Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 18 of 21
Found at i:2939375 original size:5 final size:5
Alignment explanation
Indices: 2939365--2939415 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
2939355 GTTTTCAAAT
*
2939365 ATATA ATATA ATATA ATATA ATATA TATTTA TATCATA A-ATA ATA-A
1 ATATA ATATA ATATA ATATA ATATA -ATATA -AT-ATA ATATA ATATA
2939411 ATATA
1 ATATA
2939416 TATTATATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 8 0.20
5 22 0.55
6 8 0.20
7 2 0.05
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:2939410 original size:25 final size:26
Alignment explanation
Indices: 2939363--2939437 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 26
2939353 AAGTTTTCAA
* *
2939363 ATATATAATATAATATAAT-ATAATAT
1 ATATATTATATCATA-AATAATAATAT
2939389 ATAT-TTATATCATAAATAATAA-AT
1 ATATATTATATCATAAATAATAATAT
*
2939413 ATATATTATATCATAATTAA-AATAT
1 ATATATTATATCATAAATAATAATAT
2939438 TAAAAAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 11 0.26
25 28 0.65
26 4 0.09
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATATTATATCATAAATAATAATAT
Found at i:2941363 original size:2 final size:2
Alignment explanation
Indices: 2941356--2941391 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2941346 TGAGTTTAAA
*
2941356 AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2941392 GTGCAAGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2943737 original size:2 final size:2
Alignment explanation
Indices: 2943732--2943765 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2943722 ATATATGTTA
2943732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2943766 GAAGAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2943945 original size:5 final size:5
Alignment explanation
Indices: 2943937--2944027 Score: 54
Period size: 5 Copynumber: 19.4 Consensus size: 5
2943927 ATAATAATTA
* * * *
2943937 ATATT ATA-T AAATT TTAAT ATATTT ATATT AT-TT -T-TT ATTTT ATATT
1 ATATT ATATT ATATT ATATT ATA-TT ATATT ATATT ATATT ATATT ATATT
* *
2943984 ATATT ATATT TTAATT A-ATT -TTTT ATATT ATA-T A-ATT ATATT AT
1 ATATT ATATT AT-ATT ATATT ATATT ATATT ATATT ATATT ATATT AT
2944028 GTCTAAAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
3 4 0.06
4 15 0.23
5 40 0.61
6 7 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
ATATT
Found at i:2943981 original size:17 final size:17
Alignment explanation
Indices: 2943959--2944016 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
2943949 TTTTAATATA
2943959 TTTATATTATTTTTTAT
1 TTTATATTATTTTTTAT
* *
2943976 TTTATATTATATTATAT
1 TTTATATTATTTTTTAT
2943993 TTTA-ATTAATTTTTTAT
1 TTTATATT-ATTTTTTAT
*
2944010 ATTATAT
1 TTTATAT
2944017 AATTATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 3 0.09
17 29 0.85
18 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATATTATTTTTTAT
Found at i:2947789 original size:22 final size:22
Alignment explanation
Indices: 2947759--2947828 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 22
2947749 AAAAGCTTAA
2947759 TTTATATTAAATAATTAAAATAT
1 TTTATATTAAATAA-TAAAATAT
*
2947782 TTTA-ATTAAATTATAAAATAT
1 TTTATATTAAATAATAAAATAT
** *
2947803 ATAAATATT-AA-AATAAAATCT
1 -TTTATATTAAATAATAAAATAT
2947824 TTTAT
1 TTTAT
2947829 TAATTATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
20 3 0.08
21 16 0.42
22 12 0.32
23 7 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTATATTAAATAATAAAATAT
Found at i:2951302 original size:21 final size:22
Alignment explanation
Indices: 2951278--2951318 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2951268 TTAAATTTTA
2951278 TATAATTTATA-TTTATTTAAT
1 TATAATTTATATTTTATTTAAT
*
2951299 TATATTTTATATTTTATTTA
1 TATAATTTATATTTTATTTA
2951319 TATAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATAATTTATATTTTATTTAAT
Found at i:2951629 original size:2 final size:2
Alignment explanation
Indices: 2951622--2951651 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2951612 CGAAATTTCA
*
2951622 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2951652 TCGGCTGAAG
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:2955587 original size:10 final size:10
Alignment explanation
Indices: 2955572--2955605 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2955562 AATAAGAAGC
2955572 AAAGAAAAAA
1 AAAGAAAAAA
2955582 AAAGAAAAAA
1 AAAGAAAAAA
2955592 AAA-AAAAAA
1 AAAGAAAAAA
2955601 GAAAG
1 -AAAG
2955606 GAAAGTGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:2956513 original size:15 final size:15
Alignment explanation
Indices: 2956489--2956526 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2956479 GCCAGAATCG
*
2956489 GATGACGAGGAGGAA
1 GATGAAGAGGAGGAA
*
2956504 GATGAAGAGGAGGAG
1 GATGAAGAGGAGGAA
2956519 GATGAAGA
1 GATGAAGA
2956527 TGATCCAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.47, T:0.08
Consensus pattern (15 bp):
GATGAAGAGGAGGAA
Found at i:2958834 original size:18 final size:18
Alignment explanation
Indices: 2958792--2958834 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2958782 AAAGAGAAGT
*
2958792 GATGATGATGCAGAGGAG
1 GATGATGATGCAGAGGAA
*
2958810 GAGGATGATG-ATGAGGAA
1 GATGATGATGCA-GAGGAA
2958828 GATGATG
1 GATGATG
2958835 TTGTTGAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.35, C:0.02, G:0.44, T:0.19
Consensus pattern (18 bp):
GATGATGATGCAGAGGAA
Found at i:2960720 original size:5 final size:5
Alignment explanation
Indices: 2960712--2960792 Score: 67
Period size: 5 Copynumber: 15.6 Consensus size: 5
2960702 AAAAAGGCAT
* * *
2960712 AAAGA AAAGA AAA-A AAAGA AAAGA AAA-C AGAGA AAAGGA AAGGA AAAGGAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA-GA AAAGA AAA-G-A
*
2960763 AAAGAA AAAGAA AAAGA AAATA AAAGA AAA
1 AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA
2960793 TAAATCAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
4 6 0.10
5 35 0.56
6 18 0.29
7 4 0.06
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAGA
Found at i:2960725 original size:6 final size:6
Alignment explanation
Indices: 2960697--2960782 Score: 66
Period size: 6 Copynumber: 13.5 Consensus size: 6
2960687 TAGTTTTTGG
* * *
2960697 AAAAGA AAAAGGCA TAAAG- AAAAGAA AAAAAA GAAAAGA AAACAGA GAAAAGG
1 AAAAGA AAAA-G-A AAAAGA AAAAG-A AAAAGA -AAAAGA AAA-AGA -AAAAGA
* *
2960750 AAAGGA AAAGGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA
2960783 TAAAAGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
5 4 0.06
6 38 0.58
7 16 0.25
8 7 0.11
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:2960734 original size:19 final size:19
Alignment explanation
Indices: 2960712--2960792 Score: 74
Period size: 19 Copynumber: 4.2 Consensus size: 19
2960702 AAAAAGGCAT
2960712 AAAGAAAAGAAAAAAAAGA
1 AAAGAAAAGAAAAAAAAGA
* * *
2960731 AAAGAAAACAGAGAAAAGGA
1 AAAGAAAAGA-AAAAAAAGA
* * *
2960751 AAGGAAAAGGAAAAAGA-A
1 AAAGAAAAGAAAAAAAAGA
2960769 AAAGAAAAAGAAAATAAAAGA
1 AAAG-AAAAGAAAA-AAAAGA
2960790 AAA
1 AAA
2960793 TAAATCAATA
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
18 4 0.09
19 21 0.46
20 17 0.37
21 4 0.09
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (19 bp):
AAAGAAAAGAAAAAAAAGA
Found at i:2963774 original size:27 final size:27
Alignment explanation
Indices: 2963715--2963810 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 27
2963705 TAAACACCAA
* *
2963715 TTTTGACAAACAACAA-G--CCATAAT
1 TTTTGACAAACAAAAAGGAACCATCAT
* * *
2963739 TTTTTACAAACAAAAAGGAATCATTAT
1 TTTTGACAAACAAAAAGGAACCATCAT
* * *
2963766 TTTTGACAAATATAAAGTAACCATCAT
1 TTTTGACAAACAAAAAGGAACCATCAT
*
2963793 TTTTGACAAACACAAAGG
1 TTTTGACAAACAAAAAGG
2963811 GTGGTTTTTG
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
24 14 0.25
25 1 0.02
27 41 0.73
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (27 bp):
TTTTGACAAACAAAAAGGAACCATCAT
Found at i:2968283 original size:23 final size:24
Alignment explanation
Indices: 2968256--2968307 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2968246 TCATTTTATA
*
2968256 ATAAA-AATTAATCATCAA-TTTTG
1 ATAAACAATAAATCAT-AATTTTTG
2968279 ATAAACAATAAATCATAATTTTTG
1 ATAAACAATAAATCATAATTTTTG
2968303 ATAAA
1 ATAAA
2968308 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
ATAAACAATAAATCATAATTTTTG
Found at i:2968293 original size:24 final size:23
Alignment explanation
Indices: 2968256--2968348 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 23
2968246 TCATTTTATA
*
2968256 ATAAAAATTAATCATCAA-TTTTG
1 ATAAAAATAAATCAT-AATTTTTG
2968279 ATAAACAATAAATCATAATTTTTG
1 ATAAA-AATAAATCATAATTTTTG
* * *
2968303 ATAAATAAAAAAAATCATTATTTTTT
1 AT--A-AAAATAAATCATAATTTTTG
* *
2968329 ATAAATATAAAATAATAATT
1 ATAAAAAT-AAATCATAATT
2968349 ATTTTTAACA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
23 10 0.18
24 26 0.46
26 18 0.32
27 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (23 bp):
ATAAAAATAAATCATAATTTTTG
Found at i:2968310 original size:28 final size:27
Alignment explanation
Indices: 2968255--2968343 Score: 89
Period size: 26 Copynumber: 3.4 Consensus size: 27
2968245 CTCATTTTAT
*
2968255 AATAAAAATTAATCATCAA-TTTTGAT-
1 AATAAAAATAAATCAT-AATTTTTGATA
*
2968281 -A-AACAATAAATCATAATTTTTGATA
1 AATAAAAATAAATCATAATTTTTGATA
* *
2968306 AATAAAAA-AAATCATTATTTTTTATA
1 AATAAAAATAAATCATAATTTTTGATA
2968332 AATATAAAATAA
1 AATA-AAAATAA
2968344 TAATTATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
23 2 0.04
24 18 0.35
25 1 0.02
26 21 0.40
27 8 0.15
28 2 0.04
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (27 bp):
AATAAAAATAAATCATAATTTTTGATA
Found at i:2968340 original size:27 final size:26
Alignment explanation
Indices: 2968279--2968354 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
2968269 ATCAATTTTG
*
2968279 ATAAACAATAAATCATAATTTTTGATAA
1 ATAAA-AA-AAATCATTATTTTTGATAA
*
2968307 ATAAAAAAAATCATTATTTTTTATAA
1 ATAAAAAAAATCATTATTTTTGATAA
* *
2968333 ATATAAAATAATAATTATTTTT
1 ATA-AAAAAAATCATTATTTTT
2968355 AACAAACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 20 0.47
27 18 0.42
28 5 0.12
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (26 bp):
ATAAAAAAAATCATTATTTTTGATAA
Found at i:2968355 original size:26 final size:25
Alignment explanation
Indices: 2968296--2968355 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 25
2968286 ATAAATCATA
*
2968296 ATTTTTGATAAATAAAAAAAATCATT
1 ATTTTT-ATAAATAAAAAAAATAATT
*
2968322 ATTTTTTATAAATATAAAATAATAATT
1 A-TTTTTATAAATA-AAAAAAATAATT
2968349 ATTTTTA
1 ATTTTTA
2968356 ACAAACAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
ATTTTTATAAATAAAAAAAATAATT
Found at i:2968677 original size:34 final size:35
Alignment explanation
Indices: 2968610--2968677 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
2968600 TTGACGTGTA
*
2968610 TTGACTTCATCAATTTTCTGTTTTCTTGTATGGAC
1 TTGACTTCATCAATTTTCTGTTTTCTTGAATGGAC
**
2968645 TTGACTTCATCGGTTTTCT-TTTTCTTGAATGGA
1 TTGACTTCATCAATTTTCTGTTTTCTTGAATGGA
2968678 TTTTTTACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 13 0.43
35 17 0.57
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (35 bp):
TTGACTTCATCAATTTTCTGTTTTCTTGAATGGAC
Found at i:2976236 original size:2 final size:2
Alignment explanation
Indices: 2976229--2976267 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2976219 AGCTCAAATT
2976229 TA TA 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 TA TA T
2976268 TTATTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2982669 original size:16 final size:17
Alignment explanation
Indices: 2982645--2982685 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2982635 AAGTTAAATA
*
2982645 ATTACTTATTAATTT-T
1 ATTATTTATTAATTTAT
2982661 ATTATTTATTAATTTAT
1 ATTATTTATTAATTTAT
2982678 ATT-TTTAT
1 ATTATTTAT
2982686 ATTTAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTTATTAATTTAT
Found at i:2985216 original size:6 final size:6
Alignment explanation
Indices: 2985205--2985237 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2985195 TGTAAGTTTA
*
2985205 AAAATG AAAATG AAAATG AAAATG AAAAAG AAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAA
2985238 TTAGAGGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (6 bp):
AAAATG
Found at i:2986040 original size:3 final size:3
Alignment explanation
Indices: 2986032--2986062 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2986022 CCCAAAATTC
*
2986032 TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2986063 ATCTTTTCTG
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:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:2987011 original size:23 final size:21
Alignment explanation
Indices: 2986984--2987031 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
2986974 CGATTTAAAA
*
2986984 AATAAAAAAATATTTTAATAATT
1 AATAAAAAAATA-ATTAA-AATT
*
2987007 AATAATAAAATAATTAAAATT
1 AATAAAAAAATAATTAAAATT
2987028 AATA
1 AATA
2987032 TCAAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 11 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAAAAAAATAATTAAAATT
Found at i:2988315 original size:18 final size:19
Alignment explanation
Indices: 2988277--2988317 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2988267 TGTCCACTTC
*
2988277 TTTATTTTAAAATGATTAA
1 TTTATATTAAAATGATTAA
*
2988296 TTTATATTAAAAT-TTTAA
1 TTTATATTAAAATGATTAA
2988314 TTTA
1 TTTA
2988318 AATCACCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTATATTAAAATGATTAA
Found at i:2988721 original size:28 final size:28
Alignment explanation
Indices: 2988672--2988727 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2988662 TAAATAGTAT
**
2988672 AAAAATAATTAAATTATGATATAATATA
1 AAAAATAATTAAATTAAAATATAATATA
*
2988700 AAAAATAATTCAAA-TAAAATATTATATA
1 AAAAATAATT-AAATTAAAATATAATATA
2988728 GGATTGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAAATAATTAAATTAAAATATAATATA
Found at i:2989208 original size:3 final size:3
Alignment explanation
Indices: 2989200--2989246 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2989190 AAAATTAGAG
2989200 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2989247 GAAGAAGAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2989251 original size:3 final size:3
Alignment explanation
Indices: 2989245--2989287 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2989235 TAATAATAAT
2989245 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2989288 GGACGAAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2991198 original size:18 final size:18
Alignment explanation
Indices: 2991171--2991212 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2991161 TTAAGGGAAA
*
2991171 AAAAGAAAGAAAAAAGAG
1 AAAAGGAAGAAAAAAGAG
2991189 AAAAGGAAGAAAAAAGAG
1 AAAAGGAAGAAAAAAGAG
2991207 AAAAGG
1 AAAAGG
2991213 GCTCTCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AAAAGGAAGAAAAAAGAG
Found at i:2991419 original size:37 final size:35
Alignment explanation
Indices: 2991373--2991441 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
2991363 ATATATACAA
2991373 AATAAAAAAATAATTAAAATATAAATATAATATATAT
1 AATAAAAAAAT-ATTAAAA-ATAAATATAATATATAT
* * **
2991410 AATATAAAAATTTTAAAAATTTATATAATATA
1 AATAAAAAAATATTAAAAATAAATATAATATA
2991442 AAAATTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 12 0.43
36 6 0.21
37 10 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (35 bp):
AATAAAAAAATATTAAAAATAAATATAATATATAT
Found at i:2991434 original size:26 final size:26
Alignment explanation
Indices: 2991405--2991469 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
2991395 AAATATAATA
2991405 TATATAATATAAAAATTTTAAAAATT
1 TATATAATATAAAAATTTTAAAAATT
2991431 TATATAATATAAAAATTTTAAAAATT
1 TATATAATATAAAAATTTTAAAAATT
2991457 TATATAATATAAA
1 TATATAATATAAA
2991470 TTACTAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TATATAATATAAAAATTTTAAAAATT
Found at i:2994963 original size:2 final size:2
Alignment explanation
Indices: 2994958--2994988 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2994948 TCCTTTTCCT
2994958 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 T
2994989 TCTTGGGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2995451 original size:8 final size:8
Alignment explanation
Indices: 2995440--2995481 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
2995430 TTTTATATTT
2995440 ATATTTAA
1 ATATTTAA
2995448 ATATTTAA
1 ATATTTAA
2995456 A-ATTATAAA
1 ATATT-T-AA
*
2995465 AAATTTAA
1 ATATTTAA
2995473 ATATTTAA
1 ATATTTAA
2995481 A
1 A
2995482 AAAAGAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
7 3 0.10
8 20 0.67
9 4 0.13
10 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATTTAA
Found at i:2995472 original size:17 final size:17
Alignment explanation
Indices: 2995440--2995484 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
2995430 TTTTATATTT
*
2995440 ATATTT-AAATATTTAA
1 ATATTTAAAAAATTTAA
2995456 A-ATTATAAAAAATTTAA
1 ATATT-TAAAAAATTTAA
2995473 ATATTTAAAAAA
1 ATATTTAAAAAA
2995485 AGAATCAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 17 0.68
18 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATTTAAAAAATTTAA
Found at i:2996123 original size:13 final size:13
Alignment explanation
Indices: 2996101--2996133 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2996091 ATTTATATTT
*
2996101 AAATATATATTAA
1 AAATAAATATTAA
2996114 AAATAAATATTAA
1 AAATAAATATTAA
2996127 AAA-AAAT
1 AAATAAAT
2996134 TAAAGTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATATTAA
Found at i:2998384 original size:4 final size:4
Alignment explanation
Indices: 2998375--2998402 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2998365 AATTACTTGC
2998375 AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT
2998403 CGTCTCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:3000629 original size:2 final size:2
Alignment explanation
Indices: 3000622--3000646 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3000612 TCTTTTAAAT
3000622 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3000647 TCTACTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3009686 original size:25 final size:27
Alignment explanation
Indices: 3009628--3009686 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
3009618 AAATTTAAAG
* *
3009628 TTTAAATTTTAAATTTTTAATATTTTT
1 TTTAATTTTTAAATTTATAATATTTTT
*
3009655 ATT-ATTTTTAAA-TTATAAT-TTTTT
1 TTTAATTTTTAAATTTATAATATTTTT
3009679 TTTAATTT
1 TTTAATTT
3009687 CTCCCTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 7 0.26
25 10 0.37
26 8 0.30
27 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTAATTTTTAAATTTATAATATTTTT
Found at i:3010381 original size:8 final size:8
Alignment explanation
Indices: 3010370--3010436 Score: 56
Period size: 7 Copynumber: 9.1 Consensus size: 8
3010360 TATTAAAATT
3010370 TATATAAA
1 TATATAAA
3010378 TATA-AAA
1 TATATAAA
* *
3010385 TATTTTAA
1 TATATAAA
*
3010393 -ATATAAT
1 TATATAAA
3010400 TATA-AAA
1 TATATAAA
3010407 TA-ATAAA
1 TATATAAA
*
3010414 -ATATATA
1 TATATAAA
3010421 -ATATAAA
1 TATATAAA
3010428 TATATAAA
1 TATATAAA
3010436 T
1 T
3010437 TATTATATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
6 2 0.04
7 27 0.59
8 17 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TATATAAA
Found at i:3010425 original size:22 final size:23
Alignment explanation
Indices: 3010356--3010435 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 23
3010346 AAAAAATATC
3010356 AATATATTAAAATTTATATAAATATAA
1 AATATA-TAAAA--TATAT-AATATAA
* * *
3010383 AATATTTTAAATATA-ATTATAA
1 AATATATAAAATATATAATATAA
3010405 AATA-ATAAAATATATAATAT-A
1 AATATATAAAATATATAATATAA
3010426 AATATATAAA
1 AATATATAAA
3010436 TTATTATATT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 13 0.29
22 19 0.42
24 4 0.09
26 4 0.09
27 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AATATATAAAATATATAATATAA
Found at i:3012170 original size:3 final size:3
Alignment explanation
Indices: 3012162--3012206 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
3012152 GAAAGAAAAT
*
3012162 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3012207 AGGAGAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3013338 original size:17 final size:17
Alignment explanation
Indices: 3013283--3013352 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
3013273 CTCGATATTT
*
3013283 TAAATTT-AATTTTATT
1 TAAATTTAAATTTTATA
* * *
3013299 TAATATTTGAATATAATA
1 TAA-ATTTAAATTTTATA
*
3013317 AAAATTTAAATTTTATA
1 TAAATTTAAATTTTATA
* * *
3013334 TAAATATAATTTTTTTA
1 TAAATTTAAATTTTATA
3013351 TA
1 TA
3013353 TTTTATAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
16 3 0.07
17 30 0.73
18 8 0.20
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (17 bp):
TAAATTTAAATTTTATA
Found at i:3014115 original size:2 final size:2
Alignment explanation
Indices: 3014108--3014135 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3014098 TCAGTCGCAC
3014108 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
3014136 GGGAACAGCT
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:3015764 original size:15 final size:15
Alignment explanation
Indices: 3015724--3015799 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
3015714 TAATAAATTT
* *
3015724 ATTAAAATTATTTAT
1 ATTAAAATTAATTAA
*
3015739 ATCATAAATTAATTAA
1 ATTA-AAATTAATTAA
*
3015755 ATTAAAATTAA-AAA
1 ATTAAAATTAATTAA
*
3015769 ATTTAAAA-T-ATAAA
1 A-TTAAAATTAATTAA
*
3015783 ATTAAAATTTATTAA
1 ATTAAAATTAATTAA
3015798 AT
1 AT
3015800 ATTATTTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 7 0.14
14 9 0.18
15 22 0.44
16 12 0.24
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAAATTAATTAA
Found at i:3015770 original size:14 final size:14
Alignment explanation
Indices: 3015753--3015791 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3015743 TAAATTAATT
3015753 AAATTAAAATTAAA
1 AAATTAAAATTAAA
*
3015767 AAATTTAAAA-TATA
1 AAA-TTAAAATTAAA
3015781 AAATTAAAATT
1 AAATTAAAATT
3015792 TATTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTAAAATTAAA
Found at i:3015799 original size:22 final size:23
Alignment explanation
Indices: 3015744--3015801 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
3015734 TTTATATCAT
*
3015744 AAATTAATTAAAT-TAAAATTAAA
1 AAATTTATTAAATATAAAATT-AA
3015767 AAATTTA--AAATATAAAATT-A
1 AAATTTATTAAATATAAAATTAA
3015787 AAATTTATTAAATAT
1 AAATTTATTAAATAT
3015802 TATTTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 8 0.26
21 4 0.13
22 13 0.42
23 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTATTAAATATAAAATTAA
Found at i:3023026 original size:20 final size:20
Alignment explanation
Indices: 3023001--3023072 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3022991 TTTAATAATT
*
3023001 TTTTTATCTAATTATATAAA
1 TTTTTATTTAATTATATAAA
* *
3023021 TTTTTATTTATTTTAATATAAT
1 TTTTTATTTA-ATT-ATATAAA
*
3023043 TTGTTTATTTAATTATAT-GA
1 TT-TTTATTTAATTATATAAA
3023063 TTTTTATTTA
1 TTTTTATTTA
3023073 TTTTAATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 8 0.19
20 11 0.26
21 6 0.14
22 10 0.23
23 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTTATTTAATTATATAAA
Found at i:3023051 original size:19 final size:20
Alignment explanation
Indices: 3023022--3023083 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 20
3023012 TTATATAAAT
3023022 TTTTATTTATTTTAATATAA
1 TTTTATTTATTTTAATATAA
*
3023042 -TTTGTTTA-TTTAATTATATGA
1 TTTTATTTATTTTAA-TATA--A
3023063 TTTTTATTTATTTTAATATAA
1 -TTTTATTTATTTTAATATAA
3023084 AAATAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
18 5 0.15
19 11 0.32
21 2 0.06
23 11 0.32
24 5 0.15
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTTATTTATTTTAATATAA
Found at i:3023053 original size:23 final size:21
Alignment explanation
Indices: 3023014--3023083 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
3023004 TTATCTAATT
3023014 ATATAAATTTTTATTTATTTTA
1 ATAT-AATTTTTATTTATTTTA
*
3023036 ATATAATTTGTTTATTTA-ATT-
1 ATATAA-TT-TTTATTTATTTTA
*
3023057 ATATGATTTTTATTTATTTTA
1 ATATAATTTTTATTTATTTTA
3023078 ATATAA
1 ATATAA
3023084 AAATAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 8 0.20
20 4 0.10
21 12 0.30
22 8 0.20
23 8 0.20
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (21 bp):
ATATAATTTTTATTTATTTTA
Found at i:3023079 original size:42 final size:43
Alignment explanation
Indices: 3022995--3023083 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 43
3022985 TAACATTTTA
*
3022995 ATAATTTTTTTATCTAATTATATAAATTTTTATTTATTTTAAT
1 ATAATTTGTTTATCTAATTATATAAATTTTTATTTATTTTAAT
* *
3023038 ATAATTTGTTTATTTAATTATAT-GATTTTTATTTATTTTAAT
1 ATAATTTGTTTATCTAATTATATAAATTTTTATTTATTTTAAT
3023080 ATAA
1 ATAA
3023084 AAATAATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
42 22 0.51
43 21 0.49
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (43 bp):
ATAATTTGTTTATCTAATTATATAAATTTTTATTTATTTTAAT
Found at i:3023436 original size:20 final size:20
Alignment explanation
Indices: 3023411--3023448 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3023401 AAAAATAATT
* *
3023411 TTAAAATTTTTTATTAATAC
1 TTAAAATTATTTAATAATAC
3023431 TTAAAATTATTTAATAAT
1 TTAAAATTATTTAATAAT
3023449 TTATAACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAAATTATTTAATAATAC
Found at i:3024436 original size:53 final size:53
Alignment explanation
Indices: 3024373--3024477 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
3024363 GGCTGAGATT
* *
3024373 TGGACAAGGAAATTTTTCGTCGGATGCTCTGGTAACAAATCAGGTGTCTGATC
1 TGGACAAGGAAATTGTTCGTCGGATGCTCTGGTAACAAAACAGGTGTCTGATC
* *
3024426 TGGACGAGGAAATTGTTCGTTGGATGCTCTGGTAACAAAACAGGTGTCTGAT
1 TGGACAAGGAAATTGTTCGTCGGATGCTCTGGTAACAAAACAGGTGTCTGAT
3024478 GTAGCCGATG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (53 bp):
TGGACAAGGAAATTGTTCGTCGGATGCTCTGGTAACAAAACAGGTGTCTGATC
Found at i:3025058 original size:21 final size:21
Alignment explanation
Indices: 3025025--3025078 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
3025015 TTTTGCTGTA
3025025 ATATTATTTTTATAAAACTTAC
1 ATATTA-TTTTATAAAACTTAC
3025047 ATATTATTTTATAAAACTTAC
1 ATATTATTTTATAAAACTTAC
*
3025068 AAATTATTTTA
1 ATATTATTTTA
3025079 AATTTAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTATTTTATAAAACTTAC
Found at i:3028066 original size:16 final size:16
Alignment explanation
Indices: 3028041--3028074 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3028031 TTTTAGAATC
* *
3028041 AAAATTAAAAATTAAA
1 AAAATGAAAAATGAAA
3028057 AAAATGAAAAATGAAA
1 AAAATGAAAAATGAAA
3028073 AA
1 AA
3028075 TTTAGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAATGAAAAATGAAA
Found at i:3033111 original size:2 final size:2
Alignment explanation
Indices: 3033106--3033130 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3033096 AAATTGTGTG
3033106 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3033131 TTGACTTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3041731 original size:2 final size:2
Alignment explanation
Indices: 3041724--3041749 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3041714 TTCATACCTT
3041724 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
3041750 CCCCCCCCCT
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:3042794 original size:2 final size:2
Alignment explanation
Indices: 3042789--3042817 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3042779 TAATATATAA
3042789 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
3042818 ATTCATGAAA
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:3056019 original size:19 final size:19
Alignment explanation
Indices: 3055959--3056019 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
3055949 AAATATTAAA
*
3055959 ATATTAAAATTTT-TAA-T
1 ATATTTAAATTTTATAATT
3055976 ATATTTAAACTTTTATAACTT
1 ATATTTAAA-TTTTATAA-TT
*
3055997 ATATTTATATTTTATAATT
1 ATATTTAAATTTTATAATT
3056016 ATAT
1 ATAT
3056020 ATGTCGAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 8 0.21
18 4 0.11
19 9 0.24
20 8 0.21
21 9 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTAAATTTTATAATT
Found at i:3056020 original size:21 final size:22
Alignment explanation
Indices: 3055974--3056021 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
3055964 AAAATTTTTA
3055974 ATATATTTAAACTTTTATAACT
1 ATATATTTAAACTTTTATAACT
* *
3055996 -TATATTTATA-TTTTATAATT
1 ATATATTTAAACTTTTATAACT
3056016 ATATAT
1 ATATAT
3056022 GTCGAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATATTTAAACTTTTATAACT
Found at i:3057386 original size:17 final size:18
Alignment explanation
Indices: 3057348--3057390 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
3057338 TAGTAATATT
3057348 TTATCTAAAATATAATAA
1 TTATCTAAAATATAATAA
*
3057366 TTAT-TAAAA-ATTATAA
1 TTATCTAAAATATAATAA
3057382 GTTATCTAA
1 -TTATCTAA
3057391 TATGATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (18 bp):
TTATCTAAAATATAATAA
Found at i:3057715 original size:21 final size:21
Alignment explanation
Indices: 3057690--3057739 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 21
3057680 CTGTATGACT
* * *
3057690 TGATAATATAATATGATTATA
1 TGATAATATAAAATAATTAAA
3057711 TGAT-ATA-AAAATAATTAAA
1 TGATAATATAAAATAATTAAA
3057730 T-ATAATATAA
1 TGATAATATAA
3057740 CTTTATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 5 0.21
21 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (21 bp):
TGATAATATAAAATAATTAAA
Found at i:3059876 original size:37 final size:36
Alignment explanation
Indices: 3059829--3059905 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
3059819 AAAGATTTAT
* *
3059829 TTATTAATTTAAAAATATTTTTATATT-TAATATATTA
1 TTATTAATTTAAAAAAATTATTA-ATTAT-ATATATTA
*
3059866 TTATTAATTTAAAAAAATTATTAATTATATATATTT
1 TTATTAATTTAAAAAAATTATTAATTATATATATTA
3059902 TTAT
1 TTAT
3059906 AAATATAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 14 0.39
37 22 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
TTATTAATTTAAAAAAATTATTAATTATATATATTA
Found at i:3059889 original size:17 final size:17
Alignment explanation
Indices: 3059829--3059891 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 17
3059819 AAAGATTTAT
3059829 TTATTAATTTAAAAATA
1 TTATTAATTTAAAAATA
* *
3059846 TTTTTATATTTAATATATTA
1 TTATTA-ATTTAA-A-AATA
*
3059866 TTATTAATTTAAAAAAA
1 TTATTAATTTAAAAATA
3059883 TTATTAATT
1 TTATTAATT
3059892 ATATATATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 16 0.42
18 7 0.18
19 7 0.18
20 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTAATTTAAAAATA
Found at i:3065577 original size:28 final size:28
Alignment explanation
Indices: 3065541--3065616 Score: 68
Period size: 28 Copynumber: 2.7 Consensus size: 28
3065531 ACAACATTTA
*
3065541 TATATTTATGTTATTCTGT-ATTAATTTTT
1 TATATTTATATTATT-TGTAATT-ATTTTT
*
3065570 TATA-TTATATTATTTTTAATTATTTTT
1 TATATTTATATTATTTGTAATTATTTTT
*
3065597 TAT-TATATAATTATATTGTA
1 TATATTTAT-ATTAT-TTGTA
3065617 TACAAAATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 14 0.36
28 17 0.44
29 8 0.21
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (28 bp):
TATATTTATATTATTTGTAATTATTTTT
Found at i:3066261 original size:2 final size:2
Alignment explanation
Indices: 3066256--3066282 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3066246 CAAATCTCTT
3066256 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
3066283 GTAGGAATTG
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:3068247 original size:27 final size:28
Alignment explanation
Indices: 3068195--3068254 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
3068185 AATCATTATC
**
3068195 TAAATAATAAATTATTTAAATTTAATTA
1 TAAATAATAAATTATTTAAAAATAATTA
3068223 TAAA-AATAAATT-TTTAATAAATAA-TA
1 TAAATAATAAATTATTTAA-AAATAATTA
3068249 -AAATAA
1 TAAATAA
3068255 ATTATTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
25 3 0.11
26 9 0.32
27 12 0.43
28 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAATAATAAATTATTTAAAAATAATTA
Found at i:3075250 original size:13 final size:12
Alignment explanation
Indices: 3075213--3075263 Score: 57
Period size: 12 Copynumber: 4.0 Consensus size: 12
3075203 AAAATAATAT
*
3075213 ATATTTATATAA
1 ATATTTATATTA
*
3075225 ATTTTAATATATTA
1 ATATT--TATATTA
3075239 ATAATTTATATTA
1 AT-ATTTATATTA
3075252 ATATTTATATTA
1 ATATTTATATTA
3075264 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 14 0.42
13 9 0.27
14 8 0.24
15 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATATTTATATTA
Found at i:3078924 original size:24 final size:24
Alignment explanation
Indices: 3078879--3078932 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
3078869 TCGAATAAGG
*
3078879 AAATA-ATTATTTGATATATATAT
1 AAATATATTATTTGAAATATATAT
*
3078902 ATATATATTAGTTTGAAAT-TATAT
1 AAATATATTA-TTTGAAATATATAT
3078926 AAATATA
1 AAATATA
3078933 AAAATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 15 0.58
25 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
AAATATATTATTTGAAATATATAT
Found at i:3078951 original size:28 final size:29
Alignment explanation
Indices: 3078920--3078993 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 29
3078910 TAGTTTGAAA
3078920 TTATATAAATATAAAAATA-TATTAAATT
1 TTATATAAATATAAAAATATTATTAAATT
* * *
3078948 TTATATAAATAT-ATAATATTTTTATATT
1 TTATATAAATATAAAAATATTATTAAATT
*
3078976 TT-TATAAAAATAAAAATA
1 TTATATAAATATAAAAATA
3078994 ACATAAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 13 0.33
28 26 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTATATAAATATAAAAATATTATTAAATT
Found at i:3078957 original size:20 final size:20
Alignment explanation
Indices: 3078929--3078973 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3078919 ATTATATAAA
*
3078929 TATAAAAATATATTAA-ATTT
1 TATATAAATATA-TAATATTT
3078949 TATATAAATATATAATATTT
1 TATATAAATATATAATATTT
3078969 T-TATA
1 TATATA
3078974 TTTTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATAAATATATAATATTT
Found at i:3080572 original size:26 final size:26
Alignment explanation
Indices: 3080529--3080583 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
3080519 TTTTTATATT
** *
3080529 AAAAAATATTTTTGAATTGAAATTATA
1 AAAAAATAAATTTGAATTAAAATTA-A
3080556 AAAAAATAAATTT-AATTAAAATTAA
1 AAAAAATAAATTTGAATTAAAATTAA
3080581 AAA
1 AAA
3080584 TTTAATGCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.16
26 10 0.40
27 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
AAAAAATAAATTTGAATTAAAATTAA
Found at i:3080825 original size:27 final size:28
Alignment explanation
Indices: 3080773--3080825 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
3080763 ATTCAATTCA
*
3080773 AACTATTATTTAAAGAAACTAATGGATT
1 AACTATTATTTAAAGAAACGAATGGATT
*
3080801 AACTATT-TTTTAAGAAA-GAAGTGGA
1 AACTATTATTTAAAGAAACGAA-TGGA
3080826 CTCTTTATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 2 0.09
27 13 0.59
28 7 0.32
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (28 bp):
AACTATTATTTAAAGAAACGAATGGATT
Found at i:3081485 original size:28 final size:27
Alignment explanation
Indices: 3081430--3081495 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
3081420 GTCACCTATT
*
3081430 TGTTTGTTAAAAATGGTGGTGATTTTG
1 TGTTTGTCAAAAATGGTGGTGATTTTG
**
3081457 TGTTTGTCAAAAATGGTGGTTTTCTTTG
1 TGTTTGTCAAAAATGGTGGTGAT-TTTG
*
3081485 TATTTGTCAAA
1 TGTTTGTCAAA
3081496 TATGAAGGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.59
28 14 0.41
ACGTcount: A:0.23, C:0.05, G:0.24, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTGATTTTG
Found at i:3086060 original size:28 final size:27
Alignment explanation
Indices: 3086005--3086075 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
3085995 GCCACCCATT
3086005 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
3086032 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
3086060 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
3086076 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:3087073 original size:23 final size:21
Alignment explanation
Indices: 3087032--3087080 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
3087022 CGTTATAATT
* *
3087032 TTTTTTATTATTTTATTTTTATA
1 TTTTTTATGATTGTA-TTTTA-A
*
3087055 TTTTTTATGATTGTGTTTTAA
1 TTTTTTATGATTGTATTTTAA
3087076 TTTTT
1 TTTTT
3087081 AATTTAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
22 5 0.22
23 12 0.52
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTTTTATGATTGTATTTTAA
Found at i:3093751 original size:2 final size:2
Alignment explanation
Indices: 3093739--3093775 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3093729 ATAAGGACAT
*
3093739 GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3093776 GAAAGGAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3099867 original size:137 final size:139
Alignment explanation
Indices: 3099607--3099876 Score: 300
Period size: 137 Copynumber: 1.9 Consensus size: 139
3099597 AGCAAAGCCT
* * * * *
3099607 CTAACAGAATAAATTCTGTAGATTAAAGTTAGAATGTCATTGTGACATAACATATGAGAGTCAAC
1 CTAACAGAACAAATTCTGTAGATGAAAATTAGAATGTCATTGTGACACAACACAT-AGAGTCAAC
* * **
3099672 TTAGGGTATAAAACCGTACATCCTTCCTATGAACCTGTGAATGGAGCACAGCTTAACATGCCAAC
65 TTAGGGTATAAAACCGTACATCCTTCCTATAAACCAGTGAATGGAGCACAGCGCAACATGCCAAC
3099737 AAACAATGTA
130 AAACAATGTA
* * *
3099747 CTAAGAGAACAAATTCTGTAGATGAAAATTAGAATGT-ATTTGTGACGCAA-ACAT-GAGTCTA-
1 CTAACAGAACAAATTCTGTAGATGAAAATTAGAATGTCA-TTGTGACACAACACATAGAGTCAAC
* * * * *
3099808 TTGAGGGTATAAAACTGTTCAT-CTTCCCTATAAATCAGTGAACTGG-GTACAGCGCAACATTCC
65 TT-AGGGTATAAAACCGTACATCCTT-CCTATAAACCAGTGAA-TGGAGCACAGCGCAACATGCC
3099871 AACAAA
127 AACAAA
3099877 AACAGTGTAG
Statistics
Matches: 109, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
136 5 0.05
137 55 0.50
138 3 0.03
139 4 0.04
140 42 0.39
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (139 bp):
CTAACAGAACAAATTCTGTAGATGAAAATTAGAATGTCATTGTGACACAACACATAGAGTCAACT
TAGGGTATAAAACCGTACATCCTTCCTATAAACCAGTGAATGGAGCACAGCGCAACATGCCAACA
AACAATGTA
Found at i:3103503 original size:13 final size:14
Alignment explanation
Indices: 3103485--3103513 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3103475 TACTTAGGAA
3103485 TTTAAT-TATATTT
1 TTTAATATATATTT
3103498 TTTAATATATATTT
1 TTTAATATATATTT
3103512 TT
1 TT
3103514 ATATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTAATATATATTT
Found at i:3103567 original size:18 final size:17
Alignment explanation
Indices: 3103516--3103567 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
3103506 ATATTTTTAT
*
3103516 ATTTAATAAATATTAAAA
1 ATTTAATATATA-TAAAA
* *
3103534 ATTGTAATTTAAATAAAA
1 ATT-TAATATATATAAAA
3103552 ATTTAAATATATATAA
1 ATTT-AATATATATAA
3103568 TCGAATTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 20 0.74
19 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
ATTTAATATATATAAAA
Found at i:3103703 original size:22 final size:20
Alignment explanation
Indices: 3103660--3103717 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 20
3103650 ATTTATTTTT
3103660 AATTAAATTTAAATTTTAAA
1 AATTAAATTTAAATTTTAAA
3103680 AATTAAATTT-AATTGAGTTAAA
1 AATTAAATTTAAATT---TTAAA
3103702 AATTAAATTTTAAATT
1 AATTAAA-TTTAAATT
3103718 GGTTTCGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.12
20 10 0.30
22 12 0.36
23 3 0.09
24 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AATTAAATTTAAATTTTAAA
Found at i:3110216 original size:34 final size:34
Alignment explanation
Indices: 3110178--3110246 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
3110168 TTCCCTTCTG
* *
3110178 AGACAGAGTAGCTTGTAACTTAACTATCAGAGAA
1 AGACAAAGTAGCTTGTAACTTAACTATCAAAGAA
*
3110212 AGACAAAGTTGCTTGTAACTTAACTATCAAAGAA
1 AGACAAAGTAGCTTGTAACTTAACTATCAAAGAA
3110246 A
1 A
3110247 AACTATCTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.25
Consensus pattern (34 bp):
AGACAAAGTAGCTTGTAACTTAACTATCAAAGAA
Found at i:3111223 original size:16 final size:16
Alignment explanation
Indices: 3111202--3111327 Score: 55
Period size: 17 Copynumber: 7.6 Consensus size: 16
3111192 AATATTATAA
3111202 TTATATTTAAAATATT
1 TTATATTTAAAATATT
3111218 TTATATTTATATAA-ATT
1 TTATATTTA-A-AATATT
*
3111235 TTAATATATT--AATAAT
1 TT-ATAT-TTAAAATATT
3111251 TTATATTATATAAAT-TT
1 TTATATT-TA-AAATATT
* * *
3111268 TAAAATATTAAAATTATA
1 TTATAT-TTAAAA-TATT
* *
3111286 TTATATTTTAATTATT
1 TTATATTTAAAATATT
* * *
3111302 TT-TATATAATATATAA
1 TTATATTTAAAATAT-T
3111318 TTATATTTAA
1 TTATATTTAA
3111328 TATTATCATA
Statistics
Matches: 80, Mismatches: 16, Indels: 27
0.65 0.13 0.22
Matches are distributed among these distances:
14 1 0.01
15 15 0.19
16 23 0.29
17 24 0.30
18 15 0.19
19 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:3111237 original size:27 final size:26
Alignment explanation
Indices: 3111207--3111319 Score: 77
Period size: 27 Copynumber: 4.0 Consensus size: 26
3111197 TATAATTATA
3111207 TTTAAAATATTTTATATTTATATAAAT
1 TTTAAAATATTTTATA-TTATATAAAT
3111234 TTTAATATATTAATAATTTATATTATATAAAT
1 TTTAA-A-A-T-AT--TTTATATTATATAAAT
* * *
3111266 TTTAAAATA-TTAAAATTATATTATAT
1 TTTAAAATATTTTATATTATA-TAAAT
* *
3111292 TTT-AATTATTTTTATATAATATATAAT
1 TTTAAAATA-TTTTATATTATATA-AAT
3111319 T
1 T
3111320 ATATTTAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
25 13 0.19
26 9 0.13
27 16 0.24
28 2 0.03
29 2 0.03
30 2 0.03
31 3 0.04
32 15 0.22
33 6 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTAAAATATTTTATATTATATAAAT
Found at i:3111249 original size:18 final size:18
Alignment explanation
Indices: 3111215--3111269 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
3111205 TATTTAAAAT
3111215 ATTTTATAT-TTATATAA
1 ATTTTATATATTATATAA
3111232 ATTTTAATATATTA-AT-A
1 ATTTT-ATATATTATATAA
3111249 A--TT-TATATTATATAA
1 ATTTTATATATTATATAA
3111264 ATTTTA
1 ATTTTA
3111270 AAATATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
13 7 0.23
14 2 0.06
15 4 0.13
17 9 0.29
18 6 0.19
19 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTATATATTATATAA
Found at i:3111263 original size:32 final size:32
Alignment explanation
Indices: 3111212--3111291 Score: 119
Period size: 32 Copynumber: 2.5 Consensus size: 32
3111202 TTATATTTAA
* *
3111212 AATATTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATA-TTATATAAATTTTAAAATATT
3111245 AATAATTTATATTATATAAATTTTAAAATATT
1 AATAATTTATATTATATAAATTTTAAAATATT
3111277 AA-AA-TTATATTATAT
1 AATAATTTATATTATAT
3111292 TTTAATTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 11 0.24
31 2 0.04
32 22 0.49
33 10 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
AATAATTTATATTATATAAATTTTAAAATATT
Found at i:3111306 original size:22 final size:22
Alignment explanation
Indices: 3111281--3111338 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3111271 AATATTAAAA
*
3111281 TTATATTATATTTTAATTAT-TT
1 TTATATTATA-TATAATTATATT
*
3111303 TTATATAATATATAATTATATT
1 TTATATTATATATAATTATATT
*
3111325 TAATATTATCATAT
1 TTATATTAT-ATAT
3111339 GATCGTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 8 0.27
22 18 0.60
23 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATTATATATAATTATATT
Found at i:3111929 original size:61 final size:61
Alignment explanation
Indices: 3111850--3111971 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
3111840 TTTTTCTCTC
*
3111850 TAATTTGCTTGGAAAAGAGTAGGAAGCTAGTGGTAGAATTCATGAATATAAATATAATATA
1 TAATTTGCTTAGAAAAGAGTAGGAAGCTAGTGGTAGAATTCATGAATATAAATATAATATA
*
3111911 TAATTTGTTTAGAAAAGAGTAGGAAGCTAGTGGTAGAATTCATGAATATAAATATAATATA
1 TAATTTGCTTAGAAAAGAGTAGGAAGCTAGTGGTAGAATTCATGAATATAAATATAATATA
3111972 AATATAGTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.32
Consensus pattern (61 bp):
TAATTTGCTTAGAAAAGAGTAGGAAGCTAGTGGTAGAATTCATGAATATAAATATAATATA
Found at i:3112162 original size:25 final size:25
Alignment explanation
Indices: 3112134--3112196 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
3112124 AATAAATAAT
3112134 TTTTATTTATTATATTGATAT-AAAA
1 TTTTATTTATTA-ATTGATATGAAAA
**
3112159 TTTTATTTATTAATTTTTATGAAAA
1 TTTTATTTATTAATTGATATGAAAA
3112184 -TTT-TTTATTAATT
1 TTTTATTTATTAATT
3112197 AGATTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 10 0.29
24 9 0.26
25 16 0.46
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTTATTTATTAATTGATATGAAAA
Found at i:3112350 original size:16 final size:16
Alignment explanation
Indices: 3112331--3112372 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3112321 TTTTTAATAT
3112331 TTTATTTATTAACGTA
1 TTTATTTATTAACGTA
**
3112347 TTTATTTATTAGTGTA
1 TTTATTTATTAACGTA
3112363 TTTATTTATT
1 TTTATTTATT
3112373 TTTTTTCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (16 bp):
TTTATTTATTAACGTA
Found at i:3112798 original size:28 final size:27
Alignment explanation
Indices: 3112767--3112862 Score: 77
Period size: 28 Copynumber: 3.3 Consensus size: 27
3112757 AATAAGAATG
3112767 ATTTTTTATTTTTAAAATTTTAATGATT
1 ATTTTTTATTTTTAAAATTTTAAT-ATT
* *
3112795 ATTTTTTTATTTTTTAAAAATAATTATTAATT
1 A-TTTTTTA-TTTTT-AAAAT-TTTAAT-ATT
* *
3112827 ATTTTTAATTTATT-AAATTTTATATAAT
1 ATTTTTTATTT-TTAAAATTTTA-ATATT
3112855 ATTTTTTA
1 ATTTTTTA
3112863 ATTAATATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
28 13 0.24
29 12 0.22
30 8 0.15
31 13 0.24
32 8 0.15
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (27 bp):
ATTTTTTATTTTTAAAATTTTAATATT
Found at i:3112832 original size:31 final size:30
Alignment explanation
Indices: 3112767--3112843 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 30
3112757 AATAAGAATG
* *
3112767 ATTTTTTA-TTTTT-AAAATTTTAATGATT
1 ATTTTTTATTTTTTAAAAATATTAATAATT
*
3112795 ATTTTTTTATTTTTTAAAAATAATTATTAATT
1 A-TTTTTTATTTTTTAAAAAT-ATTAATAATT
* *
3112827 ATTTTTAATTTATTAAA
1 ATTTTTTATTTTTTAAA
3112844 TTTTATATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 7 0.17
30 5 0.12
31 19 0.47
32 8 0.20
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (30 bp):
ATTTTTTATTTTTTAAAAATATTAATAATT
Found at i:3113128 original size:3 final size:3
Alignment explanation
Indices: 3113120--3113148 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3113110 TCTCATATTT
3113120 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3113149 TTATAAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3125088 original size:29 final size:29
Alignment explanation
Indices: 3125056--3125130 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
3125046 AATTTTTTTT
3125056 AATTATTATTTT-TTTAATTA-TAATATTTAA
1 AATTATTATTTTATTTAA--AGTAAT-TTTAA
* *
3125086 ATTTAATATTTTATTTAAAGTAATTTTAA
1 AATTATTATTTTATTTAAAGTAATTTTAA
3125115 AATTATTATTTTATTT
1 AATTATTATTTTATTT
3125131 TTTTCAACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 20 0.51
30 14 0.36
31 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
AATTATTATTTTATTTAAAGTAATTTTAA
Found at i:3138626 original size:6 final size:6
Alignment explanation
Indices: 3138588--3138623 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
3138578 TCAAACGAAA
*
3138588 TCCTCG TCCTCG TCCTCG TCCTCG TCCTCG ACCTCG
1 TCCTCG TCCTCG TCCTCG TCCTCG TCCTCG TCCTCG
3138624 ACCAACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.50, G:0.17, T:0.31
Consensus pattern (6 bp):
TCCTCG
Found at i:3139304 original size:2 final size:2
Alignment explanation
Indices: 3139297--3139333 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3139287 AAACAATTCT
3139297 TA 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 TA T
3139334 CTAAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3146791 original size:2 final size:2
Alignment explanation
Indices: 3146784--3146817 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3146774 TGGTTTATGA
3146784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3146818 TTTACATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3153404 original size:13 final size:13
Alignment explanation
Indices: 3153372--3153414 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3153362 TATTATCTAT
3153372 AATTAATTTTAAA
1 AATTAATTTTAAA
*
3153385 AAATAATTTTAAA
1 AATTAATTTTAAA
**
3153398 TTTTAATATTTAAA
1 AATTAAT-TTTAAA
3153412 AAT
1 AAT
3153415 CTTTTTCTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTAATTTTAAA
Found at i:3154957 original size:16 final size:17
Alignment explanation
Indices: 3154916--3154961 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
3154906 TTTATATATT
3154916 TTTTTATTATAATTATA
1 TTTTTATTATAATTATA
** *
3154933 TTTAAATTAT-TTTATA
1 TTTTTATTATAATTATA
3154949 TTTTTATTA-AATT
1 TTTTTATTATAATT
3154962 TAATACATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTATTATAATTATA
Found at i:3155668 original size:17 final size:16
Alignment explanation
Indices: 3155639--3155684 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
3155629 TATTTAAGTC
3155639 ATTATATATATATATTA
1 ATTATA-ATATATATTA
*
3155656 ATTTATAATATATTTTA
1 A-TTATAATATATATTA
3155673 A-TATAATATATA
1 ATTATAATATATA
3155685 AATAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 10 0.38
17 11 0.42
18 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATAATATATATTA
Found at i:3159995 original size:21 final size:21
Alignment explanation
Indices: 3159956--3160000 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3159946 ATATTTAATT
*
3159956 TTTTTATATATTTAAATTATA
1 TTTTTATATATTTAAATTAAA
*
3159977 TTTTTATAT-TTATATATTAAA
1 TTTTTATATATT-TAAATTAAA
3159998 TTT
1 TTT
3160001 ATTAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTATATATTTAAATTAAA
Found at i:3163976 original size:21 final size:22
Alignment explanation
Indices: 3163952--3163992 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3163942 AACTAATTCA
*
3163952 AAATTTTATATTA-TAACTTAT
1 AAATATTATATTATTAACTTAT
*
3163973 AAATATTATTTTATTAACTT
1 AAATATTATATTATTAACTT
3163993 GATGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATATTATATTATTAACTTAT
Found at i:3164117 original size:32 final size:32
Alignment explanation
Indices: 3164071--3164131 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
3164061 TCAAGTTCGA
* * *
3164071 GTTATTTCGGATTTGAGTTATTTTGGGTTCAG
1 GTTATTTCGAATTTGAGTCATTTCGGGTTCAG
* *
3164103 GTTATTTTGAATTTGGGTCATTTCGGGTT
1 GTTATTTCGAATTTGAGTCATTTCGGGTT
3164132 TAAATCATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.15, C:0.07, G:0.28, T:0.51
Consensus pattern (32 bp):
GTTATTTCGAATTTGAGTCATTTCGGGTTCAG
Found at i:3164747 original size:190 final size:190
Alignment explanation
Indices: 3164424--3164807 Score: 678
Period size: 190 Copynumber: 2.0 Consensus size: 190
3164414 AATTATATTA
* ** *
3164424 TTTTATTTAATTAATTTATATAATTACTTTTAAATATGTTAAATTTAAGCTTAACCTAGATAGTT
1 TTTTATTTAATTAATTTACATAATTACTTTTAAATATGCCAAACTTAAGCTTAACCTAGATAGTT
* *
3164489 TTTTAAGTTATTTTTAAGATTCCTCCTTGCTTAGGTCTGCTCAGTACAGTATGAGCAAGAAAAAA
66 TTTTAAGCTATTTTTAAGATTCCTCCTTGCTTAGGTCTGCTCAGTACAGTATGAACAAGAAAAAA
* *
3164554 CTGTACTGATTAGCAAGTAGGAAAACTGTATCAAAAATCTTACTCGATCGAGTTCTCTTC
131 CTGTACTGATTAGCAAGTAGAAAAACTGTACCAAAAATCTTACTCGATCGAGTTCTCTTC
*
3164614 TTTTATTTAATTAATTTACATAATTATTTTTAAATATGCCAAACTTAAGCTTAACCTAGATAGTT
1 TTTTATTTAATTAATTTACATAATTACTTTTAAATATGCCAAACTTAAGCTTAACCTAGATAGTT
*
3164679 TTTTAAGCTATTTTTAAGATTCTTCCTTGCTTAGGTCTGCTCAGTACAGTATGAACAAGAAAAAA
66 TTTTAAGCTATTTTTAAGATTCCTCCTTGCTTAGGTCTGCTCAGTACAGTATGAACAAGAAAAAA
3164744 CTGTACTGATTAGCAAGTAGAAAAACTGTACCAAAAATCTTACTCGATCGAGTTCTCTTC
131 CTGTACTGATTAGCAAGTAGAAAAACTGTACCAAAAATCTTACTCGATCGAGTTCTCTTC
3164804 TTTT
1 TTTT
3164808 CTCCCTGGGA
Statistics
Matches: 184, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
190 184 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (190 bp):
TTTTATTTAATTAATTTACATAATTACTTTTAAATATGCCAAACTTAAGCTTAACCTAGATAGTT
TTTTAAGCTATTTTTAAGATTCCTCCTTGCTTAGGTCTGCTCAGTACAGTATGAACAAGAAAAAA
CTGTACTGATTAGCAAGTAGAAAAACTGTACCAAAAATCTTACTCGATCGAGTTCTCTTC
Found at i:3166153 original size:22 final size:22
Alignment explanation
Indices: 3166128--3166171 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3166118 CTTTCCTTAC
*
3166128 AATTATAAT-TTTATAATTTTAT
1 AATT-TAATGTTTATAATATTAT
*
3166150 AATTTTATGTTTATAATATTAT
1 AATTTAATGTTTATAATATTAT
3166172 GATTCTCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
AATTTAATGTTTATAATATTAT
Found at i:3166162 original size:14 final size:14
Alignment explanation
Indices: 3166130--3166172 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
3166120 TTCCTTACAA
*
3166130 TTATAATTTTATAATT
1 TTATAATTTTAT--GT
3166146 TTATAATTTTATGT
1 TTATAATTTTATGT
*
3166160 TTATAATATTATG
1 TTATAATTTTATG
3166173 ATTCTCGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
16 12 0.48
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (14 bp):
TTATAATTTTATGT
Found at i:3166171 original size:8 final size:8
Alignment explanation
Indices: 3166130--3166157 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3166120 TTCCTTACAA
3166130 TTATAATT
1 TTATAATT
3166138 TTATAATT
1 TTATAATT
3166146 TTATAATT
1 TTATAATT
3166154 TTAT
1 TTAT
3166158 GTTTATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATAATT
Found at i:3170081 original size:49 final size:49
Alignment explanation
Indices: 3170009--3170106 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
3169999 TAGCCATTAA
3170009 AGGTTTTTAACTTTGTGCTCTGCTCAATGATAATTTTGTTGTTATTTAT
1 AGGTTTTTAACTTTGTGCTCTGCTCAATGATAATTTTGTTGTTATTTAT
*
3170058 AGGTTTTTAACTTTGTGCTCTGCTCAATGATAATTTTTTTGTTATTTAT
1 AGGTTTTTAACTTTGTGCTCTGCTCAATGATAATTTTGTTGTTATTTAT
3170107 TATTCAATTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.54
Consensus pattern (49 bp):
AGGTTTTTAACTTTGTGCTCTGCTCAATGATAATTTTGTTGTTATTTAT
Found at i:3173251 original size:17 final size:17
Alignment explanation
Indices: 3173229--3173264 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3173219 CAAGTTTATC
3173229 ATGTTTTAACAGGTTTT
1 ATGTTTTAACAGGTTTT
3173246 ATGTTTTAACAGGTTTT
1 ATGTTTTAACAGGTTTT
3173263 AT
1 AT
3173265 TTCATTCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.53
Consensus pattern (17 bp):
ATGTTTTAACAGGTTTT
Found at i:3173622 original size:20 final size:20
Alignment explanation
Indices: 3173593--3173636 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3173583 AACGTCCGTA
*
3173593 AATTTCTTAACCAAAAATTT
1 AATTTATTAACCAAAAATTT
**
3173613 AATTTATTAATTAAAAATTT
1 AATTTATTAACCAAAAATTT
3173633 AATT
1 AATT
3173637 CAATTAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTATTAACCAAAAATTT
Found at i:3173642 original size:21 final size:20
Alignment explanation
Indices: 3173605--3173645 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3173595 TTTCTTAACC
*
3173605 AAAAATTTAATTTATTAATT
1 AAAAATTTAATTAATTAATT
3173625 AAAAATTTAATTCAATTAATT
1 AAAAATTTAATT-AATTAATT
3173646 CTTATAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAAATTTAATTAATTAATT
Found at i:3179231 original size:30 final size:30
Alignment explanation
Indices: 3179195--3179256 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
3179185 AAATCTGGGG
3179195 TAAGTACTTGTAATAGTTTGAACAACATTT
1 TAAGTACTTGTAATAGTTTGAACAACATTT
*
3179225 TAAGTACTTGTAATGGTTTGAACAACATTT
1 TAAGTACTTGTAATAGTTTGAACAACATTT
3179255 TA
1 TA
3179257 CAATTATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (30 bp):
TAAGTACTTGTAATAGTTTGAACAACATTT
Found at i:3204365 original size:33 final size:33
Alignment explanation
Indices: 3204325--3204393 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
3204315 ATAATTTATA
**
3204325 TTATATAAATGTATTTTATAAATTTTAAAATAT
1 TTATATAAATGTATCATATAAATTTTAAAATAT
* *
3204358 TTATATAATTTTATCATATAAATTTTAAAATAT
1 TTATATAAATGTATCATATAAATTTTAAAATAT
3204391 TTA
1 TTA
3204394 AATATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (33 bp):
TTATATAAATGTATCATATAAATTTTAAAATAT
Found at i:3204376 original size:19 final size:18
Alignment explanation
Indices: 3204339--3204403 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
3204329 ATAAATGTAT
3204339 TTTATAAATTTTAAAATA
1 TTTATAAATTTTAAAATA
3204357 TTTATATAATTTT---ATCA
1 TTTATA-AATTTTAAAAT-A
3204374 --TATAAATTTTAAAATA
1 TTTATAAATTTTAAAATA
3204390 TTTA-AATATTTTAA
1 TTTATAA-ATTTTAA
3204404 TTTTTTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
14 6 0.15
15 4 0.10
16 3 0.08
17 5 0.13
18 15 0.38
19 6 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATAAATTTTAAAATA
Found at i:3210299 original size:13 final size:14
Alignment explanation
Indices: 3210270--3210303 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3210260 GATTAATTTA
3210270 TTAATGATAAAAAT
1 TTAATGATAAAAAT
*
3210284 TTAATGAT-ATAAT
1 TTAATGATAAAAAT
3210297 TTAATGA
1 TTAATGA
3210304 AATTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (14 bp):
TTAATGATAAAAAT
Found at i:3223115 original size:24 final size:24
Alignment explanation
Indices: 3223057--3223115 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
3223047 TTAAAAATAA
* *
3223057 AAAAATTAAATTAAATTTATATTT
1 AAAAATTAATTTAAATTAATATTT
3223081 AAAAATT-ATTTAAATTAAATATTT
1 AAAAATTAATTTAAATT-AATATTT
*
3223105 -AAATTTAATTT
1 AAAAATTAATTT
3223116 GATCAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAAATTAATTTAAATTAATATTT
Found at i:3223731 original size:2 final size:2
Alignment explanation
Indices: 3223724--3223751 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3223714 GAAATTGCAT
3223724 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3223752 ATGGGTGGGT
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):
GA
Found at i:3223760 original size:4 final size:4
Alignment explanation
Indices: 3223753--3223787 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
3223743 AGAGAGAGAA
* *
3223753 TGGG TGGG TGAG TCGG TGGG TGGG TGGG TGGG TGG
1 TGGG TGGG TGGG TGGG TGGG TGGG TGGG TGGG TGG
3223788 CGGTGACTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.03, C:0.03, G:0.69, T:0.26
Consensus pattern (4 bp):
TGGG
Done.