Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 25
Found at i:3635215 original size:21 final size:20
Alignment explanation
Indices: 3635185--3635246 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
3635175 AATATCTATT
*
3635185 AAAATTATATCAAAAATTATC
1 AAAATCATAT-AAAAATTATC
* *
3635206 CAAATCATATATAAAATTATT
1 AAAATCATATA-AAAATTATC
3635227 AAAATCATATAAAAAATTAT
1 AAAATCATAT-AAAAATTAT
3635247 ATTATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATCATATAAAAATTATC
Found at i:3637289 original size:22 final size:21
Alignment explanation
Indices: 3637245--3637285 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3637235 TAATTTTTTT
*
3637245 TTTAATTTTTATATTATTAAA
1 TTTAACTTTTATATTATTAAA
3637266 TTTAACTTTTATATT-TTAAA
1 TTTAACTTTTATATTATTAAA
3637286 AATTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAACTTTTATATTATTAAA
Found at i:3637486 original size:18 final size:18
Alignment explanation
Indices: 3637453--3637502 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
3637443 ATATAATACG
* *
3637453 TTAATATTTATCAATAT-
1 TTAATATTTTTTAATATA
3637470 TTAAATATTTTTTAATATAA
1 TT-AATATTTTTTAATAT-A
3637490 TTAATATTTTTTA
1 TTAATATTTTTTA
3637503 TTTATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 13 0.46
19 11 0.39
20 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAATATTTTTTAATATA
Found at i:3637987 original size:38 final size:38
Alignment explanation
Indices: 3637936--3638014 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
3637926 CGTTTAGGTT
3637936 AAATATACAACATAAAATTATAATATTTGAAAAGTTTC
1 AAATATACAACATAAAATTATAATATTTGAAAAGTTTC
3637974 AAATATACAACATAAAATTATAATATTTGAAAAGTTTC
1 AAATATACAACATAAAATTATAATATTTGAAAAGTTTC
3638012 AAA
1 AAA
3638015 CTTGAACATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (38 bp):
AAATATACAACATAAAATTATAATATTTGAAAAGTTTC
Found at i:3643987 original size:24 final size:25
Alignment explanation
Indices: 3643960--3644029 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 25
3643950 TATAAATATA
3643960 ATAAATATTATTATAATTTT-AATT
1 ATAAATATTATTATAATTTTAAATT
* *
3643984 ATAAATATTTATAAAAAATTTTAAATT
1 ATAAATA-TTAT-TATAATTTTAAATT
*
3644011 ATTAAATAATAATTATAAT
1 A-TAAAT-ATTATTATAAT
3644030 ATAATATTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
24 7 0.19
25 4 0.11
26 7 0.19
27 9 0.25
28 8 0.22
29 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATAAATATTATTATAATTTTAAATT
Found at i:3654200 original size:79 final size:79
Alignment explanation
Indices: 3654069--3654229 Score: 286
Period size: 79 Copynumber: 2.0 Consensus size: 79
3654059 GCGTGAAGAG
* *
3654069 AAAAAAGAGTTTGCAGACCTTTACAATGGCATTAGAGGTCCAAGTCATTCACATCCGAGTTTCAT
1 AAAAAAGAGTTTGCAGACCTCTACAAGGGCATTAGAGGTCCAAGTCATTCACATCCGAGTTTCAT
*
3654134 GGAGCAGGGTTCTA
66 GGAGCAGGGTTCGA
*
3654148 AAAAAAGAGTTTGCAGACCTCTACAAGGGCATTAGAGGTCCCAGTCATTCACATCCGAGTTTCAT
1 AAAAAAGAGTTTGCAGACCTCTACAAGGGCATTAGAGGTCCAAGTCATTCACATCCGAGTTTCAT
3654213 GGAGCAGGGTTCGA
66 GGAGCAGGGTTCGA
3654227 AAA
1 AAA
3654230 TAACCATCGG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (79 bp):
AAAAAAGAGTTTGCAGACCTCTACAAGGGCATTAGAGGTCCAAGTCATTCACATCCGAGTTTCAT
GGAGCAGGGTTCGA
Found at i:3661479 original size:2 final size:2
Alignment explanation
Indices: 3661472--3661501 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3661462 CTTGCTTGTG
*
3661472 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3661502 TATTTAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3666869 original size:4 final size:4
Alignment explanation
Indices: 3666860--3666894 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3666850 GACGGCTCCA
3666860 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3666895 CAAACAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3666911 original size:8 final size:8
Alignment explanation
Indices: 3666864--3666911 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
3666854 GCTCCAAAAT
*
3666864 AAATAAAT
1 AAATAAAC
*
3666872 AAATAAAT
1 AAATAAAC
*
3666880 AAATAAAT
1 AAATAAAC
3666888 AAATAAAC
1 AAATAAAC
*
3666896 AAACAAAC
1 AAATAAAC
*
3666904 ACATAAAC
1 AAATAAAC
3666912 GATCTTTCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (8 bp):
AAATAAAC
Found at i:3678012 original size:2 final size:2
Alignment explanation
Indices: 3678005--3678035 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3677995 TTTCTCGTCA
3678005 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3678036 TCCCCCGCGA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3679880 original size:17 final size:17
Alignment explanation
Indices: 3679849--3679883 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3679839 GTTATAAATT
3679849 TATAAATTTATTATTAA
1 TATAAATTTATTATTAA
3679866 TATAATATTTA-TATTAA
1 TATAA-ATTTATTATTAA
3679883 T
1 T
3679884 TTTATGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATAAATTTATTATTAA
Found at i:3682241 original size:23 final size:22
Alignment explanation
Indices: 3682215--3682265 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3682205 ATTTTTTTTT
3682215 ATAAAATATGATAACTTTTAATC
1 ATAAAA-ATGATAACTTTTAATC
* **
3682238 ATAAAAATTATATTTTTTAATC
1 ATAAAAATGATAACTTTTAATC
3682260 -TAAAAA
1 ATAAAAA
3682266 ATATAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.24
22 13 0.52
23 6 0.24
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (22 bp):
ATAAAAATGATAACTTTTAATC
Found at i:3682263 original size:21 final size:22
Alignment explanation
Indices: 3682215--3682276 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
3682205 ATTTTTTTTT
* *
3682215 ATAAAATATGATAACTTTTAATC
1 ATAAAAAAT-ATAATTTTTAATC
* *
3682238 ATAAAAATTATATTTTTTAATC
1 ATAAAAAATATAATTTTTAATC
3682260 -TAAAAAATATAATTTTT
1 ATAAAAAATATAATTTTT
3682277 CATTTAACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.45
22 11 0.33
23 7 0.21
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAAAAAATATAATTTTTAATC
Found at i:3687407 original size:40 final size:40
Alignment explanation
Indices: 3687352--3687433 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
3687342 AATGCACATC
*
3687352 GTAGAAGTCATGTAACCTTTCATTATTATAAAAGGAAAGA
1 GTAGAAGTCATGTAACCTTTCATTATTATAAAAGAAAAGA
3687392 GTAGAAGTCATGTAACCTTTCATTATTATAAAAGAAAAGA
1 GTAGAAGTCATGTAACCTTTCATTATTATAAAAGAAAAGA
3687432 GT
1 GT
3687434 GGACACGTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (40 bp):
GTAGAAGTCATGTAACCTTTCATTATTATAAAAGAAAAGA
Found at i:3691746 original size:6 final size:6
Alignment explanation
Indices: 3691731--3691770 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
3691721 CCAGGTTTTG
*
3691731 CCTCCA CCTCCG CCTCCA CCTCCA CCTCCA CCTCCA CCTC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTC
3691771 TATTAATCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.12, C:0.68, G:0.03, T:0.17
Consensus pattern (6 bp):
CCTCCA
Found at i:3710862 original size:26 final size:28
Alignment explanation
Indices: 3710823--3710885 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
3710813 ACCAACTCTT
*
3710823 AAAT-AATGTATTTA-TTTA-TTTTAAA
1 AAATAAATTTATTTATTTTATTTTTAAA
3710848 AAATAAATTTATTTATTTTATTTTTAAA
1 AAATAAATTTATTTATTTTATTTTTAAA
* *
3710876 TAATATATTT
1 AAATAAATTT
3710886 TAAAAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.12
26 9 0.28
27 4 0.12
28 15 0.47
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
AAATAAATTTATTTATTTTATTTTTAAA
Found at i:3711491 original size:2 final size:2
Alignment explanation
Indices: 3711484--3711509 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3711474 TCAGTTAACA
3711484 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
3711510 GCTCGCTCGC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3713890 original size:24 final size:24
Alignment explanation
Indices: 3713858--3713905 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3713848 TAGTGTACAT
3713858 GGACTTTTCTCAATAGAAATAATA
1 GGACTTTTCTCAATAGAAATAATA
*
3713882 GGACTTTTCTCAGTAGAAATAATA
1 GGACTTTTCTCAATAGAAATAATA
3713906 AGGTATAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (24 bp):
GGACTTTTCTCAATAGAAATAATA
Found at i:3720109 original size:22 final size:22
Alignment explanation
Indices: 3720084--3720140 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
3720074 CTAAAAAAAT
3720084 TTAAATATAAAATTTAATTTAA
1 TTAAATATAAAATTTAATTTAA
* *
3720106 TT-AATTTATATATTTAATTTAA
1 TTAAATATA-AAATTTAATTTAA
3720128 --AAATAATAAAATT
1 TTAAAT-ATAAAATT
3720141 CAAACCTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATATAAAATTTAATTTAA
Found at i:3720696 original size:18 final size:18
Alignment explanation
Indices: 3720673--3720712 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3720663 TTGACATGCA
3720673 TTGCTT-TGCCCTTTGCTT
1 TTGCTTGTG-CCTTTGCTT
*
3720691 TTGCTTGTGCTTTTGCTT
1 TTGCTTGTGCCTTTGCTT
3720709 TTGC
1 TTGC
3720713 CTGCCTTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.00, C:0.23, G:0.20, T:0.57
Consensus pattern (18 bp):
TTGCTTGTGCCTTTGCTT
Found at i:3721255 original size:3 final size:3
Alignment explanation
Indices: 3721247--3721281 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3721237 TCGTCAAATT
3721247 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3721282 GTTCATTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3721427 original size:18 final size:20
Alignment explanation
Indices: 3721394--3721433 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3721384 GTGAACTATC
*
3721394 AATTTGTATTAAAAA-TTAA
1 AATTTGTATGAAAAATTTAA
3721413 AATTT-TATGAAAAATTTAA
1 AATTTGTATGAAAAATTTAA
3721432 AA
1 AA
3721434 AAAATTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
AATTTGTATGAAAAATTTAA
Found at i:3724746 original size:20 final size:20
Alignment explanation
Indices: 3724723--3724771 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
3724713 CTGGACATGT
*
3724723 TAAATATGCATGAAACATAA
1 TAAAAATGCATGAAACATAA
3724743 TAAAAAAAATGCATGAAACATAA
1 T---AAAAATGCATGAAACATAA
3724766 TAAAAA
1 TAAAAA
3724772 AAATGCATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 6 0.24
23 19 0.76
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.20
Consensus pattern (20 bp):
TAAAAATGCATGAAACATAA
Found at i:3724758 original size:23 final size:23
Alignment explanation
Indices: 3724728--3724780 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
3724718 CATGTTAAAT
3724728 ATGCATGAAACATAATAAAAAAA
1 ATGCATGAAACATAATAAAAAAA
3724751 ATGCATGAAACATAATAAAAAAA
1 ATGCATGAAACATAATAAAAAAA
3724774 ATGCATG
1 ATGCATG
3724781 GTCAAAGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.19
Consensus pattern (23 bp):
ATGCATGAAACATAATAAAAAAA
Found at i:3725736 original size:20 final size:20
Alignment explanation
Indices: 3725689--3725763 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
3725679 AAAAAGACAT
*
3725689 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3725708 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3725729 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
3725749 AATGTATTGATACAT
1 AATGTATCGATACAT
3725764 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3725761 original size:40 final size:39
Alignment explanation
Indices: 3725686--3725763 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
3725676 GGTAAAAAGA
* *
3725686 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
3725725 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3725764 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3726478 original size:28 final size:28
Alignment explanation
Indices: 3726425--3727420 Score: 1034
Period size: 28 Copynumber: 35.0 Consensus size: 28
3726415 TTTAAAAATG
*
3726425 TGCCACTAACTTGCGTGGGCTTTGAAAGGA
1 TGCCACTGACTT--GTGGGCTTTGAAAGGA
3726455 TGCCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
3726482 GTGCCACTGACTCGTGGGCTTTGAAA-GA
1 -TGCCACTGACTTGTGGGCTTTGAAAGGA
*
3726510 GTGCCACTGACTCGTGGGCTTTGAAAAAGG-
1 -TGCCACTGACTTGTGGGCTTTG--AAAGGA
*
3726540 TGCCACTGACTCGTGGGCTTTGAAAAGG-
1 TGCCACTGACTTGTGGGCTTTG-AAAGGA
* *
3726568 TGCCACTGACTTGCGTGGGCTTTAAAAGGG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGA
* * *
3726598 TGCCACTAACTGGCGTGGGCTTTGAAAAGA
1 TGCCACTGACT--TGTGGGCTTTGAAAGGA
3726628 TGCCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
3726655 GTGCCACTGACTCGTGGGCTTTGAAAAGG-
1 -TGCCACTGACTTGTGGGCTTTG-AAAGGA
* * *
3726684 TGCCACTGACTCGTAGGC-TTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
3726711 TGCCACTGACTCGTGGGCTTTAAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
3726739 GTGCCACTGACTTGTGTGGGCTTTGAAAGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAAGGA
*
3726770 TGCCACTGACTTGTGGGCTTT-AAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * *
3726797 GTGCCACTAAATTGTGGGCTTCGCAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
3726826 TGCCACTGACTTGTGGGCTCTAAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
3726854 GTGCCACTGACTTGTGTGGGCTTTGAAAGGG
1 -TGCCACTGAC-T-TGTGGGCTTTGAAAGGA
3726885 TGCCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * *
3726912 GTGCCATTGAATTGTGGGCTTCGCAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
3726941 TGCCACTGACTTGTGGGCTTCGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
3726969 TGCCACTCACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * *
3726996 GTGCCACTGAATTATGGGCTTCGTAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGGA
3727025 TGCCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
3727052 GTGCCACTGACTCGTGGGCTTTGAAAAGG-
1 -TGCCACTGACTTGTGGGCTTTG-AAAGGA
*
3727081 TGCCACTGACTCGTGGGCTTTGAAAAGG-
1 TGCCACTGACTTGTGGGCTTTG-AAAGGA
* *
3727109 TGCCACTGACTTGCGTGGGCTTTAAAAGGG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGA
3727139 TGCCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
3727166 GTGCCACTGAATTGTGGGCTTCGCAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
3727195 TGCCACTGACTTGTGGGCTTCGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
3727223 TGTCACTAACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
3727250 GTGCCACTGAATTATAGGCTTTGAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGGA
3727279 TGCCACTGACTTGTGGGCTTTGAAATGG-
1 TGCCACTGACTTGTGGGCTTTGAAA-GGA
* *
3727307 TGCCACTGACTTGTGGGCTTTAAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
3727335 GTGTCACTGATTTGTGGGCTTTGAAAAGA
1 -TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
3727364 GTGCCATTGTCTTGTGGGCTTTGAAAGGA
1 -TGCCACTGACTTGTGGGCTTTGAAAGGA
3727393 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 -TGCCACTGACTTGTGGGCTTTGAAAGG
3727421 GATGAACATT
Statistics
Matches: 831, Mismatches: 96, Indels: 79
0.83 0.10 0.08
Matches are distributed among these distances:
26 5 0.01
27 34 0.04
28 518 0.62
29 144 0.17
30 101 0.12
31 29 0.03
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.27
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:3726515 original size:56 final size:56
Alignment explanation
Indices: 3726377--3727419 Score: 1195
Period size: 56 Copynumber: 18.3 Consensus size: 56
3726367 CACTGACACG
** * * *
3726377 TGTGGGCTTTGAATAGAGTGTTACTAACTTGCGTGGGCTTT-AAAAATGTGCCACTAACT
1 TGTGGGCTTTGAA-AGAGTGCCACTGACTT--GTGGGCTTTGAAAGA-GTGCCACTGACT
3726436 TGCGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
1 T--GTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
3726494 CGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACT
* * * *
3726551 CGTGGGCTTTGAAA-AGGTGCCACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGA-GTGCCACTGACTT--GTGGGCTTTGAAAGAGTGCCACTGACT
*
3726609 GGCGTGGGCTTTGAAA-AGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
1 --TGTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
3726667 CGTGGGCTTTGAAA-AGGTGCCACTGACTCGTAGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
3726722 CGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * * *
3726781 TGTGGGCTTTAAAAGAGTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
3726837 TGTGGGCTCTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * *
3726896 TGTGGGCTTTGAAAGAGTGCCATTGAATTGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
3726952 TGTGGGCTTCGAAAGGGTGCCACTCACTTGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
3727008 TATGGGCTTCGTAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* *
3727064 CGTGGGCTTTGAAA-AGGTGCCACTGACTCGTGGGCTTTGAAA-AGGTGCCACTGACT
1 TGTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACT
* * *
3727120 TGCGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGAAT
1 T--GTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * * * *
3727178 TGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGTCACTAACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
3727234 TGTGGGCTTTGAAAGAGTGCCACTGAATTATAGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
3727290 TGTGGGCTTTGAAATG-GTGCCACTGACTTGTGGGCTTTAAAAAGAGTGTCACTGATT
1 TGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTT-GAAAGAGTGCCACTGACT
* *
3727347 TGTGGGCTTTGAAAAGAGTGCCATTGTCTTGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACT
3727405 TGTGGGCTTTGAAAG
1 TGTGGGCTTTGAAAG
3727420 GGATGAACAT
Statistics
Matches: 861, Mismatches: 91, Indels: 66
0.85 0.09 0.06
Matches are distributed among these distances:
55 33 0.04
56 420 0.49
57 89 0.10
58 178 0.21
59 91 0.11
60 38 0.04
61 12 0.01
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.28
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
Found at i:3726981 original size:84 final size:84
Alignment explanation
Indices: 3726377--3727419 Score: 1282
Period size: 84 Copynumber: 12.2 Consensus size: 84
3726367 CACTGACACG
** * * ** *
3726377 TGTGGGCTTTGAATAGAGTGTTACTAACTTGCGTGGGCTTTAAAAATGTGCCACTAACTTGCGTG
1 TGTGGGCTTTGAA-AGAGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACTT--GTG
*
3726442 GGCTTTGAAAGGATGCCACTGACT
61 GGCTTTGAAAGGGTGCCACTGACT
* * *
3726466 TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
*
3726531 TGAAAAAGGTGCCACTGACT
66 TG-AAAGGGTGCCACTGACT
* * * *
3726551 CGTGGGCTTTGAAA-AGGTGCCACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTAACTGGCGTG
1 TGTGGGCTTTGAAAGA-GTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACT--TGTG
* *
3726615 GGCTTTGAAAAGATGCCACTGACT
61 GGCTTTGAAAGGGTGCCACTGACT
* * * *
3726639 TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTCGTAGGC-T
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
3726703 TGAAAGGGTGCCACTGACT
66 TGAAAGGGTGCCACTGACT
* *
3726722 CGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
1 TGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
* * * *
3726787 CTTTAAAAGAGTGCCACTAAAT
63 CTTTGAAAGGGTGCCACTGACT
* * * * *
3726809 TGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCCACTGACTTGTGTGGG
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGAC-T-TGTGGG
3726874 CTTTGAAAGGGTGCCACTGACT
63 CTTTGAAAGGGTGCCACTGACT
* * * *
3726896 TGTGGGCTTTGAAAGAGTGCCATTGAATTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
* *
3726961 CGAAAGGGTGCCACTCACT
66 TGAAAGGGTGCCACTGACT
* * * *
3726980 TGTGGGCTTTGAAAGAGTGCCACTGAATTATGGGCTTCGTAAGGGTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
*
3727045 TGAAAGAGTGCCACTGACT
66 TGAAAGGGTGCCACTGACT
* * *
3727064 CGTGGGCTTTGAAA-AGGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGG
1 TGTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGG
*
3727128 CTTTAAAAGGGTGCCACTGACT
63 CTTTGAAAGGGTGCCACTGACT
* * *
3727150 TGTGGGCTTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
* * *
3727215 CGAAAGGGTGTCACTAACT
66 TGAAAGGGTGCCACTGACT
* * *
3727234 TGTGGGCTTTGAAAGAGTGCCACTGAATTATAGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
*
3727299 TGAAATGGTGCCACTGACT
66 TGAAAGGGTGCCACTGACT
* * * * * *
3727318 TGTGGGCTTTAAAAAGAGTGTCACTGATTTGTGGGCTTTGAAAAGAGTGCCATTGTCTTGTGGGC
1 TGTGGGCTTT-GAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
3727383 TTTGAAAGGAGTGCCACTGACT
64 TTTGAAAGG-GTGCCACTGACT
3727405 TGTGGGCTTTGAAAG
1 TGTGGGCTTTGAAAG
3727420 GGATGAACAT
Statistics
Matches: 833, Mismatches: 100, Indels: 45
0.85 0.10 0.05
Matches are distributed among these distances:
83 31 0.04
84 305 0.37
85 78 0.09
86 209 0.25
87 132 0.16
88 53 0.06
89 25 0.03
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.28
Consensus pattern (84 bp):
TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
TGAAAGGGTGCCACTGACT
Found at i:3728382 original size:23 final size:24
Alignment explanation
Indices: 3728356--3728407 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
3728346 GTTATTTTGC
*
3728356 TTTTGCACTTTTTCTTTTCA-TTT
1 TTTTGCACTTTTGCTTTTCACTTT
** *
3728379 TTTTGTGCTTTTGCTTTTGACTTT
1 TTTTGCACTTTTGCTTTTCACTTT
3728403 TTTTG
1 TTTTG
3728408 TCATTTAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.06, C:0.13, G:0.12, T:0.69
Consensus pattern (24 bp):
TTTTGCACTTTTGCTTTTCACTTT
Found at i:3728383 original size:37 final size:35
Alignment explanation
Indices: 3728342--3728413 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 35
3728332 TGTTGTTTCC
* *
3728342 TTTTGTTATTTTGCTTTTGCACTTTTTCTTTTCATTT
1 TTTTGTGATTTTGCTTTTG-ACTTTTT-TTGTCATTT
*
3728379 TTTTGTGCTTTTGCTTTTGACTTTTTTTGTCATTT
1 TTTTGTGATTTTGCTTTTGACTTTTTTTGTCATTT
3728414 AAAGGTAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 8 0.25
36 7 0.22
37 17 0.53
ACGTcount: A:0.07, C:0.12, G:0.11, T:0.69
Consensus pattern (35 bp):
TTTTGTGATTTTGCTTTTGACTTTTTTTGTCATTT
Found at i:3728408 original size:24 final size:23
Alignment explanation
Indices: 3728363--3728408 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3728353 TGCTTTTGCA
*
3728363 CTTTTTCTTTTCATTTTTTTGTG
1 CTTTTGCTTTTCATTTTTTTGTG
*
3728386 CTTTTGCTTTTGACTTTTTTTGT
1 CTTTTGCTTTTCA-TTTTTTTGT
3728409 CATTTAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.04, C:0.13, G:0.11, T:0.72
Consensus pattern (23 bp):
CTTTTGCTTTTCATTTTTTTGTG
Found at i:3734575 original size:23 final size:22
Alignment explanation
Indices: 3734520--3734568 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
3734510 TGGACATGTT
3734520 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
3734542 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
3734564 AAAAA
1 AAAAA
3734569 ATACATGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:3735531 original size:20 final size:20
Alignment explanation
Indices: 3735484--3735558 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
3735474 AAAAAGACAT
*
3735484 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3735503 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3735524 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
3735544 AATGTATCGATACAT
1 AATGTATCGATACAT
3735559 CAGGGTATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3735552 original size:40 final size:39
Alignment explanation
Indices: 3735481--3735558 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3735471 GGTAAAAAGA
* *
3735481 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
3735520 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3735559 CAGGGTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3740738 original size:18 final size:20
Alignment explanation
Indices: 3740717--3740756 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
3740707 AAAATTTATA
3740717 TTATATT-TAATAT-TATTT
1 TTATATTATAATATATATTT
*
3740735 TTATATTATATTATATATTT
1 TTATATTATAATATATATTT
3740755 TT
1 TT
3740757 TAAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATATTATAATATATATTT
Found at i:3740751 original size:12 final size:11
Alignment explanation
Indices: 3740710--3740753 Score: 61
Period size: 12 Copynumber: 3.8 Consensus size: 11
3740700 AAATTTTAAA
3740710 ATTTATATTAT
1 ATTTATATTAT
3740721 ATTTAATATTAT
1 ATTT-ATATTAT
*
3740733 TTTTATATTAT
1 ATTTATATTAT
3740744 ATTATATATT
1 ATT-TATATT
3740754 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 13 0.45
12 16 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:3740752 original size:23 final size:22
Alignment explanation
Indices: 3740711--3740757 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
3740701 AATTTTAAAA
3740711 TTTATATTATATTTAATATTATT
1 TTTATATTATATTTAATATT-TT
3740734 TTTATATTATA-TTATATATTTT
1 TTTATATTATATTTA-ATATTTT
3740756 TT
1 TT
3740758 AAAATTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATATTATATTTAATATTTT
Found at i:3741746 original size:23 final size:24
Alignment explanation
Indices: 3741691--3741750 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
3741681 AGATAAAAAC
3741691 ATAATATATTT-AATAAAAATAAT
1 ATAATATATTTAAATAAAAATAAT
* *
3741714 ATAATATATTTAAATATAATTAAT
1 ATAATATATTTAAATAAAAATAAT
*
3741738 GTAAT-TA-TTAAAT
1 ATAATATATTTAAAT
3741751 TTATTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.18
23 13 0.39
24 14 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAATATATTTAAATAAAAATAAT
Found at i:3742161 original size:4 final size:4
Alignment explanation
Indices: 3742154--3742188 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3742144 CATCCACTCT
3742154 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3742189 TCATTATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3743357 original size:6 final size:6
Alignment explanation
Indices: 3743346--3743374 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3743336 CAAAGTAAAT
3743346 AATATA AATATA AATATA AATAT- AATATA
1 AATATA AATATA AATATA AATATA AATATA
3743375 GTTTGAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:3744046 original size:20 final size:18
Alignment explanation
Indices: 3743974--3744037 Score: 51
Period size: 20 Copynumber: 3.4 Consensus size: 18
3743964 TAAAAAAATT
3743974 ATATAAATATAATATGTA
1 ATATAAATATAATATGTA
* *
3743992 A-A-AAATAATTAAAATATA
1 ATATAAAT-A-TAATATGTA
*
3744010 ATATAACATAGATATATGTA
1 ATATAA-ATATA-ATATGTA
3744030 ATATAAAT
1 ATATAAAT
3744038 TATTAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
16 4 0.11
17 2 0.06
18 9 0.26
19 4 0.11
20 14 0.40
21 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (18 bp):
ATATAAATATAATATGTA
Found at i:3744071 original size:11 final size:11
Alignment explanation
Indices: 3743974--3744071 Score: 51
Period size: 11 Copynumber: 8.5 Consensus size: 11
3743964 TAAAAAAATT
3743974 ATATAAATATA
1 ATATAAATATA
*
3743985 ATATGTAAAAAATA
1 ATA--T-AAATATA
3743999 AT-TAAAATATA
1 ATAT-AAATATA
*
3744010 ATATAACATA-G
1 ATATAA-ATATA
*
3744021 ATAT--ATGTA
1 ATATAAATATA
3744030 ATATAAATTATTA
1 ATATAAA-TA-TA
*
3744043 ATATATTAAAATA
1 ATATA--AATATA
3744056 ATATAAATATA
1 ATATAAATATA
3744067 ATATA
1 ATATA
3744072 TTTTAAATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
8 2 0.03
9 4 0.06
11 30 0.45
12 5 0.07
13 15 0.22
14 9 0.13
15 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (11 bp):
ATATAAATATA
Found at i:3748094 original size:22 final size:22
Alignment explanation
Indices: 3748064--3748107 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
3748054 TTCTTTTTTT
*
3748064 ATTTTTTTAATATTTCAAAATTG
1 ATTTTTTAAATATTT-AAAATTG
3748087 ATTTTTTAAATATTTAAAATT
1 ATTTTTTAAATATTTAAAATT
3748108 TTTTCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTTTTAAATATTTAAAATTG
Found at i:3748558 original size:22 final size:20
Alignment explanation
Indices: 3748526--3748592 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 20
3748516 ATATAATATT
3748526 TTTAAAA-TAATAATATAAAAA
1 TTTAAAATTAATAA-A-AAAAA
3748547 TTTAAAATTAATCAAAAAATAAA
1 TTTAAAATTAAT--AAAAA-AAA
3748570 TTT-AAATTAA-AAAAAAAA
1 TTTAAAATTAATAAAAAAAA
3748588 TTTAA
1 TTTAA
3748593 CCCGAACCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
18 6 0.15
19 6 0.15
21 7 0.17
22 13 0.32
23 7 0.17
24 2 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTAAAATTAATAAAAAAAA
Found at i:3748569 original size:17 final size:18
Alignment explanation
Indices: 3748549--3748589 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3748539 TATAAAAATT
3748549 TAAAATT-AATCAAAAAA
1 TAAAATTAAATCAAAAAA
* *
3748566 TAAATTTAAATTAAAAAA
1 TAAAATTAAATCAAAAAA
3748584 -AAAATT
1 TAAAATT
3748590 TAACCCGAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATTAAATCAAAAAA
Found at i:3749246 original size:15 final size:15
Alignment explanation
Indices: 3749225--3749262 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3749215 ACTCTGATGT
*
3749225 TTTCTTTTTCT-TTC
1 TTTCTTTTTATGTTC
3749239 TTTACTTTTTATGTTC
1 TTT-CTTTTTATGTTC
3749255 TTTCTTTT
1 TTTCTTTT
3749263 ATCATGCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 12 0.57
16 6 0.29
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTCTTTTTATGTTC
Found at i:3751833 original size:28 final size:28
Alignment explanation
Indices: 3751793--3751849 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
3751783 CTCTTCTTTG
3751793 TGTCTTTGAGATTAGGGTGGCAGTTGGT
1 TGTCTTTGAGATTAGGGTGGCAGTTGGT
*
3751821 TGTCTTTGAGATTAGGGTGGCGGTTGGT
1 TGTCTTTGAGATTAGGGTGGCAGTTGGT
3751849 T
1 T
3751850 TACTGGCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.12, C:0.07, G:0.40, T:0.40
Consensus pattern (28 bp):
TGTCTTTGAGATTAGGGTGGCAGTTGGT
Found at i:3755848 original size:2 final size:2
Alignment explanation
Indices: 3755841--3755869 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3755831 GGAAGCATGT
3755841 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3755870 ACATATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3767952 original size:3 final size:3
Alignment explanation
Indices: 3767946--3767976 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3767936 TAAAAAAAAG
*
3767946 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3767977 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3772647 original size:14 final size:15
Alignment explanation
Indices: 3772622--3772650 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3772612 ATATTAATAA
3772622 AAAATATTTTATATT
1 AAAATATTTTATATT
3772637 AAAAT-TTTTATATT
1 AAAATATTTTATATT
3772651 TTATTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAAATATTTTATATT
Found at i:3778879 original size:33 final size:33
Alignment explanation
Indices: 3778837--3778905 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
3778827 AAGCTTGTGA
3778837 CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
1 CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
3778870 CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
1 CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
3778903 CAT
1 CAT
3778906 CGATACTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (33 bp):
CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
Found at i:3779709 original size:33 final size:33
Alignment explanation
Indices: 3779667--3779735 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
3779657 AAGCTTGTGA
3779667 CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
1 CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
3779700 CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
1 CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
3779733 CAT
1 CAT
3779736 CGATACTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (33 bp):
CATATCTTGATCTGGAACTGGGGTAGCCTCCCT
Found at i:3779898 original size:830 final size:830
Alignment explanation
Indices: 3778300--3779940 Score: 3282
Period size: 830 Copynumber: 2.0 Consensus size: 830
3778290 ATATTTGTTC
3778300 TTTTGAATAGTGGGAAAGTTGGCATATTTGCAAAAGCAAATCACATGATGTTTAACAGGAAGTAT
1 TTTTGAATAGTGGGAAAGTTGGCATATTTGCAAAAGCAAATCACATGATGTTTAACAGGAAGTAT
3778365 TGGCGGCATGCTGTAGAACTGATGCAGCGCATGCTGGTGTAAGCTTGCAAAGAAAATGGGTGATG
66 TGGCGGCATGCTGTAGAACTGATGCAGCGCATGCTGGTGTAAGCTTGCAAAGAAAATGGGTGATG
3778430 CTCCTCCTGCACATACTTTCTATGGTCAATCAACAGTGATATTTACAGGTTTGAGAGTGAGGAGA
131 CTCCTCCTGCACATACTTTCTATGGTCAATCAACAGTGATATTTACAGGTTTGAGAGTGAGGAGA
3778495 GCACCCATTGCAGTTGCCAGGAGCTGCATCATCTCATATGGACCGAGGAGGCCTCTTTGTGGATC
196 GCACCCATTGCAGTTGCCAGGAGCTGCATCATCTCATATGGACCGAGGAGGCCTCTTTGTGGATC
3778560 AAGAGGCATAGCTTGATGATCACTGAAGATGGTTAATTGAATCTGATGTGCTAGAAAAGGTAATT
261 AAGAGGCATAGCTTGATGATCACTGAAGATGGTTAATTGAATCTGATGTGCTAGAAAAGGTAATT
3778625 AGAAGCGCACATTTGCAGTAAAAGGTAGTTGTTCATCTGCACTGTGGTGGTGTCTGGAGTAGATC
326 AGAAGCGCACATTTGCAGTAAAAGGTAGTTGTTCATCTGCACTGTGGTGGTGTCTGGAGTAGATC
3778690 AACAATGTTGTGAAGCCATCATGGGTTGGTTCAGTTGCTCAACTACTGATTAGCACCTTGGCAAG
391 AACAATGTTGTGAAGCCATCATGGGTTGGTTCAGTTGCTCAACTACTGATTAGCACCTTGGCAAG
3778755 TACCAAGATTTGAGACTCATCAATAATCTCCCTTGATGGGTAATCTGTAAGTATTACTATTAACC
456 TACCAAGATTTGAGACTCATCAATAATCTCCCTTGATGGGTAATCTGTAAGTATTACTATTAACC
3778820 TTATTTGAAGCTTGTGACATATCTTGATCTGGAACTGGGGTAGCCTCCCTCATATCTTGATCTGG
521 TTATTTGAAGCTTGTGACATATCTTGATCTGGAACTGGGGTAGCCTCCCTCATATCTTGATCTGG
3778885 AACTGGGGTAGCCTCCCTCATCGATACTTTTTGGTATCAAACAATATTTTGAAACAACTGTCTTA
586 AACTGGGGTAGCCTCCCTCATCGATACTTTTTGGTATCAAACAATATTTTGAAACAACTGTCTTA
3778950 AACGTGAATTGAAAGGTCTAATGTCCATCTGATATCTATGTTGGAGCAGTTGGTGTAGAAATCAA
651 AACGTGAATTGAAAGGTCTAATGTCCATCTGATATCTATGTTGGAGCAGTTGGTGTAGAAATCAA
3779015 TTTGCTTAGGATCATAGGTGTAAATAGAATGAACTAAGTGTGGTTTGTCATATGGGACTCATGAA
716 TTTGCTTAGGATCATAGGTGTAAATAGAATGAACTAAGTGTGGTTTGTCATATGGGACTCATGAA
3779080 TTTTATTTTAATGGCAAAAGATGTCAGGATGTCAGGATGAACCACCAATA
781 TTTTATTTTAATGGCAAAAGATGTCAGGATGTCAGGATGAACCACCAATA
3779130 TTTTGAATAGTGGGAAAGTTGGCATATTTGCAAAAGCAAATCACATGATGTTTAACAGGAAGTAT
1 TTTTGAATAGTGGGAAAGTTGGCATATTTGCAAAAGCAAATCACATGATGTTTAACAGGAAGTAT
3779195 TGGCGGCATGCTGTAGAACTGATGCAGCGCATGCTGGTGTAAGCTTGCAAAGAAAATGGGTGATG
66 TGGCGGCATGCTGTAGAACTGATGCAGCGCATGCTGGTGTAAGCTTGCAAAGAAAATGGGTGATG
3779260 CTCCTCCTGCACATACTTTCTATGGTCAATCAACAGTGATATTTACAGGTTTGAGAGTGAGGAGA
131 CTCCTCCTGCACATACTTTCTATGGTCAATCAACAGTGATATTTACAGGTTTGAGAGTGAGGAGA
3779325 GCACCCATTGCAGTTGCCAGGAGCTGCATCATCTCATATGGACCGAGGAGGCCTCTTTGTGGATC
196 GCACCCATTGCAGTTGCCAGGAGCTGCATCATCTCATATGGACCGAGGAGGCCTCTTTGTGGATC
3779390 AAGAGGCATAGCTTGATGATCACTGAAGATGGTTAATTGAATCTGATGTGCTAGAAAAGGTAATT
261 AAGAGGCATAGCTTGATGATCACTGAAGATGGTTAATTGAATCTGATGTGCTAGAAAAGGTAATT
3779455 AGAAGCGCACATTTGCAGTAAAAGGTAGTTGTTCATCTGCACTGTGGTGGTGTCTGGAGTAGATC
326 AGAAGCGCACATTTGCAGTAAAAGGTAGTTGTTCATCTGCACTGTGGTGGTGTCTGGAGTAGATC
3779520 AACAATGTTGTGAAGCCATCATGGGTTGGTTCAGTTGCTCAACTACTGATTAGCACCTTGGCAAG
391 AACAATGTTGTGAAGCCATCATGGGTTGGTTCAGTTGCTCAACTACTGATTAGCACCTTGGCAAG
3779585 TACCAAGATTTGAGACTCATCAATAATCTCCCTTGATGGGTAATCTGTAAGTATTACTATTAACC
456 TACCAAGATTTGAGACTCATCAATAATCTCCCTTGATGGGTAATCTGTAAGTATTACTATTAACC
3779650 TTATTTGAAGCTTGTGACATATCTTGATCTGGAACTGGGGTAGCCTCCCTCATATCTTGATCTGG
521 TTATTTGAAGCTTGTGACATATCTTGATCTGGAACTGGGGTAGCCTCCCTCATATCTTGATCTGG
3779715 AACTGGGGTAGCCTCCCTCATCGATACTTTTTGGTATCAAACAATATTTTGAAACAACTGTCTTA
586 AACTGGGGTAGCCTCCCTCATCGATACTTTTTGGTATCAAACAATATTTTGAAACAACTGTCTTA
3779780 AACGTGAATTGAAAGGTCTAATGTCCATCTGATATCTATGTTGGAGCAGTTGGTGTAGAAATCAA
651 AACGTGAATTGAAAGGTCTAATGTCCATCTGATATCTATGTTGGAGCAGTTGGTGTAGAAATCAA
3779845 TTTGCTTAGGATCATAGGTGTAAATAGAATGAACTAAGTGTGGTTTGTCATATGGGACTCATGAA
716 TTTGCTTAGGATCATAGGTGTAAATAGAATGAACTAAGTGTGGTTTGTCATATGGGACTCATGAA
3779910 TTTTATTTTAATGGCAAAAGATGTCAGGATG
781 TTTTATTTTAATGGCAAAAGATGTCAGGATG
3779941 AACTGCCATC
Statistics
Matches: 811, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
830 811 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (830 bp):
TTTTGAATAGTGGGAAAGTTGGCATATTTGCAAAAGCAAATCACATGATGTTTAACAGGAAGTAT
TGGCGGCATGCTGTAGAACTGATGCAGCGCATGCTGGTGTAAGCTTGCAAAGAAAATGGGTGATG
CTCCTCCTGCACATACTTTCTATGGTCAATCAACAGTGATATTTACAGGTTTGAGAGTGAGGAGA
GCACCCATTGCAGTTGCCAGGAGCTGCATCATCTCATATGGACCGAGGAGGCCTCTTTGTGGATC
AAGAGGCATAGCTTGATGATCACTGAAGATGGTTAATTGAATCTGATGTGCTAGAAAAGGTAATT
AGAAGCGCACATTTGCAGTAAAAGGTAGTTGTTCATCTGCACTGTGGTGGTGTCTGGAGTAGATC
AACAATGTTGTGAAGCCATCATGGGTTGGTTCAGTTGCTCAACTACTGATTAGCACCTTGGCAAG
TACCAAGATTTGAGACTCATCAATAATCTCCCTTGATGGGTAATCTGTAAGTATTACTATTAACC
TTATTTGAAGCTTGTGACATATCTTGATCTGGAACTGGGGTAGCCTCCCTCATATCTTGATCTGG
AACTGGGGTAGCCTCCCTCATCGATACTTTTTGGTATCAAACAATATTTTGAAACAACTGTCTTA
AACGTGAATTGAAAGGTCTAATGTCCATCTGATATCTATGTTGGAGCAGTTGGTGTAGAAATCAA
TTTGCTTAGGATCATAGGTGTAAATAGAATGAACTAAGTGTGGTTTGTCATATGGGACTCATGAA
TTTTATTTTAATGGCAAAAGATGTCAGGATGTCAGGATGAACCACCAATA
Found at i:3785481 original size:16 final size:17
Alignment explanation
Indices: 3785449--3785482 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3785439 TCTTTCGAAC
*
3785449 ATAAATTTCTTTTTGAA
1 ATAAATTTCTATTTGAA
3785466 ATAAATTT-TATTTGAA
1 ATAAATTTCTATTTGAA
3785482 A
1 A
3785483 AGAGTACCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
ATAAATTTCTATTTGAA
Found at i:3785509 original size:2 final size:2
Alignment explanation
Indices: 3785504--3785535 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3785494 ATATACATCC
3785504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3785536 GAAAAAGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3787219 original size:2 final size:2
Alignment explanation
Indices: 3787212--3787249 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3787202 GAACTATAAA
3787212 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3787250 TTACCTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3793664 original size:13 final size:13
Alignment explanation
Indices: 3793646--3793671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3793636 CAACCTACAT
3793646 CAAAACCGGATAA
1 CAAAACCGGATAA
3793659 CAAAACCGGATAA
1 CAAAACCGGATAA
3793672 GCGGATATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.15, T:0.08
Consensus pattern (13 bp):
CAAAACCGGATAA
Found at i:3814228 original size:20 final size:20
Alignment explanation
Indices: 3814200--3814239 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3814190 TTTTTAAGTC
*
3814200 TTTATAAAATATAAATTTAT
1 TTTAAAAAATATAAATTTAT
*
3814220 TTTAAAAAATATCAATTTAT
1 TTTAAAAAATATAAATTTAT
3814240 ACTCTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAAAAATATAAATTTAT
Found at i:3814354 original size:15 final size:17
Alignment explanation
Indices: 3814336--3814369 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
3814326 TATTTTTTAT
3814336 TATTTTTA-TT-CAAAA
1 TATTTTTACTTACAAAA
3814351 TATTTTTACTTACAAAA
1 TATTTTTACTTACAAAA
3814368 TA
1 TA
3814370 ATGATGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTTTACTTACAAAA
Found at i:3814443 original size:27 final size:26
Alignment explanation
Indices: 3814413--3814472 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
3814403 ATTATTATTA
3814413 AATT-AAATTATTATTAAGTTATATTCT
1 AATTCAAA-TATTATTAAGTTAT-TTCT
* * *
3814440 AATTCAAATATTTTTAATTTATTTTT
1 AATTCAAATATTATTAAGTTATTTCT
3814466 AATTCAA
1 AATTCAA
3814473 TCACATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 10 0.34
27 16 0.55
28 3 0.10
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
AATTCAAATATTATTAAGTTATTTCT
Found at i:3814769 original size:24 final size:24
Alignment explanation
Indices: 3814742--3814805 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 24
3814732 TATTAATTTT
3814742 TTAAAATAAAAATAATATA-ATATA
1 TTAAAATAAAAATAATATATATA-A
* **
3814766 TTAATATCAAAGTTAATATATATAA
1 TTAAAAT-AAAAATAATATATATAA
* *
3814791 TTAAATTAAATATAA
1 TTAAAATAAAAATAA
3814806 GTTTAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
24 12 0.39
25 16 0.52
26 3 0.10
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TTAAAATAAAAATAATATATATAA
Found at i:3817934 original size:42 final size:42
Alignment explanation
Indices: 3817873--3817977 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 42
3817863 TAGAAATAAA
* *
3817873 ATAATCTTTAATAAAATTTTGA-TAACTTTTGATT-TAA-TGTTG
1 ATAATCTTTTATATAATTTTGAGTAACTTTT--TTATAACT-TTG
*
3817915 ATAATTTTTTATATAATTTT-AGTAACTTTTTTGATAACTTTG
1 ATAATCTTTTATATAATTTTGAGTAACTTTTTT-ATAACTTTG
*
3817957 ATAATCTTTTATATATTTTTG
1 ATAATCTTTTATATAATTTTG
3817978 CAACCCTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
40 2 0.04
41 1 0.02
42 49 0.92
43 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (42 bp):
ATAATCTTTTATATAATTTTGAGTAACTTTTTTATAACTTTG
Found at i:3817977 original size:21 final size:21
Alignment explanation
Indices: 3817873--3817977 Score: 90
Period size: 21 Copynumber: 5.0 Consensus size: 21
3817863 TAGAAATAAA
* *
3817873 ATAATCTTTAATAAAATTTTG
1 ATAATCTTTTATATAATTTTG
* *
3817894 ATAA-CTTTTGATTTAATGTTG
1 ATAATCTTTT-ATATAATTTTG
*
3817915 ATAATTTTTTATATAATTTT-
1 ATAATCTTTTATATAATTTTG
* *
3817935 AGTAA-CTTTTTTGATAACTTTG
1 A-TAATCTTTTAT-ATAATTTTG
*
3817957 ATAATCTTTTATATATTTTTG
1 ATAATCTTTTATATAATTTTG
3817978 CAACCCTTAA
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
20 10 0.15
21 44 0.68
22 11 0.17
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (21 bp):
ATAATCTTTTATATAATTTTG
Found at i:3828763 original size:32 final size:33
Alignment explanation
Indices: 3828722--3828811 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 33
3828712 ATAAACATGA
*
3828722 TATATATT-AATAAAATATTAAATTTTTAATTTT
1 TATATATTAAAT-AAATATAAAATTTTTAATTTT
*
3828755 TATA-ATTAAATAAATGTAAAATTTTTAATAATTT
1 TATATATTAAATAAATATAAAATTTTTAAT--TTT
*
3828789 TAAATATTAAA-AAATA-AAAATTT
1 TATATATTAAATAAATATAAAATTT
3828812 ATATAATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
32 19 0.39
33 14 0.29
34 10 0.20
35 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
TATATATTAAATAAATATAAAATTTTTAATTTT
Found at i:3829761 original size:43 final size:42
Alignment explanation
Indices: 3829691--3829772 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
3829681 TACTGAGAAT
* *
3829691 CCCTCTAAGCCTTAAAGTTCCATTATGTCTCTTTCCTTTCAAA
1 CCCTCTAACCCTTAAAGTTCCATTATGTCACTTT-CTTTCAAA
*
3829734 CCCTTTAACCCTTAAAGTTCCATTATGTCACTTTCTTTC
1 CCCTCTAACCCTTAAAGTTCCATTATGTCACTTTCTTTC
3829773 CTTTCTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 5 0.14
43 31 0.86
ACGTcount: A:0.22, C:0.30, G:0.06, T:0.41
Consensus pattern (42 bp):
CCCTCTAACCCTTAAAGTTCCATTATGTCACTTTCTTTCAAA
Found at i:3830211 original size:2 final size:2
Alignment explanation
Indices: 3830204--3830229 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3830194 CCAATTAGAA
3830204 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
3830230 GATGGGTTTC
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:3837560 original size:16 final size:16
Alignment explanation
Indices: 3837539--3837569 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3837529 GGCCCGTGCA
*
3837539 TTTCTTTTTTTCTTCC
1 TTTCTTTTCTTCTTCC
3837555 TTTCTTTTCTTCTTC
1 TTTCTTTTCTTCTTC
3837570 AGCTGCCTCT
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:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTTCTTCTTCC
Found at i:3840638 original size:18 final size:18
Alignment explanation
Indices: 3840615--3840650 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3840605 GTATTCATAA
3840615 GCTAGTTAATAGAAAACT
1 GCTAGTTAATAGAAAACT
3840633 GCTAGTTAATAGAAAACT
1 GCTAGTTAATAGAAAACT
3840651 AACCTGCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
GCTAGTTAATAGAAAACT
Found at i:3844694 original size:2 final size:2
Alignment explanation
Indices: 3844689--3844766 Score: 84
Period size: 2 Copynumber: 39.0 Consensus size: 2
3844679 AAAATATACA
** * *
3844689 TG TG TG TG TG TG TG TG TG TG TG CA CG TG TG TG TG TG TG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * *
3844731 CG CG TG CG TG CG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3844767 GTGAAGTATT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.01, C:0.09, G:0.49, T:0.41
Consensus pattern (2 bp):
TG
Found at i:3850633 original size:20 final size:20
Alignment explanation
Indices: 3850603--3850662 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
3850593 GTATATTTTA
3850603 TTAAATT-TATAAATATAAT
1 TTAAATTATATAAATATAAT
* *
3850622 TTAAATTATATAAATTTAAA
1 TTAAATTATATAAATATAAT
*
3850642 TT-AA-TATTTAAATAT-AT
1 TTAAATTATATAAATATAAT
3850659 TTAA
1 TTAA
3850663 TAAAATATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 3 0.09
18 10 0.29
19 9 0.26
20 12 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATTATATAAATATAAT
Found at i:3850639 original size:15 final size:14
Alignment explanation
Indices: 3850615--3850658 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
3850605 AAATTTATAA
3850615 ATATAATTTAAATT
1 ATATAATTTAAATT
3850629 ATATAAATTTAAATT
1 ATAT-AATTTAAATT
3850644 A-AT-ATTTAAA-T
1 ATATAATTTAAATT
3850655 ATAT
1 ATAT
3850659 TTAATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.07
12 9 0.32
14 6 0.21
15 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATAATTTAAATT
Found at i:3850689 original size:38 final size:38
Alignment explanation
Indices: 3850602--3850689 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
3850592 CGTATATTTT
* * *
3850602 ATTAAATTTATAAATATAATTTAAATTATATAAATTTAA
1 ATTAAAATT-TAAATATAATTTAAATAAAATAAATTTAA
* *
3850641 ATTAATATTTAAATAT-ATTT-AATAAAATATATTTAAA
1 ATTAAAATTTAAATATAATTTAAATAAAATAAATTT-AA
3850678 ATTAAAAATTTA
1 ATT-AAAATTTA
3850690 TCAATCAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
36 11 0.27
37 9 0.22
38 14 0.34
39 7 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (38 bp):
ATTAAAATTTAAATATAATTTAAATAAAATAAATTTAA
Found at i:3850700 original size:52 final size:52
Alignment explanation
Indices: 3850613--3850715 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 52
3850603 TTAAATTTAT
* *
3850613 AAATATAATTTAAATTATATAAATTTAAATTAATATTTAAATATATTTAATA
1 AAATATAATTTAAATTATATAAATTTAAATCAATATTGAAATATATTTAATA
* *
3850665 AAATAT-ATTTAAAATTA-A-AAATTTATCAATCAATATTGATATTTATTTAAT
1 AAATATAATTT-AAATTATATAAATTTA--AATCAATATTGAAATATATTTAAT
3850716 TATTTTAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
50 7 0.16
51 5 0.11
52 32 0.73
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (52 bp):
AAATATAATTTAAATTATATAAATTTAAATCAATATTGAAATATATTTAATA
Found at i:3850755 original size:9 final size:9
Alignment explanation
Indices: 3850741--3850810 Score: 58
Period size: 9 Copynumber: 7.9 Consensus size: 9
3850731 ATTAATAAGG
3850741 ATTAATTTA
1 ATTAATTTA
3850750 ATTAATTTTA
1 ATTAA-TTTA
*
3850760 A-T-ATTAAA
1 ATTAATT-TA
*
3850768 ATTAATTAA
1 ATTAATTTA
3850777 ATTAATTT-
1 ATTAATTTA
3850785 -TTAATTTAA
1 ATTAATTT-A
*
3850794 ATTAATTAA
1 ATTAATTTA
3850803 ATTAATTT
1 ATTAATTT
3850811 TTAATTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
7 9 0.18
8 3 0.06
9 24 0.48
10 14 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTAATTTA
Found at i:3850755 original size:31 final size:27
Alignment explanation
Indices: 3850711--3850811 Score: 105
Period size: 26 Copynumber: 3.6 Consensus size: 27
3850701 TGATATTTAT
**
3850711 TTAATTATTTTAATTTTAAAATTAATAAGGA
1 TTAATTAAATTAATTTTAAAATT-A-AA--A
* *
3850742 TTAATTTAATTAATTTTAATATTAAAA
1 TTAATTAAATTAATTTTAAAATTAAAA
* *
3850769 TTAATTAAATTAATTTT-TAATTTAAA
1 TTAATTAAATTAATTTTAAAATTAAAA
3850795 TTAATTAAATTAATTTT
1 TTAATTAAATTAATTTT
3850812 TAATTTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
26 23 0.37
27 17 0.27
29 2 0.03
30 1 0.02
31 19 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TTAATTAAATTAATTTTAAAATTAAAA
Found at i:3850795 original size:17 final size:16
Alignment explanation
Indices: 3850769--3850800 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3850759 AATATTAAAA
3850769 TTAATTAAATTAATTT
1 TTAATTAAATTAATTT
3850785 TTAATTTAAATTAATT
1 TTAA-TTAAATTAATT
3850801 AAATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTAAATTAATTT
Found at i:3850795 original size:26 final size:27
Alignment explanation
Indices: 3850741--3850817 Score: 122
Period size: 26 Copynumber: 2.9 Consensus size: 27
3850731 ATTAATAAGG
*
3850741 ATTAATTTAATTAA-TTTTAATATTAAA
1 ATTAATTAAATTAATTTTTAAT-TTAAA
3850768 ATTAATTAAATTAATTTTTAATTT-AA
1 ATTAATTAAATTAATTTTTAATTTAAA
3850794 ATTAATTAAATTAATTTTTAATTT
1 ATTAATTAAATTAATTTTTAATTT
3850818 TTTTATAATT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 26 0.54
27 15 0.31
28 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTAATTAAATTAATTTTTAATTTAAA
Found at i:3850830 original size:36 final size:34
Alignment explanation
Indices: 3850782--3850850 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
3850772 ATTAAATTAA
* * *
3850782 TTTTTAATTTAAATTAATTAAATTAATTTTTAATT
1 TTTTTAAATTAAAAT-ATTAAATTAAATTTTAATT
*
3850817 TTTTTATAATTAAAATATTTAATTAAATTTTAAT
1 TTTTTA-AATTAAAATATTAAATTAAATTTTAAT
3850851 AAATTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TTTTTAAATTAAAATATTAAATTAAATTTTAATT
Found at i:3852437 original size:28 final size:30
Alignment explanation
Indices: 3852406--3852462 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
3852396 ATATTTTTAT
3852406 ATAAAAAT-TAAAAATA-ATAAAAAATATG
1 ATAAAAATATAAAAATATATAAAAAATATG
* *
3852434 ATAAAAATATAATAATATATTAAAAATAT
1 ATAAAAATATAAAAATATATAAAAAATAT
3852463 ATATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.32
29 7 0.28
30 10 0.40
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (30 bp):
ATAAAAATATAAAAATATATAAAAAATATG
Found at i:3852457 original size:19 final size:18
Alignment explanation
Indices: 3852403--3852463 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 18
3852393 ATAATATTTT
*
3852403 TATATAAAA-ATTAAAAA
1 TATAAAAAATATTAAAAA
3852420 TAATAAAAAATATGATAAAAA
1 T-ATAAAAAATAT--TAAAAA
*
3852441 TATAATAATATATTAAAAA
1 TATAA-AAAATATTAAAAA
3852460 TATA
1 TATA
3852464 TATTATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 12 0.32
20 4 0.11
21 13 0.35
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
TATAAAAAATATTAAAAA
Found at i:3852514 original size:28 final size:26
Alignment explanation
Indices: 3852403--3852525 Score: 70
Period size: 30 Copynumber: 4.3 Consensus size: 26
3852393 ATAATATTTT
* *
3852403 TATATAAAAATTAAAAATAATAAAAAA
1 TATATAAAAA-TAAATATAATTAAAAA
3852430 TATGATAAAAATATAATAATATATTAAAAA
1 TAT-ATAAAAATA-AAT-ATA-ATTAAAAA
* *
3852460 TATATATTATATAAAT-T-ATTAACATAAA
1 TATATA-AAAATAAATATAATT-A-A-AAA
*
3852488 TATATAATAAATTAAATATAATTATAATA
1 TATATAA-AAA-TAAATATAATTA-AAAA
3852517 TACTATAAA
1 TA-TATAAA
3852526 TATTATTTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
25 3 0.04
26 1 0.01
27 7 0.09
28 20 0.27
29 19 0.25
30 22 0.29
31 3 0.04
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.36
Consensus pattern (26 bp):
TATATAAAAATAAATATAATTAAAAA
Found at i:3852525 original size:22 final size:22
Alignment explanation
Indices: 3852445--3852555 Score: 72
Period size: 22 Copynumber: 5.0 Consensus size: 22
3852435 TAAAAATATA
*
3852445 ATAATATATTAAAAATATATATT
1 ATAATATATTATAAATATA-ATT
*
3852468 AT-ATAAATTATTAACATA-AATAT
1 ATAATATATTA-TAA-ATATAAT-T
*
3852491 ATAATA-AAT-TAAATATAATT
1 ATAATATATTATAAATATAATT
* *
3852511 ATAATATACTATAAATATTATT
1 ATAATATATTATAAATATAATT
*
3852533 -TAA-ATATATATAAAATTTAATT
1 ATAATATAT-TAT-AAATATAATT
3852555 A
1 A
3852556 AAAAATTACT
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
20 13 0.19
21 14 0.20
22 27 0.39
23 10 0.14
24 6 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAATATATTATAAATATAATT
Found at i:3852527 original size:11 final size:10
Alignment explanation
Indices: 3852427--3852546 Score: 62
Period size: 11 Copynumber: 12.3 Consensus size: 10
3852417 AAATAATAAA
*
3852427 AAATATGATAA
1 AAATAT-ATAT
3852438 AAATATA-AT
1 AAATATATAT
3852447 -AATATAT-T
1 AAATATATAT
3852455 AAA-A-ATAT
1 AAATATATAT
*
3852463 ATAT-TATAT
1 AAATATATAT
3852472 AAAT-TAT-T
1 AAATATATAT
*
3852480 AACATAAATAT
1 AA-ATATATAT
*
3852491 ATAATAAAT-T
1 A-AATATATAT
3852501 AAATATA-ATT
1 AAATATATA-T
3852511 ATAATATACTAT
1 A-AATATA-TAT
*
3852523 AAATATTATTT
1 AAATA-TATAT
3852534 AAATATATAT
1 AAATATATAT
3852544 AAA
1 AAA
3852547 ATTTAATTAA
Statistics
Matches: 87, Mismatches: 7, Indels: 31
0.70 0.06 0.25
Matches are distributed among these distances:
7 2 0.02
8 14 0.16
9 20 0.23
10 14 0.16
11 31 0.36
12 5 0.06
13 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (10 bp):
AAATATATAT
Found at i:3852548 original size:11 final size:11
Alignment explanation
Indices: 3852403--3852548 Score: 50
Period size: 11 Copynumber: 13.9 Consensus size: 11
3852393 ATAATATTTT
3852403 TATATAAAA-A
1 TATATAAAATA
3852413 T-TA-AAAATA
1 TATATAAAATA
*
3852422 -ATAAAAAATA
1 TATATAAAATA
3852432 TGATA-AAAATA
1 T-ATATAAAATA
*
3852443 TA-ATAATATA
1 TATATAAAATA
*
3852453 T-TAAAAATATA
1 TATATAAA-ATA
3852464 TATTATATAAAT-
1 TA-TATA-AAATA
*
3852476 TAT-TAACATA
1 TATATAAAATA
* *
3852486 AATATATAATA
1 TATATAAAATA
*
3852497 -A-ATTAAATA
1 TATATAAAATA
*
3852506 TA-ATTATAATA
1 TATA-TAAAATA
3852517 TACTAT-AAATA
1 TA-TATAAAATA
*
3852528 T-TATTTAAATA
1 TATA-TAAAATA
3852539 TATATAAAAT
1 TATATAAAAT
3852549 TTAATTAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 39
0.66 0.09 0.25
Matches are distributed among these distances:
8 4 0.04
9 17 0.17
10 25 0.25
11 40 0.39
12 8 0.08
13 6 0.06
14 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (11 bp):
TATATAAAATA
Found at i:3860605 original size:2 final size:2
Alignment explanation
Indices: 3860598--3860630 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3860588 CCTAATTTCC
3860598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3860631 CTTAGGATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3863297 original size:13 final size:13
Alignment explanation
Indices: 3863279--3863305 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3863269 TTTTTTCTCC
3863279 TAATCTGTTAGTT
1 TAATCTGTTAGTT
3863292 TAATCTGTTAGTT
1 TAATCTGTTAGTT
3863305 T
1 T
3863306 GTTTTTGCTT
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:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TAATCTGTTAGTT
Found at i:3871920 original size:2 final size:2
Alignment explanation
Indices: 3871907--3871953 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
3871897 ATTAAGTGCC
* * *
3871907 TA TA TA TGA TA TA TA TA TA TA TA TA TA TA GA TA TA GA TA TA GA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3871950 TA TA
1 TA TA
3871954 CATGCATACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (2 bp):
TA
Found at i:3871932 original size:12 final size:12
Alignment explanation
Indices: 3871907--3871953 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
3871897 ATTAAGTGCC
3871907 TATATAT-GATA
1 TATATATAGATA
3871918 TATATAT--ATA
1 TATATATAGATA
3871928 TATATATAGATA
1 TATATATAGATA
*
3871940 TAGATATAGATA
1 TATATATAGATA
3871952 TA
1 TA
3871954 CATGCATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 10 0.30
11 7 0.21
12 16 0.48
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (12 bp):
TATATATAGATA
Found at i:3876441 original size:12 final size:12
Alignment explanation
Indices: 3876406--3876444 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3876396 ATCGAGCAAC
* *
3876406 TTTATTTTGTAA
1 TTTATTTTTTTA
*
3876418 TTTATTTATTTA
1 TTTATTTTTTTA
3876430 TTTATTTTTTTA
1 TTTATTTTTTTA
3876442 TTT
1 TTT
3876445 TTTCTGCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:3886848 original size:31 final size:31
Alignment explanation
Indices: 3886810--3886871 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3886800 AGATATTACA
3886810 CATGAATGCATGATCTGTCCAGTCAGAGACT
1 CATGAATGCATGATCTGTCCAGTCAGAGACT
*
3886841 CATGAATGCATGATCTGTCTAGTCAGAGACT
1 CATGAATGCATGATCTGTCCAGTCAGAGACT
3886872 ATCTCCGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (31 bp):
CATGAATGCATGATCTGTCCAGTCAGAGACT
Found at i:3889931 original size:17 final size:20
Alignment explanation
Indices: 3889879--3889928 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
3889869 TTTAATTTAA
3889879 AATAATTTAAAAATTATTATT
1 AATAA-TTAAAAATTATTATT
*
3889900 AATATTTAAAAATTATT-TT
1 AATAATTAAAAATTATTATT
3889919 -ATAATTAAAA
1 AATAATTAAAA
3889929 TTAAATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 2 0.07
20 12 0.44
21 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATTAAAAATTATTATT
Found at i:3890012 original size:106 final size:105
Alignment explanation
Indices: 3889869--3890149 Score: 501
Period size: 106 Copynumber: 2.7 Consensus size: 105
3889859 AAATTTTTTA
* * *
3889869 TTTAA-TTTAAAATAATTTAAAAATTATTATTAATATTTAAAAATTATTTTATAATTAAAATTAA
1 TTTAATTTTAAATTAATTAAAAAATTATTATTAGTATTTAAAAATTATTTTATAATTAAAATTAA
3889933 ATAAAGTTTATATGAAAATTTAATTTAATATAAGTTACTT
66 ATAAAGTTTATATGAAAATTTAATTTAATATAAGTTACTT
*
3889973 TTTAATTTTAAATTAATTAAAAAAATTATTATTAGTATTTAAAAATTATTTTATATTTAAAATTA
1 TTTAATTTTAAATTAATT-AAAAAATTATTATTAGTATTTAAAAATTATTTTATAATTAAAATTA
3890038 AATAAAGTTTATATGAAAATTTAATTTAATATAAGTTACTT
65 AATAAAGTTTATATGAAAATTTAATTTAATATAAGTTACTT
3890079 TTTAATTTTAAATTAATTTAAAAAATTATTATTAGTATTTAAAAATTATTTTATAATTAAAATTA
1 TTTAATTTTAAATTAA-TTAAAAAATTATTATTAGTATTTAAAAATTATTTTATAATTAAAATTA
3890144 AATAAA
65 AATAAA
3890150 AATTTACATC
Statistics
Matches: 169, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
104 5 0.03
105 11 0.07
106 151 0.89
107 2 0.01
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.48
Consensus pattern (105 bp):
TTTAATTTTAAATTAATTAAAAAATTATTATTAGTATTTAAAAATTATTTTATAATTAAAATTAA
ATAAAGTTTATATGAAAATTTAATTTAATATAAGTTACTT
Found at i:3890037 original size:17 final size:20
Alignment explanation
Indices: 3889993--3890034 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3889983 AATTAATTAA
3889993 AAAAATTATTATTAGTATTT
1 AAAAATTATTATTAGTATTT
3890013 AAAAATTATT-TTA-TATTT
1 AAAAATTATTATTAGTATTT
3890031 AAAA
1 AAAA
3890035 TTAAATAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.41
19 3 0.14
20 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAAATTATTATTAGTATTT
Found at i:3890118 original size:21 final size:19
Alignment explanation
Indices: 3890094--3890140 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
3890084 TTTTAAATTA
3890094 ATTTAAAAAATTATTATTAGT
1 ATTTAAAAAATTATT-TTA-T
3890115 ATTT-AAAAATTATTTTAT
1 ATTTAAAAAATTATTTTAT
*
3890133 AATTAAAA
1 ATTTAAAA
3890141 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.17
19 6 0.25
20 10 0.42
21 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTTAAAAAATTATTTTAT
Found at i:3890125 original size:33 final size:34
Alignment explanation
Indices: 3889873--3890131 Score: 91
Period size: 33 Copynumber: 7.5 Consensus size: 34
3889863 TTTTTATTTA
*
3889873 ATTT-AAAA-TAATTT-A-AAAATTATTATTAAT
1 ATTTAAAAATTAATTTAATAAAATTATTATTAGT
* * *
3889903 ATTTAAAAATTATTTTATAATTAAAATTA-AATAAAGT
1 ATTTAAAAATTA-ATT-TAA-TAAAATTATTAT-TAGT
* *
3889940 -TTATATGAAAATTTAATTTAATATAAGTTACTTTTTA--
1 ATT-TA--AAAA-TTAATTTAATA-AAATTA-TTATTAGT
* *
3889977 ATTT-TAAATTAA-TTAAAAAAATTATTATTAGT
1 ATTTAAAAATTAATTTAATAAAATTATTATTAGT
* * *
3890009 ATTTAAAAATTATTTTATATTTAAAATTA-AATAAAGT
1 ATTTAAAAATTAATTTA-A--TAAAATTATTAT-TAGT
* *
3890046 -TTATATGAAAATTTAATTTAATATAAGTTACTTTTTA--
1 ATT-TA--AAAA-TTAATTTAATA-AAATTA-TTATTAGT
*
3890083 ATTT-TAAATTAATTTAA-AAAATTATTATTAGT
1 ATTTAAAAATTAATTTAATAAAATTATTATTAGT
*
3890115 ATTTAAAAATTATTTTA
1 ATTTAAAAATTAATTTA
3890132 TAATTAAAAT
Statistics
Matches: 166, Mismatches: 28, Indels: 67
0.64 0.11 0.26
Matches are distributed among these distances:
30 14 0.08
31 14 0.08
32 16 0.10
33 31 0.19
34 10 0.06
35 2 0.01
36 8 0.05
37 29 0.17
38 17 0.10
39 13 0.08
40 12 0.07
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (34 bp):
ATTTAAAAATTAATTTAATAAAATTATTATTAGT
Found at i:3890143 original size:17 final size:20
Alignment explanation
Indices: 3890099--3890140 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3890089 AATTAATTTA
*
3890099 AAAAATTATTATTAGTATTT
1 AAAAATTATTATTAGTAATT
3890119 AAAAATTATT-TTA-TAATT
1 AAAAATTATTATTAGTAATT
3890137 AAAA
1 AAAA
3890141 TTAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 3 0.14
20 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAAATTATTATTAGTAATT
Found at i:3891018 original size:15 final size:15
Alignment explanation
Indices: 3890983--3891012 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3890973 TAGTCTAATA
*
3890983 AATTTTGAATAGATT
1 AATTTTGAATAAATT
3890998 AATTTTGAATAAATT
1 AATTTTGAATAAATT
3891013 TTTTTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (15 bp):
AATTTTGAATAAATT
Found at i:3891267 original size:3 final size:3
Alignment explanation
Indices: 3891259--3891294 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3891249 TCTGATATTT
3891259 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3891295 TTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3891299 original size:3 final size:3
Alignment explanation
Indices: 3891293--3891324 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3891283 ATAATAATAA
3891293 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3891325 AAAATTTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3898128 original size:14 final size:14
Alignment explanation
Indices: 3898109--3898138 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3898099 ATTTGCCTGG
3898109 TATTTCCTTCTAAA
1 TATTTCCTTCTAAA
3898123 TATTTCCTTCTAAA
1 TATTTCCTTCTAAA
3898137 TA
1 TA
3898139 ATGTCAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTCCTTCTAAA
Found at i:3905152 original size:2 final size:2
Alignment explanation
Indices: 3905140--3905184 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
3905130 GACACCTAAT
* * *
3905140 TA TA TA CA TA TA TA TA TA TA TA CA TG 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
3905182 TA T
1 TA T
3905185 TTTCTCCTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3906965 original size:31 final size:34
Alignment explanation
Indices: 3906922--3906987 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 34
3906912 TATCGATGTG
*
3906922 TTTTAATATATTTTTTCATATTTAT-C-TATATT
1 TTTTAATATATTTTTTCATATATATACTTATATT
3906954 TTTTAA-ATATTTTTTCATATATATACTTATATT
1 TTTTAATATATTTTTTCATATATATACTTATATT
3906987 T
1 T
3906988 ATAGGTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 17 0.55
32 7 0.23
33 7 0.23
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (34 bp):
TTTTAATATATTTTTTCATATATATACTTATATT
Found at i:3916085 original size:335 final size:335
Alignment explanation
Indices: 3915271--3916617 Score: 1772
Period size: 335 Copynumber: 4.0 Consensus size: 335
3915261 ATAAGTAAAA
* *
3915271 AAAATTATTTGAGATTTTGATTTAATTCAAT-AGAATTATTATTGTTTATTTTTAAAGGTTTATT
1 AAAATTAATTGAGATTTTGATTTAATTCAATGA-AATTATTATTGTTTAATTTTAAAGGTTTATT
* * * * * * *
3915335 ATATATTTAAAAATTAAGATTTTGATAAAATAGATAGAGATTTGTTTTTAAGTTAGATTAAGTTT
65 ATACATTTAAAAATTAAGATTTTGATAAAATAAATAGAGATTTGTTTTAAAATCAGATTGAGCTT
* * * * * * * * *
3915400 TTGGCATATGTTTAAAAATATTATTTAACTCGATTAGATCGTTTTAATATCTTGATTGAGTTTTT
130 TCGGCATATGTTTAAAAACATGATCTAACCCGATTAGATCGCTTTAATACCTTAATTGAGTTTAT
* * * * *
3915465 ACCTAAAATATAATTCATACTTCAAGTTATATTAGAAAAATAACTATATGATTAGCTTAATTTTA
195 ACCTAAAATATAATTCATATTTCAAGTTATATTAAAAAAATAAGTATTTGATTAGTTTAATTTTA
* * *
3915530 AAATTTTTAAAATTATATAAATTTAAAGAATCATTTGAATTTTAAAATATAAA-AAAAAATCAAA
260 AAATTTTAAAAATTATATAAATTTAAAAAATCATTTGAATTTCAAAATATAAAGAAAAAATCAAA
3915594 TTAATCAAATT
325 TTAATCAAATT
3915605 AAAATTAATTGAGATTTTGATTTAATTCAATGAAATTATTATTGTTTAATTTTAAAGGTTTATTA
1 AAAATTAATTGAGATTTTGATTTAATTCAATGAAATTATTATTGTTTAATTTTAAAGGTTTATTA
* * * *
3915670 TACATTTAAAAATTAAGATTTTGATAAAATGAATAGAGATTTGTTTTTAAGTCAGATTGAGTTTT
66 TACATTTAAAAATTAAGATTTTGATAAAATAAATAGAGATTTGTTTTAAAATCAGATTGAGCTTT
* * * * *** * *
3915735 TGGTATATATTTAAAAATATGATCTAAATTGATTAGATCGTTTTAATACCTTGATTGAGTTTATA
131 CGGCATATGTTTAAAAACATGATCTAACCCGATTAGATCGCTTTAATACCTTAATTGAGTTTATA
* * * *
3915800 CTTAAAATATAATTTATATTTCAAGTTATATTAAAAAATTAAGTATTTTATTAGTTTAATTTTAA
196 CCTAAAATATAATTCATATTTCAAGTTATATTAAAAAAATAAGTATTTGATTAGTTTAATTTTAA
* ** *
3915865 ATTTTTAAAAATTATATAAATTTAAAAAATCGCTTGAATTTCAAAGTATAAAGAAAAAATCAAAT
261 AATTTTAAAAATTATATAAATTTAAAAAATCATTTGAATTTCAAAATATAAAGAAAAAATCAAAT
** **
3915930 TAATTGAGCT
326 TAATCAAATT
* *
3915940 AAAGTTAATTGAGACTTTGATTTAATTCAATGAAATTATTATTGTTTAATTTTAAAGGTTTATTA
1 AAAATTAATTGAGATTTTGATTTAATTCAATGAAATTATTATTGTTTAATTTTAAAGGTTTATTA
* * * *
3916005 TATATTTAAAAATTAAGATTTTGACAAAATAAATAGAAATTTATTTTAAAATCAGATTGAGCTTT
66 TACATTTAAAAATTAAGATTTTGATAAAATAAATAGAGATTTGTTTTAAAATCAGATTGAGCTTT
* * * * * *
3916070 CGACATATGTTTAAAAGCATGATCTAACCCGGTTAGATCGCTTGAATACCTTAATTGAATCTATA
131 CGGCATATGTTTAAAAACATGATCTAACCCGATTAGATCGCTTTAATACCTTAATTGAGTTTATA
* * * *
3916135 CCTAAAATATAATTCACATTTCAAGTTATGTTAAAAAAATAAGAATAT-AGTTAGTTTAATTTTA
196 CCTAAAATATAATTCATATTTCAAGTTATATTAAAAAAATAAGTATTTGA-TTAGTTTAATTTTA
* * *
3916199 AAATTTTAAAAATTATATAAATTTAAAAGATCGTTTAAATTTCAAAATAT-AAGTAAAAAATCAA
260 AAATTTTAAAAATTATATAAATTTAAAAAATCATTTGAATTTCAAAATATAAAG-AAAAAATCAA
3916263 ATTAATCAAATT
324 ATTAATCAAATT
* *
3916275 AAAATTAATTGAGATTTTGATTTAATTCAAAGAAATTATTATTGTATAATTTTAAAGGTTTATTA
1 AAAATTAATTGAGATTTTGATTTAATTCAATGAAATTATTATTGTTTAATTTTAAAGGTTTATTA
* ** * * *
3916340 TACATTTAAAAATTTAGATTTTGATAAAATTGATAGAGATTTGTTTTAAAATTAGATTGACCTTC
66 TACATTTAAAAATTAAGATTTTGATAAAATAAATAGAGATTTGTTTTAAAATCAGATTGAGCTTT
* * * ** * *
3916405 CGTCATATGTTTAAAAACATAATTTAACCTAATTAGATCGCTTTAATATCTTAATTGAGTTTACA
131 CGGCATATGTTTAAAAACATGATCTAACCCGATTAGATCGCTTTAATACCTTAATTGAGTTTATA
* * *
3916470 CCTAAAATATTATTCATATTTCAAGTTATATTAAAAAAAATAAGAATCTGATTAGTTTAATTTTA
196 CCTAAAATATAATTCATATTTCAAGTTATATT-AAAAAAATAAGTATTTGATTAGTTTAATTTTA
* * * *
3916535 AAATTTTAAAAATTATATAAATTTTAAAAATTATTTGAATTTCAAAATAT-AAG--TAAACCAAA
260 AAATTTTAAAAATTATATAAATTTAAAAAATCATTTGAATTTCAAAATATAAAGAAAAAATCAAA
*
3916597 TTAATCAAACT
325 TTAATCAAATT
3916608 AAAATTAATT
1 AAAATTAATT
3916618 ATTCAATCAG
Statistics
Matches: 893, Mismatches: 114, Indels: 13
0.88 0.11 0.01
Matches are distributed among these distances:
333 27 0.03
334 283 0.32
335 505 0.57
336 77 0.09
337 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (335 bp):
AAAATTAATTGAGATTTTGATTTAATTCAATGAAATTATTATTGTTTAATTTTAAAGGTTTATTA
TACATTTAAAAATTAAGATTTTGATAAAATAAATAGAGATTTGTTTTAAAATCAGATTGAGCTTT
CGGCATATGTTTAAAAACATGATCTAACCCGATTAGATCGCTTTAATACCTTAATTGAGTTTATA
CCTAAAATATAATTCATATTTCAAGTTATATTAAAAAAATAAGTATTTGATTAGTTTAATTTTAA
AATTTTAAAAATTATATAAATTTAAAAAATCATTTGAATTTCAAAATATAAAGAAAAAATCAAAT
TAATCAAATT
Found at i:3916548 original size:9 final size:9
Alignment explanation
Indices: 3916528--3916566 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
3916518 TGATTAGTTT
3916528 AATTTT-AA
1 AATTTTAAA
3916536 AATTTTAAA
1 AATTTTAAA
* *
3916545 AATTATATA
1 AATTTTAAA
3916554 AATTTTAAA
1 AATTTTAAA
3916563 AATT
1 AATT
3916567 ATTTGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 6 0.23
9 20 0.77
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AATTTTAAA
Found at i:3924430 original size:2 final size:2
Alignment explanation
Indices: 3924423--3924457 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3924413 ATGGAGCTGT
3924423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3924458 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3926117 original size:2 final size:2
Alignment explanation
Indices: 3926110--3926163 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
3926100 ATGGCAAAAA
* * *
3926110 CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT GT CT CT GT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3926152 CT CT CT CT CT CT
1 CT CT CT CT CT CT
3926164 ATATATATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3943532 original size:49 final size:49
Alignment explanation
Indices: 3943460--3943557 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
3943450 ATGAATGTTT
* *
3943460 GAGTTTAAGGACAGTTAAATAGTCTTTAGTGATTTCCTGATTGAACATA
1 GAGTTTAAGGACAGTTAAATAGTCTTAAGTGATTCCCTGATTGAACATA
3943509 GAGTTTAAGGACAGTTAAATAGTCTTAAGTGATTCCCTGATTGAACATA
1 GAGTTTAAGGACAGTTAAATAGTCTTAAGTGATTCCCTGATTGAACATA
3943558 CACATTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (49 bp):
GAGTTTAAGGACAGTTAAATAGTCTTAAGTGATTCCCTGATTGAACATA
Found at i:3955372 original size:2 final size:2
Alignment explanation
Indices: 3955365--3955396 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3955355 AAAATGGTCC
3955365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3955397 TCCAAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3957357 original size:107 final size:107
Alignment explanation
Indices: 3957225--3957457 Score: 459
Period size: 107 Copynumber: 2.2 Consensus size: 107
3957215 ATTTAAATTT
3957225 AATT-TAAAAATTTATTTTATCAGTTCATATAAATTAAAATATATATTTTTATAATTAAATTTAA
1 AATTATAAAAATTTATTTTATCAGTTCATATAAATTAAAATATATATTTTTATAATTAAATTTAA
3957289 ATAAAATTATTTTAATTATTTAAATTGGATCGAATTTTTTTG
66 ATAAAATTATTTTAATTATTTAAATTGGATCGAATTTTTTTG
3957331 AATTATAAAAATTTATTTTATCAGTTCATATAAATTAAAATATATATTTTTATAATTAAATTTAA
1 AATTATAAAAATTTATTTTATCAGTTCATATAAATTAAAATATATATTTTTATAATTAAATTTAA
3957396 ATAAAATTATTTTAATTATTTAAATTGGATCGAATTTTTTTG
66 ATAAAATTATTTTAATTATTTAAATTGGATCGAATTTTTTTG
3957438 AATTATAAAAATTTATTTTA
1 AATTATAAAAATTTATTTTA
3957458 AAAATAAACA
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 4 0.03
107 122 0.97
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (107 bp):
AATTATAAAAATTTATTTTATCAGTTCATATAAATTAAAATATATATTTTTATAATTAAATTTAA
ATAAAATTATTTTAATTATTTAAATTGGATCGAATTTTTTTG
Found at i:3957814 original size:2 final size:2
Alignment explanation
Indices: 3957807--3957833 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3957797 CAAAATTCAA
3957807 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
3957834 TACATAGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3959940 original size:2 final size:2
Alignment explanation
Indices: 3959933--3959977 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
3959923 AGTGTAATGG
* * *
3959933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3959975 AT A
1 AT A
3959978 ACACTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3962908 original size:33 final size:35
Alignment explanation
Indices: 3962851--3962923 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 35
3962841 TTTAACATTT
* *
3962851 TTTTATATTTATATTATAATATTAATAAATTT-ATA
1 TTTTATATTAATATTATAAAATTAAT-AATTTCATA
*
3962886 TTTTATA-TAATA-TATAAAATTAATACTTTCATA
1 TTTTATATTAATATTATAAAATTAATAATTTCATA
3962919 TTTTA
1 TTTTA
3962924 AGTGAACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 4 0.12
33 19 0.56
34 4 0.12
35 7 0.21
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (35 bp):
TTTTATATTAATATTATAAAATTAATAATTTCATA
Found at i:3965023 original size:24 final size:24
Alignment explanation
Indices: 3964996--3965045 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3964986 TTTTACCTTT
*
3964996 TATTTTTTTAT-GTATAAAATATAA
1 TATTTTTTTATCAT-TAAAATATAA
3965020 TATTTTTTTATCATTAAAATATAA
1 TATTTTTTTATCATTAAAATATAA
3965044 TA
1 TA
3965046 ATCTTAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TATTTTTTTATCATTAAAATATAA
Found at i:3968369 original size:23 final size:23
Alignment explanation
Indices: 3968343--3968397 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
3968333 TTTTTATAAT
* *
3968343 TTATAAAAAATATTTAAATTTTA
1 TTATAAAAAATATATAAATATTA
3968366 TTATAAAAAATATATAAATATTA
1 TTATAAAAAATATATAAATATTA
*
3968389 ATATAAAAA
1 TTATAAAAA
3968398 TAATTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTATAAAAAATATATAAATATTA
Found at i:3968418 original size:30 final size:31
Alignment explanation
Indices: 3968384--3968444 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
3968374 AATATATAAA
*
3968384 TATTAA-TATAAA-AATAATTTTTAATTTTTT
1 TATTAATTATAAATAATAA-TTTAAATTTTTT
3968414 TATTAATTTATAAATAATAATTTAAATTTTT
1 TATTAA-TTATAAATAATAATTTAAATTTTT
3968445 AAGTAGGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 6 0.22
32 16 0.59
33 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TATTAATTATAAATAATAATTTAAATTTTTT
Found at i:3968445 original size:30 final size:30
Alignment explanation
Indices: 3968384--3968445 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
3968374 AATATATAAA
* *
3968384 TATTAATATAAAAATAATTTTTAATTTTTT
1 TATTAATATAAAAATAATATTTAATATTTT
* *
3968414 TATTAATTTATAAATAATAATTTAA-ATTTT
1 TATTAATATAAAAATAAT-ATTTAATATTTT
3968444 TA
1 TA
3968446 AGTAGGGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TATTAATATAAAAATAATATTTAATATTTT
Found at i:3968497 original size:22 final size:22
Alignment explanation
Indices: 3968466--3968536 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
3968456 AATTTAAACA
* *
3968466 TAAACAAAATTTAAAAAACTTT
1 TAAATAAAAATTAAAAAACTTT
* * **
3968488 TAAAT-TAAATCAAAATAACAAT
1 TAAATAAAAATTAAAA-AACTTT
3968510 TAAATAAAAAATTAAAAAA-TTT
1 TAAAT-AAAAATTAAAAAACTTT
3968532 TAAAT
1 TAAAT
3968537 CGTGACTACT
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
21 7 0.19
22 19 0.53
23 2 0.06
24 8 0.22
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAATAAAAATTAAAAAACTTT
Found at i:3969930 original size:21 final size:23
Alignment explanation
Indices: 3969891--3969940 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
3969881 TTTTCGATTA
3969891 AAAAATATATTTTTATATAATAT
1 AAAAATATATTTTTATATAATAT
* *
3969914 AAAAATA-ATTTTT-TATATTTT
1 AAAAATATATTTTTATATAATAT
3969935 AAAAAT
1 AAAAAT
3969941 TTTAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 6 0.24
23 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAAATATATTTTTATATAATAT
Found at i:3972148 original size:2 final size:2
Alignment explanation
Indices: 3972141--3972205 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
3972131 AATGGACAAG
*
3972141 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA 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
3972183 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
3972206 GATTTGTCTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.