (48 bp):
GATAAATAGTGATAAGAGTATAGACAGTGGAAAACCAAATTTAAAAAT
Found at i:167532 original size:3 final size:3
Alignment explanation
Indices: 167524--167561 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
167514 TGTTGTATCT
167524 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
167562 TTTTATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:178622 original size:14 final size:14
Alignment explanation
Indices: 178605--178634 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
178595 ATTCAACTAA
*
178605 ACTAAAATGATTAT
1 ACTAAAATGATCAT
178619 ACTAAAATGATCAT
1 ACTAAAATGATCAT
178633 AC
1 AC
178635 ATACTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (14 bp):
ACTAAAATGATCAT
Found at i:181448 original size:2 final size:2
Alignment explanation
Indices: 181441--181467 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
181431 CAACAGTATG
181441 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
181468 ATATTCTCAT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:188742 original size:52 final size:52
Alignment explanation
Indices: 188680--188782 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
188670 TGCTGGTTAG
* *
188680 TTGTTTTCTATGTATTAAAAATATTCCAACTTTGTCTATTTTCGCTTCTATA
1 TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTATA
188732 TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTAT
1 TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTAT
188783 GTCAATGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.50
Consensus pattern (52 bp):
TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTATA
Found at i:193207 original size:13 final size:13
Alignment explanation
Indices: 193189--193218 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
193179 ATCATTTTTT
193189 TATTTTTCAATAA
1 TATTTTTCAATAA
*
193202 TATTTTTCAATAG
1 TATTTTTCAATAA
193215 TATT
1 TATT
193219 CAATTTTACT
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:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (13 bp):
TATTTTTCAATAA
Found at i:193255 original size:21 final size:21
Alignment explanation
Indices: 193231--193285 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
193221 ATTTTACTTT
* * *
193231 TAAAATTTTTAATAGTATTTA
1 TAAAATTTTAAAAAGTATATA
*
193252 TAAAAATTTAAAAAGTATATA
1 TAAAATTTTAAAAAGTATATA
193273 -AAAATTTTAAAAA
1 TAAAATTTTAAAAA
193286 ATTAAATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAAATTTTAAAAAGTATATA
Found at i:195105 original size:26 final size:25
Alignment explanation
Indices: 195076--195162 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
195066 ATCTGGGAAG
*
195076 CCTTTCTGGCTAATCTTGTGGAAAAA
1 CCTTTGTGGCTAAT-TTGTGGAAAAA
*
195102 CCTTTGTGG-TGAATTCTCTGGAAAAA
1 CCTTTGTGGCT-AATT-TGTGGAAAAA
* * *
195128 CCTATGTGACTAATATTGTGG-AAAG
1 CCTTTGTGGCTAAT-TTGTGGAAAAA
195153 CCTTTGTGGC
1 CCTTTGTGGC
195163 ATGTTATTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
25 13 0.27
26 34 0.69
27 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (25 bp):
CCTTTGTGGCTAATTTGTGGAAAAA
Found at i:211097 original size:84 final size:84
Alignment explanation
Indices: 210951--211120 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
210941 TGAGGGAGGT
*
210951 AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCTCTAGATTGACTTGACATATCTTG
1 AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
211016 GGAGAGATCTCAGTTAAAC
66 GGAGAGATCTCAGTTAAAC
*
211035 AGTTTACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
1 AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
211100 GGAGAGATCTCAGTTAAAC
66 GGAGAGATCTCAGTTAAAC
211119 AG
1 AG
211121 GGGTGTGCAT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (84 bp):
AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
GGAGAGATCTCAGTTAAAC
Found at i:215080 original size:16 final size:15
Alignment explanation
Indices: 215055--215087 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
215045 ATTCGGTTAC
215055 TTTTTTTTGTTATTT
1 TTTTTTTTGTTATTT
215070 TTTTTTCTTGTTATTT
1 TTTTTT-TTGTTATTT
215086 TT
1 TT
215088 CACTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTTTTTGTTATTT
Found at i:216005 original size:3 final size:3
Alignment explanation
Indices: 215999--216023 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
215989 AGCAGCGGGC
215999 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
216024 AAGAAGGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:229281 original size:6 final size:7
Alignment explanation
Indices: 229266--229290 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
229256 CACTACTTGT
229266 AAAATAA
1 AAAATAA
229273 AAAATAA
1 AAAATAA
229280 AAAATAA
1 AAAATAA
229287 AAAA
1 AAAA
229291 AAGTTTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:231201 original size:21 final size:23
Alignment explanation
Indices: 231177--231221 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
231167 TTGAACTAAC
231177 TGCTACTAACAACC-ATTA-TTA
1 TGCTACTAACAACCTATTAGTTA
*
231198 TGCTACTAACGACCTATTAGTTA
1 TGCTACTAACAACCTATTAGTTA
231221 T
1 T
231222 CTTAACAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 4 0.19
23 4 0.19
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (23 bp):
TGCTACTAACAACCTATTAGTTA
Found at i:232790 original size:21 final size:21
Alignment explanation
Indices: 232745--232792 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
232735 AGATATATTT
*
232745 TAAATAAATTTATACATTTTT
1 TAAATAAATTTATACATTTTA
*
232766 TAAATAAATTTATTC-TTTTAA
1 TAAATAAATTTATACATTTT-A
232787 TAAATA
1 TAAATA
232793 GTATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATAAATTTATACATTTTA
Found at i:233539 original size:25 final size:26
Alignment explanation
Indices: 233505--233554 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
233495 TATTTTGATC
*
233505 ATTAAGATAA-TATGAAAGTTTAAAA
1 ATTAAGATAATTATAAAAGTTTAAAA
* *
233530 ATTAATATAATTTTAAAAGTTTAAA
1 ATTAAGATAATTATAAAAGTTTAAA
233555 TGAAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (26 bp):
ATTAAGATAATTATAAAAGTTTAAAA
Found at i:233601 original size:18 final size:17
Alignment explanation
Indices: 233578--233621 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
233568 AATTTAAAAT
*
233578 ATTTTAATTTGAATTTGA
1 ATTTTAATTTAAATTT-A
*
233596 ATTTTAAATTAAATTTA
1 ATTTTAATTTAAATTTA
*
233613 TTTTTAATT
1 ATTTTAATT
233622 ATTTCACAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTTAATTTAAATTTA
Found at i:233705 original size:19 final size:19
Alignment explanation
Indices: 233666--233705 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
233656 TAAATAATAA
* *
233666 TTTATTATTAAATTTTCTT
1 TTTATTATTAAATTATATT
233685 TTTATTATTAAATTATATT
1 TTTATTATTAAATTATATT
233704 TT
1 TT
233706 AAATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTATTAAATTATATT
Found at i:249517 original size:44 final size:44
Alignment explanation
Indices: 249454--249541 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
249444 AACAAAAAAA
249454 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
1 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
249498 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
1 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
249542 CTTAATTCCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (44 bp):
AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
Found at i:251125 original size:7 final size:7
Alignment explanation
Indices: 251113--251142 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
251103 GGTCTGAGTT
251113 TGAGAAA
1 TGAGAAA
251120 TGAGAAA
1 TGAGAAA
251127 TGAGAAA
1 TGAGAAA
251134 TGAGAAA
1 TGAGAAA
251141 TG
1 TG
251143 TCTAGTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (7 bp):
TGAGAAA
Found at i:256930 original size:51 final size:51
Alignment explanation
Indices: 256832--256930 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
256822 TTGGTGCCCG
* * * *
256832 TGTTGTCTGCCAGCATTGGCGTCAGAAAGTTGAAAAAGTTTTTTTTTTCCA
1 TGTTGTCTGCCAACATCGGCGTCAGAAAGTTGAAAAAATTTTCTTTTTCCA
* * *
256883 TGTTGTCTGGCAACATCGGTGTTAGAAAGTT-AAAAAATTTATCTTTTT
1 TGTTGTCTGCCAACATCGGCGTCAGAAAGTTGAAAAAATTT-TCTTTTT
256931 TTGTGTTGCC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 8 0.20
51 32 0.80
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (51 bp):
TGTTGTCTGCCAACATCGGCGTCAGAAAGTTGAAAAAATTTTCTTTTTCCA
Found at i:258948 original size:9 final size:9
Alignment explanation
Indices: 258930--258961 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
258920 ATAAGTATAA
*
258930 AATTACCCG
1 AATTAACCG
258939 AATTAACCG
1 AATTAACCG
258948 AATTAACCG
1 AATTAACCG
258957 AATTA
1 AATTA
258962 TTTGTACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:258996 original size:5 final size:6
Alignment explanation
Indices: 258981--259027 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
258971 AATTATATGT
*
258981 TTTTTA TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
259028 ATTAAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 28 0.76
7 8 0.22
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:259068 original size:13 final size:13
Alignment explanation
Indices: 259052--259076 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259042 AATTTTTATG
259052 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
259065 ATTGGGTTGGGT
1 ATTGGGTTGGGT
259077 TGAGTTGAGT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:264127 original size:14 final size:14
Alignment explanation
Indices: 264108--264134 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
264098 TCTGAAAATT
264108 AAAAATATATATTA
1 AAAAATATATATTA
264122 AAAAATATATATT
1 AAAAATATATATT
264135 TATTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATATATATTA
Found at i:269190 original size:10 final size:10
Alignment explanation
Indices: 269177--269209 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
269167 GAAAAACTTC
269177 AAAAAATTAT
1 AAAAAATTAT
269187 AAAAAA-TAT
1 AAAAAATTAT
*
269196 TAAAAATTAT
1 AAAAAATTAT
269206 AAAA
1 AAAA
269210 TGTAGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:273522 original size:3 final size:3
Alignment explanation
Indices: 273514--273541 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
273504 CTCGTGAAGA
273514 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
273542 GGTTATTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:273958 original size:28 final size:28
Alignment explanation
Indices: 273925--273986 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
273915 TTGATAAGGG
**
273925 TTATATTTAATGTGGCGTATGCTTTTAT
1 TTATATTTAATGTAACGTATGCTTTTAT
* *
273953 TTATATTTAATGTAATGTATGGTTTTAT
1 TTATATTTAATGTAACGTATGCTTTTAT
273981 TTATAT
1 TTATAT
273987 ATAAGTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (28 bp):
TTATATTTAATGTAACGTATGCTTTTAT
Found at i:276073 original size:29 final size:29
Alignment explanation
Indices: 276040--276095 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
276030 TAGCTATTTG
* * *
276040 AACTAATTAATTACATTGTTAAAATATTA
1 AACTAATTAATAACATTATAAAAATATTA
276069 AACTAATTAATAACATTATAAAAATAT
1 AACTAATTAATAACATTATAAAAATAT
276096 AGAGACCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (29 bp):
AACTAATTAATAACATTATAAAAATATTA
Found at i:283375 original size:81 final size:81
Alignment explanation
Indices: 283237--283402 Score: 269
Period size: 81 Copynumber: 2.0 Consensus size: 81
283227 TGATCACACA
* **
283237 AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCGAGGTGTTAAGCTACA
1 AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCAAAATGTTAAGCTACA
* *
283302 CGATGTTGCTTATACG
66 CGATGCTGCTCATACG
* *
283318 AGCTGTGACTGTAACATGTAACTGTATATGCTCACATGAGTTGTGGGTCAAAATGTTAAGCTACA
1 AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCAAAATGTTAAGCTACA
283383 CGATGCTGCTCATACG
66 CGATGCTGCTCATACG
283399 AGCT
1 AGCT
283403 ATGAAAAATC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (81 bp):
AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCAAAATGTTAAGCTACA
CGATGCTGCTCATACG
Found at i:291556 original size:12 final size:12
Alignment explanation
Indices: 291539--291563 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
291529 GATTTACAGC
291539 AAAAAAAGAAAG
1 AAAAAAAGAAAG
291551 AAAAAAAGAAAG
1 AAAAAAAGAAAG
291563 A
1 A
291564 GGCACGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:297551 original size:13 final size:13
Alignment explanation
Indices: 297533--297558 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
297523 TGTACCTTAA
297533 AACTCAAGTTTAC
1 AACTCAAGTTTAC
297546 AACTCAAGTTTAC
1 AACTCAAGTTTAC
297559 TAAATTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
AACTCAAGTTTAC
Found at i:297785 original size:22 final size:24
Alignment explanation
Indices: 297759--297811 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
297749 CTACTTAGGT
297759 TACCAACCTCAAGCTAAAC-A-CA
1 TACCAACCTCAAGCTAAACTATCA
* *
297781 TACCAAACTTTAAGCTAAACTATCA
1 TACC-AACCTCAAGCTAAACTATCA
297806 TACCAA
1 TACCAA
297812 ACATAGCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 13 0.50
24 3 0.12
25 6 0.23
ACGTcount: A:0.45, C:0.30, G:0.04, T:0.21
Consensus pattern (24 bp):
TACCAACCTCAAGCTAAACTATCA
Found at i:303384 original size:16 final size:17
Alignment explanation
Indices: 303353--303385 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
303343 TTTATAAGTA
303353 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
303370 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
303386 GCTTCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:303731 original size:46 final size:47
Alignment explanation
Indices: 303671--303943 Score: 369
Period size: 46 Copynumber: 5.9 Consensus size: 47
303661 TTTGACATGA
* * * * * *
303671 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCACGT
** *
303717 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCACGT
* ** *
303763 TGCCATGGTATCTTTCAACCATGGTATTATTC-GTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCACGT
*
303809 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCACGT
*
303855 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCACGT
303901 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCA
303944 AAGAGCACAC
Statistics
Matches: 213, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
45 5 0.02
46 208 0.98
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCACGT
Found at i:306101 original size:11 final size:11
Alignment explanation
Indices: 306085--306112 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
306075 ACCAAATAAT
306085 TAATAATAAAA
1 TAATAATAAAA
306096 TAATAATAAAA
1 TAATAATAAAA
306107 TAATAA
1 TAATAA
306113 AATATCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:306139 original size:20 final size:21
Alignment explanation
Indices: 306086--306161 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 21
306076 CCAAATAATT
*
306086 AATAATAAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
306105 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
306126 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
306147 TAATCATAAAATATC
1 -AATAATAAAATATC
306162 ATCAAAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.26
20 12 0.26
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:306425 original size:30 final size:30
Alignment explanation
Indices: 306358--306425 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
306348 CACCCTTAAA
* * *
306358 ATATTTGCACTATTAGTCCTTTAACTTTTC
1 ATATTTACACTATTAATCCTTTAAATTTTC
*
306388 ATATTTACACT-TTAATCCTTTAAATTTTG
1 ATATTTACACTATTAATCCTTTAAATTTTC
306417 AGTATTTAC
1 A-TATTTAC
306426 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTTAAATTTTC
Found at i:308582 original size:29 final size:30
Alignment explanation
Indices: 308535--308602 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
308525 TGGCCCAAGA
* *
308535 GTAAATACTCAAAATTTAAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTAAAGGACTAATAGT
*
308565 GTAAATATGAAAAGTTAAAGGACTAATAGT
1 GTAAATATCAAAAGTTAAAGGACTAATAGT
*
308595 GCAAATAT
1 GTAAATAT
308603 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTAAAGGACTAATAGT
Found at i:308839 original size:20 final size:21
Alignment explanation
Indices: 308790--308858 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
308780 AAAGTAATGA
* * *
308790 TATTTTGATGATATTTTATGAT
1 TATTTTAATGAGATATTAT-AT
*
308812 TA-TTTAATTAGATA-TATAT
1 TATTTTAATGAGATATTATAT
*
308831 TATTTTAATGAGATATTTTAT
1 TATTTTAATGAGATATTATAT
308852 TATTTTA
1 TATTTTA
308859 TTATTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.10
20 14 0.36
21 19 0.49
22 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (21 bp):
TATTTTAATGAGATATTATAT
Found at i:308851 original size:18 final size:20
Alignment explanation
Indices: 308810--308858 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
308800 ATATTTTATG
*
308810 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
*
308829 ATTATTTTAATGAGATATTTT
1 ATTATTTTAATGAGATA-TAT
308850 ATTATTTTA
1 ATTATTTTA
308859 TTATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
21 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:308864 original size:11 final size:11
Alignment explanation
Indices: 308848--308875 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
308838 ATGAGATATT
308848 TTATTATTTTA
1 TTATTATTTTA
308859 TTATTATTTTA
1 TTATTATTTTA
308870 TTATTA
1 TTATTA
308876 ATTATTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:311066 original size:46 final size:46
Alignment explanation
Indices: 311018--311332 Score: 445
Period size: 46 Copynumber: 6.8 Consensus size: 46
311008 GCTCTTTGAT
** * *
311018 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** *
311064 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
311110 ATGAAACGAATAATACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
311156 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
311202 A-GAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
311248 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * * *
311294 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
311333 TCATGTCAAA
Statistics
Matches: 248, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
45 2 0.01
46 245 0.99
47 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:311639 original size:16 final size:17
Alignment explanation
Indices: 311618--311650 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
311608 ATGATGAAGC
311618 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
311634 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
311651 TACTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:312772 original size:46 final size:46
Alignment explanation
Indices: 312713--312987 Score: 424
Period size: 46 Copynumber: 6.0 Consensus size: 46
312703 TTTCTGTCAT
* * *
312713 GTTGCCACGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
*
312759 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
* *
312805 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
**
312851 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
** * *
312897 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
**
312943 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCA
312988 GAGAGCACAC
Statistics
Matches: 215, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 215 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
Found at i:312880 original size:138 final size:138
Alignment explanation
Indices: 312665--312973 Score: 458
Period size: 138 Copynumber: 2.2 Consensus size: 138
312655 TTTGACATGA
* * * *
312665 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTCATTTTCTGTCATGTTGCCACGGTATCTTT
1 TGCCATGGTATCTTTCAACCATGGTC-T--T-ATTCATTTTCTGTCACGTTGCCACGGTATCTTT
** * * **
312730 CAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCAT
62 CAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
312795 TTCATATCAGGT
127 TTCATATCAGGT
*
312807 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTC-TGTCACGTTGCCACGGTATCTTTCAA
312871 CCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
65 CCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
*
312936 ATATTAGGT
130 ATATCAGGT
312945 TGCCATGGTATCTTTCAACCATGGTCTTA
1 TGCCATGGTATCTTTCAACCATGGTCTTA
312974 CACATTTCAT
Statistics
Matches: 154, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
137 5 0.03
138 124 0.81
139 1 0.01
141 1 0.01
142 23 0.15
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (138 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCTGTCACGTTGCCACGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
TATCAGGT
Found at i:314851 original size:16 final size:16
Alignment explanation
Indices: 314832--314870 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
314822 AATTTTTCCC
*
314832 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
*
314848 TTTTCCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
314864 TCTTTCC
1 TTTTTCC
314871 CCTGCTCTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:314928 original size:16 final size:18
Alignment explanation
Indices: 314899--314939 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
314889 TCATCCTTTC
314899 TTTCTTTTTCTATT-CTT
1 TTTCTTTTTCTATTCCTT
314916 TTTCTTTTT-TATTCCTT
1 TTTCTTTTTCTATTCCTT
*
314933 TTACTTT
1 TTTCTTT
314940 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTTTTTCTATTCCTT
Found at i:332131 original size:161 final size:162
Alignment explanation
Indices: 331865--332346 Score: 912
Period size: 161 Copynumber: 3.0 Consensus size: 162
331855 GACGAGTGTA
*
331865 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGAAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
331930 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGGTTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
331995 GTAATAATCTTTTCCACCAATTAAATTTGATT
131 GTAATAATCTTTTCCACCAATTAAATTTGATT
*
332027 AAGTGATGATCTATGTTACAGTGAATCC-CCTGCAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
332091 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
* *
332156 GTAATAATCTTTCCCACCAATTAAATTTGCTT
131 GTAATAATCTTTTCCACCAATTAAATTTGATT
332188 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
332253 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
332318 GTAATAATCTTTTCCACCAATTAAATTTG
131 GTAATAATCTTTTCCACCAATTAAATTTG
332347 CTTACTTTTA
Statistics
Matches: 312, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
161 156 0.50
162 156 0.50
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (162 bp):
AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
GTAATAATCTTTTCCACCAATTAAATTTGATT
Found at i:332301 original size:162 final size:162
Alignment explanation
Indices: 331865--332350 Score: 920
Period size: 162 Copynumber: 3.0 Consensus size: 162
331855 GACGAGTGTA
*
331865 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGAAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
331930 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGGTTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
*
331995 GTAATAATCTTTTCCACCAATTAAATTTGATT
131 GTAATAATCTTTTCCACCAATTAAATTTGCTT
*
332027 AAGTGATGATCTATGTTACAGTGAATCC-CCTGCAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
332091 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
*
332156 GTAATAATCTTTCCCACCAATTAAATTTGCTT
131 GTAATAATCTTTTCCACCAATTAAATTTGCTT
332188 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
332253 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
332318 GTAATAATCTTTTCCACCAATTAAATTTGCTT
131 GTAATAATCTTTTCCACCAATTAAATTTGCTT
332350 A
1 A
332351 CTTTTAAAAC
Statistics
Matches: 316, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
161 156 0.49
162 160 0.51
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (162 bp):
AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
GTAATAATCTTTTCCACCAATTAAATTTGCTT
Found at i:335481 original size:3 final size:3
Alignment explanation
Indices: 335473--335499 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
335463 GCTAAAAAAG
335473 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
335500 AAGACGAAGA
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:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:335583 original size:3 final size:3
Alignment explanation
Indices: 335575--335609 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
335565 TACCTTATGC
335575 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
335610 GGCGGCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:337183 original size:111 final size:111
Alignment explanation
Indices: 337047--337264 Score: 337
Period size: 111 Copynumber: 2.0 Consensus size: 111
337037 TTCTTCCAAT
* * * * * *
337047 TTGGAATGATGAGAGGATAGAAAATAAGAGAGAAATATATGTTAGTTTAAAATTATGAATTTTTA
1 TTGGAATCATGAGAGGAGAGAAAATAAAAGAGAAATAGATGTTAGTTCAAAATTATGAATTTTCA
* *
337112 AATTTTTTATTTTATTTTCTTTCATTTTTCAACTCTACCAAGTAAA
66 AATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAGTAAA
* *
337158 TTGGAATCATGAGATGAGAGAAAATAAAAGAGAAATGGATGTTAGTTCAAAATTATGAATTTTCA
1 TTGGAATCATGAGAGGAGAGAAAATAAAAGAGAAATAGATGTTAGTTCAAAATTATGAATTTTCA
*
337223 GATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAG
66 AATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAG
337265 CAACGAAGAA
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 96 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (111 bp):
TTGGAATCATGAGAGGAGAGAAAATAAAAGAGAAATAGATGTTAGTTCAAAATTATGAATTTTCA
AATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAGTAAA
Found at i:376723 original size:46 final size:46
Alignment explanation
Indices: 376671--377036 Score: 473
Period size: 46 Copynumber: 8.0 Consensus size: 46
376661 GCTTTCTGAA
* *
376671 ATGAAATGTGTAAGAACATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
376717 ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
376763 ATGAAAGGTGTAAGATCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
376809 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
376855 ATAAAATGTGTAAGACCATGGTTAAAAGATACCATAGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* ** * *
376901 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** ** *
376947 ATGAAATGAACAAGACCACAGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
376993 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
377037 TCAAAGATAA
Statistics
Matches: 279, Mismatches: 40, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 1 0.00
46 278 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:376813 original size:25 final size:25
Alignment explanation
Indices: 376739--376814 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
376729 AGACCATAGT
*
376739 TGAAAGATACCATGGCAACAGGATA
1 TGAAAGATACCATGGCAACATGATA
* ** * * *
376764 TGAAAGGT-GTA-AG-ATCATGGT-
1 TGAAAGATACCATGGCAACATGATA
376785 TGAAAGATACCATGGCAACATGATA
1 TGAAAGATACCATGGCAACATGATA
376810 TGAAA
1 TGAAA
376815 TGTGTAAGAC
Statistics
Matches: 34, Mismatches: 13, Indels: 8
0.62 0.24 0.15
Matches are distributed among these distances:
21 7 0.21
22 6 0.18
23 2 0.06
24 7 0.21
25 12 0.35
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (25 bp):
TGAAAGATACCATGGCAACATGATA
Found at i:377336 original size:16 final size:17
Alignment explanation
Indices: 377317--377349 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
377307 ATGATGGAGC
377317 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
377333 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
377350 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:378875 original size:19 final size:20
Alignment explanation
Indices: 378842--378879 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
378832 TTTTACCCTA
*
378842 AACCTCGAACTTTGAACTCG
1 AACCTCGAACCTTGAACTCG
378862 AACCT-GAACCTTGAACTC
1 AACCTCGAACCTTGAACTC
378880 AAAATCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.32, C:0.32, G:0.13, T:0.24
Consensus pattern (20 bp):
AACCTCGAACCTTGAACTCG
Found at i:386329 original size:19 final size:20
Alignment explanation
Indices: 386302--386339 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
386292 TTTTATATTA
386302 TTAAAAAAATTAAT-TTTTT
1 TTAAAAAAATTAATATTTTT
*
386321 TTAACAAAATTAATATTTT
1 TTAAAAAAATTAATATTTT
386340 AAAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAAAAAATTAATATTTTT
Found at i:388343 original size:29 final size:30
Alignment explanation
Indices: 388311--388369 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
388301 CTTATAATGA
388311 ACATTTTA-AATAAATAA-TTATTTTAATTT
1 ACATTTTATAAT-AATAATTTATTTTAATTT
*
388340 ACATTTTATAATAATAATTTTTTTTAATTT
1 ACATTTTATAATAATAATTTATTTTAATTT
388370 TTTCAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (30 bp):
ACATTTTATAATAATAATTTATTTTAATTT
Found at i:396663 original size:86 final size:86
Alignment explanation
Indices: 396489--396674 Score: 198
Period size: 87 Copynumber: 2.2 Consensus size: 86
396479 CTTTAAAAAG
* * * * * * * *
396489 AAAAAAG-AATTAAACTCTTTTTTTTTTCACTTAATTGAGTACTTTAACTTTCAGAATGTATAAA
1 AAAAAAGCAATTAAACCCATTTTTTTTCCACTTAACTGAGTAATTGAACTTTCAAAATATATAAA
* *
396553 AAAAGGCCTTCAAATTTTTTC
66 AAAAGACCTTCAAAATTTTTC
* * * *
396574 AAAAAAAGCAATTAAGCCCATTTTTTTTCCACTTAACTGGGTAATTGATCTTTCAAAATATAT-C
1 -AAAAAAGCAATTAAACCCATTTTTTTTCCACTTAACTGAGTAATTGAACTTTCAAAATATATAA
396638 AAAAAGACACTT-AAAATTTTTC
65 AAAAAGAC-CTTCAAAATTTTTC
*
396660 AAAAAAGCTATTAAA
1 AAAAAAGCAATTAAA
396675 ACCCTGCTCT
Statistics
Matches: 82, Mismatches: 16, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
85 13 0.16
86 23 0.28
87 46 0.56
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (86 bp):
AAAAAAGCAATTAAACCCATTTTTTTTCCACTTAACTGAGTAATTGAACTTTCAAAATATATAAA
AAAAGACCTTCAAAATTTTTC
Done.