Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 175 of 187
Found at i:52386820 original size:39 final size:41
Alignment explanation
Indices: 52386736--52386821 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 41
52386726 TATAGTTCAT
* * *
52386736 GTTTTTATGATTTTTTAATAATTTTATATCATTTTTATTTA
1 GTTTTTATGATTTTTCAATAATTTTATATCATTTTTAGTAA
* * *
52386777 -TTTTTAT-ATTTTTCAATATTTTTTTATGATTTTT-GTAA
1 GTTTTTATGATTTTTCAATAATTTTATATCATTTTTAGTAA
52386815 GTTTTTA
1 GTTTTTA
52386822 AGAAATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
38 2 0.05
39 29 0.76
40 7 0.18
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (41 bp):
GTTTTTATGATTTTTCAATAATTTTATATCATTTTTAGTAA
Found at i:52386931 original size:10 final size:10
Alignment explanation
Indices: 52386860--52386950 Score: 52
Period size: 10 Copynumber: 9.4 Consensus size: 10
52386850 TGTAAATATG
52386860 TTTTTATTAA
1 TTTTTATTAA
**
52386870 -TTTTACAAA
1 TTTTTATTAA
*
52386879 TTTTTTTATAA
1 TTTTTAT-TAA
*
52386890 TTTATTGTT-A
1 TTT-TTATTAA
52386900 TTTTTA-TAA
1 TTTTTATTAA
*
52386909 -TATTA-TAA
1 TTTTTATTAA
52386917 GTTTTTATTAA
1 -TTTTTATTAA
52386928 TTTTTA-TAA
1 TTTTTATTAA
52386937 -TTTTATATAA
1 TTTTTAT-TAA
52386947 TTTT
1 TTTT
52386951 AATATTCTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
8 13 0.21
9 13 0.21
10 21 0.34
11 12 0.19
12 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTTATTAA
Found at i:52386940 original size:19 final size:19
Alignment explanation
Indices: 52386860--52386950 Score: 64
Period size: 19 Copynumber: 4.7 Consensus size: 19
52386850 TGTAAATATG
*
52386860 TTTTTATTAA-TTTTACAAA
1 TTTTTATTAATTTTTA-TAA
* * *
52386879 TTTTTTTATAATTTATTGTTA
1 TTTTTAT-TAATTT-TTATAA
*
52386900 TTTTTA-TAA-TATTATAA
1 TTTTTATTAATTTTTATAA
52386917 GTTTTTATTAATTTTTATAA
1 -TTTTTATTAATTTTTATAA
52386937 -TTTTATATAATTTT
1 TTTTTAT-TAATTTT
52386951 AATATTCTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
17 4 0.07
18 13 0.23
19 19 0.34
20 10 0.18
21 8 0.14
22 2 0.04
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTTATTAATTTTTATAA
Found at i:52386942 original size:8 final size:9
Alignment explanation
Indices: 52386881--52386950 Score: 70
Period size: 10 Copynumber: 7.4 Consensus size: 9
52386871 TTTACAAATT
52386881 TTTTTATAA
1 TTTTTATAA
* *
52386890 TTTATTGTTA
1 TTT-TTATAA
52386900 TTTTTATAA
1 TTTTTATAA
*
52386909 -TATTATAA
1 TTTTTATAA
52386917 GTTTTTATTAA
1 -TTTTTA-TAA
52386928 TTTTTATAA
1 TTTTTATAA
52386937 TTTTATATAA
1 TTTT-TATAA
52386947 TTTT
1 TTTT
52386951 AATATTCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
8 7 0.14
9 14 0.28
10 26 0.52
11 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52386950 original size:18 final size:17
Alignment explanation
Indices: 52386899--52386951 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
52386889 ATTTATTGTT
*
52386899 ATTTTTATAATATTATA
1 ATTTTTATAATTTTATA
52386916 AGTTTTTATTAATTTTTATA
1 A-TTTTTA-TAA-TTTTATA
52386936 ATTTTATATAATTTTA
1 ATTTT-TATAATTTTA
52386952 ATATTCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.03
18 11 0.35
19 10 0.32
20 9 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTTTTATAATTTTATA
Found at i:52386951 original size:10 final size:10
Alignment explanation
Indices: 52386861--52386951 Score: 52
Period size: 9 Copynumber: 9.5 Consensus size: 10
52386851 GTAAATATGT
52386861 TTTTAT-TAA
1 TTTTATATAA
*
52386870 TTTTACA-AA
1 TTTTATATAA
*
52386879 TTTTTTTATAA
1 -TTTTATATAA
* *
52386890 -TTTATTGTTA
1 TTTTA-TATAA
52386900 TTTT-TATAA
1 TTTTATATAA
* *
52386909 TATTATA-AG
1 TTTTATATAA
52386918 TTTT-TATTAA
1 TTTTATA-TAA
52386928 TTTT-TATAA
1 TTTTATATAA
52386937 TTTTATATAA
1 TTTTATATAA
52386947 TTTTA
1 TTTTA
52386952 ATATTCTTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 17
0.68 0.13 0.19
Matches are distributed among these distances:
8 2 0.03
9 27 0.44
10 27 0.44
11 5 0.08
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTATATAA
Found at i:52386967 original size:18 final size:19
Alignment explanation
Indices: 52386946--52386986 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
52386936 ATTTTATATA
52386946 ATTTTAAT-ATTCTTTAAT
1 ATTTTAATGATTCTTTAAT
*
52386964 A-TTTAATGATTTTTTAAT
1 ATTTTAATGATTCTTTAAT
52386982 ATTTT
1 ATTTT
52386987 TATGGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 11 0.55
19 3 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTAATGATTCTTTAAT
Found at i:52389928 original size:30 final size:30
Alignment explanation
Indices: 52389885--52389942 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
52389875 TTTTATATAC
*
52389885 TATATAATTTATAATAC-ATAATCTAAATT
1 TATATAATATATAATACTATAATCTAAATT
*
52389914 TATAGTAATATATAATACTATAATGTAAA
1 TATA-TAATATATAATACTATAATCTAAA
52389943 CATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 12 0.48
31 9 0.36
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (30 bp):
TATATAATATATAATACTATAATCTAAATT
Found at i:52392983 original size:18 final size:19
Alignment explanation
Indices: 52392946--52392983 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
52392936 AAGTTCGTAA
**
52392946 TTTATTATATTATGTTATT
1 TTTATTATATTATGCAATT
52392965 TTTA-TATATTATGCAATT
1 TTTATTATATTATGCAATT
52392983 T
1 T
52392984 ATAACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATTATATTATGCAATT
Found at i:52395169 original size:31 final size:31
Alignment explanation
Indices: 52395080--52395162 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 31
52395070 ATACGCCCGT
* *
52395080 ATGTATACAATTGAATCAAAATCAAAGTTTT
1 ATGTATACAATTGAATCAAAATCAAAATTTA
* *
52395111 ATATATACATTTGAATCAAAATCAAAATTTA
1 ATGTATACAATTGAATCAAAATCAAAATTTA
*
52395142 ATGTATATAATTGAATCAAAA
1 ATGTATACAATTGAATCAAAA
52395163 ATAAAATACA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.35
Consensus pattern (31 bp):
ATGTATACAATTGAATCAAAATCAAAATTTA
Found at i:52407072 original size:61 final size:61
Alignment explanation
Indices: 52406961--52407075 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
52406951 AAAATTTAAC
* * * * * *
52406961 AAATTTAACCCTCAATATTTACAAAATTTATCATTTTAGTTCTGATTCTAAAAAAATCAAT
1 AAATTTAACCCTCAATATTTACAAAATTGATCAATTTAATTATAACTCTAAAAAAATCAAT
* *
52407022 AAATTTAACTCTCAATATTTACAAAATCTGCT-AATTTAATTATAACTCTAAAAA
1 AAATTTAACCCTCAATATTTACAAAAT-TGATCAATTTAATTATAACTCTAAAAA
52407076 CTAGAAAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (61 bp):
AAATTTAACCCTCAATATTTACAAAATTGATCAATTTAATTATAACTCTAAAAAAATCAAT
Found at i:52413785 original size:106 final size:106
Alignment explanation
Indices: 52413431--52413852 Score: 648
Period size: 106 Copynumber: 4.0 Consensus size: 106
52413421 TGGATTTAGA
* * * *
52413431 TTTAATAGGATATTTGGCTATTTGGTCGAACGAGAAATTGAAACCCAGCACGTTAGGGCACATTC
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
*
52413496 TCTTGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
* * *
52413537 TTTAAAAGGGATATTTTGCTATTTGGTCGAACGAGAAATAGAAACCCAGCACGTTAGGACACGTT
1 TTTAAAA-GGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTT
* *
52413602 TTCTCGAATTTTCAAAC-CAAAATATTGTCTTACTTTGAAAG
65 TTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
*
52413643 TTTAAAAGAATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* *
52413708 TCTCGAATTTCCAAACGCGAAATATTGCCTTACTTTGAAAT
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
* * * * *
52413749 TTTGAAAGGATATTCGGCTATTTGGTCGAACGAGAAATCGAAACCGAACAAGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* *
52413814 TCTCGAATTTCCAAACGCAAAATATTGTCTTACTCTGAA
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAA
52413853 TTTGAATGAA
Statistics
Matches: 288, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
105 69 0.24
106 152 0.53
107 67 0.23
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
Found at i:52414144 original size:23 final size:22
Alignment explanation
Indices: 52414118--52414161 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
52414108 ATTATTAAAG
52414118 ATGACAAAAAAATAAATAATGAA
1 ATGACAAAAAAAT-AATAATGAA
* **
52414141 ATGATAAAGTAATAATAATGA
1 ATGACAAAAAAATAATAATGA
52414162 CAAGAGTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (22 bp):
ATGACAAAAAAATAATAATGAA
Found at i:52424592 original size:24 final size:25
Alignment explanation
Indices: 52424540--52424612 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
52424530 ATAAGCAATT
* *
52424540 GAATTTTAAAAAATAATTTTAAAAATA
1 GAATTTT-AAAAAT-ATATAAAAAATA
* **
52424567 GATTTTTTTAAAT-TATAAAAAATA
1 GAATTTTAAAAATATATAAAAAATA
52424591 GAATTTTAAAAATATATAAAAA
1 GAATTTTAAAAATATATAAAAA
52424613 TAAAAATTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 19 0.51
25 8 0.22
26 4 0.11
27 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
GAATTTTAAAAATATATAAAAAATA
Found at i:52424613 original size:24 final size:23
Alignment explanation
Indices: 52424498--52424614 Score: 74
Period size: 24 Copynumber: 4.7 Consensus size: 23
52424488 TTTTAAAACA
* *
52424498 TAAAAATCATAAAAACA-AATTCT
1 TAAAAATTATAAAAATAGAATT-T
* *
52424521 TATAAAATTATAAGCAATTGAATTT
1 TA-AAAATTATAA-AAATAGAATTT
* *
52424546 TAAAAAATAATTTTAAAAATAGATTTT
1 T---AAA-AATTATAAAAATAGAATTT
**
52424573 TTTAAATTATAAAAAATAGAATTT
1 TAAAAATTAT-AAAAATAGAATTT
52424597 TAAAAATATATAAAAATA
1 TAAAAAT-TATAAAAATA
52424615 AAAATTATTA
Statistics
Matches: 71, Mismatches: 14, Indels: 17
0.70 0.14 0.17
Matches are distributed among these distances:
23 7 0.10
24 34 0.48
25 7 0.10
26 4 0.06
27 11 0.15
28 8 0.11
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (23 bp):
TAAAAATTATAAAAATAGAATTT
Found at i:52424620 original size:25 final size:23
Alignment explanation
Indices: 52424571--52424627 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
52424561 AAAATAGATT
* * *
52424571 TTTTTAAATTATAAAAAATAGAA
1 TTTTAAAAATATAAAAAATAAAA
52424594 TTTTAAAAATATATAAAAATAAAAA
1 TTTTAAAAATATA-AAAAAT-AAAA
52424619 TTATTAAAA
1 TT-TTAAAA
52424628 TTCATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.39
24 6 0.21
25 5 0.18
26 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TTTTAAAAATATAAAAAATAAAA
Found at i:52424628 original size:25 final size:22
Alignment explanation
Indices: 52424572--52424628 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
52424562 AAATAGATTT
* *
52424572 TTTTAAATTATAAAAAATAGAA
1 TTTTAAAATATAAAAAATAAAA
52424594 TTTTAAAAATATATAAAAATAAAAA
1 TTTT-AAAATATA-AAAAAT-AAAA
52424619 TTATTAAAAT
1 TT-TTAAAAT
52424629 TCATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 4 0.14
23 7 0.24
24 6 0.21
25 10 0.34
26 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTTAAAATATAAAAAATAAAA
Found at i:52424696 original size:32 final size:32
Alignment explanation
Indices: 52424659--52424731 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 32
52424649 TTGCAAAAAT
* * *
52424659 TTAAAATTTACAAAAAATATATATTAAAA-TTA
1 TTAAAATTT-CAAAAAATAAAAATAAAAAGTTA
*
52424691 TTAAAATTTTAAAAAATAAAAATAAAAAGTTA
1 TTAAAATTTCAAAAAATAAAAATAAAAAGTTA
52424723 TATAAAATT
1 T-TAAAATT
52424732 ATGAAAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 15 0.43
32 13 0.37
33 7 0.20
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (32 bp):
TTAAAATTTCAAAAAATAAAAATAAAAAGTTA
Found at i:52425527 original size:2 final size:2
Alignment explanation
Indices: 52425520--52425546 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52425510 TAAAATTTCT
52425520 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52425547 GTATGCAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52426008 original size:52 final size:52
Alignment explanation
Indices: 52425930--52426036 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
52425920 GAGAAAAATT
* *
52425930 TAGTGCTTTCCATTGCCCTAAATTTTTCTTTCAGCCATTTACACCTTTCCTC
1 TAGTGCTTTCCATTGCCATAAATTTTTCTTTCAGCCATTTACACCTTTCCCC
* *
52425982 TAGTGCTTTCCATTGCCATAAATTTTTCTTTGAGTCATTTACACCTTTCCCC
1 TAGTGCTTTCCATTGCCATAAATTTTTCTTTCAGCCATTTACACCTTTCCCC
52426034 TAG
1 TAG
52426037 CCATTTACCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (52 bp):
TAGTGCTTTCCATTGCCATAAATTTTTCTTTCAGCCATTTACACCTTTCCCC
Found at i:52426838 original size:23 final size:20
Alignment explanation
Indices: 52426792--52426833 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
52426782 ACTCGTCAGC
52426792 TTTTCTAAAAATAAACTAAA
1 TTTTCTAAAAATAAACTAAA
52426812 TTTTCTACTAAAATAAA-TAAA
1 TTTTCTA--AAAATAAACTAAA
52426833 T
1 T
52426834 ATTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTCTAAAAATAAACTAAA
Found at i:52432848 original size:2 final size:2
Alignment explanation
Indices: 52432841--52432871 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52432831 ATTTAAAGAA
52432841 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
52432872 AAAGGGAAGT
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:52436537 original size:10 final size:10
Alignment explanation
Indices: 52436493--52436541 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
52436483 TAATATTTTT
52436493 TTAAGTTATAA
1 TTAA-TTATAA
52436504 TTAATTAT-A
1 TTAATTATAA
*
52436513 TTAA-TAGT-T
1 TTAATTA-TAA
52436522 TTAATTATAA
1 TTAATTATAA
52436532 TTAATTATAA
1 TTAATTATAA
52436542 CAAGCTTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 2 0.06
9 11 0.33
10 16 0.48
11 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (10 bp):
TTAATTATAA
Found at i:52447070 original size:66 final size:66
Alignment explanation
Indices: 52446876--52447050 Score: 244
Period size: 66 Copynumber: 2.7 Consensus size: 66
52446866 ACACACAATT
* * * * *
52446876 GTGTGG-TTGGCCGTGTGACACAAGTCAGTATACCCTCCAGTTTTCACACGGCCTAGCACACGGG
1 GTGTGGCTTGGCCATGTGACACAAGTCAGTATACTCACTAGTTTTCACACGGCCTAGCACACGGA
52446940 C
66 C
* * * *
52446941 GTGTGGCTTGGCCATGTGTCACAAGTCAGTATGCTCATTATTTTTCACACGGCCTAGCACACGGA
1 GTGTGGCTTGGCCATGTGACACAAGTCAGTATACTCACTAGTTTTCACACGGCCTAGCACACGGA
52447006 C
66 C
* *
52447007 GTGTGGCTTGGCCATGTGACCCAAGTCAGTAAACTCACTAGTTT
1 GTGTGGCTTGGCCATGTGACACAAGTCAGTATACTCACTAGTTT
52447051 GGACACGGGA
Statistics
Matches: 94, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 6 0.06
66 88 0.94
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (66 bp):
GTGTGGCTTGGCCATGTGACACAAGTCAGTATACTCACTAGTTTTCACACGGCCTAGCACACGGA
C
Found at i:52453004 original size:2 final size:2
Alignment explanation
Indices: 52452997--52453021 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52452987 GCAAAAATTC
52452997 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 A
52453022 CTAATACTTA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52453470 original size:41 final size:41
Alignment explanation
Indices: 52453411--52453542 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 41
52453401 TGCTAAGCAC
* * *
52453411 AAAGCCCGATACATTTCACCGGCACAAAGCCTACTAGACAT
1 AAAGCCTGATATAATTCACCGGCACAAAGCCTACTAGACAT
* ** * *
52453452 AAAGTCTGATATAATTCACCGGCACTGAGCCTGCTAGGCAT
1 AAAGCCTGATATAATTCACCGGCACAAAGCCTACTAGACAT
* * * *
52453493 AAAGCCTGATGTAATTCACCGACATC-AAGCCTGCTAGGCAT
1 AAAGCCTGATATAATTCACCGGCA-CAAAGCCTACTAGACAT
*
52453534 TAAGCCTGA
1 AAAGCCTGA
52453543 AAATCTCAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 76 0.99
42 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (41 bp):
AAAGCCTGATATAATTCACCGGCACAAAGCCTACTAGACAT
Found at i:52453782 original size:65 final size:62
Alignment explanation
Indices: 52453648--52453784 Score: 154
Period size: 65 Copynumber: 2.2 Consensus size: 62
52453638 GCAAACAAAC
* ** *
52453648 ATTCGAACCACATATGTATAATTTACAACATTAAAATTCAGCTCAAAGAATTTGTAACCTAT
1 ATTCGAACCACATATGTATAAATTACAACATTAAAATTCAGCTCAAAGAATTTAAAACATAT
*
52453710 ATTCGAACCACATATGTATGTAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTAAATATA
1 ATTCGAACCACATATGTA--T-AAATTACA-ACATTAAAATTCAGCTCAAAGAA-TTTAAA-ACA
52453772 TAT
60 TAT
52453775 ATTCGAACCA
1 ATTCGAACCA
52453785 TATGTGCATA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
62 18 0.28
63 5 0.08
64 18 0.28
65 23 0.36
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (62 bp):
ATTCGAACCACATATGTATAAATTACAACATTAAAATTCAGCTCAAAGAATTTAAAACATAT
Found at i:52453894 original size:61 final size:60
Alignment explanation
Indices: 52453799--52453918 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 60
52453789 TGCATATATA
** * *
52453799 TATATATATAATTCATAATACTATGTTCAACTCAAAGAACTTATATCATACATTCAAACTT
1 TATATATATAATTCATAATACTAAATTCAACTC-AAGAAATTAAATCATACATTCAAACTT
* * *
52453860 TATATATATAATTCATAACT-TTAAATTCAACTCAAGAAATTAAATCTTACATTCGAACT
1 TATATATATAATTCATAA-TACTAAATTCAACTCAAGAAATTAAATCATACATTCAAACT
52453919 ACATATCCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 22 0.43
61 28 0.55
62 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (60 bp):
TATATATATAATTCATAATACTAAATTCAACTCAAGAAATTAAATCATACATTCAAACTT
Found at i:52454873 original size:28 final size:28
Alignment explanation
Indices: 52454838--52454894 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
52454828 TTATGTTGTT
52454838 TTTATTATAATAA-CTTTATAATATATTA
1 TTTATTATAATAACCTTTATAAT-TATTA
*
52454866 TTTATTATTATAACCTTTATAATTATTA
1 TTTATTATAATAACCTTTATAATTATTA
52454894 T
1 T
52454895 AAAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATAATAACCTTTATAATTATTA
Found at i:52456339 original size:2 final size:2
Alignment explanation
Indices: 52456332--52456367 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52456322 TTTTACCTTT
52456332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52456368 ATTTGTCAGA
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):
TA
Found at i:52459240 original size:33 final size:32
Alignment explanation
Indices: 52459097--52459257 Score: 115
Period size: 33 Copynumber: 4.8 Consensus size: 32
52459087 CATTGTTTAT
*
52459097 ATGTAAGATCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGATCATAGCTGGGCTATGGCAGTCTG
* * * * * *
52459129 ATGATAATACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGATCATAGCTGGGCTATGGCAGTCTG
* * * * * * * *
52459162 AACGTAAGACCATGGTTGGACCATGGCAATGTTTAT
1 -ATGTAAGATCATAGCTGGGCTATGGC-A-GTCT-G
52459198 ATGTAAGATCATAGCTGGGCTATGGCAGTCTG
1 ATGTAAGATCATAGCTGGGCTATGGCAGTCTG
* *
52459230 ATGATAAGATCATAACTGGGTTATGGCA
1 ATG-TAAGATCATAGCTGGGCTATGGCA
52459258 CTACGAATGT
Statistics
Matches: 96, Mismatches: 27, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
32 6 0.06
33 64 0.67
34 4 0.04
35 22 0.23
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (32 bp):
ATGTAAGATCATAGCTGGGCTATGGCAGTCTG
Found at i:52459254 original size:101 final size:101
Alignment explanation
Indices: 52459079--52459269 Score: 328
Period size: 101 Copynumber: 1.9 Consensus size: 101
52459069 ATGAACGTAA
* * *
52459079 GACCATGGCATTGTTTATATGTAAGATCATAGCTGGGCTATGGCATTCTGATGATAATACCATAA
1 GACCATGGCAATGTTTATATGTAAGATCATAGCTGGGCTATGGCAGTCTGATGATAAGACCATAA
*
52459144 CTGGGTTATGGCACTATGAACGTAAGACCATGGTTG
66 CTGGGTTATGGCACTACGAACGTAAGACCATGGTTG
*
52459180 GACCATGGCAATGTTTATATGTAAGATCATAGCTGGGCTATGGCAGTCTGATGATAAGATCATAA
1 GACCATGGCAATGTTTATATGTAAGATCATAGCTGGGCTATGGCAGTCTGATGATAAGACCATAA
*
52459245 CTGGGTTATGGCACTACGAATGTAA
66 CTGGGTTATGGCACTACGAACGTAA
52459270 ATGATGAATT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 84 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (101 bp):
GACCATGGCAATGTTTATATGTAAGATCATAGCTGGGCTATGGCAGTCTGATGATAAGACCATAA
CTGGGTTATGGCACTACGAACGTAAGACCATGGTTG
Found at i:52459520 original size:12 final size:12
Alignment explanation
Indices: 52459505--52459537 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
52459495 CAGTAAGAGA
52459505 ATGATATGTGTC
1 ATGATATGTGTC
52459517 ATGATATGTGTC
1 ATGATATGTGTC
52459529 ATGATATGT
1 ATGATATGT
52459538 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (12 bp):
ATGATATGTGTC
Found at i:52463698 original size:202 final size:201
Alignment explanation
Indices: 52463347--52463945 Score: 783
Period size: 202 Copynumber: 3.0 Consensus size: 201
52463337 ATGTGGTTGA
*
52463347 GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATAGCTTCGGTAATATGTAAACTAGA
1 GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATGGCTTCGGTAATATGTAAAC-AGA
* * * *
52463412 CTAGTAGATCACGACATGAAAATATGTATAAGTCCATAAAGGAGATACCCATAGCGCCTTTTGTG
65 CTAGCAGATCACGACATGAAAATATGTATAAGTTCATGAGGGAGATACCCATAGCGCCTTTTGTG
* *
52463477 AAAGTTCGCTAGG-ACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGTGTAATCTACTAAG
130 AAAGTT-GC-CGGAACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGCGTAATCTACTAAG
*
52463541 CT-TTTTGG
193 CTCTTCTGG
* * * * *
52463549 GACTCATGACAATATATGACTGTATGAATATTCATGGTGATGGTTTCGGTAATATGTAAATCGGA
1 GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATGGCTTCGGTAATATGTAAA-CAGA
* * *
52463614 CTAGCAGATTATGACATGAAAATATGTATAAGTTCATGAGGGAGATACCCATAGAGCCTTTTGTG
65 CTAGCAGATCACGACATGAAAATATGTATAAGTTCATGAGGGAGATACCCATAGCGCCTTTTGTG
* * * * *
52463679 AAAGTCTGCCGGAACAGTAAACATGTGATTTTGTATGATGGCATCTGTGGCGTTATCTACTAA-A
130 AAAGT-TGCCGGAACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGCGTAATCTACTAAGC
52463743 TCTTCTGG
194 TCTTCTGG
* *
52463751 GACCCATGACAAGATATGATTGTATGAATATTCATAGTGATGGCTTCGGTAACATGTAAACCAGA
1 GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATGGCTTCGGTAATATGTAAA-CAGA
* * *
52463816 TTGGCAGATCACAACATGAAAATATGTATAAG-TCTATGAGGGAGATACCCATAGCGCCTTTTGT
65 CTAGCAGATCACGACATGAAAATATGTATAAGTTC-ATGAGGGAGATACCCATAGCGCCTTTTGT
** ** * * * * *
52463880 GAAAGTTTACTAAGACAATAAACACGTGATTTTATATGATGGTCTGTGTGGCGTAATCTGCTAAG
129 GAAAGTTGCCGGA-ACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGCGTAATCTACTAAG
52463945 C
193 C
52463946 CTTTGTGGTG
Statistics
Matches: 342, Mismatches: 48, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
201 8 0.02
202 332 0.97
203 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (201 bp):
GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATGGCTTCGGTAATATGTAAACAGAC
TAGCAGATCACGACATGAAAATATGTATAAGTTCATGAGGGAGATACCCATAGCGCCTTTTGTGA
AAGTTGCCGGAACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGCGTAATCTACTAAGCTC
TTCTGG
Found at i:52463962 original size:23 final size:23
Alignment explanation
Indices: 52463926--52463977 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
52463916 TGATGGTCTG
52463926 TGTGGCGTAATCTGCTAAG-CCTT
1 TGTGGCGTAATCTG-TAAGACCTT
* * *
52463949 TGTGGTGTATTCTGTATGACCTT
1 TGTGGCGTAATCTGTAAGACCTT
52463972 TGTGGC
1 TGTGGC
52463978 AAGTTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.13, C:0.17, G:0.29, T:0.40
Consensus pattern (23 bp):
TGTGGCGTAATCTGTAAGACCTT
Found at i:52466850 original size:21 final size:21
Alignment explanation
Indices: 52466826--52466868 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
52466816 AAATCAATAT
52466826 ATATAAAATATA-AATAATTTA
1 ATATAAAATATATAAT-ATTTA
*
52466847 ATATAAATTATATAATATTTA
1 ATATAAAATATATAATATTTA
52466868 A
1 A
52466869 AAAACATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAAAATATATAATATTTA
Found at i:52467527 original size:18 final size:18
Alignment explanation
Indices: 52467496--52467538 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
52467486 TTCTTTTTAT
52467496 AAATAAATAGATCGAAAA
1 AAATAAATAGATCGAAAA
52467514 AAATGAAATA-ATCGAAAA
1 AAAT-AAATAGATCGAAAA
*
52467532 GAATAAA
1 AAATAAA
52467539 GAAAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 15 0.65
19 5 0.22
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (18 bp):
AAATAAATAGATCGAAAA
Found at i:52482695 original size:3 final size:3
Alignment explanation
Indices: 52482680--52482722 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
52482670 TGTTTATTGT
* *
52482680 TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG CTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
52482723 GTGTGTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.02, C:0.02, G:0.30, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:52497014 original size:85 final size:85
Alignment explanation
Indices: 52496871--52497033 Score: 308
Period size: 85 Copynumber: 1.9 Consensus size: 85
52496861 TAAACCATAT
*
52496871 AAGAGAAGCAACATAATACCAAAGAGAAAAGCACAATTGCCATCATAAATAACCTTTTGAATCTC
1 AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATAACCTTTTGAATCTC
52496936 AGGAGTTATATGTACAGTAC
66 AGGAGTTATATGTACAGTAC
*
52496956 AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATCACCTTTTGAATCTC
1 AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATAACCTTTTGAATCTC
52497021 AGGAGTTATATGT
66 AGGAGTTATATGT
52497034 CCAATCCTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.23
Consensus pattern (85 bp):
AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATAACCTTTTGAATCTC
AGGAGTTATATGTACAGTAC
Found at i:52506443 original size:2 final size:2
Alignment explanation
Indices: 52506436--52506463 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52506426 CGGAGAAGAA
52506436 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52506464 GTGAAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52506947 original size:12 final size:12
Alignment explanation
Indices: 52506930--52506957 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
52506920 GGAAAAATAG
52506930 CTACTTTAAGCA
1 CTACTTTAAGCA
52506942 CTACTTTAAGCA
1 CTACTTTAAGCA
52506954 CTAC
1 CTAC
52506958 GTCAATGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (12 bp):
CTACTTTAAGCA
Found at i:52510837 original size:7 final size:7
Alignment explanation
Indices: 52510825--52510870 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
52510815 AAAGAAAGGG
52510825 AGAAAAT
1 AGAAAAT
52510832 AGAAAAT
1 AGAAAAT
52510839 AGAAAA-
1 AGAAAAT
*
52510845 GGAAAA-
1 AGAAAAT
52510851 AGAAAAT
1 AGAAAAT
52510858 AGAGAAAT
1 AGA-AAAT
52510866 A-AAAA
1 AGAAAA
52510871 GGAAAATCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 13 0.37
7 17 0.49
8 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (7 bp):
AGAAAAT
Found at i:52510854 original size:26 final size:26
Alignment explanation
Indices: 52510825--52510876 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
52510815 AAAGAAAGGG
52510825 AGAAAATAGA-AAATAGAAAAGGAAAA
1 AGAAAATAGAGAAATA-AAAAGGAAAA
52510851 AGAAAATAGAGAAATAAAAAGGAAAA
1 AGAAAATAGAGAAATAAAAAGGAAAA
52510877 TCTCCCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (26 bp):
AGAAAATAGAGAAATAAAAAGGAAAA
Found at i:52518048 original size:2 final size:2
Alignment explanation
Indices: 52518041--52518065 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52518031 TACACCTCTA
52518041 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 A
52518066 ATTTATCTTG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52537761 original size:54 final size:56
Alignment explanation
Indices: 52537653--52537762 Score: 197
Period size: 54 Copynumber: 2.0 Consensus size: 56
52537643 CTTTTATTGC
*
52537653 CTAAAATAATAAAAATAAATTTTGAATATATTCTTATATTTTTATTATAGAATTTA
1 CTAAAATAATAAAAATAAATATTGAATATATTCTTATATTTTTATTATAGAATTTA
52537709 CTAAAATAAT-AAAATAAA-ATTGAATATATTCTTATATTTTTATTATAGAATTTA
1 CTAAAATAATAAAAATAAATATTGAATATATTCTTATATTTTTATTATAGAATTTA
52537763 TTCTTAATTT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
54 35 0.66
55 8 0.15
56 10 0.19
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (56 bp):
CTAAAATAATAAAAATAAATATTGAATATATTCTTATATTTTTATTATAGAATTTA
Found at i:52551689 original size:86 final size:85
Alignment explanation
Indices: 52551592--52551763 Score: 226
Period size: 86 Copynumber: 2.0 Consensus size: 85
52551582 TTAATACAAT
* *
52551592 TAACAATTAATAATTTGATGTAATTTG-ATAATTTTACTAATAATTAAT-ACAATT-A-ACAATT
1 TAACAATTAATAA-TT-A-ATAATTTGAATAATTTGA-TAAT-ATTAATAACAATTAATACAATT
52551653 AATAATTTTACTAACAAAATGTTAG
61 AATAATTTTACTAACAAAATGTTAG
* *
52551678 TAACAATTAATAATTAATAATTTGATATAATTTGATAATTTTAGTAACAATTAATACAATTAATA
1 TAACAATTAATAATTAATAATTTGA-ATAATTTGATAATATTAATAACAATTAATACAATTAATA
52551743 ATTTTACTAACAAAATGTTAG
65 ATTTTACTAACAAAATGTTAG
52551764 ATTTTACAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
83 11 0.14
84 11 0.14
85 11 0.14
86 44 0.57
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (85 bp):
TAACAATTAATAATTAATAATTTGAATAATTTGATAATATTAATAACAATTAATACAATTAATAA
TTTTACTAACAAAATGTTAG
Found at i:52551788 original size:17 final size:17
Alignment explanation
Indices: 52551752--52551791 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
52551742 AATTTTACTA
*
52551752 ACAAAATGTTAGATTTT
1 ACAAAATGTTAGATTGT
52551769 ACAAAATGTT-GATTGGT
1 ACAAAATGTTAGATT-GT
52551786 ACAAAA
1 ACAAAA
52551792 AATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (17 bp):
ACAAAATGTTAGATTGT
Found at i:52551828 original size:16 final size:16
Alignment explanation
Indices: 52551809--52551865 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
52551799 AATTTGATAC
*
52551809 AATTTTAATAATAATT
1 AATTTTAATAACAATT
*
52551825 AATTTTGATAACAATT
1 AATTTTAATAACAATT
52551841 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
52551857 AGTTTTAAT
1 AATTTTAAT
52551866 TTTAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:52551849 original size:22 final size:23
Alignment explanation
Indices: 52551839--52551900 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
52551829 TTGATAACAA
* *
52551839 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
52551861 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
52551884 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
52551901 ACGGGCCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 14 0.39
24 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:52564103 original size:20 final size:18
Alignment explanation
Indices: 52564066--52564132 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
52564056 CTTTATCAAA
*
52564066 TATATTTAAATTATTTAT
1 TATATTTAAATTAATTAT
52564084 TATATTTAATACTTAATTA-
1 TATATTTAA-A-TTAATTAT
* *
52564103 T-TATTAAAATTATTTATT
1 TATATTTAAATTAATTA-T
52564121 TAATATTTAAAT
1 T-ATATTTAAAT
52564133 CCGTTTCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
16 6 0.15
17 1 0.03
18 16 0.41
19 2 0.05
20 14 0.36
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTTAAATTAATTAT
Found at i:52564973 original size:96 final size:97
Alignment explanation
Indices: 52564808--52564994 Score: 295
Period size: 96 Copynumber: 1.9 Consensus size: 97
52564798 CCAGAATTAT
* * * *
52564808 GTATGAATGACATGGAAAAAAATTGTTGAAATGCCGTTCAATAATTAGAAAGGGGTCATGGATGA
1 GTATGAATGACATAGAAAAAAATTGTTGAAATGCCATTAAATAATTAGAAAGGGATCATGGATGA
* *
52564873 TGTGGTGGGAATGGTTCGTAAAATAATTTCTC
66 TGTGGTGGGAATGGTCCATAAAATAATTTCTC
* *
52564905 GTATGAATGACATAG-AAAAAATTGTTGAAATGTCATTAAATGATTAGAAAGGGATCATGGATGA
1 GTATGAATGACATAGAAAAAAATTGTTGAAATGCCATTAAATAATTAGAAAGGGATCATGGATGA
52564969 TGTGGTGGGAATGGTCCATAAAATAA
66 TGTGGTGGGAATGGTCCATAAAATAA
52564995 GTCTTCCCTA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 68 0.83
97 14 0.17
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (97 bp):
GTATGAATGACATAGAAAAAAATTGTTGAAATGCCATTAAATAATTAGAAAGGGATCATGGATGA
TGTGGTGGGAATGGTCCATAAAATAATTTCTC
Found at i:52570810 original size:19 final size:20
Alignment explanation
Indices: 52570786--52570823 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
52570776 CCTTTTTACA
*
52570786 TTTCTTTTT-CTTTTCTTTT
1 TTTCTTTTTACGTTTCTTTT
52570805 TTTCTTTTTACGTTTCTTT
1 TTTCTTTTTACGTTTCTTT
52570824 GGTCTACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTCTTTTTACGTTTCTTTT
Found at i:52571336 original size:10 final size:10
Alignment explanation
Indices: 52571309--52571359 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
52571299 TTTATATTTT
52571309 TAAAAAATTA
1 TAAAAAATTA
* *
52571319 TAACAAATTC
1 TAAAAAATTA
52571329 TAAAAAATATA
1 TAAAAAAT-TA
52571340 TAAAGAAA-TA
1 TAAA-AAATTA
*
52571350 AAAAAAATTA
1 TAAAAAATTA
52571360 GAATAATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.67
11 5 0.15
12 3 0.09
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:52574875 original size:15 final size:15
Alignment explanation
Indices: 52574857--52574887 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52574847 TGAAAAATGC
52574857 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
*
52574872 AAAAAGAAAAAAGAA
1 AAAAAAAAAAAAGAA
52574887 A
1 A
52574888 TTAAGCTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:52579544 original size:15 final size:14
Alignment explanation
Indices: 52579511--52579569 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
52579501 AACTCAGCAG
* *
52579511 AATACAAATAA-AA
1 AATAAAAATAATAT
52579524 AATAAAAATAATGAT
1 AATAAAAATAAT-AT
*
52579539 AATAAAACTAATAT
1 AATAAAAATAATAT
*
52579553 AATAATAAATAAAAT
1 AATAA-AAATAATAT
52579568 AA
1 AA
52579570 ACTAAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 10 0.26
14 7 0.18
15 21 0.55
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (14 bp):
AATAAAAATAATAT
Found at i:52582654 original size:27 final size:26
Alignment explanation
Indices: 52582594--52582655 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
52582584 TATAGAATAG
* *
52582594 ATAATAATATAACCATGCATATATATT
1 ATAA-AATATAAACATGCATATACATT
*
52582621 ATTAAATATTAAACATGCATATACA-T
1 ATAAAATA-TAAACATGCATATACATT
52582647 ATGAAAATA
1 AT-AAAATA
52582656 AAAGTGCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.34
Consensus pattern (26 bp):
ATAAAATATAAACATGCATATACATT
Found at i:52582866 original size:3 final size:3
Alignment explanation
Indices: 52582858--52582903 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
52582848 AAAATGAAAC
*
52582858 TAA TAA TAA TTAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52582904 GTTAAACAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52594132 original size:72 final size:73
Alignment explanation
Indices: 52593990--52594133 Score: 227
Period size: 72 Copynumber: 2.0 Consensus size: 73
52593980 CTTAGACATG
** * *
52593990 TCATTAGCTCATTAAGTTTCATTGGATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTTATT
1 TCATTAGCTCATTAAAATTCATTGCATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTGATT
52594055 GCAAACCA
66 GCAAACCA
* *
52594063 TCATTAGCTCATTAAAATTCATTGCATCAACAA-TTAAGCCTCTTGAATTGTTGTCACCTTGATT
1 TCATTAGCTCATTAAAATTCATTGCATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTGATT
52594127 GCAAACC
66 GCAAACC
52594134 TTTCAAGTAG
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
72 35 0.54
73 30 0.46
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (73 bp):
TCATTAGCTCATTAAAATTCATTGCATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTGATT
GCAAACCA
Found at i:52600785 original size:26 final size:26
Alignment explanation
Indices: 52600750--52600805 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
52600740 GTGGTTATTG
*
52600750 AACTCTTAAGGGAGTTGCCTACCTTGA
1 AACTCTTAAGCGAGTTGCCTACCTT-A
52600777 AACTC-TAAGCGAGTTGCCTACCTTA
1 AACTCTTAAGCGAGTTGCCTACCTTA
52600802 AACT
1 AACT
52600806 TACTGAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 5 0.18
26 18 0.64
27 5 0.18
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (26 bp):
AACTCTTAAGCGAGTTGCCTACCTTA
Found at i:52603121 original size:19 final size:20
Alignment explanation
Indices: 52603094--52603131 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52603084 TTAAATGTTT
*
52603094 TATATTTTA-ATATTTAAAA
1 TATAGTTTATATATTTAAAA
52603113 TATAGTTTATATATTTAAA
1 TATAGTTTATATATTTAAA
52603132 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TATAGTTTATATATTTAAAA
Found at i:52603141 original size:20 final size:20
Alignment explanation
Indices: 52603099--52603143 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
52603089 TGTTTTATAT
* *
52603099 TTTA-ATATTTAAAATATAG
1 TTTATATATTTAAAATAAAA
*
52603118 TTTATATATTTAAATTAAAA
1 TTTATATATTTAAAATAAAA
52603138 TTTATA
1 TTTATA
52603144 AATAATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTATATATTTAAAATAAAA
Found at i:52603153 original size:49 final size:51
Alignment explanation
Indices: 52603055--52603158 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 51
52603045 TGAATTTTAT
* * * * *
52603055 TTTAAATATATAATATTATGTATTTAAATTTAAATGTTTTATATTTTAATA
1 TTTAAATATATAATATTATATATTTAAATTAAAATGTTATAAATATTAATA
*
52603106 TTTAAA-ATATAGT-TTATATATTTAAATTAAAAT-TTATAAATAATTAATA
1 TTTAAATATATAATATTATATATTTAAATTAAAATGTTATAAAT-ATTAATA
52603155 TTTA
1 TTTA
52603159 TGGCTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 6 0.13
49 28 0.61
50 6 0.13
51 6 0.13
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (51 bp):
TTTAAATATATAATATTATATATTTAAATTAAAATGTTATAAATATTAATA
Found at i:52603225 original size:29 final size:29
Alignment explanation
Indices: 52603167--52603225 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
52603157 TATGGCTTAA
* * *
52603167 AAAATATTTAAAAATATATTTCATATATT
1 AAAATATTTAAAAATAAATTTAATAAATT
*
52603196 AAAATA-TTAACAATAAATTATAATAAATT
1 AAAATATTTAAAAATAAATT-TAATAAATT
52603225 A
1 A
52603226 TTTTTTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (29 bp):
AAAATATTTAAAAATAAATTTAATAAATT
Found at i:52607408 original size:19 final size:20
Alignment explanation
Indices: 52607357--52607413 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
52607347 TTCCTCAACC
*
52607357 GAAAATATTTTCTGCAATAGT
1 GAAAATATTTTTTGC-ATAGT
*
52607378 CAGAAA-ATTTTTTGCA-AGT
1 GA-AAATATTTTTTGCATAGT
52607397 GAAAATATTTTTTGCAT
1 GAAAATATTTTTTGCAT
52607414 TACCAACACT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.10
19 14 0.47
20 1 0.03
21 9 0.30
22 3 0.10
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (20 bp):
GAAAATATTTTTTGCATAGT
Found at i:52619445 original size:20 final size:21
Alignment explanation
Indices: 52619406--52619447 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
52619396 TAAAAAATTC
*
52619406 AAATATTAAAAATTAGAAAAA
1 AAATATTAAAAATCAGAAAAA
*
52619427 AAATA-TAAAAATCATAAAAA
1 AAATATTAAAAATCAGAAAAA
52619447 A
1 A
52619448 TAAAAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (21 bp):
AAATATTAAAAATCAGAAAAA
Found at i:52619471 original size:19 final size:19
Alignment explanation
Indices: 52619447--52619527 Score: 53
Period size: 19 Copynumber: 4.3 Consensus size: 19
52619437 ATCATAAAAA
52619447 ATAAAAATTGTAAAATTTT
1 ATAAAAATTGTAAAATTTT
* **
52619466 AT-AAAATCGTAAAAAAATT
1 ATAAAAATTGT-AAAATTTT
*
52619485 AT-AAAATATGTAGAAA-TAT
1 ATAAAAAT-TGTA-AAATTTT
*
52619504 A-AAAAATTTATAAAATTTT
1 ATAAAAA-TTGTAAAATTTT
52619523 ATAAA
1 ATAAA
52619528 GTTGTAAGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
18 10 0.21
19 28 0.60
20 9 0.19
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (19 bp):
ATAAAAATTGTAAAATTTT
Found at i:52619553 original size:57 final size:57
Alignment explanation
Indices: 52619449--52619565 Score: 139
Period size: 57 Copynumber: 2.0 Consensus size: 57
52619439 CATAAAAAAT
* *
52619449 AAAAATTGTAAAATTTTATAAAATCGTAAAAAAATTATAAAATATGT-AGAAATATA
1 AAAAATTATAAAATTTTATAAAATCGTAAAAAAACTATAAAATATGTAAGAAATATA
* * * *
52619505 AAAAATTTATAAAATTTTATAAAGTTGTAAGAAAACTATACGAA-ATGTAAAGAAATATA
1 AAAAA-TTATAAAATTTTATAAAATCGTAAAAAAACTATA-AAATATGT-AAGAAATATA
52619564 AA
1 AA
52619566 TTTCGTAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
56 5 0.10
57 33 0.65
58 2 0.04
59 11 0.22
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.31
Consensus pattern (57 bp):
AAAAATTATAAAATTTTATAAAATCGTAAAAAAACTATAAAATATGTAAGAAATATA
Found at i:52620049 original size:89 final size:88
Alignment explanation
Indices: 52619895--52620170 Score: 364
Period size: 88 Copynumber: 3.1 Consensus size: 88
52619885 TAATAAGAGC
*
52619895 AGGGGCTTAATTATTTTTTTGAAAAAAATTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAGT
1 AGGGGCTTAATTGTTTTTTTGAAAAAAATTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAGT
52619960 ATCTAATTGAGTGAAAAAAAATT
66 ATCTAATTGAGTGAAAAAAAATT
*
52619983 AGGCGCTTAATTGTTTTTTTGAAAAAAATTTAAGGGTCTTTTTTTATACATTTTTAAAGTTCAAG
1 AGGGGCTTAATTGTTTTTTTGAAAAAAATTTAAGGGTC-TTTTTTATACATTTTTAAAGTTCAAG
*
52620048 TATCCAATTGAGTG-AAAAAAATT
65 TATCTAATTGAGTGAAAAAAAATT
* * * * * * ** *
52620071 AGGGGCTTAATTTCTTTTTTTG-AAGAATTTTGAGGGCCTTTTTAATGTATTTTGAAAGTTCAAG
1 AGGGGCTTAA-TTGTTTTTTTGAAAAAAATTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAG
*
52620135 T-GCTCAATTGAGTGCAAAAAAAA--
65 TATCT-AATTGAGTG-AAAAAAAATT
52620158 AGGGGCTTAATTG
1 AGGGGCTTAATTG
52620171 CTTCTTCTTC
Statistics
Matches: 167, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
86 3 0.02
87 42 0.25
88 66 0.40
89 56 0.34
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.41
Consensus pattern (88 bp):
AGGGGCTTAATTGTTTTTTTGAAAAAAATTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAGT
ATCTAATTGAGTGAAAAAAAATT
Found at i:52636016 original size:29 final size:29
Alignment explanation
Indices: 52635974--52636035 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
52635964 AACTTGACAC
52635974 TCAACTCTCTAGGAGAGACATAAAAGCAA
1 TCAACTCTCTAGGAGAGACATAAAAGCAA
*
52636003 TCAACTCTCTAGGAGAGACATAAATGCAA
1 TCAACTCTCTAGGAGAGACATAAAAGCAA
52636032 TCAA
1 TCAA
52636036 AGTACAAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (29 bp):
TCAACTCTCTAGGAGAGACATAAAAGCAA
Found at i:52638236 original size:31 final size:33
Alignment explanation
Indices: 52638198--52638266 Score: 97
Period size: 35 Copynumber: 2.1 Consensus size: 33
52638188 ATACAATGTT
*
52638198 TAAAAA-A-ATCAAACAAATAACCTAGATAAAC
1 TAAAAATACATCAAACAAATAACCTAAATAAAC
52638229 TAAAAAAATACATCAAACAAATAACCTAAATAAAC
1 T--AAAAATACATCAAACAAATAACCTAAATAAAC
52638264 TAA
1 TAA
52638267 CATGAGAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
31 1 0.03
33 7 0.21
34 1 0.03
35 24 0.73
ACGTcount: A:0.65, C:0.16, G:0.01, T:0.17
Consensus pattern (33 bp):
TAAAAATACATCAAACAAATAACCTAAATAAAC
Found at i:52645684 original size:27 final size:27
Alignment explanation
Indices: 52645654--52645721 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
52645644 ATGTAGAAAC
*
52645654 AATAATAATAATAACATCATTAA-T-AAT
1 AATAATAATAATAACA--ATGAACTAAAT
** *
52645681 AATAGCAATAAAAACAATGAACTAAAT
1 AATAATAATAATAACAATGAACTAAAT
52645708 AATAATAATAATAA
1 AATAATAATAATAA
52645722 AGGGACTAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
25 4 0.12
26 1 0.03
27 27 0.84
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.26
Consensus pattern (27 bp):
AATAATAATAATAACAATGAACTAAAT
Found at i:52655282 original size:15 final size:15
Alignment explanation
Indices: 52655238--52655283 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
52655228 ACAAAAAAAT
52655238 AAAATATTTT-CT-A
1 AAAATATTTTACTGA
*
52655251 AAAATTATTTTA-GGA
1 AAAA-TATTTTACTGA
52655266 AAAATATTTTACTGA
1 AAAATATTTTACTGA
52655281 AAA
1 AAA
52655284 TTAAAGTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 4 0.15
14 13 0.48
15 10 0.37
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (15 bp):
AAAATATTTTACTGA
Found at i:52662383 original size:16 final size:16
Alignment explanation
Indices: 52662362--52662392 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52662352 AATTAATCTA
*
52662362 AATTATTTATAAAATT
1 AATTATATATAAAATT
52662378 AATTATATATAAAAT
1 AATTATATATAAAAT
52662393 ATTTTTAAAA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTATATATAAAATT
Found at i:52662390 original size:27 final size:26
Alignment explanation
Indices: 52662351--52662404 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
52662341 ATATTTCAAG
* *
52662351 TAATTAATCTAAATTATTTATAAAAT
1 TAATTAATATAAAATATTTATAAAAT
*
52662377 TAATTATATATAAAATATTTTTAAAAT
1 TAATTA-ATATAAAATATTTATAAAAT
52662404 T
1 T
52662405 TTAACATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATTAATATAAAATATTTATAAAAT
Found at i:52662763 original size:31 final size:30
Alignment explanation
Indices: 52662694--52662763 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
52662684 TACCCATATT
* *
52662694 ATTTTTTAATTTTAAAAAAAATTATATTAT
1 ATTTTTTAATTTTAAAAAAAATTATATGAA
52662724 ATTATTTTAATATTTAATAAAAAATTAT-TGAA
1 ATT-TTTTAAT-TTTAA-AAAAAATTATATGAA
52662756 ATTTTTTA
1 ATTTTTTA
52662764 TAATATCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 3 0.09
31 12 0.34
32 10 0.29
33 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
ATTTTTTAATTTTAAAAAAAATTATATGAA
Found at i:52662768 original size:33 final size:32
Alignment explanation
Indices: 52662695--52662774 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
52662685 ACCCATATTA
* *
52662695 TTTTTTAAT-TTTAAAAAAAATTATATTATAT
1 TTTTTTAATATTTAAAAAAAATTATATGAAAT
*
52662726 TATTTTAATATTTAATAAAAAATTAT-TGAAAT
1 TTTTTTAATATTTAA-AAAAAATTATATGAAAT
52662758 TTTTTATAATATCTTAA
1 TTTTT-TAATAT-TTAA
52662775 CATTATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 8 0.20
32 13 0.32
33 16 0.39
34 4 0.10
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
TTTTTTAATATTTAAAAAAAATTATATGAAAT
Found at i:52667695 original size:47 final size:47
Alignment explanation
Indices: 52667621--52667720 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 47
52667611 TATTAAGTAA
* *
52667621 TAAATATTCTATCGTTATGTGTTTGCGATGTATTAATAAAACTAACTT
1 TAAA-ATTCTATCGTTATGTGTTTGCGATGCATTAATAAAACTAACGT
* * *
52667669 TAAAATTCTATTGTTATGTGTTTGCGATGCATTAGTAAAATTAACGT
1 TAAAATTCTATCGTTATGTGTTTGCGATGCATTAATAAAACTAACGT
52667716 TAAAA
1 TAAAA
52667721 CAAGTTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 43 0.91
48 4 0.09
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (47 bp):
TAAAATTCTATCGTTATGTGTTTGCGATGCATTAATAAAACTAACGT
Found at i:52668552 original size:2 final size:2
Alignment explanation
Indices: 52668537--52668578 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
52668527 NNNNNNNNNN
52668537 TA TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52668577 TA
1 TA
52668579 AAGGACTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52674754 original size:18 final size:18
Alignment explanation
Indices: 52674716--52674754 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52674706 ATTGCTTCTC
*
52674716 AAAAGCACTTTTGGGACA
1 AAAAGCACTTTTGAGACA
* *
52674734 AAAAGTACTTTTGAGATA
1 AAAAGCACTTTTGAGACA
52674752 AAA
1 AAA
52674755 GCATTACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (18 bp):
AAAAGCACTTTTGAGACA
Found at i:52677092 original size:15 final size:16
Alignment explanation
Indices: 52677063--52677095 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52677053 TTTTTATAAC
*
52677063 TTTTTAATATTTTTAT
1 TTTTTAATATATTTAT
52677079 TTTTTAATA-ATTTAT
1 TTTTTAATATATTTAT
52677094 TT
1 TT
52677096 GTTTTGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTAATATATTTAT
Found at i:52681496 original size:25 final size:25
Alignment explanation
Indices: 52681467--52681525 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
52681457 AGGATTAACT
52681467 GAATTAAAATTTTACTTATAAAATC
1 GAATTAAAATTTTACTTATAAAATC
52681492 GAATTAAAATTTTACTTATAAAATC
1 GAATTAAAATTTTACTTATAAAATC
52681517 GAATTAAAA
1 GAATTAAAA
52681526 GTGGGTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (25 bp):
GAATTAAAATTTTACTTATAAAATC
Found at i:52684017 original size:31 final size:30
Alignment explanation
Indices: 52683976--52684050 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
52683966 TTAATGGCTC
* **
52683976 AGTGATTAAAATGTTACAACATGTT-AATGTA
1 AGTGACTAAAATGTT--AACATGTTGAACATA
* *
52684007 AGTGACTAAAACG-TAACATTTTGAACATA
1 AGTGACTAAAATGTTAACATGTTGAACATA
52684036 AGTGACTAAAATGTT
1 AGTGACTAAAATGTT
52684051 GCCTGAGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 7 0.19
29 16 0.44
30 2 0.06
31 11 0.31
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (30 bp):
AGTGACTAAAATGTTAACATGTTGAACATA
Found at i:52685425 original size:2 final size:2
Alignment explanation
Indices: 52685418--52685443 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52685408 CAAATTACAA
52685418 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
52685444 TAATTTTGTT
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:52685693 original size:42 final size:43
Alignment explanation
Indices: 52685644--52685736 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 43
52685634 GAATTACTAG
*
52685644 TTAAAAAT-TTGA-AATGGAATAGAAGTTGT-GATAATTATACAT
1 TTAAAAATATT-ATAATGGAATAGAAGTTGTAG-TAATTACACAT
* **
52685686 TTAAAAATAATTATAGTTTAATAGAAGTTGTAGTAATTACACAT
1 TTAAAAAT-ATTATAATGGAATAGAAGTTGTAGTAATTACACAT
52685730 TTAAAAA
1 TTAAAAA
52685737 CAATTTAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
42 8 0.19
43 1 0.02
44 33 0.77
45 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (43 bp):
TTAAAAATATTATAATGGAATAGAAGTTGTAGTAATTACACAT
Found at i:52685783 original size:25 final size:24
Alignment explanation
Indices: 52685738--52685788 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
52685728 ATTTAAAAAC
*
52685738 AATTTAAACTTATATTATAATTATT
1 AATTTAAAATTATATTATAATT-TT
*
52685763 AATTTAAAA-TATAATTCTAATTTT
1 AATTTAAAATTAT-ATTATAATTTT
52685787 AA
1 AA
52685789 AATAGAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTTAAAATTATATTATAATTTT
Found at i:52686159 original size:29 final size:29
Alignment explanation
Indices: 52686126--52686186 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
52686116 CATGACACTG
*
52686126 TTTGTTATATATGCCATATCAACAAATAA
1 TTTGTTATATATGCCACATCAACAAATAA
*
52686155 TTTGTTATATATTCCACATCAACAAATAA
1 TTTGTTATATATGCCACATCAACAAATAA
52686184 TTT
1 TTT
52686187 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (29 bp):
TTTGTTATATATGCCACATCAACAAATAA
Found at i:52686571 original size:40 final size:40
Alignment explanation
Indices: 52686513--52686645 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
52686503 GCATTAACGA
* * *
52686513 CGCTTTTTAACAAACGCCGC-AATAGATCAAGAATTAGCGG
1 CGCTTTTTTAGAATCGCCGCTAA-AGATCAAGAATTAGCGG
* *
52686553 CGCTTTTTTAGAATCGCCGCTAAAGATCAAGTATTGGCGG
1 CGCTTTTTTAGAATCGCCGCTAAAGATCAAGAATTAGCGG
* * * *
52686593 CGCTTTTTGAAACAT-GCCGCTAAAGATCAAGAAATAGTGG
1 CGCTTTTTTAGA-ATCGCCGCTAAAGATCAAGAATTAGCGG
*
52686633 CGCATTTTTAGAA
1 CGCTTTTTTAGAA
52686646 ATGTCGTTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 72 0.94
41 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (40 bp):
CGCTTTTTTAGAATCGCCGCTAAAGATCAAGAATTAGCGG
Found at i:52687112 original size:14 final size:14
Alignment explanation
Indices: 52687081--52687176 Score: 63
Period size: 14 Copynumber: 6.9 Consensus size: 14
52687071 TGAGCTTTAT
52687081 TTTAGGGTTT-GTGA
1 TTTAGGGTTTAG-GA
* *
52687095 TTTAGGATTTAGGG
1 TTTAGGGTTTAGGA
* *
52687109 TTTAAGGTTTAGGGT
1 TTTAGGGTTTA-GGA
* * *
52687124 TTTATGATTTATGA
1 TTTAGGGTTTAGGA
52687138 -TTAGGGTTTA-GA
1 TTTAGGGTTTAGGA
**
52687150 GTTTAAAGTTTAGGA
1 -TTTAGGGTTTAGGA
52687165 TTTAGGGTTTAG
1 TTTAGGGTTTAG
52687177 TATTCAAGAT
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
12 2 0.03
13 8 0.13
14 38 0.61
15 14 0.23
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAGGA
Found at i:52687119 original size:21 final size:21
Alignment explanation
Indices: 52687081--52687175 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 21
52687071 TGAGCTTTAT
** *
52687081 TTTAGGGTTTGTGATTTAGGA
1 TTTAGGGTTTAAGGTTTAGGA
*
52687102 TTTAGGGTTTAAGGTTTAGGGT
1 TTTAGGGTTTAAGGTTTA-GGA
* * * * *
52687124 TTTATGATTT-ATGATTAGGG
1 TTTAGGGTTTAAGGTTTAGGA
* *
52687144 TTTAGAGTTTAAAGTTTAGGA
1 TTTAGGGTTTAAGGTTTAGGA
52687165 TTTAGGGTTTA
1 TTTAGGGTTTA
52687176 GTATTCAAGA
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 9 0.16
21 37 0.66
22 10 0.18
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.47
Consensus pattern (21 bp):
TTTAGGGTTTAAGGTTTAGGA
Found at i:52687154 original size:35 final size:35
Alignment explanation
Indices: 52687081--52687176 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
52687071 TGAGCTTTAT
*
52687081 TTTAGGGTTTGTGATTTAGGATTTAGGGTTTAAGG
1 TTTAGGGTTTATGATTTAGGATTTAGGGTTTAAGG
*
52687116 TTTAGGGTTTTATGATTTATGA-TTAGGGTTT-AGAG
1 TTTAGGG-TTTATGATTTAGGATTTAGGGTTTAAG-G
** * *
52687151 TTTAAAGTTTAGGATTTAGGGTTTAG
1 TTTAGGGTTTATGATTTAGGATTTAG
52687177 TATTCAAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
34 13 0.25
35 26 0.51
36 12 0.24
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (35 bp):
TTTAGGGTTTATGATTTAGGATTTAGGGTTTAAGG
Found at i:52691997 original size:42 final size:43
Alignment explanation
Indices: 52691951--52692049 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
52691941 GAATGGTACT
*
52691951 TTTAGTGGCATTTGCGAAAAAAGTACC-CTAAAGGTCATGTTC
1 TTTAGTGGCATTTGCGAAAAAAGCACCGCTAAAGGTCATGTTC
* * *
52691993 TTTAGTGGCGA-TTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGTGGC-ATTTGCGAAAAAAGCACCGCTAAAGGTCATGTTC
* *
52692036 TTTAGCGGCGTTTG
1 TTTAGTGGCATTTG
52692050 TGATAAGAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
42 21 0.44
43 27 0.56
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
TTTAGTGGCATTTGCGAAAAAAGCACCGCTAAAGGTCATGTTC
Found at i:52692034 original size:43 final size:43
Alignment explanation
Indices: 52691978--52692176 Score: 229
Period size: 43 Copynumber: 4.7 Consensus size: 43
52691968 AAAAAGTACC
* *
52691978 CTAAAGGTCATGTTCTTTAGTGGCGATTGTGATAAAAGCGCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
* *
52692021 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAGAGCCCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
* ** ** * * ** **
52692064 TTAAAGAACATGGCCTTTAGCGGCGCTTCTCTTTGAA-CGCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
* *
52692106 CTAAAGGTCATGATCTTTAGCGGTGTTTGTGATAAAAGCGCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
*
52692149 CTAAATGTCATGTTCTTTAGCGGCGTTT
1 CTAAAGGTCATGTTCTTTAGCGGCGTTT
52692177 ATGTGAAAGA
Statistics
Matches: 123, Mismatches: 32, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
42 29 0.24
43 94 0.76
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (43 bp):
CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
Found at i:52692701 original size:22 final size:22
Alignment explanation
Indices: 52692670--52692716 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
52692660 GAATATGTTA
52692670 AAAATGTTTTAATTAT-TATTTG
1 AAAATGTTTT-ATTATATATTTG
*
52692692 AAAATTTTTTATTATAATATTTG
1 AAAATGTTTTATTAT-ATATTTG
52692715 AA
1 AA
52692717 TTAACAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 9 0.41
23 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
AAAATGTTTTATTATATATTTG
Found at i:52692705 original size:21 final size:23
Alignment explanation
Indices: 52692670--52692716 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
52692660 GAATATGTTA
52692670 AAAATGTTTTAATTAT-TATTTG
1 AAAATGTTTTAATTATATATTTG
*
52692692 AAAAT-TTTTTATTATAATATTTG
1 AAAATGTTTTAATTAT-ATATTTG
52692715 AA
1 AA
52692717 TTAACAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 5 0.23
23 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (23 bp):
AAAATGTTTTAATTATATATTTG
Found at i:52692712 original size:23 final size:24
Alignment explanation
Indices: 52692661--52692716 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
52692651 TTGTATGTTG
*
52692661 AATATGTTAAAAATGTTTTAATTAT
1 AATAT-TTGAAAATGTTTTAATTAT
*
52692686 --TATTTGAAAAT-TTTTTATTAT
1 AATATTTGAAAATGTTTTAATTAT
52692707 AATATTTGAA
1 AATATTTGAA
52692717 TTAACAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 9 0.33
22 7 0.26
23 11 0.41
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (24 bp):
AATATTTGAAAATGTTTTAATTAT
Found at i:52693098 original size:18 final size:18
Alignment explanation
Indices: 52693068--52693102 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
52693058 AAAATTGTGC
52693068 TAATTATAATTATAGTTA
1 TAATTATAATTATAGTTA
52693086 TAATT-TAATTTATAGTT
1 TAATTATAA-TTATAGTT
52693103 GTTAGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TAATTATAATTATAGTTA
Found at i:52695977 original size:116 final size:116
Alignment explanation
Indices: 52695772--52695986 Score: 349
Period size: 116 Copynumber: 1.9 Consensus size: 116
52695762 TTCGACTGTA
* * *
52695772 ACACCCTAAAACATAAGTTTGATTAAGCAACAAAATTAAGTACCAAATGGGCAACAACCTAATGA
1 ACACCCCAAAACATAAGTTCGATTAAGCAACAAAATTAAGTAACAAATGGGCAACAACCTAATGA
* *
52695837 TTAAGCTTTAGTCTCTCCCCCTTGCTTACCCAAGCGCCTTCCTCCCTTGTG
66 TTAAGCGTTAATCTCTCCCCCTTGCTTACCCAAGCGCCTTCCTCCCTTGTG
* * *
52695888 ACACCCCAAAACATAAGTTCGGTTAAGCGACAAAATTAAGTAAGAAATGGGCAACAACCTAATGA
1 ACACCCCAAAACATAAGTTCGATTAAGCAACAAAATTAAGTAACAAATGGGCAACAACCTAATGA
*
52695953 TTAAGCGTTAATCTCTCCCTCTTGCTTACCCAAG
66 TTAAGCGTTAATCTCTCCCCCTTGCTTACCCAAG
52695987 TTCGAGCCCC
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
116 90 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (116 bp):
ACACCCCAAAACATAAGTTCGATTAAGCAACAAAATTAAGTAACAAATGGGCAACAACCTAATGA
TTAAGCGTTAATCTCTCCCCCTTGCTTACCCAAGCGCCTTCCTCCCTTGTG
Found at i:52696620 original size:13 final size:13
Alignment explanation
Indices: 52696581--52696633 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
52696571 AATTTGGCAA
*
52696581 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
* * *
52696594 TACTGTGGAAAAG
1 TGCTTTTGAAAAG
*
52696607 TGCTTTTGATAAG
1 TGCTTTTGAAAAG
*
52696620 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
52696633 T
1 T
52696634 TTGATTTTAA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:52696911 original size:33 final size:35
Alignment explanation
Indices: 52696816--52696912 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
52696806 TTAATATTTT
*
52696816 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
52696851 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
52696884 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
52696913 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:52697122 original size:19 final size:19
Alignment explanation
Indices: 52697098--52697135 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52697088 AGCTTCACCC
*
52697098 TTTGAAAGGCTAAAAATTT
1 TTTGAAAAGCTAAAAATTT
52697117 TTTGAAAAGCTAAAAATTT
1 TTTGAAAAGCTAAAAATTT
52697136 CAGCTAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (19 bp):
TTTGAAAAGCTAAAAATTT
Found at i:52697144 original size:19 final size:19
Alignment explanation
Indices: 52697122--52697162 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
52697112 AATTTTTTGA
52697122 AAAGCTAAAAATTTCAGCT
1 AAAGCTAAAAATTTCAGCT
52697141 AAAGCTAAAAATTTCAGCT
1 AAAGCTAAAAATTTCAGCT
52697160 AAA
1 AAA
52697163 AGTAACTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (19 bp):
AAAGCTAAAAATTTCAGCT
Found at i:52702192 original size:14 final size:14
Alignment explanation
Indices: 52702173--52702221 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
52702163 AATTATGATT
52702173 TTAATATATTAAAA
1 TTAATATATTAAAA
*
52702187 TTAATAAATTAAATA
1 TTAATATATTAAA-A
52702202 TTAATAT-TTAAAA
1 TTAATATATTAAAA
52702215 TT-ATATA
1 TTAATATA
52702222 GAAGCTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 4 0.13
13 3 0.10
14 17 0.55
15 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAATATATTAAAA
Found at i:52702579 original size:25 final size:25
Alignment explanation
Indices: 52702529--52702581 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
52702519 AGAAATTATC
*
52702529 ATTATAAATTACAACTTTTTATAAA
1 ATTATAAATTACAACTTATTATAAA
*
52702554 ATTAT-AATTACAACATTAATTAAAAA
1 ATTATAAATTACAAC-TT-ATTATAAA
52702580 AT
1 AT
52702582 AACATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 7 0.29
26 8 0.33
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTATAAATTACAACTTATTATAAA
Found at i:52703086 original size:16 final size:16
Alignment explanation
Indices: 52703065--52703116 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
52703055 TTTGGTTCGC
*
52703065 TGTATTGGATTAGAGG
1 TGTATTGGAATAGAGG
52703081 TGTATTGGAATAGAGG
1 TGTATTGGAATAGAGG
*
52703097 TGTAATGGAATAGAGG
1 TGTATTGGAATAGAGG
52703113 TGTA
1 TGTA
52703117 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTATTGGAATAGAGG
Found at i:52703202 original size:39 final size:43
Alignment explanation
Indices: 52703097--52703206 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
52703087 GGAATAGAGG
52703097 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
52703142 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
52703182 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
52703207 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:52703372 original size:18 final size:17
Alignment explanation
Indices: 52703351--52703385 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52703341 TTATTATTAA
*
52703351 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52703369 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52703386 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52708034 original size:19 final size:21
Alignment explanation
Indices: 52708012--52708057 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
52708002 TATTTTTTGA
52708012 ATATTTTAATAATT-A-ATTT
1 ATATTTTAATAATTGATATTT
* *
52708031 ATATATTATTAATTGATATTT
1 ATATTTTAATAATTGATATTT
52708052 A-ATTTT
1 ATATTTT
52708058 TTTAAGAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.55
20 5 0.23
21 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATTTTAATAATTGATATTT
Found at i:52708175 original size:30 final size:29
Alignment explanation
Indices: 52708114--52708175 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
52708104 ATAAAACAAA
* *
52708114 CACTAAACTTTAAAAAGTTACAACTCAGT
1 CACTAAACTTTAAAAAATAACAACTCAGT
52708143 CACTAAACTTTAGAAAAATAACAAAC-CAGT
1 CACTAAACTTTA-AAAAATAAC-AACTCAGT
52708173 CAC
1 CAC
52708176 CAATAACCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 12 0.41
30 14 0.48
31 3 0.10
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (29 bp):
CACTAAACTTTAAAAAATAACAACTCAGT
Found at i:52708281 original size:3 final size:3
Alignment explanation
Indices: 52708273--52708309 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
52708263 GCTGGGCAGT
52708273 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
52708310 ATGGAGATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52709327 original size:30 final size:31
Alignment explanation
Indices: 52709263--52709327 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
52709253 ATATTAGTGG
*
52709263 GTGATTGATTTGTCACTTTTCAATAACGTTA
1 GTGATTGATTTGTCACTTTTCAATAAAGTTA
* *
52709294 GTGATTGATTTGTTA-TTTTC-CTAAAGTTGA
1 GTGATTGATTTGTCACTTTTCAATAAAGTT-A
52709324 GTGA
1 GTGA
52709328 CTACTAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 6 0.20
30 10 0.33
31 14 0.47
ACGTcount: A:0.25, C:0.09, G:0.20, T:0.46
Consensus pattern (31 bp):
GTGATTGATTTGTCACTTTTCAATAAAGTTA
Found at i:52713017 original size:20 final size:20
Alignment explanation
Indices: 52712992--52713067 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
52712982 AAATTTTAAC
52712992 TTTTTTAT-ATTTTTAAGAAT
1 TTTTTTATAATTTTT-AGAAT
52713012 TTTTTTAAATAATTTTT-GAA-
1 TTTTTT--ATAATTTTTAGAAT
*
52713032 ATTTTTATAAATATTTT-GAAT
1 TTTTTTAT-AAT-TTTTAGAAT
52713053 TTTTTTATAATTTTT
1 TTTTTTATAATTTTT
52713068 GTAATAGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.04
19 7 0.15
20 21 0.44
21 10 0.21
22 2 0.04
23 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTTTATAATTTTTAGAAT
Found at i:52713036 original size:21 final size:20
Alignment explanation
Indices: 52713012--52713068 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
52713002 TTTTAAGAAT
52713012 TTTTTTAAATAATTTTTGAAA
1 TTTTTTAAATAATTTTTG-AA
52713033 TTTTTATAAAT-A-TTTTGAA
1 TTTTT-TAAATAATTTTTGAA
*
52713052 TTTTTT-TATAATTTTTG
1 TTTTTTAAATAATTTTTG
52713069 TAATAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 12 0.38
20 5 0.16
21 6 0.19
22 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTTAAATAATTTTTGAA
Found at i:52713844 original size:106 final size:103
Alignment explanation
Indices: 52713662--52713870 Score: 373
Period size: 106 Copynumber: 2.0 Consensus size: 103
52713652 TTTTTCAATC
*
52713662 TCAAGCACACTTTCAATTAGTCTAGTTTCTTATTACGAGTAAAGATCAAACATCTAATCTTATTT
1 TCAAGCACACTTTCAATTAGTCTAGTTTCCTATTACGAGTAAAGATCAAACATCTAATCTTATTT
52713727 CTATAAGCAATCACCCCACCACACATACTTTCCTGATT
66 CTATAAGCAATCACCCCACCACACATACTTTCCTGATT
*
52713765 TCAAGCACACTTTCAATTAGTCTAGTTTCCTATTGCTACGAGTAAAGATCAAACTTCTAATCTTA
1 TCAAGCACACTTTCAATTAGTCTAGTTTCCTA-T--TACGAGTAAAGATCAAACATCTAATCTTA
52713830 TTTCTATAAGCAATCACCCCACCACACATACTTTCCTGATT
63 TTTCTATAAGCAATCACCCCACCACACATACTTTCCTGATT
52713871 CATACTTTTT
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
103 31 0.31
104 1 0.01
106 69 0.68
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (103 bp):
TCAAGCACACTTTCAATTAGTCTAGTTTCCTATTACGAGTAAAGATCAAACATCTAATCTTATTT
CTATAAGCAATCACCCCACCACACATACTTTCCTGATT
Found at i:52716324 original size:18 final size:18
Alignment explanation
Indices: 52716301--52716343 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
52716291 AGTTTAAGTG
52716301 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
52716319 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
52716337 TAATTAA
1 TAATTAA
52716344 AAATCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:52719549 original size:13 final size:13
Alignment explanation
Indices: 52719531--52719557 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52719521 GAAAAAATTC
52719531 AAATCAAGTTAGG
1 AAATCAAGTTAGG
52719544 AAATCAAGTTAGG
1 AAATCAAGTTAGG
52719557 A
1 A
52719558 TGATAAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
AAATCAAGTTAGG
Found at i:52723841 original size:35 final size:34
Alignment explanation
Indices: 52723788--52723871 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 34
52723778 TTTGTCTAAG
52723788 TATA-TATATAATTAATGAT-ACTAAAATATAATT
1 TATATTATATAATTAATGATAACTAAAATATAA-T
* * *
52723821 TATATTATATGAATTTATGATAATTAAATTATAAT
1 TATATTATAT-AATTAATGATAACTAAAATATAAT
* *
52723856 GATATTATATTATTAA
1 TATATTATATAATTAA
52723872 ATAAATTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
33 4 0.10
34 9 0.21
35 19 0.45
36 10 0.24
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (34 bp):
TATATTATATAATTAATGATAACTAAAATATAAT
Found at i:52723857 original size:25 final size:23
Alignment explanation
Indices: 52723813--52723873 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
52723803 TGATACTAAA
*
52723813 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
52723837 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
52723862 ATATTATTAAAT
1 ATATAATTAAAT
52723874 AAATTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:52724322 original size:12 final size:12
Alignment explanation
Indices: 52724290--52724330 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
52724280 AAAGTAAAAT
52724290 AAAAGAAACA-A
1 AAAAGAAACAGA
52724301 AAGAAG-AACAGA
1 AA-AAGAAACAGA
52724313 AAAAGAAACAGA
1 AAAAGAAACAGA
*
52724325 GAAAGA
1 AAAAGA
52724331 GACGAAACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAGAAACAGA
Found at i:52725124 original size:39 final size:40
Alignment explanation
Indices: 52725080--52725170 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 40
52725070 TGAATTATAG
* *
52725080 AATACTGAATATTGTTTTG-AGTACTG-AGTGAATTGTGAA
1 AATACTGAATATTGTTATGTA-TAATGTAGTGAATTGTGAA
*
52725119 AATACTGAATATTGTTATGTATAATGTATTGAATTGTGAA
1 AATACTGAATATTGTTATGTATAATGTAGTGAATTGTGAA
*
52725159 ATTACTGCAATA
1 AATACTG-AATA
52725171 CTGTGAAACT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 22 0.49
40 19 0.42
41 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (40 bp):
AATACTGAATATTGTTATGTATAATGTAGTGAATTGTGAA
Found at i:52725405 original size:39 final size:39
Alignment explanation
Indices: 52725353--52725439 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
52725343 ATGTGCCAAC
* * *
52725353 TACTGTTATTGTTACTGATTCGGTACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGATTCGGCACTTTGTATGTCGAA
52725392 TACTGTTACTGTTACTGATTCGGCACTTTGTATGTCGAA
1 TACTGTTACTGTTACTGATTCGGCACTTTGTATGTCGAA
52725431 TACTGTTAC
1 TACTGTTAC
52725440 CATTAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.44
Consensus pattern (39 bp):
TACTGTTACTGTTACTGATTCGGCACTTTGTATGTCGAA
Done.