Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 24 of 25
Found at i:3433551 original size:20 final size:20
Alignment explanation
Indices: 3433526--3433564 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3433516 TCCATGACTT
3433526 TTTATATATATATATATATG
1 TTTATATATATATATATATG
3433546 TTTATATATATATATATAT
1 TTTATATATATATATATAT
3433565 AAAAGAAAGG
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:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTATATATATATATATATG
Found at i:3434895 original size:24 final size:24
Alignment explanation
Indices: 3434863--3434910 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3434853 ATTTTAAAAA
* *
3434863 TATATTTATATCATGTAT-TATTTT
1 TATAATTATAT-ATATATATATTTT
3434887 TATAATTATATATATATATATTTT
1 TATAATTATATATATATATATTTT
3434911 ATTTATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TATAATTATATATATATATATTTT
Found at i:3435168 original size:6 final size:6
Alignment explanation
Indices: 3435157--3435193 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3435147 AAGTACGTTC
*
3435157 TTATAT TTATAT TT-TAA TTATA- TTATAT TTATAT TTA
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTA
3435194 AAATATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 9 0.32
6 19 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TTATAT
Found at i:3435185 original size:22 final size:20
Alignment explanation
Indices: 3435157--3435209 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
3435147 AAGTACGTTC
*
3435157 TTATATTTATATTTTAATTATA
1 TTATATTTATA-TTTAA-AATA
3435179 TTATATTTATATTTAAAATA
1 TTATATTTATATTTAAAATA
*
3435199 TTATATATATA
1 TTATATTTATA
3435210 ATTTGATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.45
21 5 0.17
22 11 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATATTTATATTTAAAATA
Found at i:3436087 original size:17 final size:17
Alignment explanation
Indices: 3436065--3436099 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3436055 ATATAATACG
3436065 AATTAT-TAATATATAAA
1 AATTATATAA-ATATAAA
3436082 AATTATATAAATATAAA
1 AATTATATAAATATAAA
3436099 A
1 A
3436100 TATCGTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTATATAAATATAAA
Found at i:3437757 original size:22 final size:23
Alignment explanation
Indices: 3437731--3437781 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
3437721 TTGTTTCGTA
* *
3437731 AAATTTATATTT-TTTTAAATTT
1 AAATTAATATTTGATTTAAATTT
* *
3437753 TAATTAATCTTTGATTTAAATTT
1 AAATTAATATTTGATTTAAATTT
3437776 AAATTA
1 AAATTA
3437782 TTAAATGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATTAATATTTGATTTAAATTT
Found at i:3438844 original size:33 final size:33
Alignment explanation
Indices: 3438802--3438866 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
3438792 TTCATGTGGG
3438802 AGATGAAAGTTACCCTTTCTTGGAACGAATCAT
1 AGATGAAAGTTACCCTTTCTTGGAACGAATCAT
* *
3438835 AGATGAAAGTTGCCCTTTCTTGTAACGAATCA
1 AGATGAAAGTTACCCTTTCTTGGAACGAATCA
3438867 AATATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (33 bp):
AGATGAAAGTTACCCTTTCTTGGAACGAATCAT
Found at i:3439566 original size:2 final size:2
Alignment explanation
Indices: 3439561--3439587 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3439551 ATATACGTAC
3439561 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 A
3439588 ATTAGGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3440494 original size:19 final size:22
Alignment explanation
Indices: 3440472--3440516 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
3440462 TTGTGTTCGT
3440472 TTATTTTTAAA-TATT-T-TAA
1 TTATTTTTAAAGTATTATATAA
3440491 TTATTTTTAAAGTATTATATAA
1 TTATTTTTAAAGTATTATATAA
3440513 TTAT
1 TTAT
3440517 ATATATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
20 4 0.17
21 1 0.04
22 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTTTTAAAGTATTATATAA
Found at i:3440824 original size:19 final size:19
Alignment explanation
Indices: 3440800--3440846 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
3440790 TATTTTATAA
3440800 ATATTTTTGACACATTTAT
1 ATATTTTTGACACATTTAT
* *
3440819 ATATTTGTGACATATTTAT
1 ATATTTTTGACACATTTAT
*
3440838 ATTTTTTTG
1 ATATTTTTG
3440847 TGTCGTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (19 bp):
ATATTTTTGACACATTTAT
Found at i:3441208 original size:20 final size:20
Alignment explanation
Indices: 3441180--3441254 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
3441170 TCATACCCTG
3441180 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3441200 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
3441220 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
3441240 ATGTATCGATACATT
1 ATGTATCGATACATT
3441255 ATGTCCTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3441247 original size:40 final size:39
Alignment explanation
Indices: 3441180--3441257 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3441170 TCATACCCTG
* *
3441180 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
3441220 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
3441258 TCCTTTTACC
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:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:3442164 original size:23 final size:23
Alignment explanation
Indices: 3442137--3442192 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
3442127 AGCCTTTGAC
3442137 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
3442160 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
3442182 CATGCATTTTT
1 CATGCATTTTT
3442193 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:3442199 original size:20 final size:21
Alignment explanation
Indices: 3442145--3442199 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3442135 ACCATGCATT
**
3442145 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
3442166 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
3442188 -TTTTTAACATGT
1 TTTTTTAACATGT
3442200 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:3455258 original size:24 final size:23
Alignment explanation
Indices: 3455231--3455295 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 23
3455221 TTTACACCCA
3455231 AAAAAAAAAACAAAAAAAAAACAC
1 AAAAAAAAAACAAAAAAAAAA-AC
3455255 AAAAAAAAAACAAAACAAAAAAAC
1 AAAAAAAAAACAAAA-AAAAAAAC
*
3455279 AAAAAAAAAAGAAAAAA
1 AAAAAAAAAACAAAAAA
3455296 TAGCAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 2 0.05
24 31 0.79
25 6 0.15
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAACAAAAAAAAAAAC
Found at i:3455306 original size:24 final size:22
Alignment explanation
Indices: 3455231--3455308 Score: 86
Period size: 24 Copynumber: 3.4 Consensus size: 22
3455221 TTTACACCCA
3455231 AAAAAAAAAACAAAAAAAAAACAC
1 AAAAAAAAAAC-AAAAAAAAA-AC
3455255 AAAAAAAAAACAAAACAAAAAAAC
1 AAAAAAAAAAC-AAA-AAAAAAAC
* * *
3455279 AAAAAAAAAA-GAAAAAATAGC
1 AAAAAAAAAACAAAAAAAAAAC
3455300 AAAAAAAAA
1 AAAAAAAAA
3455309 TAGAAGGGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.30
22 2 0.04
24 27 0.54
25 6 0.12
ACGTcount: A:0.87, C:0.09, G:0.03, T:0.01
Consensus pattern (22 bp):
AAAAAAAAAACAAAAAAAAAAC
Found at i:3455308 original size:1 final size:1
Alignment explanation
Indices: 3455230--3455295 Score: 69
Period size: 1 Copynumber: 66.0 Consensus size: 1
3455220 CTTTACACCC
* * * * * * *
3455230 AAAAAAAAAAACAAAAAAAAAACACAAAAAAAAAACAAAACAAAAAAACAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3455295 A
1 A
3455296 TAGCAAAAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:3455311 original size:13 final size:12
Alignment explanation
Indices: 3455229--3455288 Score: 95
Period size: 13 Copynumber: 4.9 Consensus size: 12
3455219 CCTTTACACC
3455229 CAAAAAAAAAAA
1 CAAAAAAAAAAA
3455241 C-AAAAAAAAAA
1 CAAAAAAAAAAA
3455252 CACAAAAAAAAAA
1 CA-AAAAAAAAAA
3455265 CAAAACAAAAAAA
1 CAAAA-AAAAAAA
3455278 CAAAAAAAAAA
1 CAAAAAAAAAA
3455289 GAAAAAATAG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.24
12 10 0.22
13 24 0.53
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:3456571 original size:29 final size:29
Alignment explanation
Indices: 3456529--3457505 Score: 1462
Period size: 29 Copynumber: 33.9 Consensus size: 29
3456519 ATGTTCAACC
3456529 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3456558 CTTTTCAAAGCCCACAAATCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3456586 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3456614 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
3456643 CTTTTCAAAGCCCACAAATCAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
** *
3456672 ATTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3456701 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3456729 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3456758 CCTTTCAAAGCCCACAAGTTAGTGGCGC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3456786 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3456815 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3456844 -CTTTTAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3456871 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3456900 CCTTTCAAAGACCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3456929 CCTTTCAAAGCCCATAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3456958 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3456987 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3457016 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3457045 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3457074 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3457103 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3457132 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3457161 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3457190 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3457218 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3457246 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
3457275 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3457302 CCTTTTAAAGCTCACACAAGTCAGTGGCACT
1 CCTTTCAAAGC-C-CACAAGTCAGTGGCACT
* * *
3457333 CCTTTTAAAGCTCACGCAAGTCAGTGGTAC-
1 CCTTTCAAAGC-C-CACAAGTCAGTGGCACT
*
3457363 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
3457392 -CTTTCAAAGCCCACAAGTCAGTGGTA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
3457419 CCTTTCAAAGCCCACGAGTTAGTGACA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3457447 TCTTTCAAAGCCCACGCACGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
3457477 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
3457506 ACCCTTTTCA
Statistics
Matches: 873, Mismatches: 60, Indels: 29
0.91 0.06 0.03
Matches are distributed among these distances:
27 1 0.00
28 318 0.36
29 468 0.54
30 58 0.07
31 28 0.03
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:3458021 original size:20 final size:20
Alignment explanation
Indices: 3457993--3458067 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
3457983 TCATACCCTG
3457993 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3458013 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
3458033 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
3458053 ATGTATCGATACATT
1 ATGTATCGATACATT
3458068 ATGTCCTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3458060 original size:40 final size:39
Alignment explanation
Indices: 3457993--3458070 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3457983 TCATACCCTG
* *
3457993 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
3458033 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
3458071 TCCTTTTACC
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:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:3459005 original size:23 final size:23
Alignment explanation
Indices: 3458978--3459033 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
3458968 AGCCTTTGAC
3458978 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
3459001 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
3459023 CATGCATTTTT
1 CATGCATTTTT
3459034 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:3459040 original size:20 final size:21
Alignment explanation
Indices: 3458986--3459040 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3458976 ACCATGCATT
**
3458986 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
3459007 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
3459029 -TTTTTAACATGT
1 TTTTTTAACATGT
3459041 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:3462216 original size:30 final size:29
Alignment explanation
Indices: 3462182--3462239 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3462172 TAACAGTTTG
3462182 TAACAGTTTTAAAGGAGTTAACTTATTTTT
1 TAACAGTTTTAAA-GAGTTAACTTATTTTT
* **
3462212 TAACAGTTTTACATTGTTAACTTATTTT
1 TAACAGTTTTAAAGAGTTAACTTATTTT
3462240 ATATAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (29 bp):
TAACAGTTTTAAAGAGTTAACTTATTTTT
Found at i:3463622 original size:14 final size:14
Alignment explanation
Indices: 3463603--3463632 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3463593 ATACGCATCT
3463603 AACATCTATATCCA
1 AACATCTATATCCA
3463617 AACATCTATATCCA
1 AACATCTATATCCA
3463631 AA
1 AA
3463633 GGAAAAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
AACATCTATATCCA
Found at i:3469611 original size:21 final size:19
Alignment explanation
Indices: 3469581--3469619 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
3469571 TATATATATC
*
3469581 TTAAATAATAATTAAATTTAA
1 TTAAAAAAT-ATT-AATTTAA
3469602 TTAAAAAATATTAATTTA
1 TTAAAAAATATTAATTTA
3469620 TTATTACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAAAAATATTAATTTAA
Found at i:3470281 original size:32 final size:32
Alignment explanation
Indices: 3470210--3470309 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 32
3470200 AATGATTGTC
* * *
3470210 AAATTTATAAATAATTATTTTTAATA--TATC
1 AAATTTATAAGTAATTATATTTAATATTTATT
*
3470240 AAATTTATAAGTAATT-TGGTTTAATATTTATT
1 AAATTTATAAGTAATTAT-ATTTAATATTTATT
*
3470272 AAATTTATAAGAAATTATATTT-A-ATTTATT
1 AAATTTATAAGTAATTATATTTAATATTTATT
3470302 AAATTTAT
1 AAATTTAT
3470310 GATCAATATC
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.02
30 37 0.61
31 1 0.02
32 21 0.34
33 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (32 bp):
AAATTTATAAGTAATTATATTTAATATTTATT
Found at i:3470328 original size:31 final size:30
Alignment explanation
Indices: 3470265--3470329 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
3470255 TTGGTTTAAT
* *
3470265 ATTTATTAAATTTATAAGAAATTATATTTA
1 ATTTATTAAATTTATAACAAATCATATTTA
*
3470295 ATTTATTAAATTTATGATCAATATCA-ATTTA
1 ATTTATTAAATTTAT-AACAA-ATCATATTTA
3470326 ATTT
1 ATTT
3470330 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 15 0.50
31 12 0.40
32 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATTTATTAAATTTATAACAAATCATATTTA
Found at i:3470672 original size:3 final size:3
Alignment explanation
Indices: 3470664--3470690 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3470654 ATATTAATAT
3470664 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3470691 CTTTTTTTTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3475752 original size:3 final size:3
Alignment explanation
Indices: 3475744--3475778 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3475734 GAAGGCTGTA
3475744 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
3475779 CTTTATAGAA
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:0.00, C:0.34, G:0.34, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:3476993 original size:3 final size:3
Alignment explanation
Indices: 3476987--3477022 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3476977 AATAATCACA
3476987 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
3477023 TGTGTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3477802 original size:32 final size:33
Alignment explanation
Indices: 3477744--3477810 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
3477734 AAATTTTTAA
3477744 AATATAAATAAATAAATATATCAAAATTTAAAT
1 AATATAAATAAATAAATATATCAAAATTTAAAT
* * * *
3477777 AATATAAAT-TATTAATATATTAAAATTTATAT
1 AATATAAATAAATAAATATATCAAAATTTAAAT
3477809 AA
1 AA
3477811 ATATTTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
AATATAAATAAATAAATATATCAAAATTTAAAT
Found at i:3477814 original size:33 final size:34
Alignment explanation
Indices: 3477734--3477814 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 34
3477724 GAAAAGAAAT
*
3477734 AAATTTTTA-AAATATAAATAAATAAATATATCA
1 AAATTTATATAAATATAAATAAATAAATATATCA
* * * *
3477767 AAATTTAAAT-AATATAAAT-TATTAATATATTA
1 AAATTTATATAAATATAAATAAATAAATATATCA
3477799 AAATTTATATAAATAT
1 AAATTTATATAAATAT
3477815 TTTCAACATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 19 0.47
33 21 0.52
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (34 bp):
AAATTTATATAAATATAAATAAATAAATATATCA
Found at i:3478596 original size:7 final size:8
Alignment explanation
Indices: 3478569--3478597 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3478559 GACTATGAGA
3478569 AAAACACC
1 AAAACACC
3478577 AAAACACC
1 AAAACACC
3478585 AAAACA-C
1 AAAACACC
3478592 AAAACA
1 AAAACA
3478598 AAGATCTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAACACC
Found at i:3488405 original size:2 final size:2
Alignment explanation
Indices: 3488400--3488430 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3488390 GAAAAAAAAA
3488400 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 A
3488431 CACACCAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3497520 original size:29 final size:31
Alignment explanation
Indices: 3497473--3497548 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
3497463 TTCAATTATC
3497473 AAAATATATATATAA-TT-AAT-TAATAT-TA
1 AAAATATATA-ATAATTTAAATATAATATATA
*
3497501 ATAAATATATAATAATTTAAATATGATATATA
1 A-AAATATATAATAATTTAAATATAATATATA
3497533 AAAATATATTAATAAT
1 AAAATATA-TAATAAT
3497549 ATACATCTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 5 0.12
29 11 0.27
30 3 0.07
31 12 0.29
32 10 0.24
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
AAAATATATAATAATTTAAATATAATATATA
Found at i:3497550 original size:21 final size:21
Alignment explanation
Indices: 3497495--3497551 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
3497485 TAATTAATTA
*
3497495 ATATTAATAAATATATAATAAT
1 ATATTAAT-AATATATAAAAAT
*
3497517 -T-TAAATATGATATATAAAAAT
1 ATATTAATA--ATATATAAAAAT
3497538 ATATTAATAATATA
1 ATATTAATAATATA
3497552 CATCTTGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
19 1 0.04
20 4 0.14
21 17 0.61
22 1 0.04
23 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATATTAATAATATATAAAAAT
Found at i:3500588 original size:16 final size:17
Alignment explanation
Indices: 3500567--3500604 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3500557 AAAAATTTAT
*
3500567 AATAAAAAATTAAA-AA
1 AATAAAAAAGTAAATAA
*
3500583 AATAAAAAGGTAAATAA
1 AATAAAAAAGTAAATAA
3500600 AATAA
1 AATAA
3500605 TAGTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AATAAAAAAGTAAATAA
Found at i:3500810 original size:14 final size:14
Alignment explanation
Indices: 3500793--3500946 Score: 59
Period size: 14 Copynumber: 10.1 Consensus size: 14
3500783 TTTTATTTTT
3500793 TATTATTTAATTTA
1 TATTATTTAATTTA
*
3500807 TATTATATAATTTA
1 TATTATTTAATTTA
*
3500821 TTTTAAAATATTAATTCTA
1 TATT---AT-TTAATT-TA
*
3500840 TTATATATTCTATTTTA
1 -TAT-TATT-TAATTTA
3500857 TA-TA-TTAA--TA
1 TATTATTTAATTTA
3500867 TA-TATTCTAATTTAA
1 TATTATT-TAATTT-A
3500882 TAATTTATTTATAAATTTA
1 T-A-TTA-TT-T-AATTTA
3500901 TATTATTTATATTTA
1 TATTATTTA-ATTTA
3500916 TTATTATTT-ATTTA
1 -TATTATTTAATTTA
*
3500930 TTATTTATTTTATTTA
1 -TA-TTATTTAATTTA
3500946 T
1 T
3500947 GTCACATTAT
Statistics
Matches: 111, Mismatches: 7, Indels: 43
0.69 0.04 0.27
Matches are distributed among these distances:
10 6 0.05
11 1 0.01
12 5 0.05
13 1 0.01
14 28 0.25
15 15 0.14
16 18 0.16
17 8 0.07
18 14 0.13
19 7 0.06
20 7 0.06
21 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTTAATTTA
Found at i:3500851 original size:12 final size:12
Alignment explanation
Indices: 3500834--3500875 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
3500824 TAAAATATTA
3500834 ATTCTATTATAT
1 ATTCTATTATAT
*
3500846 ATTCTATTTTAT
1 ATTCTATTATAT
*
3500858 ATAT-TAATATAT
1 AT-TCTATTATAT
3500870 ATTCTA
1 ATTCTA
3500876 ATTTAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTCTATTATAT
Found at i:3500893 original size:4 final size:4
Alignment explanation
Indices: 3500884--3500946 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
3500874 TAATTTAATA
**
3500884 ATTT ATTT ATAA ATTT ATATT ATTT A--T ATTT A-TT A-TT ATTT ATTT
1 ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3500929 A-TT ATTT ATTTT ATTT AT
1 ATTT ATTT A-TTT ATTT AT
3500947 GTCACATTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
2 2 0.04
3 9 0.18
4 30 0.61
5 8 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:3500894 original size:24 final size:23
Alignment explanation
Indices: 3500832--3500894 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
3500822 TTTAAAATAT
*
3500832 TAATTCTATTATATATTCTATTTTA
1 TAATT-TATT-TATATTCTATTTAA
* *
3500857 TATATTAATATATATTCTAATTTAA
1 TA-ATTTATTTATATTCT-ATTTAA
3500882 TAATTTATTTATA
1 TAATTTATTTATA
3500895 AATTTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 17 0.55
25 11 0.35
26 3 0.10
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
TAATTTATTTATATTCTATTTAA
Found at i:3500915 original size:27 final size:27
Alignment explanation
Indices: 3500884--3500946 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
3500874 TAATTTAATA
3500884 ATTTATTTATAAATTTA-TATTATTTAT
1 ATTTATTTAT-AATTTATTATTATTTAT
*
3500911 ATTTA-TTATTATTTATTTATTATTTAT
1 ATTTATTTATAATTTA-TTATTATTTAT
3500938 -TTTATTTAT
1 ATTTATTTAT
3500947 GTCACATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 5 0.16
26 8 0.25
27 19 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
ATTTATTTATAATTTATTATTATTTAT
Found at i:3500926 original size:7 final size:7
Alignment explanation
Indices: 3500901--3500938 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
3500891 TATAAATTTA
3500901 TATTATT
1 TATTATT
3500908 TA-TATT
1 TATTATT
3500914 TATTA-T
1 TATTATT
3500920 TATTTATT
1 TA-TTATT
3500928 TATTATT
1 TATTATT
3500935 TATT
1 TATT
3500939 TTATTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 9 0.32
7 16 0.57
8 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTATT
Found at i:3500932 original size:11 final size:11
Alignment explanation
Indices: 3500898--3500939 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
3500888 ATTTATAAAT
3500898 TTATATTATTTA
1 TTAT-TTATTTA
3500910 -TATTTA-TTA
1 TTATTTATTTA
3500919 TTATTTATTTA
1 TTATTTATTTA
3500930 TTATTTATTT
1 TTATTTATTT
3500940 TATTTATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.11
10 9 0.32
11 16 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:3501247 original size:29 final size:30
Alignment explanation
Indices: 3501215--3501282 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
3501205 TCAATAAACC
*
3501215 TATTTTTTAA-AAAAAT-ATTAGAA-ATTATT
1 TATTTTTAAATAAAAATAATTA-AATA-TATT
3501244 TA-TTTTAAATAAAAATAATTAAATATATT
1 TATTTTTAAATAAAAATAATTAAATATATT
3501273 TA-TTTTAAAT
1 TATTTTTAAAT
3501283 TATTATATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 6 0.17
29 24 0.69
30 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (30 bp):
TATTTTTAAATAAAAATAATTAAATATATT
Found at i:3501298 original size:16 final size:15
Alignment explanation
Indices: 3501258--3501299 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3501248 TTAAATAAAA
3501258 ATAATTAAATATATTT
1 ATAATTAAAT-TATTT
*
3501274 AT-TTTAAATTATTAT
1 ATAATTAAATTATT-T
3501289 ATAATTAAATT
1 ATAATTAAATT
3501300 TAAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 9 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATTAAATTATTT
Found at i:3501383 original size:79 final size:80
Alignment explanation
Indices: 3501288--3501441 Score: 206
Period size: 79 Copynumber: 1.9 Consensus size: 80
3501278 TAAATTATTA
* * *
3501288 TATAATTAAATTTAAAATATTTAACACT-TACATAAGTTAGAATAAA-TCTCATTGAAATTTAGT
1 TATAATTAAATTTAAAACATTTAACA-TGTACATAAATTAGAATAAACT-TAATTGAAATTTAGT
3501351 TAGATGGTAATAATACC
64 TAGATGGTAATAATACC
** * *
3501368 TATAATT-AATTTAAAACATTTAACATGTATGTAAATTGGGATAAACTTAATTGAAATTTAGTTA
1 TATAATTAAATTTAAAACATTTAACATGTACATAAATTAGAATAAACTTAATTGAAATTTAGTTA
3501432 GATGGTAATA
66 GATGGTAATA
3501442 CATATAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
78 1 0.02
79 56 0.86
80 8 0.12
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.38
Consensus pattern (80 bp):
TATAATTAAATTTAAAACATTTAACATGTACATAAATTAGAATAAACTTAATTGAAATTTAGTTA
GATGGTAATAATACC
Found at i:3502664 original size:29 final size:29
Alignment explanation
Indices: 3502631--3502688 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3502621 TTTTAATTAA
* *
3502631 TAAAAAATATATAAATAATGA-TAAAATTT
1 TAAAAAATAAAAAAATAAT-ACTAAAATTT
*
3502660 TAAAATATAAAAAAATAATACTAAAATTT
1 TAAAAAATAAAAAAATAATACTAAAATTT
3502689 ATATCTACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
TAAAAAATAAAAAAATAATACTAAAATTT
Found at i:3506502 original size:29 final size:27
Alignment explanation
Indices: 3506458--3506520 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 27
3506448 TCTTTAATAT
3506458 AAATAAATTTATTTAAATACAATAAAA
1 AAATAAATTTATTTAAATACAATAAAA
*
3506485 AAATAATATTTTATTTAAATATAATAAAA
1 AAATAA-A-TTTATTTAAATACAATAAAA
*
3506514 ATATAAA
1 AAATAAA
3506521 CATTTAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 6 0.19
28 2 0.06
29 24 0.75
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
AAATAAATTTATTTAAATACAATAAAA
Found at i:3506526 original size:29 final size:29
Alignment explanation
Indices: 3506463--3506532 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
3506453 AATATAAATA
3506463 AATTTATTTAAATACAATAAAAAAATAAT
1 AATTTATTTAAATACAATAAAAAAATAAT
* * *
3506492 ATTTTATTTAAATATAATAAAAATATAA-
1 AATTTATTTAAATACAATAAAAAAATAAT
*
3506520 ACATTTAATTAAA
1 A-ATTTATTTAAA
3506533 AATTAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (29 bp):
AATTTATTTAAATACAATAAAAAAATAAT
Found at i:3507047 original size:22 final size:20
Alignment explanation
Indices: 3507019--3507059 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
3507009 TTTTTATTTT
3507019 AATTTAAATTAAATTATTTAAG
1 AATTTAAATT--ATTATTTAAG
3507041 AATTTAAATTATTATTTAA
1 AATTTAAATTATTATTTAA
3507060 AAAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AATTTAAATTATTATTTAAG
Found at i:3507370 original size:5 final size:5
Alignment explanation
Indices: 3507360--3507384 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3507350 AAACATTAAA
3507360 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
3507385 TTCATGAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:3512899 original size:2 final size:2
Alignment explanation
Indices: 3512892--3512924 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3512882 ACACAACCCC
3512892 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 A
3512925 AAACAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3513364 original size:21 final size:21
Alignment explanation
Indices: 3513340--3513380 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3513330 ATCAATTTTT
3513340 AATAATTATTCAAAATTAAAA
1 AATAATTATTCAAAATTAAAA
* * *
3513361 AATATTTATTTAAATTTAAA
1 AATAATTATTCAAAATTAAA
3513381 TTATTTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATTATTCAAAATTAAAA
Found at i:3513375 original size:20 final size:19
Alignment explanation
Indices: 3513352--3513390 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3513342 TAATTATTCA
3513352 AAATTAAAAAATATTTATTT
1 AAATT-AAAAATATTTATTT
* *
3513372 AAATTTAAATTATTTATTT
1 AAATTAAAAATATTTATTT
3513391 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTAAAAATATTTATTT
Found at i:3513587 original size:14 final size:16
Alignment explanation
Indices: 3513563--3513604 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
3513553 AATTTATAGA
3513563 TAAAAATATTA-ATTT
1 TAAAAATATTATATTT
3513578 TAAAAA-ATTATATTT
1 TAAAAATATTATATTT
* *
3513593 TTAATATATTAT
1 TAAAAATATTAT
3513605 TAAATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 14 0.61
16 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAAATATTATATTT
Found at i:3513610 original size:40 final size:40
Alignment explanation
Indices: 3513566--3513659 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
3513556 TTATAGATAA
*
3513566 AAATATTAATTTTAAAAAATTATATTT-TTAATATATTATT
1 AAATA-TAATTTTAAAAAATTATATTTATAAATATATTATT
* *
3513606 AAATATAATATATT--AAAATTTTATTTATAAATATTTTATT
1 AAATATAAT-T-TTAAAAAATTATATTTATAAATATATTATT
3513646 AAATA-ATATTTTAA
1 AAATATA-ATTTTAA
3513660 TATAATATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
38 2 0.04
39 17 0.38
40 24 0.53
41 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
AAATATAATTTTAAAAAATTATATTTATAAATATATTATT
Found at i:3513641 original size:15 final size:14
Alignment explanation
Indices: 3513619--3513668 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
3513609 TATAATATAT
3513619 TAAA-ATTTTATTTA
1 TAAATATTTTA-TTA
3513633 TAAATATTTTATTA
1 TAAATATTTTATTA
* *
3513647 AATAATATTTTAATA
1 TA-AATATTTTATTA
3513662 T-AATATT
1 TAAATATT
3513669 AATTTTTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 6 0.19
14 8 0.26
15 17 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAATATTTTATTA
Found at i:3513686 original size:30 final size:32
Alignment explanation
Indices: 3513652--3513717 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
3513642 TATTAAATAA
*
3513652 TATTTTAATATAAT-ATTA-ATTTTTCTATTC
1 TATTTTAATAGAATAATTATATTTTTCTATTC
* * *
3513682 TATTTTAATCGAATAATTATATTTTTTTATTT
1 TATTTTAATAGAATAATTATATTTTTCTATTC
3513714 TATT
1 TATT
3513718 CAGCTCATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 12 0.40
31 4 0.13
32 14 0.47
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (32 bp):
TATTTTAATAGAATAATTATATTTTTCTATTC
Found at i:3514410 original size:9 final size:9
Alignment explanation
Indices: 3514398--3514475 Score: 52
Period size: 9 Copynumber: 8.2 Consensus size: 9
3514388 AATTAAATTA
3514398 ATTTTTTAT
1 ATTTTTTAT
*
3514407 A-TTTTAAT
1 ATTTTTTAT
3514415 AATTTTTTAT
1 -ATTTTTTAT
*
3514425 ATTATTTAT
1 ATTTTTTAT
3514434 ATTTATTTA-
1 ATTT-TTTAT
*
3514443 ATTTAATTAT
1 ATTT-TTTAT
*
3514453 GATATTTTATT
1 -ATTTTTTA-T
3514464 ATTTATTTAT
1 ATTT-TTTAT
3514474 AT
1 AT
3514476 AGATTATGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
8 6 0.11
9 21 0.39
10 19 0.35
11 8 0.15
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:3514437 original size:18 final size:18
Alignment explanation
Indices: 3514398--3514475 Score: 63
Period size: 18 Copynumber: 4.1 Consensus size: 18
3514388 AATTAAATTA
*
3514398 ATTTTTTATATT-TTAAT
1 ATTTTTTATATTATTTAT
3514415 AATTTTTTATATTATTTAT
1 -ATTTTTTATATTATTTAT
3514434 ATTTATTTA-ATTTAATTATGAT
1 ATTT-TTTATA-TT-ATT-T-AT
3514456 ATTTTATTAT-TTATTTAT
1 ATTTT-TTATATTATTTAT
3514474 AT
1 AT
3514476 AGATTATGTA
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
18 21 0.41
19 11 0.22
20 6 0.12
21 4 0.08
22 9 0.18
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (18 bp):
ATTTTTTATATTATTTAT
Found at i:3514467 original size:30 final size:31
Alignment explanation
Indices: 3514429--3514494 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
3514419 TTTTATATTA
*
3514429 TTTA-TATTTATTTAATTTA-ATTATG-ATAT
1 TTTATTATTTATTT-ATATAGATTATGTATAT
3514458 TTTATTATTTATTTATATAGATTATGTATAT
1 TTTATTATTTATTTATATAGATTATGTATAT
*
3514489 TATATT
1 TTTATT
3514495 TTAAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.25
30 15 0.47
31 9 0.28
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (31 bp):
TTTATTATTTATTTATATAGATTATGTATAT
Found at i:3514883 original size:2 final size:2
Alignment explanation
Indices: 3514876--3514907 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3514866 TTGGACCATT
*
3514876 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3514908 GACAAAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3514974 original size:16 final size:16
Alignment explanation
Indices: 3514953--3514987 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3514943 TTAATTTTAT
3514953 ATTTTTT-ATAAAATTA
1 ATTTTTTAAT-AAATTA
3514969 ATTTTTTAATAAATTA
1 ATTTTTTAATAAATTA
3514985 ATT
1 ATT
3514988 ATTAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTTTAATAAATTA
Found at i:3515413 original size:41 final size:41
Alignment explanation
Indices: 3515312--3515396 Score: 100
Period size: 47 Copynumber: 2.0 Consensus size: 41
3515302 GTTAAAACAA
*
3515312 AAAAATATTTATT-TTATATTTTAAAATATATTTAAATATTT
1 AAAAATATTTATTATTATATTTTAAAATAAATTTAAATA-TT
3515353 AAAAACTATTTTATATTATTATATTTTAATAATAAATTTAAATA
1 AAAAA-TA--TT-TATTATTATATTTTAA-AATAAATTTAAATA
3515397 AAAATACTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
41 5 0.14
42 2 0.05
44 2 0.05
45 4 0.11
46 11 0.30
47 13 0.35
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (41 bp):
AAAAATATTTATTATTATATTTTAAAATAAATTTAAATATT
Found at i:3515864 original size:16 final size:16
Alignment explanation
Indices: 3515843--3515873 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3515833 TTATTTTTTA
*
3515843 TTTTTTAAACAATAAT
1 TTTTTTAAAAAATAAT
3515859 TTTTTTAAAAAATAA
1 TTTTTTAAAAAATAA
3515874 GTAAAAGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTTTAAAAAATAAT
Found at i:3516113 original size:16 final size:16
Alignment explanation
Indices: 3516093--3516134 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3516083 AATAATAATA
3516093 ATTTTTTATTATTTTT
1 ATTTTTTATTATTTTT
*
3516109 CTTTTTCTA-TATTTTT
1 ATTTTT-TATTATTTTT
3516125 ATCTTTTTAT
1 AT-TTTTTAT
3516135 GCTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTTATTATTTTT
Found at i:3516261 original size:5 final size:5
Alignment explanation
Indices: 3516243--3516283 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
3516233 AAACATCTTA
*
3516243 AATAT AATTAT AATAT AATAA AATAT -ATA- AATAT AATAT AA
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AA
3516284 AAATAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 6 0.19
5 20 0.65
6 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:3516267 original size:21 final size:20
Alignment explanation
Indices: 3516241--3516289 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
3516231 TAAAACATCT
3516241 TAAATATAATTATAATATAATA
1 TAAATATAA-TA-AATATAATA
3516263 -AAATAT-ATAAATATAATA
1 TAAATATAATAAATATAATA
*
3516281 TAAAAATAA
1 TAAATATAA
3516290 ATTTTATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 9 0.38
19 7 0.29
20 2 0.08
21 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATATAATAAATATAATA
Found at i:3516313 original size:26 final size:25
Alignment explanation
Indices: 3516244--3516319 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 25
3516234 AACATCTTAA
* *
3516244 ATATAATTAT-AATAT-AATAAAAT
1 ATATAAATATAAATATAAATAAATT
*
3516267 ATATAAATATAATATAAAAATAAATT
1 ATATAAATATAA-ATATAAATAAATT
* * *
3516293 TTATCAAATTTAAATATAAATTAATT
1 ATAT-AAATATAAATATAAATAAATT
3516319 A
1 A
3516320 AATTATTAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
23 9 0.22
24 1 0.02
25 3 0.07
26 21 0.51
27 7 0.17
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATAAATATAAATATAAATAAATT
Found at i:3516589 original size:23 final size:24
Alignment explanation
Indices: 3516559--3516604 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3516549 TTGAATTAAA
3516559 AATTAATTATTTTA-ATTAAGTTT
1 AATTAATTATTTTACATTAAGTTT
*
3516582 AATTAATTTTTTTATCATTAAGT
1 AATTAATTATTTTA-CATTAAGT
3516605 GAATAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
25 7 0.35
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
AATTAATTATTTTACATTAAGTTT
Found at i:3517060 original size:14 final size:14
Alignment explanation
Indices: 3517028--3517068 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3517018 TTTTATTTAA
3517028 ATTAAT-TAT-AAT
1 ATTAATATATAAAT
*
3517040 ATAAATATATAAAT
1 ATTAATATATAAAT
3517054 ATTAATATA-AAAT
1 ATTAATATATAAAT
3517067 AT
1 AT
3517069 ATTTTTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.20
13 9 0.36
14 11 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAATATATAAAT
Found at i:3517903 original size:6 final size:6
Alignment explanation
Indices: 3517892--3517970 Score: 69
Period size: 6 Copynumber: 13.5 Consensus size: 6
3517882 TTATAAATAG
* * *
3517892 TATAAA TATAAA TAT-AA TATAGAT TATTAAA TTTAAA -ATAAA TTTTAAA
1 TATAAA TATAAA TATAAA TATA-AA TA-TAAA TATAAA TATAAA -TATAAA
3517941 TATAAA TATAAA TAT-AA TAT--A TATAAA TAT
1 TATAAA TATAAA TATAAA TATAAA TATAAA TAT
3517971 TTCATATTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.07
5 14 0.23
6 31 0.52
7 9 0.15
8 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (6 bp):
TATAAA
Found at i:3517953 original size:19 final size:20
Alignment explanation
Indices: 3517892--3517970 Score: 78
Period size: 19 Copynumber: 4.2 Consensus size: 20
3517882 TTATAAATAG
3517892 TATAAA-TA-TAAATAT-AA
1 TATAAATTATTAAATATAAA
* *
3517909 TATAGATTATTAAATTTAAA
1 TATAAATTATTAAATATAAA
3517929 -ATAAATT-TTAAATATAAA
1 TATAAATTATTAAATATAAA
* *
3517947 TATAAATATAATATATATAAA
1 TATAAAT-TATTAAATATAAA
3517968 TAT
1 TAT
3517971 TTCATATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
17 5 0.10
18 12 0.24
19 18 0.36
20 3 0.06
21 12 0.24
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (20 bp):
TATAAATTATTAAATATAAA
Found at i:3518191 original size:12 final size:12
Alignment explanation
Indices: 3518174--3518297 Score: 68
Period size: 11 Copynumber: 10.8 Consensus size: 12
3518164 TATAAAAAAT
*
3518174 TAAAATATAACA
1 TAAAATATAATA
3518186 TAAAATATAATA
1 TAAAATATAATA
3518198 TAAAATA-AATA
1 TAAAATATAATA
*
3518209 TATAATAT-AT-
1 TAAAATATAATA
*
3518219 TAAAAT-TTATA
1 TAAAATATAATA
* *
3518230 TAACAT-GAAT-
1 TAAAATATAATA
* * *
3518240 TATTAATTTATTA
1 TA-AAATATAATA
3518253 TAAATATATAATA
1 TAAA-ATATAATA
3518266 TATTAAATATAAT-
1 TA--AAATATAATA
*
3518279 TATAATAT-ATA
1 TAAAATATAATA
3518290 -AAAATATA
1 TAAAATATA
3518298 TAAACAATAA
Statistics
Matches: 86, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
9 1 0.01
10 17 0.20
11 26 0.30
12 21 0.24
13 12 0.14
14 7 0.08
15 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.40
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:3518415 original size:18 final size:18
Alignment explanation
Indices: 3518392--3518427 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3518382 CCCAACCACC
3518392 CCACCCAAGACTCCACAA
1 CCACCCAAGACTCCACAA
*
3518410 CCACCCAAGGCTCCACAA
1 CCACCCAAGACTCCACAA
3518428 GTAGAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.50, G:0.08, T:0.06
Consensus pattern (18 bp):
CCACCCAAGACTCCACAA
Found at i:3518569 original size:4 final size:4
Alignment explanation
Indices: 3518560--3518594 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3518550 TTGGGTTTGA
3518560 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3518595 ATAGAGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3518877 original size:35 final size:33
Alignment explanation
Indices: 3518836--3518960 Score: 112
Period size: 32 Copynumber: 3.6 Consensus size: 33
3518826 TATTTGTATA
* *
3518836 ATATTTATATTAATTTTACTTATATTTAA-AATTAT
1 ATATTTATATAAATTTTAATT-TA-TTAATAATT-T
*
3518871 ATATTTATATAAATTTAAATTTATTAATAATTT
1 ATATTTATATAAATTTTAATTTATTAATAATTT
3518904 ATA-TTATATAAATTTTAATTTACTTATATATTATTT
1 ATATTTATATAAATTTTAATTTA-TTA-ATA--ATTT
* *
3518940 TTAATTTAT-TATATTTTAATT
1 AT-ATTTATATAAATTTTAATT
3518961 ATTTTTATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
32 18 0.23
33 11 0.14
34 9 0.12
35 18 0.23
36 5 0.06
37 12 0.16
38 4 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (33 bp):
ATATTTATATAAATTTTAATTTATTAATAATTT
Found at i:3518883 original size:18 final size:17
Alignment explanation
Indices: 3518836--3518925 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 17
3518826 TATTTGTATA
*
3518836 ATATTTATAT-TAATTT
1 ATATTTATATAAAATTT
*
3518852 -TACTTATATTTAAAATTAT
1 ATA-TT-TATATAAAATT-T
3518871 ATATTTATAT-AAATTT
1 ATATTTATATAAAATTT
*
3518887 AAATTTAT-TAATAATTT
1 ATATTTATATAA-AATTT
*
3518904 ATA-TTATATAAATTTT
1 ATATTTATATAAAATTT
3518920 A-ATTTA
1 ATATTTA
3518926 CTTATATATT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
15 4 0.07
16 23 0.39
17 19 0.32
18 8 0.14
19 3 0.05
20 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTATATAAAATTT
Found at i:3518951 original size:14 final size:15
Alignment explanation
Indices: 3518932--3518960 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3518922 TTTACTTATA
3518932 TATTAT-TTTTAATT
1 TATTATATTTTAATT
3518946 TATTATATTTTAATT
1 TATTATATTTTAATT
3518961 ATTTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTATATTTTAATT
Found at i:3518951 original size:21 final size:21
Alignment explanation
Indices: 3518898--3518953 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
3518888 AATTTATTAA
3518898 TAATTTA-TATTATATAAATTT
1 TAATTTATTA-TATATAAATTT
* *
3518919 TAATTTACTTATATATTATTTT
1 TAATTTA-TTATATATAAATTT
3518941 TAATTTATTATAT
1 TAATTTATTATAT
3518954 TTTAATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TAATTTATTATATATAAATTT
Found at i:3521768 original size:32 final size:34
Alignment explanation
Indices: 3521724--3521788 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
3521714 TAGAATACGA
3521724 ATGTTAAATTTATAT-AATAT-AAAT-TTTTAAC
1 ATGTTAAATTTATATAAATATAAAATATTTTAAC
3521755 ATGTTAAAATTTATATAAATATAAAATATTTTAA
1 ATGTT-AAATTTATATAAATATAAAATATTTTAA
3521789 ACTGATGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 5 0.17
32 10 0.33
33 5 0.17
34 4 0.13
35 6 0.20
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (34 bp):
ATGTTAAATTTATATAAATATAAAATATTTTAAC
Found at i:3521779 original size:17 final size:17
Alignment explanation
Indices: 3521729--3521781 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3521719 TACGAATGTT
3521729 AAATTTATAT-AATAT-
1 AAATTTATATAAATATA
*
3521744 AAATTT-T-TAACATGTTA
1 AAATTTATATAA-AT-ATA
3521761 AAATTTATATAAATATA
1 AAATTTATATAAATATA
3521778 AAAT
1 AAAT
3521782 ATTTTAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 1 0.03
14 2 0.07
15 8 0.27
16 1 0.03
17 12 0.40
18 3 0.10
19 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:3523556 original size:19 final size:19
Alignment explanation
Indices: 3523529--3523568 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3523519 GACTACACTA
*
3523529 TAATATTTTCTTTACTTTT
1 TAATATTTTCTTTAATTTT
* *
3523548 TAATTTTTTTTTTAATTTT
1 TAATATTTTCTTTAATTTT
3523567 TA
1 TA
3523569 TACAAAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (19 bp):
TAATATTTTCTTTAATTTT
Found at i:3524109 original size:20 final size:19
Alignment explanation
Indices: 3524046--3524105 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 19
3524036 AATGAATTAT
*
3524046 TTATTTAAAAT-TGATTTTGT
1 TTATTTAAAATAT-ATTTT-A
3524066 TTAATTTAAAAATATATTTTA
1 TT-ATTT-AAAATATATTTTA
3524087 TTATTTAAAATATATTTTA
1 TTATTTAAAATATATTTTA
3524106 ATTAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 13 0.36
20 6 0.17
21 6 0.17
22 10 0.28
23 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTATTTAAAATATATTTTA
Found at i:3524161 original size:35 final size:34
Alignment explanation
Indices: 3524096--3524162 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
3524086 ATTATTTAAA
* **
3524096 ATATATTTTAATTAAAATTTTATATTAATATTAT
1 ATATATTTTAATTAAAATTTAATAAAAATATTAT
* *
3524130 ATATATTTTTATTTAAATTTAAATAAAAATATT
1 ATATATTTTAATTAAAATTT-AATAAAAATATT
3524163 TTTTATTGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 18 0.67
35 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
ATATATTTTAATTAAAATTTAATAAAAATATTAT
Found at i:3524381 original size:2 final size:2
Alignment explanation
Indices: 3524369--3524445 Score: 109
Period size: 2 Copynumber: 38.5 Consensus size: 2
3524359 AAGAGACAGC
* * *
3524369 TA TA TA CA TA TA TA TA TA TA TG TA TA TA TA TA CA 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
* *
3524411 TA TA TG TA TA TA TG 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 T
3524446 GTCGACATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3524403 original size:26 final size:26
Alignment explanation
Indices: 3524369--3524441 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
3524359 AAGAGACAGC
3524369 TATATACATATATATATATATGTATA
1 TATATACATATATATATATATGTATA
3524395 TATATACATATATATATATATGTATA
1 TATATACATATATATATATATGTATA
* *
3524421 TATGTATATATATATATATAT
1 TATATACATATATATATATAT
3524442 ATATGTCGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (26 bp):
TATATACATATATATATATATGTATA
Found at i:3524455 original size:26 final size:25
Alignment explanation
Indices: 3524369--3524455 Score: 106
Period size: 26 Copynumber: 3.5 Consensus size: 25
3524359 AAGAGACAGC
3524369 TATAT-ACATATATATATATATGTA
1 TATATGACATATATATATATATGTA
*
3524393 TATATATACATATATATATATATGTA
1 TATAT-GACATATATATATATATGTA
* *
3524419 TATATG-TATATATATATATATATA
1 TATATGACATATATATATATATGTA
*
3524443 TATGTCGACATAT
1 TATAT-GACATAT
3524456 TTTCACCTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
24 25 0.46
25 1 0.02
26 28 0.52
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (25 bp):
TATATGACATATATATATATATGTA
Found at i:3524584 original size:4 final size:4
Alignment explanation
Indices: 3524575--3524613 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
3524565 CCTTTCAGCT
*
3524575 AATA AATA AATA AGTA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT
3524614 TCCCTCTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:3524946 original size:17 final size:17
Alignment explanation
Indices: 3524923--3524968 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3524913 TTATTTTTAA
* *
3524923 ATATAATAATAATTATT
1 ATATAATAAAAATAATT
*
3524940 TTATAATAAAAATAATT
1 ATATAATAAAAATAATT
3524957 ATATAAATAAAA
1 ATAT-AATAAAA
3524969 TTTAAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAATAAAAATAATT
Found at i:3524953 original size:20 final size:22
Alignment explanation
Indices: 3524912--3524958 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
3524902 TAAATGTGTT
3524912 ATTATTTTTAAATATAATAATA
1 ATTATTTTTAAATATAATAATA
3524934 ATTA-TTTTATAATA-AA-AATA
1 ATTATTTTTA-AATATAATAATA
3524954 ATTAT
1 ATTAT
3524959 ATAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.35
21 7 0.30
22 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATTTTTAAATATAATAATA
Found at i:3524995 original size:23 final size:23
Alignment explanation
Indices: 3524949--3524993 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3524939 TTTATAATAA
3524949 AAATAATTATATAAATAAAATTT
1 AAATAATTATATAAATAAAATTT
* *
3524972 AAATAATT-TATTAATATAATTT
1 AAATAATTATATAAATAAAATTT
3524994 TAGATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATAATTATATAAATAAAATTT
Found at i:3526208 original size:12 final size:13
Alignment explanation
Indices: 3526183--3526207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3526173 TAAGATTTAA
3526183 AAATTAATTTTTT
1 AAATTAATTTTTT
3526196 AAATTAATTTTT
1 AAATTAATTTTT
3526208 ATTTTAAATT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAATTAATTTTTT
Found at i:3526485 original size:22 final size:22
Alignment explanation
Indices: 3526455--3526520 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
3526445 TAACTTATTT
* *
3526455 TATTATTTAAATAATATTAAAA
1 TATTTTTTAATTAATATTAAAA
* *
3526477 TATTTTTTATATTAATATTTATA
1 TATTTTTTA-ATTAATATTAAAA
*
3526500 TATTTTTATAATTAATTTTAA
1 TATTTTT-TAATTAATATTAA
3526521 TTAAAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 8 0.22
23 26 0.72
24 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTTTTAATTAATATTAAAA
Found at i:3527922 original size:87 final size:87
Alignment explanation
Indices: 3527776--3527934 Score: 257
Period size: 87 Copynumber: 1.8 Consensus size: 87
3527766 TGATATTGTC
* *
3527776 CCTGATCAAAAAGGAGTAAATGATCCAGAATTTGGTGCTTATTGGTATGGAGATAATTCAGGCAA
1 CCTGATCAAAAAGGAGTAAATGATCCAGAATTTGGAGCTTACTGGTATGGAGATAATTCAGGCAA
3527841 AGAATCTAAAATTGGAGATATT
66 AGAATCTAAAATTGGAGATATT
* *
3527863 CCTGATCAAAAAGGTA-TAAATGATCCAGAGTTTGGAGCTTACTGGTATGGTGATAATTCAGGCA
1 CCTGATCAAAAAGG-AGTAAATGATCCAGAATTTGGAGCTTACTGGTATGGAGATAATTCAGGCA
*
3527927 ATGAATCT
65 AAGAATCT
3527935 GAAAGTGATA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
87 65 0.98
88 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (87 bp):
CCTGATCAAAAAGGAGTAAATGATCCAGAATTTGGAGCTTACTGGTATGGAGATAATTCAGGCAA
AGAATCTAAAATTGGAGATATT
Found at i:3528085 original size:87 final size:87
Alignment explanation
Indices: 3527941--3528139 Score: 263
Period size: 87 Copynumber: 2.3 Consensus size: 87
3527931 ATCTGAAAGT
* ** *** * *
3527941 GATAATTTAGAAAAAGAGCCTAAACGTGAAGTTGCTCCAACAAATAAAGGAATAAATGATCCAGA
1 GATAATTCAGAAAAAGAATCTAAAAACGAAGATGCTCCAACAAACAAAGGAATAAATGATCCAGA
*
3528006 GTTTGGTGCATACTGGTATGGT
66 GTTTGGTGCATACTGGTATGGC
** * *
3528028 GATAATTCAGGCAAAGAATCTAAAAACGAAGATGCTCCAACAAACAAAGGAGTAAATGATCCTGA
1 GATAATTCAGAAAAAGAATCTAAAAACGAAGATGCTCCAACAAACAAAGGAATAAATGATCCAGA
*
3528093 GTTTGGTGCTTACTGGTATGGC
66 GTTTGGTGCATACTGGTATGGC
*
3528115 GATAATTCAGAAAAAGATTCTAAAA
1 GATAATTCAGAAAAAGAATCTAAAA
3528140 GTGATGATTC
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 95 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (87 bp):
GATAATTCAGAAAAAGAATCTAAAAACGAAGATGCTCCAACAAACAAAGGAATAAATGATCCAGA
GTTTGGTGCATACTGGTATGGC
Found at i:3528143 original size:201 final size:201
Alignment explanation
Indices: 3527785--3528344 Score: 702
Period size: 201 Copynumber: 2.8 Consensus size: 201
3527775 CCCTGATCAA
* *
3527785 AAAGGAGTAAATGATCCAGAATTTGGTGCTTATTGGTATGGAGATAATTCAGGCAAAGAATCTAA
1 AAAGGAGTAAATGATCCAGAGTTTGGTGCTTACTGGTATGGAGATAATTCAGGCAAAGAATCTAA
** * ** * * *
3527850 AATTGGAGATATTCCTGATC-AA-AAAGGTA-TAAATGATCCAGAGTTTGGAGCTTACTGGTATG
66 AAACGAAGATGCTCC--AACAAACAAAGG-AGTAAATGATCCTGAGTTTGGTGCTTACTGGTATG
* ** * * *
3527912 GTGATAATTCAGGCAATGAATCTGAAAGTGATAATTTAGA-AAAAGAGCCTAAACGTGAAGTTGC
128 GCGATAATTCAGAAAAAGAATCTAAAAGTGATAATTCA-ATAAAAGAGCCTAAACGTGAAGTTGC
*
3527976 TCCAACAAAT
192 TCCAACAAAC
* * *
3527986 AAAGGAATAAATGATCCAGAGTTTGGTGCATACTGGTATGGTGATAATTCAGGCAAAGAATCTAA
1 AAAGGAGTAAATGATCCAGAGTTTGGTGCTTACTGGTATGGAGATAATTCAGGCAAAGAATCTAA
3528051 AAACGAAGATGCTCCAACAAACAAAGGAGTAAATGATCCTGAGTTTGGTGCTTACTGGTATGGCG
66 AAACGAAGATGCTCCAACAAACAAAGGAGTAAATGATCCTGAGTTTGGTGCTTACTGGTATGGCG
* * * *
3528116 ATAATTCAGAAAAAGATTCTAAAAGTGATGATTCAATCAAAGAGTCTAAACGTGAAGTTGCTCCA
131 ATAATTCAGAAAAAGAATCTAAAAGTGATAATTCAATAAAAGAGCCTAAACGTGAAGTTGCTCCA
*
3528181 ACAAGC
196 ACAAAC
* * *
3528187 AAAGGAGTAAATGATCCAGAGTTTGGTGCTTACTGGTATGGCGATAATTCAGACAAAGAATC-CA
1 AAAGGAGTAAATGATCCAGAGTTTGGTGCTTACTGGTATGGAGATAATTCAGGCAAAGAATCTAA
* * * *
3528251 AAACTAAAGATGCTCCGACAAACAAAGGAGTAAATGATCCTGAGTTTGGTGCTTATTGGTA-CGC
66 AAAC-GAAGATGCTCCAACAAACAAAGGAGTAAATGATCCTGAGTTTGGTGCTTACTGGTATGGC
* *
3528315 TGATAATTCACG-CAAAGAATCTAAAGGTGA
130 -GATAATTCA-GAAAAAGAATCTAAAAGTGA
3528345 AGTTGCTCCA
Statistics
Matches: 315, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
199 2 0.01
200 11 0.03
201 301 0.96
202 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (201 bp):
AAAGGAGTAAATGATCCAGAGTTTGGTGCTTACTGGTATGGAGATAATTCAGGCAAAGAATCTAA
AAACGAAGATGCTCCAACAAACAAAGGAGTAAATGATCCTGAGTTTGGTGCTTACTGGTATGGCG
ATAATTCAGAAAAAGAATCTAAAAGTGATAATTCAATAAAAGAGCCTAAACGTGAAGTTGCTCCA
ACAAAC
Found at i:3528383 original size:87 final size:87
Alignment explanation
Indices: 3528153--3528363 Score: 266
Period size: 87 Copynumber: 2.4 Consensus size: 87
3528143 ATGATTCAAT
* *
3528153 CAAAGAGTCTAAACGTGAAGTTGCTCCAA-CAAGCAAAGGAGTAAATGATCCAGAGTTTGGTGCT
1 CAAAGAATCTAAAAGTGAAGTTGCTCCAACCAA-CAAAGGAGTAAATGATCCAGAGTTTGGTGCT
*
3528217 TACTGGTATGGCGATAATTCAGA
65 TACTGGTATCGCGATAATTCAGA
* * * * * * *
3528240 CAAAGAATCCAAAACTAAAGATGCTCCGACAAACAAAGGAGTAAATGATCCTGAGTTTGGTGCTT
1 CAAAGAATCTAAAAGTGAAGTTGCTCCAACCAACAAAGGAGTAAATGATCCAGAGTTTGGTGCTT
*
3528305 ATTGGTA-CGCTGATAATTCACG-
66 ACTGGTATCGC-GATAATTCA-GA
*
3528327 CAAAGAATCTAAAGGTGAAGTTGCTCCAACCAACAAA
1 CAAAGAATCTAAAAGTGAAGTTGCTCCAACCAACAAA
3528364 TTTGCAAATG
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
86 2 0.02
87 98 0.95
88 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (87 bp):
CAAAGAATCTAAAAGTGAAGTTGCTCCAACCAACAAAGGAGTAAATGATCCAGAGTTTGGTGCTT
ACTGGTATCGCGATAATTCAGA
Found at i:3528627 original size:19 final size:20
Alignment explanation
Indices: 3528603--3528647 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3528593 TATGCTTATG
3528603 TTCATACA-GCTAAACTTTT
1 TTCATACATGCTAAACTTTT
* *
3528622 TTCATATATGTTAAACTTTT
1 TTCATACATGCTAAACTTTT
3528642 TTCATA
1 TTCATA
3528648 TATTTCAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (20 bp):
TTCATACATGCTAAACTTTT
Found at i:3528638 original size:20 final size:20
Alignment explanation
Indices: 3528613--3528650 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3528603 TTCATACAGC
3528613 TAAACTTTTTTCATATATGT
1 TAAACTTTTTTCATATATGT
3528633 TAAACTTTTTTCATATAT
1 TAAACTTTTTTCATATAT
3528651 TTCAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (20 bp):
TAAACTTTTTTCATATATGT
Found at i:3539134 original size:27 final size:26
Alignment explanation
Indices: 3539097--3539172 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 26
3539087 CAAAAGTCAC
* *
3539097 TCTTTGTGTTTGTAAAAAAT-GATGGT
1 TCTTTTTGTTTGTTAAAAATAG-TGGT
3539123 TCTTTTTTGTTTGTTAAAAATAGTGGT
1 TC-TTTTTGTTTGTTAAAAATAGTGGT
*
3539150 TCTTTTTATTTGTTAAAAATAGT
1 TCTTTTTGTTTGTTAAAAATAGT
3539173 AGCATGTTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 22 0.49
27 22 0.49
28 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53
Consensus pattern (26 bp):
TCTTTTTGTTTGTTAAAAATAGTGGT
Found at i:3539974 original size:15 final size:17
Alignment explanation
Indices: 3539944--3539977 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
3539934 ATATAACAAA
3539944 AAATATATATTTTAATT
1 AAATATATATTTTAATT
3539961 AAAT-TATA-TTTAATT
1 AAATATATATTTTAATT
3539976 AA
1 AA
3539978 TTGATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 4 0.24
17 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATATATATTTTAATT
Found at i:3540452 original size:21 final size:22
Alignment explanation
Indices: 3540423--3540464 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3540413 ATTTTATTAA
* *
3540423 AATTATATTTATATATAATAAT
1 AATTATATTAATAAATAATAAT
3540445 AATT-TATTAATAAATAATAA
1 AATTATATTAATAAATAATAA
3540465 AAAGTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTATATTAATAAATAATAAT
Found at i:3541146 original size:24 final size:22
Alignment explanation
Indices: 3541110--3541203 Score: 66
Period size: 24 Copynumber: 3.9 Consensus size: 22
3541100 TTTCTTTTGA
3541110 TTAT-AATTTAAAATATTATAT
1 TTATAAATTTAAAATATTATAT
*
3541131 CTTATAAATATTAAAAT-TTAAATT
1 -TTATAAAT-TTAAAATATTATA-T
*
3541155 TATATAATTATTTTTAAAATATAATAT
1 T-TATAA--A--TTTAAAATATTATAT
3541182 TTAATAAATTTAAAATTATTAT
1 TT-ATAAATTTAAAA-TATTAT
3541204 TATAATATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
22 4 0.07
23 15 0.26
24 18 0.32
25 1 0.02
26 2 0.04
27 13 0.23
28 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATAAATTTAAAATATTATAT
Found at i:3541157 original size:22 final size:23
Alignment explanation
Indices: 3541110--3541163 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
3541100 TTTCTTTTGA
*
3541110 TTAT-AATTTAAAATATTATATC
1 TTATAAATTTAAAATATTAAATC
3541132 TTATAAATATTAAAAT-TTAAAT-
1 TTATAAAT-TTAAAATATTAAATC
3541154 TTATATAATT
1 TTATA-AATT
3541164 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 10 0.36
23 11 0.39
24 7 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATAAATTTAAAATATTAAATC
Found at i:3541942 original size:6 final size:7
Alignment explanation
Indices: 3541925--3541997 Score: 58
Period size: 7 Copynumber: 10.1 Consensus size: 7
3541915 GACAAAATTC
3541925 AAAAAAT
1 AAAAAAT
3541932 AAAAAAT
1 AAAAAAT
3541939 AAAAAAT
1 AAAAAAT
3541946 -AAAAAT
1 AAAAAAT
** *
3541952 AATTAAG
1 AAAAAAT
3541959 AAAAATTTAT
1 AAAAA---AT
*
3541969 AAAAATT
1 AAAAAAT
3541976 AAAAAAT
1 AAAAAAT
*
3541983 AAATAAT
1 AAAAAAT
*
3541990 AAATAAT
1 AAAAAAT
3541997 A
1 A
3541998 TAGTGTCCTG
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
6 6 0.11
7 41 0.77
10 6 0.11
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.23
Consensus pattern (7 bp):
AAAAAAT
Found at i:3542795 original size:30 final size:30
Alignment explanation
Indices: 3542760--3542816 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3542750 GTTTTAATTC
* *
3542760 AATTAAATTATATAATTATTTTTAAAATAT
1 AATTAAATCATATAATTATTATTAAAATAT
3542790 AATTAAATCATATAATTATTATTAAAA
1 AATTAAATCATATAATTATTATTAAAA
3542817 AAAATAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
AATTAAATCATATAATTATTATTAAAATAT
Found at i:3543193 original size:16 final size:18
Alignment explanation
Indices: 3543170--3543225 Score: 68
Period size: 16 Copynumber: 3.4 Consensus size: 18
3543160 AAATTTACAT
*
3543170 AATATAAATTATTA-ATA
1 AATATAAAATATTATATA
3543187 AAT-TAAAAT-TTATATA
1 AATATAAAATATTATATA
3543203 AATATAAAATATT-T-TA
1 AATATAAAATATTATATA
3543219 AATATAA
1 AATATAA
3543226 TTATAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
15 3 0.09
16 20 0.57
17 10 0.29
18 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATAAAATATTATATA
Found at i:3543252 original size:45 final size:48
Alignment explanation
Indices: 3543170--3543259 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 48
3543160 AAATTTACAT
3543170 AATATAAATTATTAATAAATTAAAATTTATATAAATATAAAATATTTTA
1 AATATAAATTATTAATAAATTAAAA-TTATATAAATATAAAATATTTTA
*
3543219 AATAT-AATTA-TAATATAA-TAAAA-TATATAAATATAACATAT
1 AATATAAATTATTAATA-AATTAAAATTATATAAATATAAAATAT
3543260 ACATACGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
45 17 0.44
47 10 0.26
48 7 0.18
49 5 0.13
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (48 bp):
AATATAAATTATTAATAAATTAAAATTATATAAATATAAAATATTTTA
Found at i:3543408 original size:5 final size:5
Alignment explanation
Indices: 3543398--3543433 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
3543388 TGTTTTGCCT
3543398 TTTTC TTTTC TTTTC TTTTC TTTT- TTTT- TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
3543434 GGGTTCTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.39
5 19 0.61
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (5 bp):
TTTTC
Found at i:3543954 original size:2 final size:2
Alignment explanation
Indices: 3543947--3543980 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3543937 ACGAAATCGA
*
3543947 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3543981 GGATAATACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3544402 original size:15 final size:15
Alignment explanation
Indices: 3544382--3544411 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3544372 AGAATATGTG
*
3544382 AAAAATATTTTAAAT
1 AAAAATAATTTAAAT
3544397 AAAAATAATTTAAAT
1 AAAAATAATTTAAAT
3544412 TTATGTGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAATAATTTAAAT
Found at i:3544618 original size:2 final size:2
Alignment explanation
Indices: 3544611--3544636 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3544601 TACTCTTTTA
3544611 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
3544637 TGCATCTCAT
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:3545172 original size:21 final size:21
Alignment explanation
Indices: 3545147--3545186 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3545137 ACCTTGAAAC
* *
3545147 TTTTAAGAATAATTTTTAAAT
1 TTTTAAAAATAATTATTAAAT
3545168 TTTTAAAAATAATTATTAA
1 TTTTAAAAATAATTATTAA
3545187 TCGTATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTAAAAATAATTATTAAAT
Found at i:3546032 original size:2 final size:2
Alignment explanation
Indices: 3546025--3546060 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3546015 GTATAATTTG
3546025 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
3546061 CCAATGCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3546275 original size:29 final size:29
Alignment explanation
Indices: 3546218--3546275 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
3546208 AATTATATTT
* *
3546218 ATATATTTTTATAATTAAATTTAAGTAAA
1 ATATATTTTTATAATTAAATATAAATAAA
*
3546247 ATAT-TTTTTATTATTAAATAATAAATAAA
1 ATATATTTTTATAATTAAAT-ATAAATAAA
3546276 GTTAATCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
ATATATTTTTATAATTAAATATAAATAAA
Found at i:3546799 original size:87 final size:87
Alignment explanation
Indices: 3546653--3546850 Score: 261
Period size: 87 Copynumber: 2.3 Consensus size: 87
3546643 CTGGTATGGC
* * * *
3546653 GATAATTCAGGCAAAGAATCTAAAAATGAAGATGCTCCAACAAACAAAGGAGTAAATGATCCGGA
1 GATAATTCAGACAAAGAATCTAAAAATAAAGATACTACAACAAACAAAGGAGTAAATGATCCGGA
3546718 GTTTGGTGATTACCAGCATAAA
66 GTTTGGTGATTACCAGCATAAA
* ** * *
3546740 GATAATTCAGACAAAGAATCTGAAGGTAAAGTTACTACAACAAACAAAGGAGTAAATGATCCTGA
1 GATAATTCAGACAAAGAATCTAAAAATAAAGATACTACAACAAACAAAGGAGTAAATGATCCGGA
** * *
3546805 GTTTGGTGATTACTGGTATGAA
66 GTTTGGTGATTACCAGCATAAA
* *
3546827 GATAAATCGGACAAAGAATCTAAA
1 GATAATTCAGACAAAGAATCTAAA
3546851 TGTGATAATT
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 95 1.00
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (87 bp):
GATAATTCAGACAAAGAATCTAAAAATAAAGATACTACAACAAACAAAGGAGTAAATGATCCGGA
GTTTGGTGATTACCAGCATAAA
Found at i:3548609 original size:10 final size:10
Alignment explanation
Indices: 3548591--3548649 Score: 73
Period size: 10 Copynumber: 5.8 Consensus size: 10
3548581 TTAAGTAATT
*
3548591 TAAACATAAA
1 TAAAAATAAA
3548601 TAAAAATAAA
1 TAAAAATAAA
* *
3548611 TAAAATTAATT
1 TAAAAATAA-A
3548622 TAAAAATAAA
1 TAAAAATAAA
*
3548632 TAAAACTAAA
1 TAAAAATAAA
3548642 TAAAAATA
1 TAAAAATA
3548650 TAGAAAGCAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 33 0.80
11 8 0.20
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (10 bp):
TAAAAATAAA
Done.