Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 1 of 15
Found at i:7406 original size:24 final size:22
Alignment explanation
Indices: 7379--7427 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
7369 TCTTTTTAAA
7379 ATAAATTATACGATTTTTATATAT
1 ATAAATT-T-CGATTTTTATATAT
* *
7403 ATAAATTTTGATTTTTTTATAT
1 ATAAATTTCGATTTTTATATAT
7425 ATA
1 ATA
7428 TATAACGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 1 0.04
24 7 0.30
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATAAATTTCGATTTTTATATAT
Found at i:7443 original size:24 final size:24
Alignment explanation
Indices: 7391--7446 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
7381 AAATTATACG
**
7391 ATTTTTATATATATAAATTTTGAT
1 ATTTTTATATATATAAACGTTGAT
*
7415 TTTTTTATATATATATAACGTT-AT
1 ATTTTTATATATATA-AACGTTGAT
7439 ATTTTTAT
1 ATTTTTAT
7447 TATTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTTTTATATATATAAACGTTGAT
Found at i:7922 original size:2 final size:2
Alignment explanation
Indices: 7915--7943 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7905 TAAATGTGAA
7915 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
7944 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:8756 original size:28 final size:28
Alignment explanation
Indices: 8725--8786 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
8715 TTTTTTACAA
8725 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAAGAA-AACCACCATATTTGACAAAT
*
8753 ACAAAGGAAACCACCATATTTGACAAAT
1 ACAAAGAAAACCACCATATTTGACAAAT
8781 ACAAAG
1 ACAAAG
8787 GGTGGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (28 bp):
ACAAAGAAAACCACCATATTTGACAAAT
Found at i:8787 original size:28 final size:28
Alignment explanation
Indices: 8733--8787 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
8723 AAACAAAAAT
8733 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
8761 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
8788 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:13336 original size:28 final size:28
Alignment explanation
Indices: 13305--13366 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
13295 TTTTTTACAA
13305 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAAGAA-AACCACCATATTTGACAAAT
*
13333 ACAAAGGAAACCACCATATTTGACAAAT
1 ACAAAGAAAACCACCATATTTGACAAAT
13361 ACAAAG
1 ACAAAG
13367 GGTGGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (28 bp):
ACAAAGAAAACCACCATATTTGACAAAT
Found at i:13367 original size:28 final size:28
Alignment explanation
Indices: 13313--13367 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
13303 AAACAAAAAT
13313 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
13341 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
13368 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:16355 original size:2 final size:2
Alignment explanation
Indices: 16348--16386 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
16338 AGTCTAATCG
*
16348 TA TA TA TA TA TA TA TA TA TA TA TA TG 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
16387 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16584 original size:14 final size:14
Alignment explanation
Indices: 16565--16592 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16555 GTCGATGGAA
16565 ACTTAATTAACTGG
1 ACTTAATTAACTGG
16579 ACTTAATTAACTGG
1 ACTTAATTAACTGG
16593 TGGTAATCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ACTTAATTAACTGG
Found at i:29692 original size:2 final size:2
Alignment explanation
Indices: 29685--29739 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
29675 TAGATGTGAA
29685 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29727 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
29740 AAGGAAGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33051 original size:13 final size:13
Alignment explanation
Indices: 33030--33087 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
33020 AATATTTTTT
* *
33030 ATATATTTATGTC
1 ATATTTTTATATC
33043 ATATTTTTAT-T-
1 ATATTTTTATATC
33054 AT-TTTTTATATC
1 ATATTTTTATATC
*
33066 GTATATTTTTATATT
1 --ATATTTTTATATC
33081 ATATTTT
1 ATATTTT
33088 AATTACTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 7 0.18
11 3 0.08
12 1 0.03
13 16 0.42
14 2 0.05
15 9 0.24
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (13 bp):
ATATTTTTATATC
Found at i:33076 original size:15 final size:13
Alignment explanation
Indices: 33028--33103 Score: 56
Period size: 12 Copynumber: 6.1 Consensus size: 13
33018 TTAATATTTT
* *
33028 TTATATATTTATG
1 TTATATTTTTATA
*
33041 TCATA-TTTT-TA
1 TTATATTTTTATA
33052 TTAT-TTTTTATA
1 TTATATTTTTATA
33064 TCGTATATTTTTATA
1 T--TATATTTTTATA
33079 TTATA-TTTTA-A
1 TTATATTTTTATA
33090 TTACT-TTTTTATA
1 TTA-TATTTTTATA
33103 T
1 T
33104 CATGTCGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
11 12 0.24
12 17 0.33
13 10 0.20
14 3 0.06
15 9 0.18
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (13 bp):
TTATATTTTTATA
Found at i:33077 original size:38 final size:39
Alignment explanation
Indices: 33029--33104 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 39
33019 TAATATTTTT
* *
33029 TATATATTTATGTCATATTTTTATTA-TTTTTTATATCG
1 TATATATTTATATCATATTTTAATTACTTTTTTATATCG
* *
33067 TATATTTTTATATTATATTTTAATTACTTTTTTATATC
1 TATATATTTATATCATATTTTAATTACTTTTTTATATC
33105 ATGTCGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 22 0.67
39 11 0.33
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (39 bp):
TATATATTTATATCATATTTTAATTACTTTTTTATATCG
Found at i:33099 original size:12 final size:12
Alignment explanation
Indices: 33046--33103 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
33036 TTATGTCATA
33046 TTTT-TATTATT
1 TTTTATATTATT
33057 TTTTATATCGTATAT
1 TTTTATAT--TAT-T
*
33072 TTTTATATTATA
1 TTTTATATTATT
33084 TTTTA-ATTACTT
1 TTTTATATTA-TT
33096 TTTTATAT
1 TTTTATAT
33104 CATGTCGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 8 0.21
12 14 0.36
13 5 0.13
14 3 0.08
15 9 0.23
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATATTATT
Found at i:34523 original size:2 final size:2
Alignment explanation
Indices: 34516--34541 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34506 GACTCTAATC
34516 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
34542 GTTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34667 original size:13 final size:13
Alignment explanation
Indices: 34649--34674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34639 TTTTAAGTTA
34649 TTTATATCATATT
1 TTTATATCATATT
34662 TTTATATCATATT
1 TTTATATCATATT
34675 CATGTTGCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATATCATATT
Found at i:36471 original size:22 final size:21
Alignment explanation
Indices: 36446--36486 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36436 ACAATTGATC
*
36446 AATCTAATTATGAATTTTTTGG
1 AATCT-ATCATGAATTTTTTGG
*
36468 AATCTCTCATGAATTTTTT
1 AATCTATCATGAATTTTTT
36487 TATAAATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (21 bp):
AATCTATCATGAATTTTTTGG
Found at i:36824 original size:8 final size:8
Alignment explanation
Indices: 36811--36836 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
36801 GTGTTCAAAG
36811 AAAAAATA
1 AAAAAATA
36819 AAAAAATA
1 AAAAAATA
36827 AAAAAATA
1 AAAAAATA
36835 AA
1 AA
36837 GGTTTGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:38317 original size:22 final size:22
Alignment explanation
Indices: 38292--38340 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
38282 TAAATCTTGT
*
38292 TATA-TAAATTTTGATATTTTTA
1 TATATTAAATGTT-ATATTTTTA
*
38314 TATATTTAATGTTATATTTTTA
1 TATATTAAATGTTATATTTTTA
38336 T-TATT
1 TATATT
38341 TTTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
TATATTAAATGTTATATTTTTA
Found at i:38355 original size:39 final size:39
Alignment explanation
Indices: 38312--38388 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
38302 TTGATATTTT
* *
38312 TATATATTTAATGTTATATTTTTATTA-TTTTTTATATCG
1 TATAT-TTTAATATTATATTTTAATTACTTTTTTATATCG
*
38351 TATATTTTTATATTATATTTTAATTACTTTTTTATATC
1 TATATTTTAATATTATATTTTAATTACTTTTTTATATC
38389 ATGTCGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 18 0.53
39 16 0.47
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.65
Consensus pattern (39 bp):
TATATTTTAATATTATATTTTAATTACTTTTTTATATCG
Found at i:38360 original size:15 final size:13
Alignment explanation
Indices: 38311--38387 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 13
38301 TTTGATATTT
* *
38311 TTATATATTTAATG
1 TTATAT-TTTTATA
38325 TTATA-TTTT-TA
1 TTATATTTTTATA
38336 TTAT-TTTTTATA
1 TTATATTTTTATA
38348 TCGTATATTTTTATA
1 T--TATATTTTTATA
38363 TTATA-TTTTA-A
1 TTATATTTTTATA
38374 TTACT-TTTTTATA
1 TTA-TATTTTTATA
38387 T
1 T
38388 CATGTCGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
11 13 0.25
12 17 0.32
13 6 0.11
14 8 0.15
15 9 0.17
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (13 bp):
TTATATTTTTATA
Found at i:48938 original size:27 final size:27
Alignment explanation
Indices: 48904--48978 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
48894 AGCCACAATT
48904 TGTTTGTCAAATATGGTGGCTACTTTG
1 TGTTTGTCAAATATGGTGGCTACTTTG
*
48931 TGTTTGTCAAATATGGTGGTTACTTTG
1 TGTTTGTCAAATATGGTGGCTACTTTG
* *
48958 TGTTTGTCAAAAATTGTGGCT
1 TGTTTGTCAAATATGGTGGCT
48979 TGTTGTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.45
Consensus pattern (27 bp):
TGTTTGTCAAATATGGTGGCTACTTTG
Found at i:53071 original size:27 final size:27
Alignment explanation
Indices: 53037--53101 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
53027 AGCCACCATT
53037 TGTTTGTCAAATATGGTGGCTACTTTG
1 TGTTTGTCAAATATGGTGGCTACTTTG
*
53064 TGTTTGTCAAATATGGTGGTTACTTTG
1 TGTTTGTCAAATATGGTGGCTACTTTG
53091 TGTTTGTCAAA
1 TGTTTGTCAAA
53102 ATTTGTGGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAATATGGTGGCTACTTTG
Found at i:56670 original size:20 final size:20
Alignment explanation
Indices: 56645--56684 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56635 CCCAAACTCT
56645 CGTCTTGGAAAAATTAATTA
1 CGTCTTGGAAAAATTAATTA
56665 CGTCTTGGAAAAATTAATTA
1 CGTCTTGGAAAAATTAATTA
56685 AAGTGTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
CGTCTTGGAAAAATTAATTA
Found at i:59288 original size:19 final size:22
Alignment explanation
Indices: 59261--59330 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 22
59251 ATTTTTATTA
*
59261 TATAAATTTTA-AT-AT-TTTT
1 TATATATTTTACATCATATTTT
59280 TATATA-TTTACATCATATTTT
1 TATATATTTTACATCATATTTT
* *
59301 TATTATTTTTTAGATCGTATATTTT
1 TA-TATATTTTACATC--ATATTTT
59326 TATAT
1 TATAT
59331 TATATTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 4 0.10
19 7 0.17
20 2 0.05
21 6 0.15
22 3 0.07
23 7 0.17
24 3 0.07
25 9 0.22
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (22 bp):
TATATATTTTACATCATATTTT
Found at i:59301 original size:23 final size:23
Alignment explanation
Indices: 59275--59330 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
59265 AATTTTAATA
59275 TTTTTTATATATTTACATCATAT
1 TTTTTTATATATTTACATCATAT
* * *
59298 TTTTATTAT-TTTTTAGATCGTAT
1 TTTT-TTATATATTTACATCATAT
*
59321 ATTTTTATAT
1 TTTTTTATAT
59331 TATATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 4 0.15
23 19 0.70
24 4 0.15
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTTTTATATATTTACATCATAT
Found at i:59336 original size:38 final size:39
Alignment explanation
Indices: 59280--59357 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 39
59270 TAATATTTTT
*
59280 TATATATTTACATCATATTTTTATTA-TTTTTTAGATCG
1 TATATATTTACATCATATTTTAATTACTTTTTTAGATCG
* * * *
59318 TATATTTTTATATTATATTTTAATTACTTTTTTATATCG
1 TATATATTTACATCATATTTTAATTACTTTTTTAGATCG
59357 T
1 T
59358 GTCCAAAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 22 0.65
39 12 0.35
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (39 bp):
TATATATTTACATCATATTTTAATTACTTTTTTAGATCG
Found at i:59860 original size:27 final size:27
Alignment explanation
Indices: 59818--59896 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
59808 AAACAACAAG
* *
59818 CCACAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACACAAAGGAA
* * *
59845 CCACCATTTTTAACAAATACAAAGTAA
1 CCACCATTTTTGACAAACACAAAGGAA
* *
59872 CTACCATTGTTGACAAACACAAAGG
1 CCACCATTTTTGACAAACACAAAGG
59897 GTGACTTTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACACAAAGGAA
Found at i:64421 original size:28 final size:27
Alignment explanation
Indices: 64360--64462 Score: 100
Period size: 28 Copynumber: 3.6 Consensus size: 27
64350 TAGCCACCAA
*
64360 TTTTGACAAACAACAAGCCACAAGCCACAAT
1 TTTTGACAAACAAAAAG--A-AA-CCACAAT
64391 TTTTGACAAACAAAAAGAAACCACAAT
1 TTTTGACAAACAAAAAGAAACCACAAT
* *
64418 TTTTGACAAA-AATAAGAGTAACCACCAT
1 TTTTGACAAACAA-AA-AGAAACCACAAT
* *
64446 TGTTGACAAACACAAAG
1 TTTTGACAAACAAAAAG
64463 GGTGGTTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
26 2 0.03
27 21 0.33
28 23 0.36
29 2 0.03
31 16 0.25
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (27 bp):
TTTTGACAAACAAAAAGAAACCACAAT
Found at i:65793 original size:19 final size:17
Alignment explanation
Indices: 65769--65807 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
65759 AGATTTAGCA
65769 ATTTATACATTTGTATAGT
1 ATTTATACATTT-TATA-T
*
65788 ATTTATATATTTTATAT
1 ATTTATACATTTTATAT
65805 ATT
1 ATT
65808 CATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTATACATTTTATAT
Found at i:65796 original size:11 final size:10
Alignment explanation
Indices: 65772--65839 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 10
65762 TTTAGCAATT
* *
65772 TATACATTTG
1 TATATATTTA
65782 TATAGTATTTA
1 TATA-TATTTA
65793 TATAT-TTTA
1 TATATATTTA
65802 TATATTCATATTA
1 TATA-T-AT-TTA
65815 TAT-TATTTA
1 TATATATTTA
*
65824 TATCATATTTC
1 TAT-ATATTTA
65835 TATAT
1 TATAT
65840 CATATTTATG
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
9 14 0.29
10 10 0.21
11 17 0.35
12 1 0.02
13 6 0.12
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (10 bp):
TATATATTTA
Found at i:65845 original size:13 final size:13
Alignment explanation
Indices: 65822--65846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65812 TTATATTATT
65822 TATATCATATTTC
1 TATATCATATTTC
65835 TATATCATATTT
1 TATATCATATTT
65847 ATGTTATGTA
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:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATCATATTTC
Found at i:73798 original size:18 final size:18
Alignment explanation
Indices: 73777--73811 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
73767 ATTATATTTA
*
73777 TATATTCTGTTATTTATT
1 TATATTCTATTATTTATT
*
73795 TATATTTTATTATTTAT
1 TATATTCTATTATTTAT
73812 ATCATATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (18 bp):
TATATTCTATTATTTATT
Found at i:76660 original size:28 final size:28
Alignment explanation
Indices: 76629--76689 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
76619 ATTTTTACAA
76629 ACAAAA-ATAACCACCATATTTGACAAAT
1 ACAAAAGA-AACCACCATATTTGACAAAT
76657 ACAAAAGAAACCACCATATTTGACAAAT
1 ACAAAAGAAACCACCATATTTGACAAAT
76685 ACAAA
1 ACAAA
76690 GGGTGGCATT
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:78633 original size:21 final size:22
Alignment explanation
Indices: 78595--78640 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
78585 ATCTGTTCAA
* **
78595 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
78616 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
78638 ACT
1 ACT
78641 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:81042 original size:20 final size:20
Alignment explanation
Indices: 81017--81066 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
81007 AAGAATTGAA
81017 GAGGGATAC-AAGAGAGGGAT
1 GAGGGATACTAA-AGAGGGAT
*
81037 GAGGGATACTTAAGAGGGAT
1 GAGGGATACTAAAGAGGGAT
81057 GAGGGATACT
1 GAGGGATACT
81067 TGAGAGGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.36, C:0.06, G:0.42, T:0.16
Consensus pattern (20 bp):
GAGGGATACTAAAGAGGGAT
Found at i:81067 original size:20 final size:20
Alignment explanation
Indices: 81029--81073 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
81019 GGGATACAAG
81029 AGAGGGATGAGGGATACTTA
1 AGAGGGATGAGGGATACTTA
*
81049 AGAGGGATGAGGGATACTTG
1 AGAGGGATGAGGGATACTTA
81069 AGAGG
1 AGAGG
81074 ATACAAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.44, T:0.18
Consensus pattern (20 bp):
AGAGGGATGAGGGATACTTA
Found at i:81909 original size:28 final size:25
Alignment explanation
Indices: 81850--81913 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
81840 CTATATATAT
*
81850 ATAATACAAATATAACAGGAAAAAA
1 ATAATATAAATATAACAGGAAAAAA
81875 AT--T-TAAACTATAACAGGACAAAAAA
1 ATAATATAAA-TATAACAGG--AAAAAA
81900 ATAATATAAATATA
1 ATAATATAAATATA
81914 TATAATATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
22 3 0.09
23 10 0.31
25 10 0.31
27 5 0.16
28 4 0.12
ACGTcount: A:0.64, C:0.08, G:0.06, T:0.22
Consensus pattern (25 bp):
ATAATATAAATATAACAGGAAAAAA
Found at i:82186 original size:18 final size:16
Alignment explanation
Indices: 82139--82187 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
82129 AAACATATTA
82139 AAATTTATATAAA-AT
1 AAATTTATATAAATAT
82154 AAA-TTAT-TAACATAT
1 AAATTTATATAA-ATAT
82169 CAAAGTTTATATAAATAT
1 -AAA-TTTATATAAATAT
82187 A
1 A
82188 TAGTATCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 5 0.18
16 3 0.11
17 1 0.04
18 8 0.29
19 3 0.11
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (16 bp):
AAATTTATATAAATAT
Found at i:83721 original size:27 final size:29
Alignment explanation
Indices: 83668--83754 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
83658 TTTATATTTT
*
83668 ATATATTATGTAATTATTATCA-CATAAA-A-
1 ATATA-TATGT-ATTATTAT-AGTATAAATAG
83697 ATATATATGTATTATTATAGTATAAATATG
1 ATATATATGTATTATTATAGTATAAATA-G
* *
83727 AAATATATGTAATATTATAGTATAAATA
1 ATATATATGTATTATTATAGTATAAATA
83755 TGAAAAACTA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.02
27 13 0.25
28 6 0.12
29 5 0.10
30 26 0.51
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (29 bp):
ATATATATGTATTATTATAGTATAAATAG
Found at i:83733 original size:30 final size:30
Alignment explanation
Indices: 83699--83759 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
83689 ACATAAAAAT
*
83699 ATATATGTATTATTATAGTATAAATATGAA
1 ATATATGTAATATTATAGTATAAATATGAA
83729 ATATATGTAATATTATAGTATAAATATGAA
1 ATATATGTAATATTATAGTATAAATATGAA
83759 A
1 A
83760 AACTAAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (30 bp):
ATATATGTAATATTATAGTATAAATATGAA
Found at i:83816 original size:15 final size:14
Alignment explanation
Indices: 83796--83843 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
83786 AAACTTAAAA
83796 AAAAATTAAATTAAT
1 AAAAATTAAATT-AT
*
83811 AAAAATTATAGTT-T
1 AAAAATTA-AATTAT
*
83825 AAAAAATAAATTAT
1 AAAAATTAAATTAT
83839 AAAAA
1 AAAAA
83844 GTATCCTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 3 0.11
14 14 0.50
15 8 0.29
16 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
AAAAATTAAATTAT
Found at i:83891 original size:3 final size:3
Alignment explanation
Indices: 83883--83936 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
83873 TTTTTATCCC
83883 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
83931 ATT ATT
1 ATT ATT
83937 GCTATTTCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:85023 original size:6 final size:6
Alignment explanation
Indices: 85012--85062 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
85002 AGTGAGGATG
* * * *
85012 AAATAA AAATAA AAATAA AAATAA ATATAT AAATAA ATAAGAA AATTAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A-AATAA AAATAA
85061 AA
1 AA
85063 GTGTTGAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (6 bp):
AAATAA
Found at i:86157 original size:29 final size:29
Alignment explanation
Indices: 86101--86160 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
86091 TTGATGAATT
* *
86101 TATAAAAAATCAATTCAATCGATAAAAAA
1 TATAAAAAATCAATTAAATCAATAAAAAA
*
86130 TATAAAAAATTATATTAAATCAATAAAAAA
1 TATAAAAAATCA-ATTAAATCAATAAAAAA
86160 T
1 T
86161 TAGTTTTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (29 bp):
TATAAAAAATCAATTAAATCAATAAAAAA
Found at i:87631 original size:2 final size:2
Alignment explanation
Indices: 87619--87659 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
87609 TTTTTCATAC
*
87619 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
87660 GTCTGAAAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:90950 original size:22 final size:22
Alignment explanation
Indices: 90883--90951 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
90873 ATTTAAAAAA
* *
90883 ATTAACAAATAATTAAAAATTAT
1 ATTAATAAATAATTTAAAATT-T
*
90906 ATTTATATAAAATAA--T-AATTTT
1 A-TTA-AT-AAATAATTTAAAATTT
90928 ATTAATAAATAATTTAAAATTT
1 ATTAATAAATAATTTAAAATTT
90950 AT
1 AT
90952 AAAAATGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 13
0.68 0.08 0.25
Matches are distributed among these distances:
19 6 0.17
20 2 0.06
21 4 0.11
22 9 0.25
23 5 0.14
24 3 0.08
25 1 0.03
26 6 0.17
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAATAAATAATTTAAAATTT
Found at i:93206 original size:286 final size:286
Alignment explanation
Indices: 92665--93236 Score: 921
Period size: 286 Copynumber: 2.0 Consensus size: 286
92655 AGTTAAGGAT
* * *
92665 GATTTATTATCTTTGAAAACATGGAGAAGAATTTCACAAGCGGAGCTTTTCGCAAGCAACTGGTG
1 GATTTATTATCTTTGAAAACATGAAGAAGAATTTCACAAGCCGAACTTTTCGCAAGCAACTGGTG
* *
92730 GATTTGACGAATGCAATATGCTTGGTTCAGGCAGCTTTGGATATGCATATAAAGGAAGGCTTTAA
66 GATTTGACGAATGCAATATGCTTGATTCAGGCAGCTTTGGATATGCATATAAAGGAAGCCTTTAA
* * *
92795 GATGAAATGGATGTTGCAATAAAAGTTTTCAATTTATAAATAGAAAGAGCATTTAAGAGTTTTGA
131 GATGAAATGGATGTTGCAATAAAAGTTTTCAATTTACAAATAGAAAAAACATTTAAGAGTTTTGA
*
92860 CGTTGAATGCGAAACTATGCATAATATAATTCATCGTAATCTAATCAAGATCATTACTTGTTGCT
196 CGTTGAATGCGAAACTATGCATAATATAATTCATCGTAATCTAATCAAGATCATTACTTGTTACT
92925 CCAATGTTGACTCCAAAACCTTAGTG
261 CCAATGTTGACTCCAAAACCTTAGTG
* *
92951 GATTTATTATCTTTGAAAACATGAAGAAGAATTTCCCATGCCGAAC-TTTCGCAAGCAACTGGTG
1 GATTTATTATCTTTGAAAACATGAAGAAGAATTTCACAAGCCGAACTTTTCGCAAGCAACTGGTG
* *
93015 GATTTGACGAATGCAATATGCTTGATTCAGGCAGCTTTGGATATGTATATGAAGGAAGCCTTTAA
66 GATTTGACGAATGCAATATGCTTGATTCAGGCAGCTTTGGATATGCATATAAAGGAAGCCTTTAA
* *
93080 GATGGAATGGATGTTGCAATAAAAGTTTTCAATTTACACATAGAAAAAACATTTAAAGAGTTTTG
131 GATGAAATGGATGTTGCAATAAAAGTTTTCAATTTACAAATAGAAAAAACATTT-AAGAGTTTTG
* * * * * *
93145 ACGTTGAATGCGAAGCTATGCATAATATAGTTTATCGTAATTTTATCAAGGTCATTACTTGTTAC
195 ACGTTGAATGCGAAACTATGCATAATATAATTCATCGTAATCTAATCAAGATCATTACTTGTTAC
* *
93210 TCTAATGTTGACTTCAAAACCTTAGTG
260 TCCAATGTTGACTCCAAAACCTTAGTG
93237 CTTGATTTCA
Statistics
Matches: 262, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
285 128 0.49
286 134 0.51
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.33
Consensus pattern (286 bp):
GATTTATTATCTTTGAAAACATGAAGAAGAATTTCACAAGCCGAACTTTTCGCAAGCAACTGGTG
GATTTGACGAATGCAATATGCTTGATTCAGGCAGCTTTGGATATGCATATAAAGGAAGCCTTTAA
GATGAAATGGATGTTGCAATAAAAGTTTTCAATTTACAAATAGAAAAAACATTTAAGAGTTTTGA
CGTTGAATGCGAAACTATGCATAATATAATTCATCGTAATCTAATCAAGATCATTACTTGTTACT
CCAATGTTGACTCCAAAACCTTAGTG
Found at i:95813 original size:18 final size:17
Alignment explanation
Indices: 95782--95823 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
95772 TTAAAATAAT
95782 AATATTATATTTTATTA
1 AATATTATATTTTATTA
*
95799 TATATTATAATTTTATTA
1 AATATTAT-ATTTTATTA
95817 AATATTA
1 AATATTA
95824 AATATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTATATTTTATTA
Found at i:95831 original size:14 final size:14
Alignment explanation
Indices: 95812--95840 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
95802 ATTATAATTT
95812 TATTAAATATTAAA
1 TATTAAATATTAAA
95826 TATTAAATATTAAA
1 TATTAAATATTAAA
95840 T
1 T
95841 TAATATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATTAAATATTAAA
Found at i:100083 original size:17 final size:17
Alignment explanation
Indices: 100063--100096 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
100053 TAATTTTAAA
100063 TTTTAATATTTATATTT
1 TTTTAATATTTATATTT
* *
100080 TTTTTATTTTTATATTT
1 TTTTAATATTTATATTT
100097 AACATAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTAATATTTATATTT
Found at i:100083 original size:24 final size:23
Alignment explanation
Indices: 100046--100097 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
100036 TTATTAAAAA
100046 ATTTATATAATTTTAAATTTTAAT
1 ATTTATATAATTTT-AATTTTAAT
** * *
100070 ATTTATATTTTTTTTATTTTTAT
1 ATTTATATAATTTTAATTTTAAT
100093 ATTTA
1 ATTTA
100098 ACATAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTATATAATTTTAATTTTAAT
Found at i:103716 original size:25 final size:25
Alignment explanation
Indices: 103662--103719 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
103652 TGGTAATAAG
* *
103662 AAAGTTATGTTATTTGGATTTGGACG
1 AAAG-TATGTTATTTGGATTCGGACA
* *
103688 AAAGTATTTTATTTGGATTCGGATA
1 AAAGTATGTTATTTGGATTCGGACA
103713 AAAGTAT
1 AAAGTAT
103720 ATATTTGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.41
Consensus pattern (25 bp):
AAAGTATGTTATTTGGATTCGGACA
Found at i:103815 original size:10 final size:10
Alignment explanation
Indices: 103796--103834 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
103786 ATCTGGTATT
103796 TATGTGTGAA
1 TATGTGTGAA
*
103806 TATTTGTGAAAA
1 TATGTGTG--AA
103818 TATGTGTGAA
1 TATGTGTGAA
103828 TATGTGT
1 TATGTGT
103835 ATCTTATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 16 0.64
12 9 0.36
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.44
Consensus pattern (10 bp):
TATGTGTGAA
Found at i:103869 original size:19 final size:19
Alignment explanation
Indices: 103844--103884 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
103834 TATCTTATGA
*
103844 AAAAAAAAAAGAATTAAGAT
1 AAAAAATAAA-AATTAAGAT
*
103864 AAAAAATTAAAATTAAGAT
1 AAAAAATAAAAATTAAGAT
103883 AA
1 AA
103885 CATAAATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (19 bp):
AAAAAATAAAAATTAAGAT
Found at i:104173 original size:15 final size:15
Alignment explanation
Indices: 104150--104215 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
104140 AATATATTTT
*
104150 TAATGTTTTATATTA
1 TAATATTTTATATTA
104165 TAATATTTTATATT-
1 TAATATTTTATATTA
*
104179 TAATATTTATATAATA
1 TAATATTT-TATATTA
*
104195 TAA-ATTAATATATTA
1 TAATATT-TTATATTA
104210 T-ATATT
1 TAATATT
104216 ATTTAATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 9 0.21
15 31 0.72
16 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TAATATTTTATATTA
Found at i:104190 original size:44 final size:41
Alignment explanation
Indices: 104080--104190 Score: 93
Period size: 44 Copynumber: 2.5 Consensus size: 41
104070 TTAATCATGT
104080 TATTTT-TATTTAATTTTTAATATTTTTATATTTTTAATTAAA
1 TATTTTATATTTAA-TTTT-ATATTTTTATATTTTTAATTAAA
* *
104122 T-TTATAAATATATAATTTAATATATTTTTA-ATGTTTTATATTATAA
1 TATT-T-TATATTTAATTT--TATATTTTTATAT-TTTTA-ATTA-AA
104168 TATTTTATATTTAATATTTATAT
1 TATTTTATATTTAAT-TTTATAT
104191 AATATAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
41 2 0.04
42 2 0.04
43 5 0.09
44 25 0.45
45 13 0.24
46 6 0.11
47 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (41 bp):
TATTTTATATTTAATTTTATATTTTTATATTTTTAATTAAA
Found at i:104205 original size:61 final size:60
Alignment explanation
Indices: 104088--104208 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 60
104078 GTTATTTTTA
* *
104088 TTTAATTTTTAATATTTTTATATTTTTAATTAAATTTATAAATATATAATTTAATATATT
1 TTTAATTTTTAATATTATAATATTTTTAATTAAATTTATAAATATATAATTTAATATATT
*
104148 TTTAATGTTTT-ATATTATAATATTTTATATTTAATATTTATATAATATA-AA-TTAATATATT
1 TTTAAT-TTTTAATATTATAATATTTT-TAATTAA-ATTTATA-AATATATAATTTAATATATT
104209 ATATATTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
60 19 0.35
61 20 0.37
62 9 0.17
63 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (60 bp):
TTTAATTTTTAATATTATAATATTTTTAATTAAATTTATAAATATATAATTTAATATATT
Found at i:104215 original size:7 final size:7
Alignment explanation
Indices: 104158--104217 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
104148 TTTAATGTTT
104158 TATATTA
1 TATATTA
*
104165 TAATATTT
1 T-ATATTA
104173 TATATT-
1 TATATTA
104179 TAATATTTA
1 T-ATA-TTA
*
104188 TATAATA
1 TATATTA
*
104195 TAAATTAA
1 TATATT-A
104203 TATATTA
1 TATATTA
104210 TATATTA
1 TATATTA
104217 T
1 T
104218 TTAATTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
6 1 0.02
7 24 0.56
8 17 0.40
9 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TATATTA
Found at i:104216 original size:15 final size:16
Alignment explanation
Indices: 104132--104216 Score: 65
Period size: 15 Copynumber: 5.6 Consensus size: 16
104122 TTTATAAATA
104132 TATAAT-TTAATATATT
1 TATAATATTAATATA-T
* * *
104148 TTTAATGTT-TTATAT
1 TATAATATTAATATAT
*
104163 TATAATATT-TTATAT
1 TATAATATTAATATAT
* *
104178 T-TAATATTTATATAA
1 TATAATATTAATATAT
104193 TATAA-ATTAATATAT
1 TATAATATTAATATAT
104208 TAT-ATATTA
1 TATAATATTA
104217 TTTAATTTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
14 8 0.14
15 35 0.61
16 12 0.21
17 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (16 bp):
TATAATATTAATATAT
Found at i:104899 original size:27 final size:25
Alignment explanation
Indices: 104849--104910 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 25
104839 AAAAATATAA
104849 TATTTTTAA-ATTATTTAAATTATT
1 TATTTTTAATATTATTTAAATTATT
104873 TATTTTTAATATAATATTTCAAA-TATT
1 TATTTTTAATAT--TATTT-AAATTATT
*
104900 TATATTTAATA
1 TATTTTTAATA
104911 ATTTTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 9 0.27
25 2 0.06
27 19 0.58
28 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTTTTAATATTATTTAAATTATT
Found at i:104993 original size:31 final size:31
Alignment explanation
Indices: 104955--105042 Score: 85
Period size: 31 Copynumber: 2.8 Consensus size: 31
104945 TTAATTTTTA
104955 TTTTAAATATAAATAATATAATTTTTAAA-AT
1 TTTTAAATATAAATAATATAA-TTTTAAATAT
* *
104986 TTTTAAATATATAA-AATTTTAAATTTAAATAT
1 TTTTAAATATA-AATAA-TATAATTTTAAATAT
*
105018 TTTTATAT-TAAAT-ATATAAATTTTA
1 TTTTAAATATAAATAATAT-AATTTTA
105043 TGTTAATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
29 2 0.04
30 9 0.19
31 21 0.45
32 15 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTTAAATATAAATAATATAATTTTAAATAT
Found at i:105012 original size:22 final size:23
Alignment explanation
Indices: 104954--105017 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
104944 TTTAATTTTT
*
104954 ATTTTAAATATAAATA-ATATAA
1 ATTTTAAATTTAAATATATATAA
*
104976 TTTTTAAAATTTTTAAATATATA-AA
1 ATTTT-AAA--TTTAAATATATATAA
105001 ATTTTAAATTTAAATAT
1 ATTTTAAATTTAAATAT
105018 TTTTATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
22 13 0.37
23 3 0.09
24 3 0.09
25 13 0.37
26 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTTAAATTTAAATATATATAA
Found at i:105021 original size:16 final size:15
Alignment explanation
Indices: 104978--105022 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
104968 TAATATAATT
104978 TTTAAAATTTTTAAA
1 TTTAAAATTTTTAAA
104993 TATATAAAA-TTTTAAA
1 T-T-TAAAATTTTTAAA
105009 TTTAAATATTTTTA
1 TTTAAA-ATTTTTA
105023 TATTAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 3 0.12
16 14 0.54
17 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAAATTTTTAAA
Found at i:105030 original size:21 final size:20
Alignment explanation
Indices: 105004--105057 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
104994 ATATAAAATT
105004 TTAAATTTAAATATTTTTATA
1 TTAAATTTAAATA-TTTTATA
* *
105025 TTAAATATATAA-ATTTTATG
1 TTAAATTTA-AATATTTTATA
105045 TTAATATTTAAAT
1 TTAA-ATTTAAAT
105058 TTAAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 12 0.44
21 13 0.48
22 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAAATTTAAATATTTTATA
Found at i:105056 original size:19 final size:20
Alignment explanation
Indices: 104988--105059 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 20
104978 TTTAAAATTT
*
104988 TTAAATATATAAAATTTTAAA
1 TTAAATATAT-AAATTTTATA
*
105009 TTTAA-ATAT---TTTTATA
1 TTAAATATATAAATTTTATA
*
105025 TTAAATATATAAATTTTATG
1 TTAAATATATAAATTTTATA
*
105045 TT-AATATTTAAATTT
1 TTAAATATATAAATTT
105060 AAATTTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
16 10 0.24
17 4 0.10
19 12 0.29
20 12 0.29
21 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (20 bp):
TTAAATATATAAATTTTATA
Found at i:105065 original size:12 final size:13
Alignment explanation
Indices: 105045--105073 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
105035 AAATTTTATG
105045 TTAATATTTAAAT
1 TTAATATTTAAAT
105058 TTAA-ATTTAAAT
1 TTAATATTTAAAT
105070 TTAA
1 TTAA
105074 GTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAATATTTAAAT
Found at i:109428 original size:24 final size:24
Alignment explanation
Indices: 109401--109663 Score: 313
Period size: 24 Copynumber: 10.8 Consensus size: 24
109391 CCCCATATTC
109401 CCCATGTTGTTGGGTGGCATCCCT
1 CCCATGTTGTTGGGTGGCATCCCT
*
109425 CCCATG-T-TAGGG-GGCATCCCT
1 CCCATGTTGTTGGGTGGCATCCCT
*
109446 CCCATGTTGTTGGGGGGCATCCCT
1 CCCATGTTGTTGGGTGGCATCCCT
*
109470 CCTATGTTGTTAGGCGGTGGCATCCCT
1 CCCATGTTGTT--G-GGTGGCATCCCT
109497 CCCATGTTGTTAGGAGGTGGCATCCCT
1 CCCATGTTGTT--G-GGTGGCATCCCT
*
109524 CCCATGTTGTTGGGTGGCATCCTT
1 CCCATGTTGTTGGGTGGCATCCCT
*
109548 CCCATGTTGTTGGGAGGCATCCCT
1 CCCATGTTGTTGGGTGGCATCCCT
*
109572 CCTATGTTGTTAGGAGGTGGCATCCCT
1 CCCATGTTGTT--G-GGTGGCATCCCT
* *
109599 CCCATGTTG--GAG-GGCATCCTT
1 CCCATGTTGTTGGGTGGCATCCCT
*
109620 CCCATGTTGTTGGGAGGCATCCCT
1 CCCATGTTGTTGGGTGGCATCCCT
*
109644 CCCATGTTGTTGGGAGGCAT
1 CCCATGTTGTTGGGTGGCAT
109664 TCCAGCTGTA
Statistics
Matches: 211, Mismatches: 16, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
21 32 0.15
22 6 0.03
23 8 0.04
24 96 0.45
25 1 0.00
26 2 0.01
27 66 0.31
ACGTcount: A:0.12, C:0.27, G:0.30, T:0.31
Consensus pattern (24 bp):
CCCATGTTGTTGGGTGGCATCCCT
Found at i:111788 original size:23 final size:23
Alignment explanation
Indices: 111758--111804 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
111748 CCGCGGCAGC
111758 GGCGGCAGAAAAGGAAGAGAAAG
1 GGCGGCAGAAAAGGAAGAGAAAG
* * *
111781 GGCGGCAGGAAGGGAAGAGGAAG
1 GGCGGCAGAAAAGGAAGAGAAAG
111804 G
1 G
111805 AAGTTAGGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.51, T:0.00
Consensus pattern (23 bp):
GGCGGCAGAAAAGGAAGAGAAAG
Found at i:112072 original size:11 final size:11
Alignment explanation
Indices: 112043--112206 Score: 78
Period size: 11 Copynumber: 15.1 Consensus size: 11
112033 AAAAAATATA
112043 AATAT-ATTATT
1 AATATAATTA-T
112054 AATAATAATTAT
1 AAT-ATAATTAT
112066 AATATAATTAT
1 AATATAATTAT
112077 AATATAA--A-
1 AATATAATTAT
112085 AATA-AA-TAT
1 AATATAATTAT
112094 AATATAAATATAT
1 AATAT-AAT-TAT
*
112107 AA-AAAATTAT
1 AATATAATTAT
112117 AATATAAATTATT
1 AATAT-AATTA-T
* *
112130 AAT-TTATTAA
1 AATATAATTAT
* *
112140 AATTTAAATA-
1 AATATAATTAT
*
112150 AATATATATTTT
1 AATATA-ATTAT
112162 AAATATAATTAT
1 -AATATAATTAT
* * *
112174 TATTTAA-AAT
1 AATATAATTAT
*
112184 AATATAAATAT
1 AATATAATTAT
* *
112195 TATATAAATAT
1 AATATAATTAT
112206 A
1 A
112207 TTAATTAATA
Statistics
Matches: 119, Mismatches: 18, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
7 2 0.02
8 5 0.04
9 5 0.04
10 20 0.17
11 51 0.43
12 17 0.14
13 19 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AATATAATTAT
Found at i:112073 original size:17 final size:17
Alignment explanation
Indices: 112043--112100 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
112033 AAAAAATATA
* * *
112043 AATATATTATTAATAAT
1 AATATAATAATAATTAT
112060 AATTATAAT-ATAATTAT
1 AA-TATAATAATAATTAT
* *
112077 AATATAAAAATAAATAT
1 AATATAATAATAATTAT
112094 AATATAA
1 AATATAA
112101 ATATATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 5 0.15
17 24 0.71
18 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAATAATAATTAT
Found at i:112092 original size:23 final size:22
Alignment explanation
Indices: 112035--112123 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 22
112025 TATTTTATAA
*
112035 AAAATATAAATATATTATTAATA-
1 AAAA-ATAAATATAATA-TAATAT
* *
112058 ATAATTATAATATAATTATAATAT
1 AAAAATA-AATATAA-TATAATAT
112082 AAAAATAAATATAATATAAATAT
1 AAAAATAAATATAATAT-AATAT
*
112105 ATAAAA-AATTATAATATAA
1 A-AAAATAAATATAATATAA
112124 ATTATTAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
22 7 0.13
23 37 0.67
24 11 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATAAATATAATATAATAT
Found at i:112101 original size:17 final size:17
Alignment explanation
Indices: 112069--112101 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
112059 TAATTATAAT
*
112069 ATAATTATAATATAAAA
1 ATAAATATAATATAAAA
112086 ATAAATATAATATAAA
1 ATAAATATAATATAAA
112102 TATATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAATATAATATAAAA
Found at i:112124 original size:23 final size:24
Alignment explanation
Indices: 112057--112125 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 24
112047 TATTATTAAT
112057 AATAATTATAATATAATTATAATATAAA
1 AATAATTATAATATAA--AT-ATAT-AA
*
112085 AATAAATATAATATAAATATATAA
1 AATAATTATAATATAAATATATAA
112109 AA-AATTATAATATAAAT
1 AATAATTATAATATAAAT
112126 TATTAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 14 0.36
24 4 0.10
25 4 0.10
26 2 0.05
28 15 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AATAATTATAATATAAATATATAA
Found at i:112162 original size:17 final size:17
Alignment explanation
Indices: 112142--112207 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
112132 TTTATTAAAA
112142 TTTAAATAAATATATAT
1 TTTAAATAAATATATAT
112159 TTTAAATATAAT-TATTAT
1 TTTAAATA-AATATA-TAT
* *
112177 TTAAAAT-AATATAAAT
1 TTTAAATAAATATATAT
* *
112193 ATTATATAAATATAT
1 TTTAAATAAATATAT
112208 TAATTAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 9 0.23
17 18 0.46
18 12 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATAAATATATAT
Found at i:112189 original size:21 final size:20
Alignment explanation
Indices: 112163--112219 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
112153 ATATATTTTA
112163 AATATAATTATTATTTAAAAT
1 AATATAATTATTATTT-AAAT
* *
112184 AATATAAATATTATATAAAT
1 AATATAATTATTATTTAAAT
*
112204 -ATATTAATTAATATTT
1 AATA-TAATTATTATTT
112220 TTCATTATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.10
20 13 0.43
21 14 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATAATTATTATTTAAAT
Found at i:112209 original size:34 final size:35
Alignment explanation
Indices: 112141--112214 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 35
112131 ATTTATTAAA
* *
112141 ATTT-AAATAAATATATATTTTAAATATAATTATT
1 ATTTAAAATAAATATAAATATTAAATATAATTATT
*
112175 ATTTAAAAT-AATATAAATATTATATA-AATATATT
1 ATTTAAAATAAATATAAATATTAAATATAAT-TATT
*
112209 AATTAA
1 ATTTAA
112215 TATTTTTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 3 0.09
34 27 0.79
35 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
ATTTAAAATAAATATAAATATTAAATATAATTATT
Found at i:112472 original size:6 final size:6
Alignment explanation
Indices: 112461--112487 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
112451 TAATAATATC
112461 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
112488 TTTTAAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:114426 original size:31 final size:31
Alignment explanation
Indices: 114372--114453 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
114362 ATAATTATTT
*
114372 TTAATATATTTTACATTAATATAAACTTAATATA
1 TTAATA-A-TTTATATT-ATATAAACTTAATATA
*
114406 TTAATAATTTATATTATATAAATTTAATATA
1 TTAATAATTTATATTATATAAACTTAATATA
* *
114437 TTTATATTTTATTATTA
1 TTAATAATTTA-TATTA
114454 CATTTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 24 0.56
32 12 0.28
33 1 0.02
34 6 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TTAATAATTTATATTATATAAACTTAATATA
Found at i:115201 original size:12 final size:12
Alignment explanation
Indices: 115184--115213 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
115174 TTGAGGCTAC
115184 CAGGAAGGAGGA
1 CAGGAAGGAGGA
115196 CAGGAAGGAGGA
1 CAGGAAGGAGGA
115208 -AGGAAG
1 CAGGAAG
115214 CTAGCACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.43, C:0.07, G:0.50, T:0.00
Consensus pattern (12 bp):
CAGGAAGGAGGA
Found at i:116895 original size:2 final size:2
Alignment explanation
Indices: 116884--116917 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
116874 AAAAAATTAA
* *
116884 AT AT AA AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116918 CGAATACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:120903 original size:18 final size:19
Alignment explanation
Indices: 120872--120911 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
120862 AGGTAAAGTT
120872 AATTTATTTTAAAT-ATAA
1 AATTTATTTTAAATCATAA
120890 AATTT-TTTTAAAATCATAA
1 AATTTATTTT-AAATCATAA
120909 AAT
1 AAT
120912 AAAAAAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTATTTTAAATCATAA
Found at i:121405 original size:20 final size:20
Alignment explanation
Indices: 121380--121425 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
121370 ACTACACTTG
*
121380 AATAAACATGAAATTAATGT
1 AATAAACACGAAATTAATGT
*
121400 AATAAATACGAAATTAATGT
1 AATAAACACGAAATTAATGT
121420 AATAAA
1 AATAAA
121426 TATCATATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.28
Consensus pattern (20 bp):
AATAAACACGAAATTAATGT
Found at i:121426 original size:20 final size:20
Alignment explanation
Indices: 121389--121427 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
121379 GAATAAACAT
121389 GAAATTAATGTAATAAATAC
1 GAAATTAATGTAATAAATAC
121409 GAAATTAATGTAATAAATA
1 GAAATTAATGTAATAAATA
121428 TCATATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (20 bp):
GAAATTAATGTAATAAATAC
Found at i:126818 original size:24 final size:26
Alignment explanation
Indices: 126767--126824 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
126757 TGGGTGGCTA
*
126767 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
126793 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
126817 GTCAACAA
1 GTCAACAA
126825 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:126853 original size:27 final size:27
Alignment explanation
Indices: 126814--126879 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
126804 CCACCATGTG
*
126814 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
126841 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
126868 TTTGTCAAAAAT
1 TTTGTCAAAAAT
126880 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:126909 original size:24 final size:24
Alignment explanation
Indices: 126841--126910 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
126831 TTACTTTGTA
* *
126841 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
126868 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
126892 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
126911 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:126982 original size:20 final size:20
Alignment explanation
Indices: 126957--126994 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
126947 AAAAGGAGGC
*
126957 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
126977 TCCCTCATCCCTCTCAAG
1 TCCCTCATCCCTCTCAAG
126995 CATTCTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.50, G:0.05, T:0.29
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:131427 original size:24 final size:26
Alignment explanation
Indices: 131376--131433 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
131366 TGGGTGGCTA
*
131376 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
131402 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
131426 GTCAACAA
1 GTCAACAA
131434 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:131462 original size:27 final size:27
Alignment explanation
Indices: 131423--131488 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
131413 CCACCATGTG
*
131423 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
131450 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
131477 TTTGTCAAAAAT
1 TTTGTCAAAAAT
131489 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:131518 original size:24 final size:24
Alignment explanation
Indices: 131450--131519 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
131440 TTACTTTGTA
* *
131450 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
131477 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
131501 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
131520 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:131591 original size:20 final size:20
Alignment explanation
Indices: 131566--131603 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
131556 AAAAGGAGGC
*
131566 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
131586 TCCCTCATCCCTCTCAAG
1 TCCCTCATCCCTCTCAAG
131604 CATTCTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.50, G:0.05, T:0.29
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:142784 original size:28 final size:28
Alignment explanation
Indices: 142752--142807 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
142742 TTATCAGGAG
*
142752 TATGTTATTATGTTTGTTTAAGCTAAAA
1 TATGTTATTATGTTTGTTTAAGATAAAA
142780 TATGTTATTATGTTTGTTTAAGATAAAA
1 TATGTTATTATGTTTGTTTAAGATAAAA
142808 ACTGTAAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (28 bp):
TATGTTATTATGTTTGTTTAAGATAAAA
Found at i:150802 original size:3 final size:3
Alignment explanation
Indices: 150794--150820 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
150784 TTAACTACAA
150794 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
150821 CATATATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:169191 original size:16 final size:15
Alignment explanation
Indices: 169169--169215 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
169159 CGTAATTATG
169169 TAATATAAATAAATA
1 TAATATAAATAAATA
*
169184 TAAATATAATATAAAAA
1 T-AATATAA-ATAAATA
169201 TAATATAAATTAAAT
1 TAATATAAA-TAAAT
169216 TTTTTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.07
16 18 0.67
17 7 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATATAAATAAATA
Found at i:169196 original size:11 final size:11
Alignment explanation
Indices: 169169--169210 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
169159 CGTAATTATG
169169 TAATATAAATA
1 TAATATAAATA
169180 -AATATAAATA
1 TAATATAAATA
*
169190 TAATATAAAAA
1 TAATATAAATA
169201 TAATATAAAT
1 TAATATAAAT
169211 TAAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATATAAATA
Found at i:173053 original size:18 final size:19
Alignment explanation
Indices: 173019--173054 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
173009 AATATGATTA
*
173019 TTAAAAGATATTTTTTATC
1 TTAAAAGATAATTTTTATC
173038 TTAAAA-ATAATTTTTAT
1 TTAAAAGATAATTTTTAT
173055 TTATTGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
TTAAAAGATAATTTTTATC
Found at i:176500 original size:21 final size:20
Alignment explanation
Indices: 176469--176513 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
176459 TACGATAAAA
176469 AAATTTATTAAAAATAATTT
1 AAATTTATTAAAAATAATTT
* *
176489 AAATTATATTAAAATTACTTT
1 AAATT-TATTAAAAATAATTT
176510 AAAT
1 AAAT
176514 AGTAAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTATTAAAAATAATTT
Found at i:177505 original size:20 final size:22
Alignment explanation
Indices: 177466--177507 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
177456 AGTTTTACCA
*
177466 TTAAAATAAATTAGTTAAAATT
1 TTAAAATAAATCAGTTAAAATT
177488 TTAAAA-AAATCA-TTAAAATT
1 TTAAAATAAATCAGTTAAAATT
177508 AACATATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TTAAAATAAATCAGTTAAAATT
Found at i:181987 original size:18 final size:19
Alignment explanation
Indices: 181964--182009 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
181954 AAGTTAGGTC
181964 AATTTTTTAAT-TAAATTT
1 AATTTTTTAATCTAAATTT
*
181982 AATTTTTTTATCTAAATTT
1 AATTTTTTAATCTAAATTT
182001 -ATTTTTTAA
1 AATTTTTTAA
182010 ATTTAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTTTAATCTAAATTT
Found at i:181988 original size:19 final size:18
Alignment explanation
Indices: 181966--182012 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
181956 GTTAGGTCAA
181966 TTTTTTAATTAAATTTAAT
1 TTTTTTAATTAAATTT-AT
181985 TTTTTT-ATCTAAATTTAT
1 TTTTTTAAT-TAAATTTAT
*
182003 TTTTTAAATT
1 TTTTTTAATT
182013 TAATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTTAATTAAATTTAT
Found at i:183170 original size:96 final size:96
Alignment explanation
Indices: 183006--183196 Score: 382
Period size: 96 Copynumber: 2.0 Consensus size: 96
182996 TAATCTTCCC
183006 TCTACCAACCAATTATCTGTCAGATTTTCAAACAACCAGCCAATATAGCATGTAAGTAAAAGAAG
1 TCTACCAACCAATTATCTGTCAGATTTTCAAACAACCAGCCAATATAGCATGTAAGTAAAAGAAG
183071 AGTTGATTTTGTTGACTCTTTTGGCTGAAAA
66 AGTTGATTTTGTTGACTCTTTTGGCTGAAAA
183102 TCTACCAACCAATTATCTGTCAGATTTTCAAACAACCAGCCAATATAGCATGTAAGTAAAAGAAG
1 TCTACCAACCAATTATCTGTCAGATTTTCAAACAACCAGCCAATATAGCATGTAAGTAAAAGAAG
183167 AGTTGATTTTGTTGACTCTTTTGGCTGAAA
66 AGTTGATTTTGTTGACTCTTTTGGCTGAAA
183197 TTTTCAGCCT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (96 bp):
TCTACCAACCAATTATCTGTCAGATTTTCAAACAACCAGCCAATATAGCATGTAAGTAAAAGAAG
AGTTGATTTTGTTGACTCTTTTGGCTGAAAA
Found at i:190847 original size:12 final size:12
Alignment explanation
Indices: 190827--190883 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
190817 TTTTATAATG
*
190827 TAATAATTATAA
1 TAATTATTATAA
190839 TAATTATTATAA
1 TAATTATTATAA
* *
190851 AAATTATTGTAA
1 TAATTATTATAA
190863 TAA-T-TTATAA
1 TAATTATTATAA
190873 T-ATT-TTATAA
1 TAATTATTATAA
190883 T
1 T
190884 TTTTTATTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
9 1 0.03
10 14 0.36
11 1 0.03
12 23 0.59
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
TAATTATTATAA
Found at i:191048 original size:24 final size:26
Alignment explanation
Indices: 191005--191052 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
190995 ATTTATCTTT
191005 AATTATAATAAATATCAATAATAAAA
1 AATTATAATAAATATCAATAATAAAA
*
191031 AATTATAA-AATTAT-AATAATAA
1 AATTATAATAAATATCAATAATAA
191053 GATTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 5 0.24
26 8 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AATTATAATAAATATCAATAATAAAA
Found at i:197194 original size:43 final size:43
Alignment explanation
Indices: 197133--197244 Score: 197
Period size: 43 Copynumber: 2.6 Consensus size: 43
197123 TTTCAACTTT
*
197133 TCAATTTAGATATTTATAACAAAAATCAAAACCCACACTATTC
1 TCAATTTAGAGATTTATAACAAAAATCAAAACCCACACTATTC
* *
197176 TCAATTTAGAGATTTATAACAAAAATCACAATCCACACTATTC
1 TCAATTTAGAGATTTATAACAAAAATCAAAACCCACACTATTC
197219 TCAATTTAGAGATTTATAACAAAAAT
1 TCAATTTAGAGATTTATAACAAAAAT
197245 TCACGAACCA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.31
Consensus pattern (43 bp):
TCAATTTAGAGATTTATAACAAAAATCAAAACCCACACTATTC
Found at i:199398 original size:11 final size:11
Alignment explanation
Indices: 199377--199428 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
199367 AGTTTATGAT
*
199377 AATATATATAA
1 AATAAATATAA
*
199388 AATTAATATAA
1 AATAAATATAA
*
199399 TATAAATATAA
1 AATAAATATAA
* *
199410 TATAAAAATAA
1 AATAAATATAA
199421 AATAAATA
1 AATAAATA
199429 CAATTACATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAATATAA
Found at i:199408 original size:6 final size:6
Alignment explanation
Indices: 199382--199449 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
199372 ATGATAATAT
* *
199382 ATATAA A-ATTA ATAT-A ATATAA ATAT-A ATATAA AAATAA A-ATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
* *
199426 ATACAA TTACATAA ATATAA ATAT
1 ATATAA --ATATAA ATATAA ATAT
199450 TTCGTAATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
5 19 0.38
6 27 0.54
8 4 0.08
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:199660 original size:22 final size:20
Alignment explanation
Indices: 199635--199689 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
199625 CATTTGTATC
*
199635 ATATTAATTTTATAATATTTAT
1 ATATTAATATTAT-AT-TTTAT
*
199657 ATATTTATATTATATTTTAT
1 ATATTAATATTATATTTTAT
199677 ATCATTTAATATT
1 AT-A-TTAATATT
199690 TTAATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 7 0.25
21 3 0.11
22 18 0.64
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTAATATTATATTTTAT
Found at i:199692 original size:29 final size:28
Alignment explanation
Indices: 199635--199690 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
199625 CATTTGTATC
199635 ATATTAATTTTATAATATTTATATATTT
1 ATATTAATTTTATAATATTTATATATTT
199663 ATATTATATTTTAT-ATCATTTA-ATATTT
1 ATATTA-ATTTTATAAT-ATTTATATATTT
199691 TAATTCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
ATATTAATTTTATAATATTTATATATTT
Found at i:200069 original size:8 final size:8
Alignment explanation
Indices: 200056--200170 Score: 59
Period size: 8 Copynumber: 14.4 Consensus size: 8
200046 TATTTCATAT
200056 TATATTTA
1 TATATTTA
200064 TATATTT-
1 TATATTTA
200071 TATTATATTA
1 TA-TAT-TTA
200081 TA-A-TTA
1 TATATTTA
200087 T-T-TTTA
1 TATATTTA
*
200093 AATTATTT-
1 TA-TATTTA
200101 TATATTTA
1 TATATTTA
200109 TATAAATTTAA
1 TAT--ATTT-A
200120 TATATTTA
1 TATATTTA
*
200128 TATATTCA
1 TATATTTA
200136 TATAATATTA
1 TAT-AT-TTA
200146 TAT-TTTA
1 TATATTTA
*
200153 -ATAATTTT
1 TAT-ATTTA
200161 TATA-TTA
1 TATATTTA
200168 TAT
1 TAT
200171 TCATATAATT
Statistics
Matches: 84, Mismatches: 6, Indels: 35
0.67 0.05 0.28
Matches are distributed among these distances:
6 9 0.11
7 15 0.18
8 32 0.38
9 13 0.15
10 11 0.13
11 4 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (8 bp):
TATATTTA
Found at i:200117 original size:17 final size:18
Alignment explanation
Indices: 200097--200131 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
200087 TTTTTAAATT
200097 ATTT-TATATTTATATAA
1 ATTTATATATTTATATAA
200114 ATTTAATATATTTATATA
1 ATTT-ATATATTTATATA
200132 TTCATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
19 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATATTTATATAA
Found at i:200132 original size:10 final size:10
Alignment explanation
Indices: 200038--200132 Score: 62
Period size: 10 Copynumber: 9.9 Consensus size: 10
200028 TTTGAACACC
*
200038 TTTATATTTA
1 TTTATATATA
200048 TTTCATATTATA
1 TTT-ATA-TATA
200060 TTTATATAT-
1 TTTATATATA
200069 TTTAT-TATA
1 TTTATATATA
200078 -TTATA-ATTA
1 TTTATATA-TA
200087 TTT-T-TA-A
1 TTTATATATA
* *
200094 ATTATTTTATA
1 TTTA-TATATA
*
200105 TTTATATAAA
1 TTTATATATA
200115 TTTA-ATATA
1 TTTATATATA
200124 TTTATATAT
1 TTTATATAT
200133 TCATATAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 24
0.69 0.06 0.25
Matches are distributed among these distances:
7 3 0.04
8 8 0.12
9 18 0.27
10 22 0.33
11 10 0.15
12 6 0.09
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATATATA
Found at i:200156 original size:16 final size:18
Alignment explanation
Indices: 200102--200165 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 18
200092 AAATTATTTT
200102 ATATTTATATAAATTTAAT-
1 ATATTTATAT--ATTTAATA
*
200121 ATATTTATATATTCATATA
1 ATATTTATATATTTA-ATA
200140 ATA-TTATAT-TTTAATA
1 ATATTTATATATTTAATA
*
200156 ATTTTTATAT
1 ATATTTATAT
200166 TATATTCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 5 0.13
17 13 0.33
18 8 0.21
19 13 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTTATATATTTAATA
Found at i:201057 original size:19 final size:19
Alignment explanation
Indices: 201033--201110 Score: 68
Period size: 19 Copynumber: 4.0 Consensus size: 19
201023 TAATTTATAT
201033 TATATTAATTTAAATAAAA
1 TATATTAATTTAAATAAAA
* * *
201052 TATATTATTTTAATTTATAA
1 TATATTAATTTAA-ATAAAA
* *
201072 T-TATTATTTTAAGTAAAA
1 TATATTAATTTAAATAAAA
*
201090 CTAAATTAATTTAAAATAAAA
1 -TATATTAATTT-AAATAAAA
201111 ATAAAATACA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.09
19 24 0.51
20 12 0.26
21 7 0.15
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
TATATTAATTTAAATAAAA
Found at i:201103 original size:39 final size:39
Alignment explanation
Indices: 200986--201103 Score: 102
Period size: 39 Copynumber: 3.1 Consensus size: 39
200976 ATAATTATAC
* * **
200986 TTAAATTATTATATATTAATAAAAATTAAAAT--ATTAA-
1 TTAATTTATAATATATTAATTTAAA-TAAAATAAATTAAT
* * *
201023 -TAATTTATATTATATTAATTTAAATAAAATATATTATT
1 TTAATTTATAATATATTAATTTAAATAAAATAAATTAAT
* *
201061 TTAATTTATAAT-TATTATTTTAAGTAAAACTAAATTAAT
1 TTAATTTATAATATATTAATTTAAATAAAA-TAAATTAAT
201100 TTAA
1 TTAA
201104 AATAAAAATA
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
35 6 0.09
36 19 0.29
37 4 0.06
38 15 0.23
39 21 0.32
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
TTAATTTATAATATATTAATTTAAATAAAATAAATTAAT
Found at i:201260 original size:5 final size:5
Alignment explanation
Indices: 201252--201364 Score: 51
Period size: 5 Copynumber: 22.8 Consensus size: 5
201242 TGTCTAATTT
* * * *
201252 TATAA TATAA TAGGAT TATAT TATAAA TATAA TATAAA AATAA T-TAAA
1 TATAA TATAA TA-TAA TATAA TAT-AA TATAA TAT-AA TATAA TAT-AA
* *
201300 TATAA TATAA -AT-A TTTAA -A-AA TAT-A TATAA TATATA TTATAA TATAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA-A -TATAA TATAA
* *
201347 TAAAA TAAAA TA-AA TATA
1 TATAA TATAA TATAA TATA
201365 GTATGAAATA
Statistics
Matches: 84, Mismatches: 11, Indels: 26
0.69 0.09 0.21
Matches are distributed among these distances:
3 3 0.04
4 13 0.15
5 50 0.60
6 14 0.17
7 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:201309 original size:32 final size:31
Alignment explanation
Indices: 201268--201382 Score: 91
Period size: 32 Copynumber: 3.7 Consensus size: 31
201258 ATAATAGGAT
*
201268 TATATTATAAATATAATATAAAAATAATTAAA
1 TATAATATAAATATAATATAAAAATAA-TAAA
201300 TATAATATAAATAT--T-TAAAAATATATATAA
1 TATAATATAAATATAATATAAAAATA-ATA-AA
*
201330 TAT-ATATTATAATAT-AT-TAAAATAAAATAAA
1 TATAATA-TA-AATATAATATAAAA-ATAATAAA
*
201361 TATAGTATGAAATATAA-ATAAA
1 TATAATAT-AAATATAATATAAA
201383 TTATTTTTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
29 13 0.19
30 9 0.13
31 16 0.23
32 30 0.43
33 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
TATAATATAAATATAATATAAAAATAATAAA
Found at i:201321 original size:21 final size:22
Alignment explanation
Indices: 201268--201383 Score: 97
Period size: 21 Copynumber: 5.5 Consensus size: 22
201258 ATAATAGGAT
*
201268 TATATTATAAATATAATATAAA
1 TATATAATAAATATAATATAAA
201290 -A-ATAATTAAATATAATATAAA
1 TATATAA-TAAATATAATATAAA
*
201311 TATTTAA-AAATAT-ATAT-AA
1 TATATAATAAATATAATATAAA
*
201330 TATATATTATAATAT-AT-TAAA
1 TATATAATA-AATATAATATAAA
* *
201351 -ATAAAATAAATATAGTATGAAA
1 TATATAATAAATATAATAT-AAA
201373 TATA-AATAAAT
1 TATATAATAAAT
201384 TATTTTTTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
19 12 0.16
20 16 0.21
21 32 0.42
22 11 0.14
23 6 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TATATAATAAATATAATATAAA
Found at i:201723 original size:21 final size:21
Alignment explanation
Indices: 201699--201742 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
201689 TCCTCCTCAC
201699 TTTCGCCATCGTC-TCTTTCCT
1 TTTCGCCATC-TCTTCTTTCCT
*
201720 TTTCGCCCTCTCTTCTTTCCT
1 TTTCGCCATCTCTTCTTTCCT
201741 TT
1 TT
201743 CCTCTGGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.02, C:0.39, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTCGCCATCTCTTCTTTCCT
Found at i:202225 original size:19 final size:19
Alignment explanation
Indices: 202189--202238 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
202179 AGGTTTAATT
*
202189 TAATTTTGATATAGAACAA
1 TAATTTTGATATAAAACAA
*
202208 TAATGTTTGA-ATAAAACAT
1 TAAT-TTTGATATAAAACAA
202227 TACATTTT-ATAT
1 TA-ATTTTGATAT
202239 TCGATTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 1 0.04
19 18 0.69
20 7 0.27
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (19 bp):
TAATTTTGATATAAAACAA
Done.