Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 20 of 193
Found at i:6880360 original size:26 final size:25
Alignment explanation
Indices: 6880323--6880392 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 25
6880313 CTAGAACTTT
*
6880323 TCTCTTCTTCTTCTTCTTCTTCTCC
1 TCTCTTCTTCTTTTTCTTCTTCTCC
* *
6880348 TCCTCTTCTTCTTTTTGTTCTTCTTC
1 T-CTCTTCTTCTTTTTCTTCTTCTCC
6880374 TCTGCTTCTTCTTTTTCTT
1 TCT-CTTCTTCTTTTTCTT
6880393 TTACTATCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
25 3 0.08
26 36 0.92
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (25 bp):
TCTCTTCTTCTTTTTCTTCTTCTCC
Found at i:6881801 original size:5 final size:5
Alignment explanation
Indices: 6881793--6881835 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
6881783 CCTGACCCTT
6881793 TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCC
1 TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCC
6881836 CATCCCATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.19, C:0.60, G:0.00, T:0.21
Consensus pattern (5 bp):
TCCAC
Found at i:6884829 original size:31 final size:29
Alignment explanation
Indices: 6884773--6884832 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
6884763 TATAGGATTT
* *
6884773 AATTTTAAACTTTTAAAGTATAGGGACTA
1 AATTTTAAACTTATAAAATATAGGGACTA
6884802 AATTTTAAATCTTATACAAATATAGGGACTA
1 AATTTTAAA-CTTATA-AAATATAGGGACTA
6884833 CTAGCATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 9 0.33
30 5 0.19
31 13 0.48
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (29 bp):
AATTTTAAACTTATAAAATATAGGGACTA
Found at i:6886902 original size:7 final size:7
Alignment explanation
Indices: 6886890--6886916 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
6886880 TACTATGATC
6886890 CTAGTTA
1 CTAGTTA
6886897 CTAGTTA
1 CTAGTTA
6886904 CTAGTTA
1 CTAGTTA
6886911 CTAGTT
1 CTAGTT
6886917 TGGAATGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (7 bp):
CTAGTTA
Found at i:6890969 original size:10 final size:9
Alignment explanation
Indices: 6890948--6890982 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
6890938 CCAACATCTG
6890948 TATTTTTTT
1 TATTTTTTT
6890957 TATTTTATTT
1 TATTTT-TTT
6890967 TATTTTTTT
1 TATTTTTTT
6890976 TAATTTT
1 T-ATTTT
6890983 AATTAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.42
10 14 0.58
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TATTTTTTT
Found at i:6901141 original size:30 final size:30
Alignment explanation
Indices: 6901105--6901167 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
6901095 TTTTCCTGCT
* *
6901105 TTTTTTTTTTTTCTTTTCTTTTCTTTCT-TC
1 TTTTTTTTTTTTCCTTT-TGTTCTTTCTCTC
6901135 TTTTTTTTTTTTCCTTTTGTTCTTTCTCTC
1 TTTTTTTTTTTTCCTTTTGTTCTTTCTCTC
6901165 TTT
1 TTT
6901168 CCAACATGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (30 bp):
TTTTTTTTTTTTCCTTTTGTTCTTTCTCTC
Found at i:6901157 original size:25 final size:27
Alignment explanation
Indices: 6901108--6901158 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
6901098 TCCTGCTTTT
* *
6901108 TTTTTTTTTCTTTTCTTTTCTTTCTTC
1 TTTTTTTTTCTTTCCTTTTCGTTCTTC
6901135 TTTTTTTTT-TTTCCTTTT-GTTCTT
1 TTTTTTTTTCTTTCCTTTTCGTTCTT
6901159 TCTCTCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 8 0.36
27 9 0.41
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (27 bp):
TTTTTTTTTCTTTCCTTTTCGTTCTTC
Found at i:6902603 original size:3 final size:3
Alignment explanation
Indices: 6902595--6902654 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
6902585 TTTATAATGT
* * * * * * *
6902595 TGC TGC TGC TGT TGT TGT TGC TGC TGT TGT TGA TGC TGT TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
6902643 TGC TGC TGC TGC
1 TGC TGC TGC TGC
6902655 ATTTTATTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.02, C:0.22, G:0.33, T:0.43
Consensus pattern (3 bp):
TGC
Found at i:6902616 original size:12 final size:12
Alignment explanation
Indices: 6902601--6902654 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
6902591 ATGTTGCTGC
*
6902601 TGCTGTTGTTGT
1 TGCTGCTGTTGT
6902613 TGCTGCTGTTGT
1 TGCTGCTGTTGT
* *
6902625 TGATGCTGTTGC
1 TGCTGCTGTTGT
* *
6902637 TGCTGCTGCTGC
1 TGCTGCTGTTGT
6902649 TGCTGC
1 TGCTGC
6902655 ATTTTATTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.02, C:0.20, G:0.33, T:0.44
Consensus pattern (12 bp):
TGCTGCTGTTGT
Found at i:6902646 original size:15 final size:15
Alignment explanation
Indices: 6902592--6902653 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
6902582 CAATTTATAA
*
6902592 TGTTGCTGCTGCTGT
1 TGTTGCTGCTGCTGC
* *
6902607 TGTTGTTGCTGCTGT
1 TGTTGCTGCTGCTGC
* *
6902622 TGTTGATGCTGTTGC
1 TGTTGCTGCTGCTGC
*
6902637 TGCTGCTGCTGCTGC
1 TGTTGCTGCTGCTGC
6902652 TG
1 TG
6902654 CATTTTATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.02, C:0.19, G:0.34, T:0.45
Consensus pattern (15 bp):
TGTTGCTGCTGCTGC
Found at i:6905377 original size:2 final size:2
Alignment explanation
Indices: 6905370--6905408 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
6905360 GAGGAAGAAA
*
6905370 AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6905409 AAACTGTGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6908302 original size:23 final size:23
Alignment explanation
Indices: 6908267--6908328 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
6908257 CCTTTAAAAA
*
6908267 ATGATTAAATTATAATTTAATAC
1 ATGAATAAATTATAATTTAATAC
* * *
6908290 AT-AATAAACTTATATTTTGATAT
1 ATGAATAAA-TTATAATTTAATAC
6908313 ATGAA-AAATTATAATT
1 ATGAATAAATTATAATT
6908329 AAATTCCGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 12 0.38
23 18 0.56
24 2 0.06
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (23 bp):
ATGAATAAATTATAATTTAATAC
Found at i:6915446 original size:356 final size:356
Alignment explanation
Indices: 6914757--6915463 Score: 1310
Period size: 357 Copynumber: 2.0 Consensus size: 356
6914747 TGAATCATAT
* *
6914757 ATATTTACAATAATTTCATTAAGTTATTATCCTTCAATTTGTGATTGCTTAATATGATGAATATG
1 ATATTTACAATAATTTCATTAAGTTATCATCCTTCAATTTGCGATTGCTTAATATGATGAATATG
*
6914822 TGGTCTGAAAGTAACTTGTGGCATGCGCAAGTAGGCTCTCATCAGTGCCAAACATGATACCATTC
66 TGGTCTGAAAGTAACTTGTGGCATGCGCAAGTAGGCTCTCATCAGGGCCAAACATGATACCATTC
*
6914887 ATGTCTATCAATTTCTCCACCTTATTCCTTCAACGCCTTTCAATTGTTGTATTGTGGAAAAAATT
131 ATGTCTATCAATTTCTCCACCTTATTCCTTCAACGCCTTTCAATTGCTGTATTGTGGAAAAAATT
*
6914952 TGTGTTTTTGTCCCCGTTTCGCAGGCAATTCACTCTGGCACTCTATTCCCAATACAGTTCCTCTT
196 TGTGTTTTTGTCCCCGTTTCGCAAGCAATTCACTCTGGCACTCTATTCCCAATACAGTTCCTCTT
6915017 TATTTGCTTCAATGCTAAGTGCAAGTTTGGTTTCAATAATATCGCCCAAATTAGAGATAGAACAA
261 TATTTGCTTCAATGCTAAGTGCAAGTTTGGTTTCAATAATATCGCCCAAATTAGAGATAGAACAA
6915082 TAAAAAAAACATTGAATCATATATAATTATA
326 TAAAAAAAACATTGAATCATATATAATTATA
6915113 ATATTTACAATAATTTCATTAAGTTATCATCCTTCAATTTGCGATTGCTTAATATGATGAATATG
1 ATATTTACAATAATTTCATTAAGTTATCATCCTTCAATTTGCGATTGCTTAATATGATGAATATG
6915178 TGGTCTGAAAGTAACTTGTGGCATGCGCAAGTAGGCTCTCATCAGGGCCAAACATGATACCATTC
66 TGGTCTGAAAGTAACTTGTGGCATGCGCAAGTAGGCTCTCATCAGGGCCAAACATGATACCATTC
6915243 ATGTCTATCAATTTCTCCACCTTATTCCTTCAACGCCTTT-AAGTTTGCTGTATTGTGGAAAAAA
131 ATGTCTATCAATTTCTCCACCTTATTCCTTCAACGCCTTTCAA--TTGCTGTATTGTGGAAAAAA
* *
6915307 TTTGTGTTTTTGTCCCCGTTTCGCAAGCAATTCACTCTGGCACTCTGTTCTCAATACAGTTCCTC
194 TTTGTGTTTTTGTCCCCGTTTCGCAAGCAATTCACTCTGGCACTCTATTCCCAATACAGTTCCTC
6915372 TTTATTTGCTTCAATGCTAAGTGCAAGTTTGGTTTCAATAATATCGCCCAAATTAGAGAT-GAAA
259 TTTATTTGCTTCAATGCTAAGTGCAAGTTTGGTTTCAATAATATCGCCCAAATTAGAGATAG-AA
6915436 CAATAAAAAAAACATTGAATCATATATA
323 CAATAAAAAAAACATTGAATCATATATA
6915464 TAATTAATAT
Statistics
Matches: 341, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
355 2 0.01
356 168 0.49
357 171 0.50
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (356 bp):
ATATTTACAATAATTTCATTAAGTTATCATCCTTCAATTTGCGATTGCTTAATATGATGAATATG
TGGTCTGAAAGTAACTTGTGGCATGCGCAAGTAGGCTCTCATCAGGGCCAAACATGATACCATTC
ATGTCTATCAATTTCTCCACCTTATTCCTTCAACGCCTTTCAATTGCTGTATTGTGGAAAAAATT
TGTGTTTTTGTCCCCGTTTCGCAAGCAATTCACTCTGGCACTCTATTCCCAATACAGTTCCTCTT
TATTTGCTTCAATGCTAAGTGCAAGTTTGGTTTCAATAATATCGCCCAAATTAGAGATAGAACAA
TAAAAAAAACATTGAATCATATATAATTATA
Found at i:6918695 original size:19 final size:17
Alignment explanation
Indices: 6918673--6918715 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
6918663 AAATTCATTT
*
6918673 AAATTATTTTTCAAAACAC
1 AAATTATTTGT-AAAA-AC
*
6918692 AAATTAATTGTAAAAAC
1 AAATTATTTGTAAAAAC
6918709 AAATTAT
1 AAATTAT
6918716 ATTCCAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 9 0.43
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (17 bp):
AAATTATTTGTAAAAAC
Found at i:6919606 original size:13 final size:13
Alignment explanation
Indices: 6919588--6919635 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
6919578 TCGAATTTTG
6919588 AATTTTTTGTATT
1 AATTTTTTGTATT
*
6919601 AATTTTTTTTGAATAT
1 AA--TTTTTTGTAT-T
6919617 AATTTTTTGTATT
1 AATTTTTTGTATT
6919630 AATTTT
1 AATTTT
6919636 AAGTGTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 9 0.30
14 9 0.30
15 9 0.30
16 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (13 bp):
AATTTTTTGTATT
Found at i:6919609 original size:14 final size:14
Alignment explanation
Indices: 6919590--6919635 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
6919580 GAATTTTGAA
6919590 TTTTTTGTATTAATT
1 TTTTTTGTATTAA-T
*
6919605 TTTTTTGAATATAA-
1 TTTTTTGTAT-TAAT
6919619 TTTTTTGTATTAAT
1 TTTTTTGTATTAAT
6919633 TTT
1 TTT
6919636 AAGTGTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.11
14 12 0.44
15 9 0.33
16 3 0.11
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTTTTTGTATTAAT
Found at i:6919619 original size:16 final size:15
Alignment explanation
Indices: 6919590--6919624 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6919580 GAATTTTGAA
*
6919590 TTTTTTGTATTAATT
1 TTTTTTGAATTAATT
6919605 TTTTTTGAATATAATT
1 TTTTTTGAAT-TAATT
6919621 TTTT
1 TTTT
6919625 GTATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTTTTGAATTAATT
Found at i:6922283 original size:23 final size:23
Alignment explanation
Indices: 6922257--6922308 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
6922247 TTTATCGATC
* * *
6922257 TTTGTGAAATGTTTTTCTTTTGT
1 TTTGTGAAATGCTTTTCCTCTGT
**
6922280 TTTGTGGTATGCTTTTCCTCTGT
1 TTTGTGAAATGCTTTTCCTCTGT
6922303 TTTGTG
1 TTTGTG
6922309 GCAACGCTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.08, C:0.10, G:0.21, T:0.62
Consensus pattern (23 bp):
TTTGTGAAATGCTTTTCCTCTGT
Found at i:6924165 original size:27 final size:27
Alignment explanation
Indices: 6924124--6924178 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
6924114 ATGTTAATCA
* *
6924124 AAAGGATTGGTAAAGGAAAAGTAAGGT
1 AAAGGATTGGGAAAGCAAAAGTAAGGT
6924151 AAAGGATTGGGAAAGCAAAAGTAAGGT
1 AAAGGATTGGGAAAGCAAAAGTAAGGT
6924178 A
1 A
6924179 TCTTTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.02, G:0.33, T:0.16
Consensus pattern (27 bp):
AAAGGATTGGGAAAGCAAAAGTAAGGT
Found at i:6941047 original size:21 final size:22
Alignment explanation
Indices: 6940996--6941052 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
6940986 AGCACAAAAG
*
6940996 TTTTTATCAATTATTTTTTACAT
1 TTTTTAT-AAATATTTTTTACAT
* *
6941019 TGTATTATAAATATTTTTT-TAT
1 T-TTTTATAAATATTTTTTACAT
*
6941041 TTTTTATCAATA
1 TTTTTATAAATA
6941053 AATATAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 9 0.32
22 3 0.11
23 11 0.39
24 5 0.18
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTTATAAATATTTTTTACAT
Found at i:6941593 original size:29 final size:28
Alignment explanation
Indices: 6941499--6941597 Score: 75
Period size: 29 Copynumber: 3.6 Consensus size: 28
6941489 ATAAAAATCA
* *
6941499 ATAAATATTATAAATAT-TATTAAATTTT
1 ATAAAAATTATAAAAATAT-TTAAATTTT
* *
6941527 AATAAAAAATATAAAAATACTTT---TTTG
1 -ATAAAAATTATAAAAATA-TTTAAATTTT
*
6941554 A-AAAAA-AATAAAAATATTTAAATTTT
1 ATAAAAATTATAAAAATATTTAAATTTT
6941580 ATTAAAAATTATAAAAAT
1 A-TAAAAATTATAAAAAT
6941598 CCTAAAAAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
23 3 0.05
24 9 0.16
25 5 0.09
26 5 0.09
27 3 0.05
28 5 0.09
29 22 0.40
30 2 0.04
31 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (28 bp):
ATAAAAATTATAAAAATATTTAAATTTT
Found at i:6941617 original size:20 final size:19
Alignment explanation
Indices: 6941582--6941636 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
6941572 TAAATTTTAT
6941582 TAAAAATTAT-AAAAATCC
1 TAAAAATTATAAAAAATCC
**
6941600 TAAAAAGTTATAAAAAATTG
1 TAAAAA-TTATAAAAAATCC
*
6941620 TAAAATTTTATAAAAAA
1 TAAAA-ATTATAAAAAA
6941637 ATAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 6 0.19
19 4 0.13
20 21 0.68
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (19 bp):
TAAAAATTATAAAAAATCC
Found at i:6941939 original size:10 final size:10
Alignment explanation
Indices: 6941854--6941967 Score: 66
Period size: 10 Copynumber: 11.9 Consensus size: 10
6941844 TTACGAGTTT
6941854 TATATTTCTT-
1 TATATTT-TTA
6941864 TATATTTTTA
1 TATATTTTTA
6941874 TA-ATTTTCT-
1 TATATTTT-TA
*
6941883 TACGA-TTTTA
1 TA-TATTTTTA
* * *
6941893 TAAAATATTA
1 TATATTTTTA
6941903 TAT-TTTTTA
1 TATATTTTTA
*
6941912 TATATTTCTA
1 TATATTTTTA
6941922 TATA-TTTTA
1 TATATTTTTA
6941931 TATATTTTTA
1 TATATTTTTA
**
6941941 -CGATTTTTA
1 TATATTTTTA
6941950 TA-ATTTTTA
1 TATATTTTTA
6941959 -ATAATTTTT
1 TAT-ATTTTT
6941968 TAATAATTAC
Statistics
Matches: 83, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
8 1 0.01
9 40 0.48
10 41 0.49
11 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (10 bp):
TATATTTTTA
Found at i:6941965 original size:19 final size:19
Alignment explanation
Indices: 6941828--6942033 Score: 67
Period size: 19 Copynumber: 11.0 Consensus size: 19
6941818 TTTTGATACT
6941828 ATAATTTTTATAATTTTT-
1 ATAATTTTTATAATTTTTA
** * *
6941846 ACGAGTTTTAT-ATTTCTTT
1 ATAATTTTTATAATTT-TTA
*
6941865 AT-ATTTTTATAATTTTCTT
1 ATAATTTTTATAATTTT-TA
** * *
6941884 ACGA-TTTTATAAAATATT-
1 ATAATTTTTAT-AATTTTTA
* *
6941902 ATATTTTTTATATATTTCT-
1 ATAATTTTTATA-ATTTTTA
6941921 AT-ATATTTTATATATTTTT-
1 ATAAT-TTTTATA-ATTTTTA
**
6941940 ACGATTTTTATAATTTTTA
1 ATAATTTTTATAATTTTTA
**
6941959 ATAATTTTT-TAATAATTA
1 ATAATTTTTATAATTTTTA
**
6941977 CA-ATATTTTTATTAA-AATTA
1 -ATA-ATTTTTA-TAATTTTTA
*
6941997 ATAACTTTTATAATTTTTA
1 ATAATTTTTATAATTTTTA
* *
6942016 TTGATTTTTAT-ATTTTTA
1 ATAATTTTTATAATTTTTA
6942034 TATTTTTTTG
Statistics
Matches: 144, Mismatches: 27, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
17 4 0.03
18 45 0.31
19 79 0.55
20 13 0.09
21 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
ATAATTTTTATAATTTTTA
Found at i:6941969 original size:11 final size:11
Alignment explanation
Indices: 6941944--6941975 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
6941934 ATTTTTACGA
6941944 TTTTT-ATAA-
1 TTTTTAATAAT
6941953 TTTTTAATAAT
1 TTTTTAATAAT
6941964 TTTTTAATAAT
1 TTTTTAATAAT
6941975 T
1 T
6941976 ACAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 5 0.24
10 4 0.19
11 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:6941981 original size:20 final size:20
Alignment explanation
Indices: 6941958--6941996 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6941948 TATAATTTTT
6941958 AATAATTTT-TTAATAATTAC
1 AATAATTTTATTAA-AATTAC
*
6941978 AATATTTTTATTAAAATTA
1 AATAATTTTATTAAAATTA
6941997 ATAACTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTATTAAAATTAC
Found at i:6942030 original size:8 final size:9
Alignment explanation
Indices: 6941827--6942040 Score: 100
Period size: 9 Copynumber: 23.1 Consensus size: 9
6941817 CTTTTGATAC
6941827 TATAATTTT
1 TATAATTTT
6941836 TATAATTTT
1 TATAATTTT
** *
6941845 TACGAGTTT
1 TATAATTTT
*
6941854 TATATTTCTT
1 TATAATT-TT
6941864 TAT-ATTTT
1 TATAATTTT
6941872 TATAATTTT
1 TATAATTTT
6941881 CT-TACGA-TTT
1 -TATA--ATTTT
* *
6941891 TATAAAATAT
1 TAT-AATTTT
*
6941901 TATATTTTT
1 TATAATTTT
*
6941910 TATATATTTC
1 TATA-ATTTT
6941920 TAT-ATATTT
1 TATAAT-TTT
6941929 TATATATTTT
1 TATA-ATTTT
**
6941939 TACGATTTT
1 TATAATTTT
6941948 TATAATTTT
1 TATAATTTT
6941957 TAATAATTTT
1 T-ATAATTTT
**
6941967 T-TAATAAT
1 TATAATTTT
*
6941975 TACAATATTTT
1 TA-TA-ATTTT
**
6941986 TATTAAAATT
1 TA-TAATTTT
* *
6941996 AATAACTTT
1 TATAATTTT
6942005 TATAATTTT
1 TATAATTTT
*
6942014 TATTGATTTT
1 TA-TAATTTT
6942024 TAT-ATTTT
1 TATAATTTT
6942032 TAT-ATTTT
1 TATAATTTT
6942040 T
1 T
6942041 TTGCCACATG
Statistics
Matches: 154, Mismatches: 34, Indels: 35
0.69 0.15 0.16
Matches are distributed among these distances:
8 27 0.18
9 69 0.45
10 48 0.31
11 10 0.06
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
TATAATTTT
Found at i:6942039 original size:7 final size:8
Alignment explanation
Indices: 6942002--6942040 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
6941992 AATTAATAAC
6942002 TTTTATAAT
1 TTTTAT-AT
6942011 TTTTATTGAT
1 TTTTA-T-AT
6942021 TTTTATAT
1 TTTTATAT
6942029 TTTTATAT
1 TTTTATAT
6942037 TTTT
1 TTTT
6942041 TTGCCACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 14 0.50
9 6 0.21
10 8 0.29
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (8 bp):
TTTTATAT
Found at i:6942354 original size:81 final size:84
Alignment explanation
Indices: 6942198--6942356 Score: 200
Period size: 89 Copynumber: 1.9 Consensus size: 84
6942188 TTTGAAGATT
* * *
6942198 TTTTTGATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGAAATAAAAAGTAAGAACTTAATTTC
1 TTTTTAATGCATTTCGAAAGTTCAAGTATCCAATTGAGT--AATAAAAAG-AAAAACTTAA--TC
6942263 TTTTTTTGAAAAAGTATGAGAACC
61 TTTTTTTGAAAAAGTATGAGAACC
*
6942287 TTTTTAATGCATTTCGAAAGTTCAAGTA-CCTAATTGAGT-ATAAAAA-AAAAACTTCA-CTTTT
1 TTTTTAATGCATTTCGAAAGTTCAAGTATCC-AATTGAGTAATAAAAAGAAAAACTTAATCTTTT
6942348 TTTGAAAAA
65 TTTGAAAAA
6942357 ATTAAAGATT
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
81 14 0.22
84 8 0.12
86 7 0.11
88 2 0.03
89 34 0.52
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (84 bp):
TTTTTAATGCATTTCGAAAGTTCAAGTATCCAATTGAGTAATAAAAAGAAAAACTTAATCTTTTT
TTGAAAAAGTATGAGAACC
Found at i:6942541 original size:2 final size:2
Alignment explanation
Indices: 6942534--6942573 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6942524 TACTTTCTTT
6942534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6942574 ATTTTATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6954894 original size:15 final size:14
Alignment explanation
Indices: 6954866--6954907 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
6954856 ACGAGAGAGA
6954866 CGGA-GGAA-GCGG
1 CGGAGGGAAGGCGG
6954878 CGGCAGGGAAGGCGG
1 CGG-AGGGAAGGCGG
6954893 CGGAGGCGAAGGCGG
1 CGGAGG-GAAGGCGG
6954908 AGAGTAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.12
13 1 0.04
14 7 0.27
15 15 0.58
ACGTcount: A:0.21, C:0.19, G:0.60, T:0.00
Consensus pattern (14 bp):
CGGAGGGAAGGCGG
Found at i:6955689 original size:27 final size:27
Alignment explanation
Indices: 6955630--6955688 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
6955620 CCTTTTATGT
* *
6955630 TCTTTTAACTTTCCTTTTTTTTCATTC
1 TCTTTTAATTTTCCTTGTTTTTCATTC
6955657 TCTTTTAATTTTCCTCTGTTTTTC-TTC
1 TCTTTTAATTTTCCT-TGTTTTTCATTC
6955684 -CTTTT
1 TCTTTT
6955689 TCATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.17
27 17 0.59
28 7 0.24
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.68
Consensus pattern (27 bp):
TCTTTTAATTTTCCTTGTTTTTCATTC
Found at i:6956727 original size:15 final size:16
Alignment explanation
Indices: 6956702--6956742 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
6956692 TGTAATTTAT
6956702 AATATATTAAAAAATA
1 AATATATTAAAAAATA
6956718 AATATA-TAAAAAATA
1 AATATATTAAAAAATA
*
6956733 TATAATATTA
1 AAT-ATATTA
6956743 TTCTGATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 11 0.50
16 9 0.41
17 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATATTAAAAAATA
Found at i:6962164 original size:74 final size:74
Alignment explanation
Indices: 6962073--6962268 Score: 277
Period size: 74 Copynumber: 2.6 Consensus size: 74
6962063 GTAAAATTGG
* * * *
6962073 AAAAGCCCTTCCCTGTCAATTGGAATGTCTTATGTCCTCAACTGAAAATCTTTTTTATGCTCAAA
1 AAAAGTCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAA-CTTTTTTATGCACAAA
*
6962138 AGAAGA-AGA
65 AGAAGATAAA
* * *
6962147 AGAAGTCCTTCCTTGTCAATTGGAATGTTTTGTGTCCTCAATTGAAAACTTTTTTATGCACAAAA
1 AAAAGTCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAACTTTTTTATGCACAAAA
**
6962212 TCAGATAAA
66 GAAGATAAA
*
6962221 AAAAGTCCTTCCTTGTCAATTGGGATGTTTTATGTCCTCAACTGAAAA
1 AAAAGTCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAA
6962269 AAGAATCTGT
Statistics
Matches: 107, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
73 19 0.18
74 88 0.82
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (74 bp):
AAAAGTCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAACTTTTTTATGCACAAAA
GAAGATAAA
Found at i:6975079 original size:23 final size:23
Alignment explanation
Indices: 6975018--6975080 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6975008 CTGCCTTTGC
* *
6975018 GGCACGCTTTTTCTCTACCTTGT
1 GGCACGCTTTTCCTTTACCTTGT
6975041 GGCACGCTTTTCCTTTACCTTGT
1 GGCACGCTTTTCCTTTACCTTGT
*
6975064 GGCACGCTTTTGCTTTA
1 GGCACGCTTTTCCTTTA
6975081 TGGCACGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.10, C:0.29, G:0.19, T:0.43
Consensus pattern (23 bp):
GGCACGCTTTTCCTTTACCTTGT
Found at i:6983532 original size:9 final size:10
Alignment explanation
Indices: 6983500--6983532 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
6983490 AAAAAAAACT
6983500 TTAAAAATTA
1 TTAAAAATTA
*
6983510 TAAAAAATTA
1 TTAAAAATTA
6983520 TTAAAAATT-
1 TTAAAAATTA
6983529 TTAA
1 TTAA
6983533 TATATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:6984942 original size:43 final size:43
Alignment explanation
Indices: 6984889--6984993 Score: 156
Period size: 43 Copynumber: 2.4 Consensus size: 43
6984879 ACGAGTTTAA
*
6984889 GCACTTTGTGTGCCAGTATATTTGCTTTGGCTTGTCCGATGAT
1 GCACTATGTGTGCCAGTATATTTGCTTTGGCTTGTCCGATGAT
*** * *
6984932 GCACTATGTGTATTAATATATTTGCTTTGGTTTGTCCGATGAT
1 GCACTATGTGTGCCAGTATATTTGCTTTGGCTTGTCCGATGAT
6984975 GCACTATGTGTGCCAGTAT
1 GCACTATGTGTGCCAGTAT
6984994 GCAGTTCATG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (43 bp):
GCACTATGTGTGCCAGTATATTTGCTTTGGCTTGTCCGATGAT
Found at i:6988886 original size:14 final size:16
Alignment explanation
Indices: 6988857--6988890 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
6988847 CTATAATGGC
6988857 AAAAGAATGAAAAATA
1 AAAAGAATGAAAAATA
6988873 AAAAG-ATG-AAAATA
1 AAAAGAATGAAAAATA
6988887 AAAA
1 AAAA
6988891 CTAAACCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 3 0.17
16 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAAGAATGAAAAATA
Found at i:6989087 original size:24 final size:24
Alignment explanation
Indices: 6989058--6989144 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
6989048 TAGACTAATA
6989058 AGAGTTTAACTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
6989082 CGAGTTTAACTAAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
6989106 ATAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
6989130 AGAGTTTAATTGAAA
1 AGAGTTTAACTGAAA
6989145 AATTATTTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:6996947 original size:17 final size:16
Alignment explanation
Indices: 6996911--6996972 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
6996901 ATTAAGGTAC
6996911 ATTTTTCAAAAAAAATT
1 ATTTTTCAAAAAAAA-T
6996928 ATTTTTCAAAAAAACAT
1 ATTTTTCAAAAAAA-AT
* * *
6996945 ATTTATTTATAAATATAT
1 ATTT-TTCA-AAAAAAAT
6996963 ATTTTTCAAA
1 ATTTTTCAAA
6996973 TTTTTGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 2 0.05
17 22 0.58
18 10 0.26
19 4 0.11
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTTCAAAAAAAAT
Found at i:7002152 original size:30 final size:28
Alignment explanation
Indices: 7001932--7002348 Score: 320
Period size: 30 Copynumber: 14.1 Consensus size: 28
7001922 AAAAATGAAG
*
7001932 TTTTGGAGAA-TTTGGGGTTAAAATGTAA
1 TTTTGGA-AAGTTTGGGGTTAAAATGTGA
* * * *
7001960 TTTTGTAAAAATTTAGGGGTCAAAATGTAA
1 TTTTG-GAAAGTTT-GGGGTTAAAATGTGA
*
7001990 TTCTTGGAAAGTTTAGGGTTAAAATGTGA
1 TT-TTGGAAAGTTTGGGGTTAAAATGTGA
* ** *
7002019 TTTTAGAAAAGTTCAAGGGTTAAAATATGA
1 TTTT-GGAAAGTT-TGGGGTTAAAATGTGA
* * *
7002049 TTTTAGAAAAGTTTGAGGGTCAAAATATGA
1 TTTT-GGAAAGTTTG-GGGTTAAAATGTGA
*
7002079 TTTTGGAAAAGTTTGAGAGTTAAAATGTGA
1 TTTTGG-AAAGTTTG-GGGTTAAAATGTGA
7002109 TTTTAGG-AAGTTTGGGGATTAAAATGTGA
1 TTTT-GGAAAGTTTGGGG-TTAAAATGTGA
* *
7002138 TTTTAGGAAAGTTTGGTGGTCAAAATATGA
1 TTTT-GGAAAGTTTGG-GGTTAAAATGTGA
** *
7002168 TTTTGGAAAAGTTTGGGGGCCAAAATATGA
1 TTTTGG-AAAGTTT-GGGGTTAAAATGTGA
** * *
7002198 TTTTGGGGAAA-TTCAAGGATCAAAATGTGA
1 TTTT--GGAAAGTT-TGGGGTTAAAATGTGA
* * * *
7002228 TTATGGGGAAGTTTAGGGTCAAAATGTGA
1 TT-TTGGAAAGTTTGGGGTTAAAATGTGA
7002257 TTTTGTGAAAGTTTGGGGTTTAAAATGTGA
1 TTTTG-GAAAGTTTGGGG-TTAAAATGTGA
7002287 TTTTGTGAAAGTTTGGGGCTTAAAATGTGA
1 TTTTG-GAAAGTTTGGGG-TTAAAATGTGA
* *
7002317 TTTTGTGAAAGTTTGGGG-TCAAATATGA
1 TTTTG-GAAAGTTTGGGGTTAAAATGTGA
7002345 TTTT
1 TTTT
7002349 TGGGTAAAAC
Statistics
Matches: 331, Mismatches: 37, Indels: 42
0.81 0.09 0.10
Matches are distributed among these distances:
28 25 0.08
29 83 0.25
30 208 0.63
31 13 0.04
32 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (28 bp):
TTTTGGAAAGTTTGGGGTTAAAATGTGA
Found at i:7002163 original size:119 final size:114
Alignment explanation
Indices: 7001979--7002339 Score: 354
Period size: 119 Copynumber: 3.0 Consensus size: 114
7001969 AATTTAGGGG
* * * **
7001979 TCAAAATGTAATTCTTGGAAAGTTTAGGGTTAAAATGTGATTTTAGAAAAGTTCAAGGGTTAAAA
1 TCAAAATGTGATTATTGG-AAGTTTAGGGTTAAAATGTGATTTTAGGAAAGTT-TGGGGTTAAAA
7002044 TATGATTTTAGAAAAGTTTGAGGGTCAAAATATGATTTTGGAAAAGTTTGA-GA
64 TATGATTTT-GAAAAGTTTG-GGGTCAAAATATGATTTTGG-AAAGTTTGAGGA
* * *
7002097 GTTAAAATGTGATT-TTAGGAAGTTTGGGGATTAAAATGTGATTTTAGGAAAGTTTGGTGGTCAA
1 -TCAAAATGTGATTATT-GGAAGTTTAGGG-TTAAAATGTGATTTTAGGAAAGTTTGG-GGTTAA
* **
7002161 AATATGATTTTGGAAAAGTTTGGGGGCCAAAATATGATTTTGGGGAAA-TTCAAGGA
62 AATATGATTTT-GAAAAGTTT-GGGGTCAAAATATGATTTT--GGAAAGTTTGAGGA
* *
7002217 TCAAAATGTGATTATGGGGAAGTTTAGGGTCAAAATGTGATTTT-GTGAAAGTTTGGGGTTTAAA
1 TCAAAATGTGATTAT-TGGAAGTTTAGGGTTAAAATGTGATTTTAG-GAAAGTTTGGGG-TTAAA
* * * * *
7002281 ATGTGATTTTGTGAAAGTTTGGGGCTTAAAATGTGATTTTGTGAAAGTTTG-GGG
63 ATATGATTTTG-AAAAGTTTGGGG-TCAAAATATGATTTTG-GAAAGTTTGAGGA
7002335 TCAAA
1 TCAAA
7002340 TATGATTTTT
Statistics
Matches: 203, Mismatches: 24, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
117 1 0.00
118 31 0.15
119 151 0.74
120 18 0.09
121 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35
Consensus pattern (114 bp):
TCAAAATGTGATTATTGGAAGTTTAGGGTTAAAATGTGATTTTAGGAAAGTTTGGGGTTAAAATA
TGATTTTGAAAAGTTTGGGGTCAAAATATGATTTTGGAAAGTTTGAGGA
Found at i:7002350 original size:89 final size:86
Alignment explanation
Indices: 7001942--7002348 Score: 385
Period size: 89 Copynumber: 4.6 Consensus size: 86
7001932 TTTTGGAGAA
* * * * * *
7001942 TTTGGGGTTAAAATGTAATTTTGTAAAAATTTAGGGGTCAAAATGTAATTCTTGG-AAAGTTTAG
1 TTTGGGGTTAAAATGTGATTTTG-GAAAGTTT-GGGGTCAAAATATGATT-TTGGAAAAGTTTGG
*
7002006 GGTTAAAATGTGATTTTAGAAAAG
63 GGTTAAAATGTGATTTTAGGAAAG
** * *
7002030 TTCAAGGGTTAAAATATGATTTTAGAAAAGTTTGAGGGTCAAAATATGATTTTGGAAAAGTTTGA
1 TT-TGGGGTTAAAATGTGATTTT-GGAAAGTTTG-GGGTCAAAATATGATTTTGGAAAAGTTTG-
*
7002095 GAGTTAAAATGTGATTTTAGG-AAG
62 GGGTTAAAATGTGATTTTAGGAAAG
7002119 TTTGGGGATTAAAATGTGATTTTAGGAAAGTTTGGTGGTCAAAATATGATTTTGGAAAAGTTTGG
1 TTTGGGG-TTAAAATGTGATTTT-GGAAAGTTTGG-GGTCAAAATATGATTTTGGAAAAGTTT-G
** * *
7002184 GGGCCAAAATATGATTTTGGGGAAA-
62 GGGTTAAAATGTGATTTT-AGGAAAG
** * * * * * *
7002209 TTCAAGGATCAAAATGTGATTATGGGGAAGTTTAGGGTCAAAATGTGATTTTGTG-AAAGTTTGG
1 TT-TGGGGTTAAAATGTGATT-TTGGAAAGTTTGGGGTCAAAATATGATTTTG-GAAAAGTTTGG
7002273 GGTTTAAAATGTGATTTT-GTGAAAG
63 GG-TTAAAATGTGATTTTAG-GAAAG
7002298 TTTGGGGCTTAAAATGTGATTTTGTGAAAGTTTGGGGTC-AAATATGATTTT
1 TTTGGGG-TTAAAATGTGATTTTG-GAAAGTTTGGGGTCAAAATATGATTTT
7002349 TGGGTAAAAC
Statistics
Matches: 263, Mismatches: 38, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
87 1 0.00
88 34 0.13
89 176 0.67
90 47 0.18
91 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (86 bp):
TTTGGGGTTAAAATGTGATTTTGGAAAGTTTGGGGTCAAAATATGATTTTGGAAAAGTTTGGGGT
TAAAATGTGATTTTAGGAAAG
Found at i:7003163 original size:13 final size:15
Alignment explanation
Indices: 7003133--7003169 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
7003123 AAATCAATTT
7003133 TTTTGTTTTTATATA
1 TTTTGTTTTTATATA
* *
7003148 TTTTGTTTTAATATT
1 TTTTGTTTTTATATA
7003163 TTTTGTT
1 TTTTGTT
7003170 ATTTTTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (15 bp):
TTTTGTTTTTATATA
Found at i:7006701 original size:24 final size:26
Alignment explanation
Indices: 7006643--7006705 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
7006633 CTTATATCTC
*
7006643 AGATTAATAAATAATTCAAAAATTATA
1 AGATTAA-AAATAAATCAAAAATTATA
*
7006670 A-AAT-AAAATAAATC-AAAA-TATA
1 AGATTAAAAATAAATCAAAAATTATA
7006692 AGATTAAAAATAAA
1 AGATTAAAAATAAA
7006706 AATATCATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 5 0.16
23 6 0.19
24 16 0.52
25 1 0.03
26 2 0.06
27 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (26 bp):
AGATTAAAAATAAATCAAAAATTATA
Found at i:7013873 original size:24 final size:24
Alignment explanation
Indices: 7013812--7013874 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
7013802 TAGACTAATA
* *
7013812 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
7013836 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
7013860 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
7013875 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:7015831 original size:24 final size:24
Alignment explanation
Indices: 7015803--7015861 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
7015793 TAGACTAATA
*
7015803 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
7015827 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
7015851 AGAGTTTAACT
1 AGAGTTTAACT
7015862 AAAAGATCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:7020975 original size:58 final size:58
Alignment explanation
Indices: 7020890--7021044 Score: 167
Period size: 58 Copynumber: 2.7 Consensus size: 58
7020880 ATATTATGAT
*
7020890 TTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATATTATT-AAAT-TATATACTA
1 TTTTATTAAATT-ATA-TTTAATAATAATTATATTAA-AATATGATTAAAATGTATAT-CTA
* * * * *
7020949 TTTTATTAAATTGTATTTAATAATAATCA-AGTTAAAATATGATTAAAATGTTTATTTT
1 TTTTATTAAATTATATTTAATAATAATTATA-TTAAAATATGATTAAAATGTATATCTA
7021007 TTTTATTAAATTATATTTAATAATAATCT-TATTAAAAT
1 TTTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
7021045 TTAACAACAA
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
57 9 0.11
58 55 0.67
59 14 0.17
60 4 0.05
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (58 bp):
TTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAAATGTATATCTA
Found at i:7021255 original size:16 final size:16
Alignment explanation
Indices: 7021236--7021281 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
7021226 TTATTATATT
* *
7021236 TCTATTAAATTACAGG
1 TCTATTATATTACAGC
* *
7021252 TCTATTCTATTATAGC
1 TCTATTATATTACAGC
7021268 TCTATTATATTACA
1 TCTATTATATTACA
7021282 ACGAACCAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (16 bp):
TCTATTATATTACAGC
Found at i:7021257 original size:32 final size:32
Alignment explanation
Indices: 7021221--7021281 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
7021211 GATTACAACC
* **
7021221 CTATTTTATTATATTTCTATTAAATTACAGGT
1 CTATTCTATTATAGCTCTATTAAATTACAGGT
*
7021253 CTATTCTATTATAGCTCTATTATATTACA
1 CTATTCTATTATAGCTCTATTAAATTACA
7021282 ACGAACCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (32 bp):
CTATTCTATTATAGCTCTATTAAATTACAGGT
Found at i:7024351 original size:23 final size:23
Alignment explanation
Indices: 7024303--7024357 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
7024293 GGCTTGGCTG
* * *
7024303 TTTTTTAATTTTATAATGTATTA
1 TTTTTTAATTATATAATATATAA
*
7024326 TTTTTTAATTATATATTATATAA
1 TTTTTTAATTATATAATATATAA
*
7024349 TTTTATAAT
1 TTTTTTAAT
7024358 GTATTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTTTAATTATATAATATATAA
Found at i:7027952 original size:56 final size:56
Alignment explanation
Indices: 7027888--7027994 Score: 187
Period size: 56 Copynumber: 1.9 Consensus size: 56
7027878 ATTTGGCTTC
* *
7027888 TGAGCATGAAAGGTATGTAAGTCTTTTTAATTATTTCTTCTACCTGCTTTAAATGT
1 TGAGCATGAAAGGTATGCAAGTCTTTCTAATTATTTCTTCTACCTGCTTTAAATGT
*
7027944 TGAGCATGAAAGGTATGCAAGTCTTTCTAATTGTTTCTTCTACCTGCTTTA
1 TGAGCATGAAAGGTATGCAAGTCTTTCTAATTATTTCTTCTACCTGCTTTA
7027995 GATGCGGATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (56 bp):
TGAGCATGAAAGGTATGCAAGTCTTTCTAATTATTTCTTCTACCTGCTTTAAATGT
Found at i:7035932 original size:32 final size:32
Alignment explanation
Indices: 7035881--7035970 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
7035871 ACTGTTTTGA
7035881 TGCTGTTATTTTTTTGTTGTT-TTTATTGCTATTT
1 TGCTGTTA--TTTTTGTTGTTATTT-TTGCTATTT
* *
7035915 TGCTGTTATTTTTGTTGTTATTTTTGTTGTTT
1 TGCTGTTATTTTTGTTGTTATTTTTGCTATTT
* * *
7035947 TGTTGTTATTTTTGCTGCTATTTT
1 TGCTGTTATTTTTGTTGTTATTTT
7035971 GGTTATTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
32 39 0.78
33 3 0.06
34 8 0.16
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.70
Consensus pattern (32 bp):
TGCTGTTATTTTTGTTGTTATTTTTGCTATTT
Found at i:7035940 original size:12 final size:12
Alignment explanation
Indices: 7035884--7035989 Score: 89
Period size: 12 Copynumber: 9.3 Consensus size: 12
7035874 GTTTTGATGC
7035884 TGTTATTTTT-T
1 TGTTATTTTTGT
* *
7035895 TGTTGTTTTTAT
1 TGTTATTTTTGT
* *
7035907 TGCTA-TTTTGC
1 TGTTATTTTTGT
7035918 TGTTATTTTTGT
1 TGTTATTTTTGT
7035930 TGTTATTTTTGT
1 TGTTATTTTTGT
7035942 TG----TTTTGT
1 TGTTATTTTTGT
*
7035950 TGTTATTTTTGC
1 TGTTATTTTTGT
* *
7035962 TGCTATTTTGGT
1 TGTTATTTTTGT
* *
7035974 TATTATTTTGGT
1 TGTTATTTTTGT
7035986 TGTT
1 TGTT
7035990 TGGATGTTAT
Statistics
Matches: 75, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
8 8 0.11
11 17 0.23
12 50 0.67
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:7035940 original size:44 final size:45
Alignment explanation
Indices: 7035885--7035990 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 45
7035875 TTTTGATGCT
* *
7035885 GTTATT-TTTTTGTTGTTTTTATTGCTA-TTTTGCTGTTATTTTT
1 GTTATTATTTTTGTTGTTTTTATTGCTATTTTTGCTGCTATTTTG
* * *
7035928 GTTGTTATTTTTGTTG-TTTTGTTGTTATTTTTGCTGCTATTTTG
1 GTTATTATTTTTGTTGTTTTTATTGCTATTTTTGCTGCTATTTTG
*
7035972 GTTATTATTTTGGTTGTTT
1 GTTATTATTTTTGTTGTTT
7035991 GGATGTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 14 0.26
44 37 0.70
45 2 0.04
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (45 bp):
GTTATTATTTTTGTTGTTTTTATTGCTATTTTTGCTGCTATTTTG
Found at i:7035952 original size:23 final size:24
Alignment explanation
Indices: 7035884--7035953 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 24
7035874 GTTTTGATGC
* * *
7035884 TGTTATTTTT-TTGTTGTTTTTAT
1 TGTTATTTTTGTTGTTATTGTTGT
* * *
7035907 TGCTA-TTTTGCTGTTATTTTTGT
1 TGTTATTTTTGTTGTTATTGTTGT
7035930 TGTTATTTTTGTTGTT-TTGTTGT
1 TGTTATTTTTGTTGTTATTGTTGT
7035953 T
1 T
7035954 ATTTTTGCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 4 0.11
23 25 0.66
24 9 0.24
ACGTcount: A:0.07, C:0.03, G:0.17, T:0.73
Consensus pattern (24 bp):
TGTTATTTTTGTTGTTATTGTTGT
Found at i:7035998 original size:44 final size:44
Alignment explanation
Indices: 7035912--7036003 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
7035902 TTTATTGCTA
* * * * * *
7035912 TTTTGCTGTTATTTTTGTTGTTATTTTTGTTGTTTTGTTGTTAT
1 TTTTGCTGCTATTTTGGTTATTATTTTGGTTGTTTGGATGTTAT
7035956 TTTTGCTGCTATTTTGGTTATTATTTTGGTTGTTTGGATGTTAT
1 TTTTGCTGCTATTTTGGTTATTATTTTGGTTGTTTGGATGTTAT
7036000 TTTT
1 TTTT
7036004 ATGCGTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.09, C:0.03, G:0.20, T:0.68
Consensus pattern (44 bp):
TTTTGCTGCTATTTTGGTTATTATTTTGGTTGTTTGGATGTTAT
Found at i:7036619 original size:52 final size:54
Alignment explanation
Indices: 7036536--7036657 Score: 158
Period size: 52 Copynumber: 2.3 Consensus size: 54
7036526 TATTTTTAGT
* * *
7036536 TGGCGAGCGTAAACGCGTATGAATAAGCTGACGAGCGTAAA-TA-TGTGCAAGC
1 TGGCGAGCGTAAACACATATGAATAACCTGACGAGCGTAAACTATTGTGCAAGC
* *
7036588 TGGCGAGCGTAAACACATATGAATGACCTGACGAGTGTAAACGTATTTGTGCAAGC
1 TGGCGAGCGTAAACACATATGAATAACCTGACGAGCGTAAAC-TA-TTGTGCAAGC
*
7036644 TGACGAGCGTAAAC
1 TGGCGAGCGTAAAC
7036658 GCATGATTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
52 36 0.60
54 2 0.03
56 22 0.37
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (54 bp):
TGGCGAGCGTAAACACATATGAATAACCTGACGAGCGTAAACTATTGTGCAAGC
Found at i:7038085 original size:13 final size:13
Alignment explanation
Indices: 7038067--7038124 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
7038057 CATGATTTAA
7038067 AATATTATAAATT
1 AATATTATAAATT
*
7038080 AATATTAGAACA-T
1 AATATTATAA-ATT
*
7038093 AATAATATAAATT
1 AATATTATAAATT
*
7038106 ATTATT-T-AATT
1 AATATTATAAATT
*
7038117 GATATTAT
1 AATATTAT
7038125 TTTATTACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
11 8 0.23
12 3 0.09
13 23 0.66
14 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (13 bp):
AATATTATAAATT
Found at i:7041407 original size:23 final size:23
Alignment explanation
Indices: 7041363--7041408 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
7041353 ATTTTCTAAA
* *
7041363 TATTATTATTTAGTTTATTATTT
1 TATTATAATTTAGTTTAGTATTT
7041386 TATTATAATTATAG-TTAGTATTT
1 TATTATAATT-TAGTTTAGTATTT
7041409 AACAATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (23 bp):
TATTATAATTTAGTTTAGTATTT
Found at i:7043186 original size:2 final size:2
Alignment explanation
Indices: 7043179--7043203 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7043169 GCACATTATG
7043179 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
7043204 CCAGAGGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7044249 original size:21 final size:22
Alignment explanation
Indices: 7044225--7044266 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
7044215 TTAAAATATT
7044225 ACTTGATTTA-TTTAAATTTAA
1 ACTTGATTTAGTTTAAATTTAA
* *
7044246 ACTTTATTTAGTTTAATTTTA
1 ACTTGATTTAGTTTAAATTTA
7044267 TTTTTAAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (22 bp):
ACTTGATTTAGTTTAAATTTAA
Found at i:7049604 original size:9 final size:9
Alignment explanation
Indices: 7049574--7049606 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
7049564 TTTTATGATT
7049574 TTTTAAAAA
1 TTTTAAAAA
7049583 TATTT-AAAA
1 T-TTTAAAAA
7049592 TTTTAAAAA
1 TTTTAAAAA
7049601 TTTTAA
1 TTTTAA
7049607 TTGATTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 3 0.14
9 16 0.73
10 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:7057589 original size:23 final size:22
Alignment explanation
Indices: 7057563--7057613 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
7057553 CATATAATTT
7057563 TTATTTTTATTTAAATATTTATA
1 TTATTTTTATTTAAATATTT-TA
* *
7057586 TTA-TATTATTTTAATATTTTA
1 TTATTTTTATTTAAATATTTTA
*
7057607 TAATTTT
1 TTATTTT
7057614 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.17
22 16 0.70
23 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTTTTATTTAAATATTTTA
Found at i:7059028 original size:32 final size:32
Alignment explanation
Indices: 7058992--7059055 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
7058982 ATTTCTACGA
* *
7058992 TTTTTGATAAAATTTTAAAATTAAATAATACT
1 TTTTTAATAAAATTTCAAAATTAAATAATACT
7059024 TTTTTAATAAAATTTCAAAATTAAATAATACT
1 TTTTTAATAAAATTTCAAAATTAAATAATACT
7059056 GTCCAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (32 bp):
TTTTTAATAAAATTTCAAAATTAAATAATACT
Found at i:7059486 original size:17 final size:18
Alignment explanation
Indices: 7059454--7059487 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
7059444 TAACCCTTTT
*
7059454 TTTTCATATTTTATCTTA
1 TTTTCATATTTAATCTTA
7059472 TTTTCA-ATTTAATCTT
1 TTTTCATATTTAATCTT
7059488 TCTCTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTCATATTTAATCTTA
Found at i:7060206 original size:11 final size:11
Alignment explanation
Indices: 7060190--7060232 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
7060180 CTAACCATTT
7060190 ATAAAATATTA
1 ATAAAATATTA
7060201 ATAAAATATCTTA
1 ATAAAATA--TTA
*
7060214 TTAAAATATTA
1 ATAAAATATTA
7060225 ATAAAATA
1 ATAAAATA
7060233 ATATTATCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 18 0.64
13 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAAAATATTA
Found at i:7060219 original size:24 final size:25
Alignment explanation
Indices: 7060191--7060258 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
7060181 TAACCATTTA
7060191 TAAAATATTAATAAAATATCTTAT-
1 TAAAATATTAATAAAATATCTTATC
*
7060215 TAAAATATTAATAAAATAATATTATC
1 TAAAATATTAATAAAAT-ATCTTATC
*
7060241 TAATA-ATT-ATAAAATATC
1 TAAAATATTAATAAAATATC
7060259 ATCAAATATC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 2 0.05
24 24 0.62
25 9 0.23
26 4 0.10
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAAATATTAATAAAATATCTTATC
Found at i:7062266 original size:174 final size:173
Alignment explanation
Indices: 7061982--7062658 Score: 940
Period size: 174 Copynumber: 3.9 Consensus size: 173
7061972 GCTGGCTCGA
* * * ** *
7061982 AGGACACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATCTGAAGGAGAGTCCTTTGTCTTATGA
1 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAAT-T--TGGAGAGGCAGTTGTCCTATGA
** ** *
7062047 GAAAAACCAGTGCTTGAGTGAGCCTTTGAACTTGTTTCCGGAAGATCTTCATCAGAACCACTATT
63 GAAAAACCA-TGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATT
* *
7062112 TCCTGGACCTAAATATGGCATGGGGTCAGAAACTACCTTTGATTCAG
127 TCCTGGACCAAAATATGGCATGGGGTCAGAAACTACCTTCGATTCAG
* *
7062159 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCTTGCATTTGGAGAGGCAGTTGTCCTATGAGAA
1 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTTGGAGAGGCAGTTGTCCTATGAG-A
*
7062224 AAAATCATGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCC
65 AAAACCATGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCC
** *
7062289 TGGACCAAAATGCGGCATAGGGTCAGAAACTACCTTCGATTCAG
130 TGGACCAAAATATGGCATGGGGTCAGAAACTACCTTCGATTCAG
*
7062333 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGCATTTGGAGAGGCAGTTGTCCTATGAGAA
1 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTTGGAGAGGCAGTTGTCCTATGAG-A
** *
7062398 AAAATTATGCTTGGACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCC
65 AAAACCATGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCC
* * * * *
7062463 TGGACCAAAATATGGTATGGGGTTAGAAACTAGCGTCGATTCGG
130 TGGACCAAAATATGGCATGGGGTCAGAAACTACCTTCGATTCAG
* * * * * *
7062507 AGGAAACTGTAGCTTTAAGAGTGGAAGCTTTTCCTGAATTCGGAGAGGCAGTTGTCCTGTGAGAA
1 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTTGGAGAGGCAGTTGTCCTATGAGAA
* * *
7062572 AAACCAATGCTTGAATGAGCCTTTGAACCTGTTTTAGGAAGATCTTCATCGGAATCACTATTTCC
66 AAACC-ATGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCC
* *
7062637 TGAATCAAAATATGGCATGGGG
130 TGGACCAAAATATGGCATGGGG
7062659 ATCCTTGAGG
Statistics
Matches: 452, Mismatches: 46, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
173 5 0.01
174 403 0.89
175 7 0.02
176 1 0.00
177 36 0.08
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (173 bp):
AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTTGGAGAGGCAGTTGTCCTATGAGAA
AAACCATGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCCT
GGACCAAAATATGGCATGGGGTCAGAAACTACCTTCGATTCAG
Found at i:7070839 original size:21 final size:21
Alignment explanation
Indices: 7070815--7070870 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
7070805 ATATATTATT
7070815 TATAAAATTTTA-TATATGAAA
1 TATAAAATTTTAGTATAT-AAA
7070836 TATAAAATTACTTAGTATATAAA
1 TATAAAATT--TTAGTATATAAA
7070859 TAATTAAAATTT
1 T-A-TAAAATTT
7070871 GCTATTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 9 0.30
23 8 0.27
24 6 0.20
25 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
TATAAAATTTTAGTATATAAA
Found at i:7070955 original size:17 final size:18
Alignment explanation
Indices: 7070933--7070966 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
7070923 ATGGAAACAT
7070933 AATAATTTAA-ATAAAAA
1 AATAATTTAATATAAAAA
7070950 AATAATTTAATATAAAA
1 AATAATTTAATATAAAA
7070967 TTAGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAATTTAATATAAAAA
Found at i:7071612 original size:31 final size:31
Alignment explanation
Indices: 7071577--7071637 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
7071567 ATTGATTTAA
* * *
7071577 TAATAATATTTATTAATTATATTAACACTCC
1 TAATAACATTCATTAATTACATTAACACTCC
* *
7071608 TAATAACATTCATTGATTACATTAATACTC
1 TAATAACATTCATTAATTACATTAACACTC
7071638 TTTGTATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.43
Consensus pattern (31 bp):
TAATAACATTCATTAATTACATTAACACTCC
Found at i:7073644 original size:46 final size:47
Alignment explanation
Indices: 7073556--7073654 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 47
7073546 GAACACTAGC
* *
7073556 GTGCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCCGATTAGCACGTCTCGTGCTCTCTG-TATTAGCACTGTGT
* *
7073604 GTGCTCTCCGATTAGCACTTCGT-GTGCTCTCTG-ATTAGCACTTTGT
1 GTGCTCTCCGATTAGCACGTC-TCGTGCTCTCTGTATTAGCACTGTGT
7073650 GTGCT
1 GTGCT
7073655 TAGTACTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
46 17 0.37
48 28 0.61
49 1 0.02
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (47 bp):
GTGCTCTCCGATTAGCACGTCTCGTGCTCTCTGTATTAGCACTGTGT
Found at i:7073645 original size:23 final size:23
Alignment explanation
Indices: 7073556--7073654 Score: 112
Period size: 23 Copynumber: 4.2 Consensus size: 23
7073546 GAACACTAGC
* *
7073556 GTGCTCTCTGTTTAGCACGTC-T
1 GTGCTCTCTGATTAGCACTTCGT
7073578 CGTGCTCTCTGTTATTAGCACTGT-GT
1 -GTGCTCTCTG--ATTAGCACT-TCGT
*
7073604 GTGCTCTCCGATTAGCACTTCGT
1 GTGCTCTCTGATTAGCACTTCGT
*
7073627 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTCGT
7073650 GTGCT
1 GTGCT
7073655 TAGTACTTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
22 1 0.02
23 47 0.71
25 16 0.24
26 2 0.03
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTCGT
Found at i:7073684 original size:39 final size:39
Alignment explanation
Indices: 7073615--7073693 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
7073605 TGCTCTCCGA
*
7073615 TTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGC
1 TTAGCACTTCGTGTACTCTCTGATTAGCACTTTGTGTGC
* * *
7073654 TTAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGC
1 TTAGCACTTCGTGTACTCTCTGATTAGCACTTTGTGTGC
7073693 T
1 T
7073694 CTCTGTTGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.46
Consensus pattern (39 bp):
TTAGCACTTCGTGTACTCTCTGATTAGCACTTTGTGTGC
Found at i:7073685 original size:23 final size:23
Alignment explanation
Indices: 7073654--7073748 Score: 79
Period size: 23 Copynumber: 4.1 Consensus size: 23
7073644 CTTTGTGTGC
*
7073654 TTAGTACTTTGTGTACTCTCTGT
1 TTAGCACTTTGTGTACTCTCTGT
*
7073677 TTAGCACTTTGTGTGCTCTCTGT
1 TTAGCACTTTGTGTACTCTCTGT
*
7073700 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---TAGCACTT-TGTGTACTCTCTGT
* * *
7073725 TCAGTACTTCG-GTACTCTCTGT
1 TTAGCACTTTGTGTACTCTCTGT
7073747 TT
1 TT
7073749 GTTCCGTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 22 0.37
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (23 bp):
TTAGCACTTTGTGTACTCTCTGT
Found at i:7075764 original size:6 final size:6
Alignment explanation
Indices: 7075755--7075822 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
7075745 TTTTAATTTT
*
7075755 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
7075803 CTTTGA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
7075823 AAAAATTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 8 0.15
6 39 0.74
8 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:7075769 original size:17 final size:17
Alignment explanation
Indices: 7075749--7075822 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
7075739 ATTGATTTTT
7075749 AATTTTATTTAAATTTA
1 AATTTTATTTAAATTTA
7075766 AA-TTTATTTTAAATTTA
1 AATTTTA-TTTAAATTTA
7075783 AATTTAATTATTTAAATTT-
1 AA-TT--TTATTTAAATTTA
* *
7075802 ACTTTGAATTTAAATTTA
1 AATTT-TATTTAAATTTA
7075820 AAT
1 AAT
7075823 AAAAATTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
16 5 0.11
17 24 0.51
18 4 0.09
19 2 0.04
20 9 0.19
21 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
AATTTTATTTAAATTTA
Found at i:7077540 original size:30 final size:30
Alignment explanation
Indices: 7077501--7077708 Score: 287
Period size: 30 Copynumber: 7.0 Consensus size: 30
7077491 CCCTATATTG
* * * *
7077501 TCCAGAATTACATTCTAACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
7077531 TCCTAAATTACATTTTGACCCCAAAATTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
7077561 TCCAAAATTACATTTTGA-CCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
7077590 TCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
7077620 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
7077650 TCCAAAATTATATTTTGACCCCAGAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
7077679 T-CAAAAGATATATTTTGACCCCAAAACTTT
1 TCCAAAA-TTACATTTTGACCCCAAAACTTT
7077709 CCTAAATCCC
Statistics
Matches: 161, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
28 5 0.03
29 49 0.30
30 107 0.66
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:7077586 original size:59 final size:59
Alignment explanation
Indices: 7077501--7077708 Score: 276
Period size: 59 Copynumber: 3.5 Consensus size: 59
7077491 CCCTATATTG
* * * * *
7077501 TCCAGAATTACATTCTAACCCTAAAACTTTTCCTAAATTACATTTTGACCCCAAAATTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAA-TTT
*
7077561 TCCAAAATTACATTTTGA-CCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAA-TTT
* * *
7077620 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAGAACTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAATTT
* *
7077679 T-CAAAAGATATATTTTGACCCCAAAACTTT
1 TCCAAAA-TTACATTTTGACCCCAAAACTTT
7077709 CCTAAATCCC
Statistics
Matches: 133, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
58 5 0.04
59 79 0.59
60 49 0.37
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (59 bp):
TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAATTT
Found at i:7077657 original size:89 final size:89
Alignment explanation
Indices: 7077501--7077708 Score: 294
Period size: 89 Copynumber: 2.3 Consensus size: 89
7077491 CCCTATATTG
* * * * *
7077501 TCCAGAATTACATTCTAACCCTAAAACTTTTCCTAAATTACATTTTGACCCCAAAATTTTTCCAA
1 TCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAA
7077566 AATTACATTTTGA-CCCAAAACTTT
66 AATTACATTTTGACCCCAAAAC-TT
7077590 TCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAA
1 TCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAA
* *
7077655 AATTATATTTTGACCCCAGAACTT
66 AATTACATTTTGACCCCAAAACTT
* * *
7077679 T-CAAAAGATATATTTTGACCCCAAAACTTT
1 TCCAAAA-TTACATTTTGACCCTAAAACTTT
7077709 CCTAAATCCC
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
88 5 0.05
89 95 0.89
90 7 0.07
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (89 bp):
TCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAA
AATTACATTTTGACCCCAAAACTT
Found at i:7077846 original size:59 final size:58
Alignment explanation
Indices: 7077712--7078117 Score: 546
Period size: 59 Copynumber: 6.8 Consensus size: 58
7077702 AAACTTTCCT
*
7077712 AAATCCCATTTTTAAACCCCGATTTCACCAAAATTTACCATTTTATTTTACCCCCGAAGCTTCTA
1 AAATTCCATTTTT-AACCCCGATTTCACCAAAA-TTACC-----ATTTTACCCCCGAAGCTTCTA
* *
7077777 AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCACTTTACCTCCGAAGCTTCTA
1 AAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCGAAGCTTCTA
7077836 AAA-TCTCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAAGCTTCTA
1 AAATTC-CATTTTTAACCCCGATTTCACCAAAA-TTACCATTTTACCCCCGAAGCTTCTA
* * *
7077895 AAATTCCGTTTTAAACCCCGATTTCACCAAAAATTACCATTTTACCTCCGAAGCTTCTA
1 AAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCGAAGCTTCTA
7077954 AAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCTA
1 AAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCGAAGCTTCTA
** * * * *
7078013 AAATTCTGTCTTTAACCCCGATTTCACCGAAAATTATCATTTTACTCCCGAAGCCTCTA
1 AAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCGAAGCTTCTA
* * *
7078072 AAATTCCGTTTTTAACCCCGATCTAACCAAAATTACCATTTT-CCCC
1 AAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCC
7078118 TCGGGTATCC
Statistics
Matches: 312, Mismatches: 24, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
57 3 0.01
58 19 0.06
59 248 0.79
60 6 0.02
64 20 0.06
65 16 0.05
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33
Consensus pattern (58 bp):
AAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGAAGCTTCTA
Found at i:7090109 original size:31 final size:31
Alignment explanation
Indices: 7090071--7090243 Score: 121
Period size: 31 Copynumber: 5.2 Consensus size: 31
7090061 TCTTGATCTC
7090071 TGAAATTGAAGTAAGAGCAACGCCATCCCCT
1 TGAAATTGAAGTAAGAGCAACGCCATCCCCT
* * * ***
7090102 TGAAATTGAAGTAGAGTGGATAACGCGTCTTGATCT
1 TGAAATTGAAGTA-AG-AG-CAACGC--CATCCCCT
*
7090138 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGCCATCCCCT
** * * **
7090170 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGCCATCCCCT
7090206 CTGAAATTGAAGTAAGAGCAACGCCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGCCATCCCCT
7090238 TGAAAT
1 TGAAAT
7090244 CAAAATAGAG
Statistics
Matches: 106, Mismatches: 24, Indels: 24
0.69 0.16 0.16
Matches are distributed among these distances:
31 32 0.30
32 15 0.14
33 4 0.04
34 9 0.08
35 4 0.04
36 16 0.15
37 26 0.25
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGCCATCCCCT
Found at i:7090131 original size:68 final size:69
Alignment explanation
Indices: 7090020--7090293 Score: 428
Period size: 68 Copynumber: 4.0 Consensus size: 69
7090010 CTGCAGGTCT
* *
7090020 CAACGTCATCCTC-TGAAATTGAAGTAGAGTTGGATAACACGTCTTGATCTCTGAAATTGAAGTA
1 CAACGCCATCCCCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTGATCTCTGAAATTGAAGTA
7090084 AGAG
66 AGAG
*
7090088 CAACGCCATCCCCTTGAAATTGAAGTAGAG-TGGATAACGCGTCTTGATCTCTGAAATTGAAGTA
1 CAACGCCATCCCCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTGATCTCTGAAATTGAAGTA
7090152 AGAG
66 AGAG
* *
7090156 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGCCATCCCCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTGATCTCTGAAATTGAAGTA
7090220 AGAG
66 AGAG
** * * * *
7090224 CAACGCCATCCCCTTGAAATCAAAATAGAGTTGGATAACACGCCTTTATTTCTGAAATTGAAGTA
1 CAACGCCATCCCCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTGATCTCTGAAATTGAAGTA
7090289 AGAG
66 AGAG
7090293 C
1 C
7090294 GAGATCATTT
Statistics
Matches: 191, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
68 139 0.73
69 52 0.27
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (69 bp):
CAACGCCATCCCCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTGATCTCTGAAATTGAAGTA
AGAG
Found at i:7090143 original size:37 final size:37
Alignment explanation
Indices: 7090025--7090219 Score: 162
Period size: 37 Copynumber: 5.5 Consensus size: 37
7090015 GGTCTCAACG
7090025 TCATCCTCTGAAATTGAAGTAGAGTTGGATAACACGTCT
1 TCAT-CTCTGAAATTGAAGTAGAG-TGGATAACACGTCT
* ** * *
7090064 TGATCTCTGAAATTGAAGTA-A---GAGCA-ACGCCA
1 TCATCTCTGAAATTGAAGTAGAGTGGATAACACGTCT
** *
7090096 TCCCCT-TGAAATTGAAGTAGAGTGGATAACGCGTCT
1 TCATCTCTGAAATTGAAGTAGAGTGGATAACACGTCT
* ** *
7090132 TGATCTCTGAAATTGAAGTA-A---GAGCA-ACGTCA
1 TCATCTCTGAAATTGAAGTAGAGTGGATAACACGTCT
**
7090164 TCCCCT-TGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCTCTGAAATTGAAGTAGAGTGGATAACACGTCT
7090200 TCATCTCTGAAATTGAAGTA
1 TCATCTCTGAAATTGAAGTA
7090220 AGAGCAACGC
Statistics
Matches: 116, Mismatches: 28, Indels: 26
0.68 0.16 0.15
Matches are distributed among these distances:
31 26 0.22
32 16 0.14
33 6 0.05
35 6 0.05
36 16 0.14
37 27 0.23
38 16 0.14
39 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (37 bp):
TCATCTCTGAAATTGAAGTAGAGTGGATAACACGTCT
Found at i:7090664 original size:6 final size:6
Alignment explanation
Indices: 7090655--7090722 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
7090645 TTTTAATTTT
*
7090655 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
7090703 CTTTGA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
7090723 AAAAATTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 8 0.15
6 39 0.74
8 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:7090669 original size:17 final size:17
Alignment explanation
Indices: 7090649--7090722 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
7090639 ATTGATTTTT
7090649 AATTTTATTTAAATTTA
1 AATTTTATTTAAATTTA
7090666 AA-TTTATTTTAAATTTA
1 AATTTTA-TTTAAATTTA
7090683 AATTTAATTATTTAAATTT-
1 AA-TT--TTATTTAAATTTA
* *
7090702 ACTTTGAATTTAAATTTA
1 AATTT-TATTTAAATTTA
7090720 AAT
1 AAT
7090723 AAAAATTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
16 5 0.11
17 24 0.51
18 4 0.09
19 2 0.04
20 9 0.19
21 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
AATTTTATTTAAATTTA
Found at i:7092593 original size:29 final size:30
Alignment explanation
Indices: 7092404--7092578 Score: 264
Period size: 30 Copynumber: 5.9 Consensus size: 30
7092394 AATTGTCTAG
*
7092404 AAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
7092434 AAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
7092464 AAATCACATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
7092494 AAATTACATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
7092524 AAATTACATTTTGACCCCAAAAC-TTT-CA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
7092552 AAAGATATATTTTGACCCCAAAACTTT
1 AAA-TTACATTTTGACCCCAAAACTTT
7092579 CCTAAATCCC
Statistics
Matches: 136, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
28 5 0.04
29 21 0.15
30 110 0.81
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:7092642 original size:58 final size:58
Alignment explanation
Indices: 7092582--7092924 Score: 447
Period size: 59 Copynumber: 5.8 Consensus size: 58
7092572 AAACTTTCCT
*
7092582 AAATCCCATTTTTAACCCTGATTTCACCAAAATTTACCATTTTACCCCCGAAGCTTCTA
1 AAATCCCATTTTTAACCCCGATTTCACCAAAA-TTACCATTTTACCCCCGAAGCTTCTA
** * * **
7092641 AAATTCCGTTTTTTAACCCCGATTTCACCAAAAATTACCACTTTATCTTCGAAGCTTCTA
1 AAA-TCCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCGAAGCTTCTA
* *
7092701 AAATCCCATTTTTAACCTCGATTTCACCAAAATTTACCATTTTACCCCCAAAGCTTCTA
1 AAATCCCATTTTTAACCCCGATTTCACCAAAA-TTACCATTTTACCCCCGAAGCTTCTA
*
7092760 AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTA-CCCCGAAGCTTCTA
1 AAATCCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCGAAGCTTCTA
* * * * *
7092818 AAATTCTATCTTTAA-CCCGATTTCACCGAAAATTACCATTTTACTCCCGAAGCCTCTA
1 AAATCCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCGAAGCTTCTA
* * * *
7092876 AAATTCCATTTTTAACCCCGATCTAACCAAAATTACCATTTTGCCCCCG
1 AAATCCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCG
7092925 GGTATCCATA
Statistics
Matches: 250, Mismatches: 28, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
57 28 0.11
58 74 0.30
59 93 0.37
60 51 0.20
61 4 0.02
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.34
Consensus pattern (58 bp):
AAATCCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGAAGCTTCTA
Found at i:7092660 original size:119 final size:115
Alignment explanation
Indices: 7092582--7092922 Score: 463
Period size: 119 Copynumber: 2.9 Consensus size: 115
7092572 AAACTTTCCT
7092582 AAATCCCATTTTTAACCCTGATTTCACCAAAATTTACCATTTTACCCCCGAAGCTTCTAAAATTC
1 AAATCCCATTTTTAACCCTGATTTCACCAAAATTTACCATTTTACCCCCGAAGCTTCTAAAATTC
* * **
7092647 CGTTTTTTAACCCCGATTTCACCAAAAATTACCACTTTATCTTCGAAGCTTCTA
66 C-ATTTTTAACCCCGATTTCA-C-AAAATTACCATTTTA-CCCCGAAGCTTCTA
*
7092701 AAATCCCATTTTTAA-CCTCGATTTCACCAAAATTTACCATTTTACCCCCAAAGCTTCTAAAATT
1 AAATCCCATTTTTAACCCT-GATTTCACCAAAATTTACCATTTTACCCCCGAAGCTTCTAAAATT
7092765 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCGAAGCTTCTA
65 CCATTTTTAACCCCGATTTCA-C-AAAATTACCATTTTACCCCGAAGCTTCTA
* * * * *
7092818 AAATTCTATCTTTAACCC-GATTTCACCGAAAA-TTACCATTTTACTCCCGAAGCCTCTAAAATT
1 AAATCCCATTTTTAACCCTGATTTCACC-AAAATTTACCATTTTACCCCCGAAGCTTCTAAAATT
* * *
7092881 CCATTTTTAACCCCGATCTAACCAAAATTACCATTTTGCCCC
65 CCATTTTTAACCCCGATTTCA-CAAAATTACCATTTTACCCC
7092923 CGGGTATCCA
Statistics
Matches: 204, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
115 18 0.09
116 58 0.28
117 28 0.14
118 39 0.19
119 61 0.30
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.34
Consensus pattern (115 bp):
AAATCCCATTTTTAACCCTGATTTCACCAAAATTTACCATTTTACCCCCGAAGCTTCTAAAATTC
CATTTTTAACCCCGATTTCACAAAATTACCATTTTACCCCGAAGCTTCTA
Found at i:7092778 original size:29 final size:29
Alignment explanation
Indices: 7092740--7092894 Score: 75
Period size: 29 Copynumber: 5.3 Consensus size: 29
7092730 AAATTTACCA
* *
7092740 TTTTACCCCCAAAGCTTCTAAAATTCCAT
1 TTTTAACCCCAAAGCATCTAAAATTCCAT
*** * *
7092769 TTTTAACCCCGATTTCACCGAAAATTACCA-
1 TTTTAACCCC-AAAGCATCTAAAATT-CCAT
* * *
7092799 TTTT-ACCCCGAAGCTTCTAAAATTCTAT
1 TTTTAACCCCAAAGCATCTAAAATTCCAT
* * *** * *
7092827 CTTTAACCCGATTTCACCGAAAATTACCA-
1 TTTTAACCCCAAAGCATCTAAAATT-CCAT
* *
7092856 TTTT-ACTCCCGAAGCCTCTAAAATTCCAT
1 TTTTAAC-CCCAAAGCATCTAAAATTCCAT
7092885 TTTTAACCCC
1 TTTTAACCCC
7092895 GATCTAACCA
Statistics
Matches: 84, Mismatches: 34, Indels: 16
0.63 0.25 0.12
Matches are distributed among these distances:
27 2 0.02
28 16 0.19
29 46 0.55
30 17 0.20
31 3 0.04
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (29 bp):
TTTTAACCCCAAAGCATCTAAAATTCCAT
Found at i:7092907 original size:29 final size:29
Alignment explanation
Indices: 7092587--7092917 Score: 105
Period size: 30 Copynumber: 11.2 Consensus size: 29
7092577 TTCCTAAATC
* *
7092587 CCATTTTTAACCCTGATTTCACCAAAATTTA
1 CCATTTTTAACCCCGATCT-ACCAAAA-TTA
* * * *
7092618 CCA-TTTTACCCCCGAAGCTTCTAAAATT-
1 CCATTTTTAACCCCG-ATCTACCAAAATTA
* *
7092646 CCGTTTTTTAACCCCGATTTCACCAAAAATTA
1 CC-ATTTTTAACCCCGATCT-ACC-AAAATTA
* * ** * * * *
7092678 CCA-CTTTATCTTCGAAGCTTCTAAAA-TC
1 CCATTTTTAACCCCG-ATCTACCAAAATTA
* *
7092706 CCATTTTTAACCTCGATTTCACCAAAATTTA
1 CCATTTTTAACCCCGATCT-ACCAAAA-TTA
* * * * *
7092737 CCA-TTTTACCCCCAAAGCTTCTAAAATT-
1 CCATTTTTAACCCC-GATCTACCAAAATTA
*
7092765 CCATTTTTAACCCCGATTTCACCGAAAATTA
1 CCATTTTTAACCCCGATCT-ACC-AAAATTA
* * *
7092796 CCA-TTTT-ACCCCGAAGCTTCTAAAATT-
1 CCATTTTTAACCCCG-ATCTACCAAAATTA
* * *
7092823 CTATCTTTAA-CCCGATTTCACCGAAAATTA
1 CCATTTTTAACCCCGATCT-ACC-AAAATTA
* *
7092853 CCA-TTTT-ACTCCCGAAGCCT-CTAAAATT-
1 CCATTTTTAAC-CCCG-A-TCTACCAAAATTA
7092881 CCATTTTTAACCCCGATCTAACCAAAATTA
1 CCATTTTTAACCCCGATCT-ACCAAAATTA
7092911 CCATTTT
1 CCATTTT
7092918 GCCCCCGGGT
Statistics
Matches: 209, Mismatches: 60, Indels: 63
0.63 0.18 0.19
Matches are distributed among these distances:
27 6 0.03
28 32 0.15
29 71 0.34
30 74 0.35
31 23 0.11
32 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.34
Consensus pattern (29 bp):
CCATTTTTAACCCCGATCTACCAAAATTA
Found at i:7108257 original size:29 final size:29
Alignment explanation
Indices: 7108174--7108257 Score: 68
Period size: 29 Copynumber: 2.9 Consensus size: 29
7108164 CTTTGATATT
*
7108174 GTTCTTTG-TATTCGAGTTCATCTGTAGTTTTG
1 GTTCTTTGCTATT-GAGTTC-T-TGTA-TTGTG
* * *
7108206 G-TCTTT-CAATT-AGTTTTTCTATTGTG
1 GTTCTTTGCTATTGAGTTCTTGTATTGTG
7108232 GTTCTTTGCTATTGAGTTCTTGTATT
1 GTTCTTTGCTATTGAGTTCTTGTATT
7108258 CTTATATTAC
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
26 5 0.12
27 8 0.20
28 5 0.12
29 14 0.34
31 8 0.20
32 1 0.02
ACGTcount: A:0.13, C:0.12, G:0.19, T:0.56
Consensus pattern (29 bp):
GTTCTTTGCTATTGAGTTCTTGTATTGTG
Found at i:7110907 original size:23 final size:23
Alignment explanation
Indices: 7110881--7110931 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
7110871 CCTTACTTTC
*
7110881 TATAAT-TAATAAATTTAAGTTT
1 TATAATATAATAAATTTAAATTT
*
7110903 ATATAATATAATATATTTAAATTT
1 -TATAATATAATAAATTTAAATTT
7110927 TATAA
1 TATAA
7110932 AGCGAACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATAATATAATAAATTTAAATTT
Found at i:7119089 original size:8 final size:8
Alignment explanation
Indices: 7119076--7119111 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
7119066 TTTAATACAG
7119076 AGAGAGAA
1 AGAGAGAA
7119084 AGAGAGAA
1 AGAGAGAA
7119092 AGAGAGAA
1 AGAGAGAA
7119100 AGAGAGAA
1 AGAGAGAA
7119108 AGAG
1 AGAG
7119112 CTTGGTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (8 bp):
AGAGAGAA
Found at i:7128750 original size:7 final size:7
Alignment explanation
Indices: 7128738--7128777 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
7128728 TTCAGTTTAG
7128738 CTTTGCC
1 CTTTGCC
7128745 CTTTGCC
1 CTTTGCC
7128752 CTTTGCC
1 CTTTGCC
7128759 CTTTGCC
1 CTTTGCC
7128766 CTTTGCC
1 CTTTGCC
7128773 CTTTG
1 CTTTG
7128778 TCTGTTTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.00, C:0.40, G:0.15, T:0.45
Consensus pattern (7 bp):
CTTTGCC
Found at i:7132023 original size:25 final size:24
Alignment explanation
Indices: 7131982--7132075 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 24
7131972 AACACGCCAC
*
7131982 AAAGGCTTT-TCAAAGAATTCTCCA
1 AAAGGCTTTCT-AGAGAATTCTCCA
* *
7132006 TAAGCGCTTTCTAGAGAATTCACCA
1 AAAG-GCTTTCTAGAGAATTCTCCA
*
7132031 CAAAGGCTTTCTAGGGAATTCAT-CA
1 -AAAGGCTTTCTAGAGAATTC-TCCA
*
7132056 CAAGGGCTTTCTAGAGAATT
1 -AAAGGCTTTCTAGAGAATT
7132076 TGTGTTTATT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
24 3 0.05
25 51 0.88
26 4 0.07
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (24 bp):
AAAGGCTTTCTAGAGAATTCTCCA
Found at i:7133848 original size:33 final size:33
Alignment explanation
Indices: 7133811--7133876 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
7133801 AGGTAAAAAT
7133811 GAGGTTGAAGAAAAGGAAGATATGAACAGATGA
1 GAGGTTGAAGAAAAGGAAGATATGAACAGATGA
*
7133844 GAGGTTGAAGATAAGGAAGATATGAACAGATGA
1 GAGGTTGAAGAAAAGGAAGATATGAACAGATGA
7133877 CAAGATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.33, T:0.17
Consensus pattern (33 bp):
GAGGTTGAAGAAAAGGAAGATATGAACAGATGA
Found at i:7136660 original size:45 final size:45
Alignment explanation
Indices: 7136605--7136710 Score: 133
Period size: 45 Copynumber: 2.4 Consensus size: 45
7136595 TTAGTCCGTT
* * *
7136605 TATTCTGTAATAGTTTGATTCCACTTAATGATTATTTGCACAATC
1 TATTTTGTAATAATTTGATTCCACTTAATAATTATTTGCACAATC
* * ** *
7136650 TATTTTGTAATAATTTGATTCTACTTGATAATTATTTGGTCAGTC
1 TATTTTGTAATAATTTGATTCCACTTAATAATTATTTGCACAATC
7136695 TA-TTTGTAATAATTTG
1 TATTTTGTAATAATTTG
7136711 TTACTTATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 14 0.26
45 39 0.74
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.49
Consensus pattern (45 bp):
TATTTTGTAATAATTTGATTCCACTTAATAATTATTTGCACAATC
Found at i:7143575 original size:6 final size:6
Alignment explanation
Indices: 7143564--7143590 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7143554 CTTGCTCCCA
7143564 CACACT CACACT CACACT CACACT CAC
1 CACACT CACACT CACACT CACACT CAC
7143591 TCAATCCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
CACACT
Found at i:7145386 original size:22 final size:23
Alignment explanation
Indices: 7145353--7145395 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
7145343 GATAATAATT
7145353 TTTTTATAAAATATATTTTTATA
1 TTTTTATAAAATATATTTTTATA
*
7145376 TTTTTAT-AAATGTATTTTTA
1 TTTTTATAAAATATATTTTTA
7145396 ACTTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTTATAAAATATATTTTTATA
Found at i:7150526 original size:24 final size:24
Alignment explanation
Indices: 7150481--7150526 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
7150471 TCCAATTCAT
* * *
7150481 TTTCAAATTTATAATTTTATTTTA
1 TTTCAAATATATAATGTAATTTTA
*
7150505 TTTCAAATATATTATGTAATTT
1 TTTCAAATATATAATGTAATTT
7150527 ATATGATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTCAAATATATAATGTAATTTTA
Found at i:7150758 original size:25 final size:25
Alignment explanation
Indices: 7150729--7150778 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
7150719 ATTTGAAACT
7150729 CATATTTCAAATCATGTCAAACTTG
1 CATATTTCAAATCATGTCAAACTTG
7150754 CATATTTCAAATCATGTCAAACTTG
1 CATATTTCAAATCATGTCAAACTTG
7150779 AACAGATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (25 bp):
CATATTTCAAATCATGTCAAACTTG
Found at i:7155875 original size:17 final size:15
Alignment explanation
Indices: 7155849--7155887 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
7155839 GAAATCCATA
7155849 AGCAGAATCAGTTCACC
1 AGCAGAATCA--TCACC
*
7155866 AGCAGTATCATCACC
1 AGCAGAATCATCACC
7155881 AGCAGAA
1 AGCAGAA
7155888 GAAACAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.15
Consensus pattern (15 bp):
AGCAGAATCATCACC
Found at i:7172150 original size:53 final size:54
Alignment explanation
Indices: 7172079--7172252 Score: 170
Period size: 53 Copynumber: 3.1 Consensus size: 54
7172069 TTTTCTCGAG
* *
7172079 AAAAAAATTTAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTT
1 AAAAAAA-TTCAAATTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCTATTT
* * * *** * *
7172134 AAAAAAATT-ACATTTTTGGGTGTTGACCATTGCATGATCGACACCCCCTTTTCT
1 AAAAAAATTCAAATTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCTATT-T
* *
7172188 CGAGAAAAAAATTCAAATTTTTTTTGTTTTGGCCATCAAATGGTCGACACCCCCTATTT
1 ----AAAAAAATTCAAA-TTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCTATTT
7172247 AAAAAA
1 AAAAAA
7172253 TTGCATATTT
Statistics
Matches: 93, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
53 34 0.37
54 3 0.03
55 13 0.14
58 9 0.10
59 3 0.03
60 31 0.33
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (54 bp):
AAAAAAATTCAAATTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCTATTT
Found at i:7172186 original size:113 final size:114
Alignment explanation
Indices: 7171949--7172252 Score: 345
Period size: 113 Copynumber: 2.7 Consensus size: 114
7171939 ATCAAATAGC
* * * ***
7171949 CGACACCCTCTTTTCTC-A-AAAAAAA-TT-ACA-TTTTTGTGTGTTGGTCATTGCATGGCCGAC
1 CGACACCCCCTTTTCTCGAGAAAAAAATTTAAAATTTTTTG-GTGTTGGCCATCAAATGGCCGAC
* * **
7172009 ACTCCTTATTTAAAAAAAAATCTATTTTGGGGTGTTGGTCATTGCATGGA
65 ACCCCCTATTTAAAAAAAAATCTATTTTGGGGTGTTGACCATTGCATGGA
* * *
7172059 CGACATCTCATTTTCTCGAGAAAAAAATTTAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA
1 CGACACCCCCTTTTCTCGAGAAAAAAATTTAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA
* *
7172124 CCCCCTATTT-AAAAAAATTAC-ATTTTTGGGTGTTGACCATTGCAT-GA
66 CCCCCTATTTAAAAAAAAAT-CTATTTTGGGGTGTTGACCATTGCATGGA
* * * * *
7172171 TCGACACCCCCTTTTCTCGAGAAAAAAATTCAAATTTTTTTTGTTTTGGCCATCAAATGGTCGAC
1 -CGACACCCCCTTTTCTCGAGAAAAAAATTTAAAATTTTTTGGTGTTGGCCATCAAATGGCCGAC
7172236 ACCCCCTATTTAAAAAA
65 ACCCCCTATTTAAAAAA
7172253 TTGCATATTT
Statistics
Matches: 163, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
110 13 0.08
111 1 0.01
112 9 0.06
113 98 0.60
114 36 0.22
115 6 0.04
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (114 bp):
CGACACCCCCTTTTCTCGAGAAAAAAATTTAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA
CCCCCTATTTAAAAAAAAATCTATTTTGGGGTGTTGACCATTGCATGGA
Found at i:7172385 original size:62 final size:61
Alignment explanation
Indices: 7172272--7172392 Score: 181
Period size: 62 Copynumber: 2.0 Consensus size: 61
7172262 TAGGTGTCGG
7172272 TCTTTTCTCGAGAAAAAAAATTTAAAATTTTTTTGTGTTGGCCATCAAATGGTCGACACTT
1 TCTTTTCTCGAGAAAAAAAATTTAAAATTTTTTTGTGTTGGCCATCAAATGGTCGACACTT
** **
7172333 TCTTTTCTCG-GATAAAAAAATTGTAATTTTTTTTTGTGTTGGCCATGTAATGGTCGACAC
1 TCTTTTCTCGAGA-AAAAAAATT-TAAAATTTTTTTGTGTTGGCCATCAAATGGTCGACAC
7172393 CAACTTTCCC
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
60 2 0.04
61 19 0.35
62 33 0.61
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (61 bp):
TCTTTTCTCGAGAAAAAAAATTTAAAATTTTTTTGTGTTGGCCATCAAATGGTCGACACTT
Found at i:7172589 original size:31 final size:31
Alignment explanation
Indices: 7172554--7172613 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
7172544 TACAATCGAA
* *
7172554 TTTCGGGGTTGAGCTATATACTGTCATGTAT
1 TTTCGGAGTTGAACTATATACTGTCATGTAT
*
7172585 TTTCGGAGTTGAATTATATACTGTCATGT
1 TTTCGGAGTTGAACTATATACTGTCATGT
7172614 GAAGCGGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (31 bp):
TTTCGGAGTTGAACTATATACTGTCATGTAT
Found at i:7176273 original size:89 final size:89
Alignment explanation
Indices: 7176166--7176334 Score: 293
Period size: 89 Copynumber: 1.9 Consensus size: 89
7176156 ACATGTTTTA
* *
7176166 ATTTGACAATACAATATTTATTAATTTTATATATTTAAATAAAAATTATTATTATTATTATATTA
1 ATTTGACAATACAATATTTATTAAATTTATATATTTAAATAAAAATTATTATTATAATTATATTA
*
7176231 TAATTTTTATCATATAATGTGTTG
66 CAATTTTTATCATATAATGTGTTG
* *
7176255 ATTTGATAATACATTATTTATTAAATTTATATATTTAAATAAAAATTATTATTATAATTATATTA
1 ATTTGACAATACAATATTTATTAAATTTATATATTTAAATAAAAATTATTATTATAATTATATTA
7176320 CAATTTTTATCATAT
66 CAATTTTTATCATAT
7176335 TTTAAATTTG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (89 bp):
ATTTGACAATACAATATTTATTAAATTTATATATTTAAATAAAAATTATTATTATAATTATATTA
CAATTTTTATCATATAATGTGTTG
Found at i:7178792 original size:30 final size:30
Alignment explanation
Indices: 7178758--7178831 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
7178748 ATTTTTTTTC
*
7178758 CGTTTACT-TTTTAAATTTAATTTGTAATTT
1 CGTTT-CTATTTTAAATTTAATTTCTAATTT
*
7178788 CGTTTTTATTTTAAATTTAATTTCTAATTT
1 CGTTTCTATTTTAAATTTAATTTCTAATTT
*
7178818 C-TTGTATATTTTAA
1 CGTT-TCTATTTTAA
7178832 TTTTTCTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (30 bp):
CGTTTCTATTTTAAATTTAATTTCTAATTT
Found at i:7178855 original size:31 final size:31
Alignment explanation
Indices: 7178812--7178876 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
7178802 ATTTAATTTC
* * * *
7178812 TAATTTCTTGTATATTTTAATTTTTCTTTTT
1 TAATTTCCTGTATATTCTAATTATTATTTTT
7178843 TAATTTCCTGTATATTCTAATTATTATTTTT
1 TAATTTCCTGTATATTCTAATTATTATTTTT
7178874 TAA
1 TAA
7178877 AAATTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.65
Consensus pattern (31 bp):
TAATTTCCTGTATATTCTAATTATTATTTTT
Found at i:7179803 original size:60 final size:58
Alignment explanation
Indices: 7179682--7180018 Score: 207
Period size: 60 Copynumber: 5.8 Consensus size: 58
7179672 AGGAGAAGTT
** * * * *
7179682 GGTGTCGGCCATTACATGGCCAACACAAAAAAAATTGTAATTTTTTTATCCGAAAAAAGAG
1 GGTGTCGGCCATTTGATGGCCAACA-ACAAAAAATTTTAATTTTTTTCT-CGAGAAAAG-G
*
7179743 GGTGTCGACCATTTGATGGCCAACAACAAAAAATTTTAAATTTTTTTCTCGAGAAAAGAG
1 GGTGTCGGCCATTTGATGGCCAACAACAAAAAATTTT-AATTTTTTTCTCGAGAAAAG-G
* * * ** *
7179803 GGTGTTGGCCA-TTGCATGG-CAGACACCCAAAAA-TGCAATTTTTTT-T--A-AATAGG
1 GGTGTCGGCCATTTG-ATGGCCA-ACAACAAAAAATTTTAATTTTTTTCTCGAGAAAAGG
** * *
7179856 GGTGTCGGCCATTTGATGGTAAACACCAAAAAATTTTGAA-TTTTTTCTTGAGAAAATGG
1 GGTGTCGGCCATTTGATGGCCAACAACAAAAAATTTT-AATTTTTTTCTCGAGAAAA-GG
* *** * * * ** *
7179915 GGTGTCGGCAATGCAATGACCAACATCCAAAAA-TGCAATTTTTTT-T--A-AATAGG
1 GGTGTCGGCCATTTGATGGCCAACAACAAAAAATTTTAATTTTTTTCTCGAGAAAAGG
* *
7179968 AGGTATCGGTCATTTGATGGCCAAC-ACAAGAAAATTTTGAATTTTTTTCTC
1 -GGTGTCGGCCATTTGATGGCCAACAACAA-AAAATTTT-AATTTTTTTCTC
7180019 AAACAAGGGG
Statistics
Matches: 214, Mismatches: 43, Indels: 41
0.72 0.14 0.14
Matches are distributed among these distances:
53 29 0.14
54 39 0.18
55 6 0.03
56 9 0.04
57 6 0.03
58 19 0.09
59 32 0.15
60 42 0.20
61 32 0.15
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (58 bp):
GGTGTCGGCCATTTGATGGCCAACAACAAAAAATTTTAATTTTTTTCTCGAGAAAAGG
Found at i:7179866 original size:53 final size:52
Alignment explanation
Indices: 7179802--7179994 Score: 142
Period size: 53 Copynumber: 3.5 Consensus size: 52
7179792 CGAGAAAAGA
*
7179802 GGGTGTTGGCCATTGCATGGCAGACACCCAAAAATGCAATTTTTTTTAAATAG
1 GGGTGTCGGCCATTGCATGGCA-ACACCCAAAAATGCAATTTTTTTTAAATAG
* * *
7179855 GGGTGTCGGCCATTTG-ATGGTAAACACCAAAAAATTTTG-AATTTTTTCTTGAGAAAATG
1 GGGTGTCGGCCA-TTGCATGG-CAACACCCAAAAA---TGCAATTTTTT-TT-A-AATA-G
* * *
7179914 GGGTGTCGG-CAATGCAATGACCAACATCCAAAAATGCAATTTTTTTTAAATAG
1 GGGTGTCGGCCATTGC-ATG-GCAACACCCAAAAATGCAATTTTTTTTAAATAG
* *
7179967 GAGGTATCGGTCATTTG-ATGGCCAACAC
1 G-GGTGTCGGCCA-TTGCATGG-CAACAC
7179995 AAGAAAATTT
Statistics
Matches: 109, Mismatches: 14, Indels: 33
0.70 0.09 0.21
Matches are distributed among these distances:
53 27 0.25
54 22 0.20
55 11 0.10
56 10 0.09
57 11 0.10
58 5 0.05
59 23 0.21
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (52 bp):
GGGTGTCGGCCATTGCATGGCAACACCCAAAAATGCAATTTTTTTTAAATAG
Found at i:7179886 original size:113 final size:112
Alignment explanation
Indices: 7179742--7180018 Score: 364
Period size: 113 Copynumber: 2.4 Consensus size: 112
7179732 CGAAAAAAGA
* *
7179742 GGGTGTCGACCATTTGATGGCCAACAACAAAAAATTTTAAATTTTTTTCTCGAGAAAA-GAGGGT
1 GGGTGTCGGCCATTTGATGGCCAAC-ACAAAAAATTTTGAATTTTTTTCTCGAGAAAATG-GGGT
* * *
7179806 GTTGGCCATTGC-ATG-GCAGACACCCAAAAATGCAATTTTTTTTAAATAG
64 GTCGG-CAATGCAATGACCA-ACACCCAAAAATGCAATTTTTTTTAAATAG
** *
7179855 GGGTGTCGGCCATTTGATGGTAAACACCAAAAAATTTTGAA-TTTTTTCTTGAGAAAATGGGGTG
1 GGGTGTCGGCCATTTGATGGCCAACA-CAAAAAATTTTGAATTTTTTTCTCGAGAAAATGGGGTG
*
7179919 TCGGCAATGCAATGACCAACATCCAAAAATGCAATTTTTTTTAAATAG
65 TCGGCAATGCAATGACCAACACCCAAAAATGCAATTTTTTTTAAATAG
* *
7179967 GAGGTATCGGTCATTTGATGGCCAACACAAGAAAATTTTGAATTTTTTTCTC
1 G-GGTGTCGGCCATTTGATGGCCAACACAA-AAAATTTTGAATTTTTTTCTC
7180019 AAACAAGGGG
Statistics
Matches: 143, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
111 5 0.03
112 60 0.42
113 70 0.49
114 8 0.06
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (112 bp):
GGGTGTCGGCCATTTGATGGCCAACACAAAAAATTTTGAATTTTTTTCTCGAGAAAATGGGGTGT
CGGCAATGCAATGACCAACACCCAAAAATGCAATTTTTTTTAAATAG
Found at i:7180140 original size:58 final size:55
Alignment explanation
Indices: 7180028--7180154 Score: 139
Period size: 58 Copynumber: 2.3 Consensus size: 55
7180018 CAAACAAGGG
* * * *
7180028 GCATGGCCGACACCAAAAAATGTAATTTTTTTCGAGAAAAAGGGTGTCGACCATTT
1 GCATAGCCAACACCAAAAAATGTAATTTTTTTCGAAAAAAAGAGTGTCGACCA-TT
* * *
7180084 G-ATAGCCAACACTAAAAAATTTAAATTTTTTTCTGAAAAAAAAGAGTGTCGGCCATT
1 GCATAGCCAACACCAAAAAATGT-AATTTTTTTC-G-AAAAAAAGAGTGTCGACCATT
*
7180141 GCATGGCCAACACC
1 GCATAGCCAACACC
7180155 TCAATTTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
55 17 0.29
56 11 0.19
57 4 0.07
58 26 0.45
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (55 bp):
GCATAGCCAACACCAAAAAATGTAATTTTTTTCGAAAAAAAGAGTGTCGACCATT
Found at i:7180697 original size:23 final size:23
Alignment explanation
Indices: 7180645--7180697 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
7180635 TGTTTTTATG
*
7180645 GCACGATTATGTCTGCTCCTATA
1 GCACGGTTATGTCTGCTCCTATA
*
7180668 GCACGGTTATGTCTGCTTCTATA
1 GCACGGTTATGTCTGCTCCTATA
*
7180691 GCGCGGT
1 GCACGGT
7180698 AATTTGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (23 bp):
GCACGGTTATGTCTGCTCCTATA
Found at i:7181770 original size:19 final size:19
Alignment explanation
Indices: 7181728--7181771 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
7181718 TTCTATGTTT
* *
7181728 TAAT-ATTTTTTGGATTTT
1 TAATGATTTTTTAGATTTA
*
7181746 TTATGATTTTTTAGATTTA
1 TAATGATTTTTTAGATTTA
7181765 TAATGAT
1 TAATGAT
7181772 ATGTTAAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.61
Consensus pattern (19 bp):
TAATGATTTTTTAGATTTA
Found at i:7192276 original size:15 final size:15
Alignment explanation
Indices: 7192256--7192286 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7192246 AATATCCGAA
*
7192256 TATTAACCGAATTAC
1 TATTAACCAAATTAC
7192271 TATTAACCAAATTAC
1 TATTAACCAAATTAC
7192286 T
1 T
7192287 TGAAATGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.35
Consensus pattern (15 bp):
TATTAACCAAATTAC
Found at i:7195597 original size:56 final size:56
Alignment explanation
Indices: 7195527--7195638 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
7195517 TATTAAAGGG
7195527 AACAAAAGAAAATCAGATGAATGAAAAAGGCAAATTGCATATATTTTCTAAAAGCT
1 AACAAAAGAAAATCAGATGAATGAAAAAGGCAAATTGCATATATTTTCTAAAAGCT
7195583 AACAAAAGAAAATCAGATGAATGAAAAAGGCAAATTGCATATATTTTCTAAAAGCT
1 AACAAAAGAAAATCAGATGAATGAAAAAGGCAAATTGCATATATTTTCTAAAAGCT
7195639 TTGGCTATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (56 bp):
AACAAAAGAAAATCAGATGAATGAAAAAGGCAAATTGCATATATTTTCTAAAAGCT
Found at i:7207068 original size:3 final size:3
Alignment explanation
Indices: 7207060--7207095 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
7207050 ATTGTTTTAA
7207060 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7207096 GATATTATCA
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):
AAT
Done.