Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold120
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: 299982
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.31
Warning! 45885 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4470 original size:20 final size:19
Alignment explanation
Indices: 4442--4510 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
4432 AGACATAATG
*
4442 TATCAATACATTGAAGAATA
1 TATCGATACATTGAA-AATA
* * *
4462 TATCGATACATTCATACATG
1 TATCGATACATTGA-AAATA
*
4482 TATCGATATATTGAAAA-A
1 TATCGATACATTGAAAATA
4500 TATCGATACAT
1 TATCGATACAT
4511 CTGGATAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 10 0.26
19 2 0.05
20 26 0.67
21 1 0.03
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (19 bp):
TATCGATACATTGAAAATA
Found at i:4483 original size:40 final size:37
Alignment explanation
Indices: 4435--4510 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 37
4425 GGTAAAAAGA
4435 CATAATGTATCAATACATTGAAGAATATATCGATACATT
1 CATAATGTATCAATACATTGAA-AA-ATATCGATACATT
* *
4474 CATACATGTATCGATATATTGAAAAATATCGATACAT
1 CATA-ATGTATCAATACATTGAAAAATATCGATACAT
4511 CTGGATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 12 0.35
39 6 0.18
40 16 0.47
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (37 bp):
CATAATGTATCAATACATTGAAAAATATCGATACATT
Found at i:5051 original size:29 final size:29
Alignment explanation
Indices: 5001--5063 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
4991 ATTACTTTTA
*
5001 ATTTTAAAATAAATTATCAAAATA-ATATT
1 ATTTTAAAATAAATTATAAAAATATA-ATT
*
5030 ATTTTAAAAT-TATTAATAAAAATATAATT
1 ATTTTAAAATAAATT-ATAAAAATATAATT
5059 ATTTT
1 ATTTT
5064 CCCGTGTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.10
29 26 0.87
30 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTTAAAATAAATTATAAAAATATAATT
Found at i:5398 original size:14 final size:15
Alignment explanation
Indices: 5374--5402 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5364 TAAGGCATAA
5374 AAATAATATGAATAT
1 AAATAATATGAATAT
5389 AAAT-ATATGAATAT
1 AAATAATATGAATAT
5403 TTTAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
AAATAATATGAATAT
Found at i:6492 original size:29 final size:29
Alignment explanation
Indices: 6452--6510 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
6442 ATGGGCAAAT
6452 TAATAGTATTTTGATAA-ATAGTTTTAAAA
1 TAATAGTATTTTGATAATATA-TTTTAAAA
* *
6481 TAATATTATTTTGATAATTTATTTTAAAA
1 TAATAGTATTTTGATAATATATTTTAAAA
6510 T
1 T
6511 TAAAGATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (29 bp):
TAATAGTATTTTGATAATATATTTTAAAA
Found at i:6582 original size:8 final size:8
Alignment explanation
Indices: 6569--6614 Score: 56
Period size: 8 Copynumber: 5.4 Consensus size: 8
6559 ACAGACATTA
6569 TTTTATTT
1 TTTTATTT
6577 TTTTATTT
1 TTTTATTT
6585 TTTTGAATTT
1 TTTT--ATTT
*
6595 TTTGAATTT
1 TTT-TATTT
6604 TTTTATTT
1 TTTTATTT
6612 TTT
1 TTT
6615 AATTAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 19 0.58
9 7 0.21
10 7 0.21
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (8 bp):
TTTTATTT
Found at i:6947 original size:42 final size:42
Alignment explanation
Indices: 6896--6982 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
6886 AATAAGAGCA
6896 AAAGATAATCTTAATTATGGCTTGAAGGCATTTTTAAGACTC
1 AAAGATAATCTTAATTATGGCTTGAAGGCATTTTTAAGACTC
6938 AAAGATAATCTTAATTATGGCTTGAAGGCATTTTTAAGACTC
1 AAAGATAATCTTAATTATGGCTTGAAGGCATTTTTAAGACTC
6980 AAA
1 AAA
6983 AGAGTCCTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.34
Consensus pattern (42 bp):
AAAGATAATCTTAATTATGGCTTGAAGGCATTTTTAAGACTC
Found at i:7401 original size:2 final size:2
Alignment explanation
Indices: 7394--7439 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
7384 TTTAATAGTT
7394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7436 TA TA
1 TA TA
7440 AACTTGTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7915 original size:13 final size:13
Alignment explanation
Indices: 7899--7938 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
7889 TATTAAAAAC
7899 AAATATTGTTTTA
1 AAATATTGTTTTA
*
7912 AAAT-TT-TTTAA
1 AAATATTGTTTTA
7923 AAATATTGTTTTA
1 AAATATTGTTTTA
7936 AAA
1 AAA
7939 ATAATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 8 0.35
12 4 0.17
13 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (13 bp):
AAATATTGTTTTA
Found at i:7936 original size:14 final size:14
Alignment explanation
Indices: 7899--7941 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
7889 TATTAAAAAC
7899 AAATATTGTTTT--
1 AAATATTGTTTTAA
7911 AAA-ATT-TTTTAA
1 AAATATTGTTTTAA
7923 AAATATTGTTTTAA
1 AAATATTGTTTTAA
7937 AAATA
1 AAATA
7942 ATTATTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.15
11 3 0.11
12 6 0.22
13 3 0.11
14 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (14 bp):
AAATATTGTTTTAA
Found at i:14038 original size:13 final size:13
Alignment explanation
Indices: 14005--14047 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
13995 ATATCATGTA
*
14005 TATTTATTAAATCAA
1 TATTTATTAAA--AT
14020 TATTTATTAAAAT
1 TATTTATTAAAAT
*
14033 TATTTAATAAAAT
1 TATTTATTAAAAT
14046 TA
1 TA
14048 ACATAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
TATTTATTAAAAT
Found at i:14093 original size:22 final size:23
Alignment explanation
Indices: 14050--14117 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 23
14040 TAAAATTAAC
*
14050 ATAAATAATTTAATTTATTAATA
1 ATAAATAATTTAATATATTAATA
*
14073 ATAAA-AATTTAATA-ATATAATT
1 ATAAATAATTTAATATAT-TAATA
* * *
14095 TTATATAATTAAATATTATTAAT
1 ATAAATAATTTAATA-TATTAAT
14118 TTACAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
21 2 0.06
22 15 0.42
23 13 0.36
24 4 0.11
25 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAAATAATTTAATATATTAATA
Found at i:14863 original size:27 final size:27
Alignment explanation
Indices: 14808--14861 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
14798 GTTATAAATT
*
14808 ACTAATATATATGAATATAAATATAAA
1 ACTAATATATATGAATATAAATAAAAA
* *
14835 ACTAATATATAT-TATATAATTAAAAA
1 ACTAATATATATGAATATAAATAAAAA
14861 A
1 A
14862 ACCGAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
ACTAATATATATGAATATAAATAAAAA
Found at i:17462 original size:13 final size:13
Alignment explanation
Indices: 17446--17519 Score: 62
Period size: 13 Copynumber: 5.6 Consensus size: 13
17436 TATAATTTAA
17446 AAAATATTAAATT
1 AAAATATTAAATT
17459 AAAATATTAAATT
1 AAAATATTAAATT
* *
17472 ATTAATATAAAAATT
1 A-AAATAT-TAAATT
*
17487 AAAAATATT-AACT
1 -AAAATATTAAATT
* *
17500 AATATA-AAAATT
1 AAAATATTAAATT
17512 AAAATATT
1 AAAATATT
17520 CCTTTATTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
12 13 0.28
13 17 0.37
14 5 0.11
15 10 0.22
16 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATATTAAATT
Found at i:17469 original size:8 final size:8
Alignment explanation
Indices: 17456--17519 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
17446 AAAATATTAA
17456 ATTAAAAT
1 ATTAAAAT
*
17464 ATTAAATT
1 ATTAAAAT
17472 ATT--AAT
1 ATTAAAAT
17478 A-TAAAA-
1 ATTAAAAT
17484 ATTAAAAAT
1 ATT-AAAAT
17493 ATTAACTAAT
1 ATTAA--AAT
17503 A-TAAAA-
1 ATTAAAAT
17509 ATTAAAAT
1 ATTAAAAT
17517 ATT
1 ATT
17520 CCTTTATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
5 1 0.02
6 5 0.11
7 10 0.22
8 19 0.42
9 6 0.13
10 4 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTAAAAT
Found at i:17740 original size:22 final size:22
Alignment explanation
Indices: 17708--17751 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
17698 TAAAAATATA
*
17708 TTTTATAT-AAATTAATATTTT
1 TTTTATATAAAATCAATATTTT
17729 TTTTAATATAAAATCAATATTTT
1 TTTT-ATATAAAATCAATATTTT
17752 AACAAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 12 0.60
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTATATAAAATCAATATTTT
Found at i:18869 original size:16 final size:16
Alignment explanation
Indices: 18848--18898 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
18838 TATATTAAAA
18848 ATATAATTATTTTAAT
1 ATATAATTATTTTAAT
*
18864 ATATAAATATTTTAAT
1 ATATAATTATTTTAAT
18880 A-ATTAATTAATATTTAAT
1 ATA-TAATT-AT-TTTAAT
18898 A
1 A
18899 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 1 0.03
16 20 0.67
17 2 0.07
18 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAATTATTTTAAT
Found at i:19064 original size:2 final size:2
Alignment explanation
Indices: 19059--19090 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19049 CTCTTTTTTC
19059 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19091 GCTACTCTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:19306 original size:30 final size:27
Alignment explanation
Indices: 19252--19323 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
19242 TAAAAAATAT
*
19252 TTAAATATATACATATATTATAATTTTG
1 TTAAATATATA-ATATATCATAATTTTG
19280 TTAAATATATAATACTAATCATTAATTTTG
1 TTAAATATATAATA-T-ATCA-TAATTTTG
*
19310 TTAAA-AAATAATAT
1 TTAAATATATAATAT
19324 GATATTAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 3 0.08
28 13 0.33
29 10 0.26
30 13 0.33
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (27 bp):
TTAAATATATAATATATCATAATTTTG
Found at i:20621 original size:66 final size:61
Alignment explanation
Indices: 20551--20670 Score: 143
Period size: 62 Copynumber: 1.9 Consensus size: 61
20541 TAGAGTTATA
20551 TAAATAA-TTTAAAAATAAAACTTACTTTTTTACTTATTCTCTATTTAAATAAATATTACGTACA
1 TAAATAATTTTAAAAA-AAAAC-TA-TTTTTTACTT-TT-T-TATTTAAATAAATATTACGTACA
20615 GT
60 GT
***
20617 TAAATAATTTTTTTTAAAAAACTATTTTTTACTTTTTTATTTAAATAAATATTA
1 TAAATAA-TTTTAAAAAAAAACTATTTTTTACTTTTTTATTTAAATAAATATTA
20671 TATTAAATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
62 17 0.35
63 1 0.02
64 2 0.04
65 10 0.20
66 9 0.18
67 5 0.10
68 5 0.10
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (61 bp):
TAAATAATTTTAAAAAAAAACTATTTTTTACTTTTTTATTTAAATAAATATTACGTACAGT
Found at i:20690 original size:16 final size:16
Alignment explanation
Indices: 20649--20705 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
20639 TATTTTTTAC
20649 TTTTTTATTTAAATAAA
1 TTTTTTA-TTAAATAAA
* *
20666 TATTATATTAAATAAA
1 TTTTTTATTAAATAAA
* *
20682 TTTTTTATT-TATATA
1 TTTTTTATTAAATAAA
20697 TTTTTTATT
1 TTTTTTATT
20706 TTTTATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 13 0.38
16 16 0.47
17 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTTATTAAATAAA
Found at i:20705 original size:7 final size:7
Alignment explanation
Indices: 20681--20714 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
20671 TATTAAATAA
20681 ATTTTTT
1 ATTTTTT
*
20688 ATTTATAT
1 ATTT-TTT
20696 ATTTTTT
1 ATTTTTT
20703 ATTTTTT
1 ATTTTTT
20710 ATTTT
1 ATTTT
20715 ACCCACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:21139 original size:25 final size:25
Alignment explanation
Indices: 21109--21172 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
21099 AATCTTTTAA
*
21109 AATAAATATAAATAATTTTATTTTT
1 AATAAATATAAATAATTTGATTTTT
*
21134 AATAAA-ATAATATTATTTGATTTTT
1 AATAAATATAA-ATAATTTGATTTTT
21159 AATAATATATAAAT
1 AATAA-ATATAAAT
21173 TTATATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 4 0.12
25 23 0.68
26 3 0.09
27 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
AATAAATATAAATAATTTGATTTTT
Found at i:21143 original size:20 final size:21
Alignment explanation
Indices: 21113--21151 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
21103 TTTTAAAATA
*
21113 AATATAAATAATTTTATTTTT
1 AATATAAATAATATTATTTTT
21134 AATA-AAATAATATTATTT
1 AATATAAATAATATTATTT
21152 GATTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATAAATAATATTATTTTT
Found at i:21181 original size:34 final size:34
Alignment explanation
Indices: 21143--21247 Score: 137
Period size: 34 Copynumber: 3.2 Consensus size: 34
21133 TAATAAAATA
*
21143 ATATTATTTGATTT-TTAATAATATATAAATTTAT
1 ATATTATTT-ATTTATTTATAATATATAAATTTAT
*
21177 ATATTATTAATTTATTTATAATATATAAA--TA-
1 ATATTATTTATTTATTTATAATATATAAATTTAT
* *
21208 AAATTATTTATTTATTTATAATATACAAATTTAT
1 ATATTATTTATTTATTTATAATATATAAATTTAT
21242 ATATTA
1 ATATTA
21248 ATAATAAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 26 0.43
32 2 0.03
33 6 0.10
34 27 0.44
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (34 bp):
ATATTATTTATTTATTTATAATATATAAATTTAT
Found at i:21187 original size:23 final size:24
Alignment explanation
Indices: 21160--21253 Score: 73
Period size: 23 Copynumber: 4.2 Consensus size: 24
21150 TTGATTTTTA
21160 ATAATATATAAATTTATATATTAT
1 ATAATATATAAATTTATATATTAT
21184 -TAAT-T-T--ATTTATA-A-TAT
1 ATAATATATAAATTTATATATTAT
* *
21201 ATAA-ATAAAATTATTTATTTATT-T
1 ATAATATATAA--ATTTATATATTAT
*
21225 ATAATATACAAATTTATATATTA-
1 ATAATATATAAATTTATATATTAT
21248 ATAATA
1 ATAATA
21254 AATTAAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 23
0.67 0.05 0.28
Matches are distributed among these distances:
17 3 0.05
18 5 0.09
19 7 0.13
21 1 0.02
22 1 0.02
23 26 0.47
24 6 0.11
25 6 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAATATATAAATTTATATATTAT
Found at i:21221 original size:31 final size:31
Alignment explanation
Indices: 21138--21237 Score: 121
Period size: 31 Copynumber: 3.1 Consensus size: 31
21128 ATTTTTAATA
*
21138 AAATAATATTATTTGATTT-TTAATAATATAT
1 AAATAATATTATTT-ATTTATTTATAATATAT
*
21169 AAATTTATATATTATTAATTTATTTATAATATAT
1 AAA--TA-ATATTATTTATTTATTTATAATATAT
* *
21203 AAATAAAATTATTTATTTATTTATAATATAC
1 AAATAATATTATTTATTTATTTATAATATAT
21234 AAAT
1 AAAT
21238 TTATATATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
31 30 0.50
32 2 0.03
33 6 0.10
34 22 0.37
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
AAATAATATTATTTATTTATTTATAATATAT
Found at i:21275 original size:65 final size:65
Alignment explanation
Indices: 21138--21264 Score: 170
Period size: 65 Copynumber: 2.0 Consensus size: 65
21128 ATTTTTAATA
* * * * *
21138 AAATAATATTATTTGATTTTTAATAATATATAAATTTATATATTATTAATTTATTTATAATATAT
1 AAATAAAATTATTTGATTTTTAATAATATACAAATTTATATATTAATAATTAAATTATAATATAT
*
21203 AAATAAAATTATTT-ATTTATTTATAATATACAAATTTATATATTAATAA-TAAATTA-AATATA
1 AAATAAAATTATTTGATTT-TTAATAATATACAAATTTATATATTAATAATTAAATTATAATATA
21265 AATAATTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 6 0.11
64 9 0.16
65 40 0.73
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (65 bp):
AAATAAAATTATTTGATTTTTAATAATATACAAATTTATATATTAATAATTAAATTATAATATAT
Found at i:22535 original size:20 final size:19
Alignment explanation
Indices: 22507--22558 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
22497 TTTTGTCTAT
*
22507 TATAAAATTTTATATTTTTA
1 TATATAATTTTATA-TTTTA
*
22527 TATATAATTATATATTTTA
1 TATATAATTTTATATTTTA
22546 TA-ATAATTATTAT
1 TATATAATT-TTAT
22559 TATTATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 12 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATAATTTTATATTTTA
Found at i:22562 original size:20 final size:19
Alignment explanation
Indices: 22506--22567 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
22496 ATTTTGTCTA
22506 TTATAA-AATT-TTATATTT
1 TTATAATAATTATTATA-TT
22524 TTATATATAATTA-TATATT
1 TTATA-ATAATTATTATATT
*
22543 TTATAATAATTATTAT-TA
1 TTATAATAATTATTATATT
22561 TTATAAT
1 TTATAAT
22568 TTTATTTTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
18 20 0.51
19 11 0.28
20 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATAATAATTATTATATT
Found at i:23201 original size:56 final size:56
Alignment explanation
Indices: 23138--23245 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
23128 CTCTTTCCTA
*
23138 CTTTCTTTGGCTATTTC-TTTATTACAAGTCAAGGTCTTCCAATAACTGGTTTCTTT
1 CTTTCTTTGGCTA-TTCGTTTAGTACAAGTCAAGGTCTTCCAATAACTGGTTTCTTT
23194 CTTTCTTTGGCTATTCGTTTAGTACAAGTCAAGGTCTTCCAATAACTGGTTT
1 CTTTCTTTGGCTATTCGTTTAGTACAAGTCAAGGTCTTCCAATAACTGGTTT
23246 TCTGGCCAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
55 3 0.06
56 47 0.94
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.45
Consensus pattern (56 bp):
CTTTCTTTGGCTATTCGTTTAGTACAAGTCAAGGTCTTCCAATAACTGGTTTCTTT
Found at i:24136 original size:19 final size:19
Alignment explanation
Indices: 24028--24136 Score: 53
Period size: 19 Copynumber: 5.5 Consensus size: 19
24018 TTATTTATAT
* * *
24028 TTATATAAAATTAAATTAA
1 TTATATATAATTATATTTA
* * *
24047 TTTTATATAATTTTATTATT
1 TTATATATAATTATATT-TA
* *
24067 TTATATATGATTA-ATATA
1 TTATATATAATTATATTTA
*
24085 TTA-ATA-AATTAACTATTAAA
1 TTATATATAATT-A-TATT-TA
24105 TTGAGTAATATAATTATATTTA
1 TT-A-T-ATATAATTATATTTA
24127 TTATATATAA
1 TTATATATAA
24137 AAAATTTTGA
Statistics
Matches: 65, Mismatches: 15, Indels: 20
0.65 0.15 0.20
Matches are distributed among these distances:
16 3 0.05
17 4 0.06
18 4 0.06
19 23 0.35
20 14 0.22
21 2 0.03
22 3 0.05
23 4 0.06
24 4 0.06
25 4 0.06
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (19 bp):
TTATATATAATTATATTTA
Found at i:25349 original size:29 final size:28
Alignment explanation
Indices: 25317--25381 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
25307 AGTATTAGAT
*
25317 TAAAATATGTATATA-TATAATATATAAAA
1 TAAAATATATATATATTA-AATA-ATAAAA
*
25346 TAAAATATATTTATATTAAATAATAAAA
1 TAAAATATATATATATTAAATAATAAAA
25374 TATAAATA
1 TA-AAATA
25382 AAATTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 8 0.25
29 22 0.69
30 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
TAAAATATATATATATTAAATAATAAAA
Found at i:25378 original size:35 final size:35
Alignment explanation
Indices: 25333--25431 Score: 108
Period size: 35 Copynumber: 3.1 Consensus size: 35
25323 ATGTATATAT
*
25333 ATAATATATAAAATAAAATATATTTATATTAAATA
1 ATAAAATATAAAATAAAATATATTTATATTAAATA
*
25368 ATAAAATAT-AAATAAAATTATATTTATGTTAAAT-
1 ATAAAATATAAAATAAAA-TATATTTATATTAAATA
25402 A-AAAATA-AAAAT----TA-ATTTATATTAAATA
1 ATAAAATATAAAATAAAATATATTTATATTAAATA
25430 AT
1 AT
25432 TATAAGTTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
27 12 0.21
28 3 0.05
33 10 0.18
34 9 0.16
35 23 0.40
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (35 bp):
ATAAAATATAAAATAAAATATATTTATATTAAATA
Found at i:25404 original size:25 final size:25
Alignment explanation
Indices: 25375--25452 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 25
25365 ATAATAAAAT
*
25375 ATAAATAAAATTATATTTATGTTAA
1 ATAAATAAAATTATATTTATATTAA
25400 ATAAAAATAAAAATTA-ATTTATATTAA
1 AT--AAAT-AAAATTATATTTATATTAA
* *
25427 ATAATTATAAGTTATA-TTATATTAA
1 ATAAATA-AAATTATATTTATATTAA
25452 A
1 A
25453 AATAAATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 1 0.02
25 20 0.44
26 1 0.02
27 16 0.36
28 7 0.16
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
ATAAATAAAATTATATTTATATTAA
Found at i:25436 original size:27 final size:28
Alignment explanation
Indices: 25371--25430 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
25361 TTAAATAATA
* *
25371 AAATATAAAT-AAAATTATATTTATGTT
1 AAATAAAAATAAAAATTATATTTATATT
25398 AAATAAAAATAAAAATTA-ATTTATATT
1 AAATAAAAATAAAAATTATATTTATATT
25425 AAATAA
1 AAATAA
25431 TTATAAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
AAATAAAAATAAAAATTATATTTATATT
Found at i:26175 original size:16 final size:17
Alignment explanation
Indices: 26144--26176 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
26134 TTATGTACAG
*
26144 TTAAATAAATTCTTTTT
1 TTAAATAAATTATTTTT
26161 TTAAA-AAATTATTTTT
1 TTAAATAAATTATTTTT
26177 CTACTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATAAATTATTTTT
Found at i:26657 original size:20 final size:21
Alignment explanation
Indices: 26624--26662 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
26614 TTTAAAAATA
26624 AATATAAATAATTTTATTTTT
1 AATATAAATAATTTTATTTTT
*
26645 AATA-AAATGATTTTATTT
1 AATATAAATAATTTTATTT
26663 GATTTATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
AATATAAATAATTTTATTTTT
Found at i:26694 original size:10 final size:10
Alignment explanation
Indices: 26679--26724 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
26669 TTGATAATAA
26679 ATAAATTTAT
1 ATAAATTTAT
26689 ATAAATTTAT
1 ATAAATTTAT
*
26699 ATATTATTAATAT
1 ATA-AATT--TAT
26712 ATAAATTTAT
1 ATAAATTTAT
26722 ATA
1 ATA
26725 TTATTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 19 0.61
11 3 0.10
12 3 0.10
13 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATAAATTTAT
Found at i:26715 original size:23 final size:23
Alignment explanation
Indices: 26686--26741 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
26676 TAAATAAATT
26686 TATATAAATTTATATATTATTAA
1 TATATAAATTTATATATTATTAA
26709 TATATAAATTTATATATTATTAA
1 TATATAAATTTATATATTATTAA
*
26732 AATATTAAAT
1 TATA-TAAAT
26742 ATAAATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 26 0.84
24 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATAAATTTATATATTATTAA
Found at i:26752 original size:25 final size:24
Alignment explanation
Indices: 26690--26766 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 24
26680 TAAATTTATA
* * *
26690 TAAATTTATATATTATTAATATA-
1 TAAATATAAATATTATTAAAATAT
* *
26713 TAAATTTATATATTATTAAAATAT
1 TAAATATAAATATTATTAAAATAT
** *
26737 TAAATATAAATAATTAAAAAAATTT
1 TAAATATAAAT-ATTATTAAAATAT
26762 TAAAT
1 TAAAT
26767 CTACTAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 22 0.48
24 9 0.20
25 15 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAAATATAAATATTATTAAAATAT
Found at i:27739 original size:66 final size:66
Alignment explanation
Indices: 27657--27780 Score: 167
Period size: 66 Copynumber: 1.9 Consensus size: 66
27647 ATGAAGTGAT
* * * *
27657 ATTATCTAATTAATTAACGGTGTATAAATTTATATATTATTAATACCTCAAATATAAAGAAATGA
1 ATTATCTAATTAATTAACAGTGTATAAAATTATATATTATCAATACATCAAATATAAAGAAATGA
27722 C
66 C
* * * * *
27723 ATTATTTAATTTATTAATAGTGTATAAAATTATATATTATCAATGCATTAAATATAAA
1 ATTATCTAATTAATTAACAGTGTATAAAATTATATATTATCAATACATCAAATATAAA
27781 TCTTTTGAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 49 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (66 bp):
ATTATCTAATTAATTAACAGTGTATAAAATTATATATTATCAATACATCAAATATAAAGAAATGA
C
Found at i:28011 original size:20 final size:19
Alignment explanation
Indices: 27964--28012 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
27954 TATTTTGCTA
*
27964 TTAT-ATAATTTTATATTT
1 TTATAATAATTATATATTT
*
27982 TTACACATAATTATATATATT
1 TTATA-ATAATTATATAT-TT
28003 TTATAATAAT
1 TTATAATAAT
28013 AGTTATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
20 16 0.64
21 6 0.24
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATAATAATTATATATTT
Found at i:28557 original size:2 final size:2
Alignment explanation
Indices: 28546--28587 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
28536 ACATGACAAG
* *
28546 TC TC -C TC TC TC TT TC TC TC TC TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28587 T
1 T
28588 TTGGCTATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:31694 original size:3 final size:3
Alignment explanation
Indices: 31686--31715 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31676 TGAAAAATTG
31686 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31716 TATGATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:34286 original size:13 final size:14
Alignment explanation
Indices: 34248--34288 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
34238 ACACTATATA
34248 AAATAAATAAAAAT
1 AAATAAATAAAAAT
34262 AAATAACA-AAAAAT
1 AAATAA-ATAAAAAT
*
34276 -AATAATTAAAAAT
1 AAATAAATAAAAAT
34289 TAGATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.46
14 12 0.50
15 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:35444 original size:22 final size:22
Alignment explanation
Indices: 35419--35461 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35409 GAAAATTATT
* **
35419 TTATTAAAATTTTGAATTTAAG
1 TTATTAAATTTTAAAATTTAAG
35441 TTATTAAATTTTAAAATTTAA
1 TTATTAAATTTTAAAATTTAA
35462 TTAATTTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTATTAAATTTTAAAATTTAAG
Found at i:35516 original size:15 final size:15
Alignment explanation
Indices: 35455--35536 Score: 57
Period size: 15 Copynumber: 5.7 Consensus size: 15
35445 TAAATTTTAA
*
35455 AATTT-AATTAATTT
1 AATTTGAATTATTTT
* *
35469 AATTTAAATCATTTT
1 AATTTGAATTATTTT
*
35484 GAA--TGAATTAATTT
1 -AATTTGAATTATTTT
*
35498 --TTTGAATTTTTTT
1 AATTTGAATTATTTT
35511 AATTTGAATTATTTT
1 AATTTGAATTATTTT
* *
35526 GATTCGAATTA
1 AATTTGAATTA
35537 ATTCAAGTTC
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
13 9 0.17
14 13 0.25
15 28 0.54
16 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.55
Consensus pattern (15 bp):
AATTTGAATTATTTT
Found at i:43124 original size:20 final size:19
Alignment explanation
Indices: 43074--43151 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
43064 GGTAAACAAA
43074 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* *
43093 GCAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
**
43113 CATACATGTATCGATATGTT
1 CATA-ATGTATCGATACATT
* *
43133 GAAAAATGTATCGATACAT
1 -CATAATGTATCGATACAT
43152 CTGGGTAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 3 0.07
20 41 0.89
21 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:43145 original size:40 final size:39
Alignment explanation
Indices: 43074--43151 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
43064 GGTAAACAAA
* *
43074 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
** *
43113 CATACATGTATCGATATGTTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
43152 CTGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:43854 original size:28 final size:28
Alignment explanation
Indices: 43708--44609 Score: 802
Period size: 28 Copynumber: 31.3 Consensus size: 28
43698 TTTTTTAAAA
* *
43708 AAAATGTGCCACTAACTTGTGTAGGCTTTG
1 AAAAGGTGCCACTGACTTGTG--GGCTTTG
* * *
43738 AAAAAAGTTACCACTGACACGTGTGGGCTTTG
1 --AAAAGGTGCCACTG--ACTTGTGGGCTTTG
* * *
43770 AAAAGAGTTACTACTGGCTTGTGGGCTTTG
1 AAAAG-G-TGCCACTGACTTGTGGGCTTTG
* *
43800 AAAAGAGTGTCACTGACTTGTGAGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
43829 AAAAGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
43857 AATAGATGCCACTAACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
43885 AAAAAGTGCCATTGACTTGTAGGC-TTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * **
43912 AAAAAGTACCACAAACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
43940 AAAAAGTGCCACTGACTTGTGGGC-TTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* **
43967 AAAAAGTGCCACTGACTCATGGGC-TTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
**
43994 AAAAGGTGCCACTGACTCAAT-GGCTTTG
1 AAAAGGTGCCACTGACT-TGTGGGCTTTG
* * *
44022 AAAGGGTGCCACTGGCTCGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
44050 AAAGGAGTGCCACTGACTTGCGTGGGCTTT-
1 AAAAG-GTGCCACTGACTT--GTGGGCTTTG
44080 AAAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAA-GGTGCCACTGACTT--GTGGGCTTTG
44111 -AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* *
44139 -AAAGAGTGTCACTGACTCGTGGGC-TTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
*
44166 AAAATGTGCCACTGACTTGCGTGGGCTTT-
1 AAAAGGTGCCACTGACTT--GTGGGCTTTG
44195 AAAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAA-GGTGCCACTGACTT--GTGGGCTTTG
* * *
44226 -AACGGATACCACTGACTTGTAGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
*
44254 -AAAGAGTGCCACTGACTCGTGGGC-TTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
**
44281 AAAATATGCCACTGACTTGCGTGGGCTTT-
1 AAAAGGTGCCACTGACTT--GTGGGCTTTG
*
44310 AAAAGGGTACCACTGACTTGCGTGGGCTTT-
1 AAAA-GGTGCCACTGACTT--GTGGGCTTTG
44340 AAAAGGGTGCCACTGACTTGCGTGGGCTTT-
1 AAAA-GGTGCCACTGACTT--GTGGGCTTTG
44370 AAAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
*
44399 -AAAGAGTGCCACTGACTCGTGGGC-TTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
* *
44426 AAAATGTGCCACTGACTTGCGCGGGCTTT-
1 AAAAGGTGCCACTGACTT--GTGGGCTTTG
44455 AAAAGGGTGCCACTGACTTGCGTGGGCTTT-
1 AAAA-GGTGCCACTGACTT--GTGGGCTTTG
44485 AAAAGGAGTGCCACTGACTTGCGTGGGCTTTG
1 AAAA-G-GTGCCACTGACTT--GTGGGCTTTG
*
44517 -AAAGGATGCCACTGGCTTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* *
44545 -AAAGAGTGCCACTAACTCGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
**
44573 AAAAAGGTGCCACTGACTCATGGGCTTTG
1 -AAAAGGTGCCACTGACTTGTGGGCTTTG
44602 AAAAGGTG
1 AAAAGGTG
44610 AAAGGGTTGA
Statistics
Matches: 752, Mismatches: 76, Indels: 88
0.82 0.08 0.10
Matches are distributed among these distances:
27 113 0.15
28 257 0.34
29 94 0.12
30 221 0.29
31 37 0.05
32 24 0.03
34 6 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (28 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTG
Found at i:44214 original size:115 final size:115
Alignment explanation
Indices: 43782--44604 Score: 850
Period size: 115 Copynumber: 7.2 Consensus size: 115
43772 AAGAGTTACT
* * * * *
43782 ACTGGCTTGTGGGCTTTGAAAAGAGTGTCACTGACTTGTGAGCTTTGAAAAGGTGCCACTGACTT
1 ACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAATGTGCCACTGACTT
* * * *
43847 -GTGGGCTTTGAATA-GATGCCACTAACTT--GTGGGCTTTGAAA-AAGTGCC
65 CGTGGGCTTT-AAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGA-TGCC
* * * * ** * *
43895 ATTGACTTGTAGGC-TTGAAAAAGTACCACAAACTTGTGGGCTTTGAAAAAGTGCCACTGACTT-
1 ACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAATGTGCCACTGACTTC
* * *
43958 GTGGGCTTGAAAA-AGTGCCACTGAC-T-CATGGGC-TTGAAAAGG-TGCC
66 GTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTG-AAAGGATGCC
** * *
44004 ACTGACTCAAT-GGCTTTGAAAGGGTGCCACTGGCTCGTGGGCTTTGAAAGGA-GTGCCACTGAC
1 ACTGACT-TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAA--ATGTGCCACTGAC
44067 TTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCC
63 TT-CGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCC
*
44121 ACTGACTTGTGGGCTTTGAAAGAGTGTCACTGACTCGTGGGC-TTGAAAATGTGCCACTGACTTG
1 ACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAATGTGCCACTGACTT-
* *
44185 CGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAACGGATACC
65 CGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCC
* *
44236 ACTGACTTGTAGGCTTTGAAAGAGTGCCACTGACTCGTGGGC-TTGAAAATATGCCACTGACTTG
1 ACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAATGTGCCACTGACTT-
* * *
44300 CGTGGGCTTTAAAAGGGTACCACTGACTTGCGTGGGCTTTAAAAGGGTGCC
65 CGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCC
* *
44351 ACTGACTTGCGTGGGCTTTAAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGA
1 ACTGACTT--GTGGGCTTTGAAAGAG-TGCCACTGACTCGTGGGCTTTGAAA-ATGTGCCACTGA
* * * * *
44414 C-TCGTGGGCTTGAAAA-TGTGCCACTGACTTGCGCGGGCTTTAAAAGGGTGCC
62 CTTCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCC
* *
44466 ACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTTGCGTGGGCTTTG-AAAGGATGCCACT
1 ACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGAC-T-CGTGGGCTTTGAAAATG-TGCCACT
* * * *
44530 GGCTT-GTGGGCTTTGAAAGAGTGCCACTAAC-T-CGTGGGCTTTGAAAAAGG-TGCC
60 GACTTCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTG--AAAGGATGCC
**
44584 ACTGACTCATGGGCTTTGAAA
1 ACTGACTTGTGGGCTTTGAAA
44605 AGGTGAAAGG
Statistics
Matches: 615, Mismatches: 64, Indels: 59
0.83 0.09 0.08
Matches are distributed among these distances:
109 17 0.03
110 48 0.08
111 60 0.10
112 4 0.01
113 23 0.04
114 12 0.02
115 235 0.38
116 55 0.09
117 86 0.14
118 58 0.09
119 17 0.03
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.27
Consensus pattern (115 bp):
ACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAATGTGCCACTGACTTC
GTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCC
Found at i:44219 original size:145 final size:143
Alignment explanation
Indices: 43790--44609 Score: 981
Period size: 145 Copynumber: 5.7 Consensus size: 143
43780 CTACTGGCTT
* * *
43790 GTGGGCTTTGAAAA-GAGTGTCACTGACTTGTGAGCTTTGAAA-AGGTGCCACTGACTTGTGGGC
1 GTGGGCTTT-AAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTCGTGGGC
* * * * * * * *
43853 TTTGAATAGATGCCACTAACTTGTGGGCTTTGAAAAAGTGCCATTGACTT--GTAGGCTTGAAAA
63 -TTGAAAAGGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAA
* * **
43916 -AGTACCACAAACTT--
127 GGGTGCCACTGACTTGC
* * *
43930 GTGGGCTTTGAAAAAG-TGCCACTGACTTGTGGGC-TTGAAAAAGTGCCACTGACTCATGGGCTT
1 GTGGGCTTT-AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTT
* * * *
43993 GAAAAGGTGCCACTGACTCAAT-GGCTTTGAAAGGGTGCCACTGGC-T-CGTGGGCTTTGAAAGG
65 GAAAAGGTGCCACTGACTC-GTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAAGG
44055 AGTGCCACTGACTTGC
129 -GTGCCACTGACTTGC
* *
44071 GTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGC
1 GTGGGCTTTAAAAGGATGCCACTGACTT--GTGGGCTTTGAAAGAG-TGCCACTGACTCGTGGGC
* *
44135 TTTG-AAAGAGTGTCACTGACTCGTGGGC-TTGAAAATGTGCCACTGACTTGCGTGGGCTTTAAA
63 -TTGAAAAG-GTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAA
44198 AGGGTGCCACTGACTTGC
126 AGGGTGCCACTGACTTGC
* * * *
44216 GTGGGCTTTGAACGGATACCACTGACTTGTAGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTG
1 GTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTG
** *
44281 AAAATATGCCACTGACTTGCGTGGGCTTT-AAAAGGGTACCACTGACTTGCGTGGGCTTTAAAAG
66 AAAAGGTGCCACTGAC-T-CGTGGGCTTTGAAAA-GGTGCCACTGACTTGCGTGGGCTTTAAAAG
44345 GGTGCCACTGACTTGC
128 GGTGCCACTGACTTGC
44361 GTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTG
1 GTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTG
* *
44426 AAAATGTGCCACTGACTTGCGCGGGCTTT-AAAAGGGTGCCACTGACTTGCGTGGGCTTTAAAAG
66 AAAAGGTGCCACTGAC-T-CGTGGGCTTTGAAAA-GGTGCCACTGACTTGCGTGGGCTTTAAAAG
44490 GAGTGCCACTGACTTGC
128 G-GTGCCACTGACTTGC
* * *
44507 GTGGGCTTTGAAAGGATGCCACTGGCTTGTGGGCTTTGAAAGAGTGCCACTAACTCGTGGGCTTT
1 GTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGC-TT
*
44572 GAAAAAGGTGCCACTGACTCATGGGCTTTGAAAAGGTG
65 G-AAAAGGTGCCACTGACTCGTGGGCTTTGAAAAGGTG
44610 AAAGGGTTGA
Statistics
Matches: 598, Mismatches: 54, Indels: 50
0.85 0.08 0.07
Matches are distributed among these distances:
136 1 0.00
137 46 0.08
138 24 0.04
139 27 0.05
140 19 0.03
141 22 0.04
142 12 0.02
143 41 0.07
144 55 0.09
145 227 0.38
146 101 0.17
147 8 0.01
148 15 0.03
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (143 bp):
GTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTG
AAAAGGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAAGGGT
GCCACTGACTTGC
Found at i:45895 original size:5 final size:5
Alignment explanation
Indices: 45856--45893 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
45846 TTTCTTAGTT
*
45856 TTTTG TTTTG TTTTG TTTTG TTTTT TTTTG TTTT- TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
45894 TTGGTGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (5 bp):
TTTTG
Found at i:58961 original size:18 final size:20
Alignment explanation
Indices: 58940--58979 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
58930 TGAGATGCTG
58940 GAAATAT-T-AAAAATGCAT
1 GAAATATATAAAAAATGCAT
58958 GAAATATAATAAAAAATGCAT
1 GAAATAT-ATAAAAAATGCAT
58979 G
1 G
58980 GTCAAAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (20 bp):
GAAATATATAAAAAATGCAT
Found at i:59865 original size:20 final size:20
Alignment explanation
Indices: 59840--59889 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
59830 TTTTAACTAG
59840 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
59860 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
*
59880 ATGGATCGAT
1 ATGTATCGAT
59890 TCATCTAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTATTCA
Found at i:59939 original size:20 final size:20
Alignment explanation
Indices: 59910--59984 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
59900 AAAAAGACAT
*
59910 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
59930 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
59950 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
59970 AATGTATCGATACAT
1 AATGTATCGATACAT
59985 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:59978 original size:40 final size:39
Alignment explanation
Indices: 59907--59984 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
59897 GGTAAAAAGA
* *
59907 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
59946 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
59985 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:61088 original size:3 final size:3
Alignment explanation
Indices: 61074--61113 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
61064 ATGCTTCTTT
* * *
61074 TTA TTG TTA TTA TTA TTG TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
61114 CATCATCATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:61091 original size:12 final size:12
Alignment explanation
Indices: 61074--61113 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
61064 ATGCTTCTTT
61074 TTATTGTTATTA
1 TTATTGTTATTA
*
61086 TTATTGTTGTTA
1 TTATTGTTATTA
*
61098 TTATTATTATTA
1 TTATTGTTATTA
61110 TTAT
1 TTAT
61114 CATCATCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (12 bp):
TTATTGTTATTA
Found at i:62082 original size:21 final size:21
Alignment explanation
Indices: 62033--62096 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
62023 AAAATATGTA
*
62033 TTTGGATGAAATG-ATGCAATGG
1 TTTGGATGAAA-GAATGCAAT-T
62055 TTT-GATGAAAGAATGCAATT
1 TTTGGATGAAAGAATGCAATT
* *
62075 TTTGGATGAAAAAATGTAATT
1 TTTGGATGAAAGAATGCAATT
62096 T
1 T
62097 CTATAACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.11
21 30 0.81
22 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTGGATGAAAGAATGCAATT
Found at i:65323 original size:21 final size:21
Alignment explanation
Indices: 65284--65340 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
65274 AAATGTGTAT
*
65284 TTGGATGAAATG-ATACAATGG
1 TTGGATGAAA-GAATGCAATGG
**
65305 TTGGATGAAAGAATGCAATTT
1 TTGGATGAAAGAATGCAATGG
*
65326 TTGGATGAAAAAATG
1 TTGGATGAAAGAATG
65341 TAACTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGGATGAAAGAATGCAATGG
Found at i:65348 original size:21 final size:21
Alignment explanation
Indices: 65305--65348 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
65295 GATACAATGG
* *
65305 TTGGATGAAAGAATGCAATTT
1 TTGGATGAAAAAATGCAACTT
*
65326 TTGGATGAAAAAATGTAACTT
1 TTGGATGAAAAAATGCAACTT
65347 TT
1 TT
65349 ATAACCAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (21 bp):
TTGGATGAAAAAATGCAACTT
Found at i:66174 original size:20 final size:20
Alignment explanation
Indices: 66149--66226 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
66139 ACTGCCAAGG
66149 AAATGTATCGATACATTAAT
1 AAATGTATCGATACATTAAT
* ***
66169 AAATGTATCGATCCATGCTT
1 AAATGTATCGATACATTAAT
*
66189 CAAATTGTATCGATACATTTAT
1 -AAA-TGTATCGATACATTAAT
* *
66211 CATTGTATCGATACAT
1 AAATGTATCGATACAT
66227 CTGGGTTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
20 29 0.63
21 4 0.09
22 13 0.28
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (20 bp):
AAATGTATCGATACATTAAT
Found at i:71192 original size:23 final size:23
Alignment explanation
Indices: 71165--71209 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
71155 TTAACTTGCC
71165 TTAATTTCAACTTAAAACCTACT
1 TTAATTTCAACTTAAAACCTACT
71188 TTAATTTCAACTTAAAACCTAC
1 TTAATTTCAACTTAAAACCTAC
71210 ATTAGCTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAATTTCAACTTAAAACCTACT
Found at i:72136 original size:3 final size:3
Alignment explanation
Indices: 72088--72122 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
72078 AACGCCTTTA
72088 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
72123 GAGAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:73092 original size:2 final size:2
Alignment explanation
Indices: 73085--73119 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
73075 TATTAATCTA
73085 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 A
73120 CACACATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:74044 original size:16 final size:16
Alignment explanation
Indices: 73999--74044 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
73989 CAACCCGAAT
*
73999 AATATTTTTCT-ATTA
1 AATATTTTTATAATTA
*
74014 AAAATTTTATATAATTA
1 AATATTTT-TATAATTA
74031 AATATTTTTATAAT
1 AATATTTTTATAAT
74045 AATAGTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 7 0.27
16 8 0.31
17 11 0.42
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
AATATTTTTATAATTA
Found at i:74200 original size:19 final size:21
Alignment explanation
Indices: 74176--74214 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
74166 AAAATTCAAT
74176 TAAAAACAT-AT-TTAAAAAA
1 TAAAAACATAATATTAAAAAA
*
74195 TAAAAATATAATATTAAAAA
1 TAAAAACATAATATTAAAAA
74215 TCTAGACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 2 0.12
21 7 0.41
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAACATAATATTAAAAAA
Found at i:74390 original size:2 final size:2
Alignment explanation
Indices: 74379--74416 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
74369 CCATGTCGTG
74379 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
74417 TTGGCTATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:75239 original size:23 final size:21
Alignment explanation
Indices: 75213--75265 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
75203 TTTTAATATT
75213 TTTAAATTTATATGTGAGAATCA
1 TTTAAATTTATATGTGA-AAT-A
* * *
75236 TTTAACTTTATTTGTGAAATT
1 TTTAAATTTATATGTGAAATA
75257 TTTAAATTT
1 TTTAAATTT
75266 GATTATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 8 0.31
22 3 0.12
23 15 0.58
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTAAATTTATATGTGAAATA
Found at i:75583 original size:11 final size:11
Alignment explanation
Indices: 75569--75599 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
75559 TCGTTTCATA
75569 TTTTATATTAT
1 TTTTATATTAT
*
75580 TTTTATGTTAT
1 TTTTATATTAT
75591 TTTTATATT
1 TTTTATATT
75600 TTTAGCTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:77606 original size:2 final size:2
Alignment explanation
Indices: 77550--77588 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
77540 TAATTATAGT
77550 TA TA TA TA 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 TA TA TA TA T
77589 GCTATGGTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:78438 original size:3 final size:3
Alignment explanation
Indices: 78384--78424 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
78374 AACACCTTTA
78384 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
78425 GAGAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:80508 original size:18 final size:20
Alignment explanation
Indices: 80485--80523 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
80475 AAAATTCAAT
80485 TAAAAACAT-AT-TTAAAAA
1 TAAAAACATAATATTAAAAA
*
80503 TAAAAATATAATATTAAAAA
1 TAAAAACATAATATTAAAAA
80523 T
1 T
80524 CCAGACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 2 0.11
20 8 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAACATAATATTAAAAA
Found at i:81076 original size:18 final size:18
Alignment explanation
Indices: 81036--81076 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
81026 TATTTAATAT
* *
81036 AATATTATTATTTTAAAT
1 AATATAATTATTTTAAAA
*
81054 CATATAATTATTTTAAAA
1 AATATAATTATTTTAAAA
81072 AATAT
1 AATAT
81077 CCTTAAATCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATAATTATTTTAAAA
Found at i:81924 original size:6 final size:6
Alignment explanation
Indices: 81915--81943 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
81905 TAGATTTAAT
81915 TTTTTA TTTTTA TTTTTA -TTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
81944 AATAATGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:82637 original size:15 final size:15
Alignment explanation
Indices: 82617--82662 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
82607 TTATAAAAAC
82617 TAATAAATAATTATT
1 TAATAAATAATTATT
*
82632 TAATAAA-ATTTAATT
1 TAATAAATAATT-ATT
*
82647 TAA-AAATAATTTTT
1 TAATAAATAATTATT
82661 TA
1 TA
82663 TTATTAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATAAATAATTATT
Found at i:83879 original size:3 final size:3
Alignment explanation
Indices: 83871--83904 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
83861 TGAAAAATTG
*
83871 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
83905 ATGATGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:95086 original size:17 final size:17
Alignment explanation
Indices: 95064--95098 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
95054 AAAATAGTAT
*
95064 ATTTCAGTTTCTATACC
1 ATTTCAATTTCTATACC
*
95081 ATTTCAATTTGTATACC
1 ATTTCAATTTCTATACC
95098 A
1 A
95099 AATGTACTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.46
Consensus pattern (17 bp):
ATTTCAATTTCTATACC
Found at i:95643 original size:20 final size:20
Alignment explanation
Indices: 95604--95643 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
95594 AATTTATATA
*
95604 TTTGTATTATGTTTATTTTT
1 TTTGTATTATGATTATTTTT
*
95624 TTTGTATTAT-ATTATGTTT
1 TTTGTATTATGATTATTTTT
95643 T
1 T
95644 ATATTGCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TTTGTATTATGATTATTTTT
Found at i:95976 original size:26 final size:28
Alignment explanation
Indices: 95947--96012 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 28
95937 TAAAAGGAAA
95947 TAATTTTTTTAACAAA-AAA-TTACATT
1 TAATTTTTTTAACAAACAAATTTACATT
*
95973 TAATTTTTCT--CAAACAAATTTACATT
1 TAATTTTTTTAACAAACAAATTTACATT
95999 TAATTAATTTTTAA
1 TAATT--TTTTTAA
96013 TGACACCGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
24 4 0.12
25 3 0.09
26 21 0.66
28 4 0.12
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (28 bp):
TAATTTTTTTAACAAACAAATTTACATT
Found at i:97113 original size:8 final size:8
Alignment explanation
Indices: 97092--97125 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
97082 TTCTTTTCTA
*
97092 TTTTTAAT
1 TTTTTATT
*
97100 TCTTTATT
1 TTTTTATT
97108 TTTTTATT
1 TTTTTATT
97116 TTTTTATT
1 TTTTTATT
97124 TT
1 TT
97126 GGTGAAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTATT
Found at i:97113 original size:16 final size:16
Alignment explanation
Indices: 97070--97125 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
97060 TTCAATTATC
97070 ATTTATTTTCAATTCTTT
1 ATTT-TTTT-AATTCTTT
97088 -TCTATTTTTAATTCTTT
1 AT-T-TTTTTAATTCTTT
* *
97105 ATTTTTTTATTTTTTT
1 ATTTTTTTAATTCTTT
97121 ATTTT
1 ATTTT
97126 GGTGAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 16 0.48
17 10 0.30
18 6 0.18
19 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTTTAATTCTTT
Found at i:97440 original size:3 final size:3
Alignment explanation
Indices: 97432--97506 Score: 143
Period size: 3 Copynumber: 25.3 Consensus size: 3
97422 ACATGCTTCT
97432 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
97479 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
97507 CTTTTTCTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:98978 original size:62 final size:58
Alignment explanation
Indices: 98912--99045 Score: 148
Period size: 56 Copynumber: 2.3 Consensus size: 58
98902 GTAGCTTTCT
* *
98912 TGGTGTTTGAATTTATCGAAATTGCA-ATTTTCCAATTATCTTTTTTTGTTGTTGGTGTTAAA
1 TGGTGTTAGAATTTAT---AATTGCACATTCT-CAATTATC-TTTTTTGTTGTTGGTGTTAAA
* * *
98974 TGGTGTTAG-ATTT-TATTTTCACATTCTCGATTATCTTTTTTGTTGTTGGTGTTAAA
1 TGGTGTTAGAATTTATAATTGCACATTCTCAATTATCTTTTTTGTTGTTGGTGTTAAA
*
99030 TGGTGTTAGATTTTAT
1 TGGTGTTAGAATTTAT
99046 TTTCACATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
56 30 0.48
57 15 0.24
58 5 0.08
60 1 0.02
61 4 0.06
62 8 0.13
ACGTcount: A:0.20, C:0.07, G:0.19, T:0.54
Consensus pattern (58 bp):
TGGTGTTAGAATTTATAATTGCACATTCTCAATTATCTTTTTTGTTGTTGGTGTTAAA
Found at i:99020 original size:56 final size:57
Alignment explanation
Indices: 98946--99054 Score: 211
Period size: 56 Copynumber: 1.9 Consensus size: 57
98936 CAATTTTCCA
98946 ATTATCTTTTTTTGTTGTTGGTGTTAAATGGTGTTAGATTTTATTTTCACATTCTCG
1 ATTATCTTTTTTTGTTGTTGGTGTTAAATGGTGTTAGATTTTATTTTCACATTCTCG
99003 ATTATC-TTTTTTGTTGTTGGTGTTAAATGGTGTTAGATTTTATTTTCACATT
1 ATTATCTTTTTTTGTTGTTGGTGTTAAATGGTGTTAGATTTTATTTTCACATT
99055 TACATTAGCA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 46 0.88
57 6 0.12
ACGTcount: A:0.18, C:0.07, G:0.17, T:0.57
Consensus pattern (57 bp):
ATTATCTTTTTTTGTTGTTGGTGTTAAATGGTGTTAGATTTTATTTTCACATTCTCG
Found at i:99171 original size:21 final size:20
Alignment explanation
Indices: 99147--99186 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
99137 GTATGTAAAA
99147 CATTAGTGTGTAACAATAGAT
1 CATTAGTGTGT-ACAATAGAT
* *
99168 CATTATTTTGTACAATAGA
1 CATTAGTGTGTACAATAGA
99187 GTTTTTTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
CATTAGTGTGTACAATAGAT
Found at i:101963 original size:24 final size:24
Alignment explanation
Indices: 101935--101980 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
101925 AATAAAAATT
101935 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
*
101959 AGCCACCAATTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
101981 AAATAACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:102010 original size:27 final size:28
Alignment explanation
Indices: 101977--102037 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
101967 ATTTTTACAA
101977 ACAAAA-ATAACCACCATATTTGACAAAT
1 ACAAAAGA-AACCACCATATTTGACAAAT
102005 ACAAAAGAAACCACCATATTTGACAAAT
1 ACAAAAGAAACCACCATATTTGACAAAT
102033 ACAAA
1 ACAAA
102038 GGTGGCATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.18
Consensus pattern (28 bp):
ACAAAAGAAACCACCATATTTGACAAAT
Found at i:109013 original size:21 final size:20
Alignment explanation
Indices: 108972--109019 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
108962 AAGGAAAATA
*
108972 CAAAAACAAAAAACAGTTTT
1 CAAAAACAAAAAACAATTTT
* *
108992 CAAAAATAAAAAATAATGTTT
1 CAAAAACAAAAAACAAT-TTT
109013 CACAAAA
1 CA-AAAA
109020 AATTACTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 14 0.61
21 5 0.22
22 4 0.17
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.21
Consensus pattern (20 bp):
CAAAAACAAAAAACAATTTT
Found at i:109347 original size:7 final size:7
Alignment explanation
Indices: 109335--109360 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
109325 ATCCTAGTCT
109335 TATAATA
1 TATAATA
109342 TATAATA
1 TATAATA
109349 TATAATA
1 TATAATA
109356 TATAA
1 TATAA
109361 CATAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TATAATA
Found at i:110289 original size:16 final size:16
Alignment explanation
Indices: 110256--110301 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
110246 TTGATAACAA
*
110256 ATTTGAAATTT-TAGAT
1 ATTTAAAATTTATA-AT
110272 A-TTAAATATTTATAAT
1 ATTTAAA-ATTTATAAT
110288 ATTTAAAATTTATA
1 ATTTAAAATTTATA
110302 TTTACATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
ATTTAAAATTTATAAT
Found at i:110886 original size:21 final size:19
Alignment explanation
Indices: 110860--110898 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
110850 TTTTTTATCA
110860 TTAAAAATAAACTTAAATTTG
1 TTAAAAATAAA--TAAATTTG
*
110881 TTAAAAGTAAATAAATTT
1 TTAAAAATAAATAAATTT
110899 TTTACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAAAAATAAATAAATTTG
Found at i:111680 original size:30 final size:26
Alignment explanation
Indices: 111612--111663 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
111602 ATGATTAATG
111612 ATTTAATAATTTAAAAAAATAAATAA
1 ATTTAATAATTTAAAAAAATAAATAA
*
111638 ATTTAATAATTTACAAAAATAAATAA
1 ATTTAATAATTTAAAAAAATAAATAA
111664 GATGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATTTAATAATTTAAAAAAATAAATAA
Found at i:112406 original size:3 final size:3
Alignment explanation
Indices: 112398--112426 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
112388 ATATGCTTCT
112398 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
112427 TTCATTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:114847 original size:78 final size:77
Alignment explanation
Indices: 114716--114872 Score: 201
Period size: 78 Copynumber: 2.0 Consensus size: 77
114706 CTACTGATAG
* * * *
114716 ATAGAGTTTTTAAATTCGATAACTACATTTACGTAATTTATAGATATTCACTAAACTATAACTAA
1 ATAGAGTTTTTAAATTCGATAAATACATTTACGTAATTCATAAATATTCACTAAACTATAAATAA
*
114781 TGAAATTAT-AA
66 AGAAATTATGAA
* * *
114792 ATAGAGTTTTTAAACTT-GATAAAAATATATTTACGTAATTCATAAATATTTACTAAATTATAAA
1 ATAGAGTTTTTAAA-TTCGAT--AAATACATTTACGTAATTCATAAATATTCACTAAACTATAAA
114856 TAAAGAAATTATGAA
63 TAAAGAAATTATGAA
114871 AT
1 AT
114873 TATTTTTGCA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
76 17 0.25
77 2 0.03
78 46 0.67
79 4 0.06
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (77 bp):
ATAGAGTTTTTAAATTCGATAAATACATTTACGTAATTCATAAATATTCACTAAACTATAAATAA
AGAAATTATGAA
Found at i:114856 original size:18 final size:19
Alignment explanation
Indices: 114818--114857 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
114808 TGATAAAAAT
114818 ATATTTACGTAATTCATAA
1 ATATTTACGTAATTCATAA
114837 ATATTTAC-TAAATT-ATAA
1 ATATTTACGT-AATTCATAA
114855 ATA
1 ATA
114858 AAGAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (19 bp):
ATATTTACGTAATTCATAA
Found at i:115655 original size:36 final size:36
Alignment explanation
Indices: 115613--115685 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
115603 TGTAATTTTA
115613 ACTTATTGATTGATGTAAAACAATTAAAATTTGATT
1 ACTTATTGATTGATGTAAAACAATTAAAATTTGATT
115649 ACTTATTGATTGATGTAAAACAATTAAAATTTGATT
1 ACTTATTGATTGATGTAAAACAATTAAAATTTGATT
115685 A
1 A
115686 ATCAATCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.41
Consensus pattern (36 bp):
ACTTATTGATTGATGTAAAACAATTAAAATTTGATT
Found at i:116227 original size:28 final size:27
Alignment explanation
Indices: 116172--116242 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
116162 GCCACCCATT
116172 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
116199 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
116227 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
116243 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:116261 original size:25 final size:25
Alignment explanation
Indices: 116227--116276 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
116217 GTTTCCTTTG
116227 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGAGGCTTGTT
*
116252 TATTTGTCAAAATTGGTGGCTTGTT
1 TATTTGTCAAAATTGGAGGCTTGTT
116277 GTTCATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (25 bp):
TATTTGTCAAAATTGGAGGCTTGTT
Found at i:116367 original size:13 final size:13
Alignment explanation
Indices: 116349--116376 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
116339 AGGCTCCCAA
116349 ATCCCTCTCAAGC
1 ATCCCTCTCAAGC
116362 ATCCCTCTCAAGC
1 ATCCCTCTCAAGC
116375 AT
1 AT
116377 TCTCTCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.43, G:0.07, T:0.25
Consensus pattern (13 bp):
ATCCCTCTCAAGC
Found at i:120827 original size:28 final size:27
Alignment explanation
Indices: 120772--120842 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
120762 GCCACCTATT
120772 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
120799 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
120827 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
120843 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:120861 original size:25 final size:25
Alignment explanation
Indices: 120827--120876 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
120817 GTTTCCTTTG
120827 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGAGGCTTGTT
*
120852 TATTTGTCAAAATTGGTGGCTTGTT
1 TATTTGTCAAAATTGGAGGCTTGTT
120877 GTTCATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (25 bp):
TATTTGTCAAAATTGGAGGCTTGTT
Found at i:120967 original size:13 final size:13
Alignment explanation
Indices: 120949--120976 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
120939 AGGCTCCCAA
120949 ATCCCTCTCAAGC
1 ATCCCTCTCAAGC
120962 ATCCCTCTCAAGC
1 ATCCCTCTCAAGC
120975 AT
1 AT
120977 TCTCTCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.43, G:0.07, T:0.25
Consensus pattern (13 bp):
ATCCCTCTCAAGC
Found at i:121304 original size:20 final size:20
Alignment explanation
Indices: 121279--121318 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
121269 CTTTACTTAT
* *
121279 AATTATATTATAAAATATAA
1 AATTATAATATAAAACATAA
121299 AATTATAATATAAAACATAA
1 AATTATAATATAAAACATAA
121319 TTCTGGCCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTATAATATAAAACATAA
Found at i:121974 original size:23 final size:21
Alignment explanation
Indices: 121925--121974 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
121915 ATGAATTGAT
121925 AAAAAGAAAATATTTATTTAA
1 AAAAAGAAAATATTTATTTAA
* *
121946 ATAAAAGCAAATATTCTTTTTAGA
1 A-AAAAGAAAATATT-TATTTA-A
121970 AAAAA
1 AAAAA
121975 AACAAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 12 0.50
23 9 0.38
24 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (21 bp):
AAAAAGAAAATATTTATTTAA
Found at i:122301 original size:17 final size:17
Alignment explanation
Indices: 122279--122314 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
122269 GAATTTAAGT
122279 ATACAAATTCCGATTAA
1 ATACAAATTCCGATTAA
122296 ATACAAATTCCGATTAA
1 ATACAAATTCCGATTAA
122313 AT
1 AT
122315 GTCGATACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (17 bp):
ATACAAATTCCGATTAA
Found at i:123163 original size:21 final size:20
Alignment explanation
Indices: 123122--123169 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
123112 AAGGAAAATA
*
123122 CAAAAACAAAAAACAGTTTT
1 CAAAAACAAAAAACAATTTT
* *
123142 CAAAAATAAAAAATAATGTTT
1 CAAAAACAAAAAACAAT-TTT
123163 CACAAAA
1 CA-AAAA
123170 AATTACTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 14 0.61
21 5 0.22
22 4 0.17
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.21
Consensus pattern (20 bp):
CAAAAACAAAAAACAATTTT
Found at i:124430 original size:16 final size:16
Alignment explanation
Indices: 124402--124442 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
124392 AACAAGTTAG
124402 AAATTT-TAGATA-TTA
1 AAATTTATA-ATATTTA
124417 AATATTTATAATATTTA
1 AA-ATTTATAATATTTA
124434 AAATTTATA
1 AAATTTATA
124443 CTTACATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 14 0.61
17 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
AAATTTATAATATTTA
Found at i:125025 original size:21 final size:19
Alignment explanation
Indices: 124999--125037 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
124989 TTTTTTATCA
124999 TTAAAAATAAACTTAAATTTG
1 TTAAAAATAAA--TAAATTTG
*
125020 TTAAAAGTAAATAAATTT
1 TTAAAAATAAATAAATTT
125038 TTTACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAAAAATAAATAAATTTG
Found at i:125825 original size:30 final size:26
Alignment explanation
Indices: 125757--125808 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
125747 ATGATTAATG
125757 ATTTAATAATTTAAAAAAATAAATAA
1 ATTTAATAATTTAAAAAAATAAATAA
*
125783 ATTTAATAATTTACAAAAATAAATAA
1 ATTTAATAATTTAAAAAAATAAATAA
125809 GATGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATTTAATAATTTAAAAAAATAAATAA
Found at i:126568 original size:3 final size:3
Alignment explanation
Indices: 126560--126612 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
126550 ATATGCTTCT
126560 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
126608 TTA TT
1 TTA TT
126613 TTCATTTTCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:175710 original size:44 final size:43
Alignment explanation
Indices: 175642--175732 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 43
175632 ATATACATGT
* *
175642 TAACGCACCTAACATTCTCACCAAATACATCCACCTAACACACC
1 TAACACACCTAACATTCTCACCAAACACAT-CACCTAACACACC
175686 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACC
175729 -AACA
1 TAACA
175733 TTCACCCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 4 0.09
43 13 0.29
44 28 0.62
ACGTcount: A:0.42, C:0.41, G:0.01, T:0.16
Consensus pattern (43 bp):
TAACACACCTAACATTCTCACCAAACACATCACCTAACACACC
Found at i:175748 original size:32 final size:34
Alignment explanation
Indices: 175682--175835 Score: 167
Period size: 32 Copynumber: 4.5 Consensus size: 34
175672 CCACCTAACA
*
175682 CACCTAACACACCTAACATTCTCACCAAACACAT
1 CACCTAACACACCTAACATTCACACCAAACACAT
*
175716 CACCTAACACACC-AACATTCAC-CCAAATACAT
1 CACCTAACACACCTAACATTCACACCAAACACAT
*
175748 CACCAACACCTAACACCACTAACATTC-CACC-AACACAT
1 CACCTA-A-C--ACA-C-CTAACATTCACACCAAACACAT
* *
175786 CACCTAACACACCTAACATT-TCACC-AATACAT
1 CACCTAACACACCTAACATTCACACCAAACACAT
175818 CACCTAACACACCTAACA
1 CACCTAACACACCTAACA
175836 AAGAAATTAA
Statistics
Matches: 105, Mismatches: 6, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
32 50 0.48
33 10 0.10
34 17 0.16
36 4 0.04
37 2 0.02
38 13 0.12
39 9 0.09
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (34 bp):
CACCTAACACACCTAACATTCACACCAAACACAT
Found at i:175751 original size:44 final size:44
Alignment explanation
Indices: 175642--175753 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 44
175632 ATATACATGT
* * * *
175642 TAACGCACCTAACATTCTCACCAAATACATCCACCTAACACACC
1 TAACACACCCAACATACTCACCAAACACATCCACCTAACACACC
* *
175686 TAACACACCTAACATTCTCACCAAACACAT-CACCTAACACACC
1 TAACACACCCAACATACTCACCAAACACATCCACCTAACACACC
175729 -AACATTCACCCAA-ATACATCACCAA
1 TAACA--CACCCAACATAC-TCACCAA
175754 CACCTAACAC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
42 4 0.07
43 16 0.26
44 41 0.67
ACGTcount: A:0.42, C:0.40, G:0.01, T:0.17
Consensus pattern (44 bp):
TAACACACCCAACATACTCACCAAACACATCCACCTAACACACC
Found at i:175800 original size:9 final size:10
Alignment explanation
Indices: 175668--175835 Score: 75
Period size: 9 Copynumber: 16.3 Consensus size: 10
175658 CTCACCAAAT
175668 ACATCCACCTA
1 ACAT-CACCTA
175679 ACA-CACCTA
1 ACATCACCTA
175688 ACA-CACCTA
1 ACATCACCTA
*
175697 ACATTCTCACCAAA
1 ACA---TCACC-TA
175711 CACATCACCTA
1 -ACATCACCTA
175722 ACA-CACC-A
1 ACATCACCTA
*
175730 ACATTCACCCA
1 ACA-TCACCTA
*
175741 A-AT-ACATCA
1 ACATCACCT-A
* *
175750 CCAACACCTA
1 ACATCACCTA
*
175760 ACACCA-CTA
1 ACATCACCTA
*
175769 ACATTCCACCAA
1 ACA-T-CACCTA
175781 CACATCACCTA
1 -ACATCACCTA
175792 ACA-CACCTA
1 ACATCACCTA
*
175801 ACATTTCACCAA
1 ACA--TCACCTA
175813 TACATCACCTA
1 -ACATCACCTA
175824 ACA-CACCTA
1 ACATCACCTA
175833 ACA
1 ACA
175836 AAGAAATTAA
Statistics
Matches: 123, Mismatches: 14, Indels: 42
0.69 0.08 0.23
Matches are distributed among these distances:
8 6 0.05
9 48 0.39
10 20 0.16
11 22 0.18
12 13 0.11
13 10 0.08
14 1 0.01
15 3 0.02
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (10 bp):
ACATCACCTA
Found at i:181168 original size:34 final size:34
Alignment explanation
Indices: 181096--181312 Score: 303
Period size: 34 Copynumber: 6.4 Consensus size: 34
181086 TGGAGGAGGG
* *
181096 TGTTGATTAAATGGTA-ATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
181129 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* *
181163 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
*
181197 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* *
181231 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* *
181265 TGTTGACTAAATGGGAGATTTGGTAAG-TTGCCAT
1 TGTTGATTAAATGGGAGATTTGGT-AGTTTACCAT
181299 TGTTGATTAAATGG
1 TGTTGATTAAATGG
181313 TGGTTTTTAC
Statistics
Matches: 163, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 14 0.09
34 148 0.91
35 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
Found at i:181271 original size:102 final size:101
Alignment explanation
Indices: 181096--181312 Score: 364
Period size: 102 Copynumber: 2.1 Consensus size: 101
181086 TGGAGGAGGG
* * *
181096 TGTTGATTAAATGGTAATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGGAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
181161 ATTGTTGACTAAATGGGAGATTTGGT-AGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAAG-TTACCAT
*
181197 TGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTAC
1 TGTTGATTAAATGGGA-ATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTAC
*
181262 CATTGTTGACTAAATGGGAGATTTGGTAAGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAAGTTACCAT
181299 TGTTGATTAAATGG
1 TGTTGATTAAATGG
181313 TGGTTTTTAC
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
101 15 0.14
102 92 0.84
103 2 0.02
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGGAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
ATTGTTGACTAAATGGGAGATTTGGTAAGTTACCAT
Found at i:181656 original size:19 final size:19
Alignment explanation
Indices: 181619--181665 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
181609 TTGGTTGTCG
**
181619 AGGTACTGTTCACGTATAC
1 AGGTACTGTTCACACATAC
*
181638 AGGTACTGTTCATACATAC
1 AGGTACTGTTCACACATAC
181657 -GGTTACTGT
1 AGG-TACTGT
181666 GCACGTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (19 bp):
AGGTACTGTTCACACATAC
Done.