Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1996
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: 77693
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:275 original size:13 final size:13
Alignment explanation
Indices: 257--294 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
247 ACAGCATTTT
257 TTGTATCGATACA
1 TTGTATCGATACA
270 TTGTATCGATACA
1 TTGTATCGATACA
*
283 CTGTATCGATAC
1 TTGTATCGATAC
295 CGTGGGATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:780 original size:20 final size:20
Alignment explanation
Indices: 731--772 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
721 CCCCTAGGCA
*
731 GCACCCACCAGGTCGCGACCG
1 GCACCC-CCAGGTCGCAACCG
*
752 GCACTCCCAGGTCGCAACCG
1 GCACCCCCAGGTCGCAACCG
772 G
1 G
773 GGCCCCCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.19, C:0.45, G:0.29, T:0.07
Consensus pattern (20 bp):
GCACCCCCAGGTCGCAACCG
Found at i:5451 original size:13 final size:13
Alignment explanation
Indices: 5429--5467 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
5419 ATAATCCCCC
* *
5429 TGTATTGATACAG
1 TGTATCGATACAA
5442 TGTATCGATACAA
1 TGTATCGATACAA
5455 TGTATCGATACAA
1 TGTATCGATACAA
5468 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:7553 original size:15 final size:15
Alignment explanation
Indices: 7533--7568 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
7523 ATCGATTTTG
*
7533 TTTTGAGCTTCTTCA
1 TTTTGAGCTTCCTCA
7548 TTTTGAGCTTCCTCA
1 TTTTGAGCTTCCTCA
*
7563 ATTTGA
1 TTTTGA
7569 ACATTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (15 bp):
TTTTGAGCTTCCTCA
Found at i:12856 original size:13 final size:13
Alignment explanation
Indices: 12838--12862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12828 ACATATAGTA
12838 TGTATCGATACAT
1 TGTATCGATACAT
12851 TGTATCGATACA
1 TGTATCGATACA
12863 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12879 original size:33 final size:32
Alignment explanation
Indices: 12818--12885 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
12808 GCAGCTAAAC
* **
12818 TTGTATCGATACATATAGTATGTATCGATACA
1 TTGTATCGATACACATAAAATGTATCGATACA
12850 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACA-CATAAAATGTATCGATACA
12883 TTG
1 TTG
12886 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACACATAAAATGTATCGATACA
Found at i:15588 original size:20 final size:21
Alignment explanation
Indices: 15559--15599 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
15549 TATTTTTGTT
15559 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
15578 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
15600 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:15749 original size:13 final size:13
Alignment explanation
Indices: 15731--15769 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
15721 ATAATCCCCT
15731 TGTATCGATACAG
1 TGTATCGATACAG
*
15744 TGTATCGATACAA
1 TGTATCGATACAG
15757 TGTATCGATACAG
1 TGTATCGATACAG
15770 AGAATGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:20782 original size:20 final size:21
Alignment explanation
Indices: 20757--20923 Score: 89
Period size: 20 Copynumber: 7.8 Consensus size: 21
20747 GTAAAAAAAC
20757 AGAATGTATCGATACATT-AA
1 AGAATGTATCGATACATTAAA
* *
20777 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATTAAA
* * *
20798 A-CATGTATCAATACATTGAA
1 AGAATGTATCGATACATTAAA
20818 A-AATGTATCGATACATCTGGGTAAAAAGA
1 AGAATGTATCGATACA--T---T--A-A-A
* *
20847 CAGAATGTATCGACACATT-GA
1 -AGAATGTATCGATACATTAAA
*
20868 AGAATGTATCGATACATTCATA
1 AGAATGTATCGATACATT-AAA
* *
20890 CG--TGTATCGATACATT-GA
1 AGAATGTATCGATACATTAAA
20908 A-AATGTATCGATACAT
1 AGAATGTATCGATACAT
20924 CTGGGTAAAA
Statistics
Matches: 116, Mismatches: 15, Indels: 33
0.71 0.09 0.20
Matches are distributed among these distances:
18 1 0.01
19 13 0.11
20 77 0.66
21 3 0.03
22 3 0.03
25 1 0.01
26 1 0.01
28 1 0.01
29 2 0.02
30 1 0.01
31 13 0.11
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (21 bp):
AGAATGTATCGATACATTAAA
Found at i:20785 original size:71 final size:70
Alignment explanation
Indices: 20662--20794 Score: 196
Period size: 71 Copynumber: 1.9 Consensus size: 70
20652 TTATTCAATG
* * * **
20662 TATCGATAATCTGGGTAATAAGACAGAATGTATCGATACATTCATACTTGTATCGATACATTGAA
1 TATCGATAATCTGGGTAAAAAAACAGAATGTATCGATACATTCAAAAATGTATCGATACATTGAA
20727 AAATT
66 AAATT
20732 TATCGATATATCTGGGTAAAAAAACAGAATGTATCGATACATT-AAAGAATGTATCGATACATT
1 TATCGATA-ATCTGGGTAAAAAAACAGAATGTATCGATACATTCAAA-AATGTATCGATACATT
20795 CATACATGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
70 10 0.18
71 46 0.82
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (70 bp):
TATCGATAATCTGGGTAAAAAAACAGAATGTATCGATACATTCAAAAATGTATCGATACATTGAA
AAATT
Found at i:20787 original size:51 final size:51
Alignment explanation
Indices: 20710--20884 Score: 185
Period size: 51 Copynumber: 3.6 Consensus size: 51
20700 CATTCATACT
* *
20710 TGTATCGATACATTGAAAAATTTATCGATATATCTGGGTAAAAAAACAGAA
1 TGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAACAGAA
* *
20761 TGTATCGATACATT-AAAGAATGTATCGATACA--T---T---CATAC---A
1 TGTATCGATACATTGAAA-AATGTATCGATACATCTGGGTAAAAAAACAGAA
* *
20801 TGTATCAATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAA
1 TGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAACAGAA
* *
20852 TGTATCGACACATTGAAGAATGTATCGATACAT
1 TGTATCGATACATTGAAAAATGTATCGATACAT
20885 TCATACGTGT
Statistics
Matches: 101, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
40 28 0.28
41 3 0.03
42 1 0.01
43 3 0.03
45 1 0.01
46 1 0.01
48 3 0.03
49 1 0.01
50 3 0.03
51 57 0.56
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAACAGAA
Found at i:20841 original size:91 final size:91
Alignment explanation
Indices: 20686--20934 Score: 419
Period size: 91 Copynumber: 2.7 Consensus size: 91
20676 GTAATAAGAC
* * *
20686 AGAATGTATCGATACATTCATACTTGTATCGATACATTGAAAAATTTATCGATATATCTGGGTAA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
*
20751 AAAAACAGAATGTATCGATACATTAA
66 AAAAACAGAATGTATCGACACATTAA
*
20777 AGAATGTATCGATACATTCATACATGTATCAATACATTGAAAAATGTATCGATACATCTGGGTAA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
* *
20842 AAAGACAGAATGTATCGACACATTGA
66 AAAAACAGAATGTATCGACACATTAA
*
20868 AGAATGTATCGATACATTCATACGTGTATCGATACATTG-AAAATGTATCGATACATCTGGGTAA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
20932 AAA
66 AAA
20935 TATGACTTTT
Statistics
Matches: 149, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
90 28 0.19
91 121 0.81
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (91 bp):
AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
AAAAACAGAATGTATCGACACATTAA
Found at i:22297 original size:22 final size:23
Alignment explanation
Indices: 22262--22307 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
22252 TTCTTCGAAG
22262 AAATTAAAAATAAAT-A-AACAA
1 AAATTAAAAATAAATCATAACAA
*
22283 AAATTGAAAGATAAATCATAACAA
1 AAATT-AAAAATAAATCATAACAA
22307 A
1 A
22308 TATATATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 1 0.05
24 6 0.29
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (23 bp):
AAATTAAAAATAAATCATAACAA
Found at i:23058 original size:2 final size:2
Alignment explanation
Indices: 23051--23087 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
23041 AAAATATTAG
*
23051 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23088 GAATTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29627 original size:21 final size:21
Alignment explanation
Indices: 29603--29656 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
29593 AATATACTTA
*
29603 AATA-TTTATATATATATTAAT
1 AATAGTTTATA-ATAGATTAAT
*
29624 AATAGTTTATAATAGATTAAA
1 AATAGTTTATAATAGATTAAT
*
29645 AAT-GTGTATAAT
1 AATAGTTTATAAT
29657 TTTTTTAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.28
21 15 0.52
22 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
AATAGTTTATAATAGATTAAT
Found at i:33468 original size:7 final size:7
Alignment explanation
Indices: 33456--33513 Score: 55
Period size: 7 Copynumber: 8.0 Consensus size: 7
33446 TAATAATAAG
33456 TAAAAAA
1 TAAAAAA
33463 TAAAAACAA
1 T-AAAA-AA
33472 TTAAAAAA
1 -TAAAAAA
**
33480 -ATCAAA
1 TAAAAAA
*
33486 TTAAAAA
1 TAAAAAA
33493 TAAAAAA
1 TAAAAAA
33500 TAAAAAA
1 TAAAAAA
33507 TAAAAAA
1 TAAAAAA
33514 ATCAATTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
6 4 0.10
7 24 0.59
8 6 0.15
9 6 0.15
10 1 0.02
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:33516 original size:34 final size:37
Alignment explanation
Indices: 33456--33526 Score: 112
Period size: 34 Copynumber: 2.0 Consensus size: 37
33446 TAATAATAAG
33456 TAAAAAATAAAAACAATTAAAAAAATCAAATTAAAAA
1 TAAAAAATAAAAACAATTAAAAAAATCAAATTAAAAA
*
33493 TAAAAAAT-AAAA-AA-TAAAAAAATCAATTTAAAAA
1 TAAAAAATAAAAACAATTAAAAAAATCAAATTAAAAA
33527 AAAGAAGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 19 0.58
35 2 0.06
36 4 0.12
37 8 0.24
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (37 bp):
TAAAAAATAAAAACAATTAAAAAAATCAAATTAAAAA
Found at i:34236 original size:18 final size:18
Alignment explanation
Indices: 34191--34225 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
34181 AGCGACCACC
34191 GCAACTTCCAGCAGCTCA
1 GCAACTTCCAGCAGCTCA
34209 GCAACTTCCAGCAGCTC
1 GCAACTTCCAGCAGCTC
34226 CACAGCTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.40, G:0.17, T:0.17
Consensus pattern (18 bp):
GCAACTTCCAGCAGCTCA
Found at i:34417 original size:102 final size:102
Alignment explanation
Indices: 34295--34481 Score: 266
Period size: 102 Copynumber: 1.8 Consensus size: 102
34285 ACAATAACTT
* * * *
34295 CCACAGCTCCCATAGCAACTTCCAGCAGCTCCAGTAGCTTCCACGGCAACCTCTAGTAGCTCCCA
1 CCACAGCTCCCACAGCAACTTCCAGCAGCTCCAGCAGCTTCCACGGCAACCTCCAGCAGCTCCCA
** **
34360 CGGTAGCCTTTAGCAGCTCAGCAATCCCGAGCAGCTC
66 CGACAGCCTCCAGCAGCTCAGCAATCCCGAGCAGCTC
* * * *
34397 CCACAGCTCCCACAGCAACTTCCAGCAGCTCTAGCAGCTTCCATGGTAGCCTCCAGCAGCTCCCA
1 CCACAGCTCCCACAGCAACTTCCAGCAGCTCCAGCAGCTTCCACGGCAACCTCCAGCAGCTCCCA
34462 CGACAGCCTCCAGCAGCTCA
66 CGACAGCCTCCAGCAGCTCA
34482 ACTCCCACAG
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 73 1.00
ACGTcount: A:0.24, C:0.41, G:0.18, T:0.17
Consensus pattern (102 bp):
CCACAGCTCCCACAGCAACTTCCAGCAGCTCCAGCAGCTTCCACGGCAACCTCCAGCAGCTCCCA
CGACAGCCTCCAGCAGCTCAGCAATCCCGAGCAGCTC
Found at i:42418 original size:20 final size:20
Alignment explanation
Indices: 42365--42410 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
42355 AAACCCTTGT
*
42365 ATGTATCAATACACATCCAG
1 ATGTATCAATACATATCCAG
42385 ATGTATCAATACATATCCAG
1 ATGTATCAATACATATCCAG
42405 ATGTAT
1 ATGTAT
42411 TGATACATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (20 bp):
ATGTATCAATACATATCCAG
Found at i:42845 original size:13 final size:13
Alignment explanation
Indices: 42827--42912 Score: 59
Period size: 13 Copynumber: 5.9 Consensus size: 13
42817 CATAAAGTGT
42827 TGTATCGATACAA
1 TGTATCGATACAA
42840 TGTATCGATACATAA
1 TGTATCGATAC--AA
42855 GTGTTGTATCGAT--AA
1 ----TGTATCGATACAA
42870 TGTATCGATACATA
1 TGTATCGATACA-A
42884 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
42901 TGTATCGATACA
1 TGTATCGATACA
42913 TAAGTTTTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 26
0.70 0.00 0.30
Matches are distributed among these distances:
11 9 0.15
13 24 0.40
14 1 0.02
15 4 0.07
17 1 0.02
18 12 0.20
19 9 0.15
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:42862 original size:32 final size:32
Alignment explanation
Indices: 42807--42933 Score: 215
Period size: 32 Copynumber: 4.0 Consensus size: 32
42797 TTTAACGATT
42807 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
42840 TGTATCGATACATAAGTGTTGTATCGAT--AA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
42870 TGTATCGATACAT-AGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
42901 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
42933 T
1 T
42934 ATAAGCTATT
Statistics
Matches: 90, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
29 14 0.16
30 15 0.17
31 15 0.17
32 33 0.37
33 13 0.14
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:42904 original size:61 final size:62
Alignment explanation
Indices: 42807--42929 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 62
42797 TTTAACGATT
42807 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATAA
*
42870 TGTATCGATACAT-AGTGTTGTATCGATACAATGTATCGATACATAAGTTTTGTATCGATA
1 TGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATA
42930 CAATATAAGC
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 46 0.78
63 13 0.22
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (62 bp):
TGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATAA
Found at i:43001 original size:19 final size:19
Alignment explanation
Indices: 42950--43004 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
42940 TATTGCCAAA
*
42950 AAATGTATCGATAAATTTC
1 AAATGTATCGATACATTTC
42969 AAATGTATCGATACATTTC
1 AAATGTATCGATACATTTC
42988 AAATGTATCGATACATT
1 AAATGTATCGATACATT
43005 GTATCGATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (19 bp):
AAATGTATCGATACATTTC
Found at i:43009 original size:13 final size:13
Alignment explanation
Indices: 42991--43015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42981 ACATTTCAAA
42991 TGTATCGATACAT
1 TGTATCGATACAT
43004 TGTATCGATACA
1 TGTATCGATACA
43016 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:46573 original size:36 final size:36
Alignment explanation
Indices: 46524--46600 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
46514 TTCATTGTTA
*
46524 TTATTTTTTGAAAGCTCTTTTGTATTTGTTTTGAGC
1 TTATTTTTCGAAAGCTCTTTTGTATTTGTTTTGAGC
46560 TTATTTTTCGAAAGCTCTTTTGTATTTGTTTTGAGC
1 TTATTTTTCGAAAGCTCTTTTGTATTTGTTTTGAGC
46596 TTATT
1 TTATT
46601 CCTTCACAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.17, C:0.09, G:0.16, T:0.58
Consensus pattern (36 bp):
TTATTTTTCGAAAGCTCTTTTGTATTTGTTTTGAGC
Found at i:53025 original size:42 final size:42
Alignment explanation
Indices: 52954--54052 Score: 886
Period size: 42 Copynumber: 26.2 Consensus size: 42
52944 ATTAAACTTT
*
52954 TGGAGACTTTCCTT-CCTTAGTCTGCCTGTCGGCTTTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * *
52995 TGGAAACTTTCTTTCCCTTAGTCTGTCTGTCGGCTTTGACAC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * *
53037 TGGAGACTTTCCTACCCTTAGTCTACCTATCAGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * *
53079 TAGAGACTTTCTTTCCCTTAGTTTGCTTGTCGGCTTTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
**
53121 TGGAGACTTTCCTTCCCTTAGTCCACCTGTCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * *
53163 TAGAGACTTT-TTTCCCCTTAGTCTGCCTGTCAGCTTTGACCC
1 TGGAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACCC
53205 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * ** *
53247 TAGAGACTTTCCTTCCCTTAGTCTGCCTATTAGCTTTGTCACC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGAC-CC
*
53290 TGGAGACTTTTCTAT-CCTTAGTCTGCCTGTCGGCTTTGA-CC
1 TGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * *
53331 TCGGAGACTTTCCTTCCCTTAGTCTACCTGTTGGCTTTGACCT
1 T-GGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * * *
53374 TGGAGACTTTTCTACCTTTAGCCTGCCTGTTGGCTTTAACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * * * *
53416 TAGAGATTTTCATGCCCTCACTTTGCCTGTCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * *
53458 TGGAGACTTTTCTACCCTTAGTTTGCTTGTCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * *
53500 TGGAGA-TTGCCTT--CTCAGTCTGCCTATCGGCTTTGACCC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * ** *
53539 TGGAGACTTTCCTGCCCTCAGTCTGCCTATCGATTTTGACAC
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * * *
53581 TAGATACTTTCCTACCCTCAGTCTGCCTATCGGCTTTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * * *
53623 TGGAGAC-TGCC-TCATCTAAAGTTTGCTTGTCGACTTTGACCC
1 TGGAGACTTTCCTTC-CCT-TAGTCTGCCTGTCGGCTTTGACCC
* * * * * * *
53665 TGAAGACTTTCCTACCCTCAGTCTGCTTGTCAGCTCTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * *
53707 TGGAGACTTT-CTTACCCTCAGTCTACCTGTCGACTTTGACCC
1 TGGAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACCC
* ** * * *
53749 TGGAGACTGT-CTTATCTAAAGTCTGCTTGTCGGCTTTGACCT
1 TGGAGACTTTCCTTCCCT-TAGTCTGCCTGTCGGCTTTGACCC
* * * *
53791 TGGAGACTTTCCTAT-CCTTAAG-CTGCTTATCGACTTTGACCT
1 TGGAGACTTTCCT-TCCCTT-AGTCTGCCTGTCGGCTTTGACCC
* * * **
53833 TGGAGACTTTCCTAT-CCTTAATCTGCTTGTTGGCTTTGACTT
1 TGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * *
53875 TGGAGAC-TGCC-TCATCTAAAGTTTGCCTGTTGGCTTTGACCC
1 TGGAGACTTTCCTTC-CCT-TAGTCTGCCTGTCGGCTTTGACCC
* * * * * *
53917 TGGAGACTTTCCTACCCTCAATCTGTCTGTTGGCTTTGACCT
1 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
* * * * * * * * *
53959 TGGAGAC-TGCC-TCATCTAAAGTTTGCCTATCGGCGTTAATCT
1 TGGAGACTTTCCTTC-CCT-TAGTCTGCCTGTCGGCTTTGACCC
* * * *
54001 TGGAGACTTT-CTTACCCTCAGTTTGCCTGCCAGCTTTGACCC
1 TGGAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACCC
54043 TGGAGACTTT
1 TGGAGACTTT
54053 TTTACTTTTT
Statistics
Matches: 844, Mismatches: 183, Indels: 61
0.78 0.17 0.06
Matches are distributed among these distances:
39 29 0.03
40 7 0.01
41 42 0.05
42 704 0.83
43 57 0.07
44 5 0.01
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.37
Consensus pattern (42 bp):
TGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCC
Found at i:54087 original size:42 final size:43
Alignment explanation
Indices: 54021--54104 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
54011 CTTACCCTCA
* * *
54021 GTTTGCCTGCCAGCTTTGACCCT-GGAGACTTTTTTACTTTTTT
1 GTTTGCCTGCCAGCTTTGAACCTGGGAGAATCTTTT-CTTTTTT
**
54064 GTTTGCCTGTTAGCTTT-AACCTGGGAGAATCTTTTCTTTTT
1 GTTTGCCTGCCAGCTTTGAACCTGGGAGAATCTTTTCTTTTT
54105 ACCTGTCGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
42 10 0.29
43 25 0.71
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (43 bp):
GTTTGCCTGCCAGCTTTGAACCTGGGAGAATCTTTTCTTTTTT
Found at i:54581 original size:17 final size:18
Alignment explanation
Indices: 54526--54590 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 18
54516 TGTAAAATAT
* *
54526 AATAATAAGTAAAAAAACA
1 AATAATAAAT-AAAAATCA
* *
54545 AAAAATATA-AAAAATCA
1 AATAATAAATAAAAATCA
54562 AATTAA-AAATAAAAAT-A
1 AA-TAATAAATAAAAATCA
54579 AATAATAAATAA
1 AATAATAAATAA
54591 TTAAAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 3 0.08
17 20 0.54
18 8 0.22
19 6 0.16
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (18 bp):
AATAATAAATAAAAATCA
Found at i:54592 original size:27 final size:27
Alignment explanation
Indices: 54519--54597 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
54509 TATTCAATGT
*
54519 AAAATATAATAATAAGTAA--AAAAACA
1 AAAATA-AATAATAAATAATTAAAAACA
* * *
54545 AAAA-ATATAAAAAATCAAATTAAAAATA
1 AAAATAAATAATAAAT--AATTAAAAACA
54573 AAAATAAATAATAAATAATTAAAAA
1 AAAATAAATAATAAATAATTAAAAA
54598 AAATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
24 7 0.17
25 1 0.02
26 6 0.14
27 9 0.21
28 10 0.24
29 9 0.21
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.22
Consensus pattern (27 bp):
AAAATAAATAATAAATAATTAAAAACA
Found at i:54702 original size:43 final size:41
Alignment explanation
Indices: 54641--54723 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 41
54631 AGGATTTGTA
* * * *
54641 GCCACCTAATTGACTTAGGTGGCATTGCATTGCATTGCATGCT
1 GCCACCTAAATCAATTAGGTGGCAATGCA-TGCATT-CATGCT
54684 GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGC
1 GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGC
54724 ATGAAATTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 5 0.14
42 6 0.17
43 25 0.69
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGCT
Found at i:55374 original size:49 final size:48
Alignment explanation
Indices: 55280--55374 Score: 127
Period size: 49 Copynumber: 2.0 Consensus size: 48
55270 AGTGACCACC
* *
55280 GCAACCTCCAGCAGCCCAGTAACTCCCACGACAGCCTTCAACAGCTAA
1 GCAACCTCCAGCAGCCCAGCAACTCCCACGACAGCCTCCAACAGCTAA
* * * *
55328 GCAACTTCCAGCAGCTCCAGCAACTTCCATGGCAGCCTCCAACAGCT
1 GCAACCTCCAGCAGC-CCAGCAACTCCCACGACAGCCTCCAACAGCT
55375 CCTACGACAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 14 0.35
49 26 0.65
ACGTcount: A:0.28, C:0.41, G:0.16, T:0.15
Consensus pattern (48 bp):
GCAACCTCCAGCAGCCCAGCAACTCCCACGACAGCCTCCAACAGCTAA
Found at i:55467 original size:30 final size:31
Alignment explanation
Indices: 55427--55512 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
55417 TATAGCTCCT
*
55427 ACAGTAACTTTCAGCAGCTCCCACAGC-TCC
1 ACAGCAACTTTCAGCAGCTCCCACAGCTTCC
* *
55457 ATAGCAACTTTCAGCAGCT-CTAGCAGCTTCC
1 ACAGCAACTTTCAGCAGCTCCCA-CAGCTTCC
* * *
55488 ACAGCAACCTCCAACAGCTCCCACA
1 ACAGCAACTTTCAGCAGCTCCCACA
55513 ACAGCCTCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
29 2 0.04
30 21 0.47
31 20 0.44
32 2 0.04
ACGTcount: A:0.29, C:0.40, G:0.13, T:0.19
Consensus pattern (31 bp):
ACAGCAACTTTCAGCAGCTCCCACAGCTTCC
Found at i:55506 original size:22 final size:22
Alignment explanation
Indices: 55480--55570 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 22
55470 GCAGCTCTAG
55480 CAGCTTCCACAGCAACCTCCAA
1 CAGCTTCCACAGCAACCTCCAA
* * * *
55502 CAGCTCCCACAACAGCCTCCAG
1 CAGCTTCCACAGCAACCTCCAA
* *
55524 CAGCTT--A-A-CAATC-CCAGG
1 CAGCTTCCACAGCAACCTCCA-A
* *
55542 CAGCTCCCACAGCAACTTCCAA
1 CAGCTTCCACAGCAACCTCCAA
55564 CAGCTTC
1 CAGCTTC
55571 AGCAGCTTCC
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
17 3 0.06
18 9 0.18
19 1 0.02
20 2 0.04
21 1 0.02
22 32 0.63
23 3 0.06
ACGTcount: A:0.30, C:0.44, G:0.12, T:0.14
Consensus pattern (22 bp):
CAGCTTCCACAGCAACCTCCAA
Found at i:55614 original size:31 final size:31
Alignment explanation
Indices: 55541--55630 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
55531 ACAATCCCAG
* * * * *
55541 GCAGCTCCCACAGCAACTTCCAACAGCTTCA
1 GCAGCTCCCACGGTAGCCTCCAGCAGCTTCA
*
55572 GCAGCTTCCACGGTAGCCTCCAGCAGCTTCA
1 GCAGCTCCCACGGTAGCCTCCAGCAGCTTCA
55603 GCAGCTCCCACGGTAGCCTCCAGCAGCT
1 GCAGCTCCCACGGTAGCCTCCAGCAGCT
55631 CCCACGACAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.22, C:0.41, G:0.20, T:0.17
Consensus pattern (31 bp):
GCAGCTCCCACGGTAGCCTCCAGCAGCTTCA
Found at i:55629 original size:22 final size:22
Alignment explanation
Indices: 55601--55667 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
55591 CCAGCAGCTT
**
55601 CAGCAGCTCCCACGGTAGCCTC
1 CAGCAGCTCCCACGACAGCCTC
55623 CAGCAGCTCCCACGACAGCCTC
1 CAGCAGCTCCCACGACAGCCTC
*
55645 TAGCAGCT--CA-G-CAGCCTC
1 CAGCAGCTCCCACGACAGCCTC
55663 CAGCA
1 CAGCA
55668 ACTTCCAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.27
19 1 0.02
20 2 0.05
22 27 0.66
ACGTcount: A:0.22, C:0.45, G:0.21, T:0.12
Consensus pattern (22 bp):
CAGCAGCTCCCACGACAGCCTC
Found at i:63946 original size:97 final size:95
Alignment explanation
Indices: 63783--64022 Score: 329
Period size: 97 Copynumber: 2.5 Consensus size: 95
63773 AATTTTATTT
* **
63783 ATCGGGGATACTCCAACCTTATTCCTCCGAGGGGATACTCCAACCTCGCTTTTAAACACACTAAA
1 ATCGGGGACACTCCAACCCCATTCCTCCGA-GGGATACTCCAACC-CGCTTTTAAACACACTAAA
63848 GTTTAAATCTTATTCTCACTTAAATTGTCACC
64 GTTTAAATCTTATTCTCACTTAAATTGTCACC
* ** *
63880 ATCGGGGACACTTCAACCCCATTTTTCCGAGGGAATACTCCAACCCGACTTTTAAACGCA-TCAA
1 ATCGGGGACACTCCAACCCCATTCCTCCGAGGG-ATACTCCAACCCG-CTTTTAAACACACT-AA
* *
63944 AGTTTAAATTTTATTCTCACTTAAATTGTCATC
63 AGTTTAAATCTTATTCTCACTTAAATTGTCACC
*
63977 ATCGGGGACACTCCAACCCCATTCCTCCGAAGGGATACTCTAACCC
1 ATCGGGGACACTCCAACCCCATTCCTCCG-AGGGATACTCCAACCC
64023 TGTTTTTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
96 6 0.05
97 116 0.92
98 4 0.03
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (95 bp):
ATCGGGGACACTCCAACCCCATTCCTCCGAGGGATACTCCAACCCGCTTTTAAACACACTAAAGT
TTAAATCTTATTCTCACTTAAATTGTCACC
Found at i:67244 original size:52 final size:52
Alignment explanation
Indices: 67166--67293 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
67156 CGAAATATAA
*
67166 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
67218 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
67270 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
67294 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:67320 original size:13 final size:13
Alignment explanation
Indices: 67302--67326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67292 CAAAGATCAG
67302 TGTATCGATACAA
1 TGTATCGATACAA
67315 TGTATCGATACA
1 TGTATCGATACA
67327 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:67410 original size:13 final size:13
Alignment explanation
Indices: 67392--67449 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
67382 CAAAAAAATA
67392 TGTATCGATACAT
1 TGTATCGATACAT
67405 TGTATCGATACAACATTTT
1 TGTATCGAT---ACA---T
67424 ATGTATCGATACAT
1 -TGTATCGATACAT
67438 TGTATCGATACA
1 TGTATCGATACA
67450 ACATTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:67430 original size:20 final size:20
Alignment explanation
Indices: 67405--67470 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
67395 ATCGATACAT
67405 TGTATCGATACAACATTTTA
1 TGTATCGATACAACATTTTA
67425 TGTATCGAT---ACA---T-
1 TGTATCGATACAACATTTTA
67438 TGTATCGATACAACATTTTA
1 TGTATCGATACAACATTTTA
*
67458 TGTATTGATACAA
1 TGTATCGATACAA
67471 ATCGTTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 21 0.55
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
TGTATCGATACAACATTTTA
Found at i:67451 original size:33 final size:33
Alignment explanation
Indices: 67370--67469 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
67360 AGTAGCTTAA
* ***
67370 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAACATTTTATGTATCGATAC
67403 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACATTTTATGTATCGATAC
*
67436 ATTGTATCGATACAACATTTTATGTATTGATAC
1 ATTGTATCGATACAACATTTTATGTATCGATAC
67469 A
1 A
67470 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (33 bp):
ATTGTATCGATACAACATTTTATGTATCGATAC
Found at i:71977 original size:52 final size:52
Alignment explanation
Indices: 71907--72027 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
71897 GAAAATTTAT
* *
71907 CTGCATGTATCGCTACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
71959 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
72011 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
72028 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:72040 original size:52 final size:52
Alignment explanation
Indices: 71907--72047 Score: 196
Period size: 52 Copynumber: 2.7 Consensus size: 52
71897 GAAAATTTAT
* *
71907 CTGCATGTATCGCTACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
*** *
71959 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
72011 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
72048 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 4 0.05
52 76 0.95
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:72054 original size:13 final size:13
Alignment explanation
Indices: 72036--72060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72026 CAAAGATCAG
72036 TGTATCGATACAA
1 TGTATCGATACAA
72049 TGTATCGATACA
1 TGTATCGATACA
72061 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:72143 original size:13 final size:13
Alignment explanation
Indices: 72125--72149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72115 CAAAAAAATA
72125 TGTATCGATACAT
1 TGTATCGATACAT
72138 TGTATCGATACA
1 TGTATCGATACA
72150 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:72143 original size:33 final size:33
Alignment explanation
Indices: 72103--72169 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
72093 AGTAGCTTAA
72103 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
72136 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
72169 A
1 A
72170 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:73255 original size:49 final size:49
Alignment explanation
Indices: 73046--73976 Score: 1193
Period size: 49 Copynumber: 19.7 Consensus size: 49
73036 AAAAGGATGT
*
73046 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
73098 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
73141 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
73189 CAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
73238 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
73286 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
73335 CAATGTGCTGAGTCAAGGCCAGCTACAGTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
73384 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
73427 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
73476 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTAC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
73519 CAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
73567 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
73610 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
73659 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
73702 CAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
73751 CAATGTGCTGAGTCAAGGCCAGCTACATTAGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
73794 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
73843 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
73892 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
73941 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
73977 GAAGGGTTGC
Statistics
Matches: 774, Mismatches: 68, Indels: 77
0.84 0.07 0.08
Matches are distributed among these distances:
43 232 0.30
45 5 0.01
46 1 0.00
47 4 0.01
48 132 0.17
49 369 0.48
52 31 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:73459 original size:92 final size:92
Alignment explanation
Indices: 73037--73981 Score: 1338
Period size: 92 Copynumber: 10.1 Consensus size: 92
73027 AGATGATGAA
* * *
73037 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAAT
73102 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
73133 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
73197 TGATTCAAGGCCAGCTACATTGGATTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
73224 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGCCA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
* *
73288 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
60 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
73321 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACAGTGGACTTAAAGATGATGATGCCA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
*
73386 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
60 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
73419 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
73484 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * *
73511 AAAGGTACCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
73575 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * *
73602 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGTCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
73667 TGAGTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * *
73694 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* * *
73759 TGAGTCAAGGCCAGCTACATTAGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
73786 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
73851 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
73878 AATGGTGAAGGTGTCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
1 -A-----AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
* *
73943 ATATGCTGATTCAGGGCCAGCTATATTGGGCTT
60 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
73976 AGAAGG
1 A-AAGG
73982 GTTGCCACCG
Statistics
Matches: 790, Mismatches: 45, Indels: 31
0.91 0.05 0.04
Matches are distributed among these distances:
91 125 0.16
92 345 0.44
93 6 0.01
94 2 0.00
95 42 0.05
96 5 0.01
97 143 0.18
98 122 0.15
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:73503 original size:22 final size:22
Alignment explanation
Indices: 73476--73541 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
73466 ATGAAGGTGC
73476 CAATATGCTGATTCAAGGCCAG
1 CAATATGCTGATTCAAGGCCAG
* * * *
73498 CGATAT--TGGACTTAAAGG-TAC
1 CAATATGCT-GA-TTCAAGGCCAG
73519 CAATATGCTGATTCAAGGCCAG
1 CAATATGCTGATTCAAGGCCAG
73541 C
1 C
73542 TACATTGGAC
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
20 1 0.03
21 14 0.45
22 15 0.48
23 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (22 bp):
CAATATGCTGATTCAAGGCCAG
Found at i:73536 original size:21 final size:21
Alignment explanation
Indices: 73469--73536 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
73459 CTTAAAGATG
*
73469 AAGGTGCCAATATGCTGATTC
1 AAGGTACCAATATGCTGATTC
* * * *
73490 AAGGCCAGCGATAT--TGGACTTA
1 AAGG-TACCAATATGCT-GA-TTC
73512 AAGGTACCAATATGCTGATTC
1 AAGGTACCAATATGCTGATTC
73533 AAGG
1 AAGG
73537 CCAGCTACAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
20 1 0.03
21 18 0.55
22 13 0.39
23 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (21 bp):
AAGGTACCAATATGCTGATTC
Found at i:74020 original size:33 final size:35
Alignment explanation
Indices: 73976--74045 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
73966 TATTGGGCTT
73976 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
74010 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
74044 AG
1 AG
74046 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:74132 original size:34 final size:33
Alignment explanation
Indices: 74055--74821 Score: 773
Period size: 34 Copynumber: 23.6 Consensus size: 33
74045 GGGAGAAAGA
* * *
74055 TGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAAAG
1 TGCCACGGAGTTGTGGGCTTTAAAA--G-AAGAAGG
74090 TGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGG
1 TGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGG
74124 TGCCACGGAGTTGTGGGCTTT---A-AAG-A-G
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
* *
74151 TGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGG
1 TGCCACGGAGTTGTGGGCTTTAAAA-GAAGAA--GG
* * *
74187 TGCCACGGAGTTATGGGC-TTAGAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTTTA-AAAGAAGAAG-G
* *
74221 TGCCACAGAGTTGTGGGCTTTTAAA-AA-AA-G
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
*
74251 TGCCACGGAGTTGTGGGCTTTGAAAGAAGAAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
74284 TGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGG
1 TGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGG
*
74318 TGCCACGGAGTTGTGGGCTTTAAAGGAA-AAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
* * *
74350 TGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAG
1 TGCCACGGAGTTGTGGGCTTTAAA-A-GAAGAAGG
*
74384 TGCCACGGAATTGTGGGCTTT--AA-AAG--GG
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
*
74412 TGCCACGGAGTTGTGGGCTTTAAAGGAA-AAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
74444 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGG
1 TGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGG
74478 TGCCACGGAGTTGTGGGCTTT-----AAG-A-G
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
* *
74504 TGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGG
1 TGCCACGGAGTTGTGGGCTTTAAAA-GAAGAA-GG
* * *
74539 TTGCCACGGAGTTATGGGC-TTAGAAGGAAAAAGAG
1 -TGCCACGGAGTTGTGGGCTTTA-AAAGAAGAAG-G
* *
74574 TGCCACAGAGTTGTGGGCTTTTAAA-AA-AA-G
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
74604 TGCCACGGAGTTGTGGGCTTTGAAAAAGAAGAAGG
1 TGCCACGGAGTTGTGGGCTTT--AAAAGAAGAAGG
74639 TGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGG
1 TGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGG
*
74673 TGCCACGGAGTTTGTGGGCTTT-AAAGGA-AAGG
1 TGCCACGGAG-TTGTGGGCTTTAAAAGAAGAAGG
* * *
74705 TTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAG
1 -TGCCACGGAGTTGTGGGCTTTAAA-A-GAAGAAGG
*
74740 TGCCACGGAATTGTGGGCTTTAAAA-AAG--GG
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
*
74770 TGCCACGGAGTTGTGGGCTTTAAAGGAA-AAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
74802 -GCCACGGAGTTGTGGGCTTT
1 TGCCACGGAGTTGTGGGCTTT
74822 GAAGAAAAAA
Statistics
Matches: 628, Mismatches: 47, Indels: 118
0.79 0.06 0.15
Matches are distributed among these distances:
26 21 0.03
27 22 0.04
28 25 0.04
29 3 0.00
30 74 0.12
31 33 0.05
32 75 0.12
33 63 0.10
34 184 0.29
35 85 0.14
36 39 0.06
37 4 0.01
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22
Consensus pattern (33 bp):
TGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGG
Found at i:74301 original size:160 final size:160
Alignment explanation
Indices: 74082--74830 Score: 796
Period size: 160 Copynumber: 4.6 Consensus size: 160
74072 CTTAAAAGGG
74082 AAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-A
1 AAAAAAAGTGCCACGGAGTTGTGGGCTTT--AAAGAA-AAGGTGCCACGGAGTTGTGGGCTTTAA
* *
74146 -AAG-A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGGTGCCACGGAGTTATGGGC-TT
63 GAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAGG-AAAA--GGTGCCACGGAGTTGTGGGCTTT
*
74207 AGAAGGAAAAAGAG-TGCCACAGAGTTGTGGGCTT-TT
124 A-AAGGAAAAAGAGTTGCCACGGAGTTGTGGGCTTATT
74243 AAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAGAA-AAGGTGCCACGGAGTTGTGGGCTTT---
*
74308 AAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGAC-TTAA
61 AAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAA
*
74372 AGATGAAAAA-AG-TGCCACGGAATTGTGGGC-T-TT
126 AG--GAAAAAGAGTTGCCACGGAGTTGTGGGCTTATT
**
74405 -AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
1 AAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA-GAAAAGGTGCCACGGAGTTGTGGGCTTT---A
*
74469 AGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AA-G---A-GTGCCACGGAGTCGTGGGCTTTAAA
62 AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTT-AA
* * **
74528 AGGAAAAAGGGTTGCCACGGAGTTATGGGCTTAGA
126 AGGAAAAAGAGTTGCCACGGAGTTGTGGGCTTATT
*
74563 AGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTTAAA-AAAA-GTGCCACGGAGTTGTGGGCTTTG
1 A--AAAAA-AGTGCCACGGAGTTGTGGGC-TTTAAAGAAAAGGTGCCACGGAGTTGTGGGCTTT-
*
74626 AAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTTGTGGG
61 ---AAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAGGAA-AAGGTGCCACGGAG-TTGTGGG
* *
74691 CTTTAAAGG--AAAG-GTTGCCACGGAGTTGTGGACTTAAAGAT
120 CTTTAAAGGAAAAAGAGTTGCCACGGAGTTGTGGGCTT--A-TT
* * *
74732 GAAAAAAGTGCCACGGAATTGTGGGCTTTAAA-AAAGGGTGCCACGGAGTTGTGGGCTTTAAAGG
1 AAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAGAAAAGGTGCCACGGAGTTGTGGGCTTT-AA-G
* *
74796 AA-AAGG-GCCACGGAGTTGTGGGCTTTGAAGAAAAA
64 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAA
74831 ATGCCATTGA
Statistics
Matches: 520, Mismatches: 32, Indels: 73
0.83 0.05 0.12
Matches are distributed among these distances:
154 23 0.04
155 4 0.01
156 20 0.04
157 1 0.00
158 1 0.00
159 2 0.00
160 117 0.22
161 103 0.20
162 44 0.08
163 54 0.10
164 11 0.02
165 16 0.03
166 66 0.13
167 30 0.06
168 2 0.00
169 16 0.03
170 10 0.02
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (160 bp):
AAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAGAA
GAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAA
AAAGAGTTGCCACGGAGTTGTGGGCTTATT
Found at i:74509 original size:26 final size:26
Alignment explanation
Indices: 74477--74526 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
74467 AAAGAAGAAG
*
74477 GTGCCACGGAGTTGTGGGCTTTAAGA
1 GTGCCACGGAGTCGTGGGCTTTAAGA
74503 GTGCCACGGAGTCGTGGGCTTTAA
1 GTGCCACGGAGTCGTGGGCTTTAA
74527 AAGGAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.38, T:0.26
Consensus pattern (26 bp):
GTGCCACGGAGTCGTGGGCTTTAAGA
Found at i:74692 original size:100 final size:96
Alignment explanation
Indices: 74030--74821 Score: 750
Period size: 97 Copynumber: 8.1 Consensus size: 96
74020 CACCGACTTG
* * * * * *
74030 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAAAGTGCC
1 TGTGGGCTTTA--AAAGGA-AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-AG-AAGAAGGTGCC
74094 ACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGT
61 ACGGAGTTGTGGGCTTT--AAA-AA-AA-GTGCCACGGAGT
* * *
74135 TGTGGGCTTT-AAA-G---A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGGTGCCACG
1 TGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAA--GGTGCCACG
* * *
74194 GAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGT
64 GAGTTGTGGGCTT--TA--AAAAA-AGTGCCACGGAGT
* *
74232 TGTGGGCTTTTAAA--AAAA-GTGCCACGGAGTTGTGGGCTTT-GAAAGAAGAAGGTGCCACGGA
1 TGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGA
74293 GTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGT
66 GTTGTGGGCTTT--AAA-AA-AA-GTGCCACGGAGT
* * * *
74329 TGTGGGCTTT-AAAGGAAAAGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACGG
1 TGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAA-AAGAAGAAGGTGCCACGG
* **
74392 AATTGTGGGCTTT-AAAAGGGTGCCACGGAGT
65 AGTTGTGGGCTTTAAAAAAAGTGCCACGGAGT
*
74423 TGTGGGCTTT-AAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGA
1 TGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGA
*
74487 GTTGTGGGCTTT---AAGAGTGCCACGGAGT
66 GTTGTGGGCTTTAAAAAAAGTGCCACGGAGT
* * * * *
74515 CGTGGGCTTTAAAAGGAAAAAGGGTTGCCACGGAGTTATGGGC-TTAGAAGGAAAAAGAGTGCCA
1 TGTGGGCTTTAAAAGG-AAAA-GG-TGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAG-GTGCCA
*
74579 CAGAGTTGTGGGCTTTTAAAAAAAGTGCCACGGAGT
62 CGGAGTTGTGGGC-TTTAAAAAAAGTGCCACGGAGT
*
74615 TGTGGGCTTTGAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACG
1 TGTGGGCTTT-AAAAGGAA-AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACG
*
74680 GAGTTTGTGGGCTTTAAAGGAAAGGTTGCCACGGAGT
64 GAG-TTGTGGGCTTTAAA--AAAAG-TGCCACGGAGT
* * * *
74717 TGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT-AAAA-AAG--GGTGCCACG
1 TGTGGGCTTTAAA-A-GGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACG
*
74777 GAGTTGTGGGCTTTAAAGGAAAAGGGCCACGGAGT
64 GAGTTGTGGGCTTTAAA--AAAAGTGCCACGGAGT
74812 TGTGGGCTTT
1 TGTGGGCTTT
74822 GAAGAAAAAA
Statistics
Matches: 591, Mismatches: 54, Indels: 93
0.80 0.07 0.13
Matches are distributed among these distances:
92 24 0.04
93 5 0.01
94 81 0.14
95 39 0.07
96 83 0.14
97 111 0.19
98 12 0.02
99 64 0.11
100 103 0.17
101 38 0.06
102 21 0.04
105 10 0.02
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.22
Consensus pattern (96 bp):
TGTGGGCTTTAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGA
GTTGTGGGCTTTAAAAAAAGTGCCACGGAGT
Found at i:74870 original size:29 final size:30
Alignment explanation
Indices: 74823--74909 Score: 113
Period size: 29 Copynumber: 2.9 Consensus size: 30
74813 GTGGGCTTTG
* *
74823 AAGAAAAAATGCCATTGAGTCGTGGCCCT-
1 AAGAAAAAATGCCACTGAGTCGTGGACCTA
* * *
74852 GAGACAAAATGCCACTGAGTCGTGGACTTA
1 AAGAAAAAATGCCACTGAGTCGTGGACCTA
74882 AAGAAAAAGATGCCACTGAGTCGTGGAC
1 AAGAAAAA-ATGCCACTGAGTCGTGGAC
74910 TTTGAGCAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
29 24 0.49
30 6 0.12
31 19 0.39
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (30 bp):
AAGAAAAAATGCCACTGAGTCGTGGACCTA
Found at i:74895 original size:60 final size:62
Alignment explanation
Indices: 74823--74943 Score: 160
Period size: 60 Copynumber: 2.0 Consensus size: 62
74813 GTGGGCTTTG
*
74823 AAGAAAAAATGCCATTGAGTCGTGG-CCCTGAGACA-A-AATGCCACT-GAGTCGTGGACTTA
1 AAGAAAAAATGCCACTGAGTCGTGGACCCTGAG-CAGAGAATGCCACTAGAGTCGTGGACTTA
** *
74882 AAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTAGAGTCGTGGACTT
1 AAGAAAAA-ATGCCACTGAGTCGTGGACCCTGAGCAGAGAATGCCACTAGAGTCGTGGACTT
74944 TTTTTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
59 8 0.15
60 18 0.34
61 6 0.11
62 8 0.15
63 13 0.25
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.21
Consensus pattern (62 bp):
AAGAAAAAATGCCACTGAGTCGTGGACCCTGAGCAGAGAATGCCACTAGAGTCGTGGACTTA
Found at i:74898 original size:31 final size:31
Alignment explanation
Indices: 74050--74911 Score: 256
Period size: 34 Copynumber: 26.8 Consensus size: 31
74040 AGGAAGGGAG
*
74050 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTCGTGGACTT-AAA--GAA
* * *
74084 AAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTCGTGGAC-TT--AAAGAA
* * * *
74119 GAAGGTGCCACGGAGTTGTGGGCTTTAAAG--
1 AAAGATGCCACGGAGTCGTGGAC-TTAAAGAA
*
74149 --AG-TGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGATGCCACGGAGTCGTGGAC-TT-AAA-GAA
* ** *
74180 AAAGGGGTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA--GATGCCACGGAGTCGTGGACTTA-AA-GAA
* * * *
74215 AAAGAGTGCCACAGAGTTGTGGGCTTTTAA-AA
1 AAAGA-TGCCACGGAGTCGTGGAC-TTAAAGAA
* *
74247 AAAG-TGCCACGGAGTTGTGGGCTTTGAAAGAA
1 AAAGATGCCACGGAGTCGTGGAC-TT-AAAGAA
* * * *
74279 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTCGTGGAC-TT--AAAGAA
* * * * *
74313 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGGA
1 AAAGATGCCACGGAGTCGTGGAC-TTAAAGAA
* *
74345 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGA
1 AAAGATGCCACGGAGTCGTGGACTTAAAGA--A
* * * * *
74378 AAAAAGTGCCACGGAATTGTGGGCTT---TAA
1 AAAGA-TGCCACGGAGTCGTGGACTTAAAGAA
* * * * *
74407 AAGGGTGCCACGGAGTTGTGGGCTTTAAAGGA
1 AAAGATGCCACGGAGTCGTGGAC-TTAAAGAA
* * *
74439 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 AAAGATGCCACGGAGTCGTGGAC-TT--AAAGAA
* * * * *
74473 GAAGGTGCCACGGAGTTGTGGGCTTTAAG--
1 AAAGATGCCACGGAGTCGTGGACTTAAAGAA
*
74502 --AG-TGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGATGCCACGGAGTCGTGGAC-TT-AAA-GAA
* ** *
74533 AAAGGGTTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA--GATGCCACGGAGTCGTGGACTTA-AA-GAA
* * * *
74568 AAAGAGTGCCACAGAGTTGTGGGCTTTTAA-AA
1 AAAGA-TGCCACGGAGTCGTGGAC-TTAAAGAA
* *
74600 AAAG-TGCCACGGAGTTGTGGGCTTTGAAAAAGAA
1 AAAGATGCCACGGAGTCGTGGAC-TT---AAAGAA
* * * *
74634 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTCGTGGAC-TT--AAAGAA
* * * * *
74668 GAAGGTGCCACGGAGTTTGTGGGCTTTAAAGGA
1 AAAGATGCCACGGAG-TCGTGGAC-TTAAAGAA
* * *
74701 AAGGTTGCCACGGAGTTGTGGACTTAAAGATGA
1 AAAGATGCCACGGAGTCGTGGACTTAAAGA--A
* * * * *
74734 AAAAAGTGCCACGGAATTGTGGGCTTTAA-AA
1 AAAGA-TGCCACGGAGTCGTGGACTTAAAGAA
* * * * *
74765 AAGGGTGCCACGGAGTTGTGGGCTTTAAAGGA
1 AAAGATGCCACGGAGTCGTGGAC-TTAAAGAA
* * * *
74797 AAAG-GGCCACGGAGTTGTGGGCTTTGAAGAA
1 AAAGATGCCACGGAGTCGTGGAC-TTAAAGAA
** * * * *
74828 AAA-ATGCCATTGAGTCGTGGCCCT-GAGAC
1 AAAGATGCCACGGAGTCGTGGACTTAAAGAA
*
74857 AAA-ATGCCACTGAGTCGTGGACTTAAAGAA
1 AAAGATGCCACGGAGTCGTGGACTTAAAGAA
*
74887 AAAGATGCCACTGAGTCGTGGACTT
1 AAAGATGCCACGGAGTCGTGGACTT
74912 TGAGCAGAGA
Statistics
Matches: 692, Mismatches: 81, Indels: 113
0.78 0.09 0.13
Matches are distributed among these distances:
26 17 0.02
27 24 0.03
28 24 0.03
29 31 0.04
30 64 0.09
31 86 0.12
32 84 0.12
33 54 0.08
34 188 0.27
35 82 0.12
36 34 0.05
37 4 0.01
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.21
Consensus pattern (31 bp):
AAAGATGCCACGGAGTCGTGGACTTAAAGAA
Found at i:74940 original size:32 final size:31
Alignment explanation
Indices: 74565--74944 Score: 132
Period size: 31 Copynumber: 11.9 Consensus size: 31
74555 GGCTTAGAAG
* * *
74565 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTTAA
1 GAAAAAGA-TGCCACTGAGTCGTGGAC-TTTAA
* * *
74598 -AAAAAG-TGCCACGGAGTTGTGGGCTTTGAA
1 GAAAAAGATGCCACTGAGTCGTGGACTTT-AA
* * *
74628 -AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
1 GAAA-AAG-A--TGCCACTGAGTCGTGGACTTTAA
* * *
74662 -AAAGAAGAAGGTGCCACGGAGTTTGTGGGCTTTAAA
1 GAAA-AAG-A--TGCCACTGAG-TCGTGGACTTT-AA
* * * * * *
74698 GGAAAGGTTGCCACGGAGTTGTGGACTTAAA
1 GAAAAAGATGCCACTGAGTCGTGGACTTTAA
* * * * *
74729 GATGAAAAAAGTGCCACGGAATTGTGGGCTTTAA
1 GA--AAAAGA-TGCCACTGAGTCGTGGACTTTAA
* * * * *
74763 -AAAAGGGTGCCACGGAGTTGTGGGCTTTAAA
1 GAAAAAGATGCCACTGAGTCGTGGACTTT-AA
* * * * *
74794 GGAAAAG-GGCCACGGAGTTGTGGGCTTTGAA
1 GAAAAAGATGCCACTGAGTCGTGGACTTT-AA
* ** *
74825 GAAAAA-ATGCCATTGAGTCGTGG-CCCTGA
1 GAAAAAGATGCCACTGAGTCGTGGACTTTAA
* *
74854 GACAAA-ATGCCACTGAGTCGTGGACTTAAA
1 GAAAAAGATGCCACTGAGTCGTGGACTTTAA
*
74884 GAAAAAGATGCCACTGAGTCGTGGACTTTGA
1 GAAAAAGATGCCACTGAGTCGTGGACTTTAA
* *
74915 G-CAGAGATTGCCACTAGAGTCGTGGACTTT
1 GAAAAAGA-TGCCACT-GAGTCGTGGACTTT
74945 TTTTTTTTTT
Statistics
Matches: 288, Mismatches: 40, Indels: 39
0.78 0.11 0.11
Matches are distributed among these distances:
29 25 0.09
30 55 0.19
31 80 0.28
32 33 0.11
33 14 0.05
34 43 0.15
35 32 0.11
36 4 0.01
37 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.22
Consensus pattern (31 bp):
GAAAAAGATGCCACTGAGTCGTGGACTTTAA
Found at i:76006 original size:15 final size:15
Alignment explanation
Indices: 75972--76005 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
75962 CTCACCGAGA
75972 TTTTTCTGTTTTGTT
1 TTTTTCTGTTTTGTT
*
75987 TTTTTCT-TTTTCTT
1 TTTTTCTGTTTTGTT
76001 TTTTT
1 TTTTT
76006 TGTGTTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTTCTGTTTTGTT
Done.