Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015303.1 Kokia drynarioides strain JFW-HI SEQ_130348, 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: 387286
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 929 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2669 original size:23 final size:23
Alignment explanation
Indices: 2639--2682 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2629 ATTGAGTTAA
2639 TTCTCTCTGCTTCATAGCACGAT
1 TTCTCTCTGCTTCATAGCACGAT
* *
2662 TTCTCTCTGTTTTATAGCACG
1 TTCTCTCTGCTTCATAGCACG
2683 TTTTTCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (23 bp):
TTCTCTCTGCTTCATAGCACGAT
Found at i:2751 original size:20 final size:19
Alignment explanation
Indices: 2700--2754 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
2690 TTTCTTTTTT
2700 TCTCTCGTCTTTTTCTTCTTC
1 TCTCTC-TCTTTTT-TTCTTC
* *
2721 T-TTTCTGTTTTTTTCTCTC
1 TCTCTCTCTTTTTTTCT-TC
2740 TCTCTCTCTTTTTTT
1 TCTCTCTCTTTTTTT
2755 TTTTTTTTTN
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 14 0.50
21 1 0.04
ACGTcount: A:0.00, C:0.27, G:0.04, T:0.69
Consensus pattern (19 bp):
TCTCTCTCTTTTTTTCTTC
Found at i:2752 original size:21 final size:20
Alignment explanation
Indices: 2700--2755 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
2690 TTTCTTTTTT
*
2700 TCTCTCGTCTTTTTCTTCTTC
1 TCTCTC-TCTTTTTTTTCTTC
2721 T-T-T-TCTGTTTTTTTCTCTC
1 TCTCTCTCT-TTTTTTTCT-TC
2740 TCTCTCTCTTTTTTTT
1 TCTCTCTCTTTTTTTT
2756 TTTTTTTTNT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
17 3 0.10
18 8 0.28
19 4 0.14
20 2 0.07
21 9 0.31
22 3 0.10
ACGTcount: A:0.00, C:0.27, G:0.04, T:0.70
Consensus pattern (20 bp):
TCTCTCTCTTTTTTTTCTTC
Found at i:25124 original size:59 final size:59
Alignment explanation
Indices: 25051--25164 Score: 210
Period size: 59 Copynumber: 1.9 Consensus size: 59
25041 TATTTTTTTT
*
25051 TAAGTGGTTGTTTTCTTTAATTTAAAATTGAAATTAATATTTATTTAGTGGAGTCGTAG
1 TAAGTGGCTGTTTTCTTTAATTTAAAATTGAAATTAATATTTATTTAGTGGAGTCGTAG
*
25110 TAAGTGGCTGTTTTCTTTAATTTAAAATTGAAATTAATATTTATTTGGTGGAGTC
1 TAAGTGGCTGTTTTCTTTAATTTAAAATTGAAATTAATATTTATTTAGTGGAGTC
25165 ATAGATAATG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.47
Consensus pattern (59 bp):
TAAGTGGCTGTTTTCTTTAATTTAAAATTGAAATTAATATTTATTTAGTGGAGTCGTAG
Found at i:27383 original size:42 final size:44
Alignment explanation
Indices: 27336--27425 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
27326 AAATATACAC
*
27336 TTATTTGTTTATTTATTTT-TAAT-TTTTTTTAAGAAATTTAAT
1 TTATTTGTTTATTTATTTTAAAATATTTTTTTAAGAAATTTAAT
27378 TTATTTGTTTATTTATTTTAAAATATTTTTTTAAGAAATTTAAT
1 TTATTTGTTTATTTATTTTAAAATATTTTTTTAAGAAATTTAAT
27422 TTAT
1 TTAT
27426 GCTTGTTATA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 19 0.42
43 3 0.07
44 23 0.51
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (44 bp):
TTATTTGTTTATTTATTTTAAAATATTTTTTTAAGAAATTTAAT
Found at i:27419 original size:22 final size:22
Alignment explanation
Indices: 27359--27420 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
27349 TATTTTTAAT
**
27359 TTTTTTTAAGAAATTTAATTTA
1 TTTTTTTAAGAAATTTAAAATA
* *** *
27381 TTTGTTTATTTATTTTAAAATA
1 TTTTTTTAAGAAATTTAAAATA
27403 TTTTTTTAAGAAATTTAA
1 TTTTTTTAAGAAATTTAA
27421 TTTATGCTTG
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTTTTTAAGAAATTTAAAATA
Found at i:28047 original size:23 final size:24
Alignment explanation
Indices: 28021--28065 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
28011 AGAACACGGT
28021 ATGT-AACACTCTAAAAT-TGTATC
1 ATGTCAACAC-CTAAAATATGTATC
*
28044 ATGTCATCACCTAAAATATGTA
1 ATGTCAACACCTAAAATATGTA
28066 GAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (24 bp):
ATGTCAACACCTAAAATATGTATC
Found at i:33368 original size:9 final size:9
Alignment explanation
Indices: 33350--33449 Score: 64
Period size: 9 Copynumber: 11.2 Consensus size: 9
33340 AAAATTATTA
33350 TTTTAAATT
1 TTTTAAATT
*
33359 TTTTACA-T
1 TTTTAAATT
*
33367 TTTTAACTT
1 TTTTAAATT
*
33376 TTTATATAATC
1 TTT-TA-AATT
*
33387 TTTAAAATT
1 TTTTAAATT
*
33396 TTTTATATT
1 TTTTAAATT
33405 TTTTAAA--
1 TTTTAAATT
* *
33412 ATATAAA-T
1 TTTTAAATT
*
33420 TTTAAAATT
1 TTTTAAATT
*
33429 TTTATAAATA
1 TTT-TAAATT
33439 TTTTAAATT
1 TTTTAAATT
33448 TT
1 TT
33450 AAAAAATATT
Statistics
Matches: 67, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
7 5 0.07
8 10 0.15
9 37 0.55
10 10 0.15
11 5 0.07
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTAAATT
Found at i:33424 original size:33 final size:36
Alignment explanation
Indices: 33378--33445 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
33368 TTTAACTTTT
* *
33378 TATATAATCTTTAAAATTTTT-TATATTTTTTAAAA
1 TATATAATCTTTAAAATTTTTATAAATATTTTAAAA
33413 TATA-AAT-TTTAAAATTTTTATAAATATTTTAAA
1 TATATAATCTTTAAAATTTTTATAAATATTTTAAA
33446 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 12 0.40
34 14 0.47
35 4 0.13
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (36 bp):
TATATAATCTTTAAAATTTTTATAAATATTTTAAAA
Found at i:33456 original size:19 final size:19
Alignment explanation
Indices: 33418--33462 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
33408 TAAAATATAA
* *
33418 ATTTTAAAATTTTTATAAAT
1 ATTTT-AAATTTTAAAAAAT
33438 ATTTTAAATTTTAAAAAAT
1 ATTTTAAATTTTAAAAAAT
33457 ATTTTA
1 ATTTTA
33463 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAAATTTTAAAAAAT
Found at i:34661 original size:19 final size:19
Alignment explanation
Indices: 34627--34678 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
34617 AAATTATCAA
34627 AAAAATTCAAATATATTT-T
1 AAAAATTCAAA-ATATTTAT
*
34646 CAAAAATTCCAAATATTTAT
1 -AAAAATTCAAAATATTTAT
*
34666 AAAAATTCTAAAT
1 AAAAATTCAAAAT
34679 TTTCATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:35014 original size:19 final size:19
Alignment explanation
Indices: 34992--35030 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
34982 CATGATATTG
*
34992 TGAAGTAAAAAAAAATTAA
1 TGAAGGAAAAAAAAATTAA
* *
35011 TGAAGGGATAAAAAATTAA
1 TGAAGGAAAAAAAAATTAA
35030 T
1 T
35031 TTTATTGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (19 bp):
TGAAGGAAAAAAAAATTAA
Found at i:36561 original size:18 final size:20
Alignment explanation
Indices: 36528--36569 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
36518 TAAATGATTT
36528 TAAAATTATTTTTTAAAA-TA
1 TAAAATTA-TTTTTAAAATTA
36548 TAAAATTA-TTTTAAAATTA
1 TAAAATTATTTTTAAAATTA
36567 TAA
1 TAA
36570 TCATCATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAATTATTTTTAAAATTA
Found at i:37409 original size:21 final size:22
Alignment explanation
Indices: 37383--37425 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
37373 GAATGATTTT
*
37383 AATAATTTT-ATATTTTTAAAA
1 AATAATTTTAATAATTTTAAAA
37404 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
37426 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:37722 original size:13 final size:14
Alignment explanation
Indices: 37686--37720 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
37676 TGACACATGC
*
37686 TTTTTGTATAATTT
1 TTTTTTTATAATTT
37700 TTTTCTTTATAATTT
1 TTTT-TTTATAATTT
37715 TTTTTT
1 TTTTTT
37721 ATGTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTTTATAATTT
Found at i:46242 original size:31 final size:31
Alignment explanation
Indices: 46191--46253 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
46181 GAGTCCAATT
*
46191 ACTTTAATAAAATTTTTTGAATAGATT-AGTG
1 ACTTAAATAAAATTTTTTGAATAG-TTCAGTG
46222 ACTTAAATGAAAA-TTTTTGAATAGTTCAGTG
1 ACTTAAAT-AAAATTTTTTGAATAGTTCAGTG
46253 A
1 A
46254 TCATTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 23 0.79
32 4 0.14
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (31 bp):
ACTTAAATAAAATTTTTTGAATAGTTCAGTG
Found at i:53949 original size:51 final size:51
Alignment explanation
Indices: 53861--53998 Score: 188
Period size: 51 Copynumber: 2.7 Consensus size: 51
53851 TTCGGATCCA
* * *
53861 TGTTCTCCGTACTCTGGTTTCCTGCCATACCCAGATCCGTACTCAGATTCT
1 TGTTCGCCATACTCTGGTTTCCGGCCATACCCAGATCCGTACTCAGATTCT
* * *
53912 TTTTCGCCATACTCTGGTTTCCGGCCATACCCGGATCCGTACTCGGATTCT
1 TGTTCGCCATACTCTGGTTTCCGGCCATACCCAGATCCGTACTCAGATTCT
* *
53963 TGTTCGCCATACT-TGGGTCTCCGACCATACCCAGAT
1 TGTTCGCCATACTCT-GGTTTCCGGCCATACCCAGAT
53999 TCAAATTCAG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
50 1 0.01
51 75 0.99
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (51 bp):
TGTTCGCCATACTCTGGTTTCCGGCCATACCCAGATCCGTACTCAGATTCT
Found at i:54038 original size:54 final size:54
Alignment explanation
Indices: 53977--54086 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 54
53967 CGCCATACTT
* *
53977 GGGTCTCCGACCATACCCAGATTCAAATTCAGGAGGCGGAGGCTGCTCAAATTC
1 GGGTCTCCGACCATACCCAGATCCAAACTCAGGAGGCGGAGGCTGCTCAAATTC
* * *
54031 GGGTCTCCGTCCATACCCAGATCCAAACTCAGGCGGCGGAGGCTGCTCATATTC
1 GGGTCTCCGACCATACCCAGATCCAAACTCAGGAGGCGGAGGCTGCTCAAATTC
54085 GG
1 GG
54087 ATTTCCGTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (54 bp):
GGGTCTCCGACCATACCCAGATCCAAACTCAGGAGGCGGAGGCTGCTCAAATTC
Found at i:57890 original size:15 final size:15
Alignment explanation
Indices: 57870--57917 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
57860 ACCTATTTCC
57870 AACATACTTTTGTCG
1 AACATACTTTTGTCG
*** *
57885 AACATA-TAAAGTTG
1 AACATACTTTTGTCG
57899 AACATACTTTTGTCG
1 AACATACTTTTGTCG
57914 AACA
1 AACA
57918 CATACCTTAT
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (15 bp):
AACATACTTTTGTCG
Found at i:75623 original size:21 final size:21
Alignment explanation
Indices: 75594--75634 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
75584 TTCTAAAGGT
*
75594 ATCCTTTTTTATTTAATTTTG
1 ATCCATTTTTATTTAATTTTG
* *
75615 ATCCATTTTTGTTTACTTTT
1 ATCCATTTTTATTTAATTTT
75635 TCTGGGTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.66
Consensus pattern (21 bp):
ATCCATTTTTATTTAATTTTG
Found at i:80327 original size:27 final size:28
Alignment explanation
Indices: 80288--80340 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
80278 CAGTATTGTT
80288 ATTTTTTAATAAAAATTTATAATTTTAA
1 ATTTTTTAATAAAAATTTATAATTTTAA
**
80316 ATTTTTT-ATAAATTTTTATAATTTT
1 ATTTTTTAATAAAAATTTATAATTTT
80341 TAATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTTTTAATAAAAATTTATAATTTTAA
Found at i:80350 original size:2 final size:2
Alignment explanation
Indices: 80343--80368 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
80333 ATAATTTTTA
80343 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
80369 CTTTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87975 original size:21 final size:20
Alignment explanation
Indices: 87946--87990 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
87936 TACTTAATTT
* *
87946 AATACATTTTTAATTATTTAA
1 AATACATTTATAATT-TATAA
*
87967 AATATATTTATAATTTATAA
1 AATACATTTATAATTTATAA
87987 AATA
1 AATA
87991 AAGATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATACATTTATAATTTATAA
Found at i:99480 original size:19 final size:19
Alignment explanation
Indices: 99452--99488 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
99442 TATTTTAGGC
*
99452 CCACCTATATTATTTTTTA
1 CCACCCATATTATTTTTTA
99471 CCACCCATATTATTTTTT
1 CCACCCATATTATTTTTT
99489 CAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (19 bp):
CCACCCATATTATTTTTTA
Found at i:99702 original size:90 final size:90
Alignment explanation
Indices: 99608--99874 Score: 516
Period size: 90 Copynumber: 3.0 Consensus size: 90
99598 GTAGTATTAT
99608 ATATTTAATATAAGTTTTTTATGTGTTCTAAATTACATAATATATAAAAATAACATAATATAAAA
1 ATATTTAATATAAGTTTTTTATGTGTTCTAAATTACATAATATATAAAAATAACATAATATAAAA
99673 TATTATAAACTTAAAAATGAGTCCG
66 TATTATAAACTTAAAAATGAGTCCG
*
99698 ATATTTAATATAAGTTTTTTATGTGTTCTAAATTACATAATATATAAAAATAATATAATATAAAA
1 ATATTTAATATAAGTTTTTTATGTGTTCTAAATTACATAATATATAAAAATAACATAATATAAAA
99763 TATTATAAACTTAAAAATGAGTCCG
66 TATTATAAACTTAAAAATGAGTCCG
*
99788 ATATTTAATATAAGTTTTTTATGTGTTCCAAATTACATAATATATAAAAATAACATAATATAAAA
1 ATATTTAATATAAGTTTTTTATGTGTTCTAAATTACATAATATATAAAAATAACATAATATAAAA
99853 TATTATAAACTTAAAAATGAGT
66 TATTATAAACTTAAAAATGAGT
99875 TCGGGCACGT
Statistics
Matches: 174, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 174 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (90 bp):
ATATTTAATATAAGTTTTTTATGTGTTCTAAATTACATAATATATAAAAATAACATAATATAAAA
TATTATAAACTTAAAAATGAGTCCG
Found at i:100666 original size:2 final size:2
Alignment explanation
Indices: 100659--100689 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
100649 TAAAAATAAT
100659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
100690 GTGAAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:104348 original size:24 final size:25
Alignment explanation
Indices: 104316--104365 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
104306 TATCTCTGAA
104316 ATAATCAGAGTTTAACTGAGAA-AAG
1 ATAATCAGAGTTTAACT-AGAAGAAG
104341 ATAA-CAGAGTTTAACTAGAAGAAG
1 ATAATCAGAGTTTAACTAGAAGAAG
104365 A
1 A
104366 ATACGAGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 4 0.17
24 16 0.67
25 4 0.17
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.22
Consensus pattern (25 bp):
ATAATCAGAGTTTAACTAGAAGAAG
Found at i:104646 original size:27 final size:27
Alignment explanation
Indices: 104616--104668 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
104606 ATCAAACACT
104616 TAAA-AAATTAAAACAAACATTAAAAAA
1 TAAATAAATTAAAA-AAACATTAAAAAA
* *
104643 TAAATAAATTTAAAATACATTAAAAA
1 TAAATAAATTAAAAAAACATTAAAAA
104669 TTCTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (27 bp):
TAAATAAATTAAAAAAACATTAAAAAA
Found at i:104808 original size:20 final size:20
Alignment explanation
Indices: 104785--104853 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 20
104775 AAAATGCATA
*
104785 AAAAATAACATCCAAACAAC
1 AAAAATAACATCAAAACAAC
*
104805 AAAAAAAACAATCAAAACAGTAGC
1 AAAAATAAC-ATCAAAACA--A-C
104829 AAAAATAACATCAAAACAAC
1 AAAAATAACATCAAAACAAC
104849 AAAAA
1 AAAAA
104854 ATAGCAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 14 0.33
21 9 0.21
23 10 0.24
24 9 0.21
ACGTcount: A:0.70, C:0.19, G:0.03, T:0.09
Consensus pattern (20 bp):
AAAAATAACATCAAAACAAC
Found at i:104812 original size:23 final size:23
Alignment explanation
Indices: 104784--104854 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
104774 AAAAATGCAT
*
104784 AAAAAATAACATCCAAACAACAA
1 AAAAAATAACATCAAAACAACAA
* ** *
104807 AAAAAA-CA-ATCAAAACAGTAG
1 AAAAAATAACATCAAAACAACAA
*
104828 CAAAAATAACATCAAAACAACAA
1 AAAAAATAACATCAAAACAACAA
104851 AAAA
1 AAAA
104855 TAGCAATAAA
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
21 14 0.40
22 2 0.06
23 19 0.54
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.08
Consensus pattern (23 bp):
AAAAAATAACATCAAAACAACAA
Found at i:104838 original size:44 final size:44
Alignment explanation
Indices: 104785--104868 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
104775 AAAATGCATA
*
104785 AAAAATAACATCCAAACAACAAAAAA-AACAATCAAAACAGTAGC
1 AAAAATAACATCAAAACAACAAAAAATAACAAT-AAAACAGTAGC
*
104829 AAAAATAACATCAAAACAACAAAAAATAGCAATAAAACAG
1 AAAAATAACATCAAAACAACAAAAAATAACAATAAAACAG
104869 CACCAAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 32 0.86
45 5 0.14
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.10
Consensus pattern (44 bp):
AAAAATAACATCAAAACAACAAAAAATAACAATAAAACAGTAGC
Found at i:104865 original size:21 final size:22
Alignment explanation
Indices: 104784--104867 Score: 88
Period size: 21 Copynumber: 3.9 Consensus size: 22
104774 AAAAATGCAT
*
104784 AAAAAATAAC-ATCCAAACAAC
1 AAAAAATAACAATCAAAACAAC
104805 AAAAAA-AACAATCAAAACAGTAGC
1 AAAAAATAACAATCAAAACA--A-C
104829 -AAAAATAAC-ATCAAAACAAC
1 AAAAAATAACAATCAAAACAAC
*
104849 AAAAAATAGCAAT-AAAACA
1 AAAAAATAACAATCAAAACA
104868 GCACCAAAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.07
21 29 0.54
22 2 0.04
23 15 0.28
24 4 0.07
ACGTcount: A:0.69, C:0.18, G:0.04, T:0.10
Consensus pattern (22 bp):
AAAAAATAACAATCAAAACAAC
Found at i:105921 original size:2 final size:2
Alignment explanation
Indices: 105914--105938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
105904 AGTTTATCAC
105914 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
105939 CCAATCTTAT
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:107085 original size:3 final size:3
Alignment explanation
Indices: 107077--107104 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
107067 AAAAGATATA
107077 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
107105 TAATATTTTG
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:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:109770 original size:17 final size:17
Alignment explanation
Indices: 109748--109781 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
109738 TAACATTGTG
*
109748 TAAAAAACTATATAAAA
1 TAAAAAACTAAATAAAA
*
109765 TAAAAAATTAAATAAAA
1 TAAAAAACTAAATAAAA
109782 AAATTCAATT
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:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAAACTAAATAAAA
Found at i:110417 original size:16 final size:17
Alignment explanation
Indices: 110400--110435 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
110390 TAATATATAA
110400 TTTCTTTAATGGTAAAT
1 TTTCTTTAATGGTAAAT
*
110417 TTTTTTTAATGGT-AAT
1 TTTCTTTAATGGTAAAT
110433 TTT
1 TTT
110436 TTTCTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.61
Consensus pattern (17 bp):
TTTCTTTAATGGTAAAT
Found at i:110436 original size:16 final size:17
Alignment explanation
Indices: 110404--110438 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
110394 ATATAATTTC
110404 TTTAATGGTAAATTTTT
1 TTTAATGGTAAATTTTT
110421 TTTAATGGT-AATTTTT
1 TTTAATGGTAAATTTTT
110437 TT
1 TT
110439 CTTTTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (17 bp):
TTTAATGGTAAATTTTT
Found at i:115355 original size:23 final size:22
Alignment explanation
Indices: 115305--115355 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
115295 ATATTGTTTT
115305 TAAT-TTTTTTTAAAATATTTA
1 TAATGTTTTTTTAAAATATTTA
*
115326 TATTGTTTTATTT-AAATATTTAA
1 TAATGTTTT-TTTAAAATATTT-A
115349 TAATGTT
1 TAATGTT
115356 ATACATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 3 0.12
22 12 0.48
23 10 0.40
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TAATGTTTTTTTAAAATATTTA
Found at i:124625 original size:61 final size:61
Alignment explanation
Indices: 124434--124616 Score: 357
Period size: 61 Copynumber: 3.0 Consensus size: 61
124424 TTTATTAAAA
124434 ATTTCATATATTTGTACAATTGAAAACTGGCGTAATTGACGGAATAACTAGACAGTGACAT
1 ATTTCATATATTTGTACAATTGAAAACTGGCGTAATTGACGGAATAACTAGACAGTGACAT
*
124495 ATTTCATATATTTGTACAATTGAAAACTGACGTAATTGACGGAATAACTAGACAGTGACAT
1 ATTTCATATATTTGTACAATTGAAAACTGGCGTAATTGACGGAATAACTAGACAGTGACAT
124556 ATTTCATATATTTGTACAATTGAAAACTGGCGTAATTGACGGAATAACTAGACAGTGACAT
1 ATTTCATATATTTGTACAATTGAAAACTGGCGTAATTGACGGAATAACTAGACAGTGACAT
124617 GTGGCATATG
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 120 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (61 bp):
ATTTCATATATTTGTACAATTGAAAACTGGCGTAATTGACGGAATAACTAGACAGTGACAT
Found at i:130641 original size:25 final size:24
Alignment explanation
Indices: 130613--130659 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
130603 TAGATATAAG
130613 ATATCA-AACATAAATATTAATAATT
1 ATATCATAA-ATAAATA-TAATAATT
*
130638 ATATTATAAATAAATATAATAA
1 ATATCATAAATAAATATAATAA
130660 ACATCTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATCATAAATAAATATAATAATT
Found at i:132143 original size:12 final size:13
Alignment explanation
Indices: 132128--132156 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
132118 TAAATAATTT
132128 AAAAATT-ATAAA
1 AAAAATTCATAAA
132140 AAAAATTCATAAA
1 AAAAATTCATAAA
132153 AAAA
1 AAAA
132157 CATGACGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAATTCATAAA
Found at i:139787 original size:14 final size:13
Alignment explanation
Indices: 139768--139806 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
139758 TTCTTTGAGG
139768 TTTTGAATTTTAGA
1 TTTTGAATTTT-GA
139782 TTTTGAATTTTGA
1 TTTTGAATTTTGA
*
139795 ATTTGATATTTT
1 TTTTGA-ATTTT
139807 TGTATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (13 bp):
TTTTGAATTTTGA
Found at i:139851 original size:13 final size:13
Alignment explanation
Indices: 139813--139851 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
139803 TTTTTGTATT
139813 TATTTATATTTAA
1 TATTTATATTTAA
* *
139826 TAATTATAATTAA
1 TATTTATATTTAA
*
139839 TATTTATTTTTAA
1 TATTTATATTTAA
139852 ACCCTTAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:141403 original size:19 final size:18
Alignment explanation
Indices: 141365--141410 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
141355 ATTCTTTTAA
*
141365 CTTTCTTTT-TTTTTTTC
1 CTTTCTTTTCTTTTATTC
141382 CTTTCTTTTCTATTTATTC
1 CTTTCTTTTCT-TTTATTC
*
141401 CTTTGTTTTC
1 CTTTCTTTTC
141411 CTCCCTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 1 0.04
19 15 0.60
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (18 bp):
CTTTCTTTTCTTTTATTC
Found at i:144179 original size:19 final size:19
Alignment explanation
Indices: 144155--144195 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
144145 AACTACGATG
*
144155 ACTACTTAATTTAATTTTC
1 ACTACTTAATATAATTTTC
144174 ACTACTTAATATAATTTTC
1 ACTACTTAATATAATTTTC
144193 ACT
1 ACT
144196 TTGAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (19 bp):
ACTACTTAATATAATTTTC
Found at i:148250 original size:121 final size:121
Alignment explanation
Indices: 148031--148277 Score: 485
Period size: 121 Copynumber: 2.0 Consensus size: 121
148021 GAATTTGCTG
*
148031 AATATTGATTAGAAATTTAAAGTTCGGTTTCGTTTTTAAAAAAAATATATTTTCATTTTCATTTT
1 AATAATGATTAGAAATTTAAAGTTCGGTTTCGTTTTTAAAAAAAATATATTTTCATTTTCATTTT
148096 AAAACAATTTTCCTTTTTTTATTTTTAAAATTTGAAAAACATGTTTGGTAATTAGA
66 AAAACAATTTTCCTTTTTTTATTTTTAAAATTTGAAAAACATGTTTGGTAATTAGA
148152 AATAATGATTAGAAATTTAAAGTTCGGTTTCGTTTTTAAAAAAAATATATTTTCATTTTCATTTT
1 AATAATGATTAGAAATTTAAAGTTCGGTTTCGTTTTTAAAAAAAATATATTTTCATTTTCATTTT
148217 AAAACAATTTTCCTTTTTTTATTTTTAAAATTTGAAAAACATGTTTGGTAATTAGA
66 AAAACAATTTTCCTTTTTTTATTTTTAAAATTTGAAAAACATGTTTGGTAATTAGA
148273 AATAA
1 AATAA
148278 AAATTTGTTT
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 125 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (121 bp):
AATAATGATTAGAAATTTAAAGTTCGGTTTCGTTTTTAAAAAAAATATATTTTCATTTTCATTTT
AAAACAATTTTCCTTTTTTTATTTTTAAAATTTGAAAAACATGTTTGGTAATTAGA
Found at i:153913 original size:22 final size:21
Alignment explanation
Indices: 153885--153941 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
153875 CATAACATGC
153885 TTGTCTCGAGACATTGGGTGG-T
1 TTGTCTCGAGACATT--GTGGAT
*
153907 TTGTCTCAAGACATTGTGGCAT
1 TTGTCTCGAGACATTGTGG-AT
153929 TTGTCTCGAGACA
1 TTGTCTCGAGACA
153942 CAAAACATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 4 0.13
22 27 0.87
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (21 bp):
TTGTCTCGAGACATTGTGGAT
Found at i:158318 original size:28 final size:28
Alignment explanation
Indices: 158287--158343 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
158277 TAGCTATCAA
158287 AATGAATACTGAAAAAGGCTACGAAATT
1 AATGAATACTGAAAAAGGCTACGAAATT
158315 AATGAATACTGAAAAAGGCTACGAAATT
1 AATGAATACTGAAAAAGGCTACGAAATT
158343 A
1 A
158344 GTTTTTAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.21
Consensus pattern (28 bp):
AATGAATACTGAAAAAGGCTACGAAATT
Found at i:164941 original size:2 final size:2
Alignment explanation
Indices: 164886--164926 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
164876 AAAACACAAA
164886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
164927 AAATAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:167015 original size:160 final size:160
Alignment explanation
Indices: 166744--167058 Score: 470
Period size: 160 Copynumber: 2.0 Consensus size: 160
166734 TGCTGTTATG
*
166744 GGGTAAATATAAAAAATAGGAAAAGTGTATAATAAGGGTAAAATGATGCGTTGACTGTGTGCGGT
1 GGGTAAATATAAAAAATAGGAAAAGTGAATAATAAGGGTAAAATGATGCGTTGACTGTGTGCGGT
* * * * *
166809 GTTACTGAAATGGTGCATATAGATTTAGTAAAACAGTGCGTTTAGGGAGTAACGGTCACAGCTGT
66 ATTACTGAAACGGTGCATATAGATCTAGTAAAACAGTGCATTTAGGGAGTAACGGCCACAGCTGT
166874 AAGGGACTTAACAAACTCTTGTAAAGCCGC
131 AAGGGACTTAACAAACTCTTGTAAAGCCGC
* * *
166904 GGGTAAATATAAAAAATAGGAAAAGTGAATAACT-AGGGTAAAATGATGTGTTGAGTGTGTGTGG
1 GGGTAAATATAAAAAATAGGAAAAGTGAATAA-TAAGGGTAAAATGATGCGTTGACTGTGTGCGG
** * *
166968 TATTACTGAAACGGTGTGTTTAGATCTAGTAAAACAGTGCATTTAGGGAGTAATGGCCACAGCTG
65 TATTACTGAAACGGTGCATATAGATCTAGTAAAACAGTGCATTTAGGGAGTAACGGCCACAGCTG
** *
167033 TAAGGGGTTTAACTAACTCTTGTAAA
130 TAAGGGACTTAACAAACTCTTGTAAA
167059 AGTCACCTTA
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
160 137 0.99
161 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.28
Consensus pattern (160 bp):
GGGTAAATATAAAAAATAGGAAAAGTGAATAATAAGGGTAAAATGATGCGTTGACTGTGTGCGGT
ATTACTGAAACGGTGCATATAGATCTAGTAAAACAGTGCATTTAGGGAGTAACGGCCACAGCTGT
AAGGGACTTAACAAACTCTTGTAAAGCCGC
Found at i:170504 original size:27 final size:28
Alignment explanation
Indices: 170474--170526 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
170464 CCAACATAAT
*
170474 TTCTAT-AAAATACTAAAAATTTAACCG
1 TTCTATAAAAATACTAAAAAATTAACCG
170501 TTCTATAAAAATACTAAAAAATTAAC
1 TTCTATAAAAATACTAAAAAATTAAC
170527 AAAAGAGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (28 bp):
TTCTATAAAAATACTAAAAAATTAACCG
Found at i:170569 original size:18 final size:19
Alignment explanation
Indices: 170546--170582 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
170536 GCTTAATAAT
170546 TCAATTTAA-TTATATTAA
1 TCAATTTAATTTATATTAA
170564 TCAATTTAATTTATATTAA
1 TCAATTTAATTTATATTAA
170583 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TCAATTTAATTTATATTAA
Found at i:171193 original size:94 final size:94
Alignment explanation
Indices: 171036--171284 Score: 335
Period size: 94 Copynumber: 2.7 Consensus size: 94
171026 TTGTAAATTA
* * *
171036 GTATAAATTTAAAATTTTATTTTGATTTAAATAAATAATTTTACTTATTTAATTATTTTTAAATT
1 GTATAAATTTAAAATTTCATTTTGATTTAAATACA-AATTTTATTTATTTAATTATTTTTAAATT
171101 ATAAAATTTTAACT-GGATAACAATGATAAT
65 ATAAAATTTTAA-TGGGATAACAATGATAAT
*
171131 GTATAGAATTT-AAATTTCATTTTGATTTAAATACAAATTTTATTTATTTAGTTATTTTTAAATT
1 GTATA-AATTTAAAATTTCATTTTGATTTAAATACAAATTTTATTTATTTAATTATTTTTAAATT
* * *
171195 GTAAAATTTTAATGGGGTAACCATGATAAT
65 ATAAAATTTTAATGGGATAACAATGATAAT
* ** * *
171225 ATATAAATTTCGAATTCCATTTTGACTTAAATACAAATTTT-TTT-TTTAATTATTTTTAAA
1 GTATAAATTTAAAATTTCATTTTGATTTAAATACAAATTTTATTTATTTAATTATTTTTAAA
171285 AATTTTAATG
Statistics
Matches: 139, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
92 15 0.11
93 9 0.06
94 83 0.60
95 27 0.19
96 5 0.04
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (94 bp):
GTATAAATTTAAAATTTCATTTTGATTTAAATACAAATTTTATTTATTTAATTATTTTTAAATTA
TAAAATTTTAATGGGATAACAATGATAAT
Found at i:177094 original size:90 final size:90
Alignment explanation
Indices: 177000--177238 Score: 263
Period size: 90 Copynumber: 2.6 Consensus size: 90
176990 ACACATATTG
* *
177000 ATAGTCCAAGTATCATATTGAACATTTT-AAGAGTATAAGTACCATATTGGACATTTTATAGAAA
1 ATAGTTCAAGTATCATATTGAACATTTTCAA-AGTATAAGTACCACATTGGACATTTTAT-GAAA
* *
177064 -CATAGATACTAAATAAT-ACATAAATA
64 GCACAAATACTAAATAATGACA-AAATA
* * * *
177090 ATAGTTCACGTATCATATTGAACATTTTCAAAATATATA-TACCACATTGCATATTTTATGAAAG
1 ATAGTTCAAGTATCATATTGAACATTTTCAAAGTATA-AGTACCACATTGGACATTTTATGAAAG
* *
177154 TACAAATACTAAATAATGGACAAATTA
65 CACAAATACTAAATAAT-GACAAAATA
* * * *
177181 ATAGTTTAAGTATCATATT-ATACATTTTCAAAGTACAAGTACCACAATAGACATTTTA
1 ATAGTTCAAGTATCATATTGA-ACATTTTCAAAGTATAAGTACCACATTGGACATTTTA
177239 AAAAAGTACA
Statistics
Matches: 124, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
89 4 0.03
90 64 0.52
91 53 0.43
92 3 0.02
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (90 bp):
ATAGTTCAAGTATCATATTGAACATTTTCAAAGTATAAGTACCACATTGGACATTTTATGAAAGC
ACAAATACTAAATAATGACAAAATA
Found at i:178392 original size:22 final size:19
Alignment explanation
Indices: 178343--178387 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
178333 GATGCTAGCT
178343 TTTAACAGTAGTACTACTC
1 TTTAACAGTAGTACTACTC
178362 TTTAACAGTAGTACTACTC
1 TTTAACAGTAGTACTACTC
178381 TTTAACA
1 TTTAACA
178388 ACAGTGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (19 bp):
TTTAACAGTAGTACTACTC
Found at i:180272 original size:55 final size:55
Alignment explanation
Indices: 180188--180297 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
180178 TGTATCTCAT
* * * *
180188 AGATATACAGATGTTGGTGTGAGTGTATGATTCTTCAAATATGTGGAGAAACTTG
1 AGATACACAGATGTTGGTATGACTGTATGATTCTTCAAATATGTGGAAAAACTTG
*
180243 AGATACACAGATGTTGGTATGACTGTATGATTCTTCAAATGTGTGGAAAAACTTG
1 AGATACACAGATGTTGGTATGACTGTATGATTCTTCAAATATGTGGAAAAACTTG
180298 GAAAAAGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (55 bp):
AGATACACAGATGTTGGTATGACTGTATGATTCTTCAAATATGTGGAAAAACTTG
Found at i:182178 original size:25 final size:25
Alignment explanation
Indices: 182150--182197 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
182140 AAAATAAATT
*
182150 AATCTCATTTTAT-TTTCTCGAAAAA
1 AATCTC-TTATATATTTCTCGAAAAA
182175 AATCTCTTATATATTTCTCGAAA
1 AATCTCTTATATATTTCTCGAAA
182198 TAATATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (25 bp):
AATCTCTTATATATTTCTCGAAAAA
Found at i:182210 original size:26 final size:26
Alignment explanation
Indices: 182163--182215 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
182153 CTCATTTTAT
**
182163 TTTCTCGAAAAAAATCTCTTAT-ATA
1 TTTCTCGAAAAAAATCAATTATGATA
*
182188 TTTCTCGAAATAATATCAATTATGATA
1 TTTCTCGAAA-AAAATCAATTATGATA
182215 T
1 T
182216 CAGAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.43
26 9 0.39
27 4 0.17
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.42
Consensus pattern (26 bp):
TTTCTCGAAAAAAATCAATTATGATA
Found at i:193544 original size:18 final size:18
Alignment explanation
Indices: 193504--193546 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
193494 TTTTTTCTAG
193504 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
193522 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
193540 TAATTAA
1 TAATTAA
193547 AAATCAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:195019 original size:58 final size:57
Alignment explanation
Indices: 194878--195025 Score: 163
Period size: 59 Copynumber: 2.5 Consensus size: 57
194868 AAGGGGTGTC
* * * * *
194878 CCAACACCCAAAAATTTGATTTTTTTTATCAGATAAATAGAGGTGTCGGTCATTGTATGG
1 CCAACACCC-AAAA-TT-ATTTTTTTTATCAGAAAAAAAGAGGTGTCGGCCATTGCATGA
** * *
194938 CCAACACAAAAAAATTATATTTTTTATCTGACAAAAAAGAGGTGTCGGCCATTGCATGA
1 CCAACAC-CCAAAATTATTTTTTTTATCAGA-AAAAAAGAGGTGTCGGCCATTGCATGA
194997 CCAACACCCAAAATTA-TTTTTTTATCAGA
1 CCAACACCCAAAATTATTTTTTTTATCAGA
195026 TTAATTTTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
57 11 0.15
58 20 0.27
59 31 0.42
60 11 0.15
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (57 bp):
CCAACACCCAAAATTATTTTTTTTATCAGAAAAAAAGAGGTGTCGGCCATTGCATGA
Found at i:205890 original size:21 final size:22
Alignment explanation
Indices: 205865--205910 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
205855 TAAAAAATAT
*
205865 AAACATAAACAATATAATT-AA
1 AAACATAAACAAAATAATTGAA
*
205886 AAACATAAATAAAATAATTGAA
1 AAACATAAACAAAATAATTGAA
205908 AAA
1 AAA
205911 AAATATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.22
Consensus pattern (22 bp):
AAACATAAACAAAATAATTGAA
Found at i:206780 original size:20 final size:19
Alignment explanation
Indices: 206751--206804 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
206741 AGCTGTAATA
* *
206751 TTTTTAAATTTTTTTATCT
1 TTTTTTAATTTTTTTATAT
*
206770 TTTTTGTAATTTTGTATATAT
1 TTTTT-TAATTTT-TTTATAT
206791 TTTTTTAATTTTTT
1 TTTTTTAATTTTTT
206805 ATCATTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.21
20 13 0.45
21 10 0.34
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTTTAATTTTTTTATAT
Found at i:206944 original size:17 final size:18
Alignment explanation
Indices: 206908--206947 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
206898 ATTTATAATA
**
206908 ATTTTAATAATTTTTTAT
1 ATTTTAATAATTTTCCAT
206926 ATTTTAA-AATTTTCCAT
1 ATTTTAATAATTTTCCAT
206943 ATTTT
1 ATTTT
206948 TTACAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTAATAATTTTCCAT
Found at i:207351 original size:17 final size:17
Alignment explanation
Indices: 207303--207356 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
207293 TCACATCACC
207303 AAATATTTTTTAAAAAAT
1 AAAT-TTTTTTAAAAAAT
** ** *
207321 AAAAATCATAAAAAAAT
1 AAATTTTTTTAAAAAAT
207338 AAATTTTTTTAAAAAAT
1 AAATTTTTTTAAAAAAT
207355 AA
1 AA
207357 TTATTTAAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 1
0.70 0.27 0.03
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTTTTTAAAAAAT
Found at i:207695 original size:11 final size:10
Alignment explanation
Indices: 207676--207769 Score: 54
Period size: 10 Copynumber: 9.5 Consensus size: 10
207666 CCAAGCATGG
207676 TTTTTAATAA
1 TTTTTAATAA
207686 TTTTTAA-ATA
1 TTTTTAATA-A
*
207696 TTATTT--TCA
1 TT-TTTAATAA
*
207705 TTTTAAAATAA
1 TTTT-TAATAA
*
207716 AT-TTAATAA
1 TTTTTAATAA
*
207725 TTTTTTATAA
1 TTTTTAATAA
207735 TTTCTT-ATAA
1 TTT-TTAATAA
*
207745 TTATTAATAA
1 TTTTTAATAA
* *
207755 TTTTAAATAG
1 TTTTTAATAA
207765 TTTTT
1 TTTTT
207770 TTATCAATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
8 2 0.03
9 12 0.19
10 41 0.65
11 8 0.13
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:219145 original size:18 final size:19
Alignment explanation
Indices: 219117--219152 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
219107 TTTTGTTGTT
219117 ATTATAATTAAAAAAAATC
1 ATTATAATTAAAAAAAATC
*
219136 ATTA-AATTAAAATAAAT
1 ATTATAATTAAAAAAAAT
219153 AATCTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTATAATTAAAAAAAATC
Found at i:219408 original size:17 final size:17
Alignment explanation
Indices: 219370--219413 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
219360 AAAACCATTT
219370 TATTTTAAAAAATTAAA
1 TATTTTAAAAAATTAAA
*
219387 -ATTTTAAAAAATCTCAA
1 TATTTTAAAAAAT-TAAA
*
219404 TTTTTTAAAA
1 TATTTTAAAA
219414 TGAAATGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 12 0.52
17 3 0.13
18 8 0.35
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TATTTTAAAAAATTAAA
Found at i:219906 original size:2 final size:2
Alignment explanation
Indices: 219876--219957 Score: 128
Period size: 2 Copynumber: 41.0 Consensus size: 2
219866 ATTTTTACTA
* * * *
219876 AT AT CT AT AT CT AT AT CT AT AT TT 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 AT AT AT AT
219918 AT AT AT 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 AT AT AT
219958 CATTATTAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:220844 original size:21 final size:21
Alignment explanation
Indices: 220819--220861 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
220809 AGTGAAGGAA
220819 AAAAGAGTACATAATCCTTTG
1 AAAAGAGTACATAATCCTTTG
220840 AAAAGAGTACATAATCCTTTG
1 AAAAGAGTACATAATCCTTTG
220861 A
1 A
220862 TACATAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
AAAAGAGTACATAATCCTTTG
Found at i:230389 original size:30 final size:30
Alignment explanation
Indices: 230331--230389 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
230321 CAAATTTTTG
* **
230331 TTGTTCATGTTCGTTTGTTTATTTTTAAGC
1 TTGTTCATGTTCGTTTGTGTATCGTTAAGC
230361 TTGTTCATGTTCAGTTTGTGT-TCGTTAAG
1 TTGTTCATGTTC-GTTTGTGTATCGTTAAG
230390 AATTTCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.14, C:0.10, G:0.20, T:0.56
Consensus pattern (30 bp):
TTGTTCATGTTCGTTTGTGTATCGTTAAGC
Found at i:230486 original size:23 final size:24
Alignment explanation
Indices: 230459--230518 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 24
230449 TTTAATGTCC
**
230459 ACGAACATGTTCATTTAAC-TTAA
1 ACGAACATGTTCATCGAACATTAA
* * *
230482 TCGAATATATTCA-CGAACATTAA
1 ACGAACATGTTCATCGAACATTAA
230505 ACGAACATGTTCAT
1 ACGAACATGTTCAT
230519 AAATATATAA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (24 bp):
ACGAACATGTTCATCGAACATTAA
Found at i:230653 original size:12 final size:12
Alignment explanation
Indices: 230636--230670 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
230626 ATCATTAATA
*
230636 AATAAACGAGTC
1 AATAAACGAGCC
230648 AATAAACGAGCC
1 AATAAACGAGCC
230660 AATAAACGAGC
1 AATAAACGAGC
230671 TTGTTCGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.51, C:0.20, G:0.17, T:0.11
Consensus pattern (12 bp):
AATAAACGAGCC
Found at i:230837 original size:48 final size:48
Alignment explanation
Indices: 230783--230878 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
230773 AACGAACATA
230783 AACGAACGTTATACAAACGATTCACAAATAGTTCATCGAACGTTCTGT
1 AACGAACGTTATACAAACGATTCACAAATAGTTCATCGAACGTTCTGT
*
230831 AACGAACGTTATACAAACGATTCACGAATAGTTCATCGAACGTTCTGT
1 AACGAACGTTATACAAACGATTCACAAATAGTTCATCGAACGTTCTGT
230879 TTATTTACAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (48 bp):
AACGAACGTTATACAAACGATTCACAAATAGTTCATCGAACGTTCTGT
Found at i:245767 original size:15 final size:15
Alignment explanation
Indices: 245747--245778 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
245737 TAAGTGGCAC
245747 ATCAGAATTTTGACA
1 ATCAGAATTTTGACA
245762 ATCAGAATTTTGACA
1 ATCAGAATTTTGACA
245777 AT
1 AT
245779 TGAAAGCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (15 bp):
ATCAGAATTTTGACA
Found at i:249913 original size:183 final size:183
Alignment explanation
Indices: 249605--249977 Score: 647
Period size: 183 Copynumber: 2.0 Consensus size: 183
249595 ATAAGCTTTG
* * * * *
249605 TATCAAGATTTTGCTTTCAATGTTGTTAGGAAACATGTTGATGCGAGTATGAGGGCTCAATTTTG
1 TATCAAGATTTTGCTTTCAATGTTGTTAAGAAACATGTTGATGCAAGTATAAGGGCCCAATTTTC
* *
249670 AGCCCAAGAACATGTTGGGCTTATCCTTTTACAAAGCCTACTTGACAAGCTCAAAAGATCACAAA
66 AGCCCAAGAACATGTTGGGCTTAACCTTCTACAAAGCCTACTTGACAAGCTCAAAAGATCACAAA
* *
249735 ACTCAAGGACCAACTTTGGATGGGATTCGAGCATCCTTGGCGTTGAGCAAGAT
131 AATCAAGGACCAACTTTGGATGGGATTCGAGCATCCTTGGAGTTGAGCAAGAT
249788 TATCAAGATTTTGCTTTCAATGTTGTTAAGAAACATGTTGATGCAAGTATAAGGGCCCAATTTTC
1 TATCAAGATTTTGCTTTCAATGTTGTTAAGAAACATGTTGATGCAAGTATAAGGGCCCAATTTTC
249853 AGCCCAAGAACATGTTGGGCTTAACCTTCTACAAAGCCTACTTGACAAGCTCAAAAGATCACAAA
66 AGCCCAAGAACATGTTGGGCTTAACCTTCTACAAAGCCTACTTGACAAGCTCAAAAGATCACAAA
**
249918 AATTGAGGACCAACTTTGGATGGGATTCGAGCATCCTTGGAGTTGAGCAAGAT
131 AATCAAGGACCAACTTTGGATGGGATTCGAGCATCCTTGGAGTTGAGCAAGAT
249971 TATCAAG
1 TATCAAG
249978 GCTTTGAATC
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
183 179 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (183 bp):
TATCAAGATTTTGCTTTCAATGTTGTTAAGAAACATGTTGATGCAAGTATAAGGGCCCAATTTTC
AGCCCAAGAACATGTTGGGCTTAACCTTCTACAAAGCCTACTTGACAAGCTCAAAAGATCACAAA
AATCAAGGACCAACTTTGGATGGGATTCGAGCATCCTTGGAGTTGAGCAAGAT
Found at i:251501 original size:20 final size:19
Alignment explanation
Indices: 251459--251501 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
251449 GTTACTATTT
*
251459 TTTTACTGTTTTGGTGTTT
1 TTTTACTGTTTTGGTGTTG
*
251478 TTTTACTGTTTTGATTGTTG
1 TTTTACTGTTTTG-GTGTTG
251498 TTTT
1 TTTT
251502 GGTGCTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.70
Consensus pattern (19 bp):
TTTTACTGTTTTGGTGTTG
Found at i:251541 original size:12 final size:12
Alignment explanation
Indices: 251520--251600 Score: 83
Period size: 12 Copynumber: 6.8 Consensus size: 12
251510 TTTTCTATTG
* *
251520 TTTTGGTGTTGT
1 TTTTGTTGTTAT
*
251532 TTTTGCTGTTAT
1 TTTTGTTGTTAT
*
251544 TTTTGTTGCTAT
1 TTTTGTTGTTAT
*
251556 TTTTGTTATTAT
1 TTTTGTTGTTAT
* *
251568 TTTTGTTGCTGT
1 TTTTGTTGTTAT
*
251580 TTTTGTTGTT-G
1 TTTTGTTGTTAT
251591 TTTTGTTGTT
1 TTTTGTTGTT
251601 TTGATTGTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
11 10 0.17
12 48 0.83
ACGTcount: A:0.05, C:0.04, G:0.21, T:0.70
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:251558 original size:24 final size:24
Alignment explanation
Indices: 251531--251598 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
251521 TTTGGTGTTG
*
251531 TTTTTGCTGTTATTTTTGTTGCTA
1 TTTTTGTTGTTATTTTTGTTGCTA
* *
251555 TTTTTGTTATTATTTTTGTTGCTG
1 TTTTTGTTGTTATTTTTGTTGCTA
*
251579 TTTTTGTTGTT-GTTTTGTTG
1 TTTTTGTTGTTATTTTTGTTG
251599 TTTTGATTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 8 0.21
24 31 0.79
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.71
Consensus pattern (24 bp):
TTTTTGTTGTTATTTTTGTTGCTA
Found at i:251602 original size:20 final size:22
Alignment explanation
Indices: 251577--251622 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
251567 TTTTTGTTGC
*
251577 TGTTTTTG-TTGTTGTTTT-GT
1 TGTTTTTGATTGTTATTTTGGT
251597 TG-TTTTGATTGTTATTTTGGT
1 TGTTTTTGATTGTTATTTTGGT
251618 TGTTT
1 TGTTT
251623 AGATGTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 5 0.23
20 11 0.50
21 4 0.18
22 2 0.09
ACGTcount: A:0.04, C:0.00, G:0.24, T:0.72
Consensus pattern (22 bp):
TGTTTTTGATTGTTATTTTGGT
Found at i:251634 original size:21 final size:20
Alignment explanation
Indices: 251585--251635 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
251575 GCTGTTTTTG
* *
251585 TTGTTGTTTTGTTGTTTTGA
1 TTGTTATTTTGTTGTTTAGA
251605 TTGTTATTTTGGTTGTTTAGA
1 TTGTTATTTT-GTTGTTTAGA
251626 -TGTTAATTTT
1 TTGTT-ATTTT
251636 ATACATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.12, C:0.00, G:0.22, T:0.67
Consensus pattern (20 bp):
TTGTTATTTTGTTGTTTAGA
Found at i:254964 original size:253 final size:253
Alignment explanation
Indices: 254634--255146 Score: 771
Period size: 253 Copynumber: 2.0 Consensus size: 253
254624 TTTGGATAGT
*
254634 TTTATGCATATATGTAATATAACAAGTAGTAATGCTATGTTTATTTACTTTGTTTTATGAAGGTA
1 TTTATGCA-ATATGTAATATAACAAGTAGTAATGCTATGTTTATTTACTATGTTTTATGAAGGTA
* **
254699 CCATTAAGCTTTATTACTCAACATATGGTTTGTTTTCTCCATGTGCA-A-GTAGAATAGATTACC
65 CCACTAAGCTTTATTACTCAACATACAGTTTGTTTTCTCC--GTGCACATGTAGAATAGATTACC
* * *
254762 GAGAATTTGAGCAGTAGATCCAACATCCAAGAAGTGATCCCTCGACTCAACAATATTTGTATAAA
128 AAGAATTCGAGCAATAGATCCAACATCCAAGAAGTGATCCCTCGACTCAACAATATTTGTATAAA
254827 TCTCGTTTTATTTAAGTATGGCATGTACCTAGATTGAGTTGGTTTTTGGGCTTAATATGTG
193 TCTCGTTTTATTTAAGTATGGCATGTACCTAGATTGAGTTGGTTTTTGGGCTTAATATGTG
* *
254888 TTTATGC-ATATGTAATATAACAAATTAGTAATGTTATGTTTATTTACTATGTTTTATGAAGGTA
1 TTTATGCAATATGTAATATAAC-AAGTAGTAATGCTATGTTTATTTACTATGTTTTATGAAGGTA
* * *** * *
254952 CCACTGAGCTTTATTGCTCAGTGTACAGTTTGTTTTCTCCGTGCACATGTATAATAGATTCCCAA
65 CCACTAAGCTTTATTACTCAACATACAGTTTGTTTTCTCCGTGCACATGTAGAATAGATTACCAA
* *
255017 GAGTTCGAGCAATAGATCCAACATCCAAGAAGTGATCCCTCGACTCAACAATGTTTGTATAAATC
130 GAATTCGAGCAATAGATCCAACATCCAAGAAGTGATCCCTCGACTCAACAATATTTGTATAAATC
* * *
255082 TTGTTTTGTTTAAGTATGGCATGTACCTAGGTTGAGTTGGTTTTTGGGCTTAATATGTG
195 TCGTTTTATTTAAGTATGGCATGTACCTAGATTGAGTTGGTTTTTGGGCTTAATATGTG
*
255141 CTTATG
1 TTTATG
255147 TAAATGATTG
Statistics
Matches: 234, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
251 5 0.02
252 15 0.06
253 207 0.88
254 7 0.03
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (253 bp):
TTTATGCAATATGTAATATAACAAGTAGTAATGCTATGTTTATTTACTATGTTTTATGAAGGTAC
CACTAAGCTTTATTACTCAACATACAGTTTGTTTTCTCCGTGCACATGTAGAATAGATTACCAAG
AATTCGAGCAATAGATCCAACATCCAAGAAGTGATCCCTCGACTCAACAATATTTGTATAAATCT
CGTTTTATTTAAGTATGGCATGTACCTAGATTGAGTTGGTTTTTGGGCTTAATATGTG
Found at i:255885 original size:20 final size:20
Alignment explanation
Indices: 255847--255887 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
255837 TCTTTATATA
* * *
255847 TTTTTTTAATTTTTTAATTT
1 TTTTTTTAAATTATAAATTT
255867 TTTTTTTAAATTATAAATTT
1 TTTTTTTAAATTATAAATTT
255887 T
1 T
255888 GGAATTTATA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTTAAATTATAAATTT
Found at i:255911 original size:17 final size:16
Alignment explanation
Indices: 255877--255915 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
255867 TTTTTTTAAA
255877 TTATAAATTTTGGAAT
1 TTATAAATTTTGGAAT
*
255893 TTATAAATATTTTGAAT
1 TTATAAAT-TTTGGAAT
255910 TT-TAAA
1 TTATAAA
255916 AATTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
TTATAAATTTTGGAAT
Found at i:255925 original size:12 final size:11
Alignment explanation
Indices: 255908--255944 Score: 51
Period size: 9 Copynumber: 3.5 Consensus size: 11
255898 AATATTTTGA
255908 ATTTTAAAAATT
1 ATTTT-AAAATT
255920 ATTTTAAAA-T
1 ATTTTAAAATT
255930 -TTTTAAAATT
1 ATTTTAAAATT
255940 ATTTT
1 ATTTT
255945 GTAATTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.35
10 2 0.09
11 8 0.35
12 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTAAAATT
Found at i:255950 original size:20 final size:19
Alignment explanation
Indices: 255883--255953 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
255873 TAAATTATAA
*
255883 ATTTTGGAATTTAT-AAA-T
1 ATTTT-GAATTTTTAAAATT
*
255901 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
*
255920 ATTTTAAAATTTTTAAAATT
1 ATTTT-GAATTTTTAAAATT
255940 ATTTTGTAATTTTT
1 ATTTTG-AATTTTT
255954 GTTGTGAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.14
18 8 0.18
19 6 0.14
20 24 0.55
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:258312 original size:19 final size:20
Alignment explanation
Indices: 258288--258345 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 20
258278 AAACAAACTT
258288 AAAATAATTTTTAAAATT-C
1 AAAATAATTTTTAAAATTCC
*
258307 AAAAT-ATTTATAAAAATTCC
1 AAAATAATTT-TTAAAATTCC
258327 AAAATTTACATTTTTAAAA
1 AAAA--TA-ATTTTTAAAA
258346 ATTACAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 4 0.13
19 12 0.39
20 5 0.16
22 1 0.03
23 5 0.16
24 4 0.13
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATAATTTTTAAAATTCC
Found at i:258320 original size:18 final size:21
Alignment explanation
Indices: 258288--258354 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 21
258278 AAACAAACTT
*
258288 AAAATAATTT-TTAAAATT-C
1 AAAATAATTTATAAAAATTCC
258307 AAAAT-ATTTATAAAAATTCC
1 AAAATAATTTATAAAAATTCC
* *
258327 AAAATTTACATTTTTAAAAATTAC
1 AAAA--TA-ATTTATAAAAATTCC
258351 AAAA
1 AAAA
258355 ATTTCAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
20 5 0.13
22 1 0.03
24 17 0.44
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATAATTTATAAAAATTCC
Found at i:261110 original size:13 final size:13
Alignment explanation
Indices: 261092--261123 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
261082 AATTTGAAAA
261092 AGTATAAGAACTT
1 AGTATAAGAACTT
261105 AGTATAAGAACTT
1 AGTATAAGAACTT
261118 AG-ATAA
1 AGTATAA
261124 TATAGACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (13 bp):
AGTATAAGAACTT
Found at i:262023 original size:31 final size:33
Alignment explanation
Indices: 261953--262029 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 33
261943 CTCAGGTTAT
* *
261953 ATTTTAGTCATTTATGTTTGAAATGTTATGTTAC
1 ATTTTAGTCACTTATGTTT-AAATGTTATGTAAC
* *
261987 ATTTTAGTCACTTATG-TT-ATTGTTTTGTAAC
1 ATTTTAGTCACTTATGTTTAAATGTTATGTAAC
262018 ATTTTAGTCACT
1 ATTTTAGTCACT
262030 GTGCCGTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 22 0.56
33 2 0.05
34 15 0.38
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.53
Consensus pattern (33 bp):
ATTTTAGTCACTTATGTTTAAATGTTATGTAAC
Found at i:263802 original size:2 final size:2
Alignment explanation
Indices: 263795--263819 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
263785 ATAACCAGTT
263795 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
263820 ATATATAGAG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:281035 original size:24 final size:26
Alignment explanation
Indices: 280989--281042 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
280979 AAATATTCCT
* **
280989 AAAATAATTAAATTTTATTTGAGA-A
1 AAAATAATTAAATTTAAACTGAGAGA
281014 AAAATAATTAAA-TTAAACTGAGAGA
1 AAAATAATTAAATTTAAACTGAGAGA
281039 AAAA
1 AAAA
281043 CTGGAGACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (26 bp):
AAAATAATTAAATTTAAACTGAGAGA
Found at i:289745 original size:44 final size:45
Alignment explanation
Indices: 289694--289785 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 45
289684 ATTGAAATAA
* *
289694 AATAGAAGTTGTGATAATTATATATTTAAAAATACTTATAATT-T
1 AATAGAAGTTGTGATAATTACATATTTAAAAATAATTATAATTGT
*
289738 AATAGAAGTTGTGATAATTACATGTTTAAAAATAATTATAATTGT
1 AATAGAAGTTGTGATAATTACATATTTAAAAATAATTATAATTGT
289783 AAT
1 AAT
289786 TTATAATTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 40 0.91
45 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (45 bp):
AATAGAAGTTGTGATAATTACATATTTAAAAATAATTATAATTGT
Found at i:290869 original size:22 final size:22
Alignment explanation
Indices: 290833--290878 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
290823 GCGAAATGAT
*
290833 AGTAAAACAACAACATAACAAC
1 AGTAAAACAACAACAAAACAAC
* * *
290855 AGTAAAATAATAACAAAATAAC
1 AGTAAAACAACAACAAAACAAC
290877 AG
1 AG
290879 GGAAAAATTA
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:0.65, C:0.15, G:0.07, T:0.13
Consensus pattern (22 bp):
AGTAAAACAACAACAAAACAAC
Found at i:291245 original size:21 final size:19
Alignment explanation
Indices: 291221--291260 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 19
291211 ATTTATTCTT
291221 AATATATATGTCAAAATTAAA
1 AATATATAT-T-AAAATTAAA
291242 AATATATATTAAAATTAAA
1 AATATATATTAAAATTAAA
291261 TAAAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 1 0.05
21 9 0.47
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
AATATATATTAAAATTAAA
Found at i:291817 original size:26 final size:26
Alignment explanation
Indices: 291783--291841 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 26
291773 TCTCATTTAA
* *
291783 ATAACAAATGTATATTTTTTAA-ATATT
1 ATAA-AAAT-TATATTATTTAATAAATT
291810 ATAAAAA-TATATTATTTAATAAATT
1 ATAAAAATTATATTATTTAATAAATT
291835 -TAAAAAT
1 ATAAAAAT
291842 AAATATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
24 17 0.61
25 4 0.14
26 3 0.11
27 4 0.14
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
ATAAAAATTATATTATTTAATAAATT
Found at i:291827 original size:24 final size:24
Alignment explanation
Indices: 291793--291842 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
291783 ATAACAAATG
* *
291793 TATATTTTTTAA-ATATTATAAAAA
1 TATATTATTTAATAAATT-TAAAAA
291817 TATATTATTTAATAAATTTAAAAA
1 TATATTATTTAATAAATTTAAAAA
291841 TA
1 TA
291843 AATATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATTATTTAATAAATTTAAAAA
Found at i:292688 original size:2 final size:2
Alignment explanation
Indices: 292681--292712 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
292671 TAAGAAATGG
292681 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
292713 TTTTTTTTTA
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):
AT
Found at i:293174 original size:21 final size:22
Alignment explanation
Indices: 293130--293176 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
293120 TTTTTTGAAC
* *
293130 TTTATGAATTTTATTTAATATT
1 TTTATGAATTCTATATAATATT
*
293152 TTTATGAATTCTA-ATAATGTT
1 TTTATGAATTCTATATAATATT
293173 TTTA
1 TTTA
293177 CAAATTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (22 bp):
TTTATGAATTCTATATAATATT
Found at i:322732 original size:6 final size:6
Alignment explanation
Indices: 322723--322765 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
322713 TTTTGGTTTA
*
322723 GCGGTA GCGGTT GCGGTT GCGGTT GCGGTT GCGGTT GCGGTT G
1 GCGGTT GCGGTT GCGGTT GCGGTT GCGGTT GCGGTT GCGGTT G
322766 GGGCATTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.02, C:0.16, G:0.51, T:0.30
Consensus pattern (6 bp):
GCGGTT
Found at i:324578 original size:20 final size:21
Alignment explanation
Indices: 324542--324581 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
324532 TAAAAATCTA
324542 AATTAATAAAAAGTAAGATAT
1 AATTAATAAAAAGTAAGATAT
*
324563 AATTAA-AAAAATTAAGATA
1 AATTAATAAAAAGTAAGATA
324582 ATTGCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (21 bp):
AATTAATAAAAAGTAAGATAT
Found at i:334767 original size:99 final size:99
Alignment explanation
Indices: 334596--334793 Score: 387
Period size: 99 Copynumber: 2.0 Consensus size: 99
334586 TGATATGAAT
334596 ATTGTTGCCCATACAGGAGGATATGGATTCGAATGCTTTAAAACTCATAATAAGATTATTCAAAA
1 ATTGTTGCCCATACAGGAGGATATGGATTCGAATGCTTTAAAACTCATAATAAGATTATTCAAAA
334661 AAAATAGTACAAATAACCGATGTCGAAACCACCC
66 AAAATAGTACAAATAACCGATGTCGAAACCACCC
334695 ATTGTTGCCCATACAGGAGGATATGGATTCGAATGCTTTAAAACTCATAATAAGATTATTCAAAA
1 ATTGTTGCCCATACAGGAGGATATGGATTCGAATGCTTTAAAACTCATAATAAGATTATTCAAAA
*
334760 AAAATAGTACAAATAACTGATGTCGAAACCACCC
66 AAAATAGTACAAATAACCGATGTCGAAACCACCC
334794 CTTTTTGCAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (99 bp):
ATTGTTGCCCATACAGGAGGATATGGATTCGAATGCTTTAAAACTCATAATAAGATTATTCAAAA
AAAATAGTACAAATAACCGATGTCGAAACCACCC
Found at i:335746 original size:59 final size:58
Alignment explanation
Indices: 335683--336023 Score: 174
Period size: 59 Copynumber: 5.8 Consensus size: 58
335673 AGGATTCTCA
*
335683 AGGGTAAAATGGTATTTTTGGGAAAG-TTCGAGGGTTAAAATGGAATTTTTAGATATTCG
1 AGGGTAAAATGGTATTTTT--GAAAGTTTCGAGGGTTAAAATGGAATTTTTAGACATTCG
* * * * * * * * *
335742 AGGGTAAAAGGGTAATTTTGAGAGTTTTGA-CGTCGAAAATGGAGTTTTTAGACATCCA
1 AGGGTAAAATGGTATTTTTGAAAGTTTCGAGGGT-TAAAATGGAATTTTTAGACATTCG
* * **
335800 AGGGCAAAATGGTAATTTTTGAAAGTTTC--GGGTTCAAAAATGGAAAATTTT-GAGGTTCG
1 AGGGTAAAATGGT-ATTTTTGAAAGTTTCGAGGGTT--AAAATGG-AATTTTTAGACATTCG
* * * * * * *
335859 AGGGTAAAATGGAATTTTTGGAAGCTTT--AGGATCAAAAATAGAATTTTTGGA-AGTTTTG
1 AGGGTAAAATGGTATTTTTGAAAG-TTTCGAGGGT-TAAAATGGAATTTTTAGACA--TTCG
* * *
335918 -GGGTTAAAATGGAATTTTTCG-AAG-TTCGAGGGTAAAAATGGAATTTTTGGA-AGTTTCG
1 AGGG-TAAAATGGTATTTTT-GAAAGTTTCGAGGGTTAAAATGGAATTTTTAGACA--TTCG
* *
335976 -GGGTCAAAAATGGAATTTTTGGAAGTTT--AGTGG-TAAAATGGAATTTTT
1 AGGGT--AAAATGGTATTTTTGAAAGTTTCGAG-GGTTAAAATGGAATTTTT
336024 GGGGTCAAAA
Statistics
Matches: 224, Mismatches: 36, Indels: 45
0.73 0.12 0.15
Matches are distributed among these distances:
57 15 0.07
58 100 0.45
59 101 0.45
60 8 0.04
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (58 bp):
AGGGTAAAATGGTATTTTTGAAAGTTTCGAGGGTTAAAATGGAATTTTTAGACATTCG
Found at i:335758 original size:29 final size:31
Alignment explanation
Indices: 335683--336024 Score: 101
Period size: 29 Copynumber: 11.7 Consensus size: 31
335673 AGGATTCTCA
*
335683 AGGGTAAAATGGT-ATTTTTGGGAAAGTTCG
1 AGGGTAAAATGGTAATTTTTGAGAAAGTTCG
*
335713 AGGGTTAAAATGG-AATTTTT-AGATA-TTCG
1 AGGG-TAAAATGGTAATTTTTGAGAAAGTTCG
* *
335742 AGGGTAAAAGGGTAA-TTTTGAG--AGTTTTG
1 AGGGTAAAATGGTAATTTTTGAGAAAG-TTCG
* * * * *
335771 A-CGTCGAAAATGG-AGTTTTT-AGACA-TCCA
1 AGGGT--AAAATGGTAATTTTTGAGAAAGTTCG
*
335800 AGGGCAAAATGGTAATTTTT--GAAAGTTTCG
1 AGGGTAAAATGGTAATTTTTGAGAAAG-TTCG
* * *
335830 -GGTTCAAAAATGGAAAATTTTGAG---GTTCG
1 AGGGT--AAAATGGTAATTTTTGAGAAAGTTCG
*
335859 AGGGTAAAATGG-AATTTTTG-G-AAGCTT-T
1 AGGGTAAAATGGTAATTTTTGAGAAAG-TTCG
* * *
335887 AGGATCAAAAATAG-AATTTTTG-G-AAGTTTTG
1 AGGGT--AAAATGGTAATTTTTGAGAAAG-TTCG
*
335918 -GGGTTAAAATGG-AATTTTT-CG-AAGTTCG
1 AGGG-TAAAATGGTAATTTTTGAGAAAGTTCG
335946 AGGGTAAAAATGG-AATTTTTG-G-AAGTTTCG
1 AGGGT-AAAATGGTAATTTTTGAGAAAG-TTCG
*
335976 -GGGTCAAAAATGG-AATTTTTG-G-AAGTT-T
1 AGGGT--AAAATGGTAATTTTTGAGAAAGTTCG
336004 AGTGGTAAAATGG-AATTTTTG
1 AG-GGTAAAATGGTAATTTTTG
336025 GGGTCAAAAA
Statistics
Matches: 246, Mismatches: 31, Indels: 72
0.70 0.09 0.21
Matches are distributed among these distances:
26 1 0.00
27 8 0.03
28 54 0.22
29 80 0.33
30 73 0.30
31 29 0.12
33 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (31 bp):
AGGGTAAAATGGTAATTTTTGAGAAAGTTCG
Found at i:335897 original size:58 final size:57
Alignment explanation
Indices: 335805--336025 Score: 218
Period size: 58 Copynumber: 3.8 Consensus size: 57
335795 ATCCAAGGGC
* * * * *
335805 AAAATGGTAATTTTTGAAAGTTTCGGGTTCAAAAATGGAAAATTTT-G-AGGTTCGAGGGT
1 AAAATGG-AATTTTTGGAAGTTT-AGGATCAAAAATGG-AATTTTTGGAAGTTTCG-GGGT
* *
335864 AAAATGGAATTTTTGGAAGCTTTAGGATCAAAAATAGAATTTTTGGAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAG-TTTAGGATCAAAAATGGAATTTTTGGAAGTTTCGGGG-T
* * *
335923 AAAATGGAATTTTTCGAAGTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTCGGGGT
1 AAAATGGAATTTTTGGAAGTT-TAGGATCAAAAATGGAATTTTTGGAAGTTTCGGGGT
*
335980 CAAAAATGGAATTTTTGGAAGTTTAGTGGT--AAAATGGAATTTTTGG
1 --AAAATGGAATTTTTGGAAGTTTAG-GATCAAAAATGGAATTTTTGG
336026 GGTCAAAAAT
Statistics
Matches: 140, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
57 7 0.05
58 72 0.51
59 61 0.44
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (57 bp):
AAAATGGAATTTTTGGAAGTTTAGGATCAAAAATGGAATTTTTGGAAGTTTCGGGGT
Found at i:335904 original size:30 final size:28
Alignment explanation
Indices: 335805--336144 Score: 263
Period size: 30 Copynumber: 11.9 Consensus size: 28
335795 ATCCAAGGGC
* *
335805 AAAATGGTAATTTTTGAAAGTTTCGGGTTCA
1 AAAATGG-AATTTTTGGAAGTTTAGGG-T-A
* * *
335836 AAAATGGAAAATTTT-GAGGTTCGAGGGT-
1 AAAATGG-AATTTTTGGAAGTT-TAGGGTA
*
335864 AAAATGGAATTTTTGGAAGCTTTAGGATCA
1 AAAATGGAATTTTTGGAAG-TTTAGGGT-A
* * *
335894 AAAATAGAATTTTTGGAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAG-TTTAGGGTA
* *
335923 AAAATGGAATTTTTCGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTT-TAGGGTA
*
335952 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTT-AGGGT-A
335982 AAAATGGAATTTTTGGAAGTTTAGTGGT-
1 AAAATGGAATTTTTGGAAGTTTAG-GGTA
336010 AAAATGGAATTTTT----G----GGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGT-A
*
336031 AAAATGGAATTTTTGGAAGTTTTGGGGT-
1 AAAATGGAATTTTTGGAAG-TTTAGGGTA
* *
336059 AAAATAGAATTTTTAGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTAGGGT-A
* * **
336089 AAAATGTAATTTTTGTAAGTTCGGTGGTA
1 AAAATGGAATTTTTGGAAGTTTAG-GGTA
336118 AAAATGGAATTTTTGGACAGTTTAGGG
1 AAAATGGAATTTTTGGA-AGTTTAGGG
336145 ACCTTTAAGG
Statistics
Matches: 248, Mismatches: 37, Indels: 50
0.74 0.11 0.15
Matches are distributed among these distances:
19 3 0.01
20 1 0.00
21 14 0.06
24 1 0.00
25 1 0.00
27 6 0.02
28 55 0.22
29 69 0.28
30 82 0.33
31 16 0.06
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTAGGGTA
Found at i:335966 original size:49 final size:48
Alignment explanation
Indices: 335907--336072 Score: 147
Period size: 49 Copynumber: 3.2 Consensus size: 48
335897 ATAGAATTTT
* * *
335907 TGGAAGTTTTGGGGT-TAAAATGGAATTTTTCGAAGTTCGAGGGTAAAAA
1 TGGAATTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT-GAGGGT-AAAA
*
335956 TGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTAGTGGTAAAA
1 TGGAA---TT-----TTT-GGGGTCAAAAATGGAATTTTTGGAAGTTGAG-GGTAAAA
336014 TGGAATTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTG-GGGTAAAA
1 TGGAATTTTTGGGGTCAAAAATGGAATTTTTGGAAG--TTGAGGGTAAAA
*
336063 TAGAATTTTT
1 TGGAATTTTT
336073 AGAAGTTTTA
Statistics
Matches: 98, Mismatches: 6, Indels: 26
0.75 0.05 0.20
Matches are distributed among these distances:
49 47 0.48
50 4 0.04
51 2 0.02
52 1 0.01
55 2 0.02
57 3 0.03
58 16 0.16
59 23 0.23
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (48 bp):
TGGAATTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTGAGGGTAAAA
Found at i:336089 original size:58 final size:60
Alignment explanation
Indices: 336020--336144 Score: 159
Period size: 58 Copynumber: 2.1 Consensus size: 60
336010 AAAATGGAAT
* *
336020 TTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTGG-GGT-AAAATAGAATTTTTAGA-AG
1 TTTTAGGGTCAAAAATGGAATTTTTGGAAG-TTCGGTGGTAAAAATAGAATTTTTAGACAG
* * * *
336078 TTTTAGGGTCAAAAATGTAATTTTTGTAAGTTCGGTGGTAAAAATGGAATTTTTGGACAG
1 TTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGGTGGTAAAAATAGAATTTTTAGACAG
336138 -TTTAGGG
1 TTTTAGGG
336145 ACCTTTAAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
57 4 0.07
58 30 0.52
59 22 0.38
60 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.38
Consensus pattern (60 bp):
TTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGGTGGTAAAAATAGAATTTTTAGACAG
Found at i:336093 original size:107 final size:108
Alignment explanation
Indices: 335907--336133 Score: 307
Period size: 107 Copynumber: 2.1 Consensus size: 108
335897 ATAGAATTTT
* * * *
335907 TGGAAGTTTTGGGGTTAAAATGGAATTTTTCGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGT
1 TGGAATTTTTGGGGTAAAAATGGAATTTTTCGAAGTTCGAGGGTAAAAATAGAATTTTTAGAAGT
* *
335972 TTCGGGGTCAAAAATGGAATTTTTGGAAGTTTAGTGGT-AAAA
66 TTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAGTGGTAAAAA
* *
336014 TGGAATTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTG-GGGT-AAAATAGAATTTTTAGAA
1 TGGAATTTTTGGGGT-AAAAATGGAATTTTTCGAAG-TTCGAGGGTAAAAATAGAATTTTTAGAA
* * * *
336077 GTTTTAGGGTCAAAAATGTAATTTTTGTAAGTTCGGTGGTAAAAA
64 GTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAGTGGTAAAAA
336122 TGGAATTTTTGG
1 TGGAATTTTTGG
336134 ACAGTTTAGG
Statistics
Matches: 105, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
107 64 0.61
108 38 0.36
109 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (108 bp):
TGGAATTTTTGGGGTAAAAATGGAATTTTTCGAAGTTCGAGGGTAAAAATAGAATTTTTAGAAGT
TTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAGTGGTAAAAA
Found at i:337230 original size:15 final size:15
Alignment explanation
Indices: 337198--337231 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
337188 ATTAGTATTA
*
337198 ATTATTATTAATATT
1 ATTATTATTAATACT
*
337213 ATTATTATTAATGCT
1 ATTATTATTAATACT
337228 ATTA
1 ATTA
337232 AAACATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (15 bp):
ATTATTATTAATACT
Found at i:337248 original size:2 final size:2
Alignment explanation
Indices: 337241--337274 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
337231 AAAACATTTA
337241 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
337275 TTATTACACT
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:338054 original size:23 final size:24
Alignment explanation
Indices: 338027--338075 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
338017 TATAATAAGT
*
338027 TTTAAA-TTTAAATATAAA-TTAAA
1 TTTAAATTTTAAA-ACAAATTTAAA
338050 TTTAAATTTTAAAACAAATTTAAA
1 TTTAAATTTTAAAACAAATTTAAA
338074 TT
1 TT
338076 CAAAATCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAATTTTAAAACAAATTTAAA
Found at i:338088 original size:17 final size:18
Alignment explanation
Indices: 338047--338080 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
338037 AATATAAATT
*
338047 AAATTTAAATTTTAAAAC
1 AAATTTAAATTTCAAAAC
338065 AAATTTAAA-TTCAAAA
1 AAATTTAAATTTCAAAA
338081 TCAATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTTAAATTTCAAAAC
Found at i:346701 original size:3 final size:3
Alignment explanation
Indices: 346695--346720 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
346685 ATTCATCATT
346695 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
346721 TAAAAAAAAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:346808 original size:16 final size:16
Alignment explanation
Indices: 346766--346800 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
346756 TACACATGCA
346766 ATAATA-AAATATATC
1 ATAATATAAATATATC
346781 ATAATATAAATATA-C
1 ATAATATAAATATATC
346796 ATAAT
1 ATAAT
346801 CGTAAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATATAAATATATC
Found at i:348136 original size:14 final size:14
Alignment explanation
Indices: 348119--348151 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
348109 TTATATCTTA
348119 TTTTTTGTTTTTAT
1 TTTTTTGTTTTTAT
348133 TTTTTTGTTTTTAT
1 TTTTTTGTTTTTAT
348147 TTTTT
1 TTTTT
348152 AAGCCTGGAT
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:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (14 bp):
TTTTTTGTTTTTAT
Found at i:362856 original size:26 final size:27
Alignment explanation
Indices: 362791--362858 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 27
362781 AATCACCGGA
362791 ATATA-TTATGTTATAAAAAATATTAT
1 ATATATTTATGTTATAAAAAATATTAT
* * *
362817 ATAAATTATATATGTTA-AATAATTATTAT
1 AT--A-TATTTATGTTATAAAAAATATTAT
362846 ATATATTTATGTT
1 ATATATTTATGTT
362859 TATATTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
26 11 0.32
27 1 0.03
28 1 0.03
29 14 0.41
30 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (27 bp):
ATATATTTATGTTATAAAAAATATTAT
Found at i:372589 original size:92 final size:92
Alignment explanation
Indices: 372383--372560 Score: 229
Period size: 92 Copynumber: 2.0 Consensus size: 92
372373 AATTTTTTTC
* ** * **
372383 AAAAAAACAATTAA-ACTCC-TACTT-TTTTGCATTCACTTGGGTACTTGAATTTTCAAAATGCA
1 AAAAAAACAATTAAGCCTCCGTTTTTATTTTGCATTCAATTAAGTACTTGAATTTTCAAAATGCA
372445 TCAAAAAAGTCCTCAAAATTTTTCAAG
66 TCAAAAAAGTCCTCAAAATTTTTCAAG
*
372472 AAAAAAACAATTAAGCCTCTGTTTTTATTTTGCATTCAATTAAGTACTTGAACTTTT-AAAATGC
1 AAAAAAACAATTAAGCCTCCGTTTTTATTTTGCATTCAATTAAGTACTTGAA-TTTTCAAAATGC
* *
372536 ATCAAAAAAAGTCTTCAAACTTTTT
65 ATC-AAAAAAGTCCTCAAAATTTTT
372561 TAAAAAAGGC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
89 14 0.19
90 3 0.04
91 3 0.04
92 32 0.43
93 23 0.31
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (92 bp):
AAAAAAACAATTAAGCCTCCGTTTTTATTTTGCATTCAATTAAGTACTTGAATTTTCAAAATGCA
TCAAAAAAGTCCTCAAAATTTTTCAAG
Found at i:372773 original size:9 final size:9
Alignment explanation
Indices: 372737--372822 Score: 61
Period size: 9 Copynumber: 9.6 Consensus size: 9
372727 CATATGGTAA
372737 AAAAATTAT
1 AAAAATTAT
372746 AAAAA--AT
1 AAAAATTAT
*
372753 AAAAATCAAT
1 AAAAAT-TAT
372763 AAAAATTAT
1 AAAAATTAT
*
372772 AAAAATGATT
1 AAAAATTA-T
**
372782 AAATTTTAAT
1 AAAAATT-AT
372792 AAAAA-TAT
1 AAAAATTAT
* *
372800 AAAATTTTT
1 AAAAATTAT
*
372809 AAAAATTAG
1 AAAAATTAT
372818 AAAAA
1 AAAAA
372823 AAAATATAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
7 7 0.12
8 6 0.10
9 28 0.47
10 17 0.29
11 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:372784 original size:19 final size:17
Alignment explanation
Indices: 372751--372814 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
372741 ATTATAAAAA
*
372751 ATAAAAATCAATAAAAATT
1 ATAAAAAT--ATAAAATTT
*
372770 ATAAAAATGATTAAATTTT
1 ATAAAAAT-A-TAAAATTT
372789 AATAAAAATATAAAATTT
1 -ATAAAAATATAAAATTT
*
372807 TTAAAAAT
1 ATAAAAAT
372815 TAGAAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 15 0.39
20 8 0.21
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
ATAAAAATATAAAATTT
Found at i:372810 original size:20 final size:20
Alignment explanation
Indices: 372770--372807 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
372760 AATAAAAATT
*
372770 ATAAAAATGATTAAATTTTA
1 ATAAAAATGATAAAATTTTA
372790 ATAAAAAT-ATAAAATTTT
1 ATAAAAATGATAAAATTTT
372808 TAAAAATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
ATAAAAATGATAAAATTTTA
Done.