Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 22 of 131
Found at i:5302032 original size:11 final size:11
Alignment explanation
Indices: 5302018--5302047 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
5302008 TTTTATATTA
5302018 ATAATATAAAT
1 ATAATATAAAT
5302029 ATAATATAAAT
1 ATAATATAAAT
5302040 ATTAATAT
1 A-TAATAT
5302048 TAATCCTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:5306307 original size:28 final size:29
Alignment explanation
Indices: 5306270--5306334 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
5306260 TAAAATATTC
*
5306270 AATATAATATTTATATT-TAAATATTTTT
1 AATATAATATTTAAATTATAAATATTTTT
* *
5306298 AATATGATATTTAAATTATGAATA-TTTT
1 AATATAATATTTAAATTATAAATATTTTT
5306326 AAT-TAATAT
1 AATATAATAT
5306335 GATACTCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 5 0.16
28 22 0.69
29 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
AATATAATATTTAAATTATAAATATTTTT
Found at i:5310507 original size:64 final size:63
Alignment explanation
Indices: 5310435--5310639 Score: 166
Period size: 63 Copynumber: 3.2 Consensus size: 63
5310425 AAAAATATCA
*
5310435 TCAATAATCCCCTCTAAAAAAATATGAGAGGATTATTGAAGGTATTTTTTGGTAAAAAATGCCT
1 TCAATAATCCTCTCTAAAAAAATATGAGAGGATTATTGAAGGTATTTTTT-GTAAAAAATGCCT
* * * * * * * *
5310499 TCAATAATCTTTTC-ATATAAA-ATGAAGTGGACTATTGAAAGCGT-TTTTTTGCAGAAAATGCC
1 TCAATAATCCTCTCTAAAAAAATATG-AGAGGATTATTG-AAG-GTATTTTTTGTAAAAAATGCC
5310561 T
63 T
* * * * * * * *
5310562 TTAATAATCCTCTTTAAAAAATTAGGAGA-AATTATTGAAAGCATTTTTTATAAAAAAAAATGCC
1 TCAATAATCCTCTCTAAAAAAATATGAGAGGATTATTGAAGGTATTTTTTGT---AAAAAATGCC
5310626 T
63 T
5310627 TCAATAATCCTCT
1 TCAATAATCCTCT
5310640 TTGCAAATAG
Statistics
Matches: 106, Mismatches: 26, Indels: 17
0.71 0.17 0.11
Matches are distributed among these distances:
61 1 0.01
62 11 0.10
63 42 0.40
64 26 0.25
65 26 0.25
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (63 bp):
TCAATAATCCTCTCTAAAAAAATATGAGAGGATTATTGAAGGTATTTTTTGTAAAAAATGCCT
Found at i:5317770 original size:62 final size:62
Alignment explanation
Indices: 5317673--5317797 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
5317663 ACCAATGAAC
5317673 TGATCACTTTCGATCAACTTAAGGAGTATGGAGCATATTGGAAGGAAGGCCTTAAAAGACAT
1 TGATCACTTTCGATCAACTTAAGGAGTATGGAGCATATTGGAAGGAAGGCCTTAAAAGACAT
* *
5317735 TGATCACTTTCGATCAACTTGAGGAGTATGGAGCATTTTGGAAGGAAGGCCTTAAAAGACAT
1 TGATCACTTTCGATCAACTTAAGGAGTATGGAGCATATTGGAAGGAAGGCCTTAAAAGACAT
5317797 T
1 T
5317798 TTCACAAACA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (62 bp):
TGATCACTTTCGATCAACTTAAGGAGTATGGAGCATATTGGAAGGAAGGCCTTAAAAGACAT
Found at i:5323860 original size:12 final size:13
Alignment explanation
Indices: 5323834--5323866 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5323824 TCTTTGAATT
5323834 TCAACTTTAAATC
1 TCAACTTTAAATC
5323847 TCAACTTT-AATC
1 TCAACTTTAAATC
*
5323859 TCTACTTT
1 TCAACTTT
5323867 CTTACTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.45
Consensus pattern (13 bp):
TCAACTTTAAATC
Found at i:5323910 original size:15 final size:15
Alignment explanation
Indices: 5323892--5323923 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5323882 CGATTATTTT
5323892 AAATCAAATTAATCA
1 AAATCAAATTAATCA
*
5323907 AAATCGAATTAATCA
1 AAATCAAATTAATCA
5323922 AA
1 AA
5323924 GTATTCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.25
Consensus pattern (15 bp):
AAATCAAATTAATCA
Found at i:5325402 original size:31 final size:31
Alignment explanation
Indices: 5325367--5325447 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
5325357 AATGTTATAA
* *
5325367 ATAAT-TTATAAACTATAATAAAATATTTAAT
1 ATAATATT-TAAACTATAAAAAAAAATTTAAT
* *
5325398 ATAATATTTAAATTTTAAAAAAAAATTTAAT
1 ATAATATTTAAACTATAAAAAAAAATTTAAT
* *
5325429 GTAATATTTGAACTATAAA
1 ATAATATTTAAACTATAAA
5325448 TATGTTAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (31 bp):
ATAATATTTAAACTATAAAAAAAAATTTAAT
Found at i:5325999 original size:20 final size:21
Alignment explanation
Indices: 5325963--5326014 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5325953 TCCGAAATTA
5325963 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
5325985 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
5326006 AT-AAATATT
1 ATAAAATATT
5326015 TTAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:5326005 original size:21 final size:22
Alignment explanation
Indices: 5325963--5326014 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5325953 TCCGAAATTA
5325963 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
5325985 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
5326006 AT-AAATATT
1 ATAAAATATT
5326015 TTAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:5328483 original size:29 final size:26
Alignment explanation
Indices: 5328426--5328489 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 26
5328416 TTTTATCTTG
*
5328426 TATATTTAA-ATAATTTTTTATAAATA
1 TATA-TTAATATAATTTTTTATAAAAA
5328452 TATATTAATATATATTTTTTCAATAAAAA
1 TATATTAATATA-ATTTTTT--ATAAAAA
5328481 TATATTAAT
1 TATATTAAT
5328490 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 4 0.12
26 7 0.21
27 7 0.21
29 15 0.45
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATATTAATATAATTTTTTATAAAAA
Found at i:5329782 original size:18 final size:18
Alignment explanation
Indices: 5329756--5329791 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5329746 TCGACAATTC
5329756 CACAGTTTCTAATTAATG
1 CACAGTTTCTAATTAATG
*
5329774 CACATTTTCTAATTAATG
1 CACAGTTTCTAATTAATG
5329792 ATAATGTATT
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:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (18 bp):
CACAGTTTCTAATTAATG
Found at i:5331219 original size:142 final size:142
Alignment explanation
Indices: 5330958--5331242 Score: 552
Period size: 142 Copynumber: 2.0 Consensus size: 142
5330948 AAGAAAGAAG
*
5330958 CTCAAGCACATTTATATCAGCCTAGGCTCATATTTTGTACTGAGACAATCTTGAATACAAAAATA
1 CTCAAGCACATTTATATCAGCCTAGGCTCATATTTTGTACCGAGACAATCTTGAATACAAAAATA
*
5331023 GAATCGTTTAAAGTATCCCCATTCACACCAGGTCTTGTTTAGGGGGAAATCTAATGAGCCACAAA
66 GAATCGTTTAAAGTATCCCCATTCACACCAGGTCTTGTTTAGGGGGAAAACTAATGAGCCACAAA
5331088 TAGAAGCATATA
131 TAGAAGCATATA
5331100 CTCAAGCACATTTATATCAGCCTAGGCTCATATTTTGTACCGAGACAATCTTGAATACAAAAATA
1 CTCAAGCACATTTATATCAGCCTAGGCTCATATTTTGTACCGAGACAATCTTGAATACAAAAATA
5331165 GAATCGTTTAAAGTATCCCCATTCACACCAGGTCTTGTTTAGGGGGAAAACTAATGAGCCACAAA
66 GAATCGTTTAAAGTATCCCCATTCACACCAGGTCTTGTTTAGGGGGAAAACTAATGAGCCACAAA
5331230 TAGAAGCATATA
131 TAGAAGCATATA
5331242 C
1 C
5331243 CAGGAAATCT
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (142 bp):
CTCAAGCACATTTATATCAGCCTAGGCTCATATTTTGTACCGAGACAATCTTGAATACAAAAATA
GAATCGTTTAAAGTATCCCCATTCACACCAGGTCTTGTTTAGGGGGAAAACTAATGAGCCACAAA
TAGAAGCATATA
Found at i:5343543 original size:18 final size:18
Alignment explanation
Indices: 5343512--5343546 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5343502 ACGACTTATC
5343512 TTTTCTTTTGACTTTTGT
1 TTTTCTTTTGACTTTTGT
5343530 TTTTACTTTT-ACTTTTG
1 TTTT-CTTTTGACTTTTG
5343547 CAGTCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.09, C:0.11, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTTCTTTTGACTTTTGT
Found at i:5348064 original size:22 final size:22
Alignment explanation
Indices: 5348038--5348079 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5348028 TGTATATTTA
* *
5348038 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
5348060 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
5348080 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:5352017 original size:22 final size:22
Alignment explanation
Indices: 5351991--5352032 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5351981 TGTATATTTA
* *
5351991 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
5352013 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
5352033 GGATAGGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:5358348 original size:41 final size:41
Alignment explanation
Indices: 5358302--5358384 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
5358292 ATTCTTTTCA
5358302 GAACTTAACTGCTTTATGAATGCTTAGATTCTCTATCTATT
1 GAACTTAACTGCTTTATGAATGCTTAGATTCTCTATCTATT
5358343 GAACTTAACTGCTTTATGAATGCTTAGATTCTCTATCTATT
1 GAACTTAACTGCTTTATGAATGCTTAGATTCTCTATCTATT
5358384 G
1 G
5358385 CTTGTTGTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (41 bp):
GAACTTAACTGCTTTATGAATGCTTAGATTCTCTATCTATT
Found at i:5358349 original size:22 final size:23
Alignment explanation
Indices: 5358318--5358384 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 23
5358308 AACTGCTTTA
5358318 TGAATGCTTAGATTCTCTATCTAT
1 TGAA-GCTTAGATTCTCTATCTAT
5358342 TGAA-CTTA-A--CTGCT-T-TA-
1 TGAAGCTTAGATTCT-CTATCTAT
5358359 TGAATGCTTAGATTCTCTATCTAT
1 TGAA-GCTTAGATTCTCTATCTAT
5358383 TG
1 TG
5358385 CTTGTTGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 18
0.65 0.00 0.35
Matches are distributed among these distances:
17 4 0.12
18 2 0.06
19 7 0.21
20 3 0.09
21 3 0.09
22 7 0.21
23 2 0.06
24 6 0.18
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (23 bp):
TGAAGCTTAGATTCTCTATCTAT
Found at i:5359938 original size:2 final size:2
Alignment explanation
Indices: 5359901--5359926 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5359891 CCAAACAACC
5359901 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
5359927 GGTTGTATAT
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:5362369 original size:2 final size:2
Alignment explanation
Indices: 5362362--5362400 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5362352 GTTTTTGCGT
* *
5362362 TA TA TA TA TA TA TA TA TA TA TG 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
5362401 GGATAGATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5364052 original size:21 final size:21
Alignment explanation
Indices: 5364028--5364084 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
5364018 TTTTATAAGT
5364028 TTATTTTAAAATTTAACAAAA
1 TTATTTTAAAATTTAACAAAA
*** * *
5364049 TTATAAAAAAATTTAACTACA
1 TTATTTTAAAATTTAACAAAA
*
5364070 -TATTTTATAATTTAA
1 TTATTTTAAAATTTAA
5364085 TCTAACAAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TTATTTTAAAATTTAACAAAA
Found at i:5364766 original size:10 final size:10
Alignment explanation
Indices: 5364753--5364777 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5364743 TGTTTTTGGA
5364753 TTTTTTATTT
1 TTTTTTATTT
5364763 TTTTTTATTT
1 TTTTTTATTT
5364773 TTTTT
1 TTTTT
5364778 GCAGGGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:5364808 original size:17 final size:16
Alignment explanation
Indices: 5364768--5364810 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5364758 TATTTTTTTT
**
5364768 TATTTTTTTTGCAGGG
1 TATTTTTTTTGCAGAA
*
5364784 TATCTTTTTTGACAGAA
1 TATTTTTTTTG-CAGAA
5364801 TATTTTTTTT
1 TATTTTTTTT
5364811 TATTCTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.19, C:0.07, G:0.14, T:0.60
Consensus pattern (16 bp):
TATTTTTTTTGCAGAA
Found at i:5367466 original size:18 final size:19
Alignment explanation
Indices: 5367433--5367471 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5367423 TATGGCATAT
5367433 TTAAAAAGTTAATAAATTA
1 TTAAAAAGTTAATAAATTA
*
5367452 TTAAAAA-TTATTAAATTA
1 TTAAAAAGTTAATAAATTA
5367470 TT
1 TT
5367472 TATTTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TTAAAAAGTTAATAAATTA
Found at i:5367622 original size:22 final size:22
Alignment explanation
Indices: 5367594--5367635 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5367584 ATAAAAAAAT
5367594 TTTATAAAATATTATAAATGGA
1 TTTATAAAATATTATAAATGGA
* *
5367616 TTTATAATATTTTATAAATG
1 TTTATAAAATATTATAAATG
5367636 AATATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTATAAAATATTATAAATGGA
Found at i:5370041 original size:41 final size:42
Alignment explanation
Indices: 5369955--5370069 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 42
5369945 GACTTATATG
** **
5369955 TTATGTCTAATCACTTT-TGTAATGATCCATACGCGTATAATT
1 TTATGTCTAATCACTTTGT-TAATGATCCATATACACATAATT
*
5369997 TTATGTGTAATCACTTTGTTAATGATCCATATACACATAA-T
1 TTATGTCTAATCACTTTGTTAATGATCCATATACACATAATT
*
5370038 TTATGTCTAATCACTTTGTTAATGATTCATAT
1 TTATGTCTAATCACTTTGTTAATGATCCATAT
5370070 GCATTCTAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 31 0.48
42 33 0.51
43 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.44
Consensus pattern (42 bp):
TTATGTCTAATCACTTTGTTAATGATCCATATACACATAATT
Found at i:5371058 original size:33 final size:32
Alignment explanation
Indices: 5371020--5371120 Score: 80
Period size: 33 Copynumber: 3.0 Consensus size: 32
5371010 TTTATTTAAA
*
5371020 TTTAATTTAATATAATAATTAAAAAATATTATT
1 TTTAATTTAATATAATAATTAAAAAATA-AATT
* *
5371053 TTTAATATAA-ATTAACT-ATTAAATAATAAATT
1 TTTAATTTAATA-TAA-TAATTAAAAAATAAATT
*
5371085 TTTAATATAATAATATATATAATTAAATAATTAAAT
1 TTTAAT-T--TAATATA-ATAATTAAA-AAATAAAT
5371121 AAATAATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
32 10 0.19
33 22 0.42
34 1 0.02
35 6 0.11
36 8 0.15
37 6 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
TTTAATTTAATATAATAATTAAAAAATAAATT
Found at i:5371819 original size:9 final size:9
Alignment explanation
Indices: 5371772--5371819 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
5371762 GTTTTTTTTC
5371772 AAAATTATATT
1 AAAATT-TA-T
*
5371783 AAAATTTTT
1 AAAATTTAT
5371792 AAAATTTAT
1 AAAATTTAT
* *
5371801 AACATATAT
1 AAAATTTAT
5371810 AAAATTTAT
1 AAAATTTAT
5371819 A
1 A
5371820 TATACTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
9 24 0.77
10 1 0.03
11 6 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTAT
Found at i:5372798 original size:21 final size:22
Alignment explanation
Indices: 5372774--5372826 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
5372764 TAATTTATAA
5372774 TTAAAAAACTATTTTAC-TCAT
1 TTAAAAAACTATTTTACATCAT
*
5372795 TTAAAAAGCTATTTTACATGTCAT
1 TTAAAAAACTATTTTACA--TCAT
5372819 TTAAAAAA
1 TTAAAAAA
5372827 ATTATCTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 16 0.59
24 11 0.41
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (22 bp):
TTAAAAAACTATTTTACATCAT
Found at i:5372877 original size:2 final size:2
Alignment explanation
Indices: 5372870--5372901 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5372860 ATCAAATCTA
5372870 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5372902 ACAATATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5381418 original size:6 final size:7
Alignment explanation
Indices: 5381396--5381426 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5381386 TCTATTTTAA
5381396 TTTGATT
1 TTTGATT
*
5381403 TTTCATT
1 TTTGATT
5381410 TTTGATT
1 TTTGATT
5381417 TTTGATT
1 TTTGATT
5381424 TTT
1 TTT
5381427 TTCCTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.03, G:0.10, T:0.74
Consensus pattern (7 bp):
TTTGATT
Found at i:5381827 original size:30 final size:30
Alignment explanation
Indices: 5381771--5381827 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
5381761 ACATGAGGTA
* *
5381771 AATTTTGTATTTGATTATTGTAATTTATTG
1 AATTGTGTATTTGATTATTATAATTTATTG
*
5381801 AATTGTGTATTTTATT-TTATATATTTA
1 AATTGTGTATTTGATTATTATA-ATTTA
5381828 AATTAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (30 bp):
AATTGTGTATTTGATTATTATAATTTATTG
Found at i:5381995 original size:15 final size:15
Alignment explanation
Indices: 5381975--5382006 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5381965 TGTGTTTAAT
*
5381975 ATTTAAATATTAAAA
1 ATTTAAATAATAAAA
5381990 ATTTAAATAATAAAA
1 ATTTAAATAATAAAA
5382005 AT
1 AT
5382007 GGTAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTTAAATAATAAAA
Found at i:5384782 original size:33 final size:33
Alignment explanation
Indices: 5384745--5384811 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5384735 TTGTCACCTT
5384745 TCATATGCCCTATCTTTTCCCTTACAAGAATGA
1 TCATATGCCCTATCTTTTCCCTTACAAGAATGA
5384778 TCATATGCCCTATCTTTTCCCTTACAAGAATGA
1 TCATATGCCCTATCTTTTCCCTTACAAGAATGA
5384811 T
1 T
5384812 AAGAAGGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.37
Consensus pattern (33 bp):
TCATATGCCCTATCTTTTCCCTTACAAGAATGA
Found at i:5390650 original size:13 final size:14
Alignment explanation
Indices: 5390618--5390670 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
5390608 ACAATTAAAG
*
5390618 TTGCATTTATGACA
1 TTGCATTCATGACA
*
5390632 TTGCATTCATG-CT
1 TTGCATTCATGACA
*
5390645 TTGCATTCATAAACA
1 TTGCATTCAT-GACA
*
5390660 TTGTATTCATG
1 TTGCATTCATG
5390671 TAATTTGTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 11 0.35
14 10 0.32
15 10 0.32
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (14 bp):
TTGCATTCATGACA
Found at i:5391082 original size:44 final size:44
Alignment explanation
Indices: 5391016--5391225 Score: 189
Period size: 44 Copynumber: 4.8 Consensus size: 44
5391006 CTTGGTTAAG
* * * * *
5391016 AAGCCTTTTATAATTTTTTAAAGTTATTGAGCTTTTAATGAGAT
1 AAGCCTTTTAAAATTTTCTAAAGTTATTAAGCTTCTGATGAGAT
* * * * *
5391060 AAGCCTTTTATAATTTTCTAAAGTTGTTTAGCCTCTGATGAGAG
1 AAGCCTTTTAAAATTTTCTAAAGTTATTAAGCTTCTGATGAGAT
* * * *
5391104 AAGACTTTTAAAATTTT-TCAAAGTTGTTAAGCCTCTGATGA-AA
1 AAGCCTTTTAAAATTTTCT-AAAGTTATTAAGCTTCTGATGAGAT
*
5391147 AAGGCTTTTTAAAATTTTC-AAAGTTATTAAG-TCTCTGATGAGAT
1 AA-GCCTTTTAAAATTTTCTAAAGTTATTAAGCT-TCTGATGAGAT
* *
5391191 GAA-CTTTTTAAAATTTTC-AAAGTTATTGAGCTTCT
1 -AAGCCTTTTAAAATTTTCTAAAGTTATTAAGCTTCT
5391226 ATTTAGAATA
Statistics
Matches: 142, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
43 52 0.37
44 88 0.62
45 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (44 bp):
AAGCCTTTTAAAATTTTCTAAAGTTATTAAGCTTCTGATGAGAT
Found at i:5391169 original size:43 final size:43
Alignment explanation
Indices: 5391053--5391214 Score: 195
Period size: 43 Copynumber: 3.7 Consensus size: 43
5391043 TGAGCTTTTA
* * * *
5391053 ATGAGATAAGCCTTTTATAATTTTCTAAAGTTGTTTAGCCTCTG
1 ATGAGAGAAGCTTTTTAAAATTTTC-AAAGTTGTTAAGCCTCTG
5391097 ATGAGAGAAGAC-TTTTAAAATTTTTCAAAGTTGTTAAGCCTCTG
1 ATGAGAGAAG-CTTTTTAAAA-TTTTCAAAGTTGTTAAGCCTCTG
* * *
5391141 ATGA-AAAAGGCTTTTTAAAATTTTCAAAGTTATTAAGTCTCTG
1 ATGAGAGAA-GCTTTTTAAAATTTTCAAAGTTGTTAAGCCTCTG
5391184 ATGAGATGAA-CTTTTTAAAATTTTCAAAGTT
1 ATGAGA-GAAGCTTTTTAAAATTTTCAAAGTT
5391215 ATTGAGCTTC
Statistics
Matches: 105, Mismatches: 7, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
43 50 0.48
44 47 0.45
45 8 0.08
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.40
Consensus pattern (43 bp):
ATGAGAGAAGCTTTTTAAAATTTTCAAAGTTGTTAAGCCTCTG
Found at i:5391242 original size:87 final size:87
Alignment explanation
Indices: 5391014--5391242 Score: 218
Period size: 88 Copynumber: 2.6 Consensus size: 87
5391004 ACCTTGGTTA
* * * * *
5391014 AGAAGCCTTTTATAATTTTTTAAAGTTATTGAGCTTTTAATGAG-ATAAGCC-TTTTATAATTTT
1 AGAAGACTTTTA-AAATTTTCAAAGTTATTGAGCTTCT-ATGAGAAT-AGCCTTTTTAAAATTTT
* *
5391077 CTAAAGTTGTTTAGCCTCTGATGAG
63 CTAAAGTTATTAAGCCTCTGATGAG
* * * * *
5391102 AGAAGACTTTTAAAATTTTTCAAAGTTGTTAAGCCTCTGATGA-AAAAGGCTTTTTAAAATTTTC
1 AGAAGACTTTTAAAA-TTTTCAAAGTTATTGAGCTTCT-ATGAGAATAGCCTTTTTAAAATTTTC
*
5391166 -AAAGTTATTAAGTCTCTGATGAG
64 TAAAGTTATTAAGCCTCTGATGAG
*
5391189 ATG-A-ACTTTTTAAAATTTTCAAAGTTATTGAGCTTCTATTTAGAATAGCCTTTT
1 A-GAAGAC-TTTTAAAATTTTCAAAGTTATTGAGCTTCTA-TGAGAATAGCCTTTT
5391243 ATGTCATTCA
Statistics
Matches: 114, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
85 1 0.01
86 23 0.20
87 44 0.39
88 46 0.40
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (87 bp):
AGAAGACTTTTAAAATTTTCAAAGTTATTGAGCTTCTATGAGAATAGCCTTTTTAAAATTTTCTA
AAGTTATTAAGCCTCTGATGAG
Found at i:5391243 original size:43 final size:43
Alignment explanation
Indices: 5391017--5391243 Score: 169
Period size: 43 Copynumber: 5.2 Consensus size: 43
5391007 TTGGTTAAGA
* * * * *
5391017 AGCCTTTTATAATTTTTTAAAGTTATTGAGCTTTTAATGAG-AT
1 AGCCTTTTA-AAATTTTCAAAGTTATTAAGCTTCTGATGAGAAT
* * * *
5391060 AAGCCTTTTATAATTTTCTAAAGTTGTTTAGCCTCTGATGAGAGA-
1 -AGCCTTTTAAAATTTTC-AAAGTTATTAAGCTTCTGATGAGA-AT
* * * *
5391105 AGACTTTTAAAATTTTTCAAAGTTGTTAAGCCTCTGATGA-AAA
1 AGCCTTTTAAAA-TTTTCAAAGTTATTAAGCTTCTGATGAGAAT
*
5391148 AGGCTTTTTAAAATTTTCAAAGTTATTAAG-TCTCTGATGAG-AT
1 A-GCCTTTTAAAATTTTCAAAGTTATTAAGCT-TCTGATGAGAAT
* * * *
5391191 GAACTTTTTAAAATTTTCAAAGTTATTGAGCTTCT-ATTTAGAAT
1 -AGCCTTTTAAAATTTTCAAAGTTATTAAGCTTCTGA-TGAGAAT
5391235 AGCCTTTTA
1 AGCCTTTTA
5391244 TGTCATTCAA
Statistics
Matches: 150, Mismatches: 21, Indels: 25
0.77 0.11 0.13
Matches are distributed among these distances:
42 2 0.01
43 71 0.47
44 71 0.47
45 5 0.03
46 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (43 bp):
AGCCTTTTAAAATTTTCAAAGTTATTAAGCTTCTGATGAGAAT
Found at i:5391975 original size:16 final size:16
Alignment explanation
Indices: 5391954--5391984 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5391944 TTTGTTTGAA
5391954 TTTTTTGAATTTTTTT
1 TTTTTTGAATTTTTTT
*
5391970 TTTTTTGAGTTTTTT
1 TTTTTTGAATTTTTT
5391985 CTGGAAATCT
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:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (16 bp):
TTTTTTGAATTTTTTT
Found at i:5392352 original size:14 final size:14
Alignment explanation
Indices: 5392316--5392345 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5392306 TCTATTTTCA
5392316 TTTGA-TTTTTAGT
1 TTTGATTTTTTAGT
5392329 TTTGATTTTTTAGT
1 TTTGATTTTTTAGT
5392343 TTT
1 TTT
5392346 TCTTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (14 bp):
TTTGATTTTTTAGT
Found at i:5392452 original size:16 final size:17
Alignment explanation
Indices: 5392433--5392468 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
5392423 TCTTTTATTT
*
5392433 ATTTGATTTGTAAAA-A
1 ATTTAATTTGTAAAACA
5392449 ATTTAATTTGTAAAACA
1 ATTTAATTTGTAAAACA
5392466 ATT
1 ATT
5392469 AAAGATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTTAATTTGTAAAACA
Found at i:5400173 original size:22 final size:20
Alignment explanation
Indices: 5400147--5400199 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
5400137 ACCATTTGCA
**
5400147 TTTTCTTTTTTTATTTTTCTT
1 TTTTCTTTTTTT-TCCTTCTT
5400168 TGTTTCTTTATTTTTCCTTCTT
1 T-TTTCTTT-TTTTTCCTTCTT
5400190 TTTTCTTTTT
1 TTTTCTTTTT
5400200 CCTTCTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 8 0.29
22 14 0.50
23 4 0.14
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTCTTTTTTTTCCTTCTT
Found at i:5400198 original size:17 final size:17
Alignment explanation
Indices: 5400153--5400206 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
5400143 TGCATTTTCT
* *
5400153 TTTTTTATTTTTCTTTG
1 TTTTTTATTTTTCCTTC
5400170 TTTCTTTATTTTTCCTTC
1 TTT-TTTATTTTTCCTTC
*
5400188 TTTTTTCTTTTTCCTTC
1 TTTTTTATTTTTCCTTC
5400205 TT
1 TT
5400207 CTTCTTTCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTTATTTTTCCTTC
Found at i:5401840 original size:39 final size:33
Alignment explanation
Indices: 5401770--5401841 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 33
5401760 AAAAATTTTT
5401770 TTTATAAAAATAAAAAAATAAAAAATTAACTAA
1 TTTATAAAAATAAAAAAATAAAAAATTAACTAA
5401803 TTTATTAAAAATAATTAAAAATAATAATAATATAACTAA
1 TTTA-TAAAAATAA--AAAAATAA-AA-AAT-TAACTAA
5401842 GGAAAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
33 4 0.12
34 9 0.27
36 8 0.24
37 2 0.06
38 3 0.09
39 7 0.21
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (33 bp):
TTTATAAAAATAAAAAAATAAAAAATTAACTAA
Found at i:5403337 original size:21 final size:21
Alignment explanation
Indices: 5403312--5403355 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5403302 CATCCTTACA
*
5403312 TTAACTCAATTTTGTTTCATT
1 TTAACTCAAATTTGTTTCATT
5403333 TTAACTCAAATTTGTTTCATT
1 TTAACTCAAATTTGTTTCATT
5403354 TT
1 TT
5403356 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.57
Consensus pattern (21 bp):
TTAACTCAAATTTGTTTCATT
Found at i:5413069 original size:20 final size:19
Alignment explanation
Indices: 5413046--5413094 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
5413036 ATATTTTCCT
5413046 TAAAAAAGAGAATAAAAAAA
1 TAAAAAAGAG-ATAAAAAAA
* * *
5413066 TAAAAAAAAGGTAAAAAAG
1 TAAAAAAGAGATAAAAAAA
5413085 TGAAAAAAGA
1 T-AAAAAAGA
5413095 ATGACATATC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (19 bp):
TAAAAAAGAGATAAAAAAA
Found at i:5413958 original size:48 final size:48
Alignment explanation
Indices: 5413906--5414106 Score: 192
Period size: 48 Copynumber: 4.1 Consensus size: 48
5413896 CATATGAGAT
5413906 TTTTTAAAGTTGTTAAGCCTTTGCTTAGAGGAGCTTTTTCAAAAT-AAA
1 TTTTTAAAGTTGTTAAGCCTTTGCTTAGAGGAGCTTTTTC-AAATGAAA
* * * *
5413954 TTTTTAAAATTGTTAAGCCTTTGCTTAGATGAGCTTTTTCAGATGATA
1 TTTTTAAAGTTGTTAAGCCTTTGCTTAGAGGAGCTTTTTCAAATGAAA
* * * * *
5414002 TTTTTAAAGTTATTAAGCCTCTACTTAGAGGAGCTTTTCCAGGATGATAA
1 TTTTTAAAGTTGTTAAGCCTTTGCTTAGAGGAGCTTTTTCA-AATGA-AA
* * * * **
5414052 ATTTTAAAGTTATTGAG-CTTCTACTTAGATAAGCCTTTTTCAAAT-AAGA
1 TTTTTAAAGTTGTTAAGCCTT-TGCTTAGAGGAG-CTTTTTCAAATGAA-A
5414101 TTTTTA
1 TTTTTA
5414107 CTGCTTAAAT
Statistics
Matches: 128, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
47 3 0.02
48 76 0.59
49 14 0.11
50 28 0.22
51 7 0.05
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (48 bp):
TTTTTAAAGTTGTTAAGCCTTTGCTTAGAGGAGCTTTTTCAAATGAAA
Found at i:5414164 original size:49 final size:49
Alignment explanation
Indices: 5414110--5414514 Score: 310
Period size: 49 Copynumber: 8.3 Consensus size: 49
5414100 ATTTTTACTG
* * *
5414110 CTTAAATGAGCCTTTTCCAAATAAGATTTTTAAAGTTATTAAGCCTTTA
1 CTTAAATGAGCCTTTTTCAGATAAGATTTTTAAAGTTGTTAAGCCTTTA
* ** * * *
5414159 TTTAAA-GAAGTTTTTTTTAGATAAGATTTTTAAAGTTGTTAAGCCTCTG
1 CTTAAATG-AGCCTTTTTCAGATAAGATTTTTAAAGTTGTTAAGCCTTTA
* * * * *
5414208 CTTAGAA-GAG-CTTTTTCAGGATGATGAATTTTAAAGTTGTTGAGTCTCTA
1 CTTA-AATGAGCCTTTTTCA-GAT-AAGATTTTTAAAGTTGTTAAGCCTTTA
* * * *
5414258 TTTAGATGAGCCTTTTT---A-AA-TTTTTTAAAGTTGTTGAGCCTTTA
1 CTTAAATGAGCCTTTTTCAGATAAGATTTTTAAAGTTGTTAAGCCTTTA
* * *
5414302 CTTAAATGAGCATTTTTCAGATAAGATTTTTAAAGTTGTTGAGCCTCTA
1 CTTAAATGAGCCTTTTTCAGATAAGATTTTTAAAGTTGTTAAGCCTTTA
* * * *
5414351 CTTAGATGAACCTTTTT-AGATAAGATTTTTAAAGTTATTAAGCCTTTG
1 CTTAAATGAGCCTTTTTCAGATAAGATTTTTAAAGTTGTTAAGCCTTTA
* * ** * * *
5414399 TTTAAAGGAGTTTTTTTCAGATAAAATTTTTAAAATTGTTAAGCCTTTG
1 CTTAAATGAGCCTTTTTCAGATAAGATTTTTAAAGTTGTTAAGCCTTTA
* * * * * *
5414448 CTGAGA-GAAG-CTTTTTCAGGATAATGAATTTTAAAGTTGTTGAGCCTCTG
1 CTTAAATG-AGCCTTTTTCA-GATAA-GATTTTTAAAGTTGTTAAGCCTTTA
* *
5414498 CTTAGATGAGCTTTTTT
1 CTTAAATGAGCCTTTTT
5414515 AAATTTTCAA
Statistics
Matches: 283, Mismatches: 56, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
44 34 0.12
45 1 0.00
47 2 0.01
48 55 0.19
49 121 0.43
50 58 0.20
51 12 0.04
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (49 bp):
CTTAAATGAGCCTTTTTCAGATAAGATTTTTAAAGTTGTTAAGCCTTTA
Found at i:5414272 original size:183 final size:180
Alignment explanation
Indices: 5413927--5414278 Score: 456
Period size: 183 Copynumber: 1.9 Consensus size: 180
5413917 GTTAAGCCTT
* * * * *
5413927 TGCTTAGAGGAGCTTTTTCAAAATAAATTTTTAAAATTGTTAAGCCTTTGCTTAGATGAGCTTTT
1 TGCTTAAAGGAGCCTTTTCAAAATAAATTTTTAAAATTATTAAGCCTTTACTTAGAAGAGCTTTT
* * *
5413992 TCAGATGATATTTTTAAAGTTATTAAGCCTCTACTTAGAGGAGCTTTTCCAGGATGATAAATTTT
66 TCAGATAAGATTTTTAAAGTTATTAAGCCTCTACTTAGAAGAGCTTTTCCAGGATGATAAATTTT
5414057 AAAGTTATTGAGCTTCTACTTAGATAAGCCTTTTTCAAATAAGATTTTTAC
131 AAAGTTATTGAGCTTCTACTTAGATAAGCCTTTTT-AAATAAGATTTTTAC
* * * * *
5414108 TGCTTAAATGAGCCTTTTCCAAATAAGATTTTTAAAGTTATTAAGCCTTTATTTA-AAGAAGTTT
1 TGCTTAAAGGAGCCTTTTCAAAATAA-ATTTTTAAAATTATTAAGCCTTTACTTAGAAG-AG-CT
* * * * *
5414172 TTTTTAGATAAGATTTTTAAAGTTGTTAAGCCTCTGCTTAGAAGAGCTTTTTCAGGATGATGAAT
63 TTTTCAGATAAGATTTTTAAAGTTATTAAGCCTCTACTTAGAAGAGCTTTTCCAGGATGATAAAT
* * *
5414237 TTTAAAGTTGTTGAG-TCTCTATTTAGATGAGCCTTTTTAAAT
128 TTTAAAGTTATTGAGCT-TCTACTTAGATAAGCCTTTTTAAAT
5414279 TTTTTAAAGT
Statistics
Matches: 146, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
181 24 0.16
182 31 0.21
183 91 0.62
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (180 bp):
TGCTTAAAGGAGCCTTTTCAAAATAAATTTTTAAAATTATTAAGCCTTTACTTAGAAGAGCTTTT
TCAGATAAGATTTTTAAAGTTATTAAGCCTCTACTTAGAAGAGCTTTTCCAGGATGATAAATTTT
AAAGTTATTGAGCTTCTACTTAGATAAGCCTTTTTAAATAAGATTTTTAC
Found at i:5414295 original size:44 final size:46
Alignment explanation
Indices: 5414179--5414556 Score: 232
Period size: 49 Copynumber: 8.0 Consensus size: 46
5414169 TTTTTTTTAG
* * *
5414179 ATAAGATTTTTAAAGTTGTTAAGCCTCTGCTTAGAAGAG-CTTTTT
1 ATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAGCCTTTTT
* * * *
5414224 CAGGATGATGAATTTTAAAGTTGTTGAGTCTCTATTTAGATGAGCCTTTTT
1 ----AT-AAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAGCCTTTTT
* * * *
5414275 A-AA-TTTTTTAAAGTTGTTGAGCCTTTACTTAAATGAGCATTTTT
1 ATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAGCCTTTTT
*
5414319 CAGATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAACCTTTTT
1 ---ATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAGCCTTTTT
* * * ** * * **
5414368 AGATAAGATTTTTAAAGTTATTAAGCCTTTGTTTAAAGGAGTTTTTTT
1 --ATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAGCCTTTTT
* * * * * *
5414416 CAGATAAAATTTTTAAAATTGTTAAGCCTTTGCTGAGA-GAAG-CTTTTT
1 ---ATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATG-AGCCTTTTT
* *
5414464 CAGGATAATGAATTTTAAAGTTGTTGAGCCTCTGCTTAGATGAG-CTTTTT
1 ----ATAA-GATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAGCCTTTTT
* * *
5414514 -TAA-ATTTTCAAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTT
1 ATAAGATTTT-TAAAGTTGTTGAGCCTCTACTTAGATGAGCCTTT
5414557 GTAATTTTTC
Statistics
Matches: 267, Mismatches: 48, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
43 4 0.01
44 61 0.23
45 8 0.03
47 2 0.01
48 46 0.17
49 76 0.28
50 63 0.24
51 7 0.03
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (46 bp):
ATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAGCCTTTTT
Found at i:5414343 original size:93 final size:94
Alignment explanation
Indices: 5414108--5414561 Score: 334
Period size: 97 Copynumber: 4.7 Consensus size: 94
5414098 AGATTTTTAC
* * * * * * * **
5414108 TGCTTAAATGAGCCTTTTCCAAATAAGATTTTTAAAGTTATTAAGCCTTTATTTA-AAGAAGTTT
1 TGCTTAAA-GAG-CTTTTTCAGATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAA--CC
*
5414172 TTTTTAGATAAGATTTTTAAAGTTGTTAAGCCTC
62 TTTTTA-ATAAGATTTTTAAAGTTGTTAAGCCTT
* * * * *
5414206 TGCTTAGAAGAGCTTTTTCAGGATGATGAATTTTAAAGTTGTTGAGTCTCTATTTAGATGAGCCT
1 TGCTTA-AAGAGCTTTTTCA-GAT-AAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAACCT
* *
5414271 TTTT-A-AA-TTTTTTAAAGTTGTTGAGCCTT
63 TTTTAATAAGATTTTTAAAGTTGTTAAGCCTT
*
5414300 TACTTAAATGAGCATTTTTCAGATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAACCTT
1 TGCTTAAA-GAGC-TTTTTCAGATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAACCTT
*
5414365 TTTAGATAAGATTTTTAAAGTTATTAAGCCTT
64 TTTA-ATAAGATTTTTAAAGTTGTTAAGCCTT
* * * * * * * * *
5414397 TGTTTAAAGGAGTTTTTTTCAGATAAAATTTTTAAAATTGTTAAGCCTTTGCTGAGA-GAAGCTT
1 TGCTTAAA-GAG-CTTTTTCAGATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAACCTT
* * *
5414461 TTTCAGGATAATGAATTTTAAAGTTGTTGAGCCTC
64 TTT-A--ATAA-GATTTTTAAAGTTGTTAAGCCTT
* * * * *
5414496 TGCTTAGATGAGCTTTTT----TAA-ATTTTCAAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTT
1 TGCTTA-AAGAGCTTTTTCAGATAAGATTTT-TAAAGTTGTTGAGCCTCTACTTAGATGAACCTT
*
5414556 TGTAAT
64 TTTAAT
5414562 TTTTCAAAAG
Statistics
Matches: 289, Mismatches: 50, Indels: 40
0.76 0.13 0.11
Matches are distributed among these distances:
92 2 0.01
93 46 0.16
94 55 0.19
95 17 0.06
96 12 0.04
97 73 0.25
98 26 0.09
99 54 0.19
100 4 0.01
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (94 bp):
TGCTTAAAGAGCTTTTTCAGATAAGATTTTTAAAGTTGTTGAGCCTCTACTTAGATGAACCTTTT
TAATAAGATTTTTAAAGTTGTTAAGCCTT
Found at i:5414640 original size:45 final size:44
Alignment explanation
Indices: 5414480--5414641 Score: 177
Period size: 44 Copynumber: 3.7 Consensus size: 44
5414470 AATGAATTTT
*
5414480 AAAGTTGTTGAGCCTCTGCTTAGATGAGCTTTTTTAAA-TTTTCA
1 AAAGTTGTTGAGCCTCTGCTTAGAAGAGC-TTTTTAAATTTTTCA
* *
5414524 AAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTGT-AATTTTTCA
1 AAAGTTGTTGAGCCTCTGCTTAGAAGAG-CTTTTTAAATTTTTCA
* * *
5414568 AAAGTTGTTGAGCTTCTG-TTACAAAGAGCTTTTTAAATTTTTAA
1 AAAGTTGTTGAGCCTCTGCTTA-GAAGAGCTTTTTAAATTTTTCA
* * * *
5414612 AAATATTGTTGAACTTCTGTTTAGAAGAGC
1 AAA-GTTGTTGAGCCTCTGCTTAGAAGAGC
5414642 CCTAAAAAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
43 10 0.10
44 69 0.68
45 20 0.20
46 3 0.03
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (44 bp):
AAAGTTGTTGAGCCTCTGCTTAGAAGAGCTTTTTAAATTTTTCA
Found at i:5414766 original size:10 final size:9
Alignment explanation
Indices: 5414753--5414787 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5414743 TCATTTTATA
5414753 TTTTTTTCT
1 TTTTTTTCT
5414762 TTTTTTTCCT
1 TTTTTTT-CT
*
5414772 TTTTTTCCT
1 TTTTTTTCT
5414781 TTTTTTT
1 TTTTTTT
5414788 TTCTTATCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:5415176 original size:21 final size:21
Alignment explanation
Indices: 5415152--5415191 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5415142 CGAGGACCAC
5415152 AACACCAAACA-ATAAAAAACA
1 AACA-CAAACACATAAAAAACA
*
5415173 AACACAGACACATAAAAAA
1 AACACAAACACATAAAAAA
5415192 ATTTTTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.70, C:0.23, G:0.03, T:0.05
Consensus pattern (21 bp):
AACACAAACACATAAAAAACA
Found at i:5418545 original size:21 final size:22
Alignment explanation
Indices: 5418504--5418547 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
5418494 AAACTATTCA
*
5418504 TGAATCATTTAAGTTTGATTTG
1 TGAATCATTTAAGTTTAATTTG
5418526 TGAAT-ATTTGAA-TTTAATTTG
1 TGAATCATTT-AAGTTTAATTTG
5418547 T
1 T
5418548 TTATTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (22 bp):
TGAATCATTTAAGTTTAATTTG
Found at i:5423938 original size:29 final size:30
Alignment explanation
Indices: 5423904--5423963 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
5423894 ATTTTGATTT
*
5423904 AAATTTTATTTTA-ATTTTTAATT-TTTAAA
1 AAATTTTA-ATTACATTTTTAATTGTTTAAA
5423933 AAATTTTAATTACATTTTTAATTGTTTAAA
1 AAATTTTAATTACATTTTTAATTGTTTAAA
5423963 A
1 A
5423964 TTATCTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 3 0.11
29 18 0.64
30 7 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (30 bp):
AAATTTTAATTACATTTTTAATTGTTTAAA
Found at i:5424227 original size:29 final size:25
Alignment explanation
Indices: 5424163--5424227 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 25
5424153 ATATTAACTT
*
5424163 TAAAATTATATTTTTTATTTTTTTG
1 TAAAATTATATTTATTATTTTTTTG
*
5424188 TAATA-TA-ATTTATTAGTTTTTTTTAG
1 TAAAATTATATTTATTA--TTTTTTT-G
5424214 TAGAAATTATATTT
1 TA-AAATTATATTT
5424228 TCAAAAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 7 0.23
24 2 0.06
25 11 0.35
26 3 0.10
27 2 0.06
28 2 0.06
29 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (25 bp):
TAAAATTATATTTATTATTTTTTTG
Found at i:5424272 original size:22 final size:21
Alignment explanation
Indices: 5424246--5424296 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5424236 GAAAATTAGG
* * *
5424246 TTAAAATTTTCAAATTTCTTTT
1 TTAAAATATTC-AATATCATTT
*
5424268 TTAAAAAATTCAATATCATTT
1 TTAAAATATTCAATATCATTT
5424289 TTAAAATA
1 TTAAAATA
5424297 AAAAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAAATATTCAATATCATTT
Found at i:5424559 original size:25 final size:23
Alignment explanation
Indices: 5424506--5424559 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
5424496 TTTTTGATAG
*
5424506 AAAATAAATTTTTGAATAGATTA
1 AAAATAAATTTTTGAAAAGATTA
* *
5424529 ATAAATATATTTTTTAAAATGATATA
1 A-AAATAAATTTTTGAAAA-GAT-TA
5424555 AAAAT
1 AAAAT
5424560 TTTTACATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 14 0.56
25 7 0.28
26 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (23 bp):
AAAATAAATTTTTGAAAAGATTA
Found at i:5424666 original size:19 final size:20
Alignment explanation
Indices: 5424620--5424672 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
5424610 AAATGAAGAG
5424620 GAATTTTTTAAAATTATTTT
1 GAATTTTTTAAAATTATTTT
* *
5424640 GAAATTTTT-AACTTAATTTT
1 GAATTTTTTAAAATT-ATTTT
5424660 -AATTTTTTTAAAA
1 GAA-TTTTTTAAAA
5424673 ATATATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 6 0.23
20 18 0.69
21 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
GAATTTTTTAAAATTATTTT
Found at i:5429174 original size:17 final size:18
Alignment explanation
Indices: 5429149--5429182 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5429139 TTTGCCACCA
5429149 CATTATCTT-TTCTTTTC
1 CATTATCTTCTTCTTTTC
*
5429166 CATTTTCTTCTTCTTTT
1 CATTATCTTCTTCTTTT
5429183 AAGTTTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (18 bp):
CATTATCTTCTTCTTTTC
Found at i:5430759 original size:31 final size:32
Alignment explanation
Indices: 5430700--5430761 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
5430690 AATATTCTAA
* *
5430700 TAATAAATATTAATATTTTAATATTATTATAT
1 TAATAAATAATAATATTTTAATACTATTATAT
5430732 TAATAAA-AATAATATTTTAA-AGCTATTATA
1 TAATAAATAATAATATTTTAATA-CTATTATA
5430762 AATATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 1 0.04
31 19 0.70
32 7 0.26
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (32 bp):
TAATAAATAATAATATTTTAATACTATTATAT
Found at i:5430888 original size:30 final size:30
Alignment explanation
Indices: 5430852--5430911 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5430842 TAATATTAAA
* *
5430852 TAATATTATTAAAAATATATT-TTTTAATAT
1 TAATATT-TTAAAAATAAATTATTTCAATAT
*
5430882 TAATATTTTAATAATAAATTATTTCAATAT
1 TAATATTTTAAAAATAAATTATTTCAATAT
5430912 ATTTTAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TAATATTTTAAAAATAAATTATTTCAATAT
Found at i:5430944 original size:25 final size:25
Alignment explanation
Indices: 5430883--5430947 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
5430873 TTTTAATATT
*
5430883 AATATTTTAATAATAAATTATTTCA
1 AATATTTTAATAATAAATAATTTCA
**
5430908 ATATATTTTAATCCTAAATAATTCTC-
1 A-ATATTTTAATAATAAATAATT-TCA
5430934 AATATTTTAATAAT
1 AATATTTTAATAAT
5430948 TATATCAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 12 0.36
26 19 0.58
27 2 0.06
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.48
Consensus pattern (25 bp):
AATATTTTAATAATAAATAATTTCA
Found at i:5431076 original size:14 final size:15
Alignment explanation
Indices: 5431057--5431086 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5431047 TGTTTAATGT
5431057 AAATA-TTTTTAAAA
1 AAATATTTTTTAAAA
5431071 AAATATTTTTTAAAA
1 AAATATTTTTTAAAA
5431086 A
1 A
5431087 TTAATTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATATTTTTTAAAA
Found at i:5436156 original size:2 final size:2
Alignment explanation
Indices: 5436149--5436211 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
5436139 ACCACCAAAA
5436149 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5436191 TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
5436212 ATATATATAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5436263 original size:16 final size:16
Alignment explanation
Indices: 5436242--5436275 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5436232 TAATATAAAA
5436242 TTTTTAATT-TTATATT
1 TTTTTAATTATTA-ATT
5436258 TTTTTAATTATTAATT
1 TTTTTAATTATTAATT
5436274 TT
1 TT
5436276 AATAAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTAATTATTAATT
Found at i:5437423 original size:4 final size:4
Alignment explanation
Indices: 5437416--5437448 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
5437406 CTATAATATA
5437416 TATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
5437449 GACTTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:5438163 original size:2 final size:2
Alignment explanation
Indices: 5438156--5438181 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5438146 TGAAAGGGAG
5438156 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
5438182 TGTTCTATCA
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:5440723 original size:27 final size:27
Alignment explanation
Indices: 5440686--5440743 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 27
5440676 CAGAAAAATA
5440686 TTTTTATTTTAAA-T-ATTTTCTATTCT
1 TTTTTATTTTAAATTCATTTTCTATT-T
5440712 TTTTTATATTTAAATTTCATTTTCTATTT
1 TTTTTAT-TTTAAA-TTCATTTTCTATTT
5440741 TTT
1 TTT
5440744 ATAATGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 7 0.25
27 6 0.21
29 5 0.18
30 10 0.36
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTTATTTTAAATTCATTTTCTATTT
Found at i:5441716 original size:13 final size:14
Alignment explanation
Indices: 5441700--5441733 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5441690 TTTTTTATTC
5441700 TTTAGTTTT-TATA
1 TTTAGTTTTGTATA
5441713 TTTA-TTTTGTATA
1 TTTAGTTTTGTATA
5441726 TTTAGTTT
1 TTTAGTTT
5441734 ATTTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 12 0.63
14 3 0.16
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (14 bp):
TTTAGTTTTGTATA
Found at i:5445989 original size:25 final size:25
Alignment explanation
Indices: 5445944--5445999 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
5445934 GATTTAGTTA
*
5445944 AATA-ATT-TTTTAATTTAATTTTT
1 AATATATTATTTTAATATAATTTTT
* *
5445967 TATATATTATTTTAATATGATTTTT
1 AATATATTATTTTAATATAATTTTT
5445992 AATATATT
1 AATATATT
5446000 TAAGTAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 3 0.11
25 21 0.78
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
AATATATTATTTTAATATAATTTTT
Found at i:5446059 original size:18 final size:19
Alignment explanation
Indices: 5446036--5446078 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
5446026 ATTTTTATTT
*
5446036 TATAAAAACT-TTAAAATA
1 TATAAAAACTATAAAAATA
5446054 TATAAAAACTAATAAAAATA
1 TATAAAAACT-ATAAAAATA
5446074 TATAA
1 TATAA
5446079 TTTGATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
TATAAAAACTATAAAAATA
Found at i:5446349 original size:2 final size:2
Alignment explanation
Indices: 5446342--5446375 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5446332 CTAGGAAGGT
5446342 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5446376 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5449073 original size:9 final size:9
Alignment explanation
Indices: 5449059--5449083 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5449049 ATAATATCAT
5449059 TATTTATTA
1 TATTTATTA
5449068 TATTTATTA
1 TATTTATTA
5449077 TATTTAT
1 TATTTAT
5449084 ATTTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TATTTATTA
Found at i:5463094 original size:17 final size:17
Alignment explanation
Indices: 5463072--5463105 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5463062 CCCATCAACA
5463072 AAATGATGAAGAATTAC
1 AAATGATGAAGAATTAC
5463089 AAATGATGAAGAATTAC
1 AAATGATGAAGAATTAC
5463106 GCTCCACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
AAATGATGAAGAATTAC
Found at i:5463628 original size:2 final size:2
Alignment explanation
Indices: 5463585--5463616 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5463575 ATCAAATCTA
5463585 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5463617 ACAACATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5465203 original size:27 final size:27
Alignment explanation
Indices: 5465149--5465203 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5465139 GGGTGTCTTA
* * * *
5465149 GTTAGAATGGGATAAGGAGATATTGAG
1 GTTAGAATAGGATAACGAGAGATGGAG
*
5465176 GTTAGAATAGGATGACGAGAGATGGAG
1 GTTAGAATAGGATAACGAGAGATGGAG
5465203 G
1 G
5465204 ATAAGAGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.40, T:0.22
Consensus pattern (27 bp):
GTTAGAATAGGATAACGAGAGATGGAG
Found at i:5467557 original size:21 final size:22
Alignment explanation
Indices: 5467532--5467574 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5467522 TCTCATCAGT
5467532 ATGAA-TTTTTTCAACAGCATC
1 ATGAATTTTTTTCAACAGCATC
5467553 ATGAATTTTTTTCAACAGCATC
1 ATGAATTTTTTTCAACAGCATC
5467575 TACTATTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (22 bp):
ATGAATTTTTTTCAACAGCATC
Found at i:5468244 original size:107 final size:107
Alignment explanation
Indices: 5468058--5468264 Score: 351
Period size: 107 Copynumber: 1.9 Consensus size: 107
5468048 ATGAGCAATA
* * * *
5468058 TCAGGTCGTGTACAAATCATAAGATAATTAAAAAACTGACTGTAGGAGAATAAAAAATATTAAAC
1 TCAGGTCATATACAAATCATAAGATAATTAAAAAACTAACTGCAGGAGAATAAAAAATATTAAAC
* *
5468123 ATAGCTAGTTGCTCTTTTTTAATCGTTAGAGAATAAAAAATG
66 ATAGCTAGTTGCTCTTTTTTAATCGTCAGACAATAAAAAATG
*
5468165 TCAGGTCATATACAAATCATAAGATAATTAAAAAACTAACTGCAGGAGAATAAAAAATATTAGAC
1 TCAGGTCATATACAAATCATAAGATAATTAAAAAACTAACTGCAGGAGAATAAAAAATATTAAAC
5468230 ATAGCTAGTTGCTCTTTTTTAATCGTCAGACAATA
66 ATAGCTAGTTGCTCTTTTTTAATCGTCAGACAATA
5468265 TTTCTTACTC
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 93 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.29
Consensus pattern (107 bp):
TCAGGTCATATACAAATCATAAGATAATTAAAAAACTAACTGCAGGAGAATAAAAAATATTAAAC
ATAGCTAGTTGCTCTTTTTTAATCGTCAGACAATAAAAAATG
Found at i:5477900 original size:17 final size:15
Alignment explanation
Indices: 5477880--5477926 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
5477870 TTTTAACATA
5477880 TTGTTAGTTATTATATT
1 TTGTT-GTTA-TATATT
5477897 TTGTTGTTATATATT
1 TTGTTGTTATATATT
*
5477912 AT-TTGTTA-ATATT
1 TTGTTGTTATATATT
5477925 TT
1 TT
5477927 ATTATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 7 0.25
16 4 0.14
17 5 0.18
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (15 bp):
TTGTTGTTATATATT
Found at i:5478068 original size:14 final size:15
Alignment explanation
Indices: 5478051--5478083 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5478041 AACTATTCAT
*
5478051 TTTTTATAT-TATTA
1 TTTTTAAATATATTA
5478065 TTTTTAAATATATTA
1 TTTTTAAATATATTA
5478080 TTTT
1 TTTT
5478084 ATGAGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAAATATATTA
Found at i:5478403 original size:61 final size:61
Alignment explanation
Indices: 5478332--5478448 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
5478322 GATGTTTGAA
* *
5478332 TTTTAGTTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGGTGAGAATTTGTGAG
1 TTTTAATTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGGTGAAAATTTGTGAG
* * * * *
5478393 TTTTAATTTACTAAGTTTTATGTATTTTATAATTTCATTATTTATGGTGAAAATTT
1 TTTTAATTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGGTGAAAATTT
5478449 ATAAGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (61 bp):
TTTTAATTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGGTGAAAATTTGTGAG
Found at i:5479393 original size:2 final size:2
Alignment explanation
Indices: 5479388--5479418 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5479378 TATATATATA
*
5479388 TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
5479419 ATGTATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5479419 original size:8 final size:8
Alignment explanation
Indices: 5479386--5479422 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
5479376 TATATATATA
5479386 TATGTGTG
1 TATGTGTG
*
5479394 TGTGTGTG
1 TATGTGTG
*
5479402 TGTGTGTG
1 TATGTGTG
5479410 TATGTGTG
1 TATGTGTG
5479418 TATGT
1 TATGT
5479423 ATATAACAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.08, C:0.00, G:0.41, T:0.51
Consensus pattern (8 bp):
TATGTGTG
Found at i:5483944 original size:21 final size:21
Alignment explanation
Indices: 5483907--5483947 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5483897 TTCACAAAAG
5483907 AAAAAATCAAGAGAATTAAAC
1 AAAAAATCAAGAGAATTAAAC
*
5483928 AAAAATATCATGA-AATTAAA
1 AAAAA-ATCAAGAGAATTAAA
5483948 TATATACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAAATCAAGAGAATTAAAC
Found at i:5486527 original size:16 final size:17
Alignment explanation
Indices: 5486498--5486530 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5486488 TATTATTTTA
*
5486498 TAAAAAAATGTTATAAT
1 TAAAAAAATATTATAAT
5486515 TAAAAAAA-ATTATAAT
1 TAAAAAAATATTATAAT
5486531 AAATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAAAAATATTATAAT
Found at i:5486733 original size:2 final size:2
Alignment explanation
Indices: 5486728--5486752 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5486718 TTCCTTTATG
5486728 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5486753 CAACATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5487649 original size:15 final size:15
Alignment explanation
Indices: 5487625--5487659 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5487615 TTCTTCCGGC
*
5487625 TTCTTTGGCTCTTCT
1 TTCTTGGGCTCTTCT
5487640 TTCTTGGGCTCTTCT
1 TTCTTGGGCTCTTCT
5487655 TTCTT
1 TTCTT
5487660 CTTCTCTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.26, G:0.14, T:0.60
Consensus pattern (15 bp):
TTCTTGGGCTCTTCT
Found at i:5488268 original size:2 final size:2
Alignment explanation
Indices: 5488263--5488287 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5488253 ATATATATAT
5488263 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5488288 AAAGATGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5488981 original size:17 final size:17
Alignment explanation
Indices: 5488952--5488986 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5488942 ATATTTTATA
5488952 ATTTTTAATTTATTTTT
1 ATTTTTAATTTATTTTT
5488969 ATTTTATAA-TTATTTTT
1 ATTTT-TAATTTATTTTT
5488986 A
1 A
5488987 ACTTAATAAA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTAATTTATTTTT
Found at i:5489062 original size:13 final size:13
Alignment explanation
Indices: 5489044--5489068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5489034 TTTTATTGTA
5489044 ATTTATTTTTTAT
1 ATTTATTTTTTAT
5489057 ATTTATTTTTTA
1 ATTTATTTTTTA
5489069 AACCAAAATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTATTTTTTAT
Found at i:5505396 original size:12 final size:14
Alignment explanation
Indices: 5505381--5505423 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
5505371 AATTATAATT
5505381 AAAAATTT-TA-TA
1 AAAAATTTATATTA
5505393 AAAAATTTATATTA
1 AAAAATTTATATTA
5505407 AATAAATTTA-ATTA
1 AA-AAATTTATATTA
5505421 AAA
1 AAA
5505424 TTAACATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.29
13 3 0.11
14 10 0.36
15 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAATTTATATTA
Found at i:5506791 original size:42 final size:39
Alignment explanation
Indices: 5506740--5506831 Score: 96
Period size: 38 Copynumber: 2.3 Consensus size: 39
5506730 TAAAAAAGAA
* * * *
5506740 ATATCTATATATAAAATTAATAAAAAAGAAATATTTATATTT
1 ATATTTATATATAAAATCAAT-AAAAAGAAA-A-TTAAAATT
*
5506782 ATATTTATATA-AAAATCAGTAAAAAGAAAATTAAAATT
1 ATATTTATATATAAAATCAATAAAAAGAAAATTAAAATT
*
5506820 ATTTTTATATAT
1 ATATTTATATAT
5506832 TTTATATGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 16 0.37
39 1 0.02
40 9 0.21
41 7 0.16
42 10 0.23
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.40
Consensus pattern (39 bp):
ATATTTATATATAAAATCAATAAAAAGAAAATTAAAATT
Found at i:5506943 original size:19 final size:19
Alignment explanation
Indices: 5506918--5506965 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5506908 ATAATTAATC
5506918 ATTTTTATTAACATTT-TAT
1 ATTTTTATTAA-ATTTATAT
*
5506937 TTTTTTATTAAATTTATAT
1 ATTTTTATTAAATTTATAT
*
5506956 ATTATTATTA
1 ATTTTTATTA
5506966 TTTTTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTATTAAATTTATAT
Found at i:5511105 original size:14 final size:14
Alignment explanation
Indices: 5511079--5511111 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5511069 ATTTAATAAA
*
5511079 TTTT-GATATATAT
1 TTTTAGATAGATAT
5511092 TTTTAGATAGATAT
1 TTTTAGATAGATAT
5511106 TTTTAG
1 TTTTAG
5511112 TAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (14 bp):
TTTTAGATAGATAT
Found at i:5511260 original size:12 final size:12
Alignment explanation
Indices: 5511219--5511259 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
5511209 CGGTTTGAAT
5511219 TTTTTATTAAAA
1 TTTTTATTAAAA
5511231 TTTTTATT-AAA
1 TTTTTATTAAAA
5511242 TTATTT-TTAAAA
1 TT-TTTATTAAAA
5511254 GTTTTT
1 -TTTTT
5511260 TTTTACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.27
12 17 0.65
13 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTTTTATTAAAA
Found at i:5526251 original size:16 final size:16
Alignment explanation
Indices: 5526198--5526263 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
5526188 TTAAATTTTA
*
5526198 AAAAGTATTTTGATTTTT
1 AAAA-TATTTT-ATATTT
* * *
5526216 AAAAAATATAATATTT
1 AAAATATTTTATATTT
* *
5526232 -AAATTTTTTATTTTT
1 AAAATATTTTATATTT
5526247 AAAATATTTTATATTT
1 AAAATATTTTATATTT
5526263 A
1 A
5526264 GATTCATTTG
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
15 10 0.28
16 19 0.53
17 3 0.08
18 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AAAATATTTTATATTT
Found at i:5526315 original size:14 final size:15
Alignment explanation
Indices: 5526288--5526316 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5526278 ATTGAAAAAA
5526288 TTTTATATATATTAT
1 TTTTATATATATTAT
5526303 TTTTATATA-ATTAT
1 TTTTATATATATTAT
5526317 CATAATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTATATATATTAT
Found at i:5527107 original size:134 final size:131
Alignment explanation
Indices: 5526781--5527164 Score: 408
Period size: 129 Copynumber: 2.9 Consensus size: 131
5526771 CCCTTGAACA
* * * * * *
5526781 ATCTTTTTATTTTTTTTTTAACGTCTTAATTGTTTAATCATTTAAGAGATTTCTGTATATAAACA
1 ATCTTTTTA-TTTTTTTATAACGTCTTAATTGATCAATCATTTAAGAG-TTTCTGTACACAAATA
*
5526846 CCTTAATTGA-C---TTTTTTTTTATAACTAATCAATTAAGATGTTTATGTGCAAAAATACATTA
64 -CTTAATTGATCTTTTTTTTTTTTATAACTAATCAATTAAGATGTTTATGTACAAAAATACATTA
5526907 AATG
128 AATG
* *
5526911 ATC---TT-TTTTTTTATAACGTTTTAATTGATCAATCATTTAAGGTGTTTCTGTACACAAATAC
1 ATCTTTTTATTTTTTTATAACGTCTTAATTGATCAATCATTTAA-GAGTTTCTGTACACAAATAC
* * * *
5526972 TTAATTGATCTTTTTGTTTTTTTATAACTAATTAATTAAGGTGTTTATGTACATAAATGTC-TTA
65 TTAATTGATCTTTTT-TTTTTTTATAACTAATCAATTAAGATGTTTATGTACAAAAAT-ACATTA
5527036 AATG
128 AATG
* * *
5527040 ATCTTTTTATTTTTCTTATAATGCCTTAATTGATCAATCATTTAAGACGTTTTTGTACACAAATA
1 ATCTTTTTATTTTT-TTATAACGTCTTAATTGATCAATCATTTAAGA-GTTTCTGTACACAAATA
* * * * * *
5527105 CTTTACTTTATTTTTTTATTTTTTTATAACTGATCAATTAAGATATTTGTGTACAGAAAA
64 C-TTAATTGATCTTTTT-TTTTTTTATAACTAATCAATTAAGATGTTTATGTACA-AAAA
5527165 GCTTTATATG
Statistics
Matches: 211, Mismatches: 28, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
124 9 0.04
125 45 0.21
126 2 0.01
127 2 0.01
128 2 0.01
129 48 0.23
130 4 0.02
132 2 0.01
133 6 0.03
134 44 0.21
135 44 0.21
136 3 0.01
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (131 bp):
ATCTTTTTATTTTTTTATAACGTCTTAATTGATCAATCATTTAAGAGTTTCTGTACACAAATACT
TAATTGATCTTTTTTTTTTTTATAACTAATCAATTAAGATGTTTATGTACAAAAATACATTAAAT
G
Found at i:5527864 original size:25 final size:24
Alignment explanation
Indices: 5527814--5527865 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
5527804 TGTTATGTTT
*
5527814 TATTGGTTTATTTACTGTAGTGGA
1 TATTGGTTTATTTACTATAGTGGA
*
5527838 TATTGGTTGTTTTTACTAT-GTGTGA
1 TATTGGTT-TATTTACTATAGTG-GA
5527863 TAT
1 TAT
5527866 ATAGAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.19, C:0.04, G:0.23, T:0.54
Consensus pattern (24 bp):
TATTGGTTTATTTACTATAGTGGA
Found at i:5530007 original size:20 final size:20
Alignment explanation
Indices: 5529982--5530020 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5529972 ATGAAATCTA
*
5529982 ATATCATGCCTATTATTTTT
1 ATATCATGCCAATTATTTTT
5530002 ATATCATGCCAATTATTTT
1 ATATCATGCCAATTATTTT
5530021 ACAGGTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.51
Consensus pattern (20 bp):
ATATCATGCCAATTATTTTT
Found at i:5530722 original size:22 final size:22
Alignment explanation
Indices: 5530680--5530734 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
5530670 AAAGACAGTA
* *
5530680 TGATTGG-ATATTTGTTAATTT
1 TGATTGGTTTATTAGTTAATTT
*
5530701 TGATTGGTTTATTAGTTTATTT
1 TGATTGGTTTATTAGTTAATTT
* *
5530723 TTATTAGTTTAT
1 TGATTGGTTTAT
5530735 ATTTGTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (22 bp):
TGATTGGTTTATTAGTTAATTT
Found at i:5530727 original size:14 final size:14
Alignment explanation
Indices: 5530708--5530734 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5530698 TTTTGATTGG
5530708 TTTATTAGTTTATT
1 TTTATTAGTTTATT
5530722 TTTATTAGTTTAT
1 TTTATTAGTTTAT
5530735 ATTTGTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTTATTAGTTTATT
Found at i:5534658 original size:41 final size:41
Alignment explanation
Indices: 5534573--5534660 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
5534563 AAACACTATA
* * * *
5534573 TAATTGATGATCAATTAAGGCGTTTTTGTATACAAATGCTT
1 TAATTGATGATCAATTAAGGCATTTTTGCATACAAATACCT
* **
5534614 TAATTGATTATCAATTAAGGCATTTCTT-CATTGAAATACCT
1 TAATTGATGATCAATTAAGGCATTT-TTGCATACAAATACCT
5534655 TAATTG
1 TAATTG
5534661 CAATATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (41 bp):
TAATTGATGATCAATTAAGGCATTTTTGCATACAAATACCT
Found at i:5543624 original size:25 final size:24
Alignment explanation
Indices: 5543575--5543624 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
5543565 ACACATAAAA
*
5543575 TTTTAAATTTATTTTTTTAGCTTTT
1 TTTTAAATTTATTTTTATA-CTTTT
5543600 TTTTAAATTTTATTTTATATA-TTTT
1 TTTTAAA-TTTATTTT-TATACTTTT
5543625 GGTGAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 11 0.50
26 8 0.36
27 3 0.14
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTTAAATTTATTTTTATACTTTT
Found at i:5543662 original size:14 final size:16
Alignment explanation
Indices: 5543631--5543667 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
5543621 TTTTGGTGAA
5543631 TTTTT-ATAAATATAT
1 TTTTTAATAAATATAT
5543646 TTTTTAATAAA-AT-T
1 TTTTTAATAAATATAT
5543660 TTTTTAAT
1 TTTTTAAT
5543668 TTTAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 7 0.33
16 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAATAAATATAT
Found at i:5543687 original size:20 final size:21
Alignment explanation
Indices: 5543664--5543718 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 21
5543654 AAAATTTTTT
5543664 TAATTTTAATTATTT-TAAAA
1 TAATTTTAATTATTTATAAAA
5543684 TAATAATTTATATTATTTAATAAAA
1 TAAT--TTTA-ATTATTT-ATAAAA
5543709 -AA-TTTAATTA
1 TAATTTTAATTA
5543719 CTAAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
20 8 0.27
21 4 0.13
22 4 0.13
23 7 0.23
24 2 0.07
25 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTTTAATTATTTATAAAA
Found at i:5543742 original size:15 final size:14
Alignment explanation
Indices: 5543722--5543751 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5543712 TTAATTACTA
5543722 AATATATATAAATAT
1 AATATATAT-AATAT
5543737 AATATATATAATAT
1 AATATATATAATAT
5543751 A
1 A
5543752 TGATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATATATAATAT
Found at i:5557070 original size:30 final size:30
Alignment explanation
Indices: 5557036--5557097 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
5557026 TGAGGTTCCT
*
5557036 TAGTCTGCAGCTCTTCACTTGTCACATAAA
1 TAGTCTGCAGCTCTTCACTTGTCACAGAAA
5557066 TAGTCTGCAGCTCTTCACTTGTCACAGAAA
1 TAGTCTGCAGCTCTTCACTTGTCACAGAAA
5557096 TA
1 TA
5557098 TTATACACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (30 bp):
TAGTCTGCAGCTCTTCACTTGTCACAGAAA
Found at i:5557201 original size:81 final size:81
Alignment explanation
Indices: 5557066--5557220 Score: 274
Period size: 81 Copynumber: 1.9 Consensus size: 81
5557056 GTCACATAAA
* *
5557066 TAGTCTGCAGCTCTTCACTTGTCACAGAAATATTATACACAGCATCCTTTTGAGAATCAACATTC
1 TAGTCTGCAGCACTTCACCTGTCACAGAAATATTATACACAGCATCCTTTTGAGAATCAACATTC
5557131 CCACCATCAGAAGGCT
66 CCACCATCAGAAGGCT
* *
5557147 TAGTCTGCAGCACTTCACCTGTCACAGAAATATTATCCACAGCATCCTTTTGAGAATCAACATTT
1 TAGTCTGCAGCACTTCACCTGTCACAGAAATATTATACACAGCATCCTTTTGAGAATCAACATTC
5557212 CCACCATCA
66 CCACCATCA
5557221 CAGGGCCAAG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (81 bp):
TAGTCTGCAGCACTTCACCTGTCACAGAAATATTATACACAGCATCCTTTTGAGAATCAACATTC
CCACCATCAGAAGGCT
Found at i:5560189 original size:3 final size:3
Alignment explanation
Indices: 5560181--5560222 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5560171 ACTATTTCAC
5560181 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5560223 GGTTGTGGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:5560935 original size:26 final size:26
Alignment explanation
Indices: 5560906--5560961 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
5560896 AATAGAATAA
5560906 ATAAAT-TAAAATTAAAACAAGTACTC
1 ATAAATATAAAATTAAAACAA-TACTC
*
5560932 ATAAATATAAAATTAAAACAATACTT
1 ATAAATATAAAATTAAAACAATACTC
5560958 ATAA
1 ATAA
5560962 GACAAAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.29
Consensus pattern (26 bp):
ATAAATATAAAATTAAAACAATACTC
Found at i:5561355 original size:18 final size:19
Alignment explanation
Indices: 5561334--5561384 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
5561324 TATTTTGTAC
**
5561334 ATATATAATTTT-TTATAA
1 ATATATAATTTTAAAATAA
5561352 ATATAT-ATTTTAAAATAA
1 ATATATAATTTTAAAATAA
5561370 ATATATTAATTTTAA
1 ATATA-TAATTTTAA
5561385 TTAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 5 0.18
18 15 0.54
19 1 0.04
20 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATAATTTTAAAATAA
Found at i:5561430 original size:18 final size:19
Alignment explanation
Indices: 5561393--5561434 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5561383 AATTAATTTA
* *
5561393 AAATAAAATTTATATTATT
1 AAATAAAAATAATATTATT
5561412 AAATAAAAATAAT-TTATT
1 AAATAAAAATAATATTATT
5561430 AAATA
1 AAATA
5561435 TATTATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATAAAAATAATATTATT
Found at i:5564564 original size:2 final size:2
Alignment explanation
Indices: 5564559--5564583 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5564549 ACTCTCTAGA
5564559 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5564584 CTTGCTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5570662 original size:30 final size:30
Alignment explanation
Indices: 5570626--5570686 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
5570616 ACTGTAAAGA
* **
5570626 TTTGTATAAGTCGGTATTAGGTGATTTAGT
1 TTTGTATAAGCCAATATTAGGTGATTTAGT
*
5570656 TTTGTATAAGCCAATATTTGGTGATTTAGT
1 TTTGTATAAGCCAATATTAGGTGATTTAGT
5570686 T
1 T
5570687 AAGCCAGCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.48
Consensus pattern (30 bp):
TTTGTATAAGCCAATATTAGGTGATTTAGT
Found at i:5572299 original size:17 final size:17
Alignment explanation
Indices: 5572277--5572309 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5572267 AACACCACAG
*
5572277 CATAGTAATAAGCCAGC
1 CATAGTAATAAACCAGC
5572294 CATAGTAATAAACCAG
1 CATAGTAATAAACCAG
5572310 ATGCAATCAA
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:0.45, C:0.21, G:0.15, T:0.18
Consensus pattern (17 bp):
CATAGTAATAAACCAGC
Found at i:5578836 original size:51 final size:51
Alignment explanation
Indices: 5578781--5578932 Score: 164
Period size: 51 Copynumber: 3.0 Consensus size: 51
5578771 ATAAGAAAAT
*
5578781 TTGTAA-AAAAAAATTTTAAGAGAAAGATGATTTTTAATAGGTAAGTTTGAC
1 TTGTAAGAAAAAAATTTTAAGAGAAAGA-GATTTTTAATAGGTAAGTTTAAC
* * * * *
5578832 TTGTAAGAGAAAAATTTTTAA-AAAAAAAAATTTTTAATAAGTAAGTTTAAC
1 TTGTAAGA-AAAAAATTTTAAGAGAAAGAGATTTTTAATAGGTAAGTTTAAC
* * * * *
5578883 TTATAAGAGAAGAATTTTAAGAGAAGAGAGATTCTTAATAGGTAAATTTA
1 TTGTAAGAAAAAAATTTTAAGAGAA-AGAGATTTTTAATAGGTAAGTTTA
5578933 TATCAGAGTT
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
50 9 0.11
51 36 0.44
52 25 0.31
53 11 0.14
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (51 bp):
TTGTAAGAAAAAAATTTTAAGAGAAAGAGATTTTTAATAGGTAAGTTTAAC
Found at i:5579063 original size:24 final size:24
Alignment explanation
Indices: 5578979--5579063 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
5578969 GAGCTGAATA
*
5578979 TTCGAAATGTGAGAAGAGTTG-AAG
1 TTCGAAATGTGA-AAGAGTCGAAAG
* *
5579003 ATTC-AATATATGAATGAGTCGAAAG
1 -TTCGAA-ATGTGAAAGAGTCGAAAG
* * *
5579028 TTCGAGACGTGAAAGAGCCGAAAG
1 TTCGAAATGTGAAAGAGTCGAAAG
5579052 TTCGAAATGTGA
1 TTCGAAATGTGA
5579064 GAAAAAAACT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
24 35 0.74
25 12 0.26
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.24
Consensus pattern (24 bp):
TTCGAAATGTGAAAGAGTCGAAAG
Done.