Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 122 of 136
Found at i:41507515 original size:66 final size:68
Alignment explanation
Indices: 41507443--41507588 Score: 206
Period size: 75 Copynumber: 2.1 Consensus size: 68
41507433 AAATTAATTG
*
41507443 TTAGTAAAATTATCAAATTATTAATTG-TTAATTG-TATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTTATTAATTGTTGTAACAAAATCTAACATT
41507506 TGA
66 TGA
41507509 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTTAATTATATTAATTGTTGTAACAAAATC
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTG-----T-TATTAATTGTTGTAACAAAATC
41507574 TAACATTTGA
59 TAACATTTGA
41507584 TTAGT
1 TTAGT
41507589 TTACATTTTT
Statistics
Matches: 70, Mismatches: 1, Indels: 9
0.88 0.01 0.11
Matches are distributed among these distances:
66 27 0.39
68 7 0.10
75 36 0.51
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTTATTAATTGTTGTAACAAAATCTAACATT
TGA
Found at i:41507548 original size:16 final size:16
Alignment explanation
Indices: 41507524--41507562 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
41507514 AAAATTATCA
* *
41507524 AATTATTAATTGTATT
1 AATTGTTAATTATATT
41507540 AATTGTTAATTATATT
1 AATTGTTAATTATATT
41507556 AATTGTT
1 AATTGTT
41507563 GTAACAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (16 bp):
AATTGTTAATTATATT
Found at i:41507826 original size:19 final size:20
Alignment explanation
Indices: 41507799--41507865 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
41507789 TCTGTCGGGG
*
41507799 AAATGAAATTGAAAAC-TAA
1 AAATAAAATTGAAAACATAA
41507818 AAATAAAATTGAAAACATAA
1 AAATAAAATTGAAAACATAA
*
41507838 AAATAAAATTGAAAACTTAA
1 AAATAAAATTGAAAACATAA
*
41507858 ACATAAAA
1 AAATAAAA
41507866 ATAAATAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 15 0.34
20 29 0.66
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (20 bp):
AAATAAAATTGAAAACATAA
Found at i:41516195 original size:2 final size:2
Alignment explanation
Indices: 41516188--41516223 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
41516178 TTATTAAATC
*
41516188 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
41516224 TTAATAAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:41516612 original size:5 final size:5
Alignment explanation
Indices: 41516602--41516627 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41516592 TGAGCATTCG
41516602 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
41516628 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:41516725 original size:5 final size:5
Alignment explanation
Indices: 41516717--41516742 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41516707 GAGATGGAAT
41516717 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
41516743 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:41516742 original size:26 final size:26
Alignment explanation
Indices: 41516691--41516742 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
41516681 TGAAGTTTTC
* * *
41516691 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
41516717 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
41516743 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:41517571 original size:9 final size:9
Alignment explanation
Indices: 41517557--41517593 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41517547 TATAGTTTGA
41517557 TATTCGAAT
1 TATTCGAAT
41517566 TATTCGAAT
1 TATTCGAAT
*
41517575 TATTCGAGT
1 TATTCGAAT
41517584 TATTCGAAT
1 TATTCGAAT
41517593 T
1 T
41517594 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41517875 original size:41 final size:41
Alignment explanation
Indices: 41517830--41517927 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
41517820 GGCTTTGTAC
*
41517830 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACCTTACGT
41517871 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACCTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACCTTACGT
*
41517912 CTAGCAGGTTTAATGC
1 CTAGCAGGCTTAATGC
41517928 TAGTGTATTG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACCTTACGT
Found at i:41523392 original size:14 final size:14
Alignment explanation
Indices: 41523373--41523401 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41523363 ATCACTTGAT
41523373 TGTCTCTGGTGAAC
1 TGTCTCTGGTGAAC
41523387 TGTCTCTGGTGAAC
1 TGTCTCTGGTGAAC
41523401 T
1 T
41523402 TAGACACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.38
Consensus pattern (14 bp):
TGTCTCTGGTGAAC
Found at i:41524913 original size:19 final size:20
Alignment explanation
Indices: 41524889--41524935 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
41524879 GTAACTTCCT
*
41524889 TAACTAACTAAC-TGCTCAC
1 TAACTAACTAACTTGATCAC
* *
41524908 TAACT-ACTGACTTGATGAC
1 TAACTAACTAACTTGATCAC
41524927 TAACTAACT
1 TAACTAACT
41524936 TCCTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 15 0.65
20 3 0.13
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.30
Consensus pattern (20 bp):
TAACTAACTAACTTGATCAC
Found at i:41526813 original size:14 final size:14
Alignment explanation
Indices: 41526796--41526822 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41526786 ATTTGGTGAG
41526796 AGAAAAAATTTTAA
1 AGAAAAAATTTTAA
41526810 AGAAAAAATTTTA
1 AGAAAAAATTTTA
41526823 TGTTAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
AGAAAAAATTTTAA
Found at i:41526830 original size:13 final size:13
Alignment explanation
Indices: 41526814--41526856 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
41526804 TTTTAAAGAA
41526814 AAAATTTTATGTT
1 AAAATTTTATGTT
41526827 AAAATTTTA----
1 AAAATTTTATGTT
41526836 AAAATTTTATGTT
1 AAAATTTTATGTT
41526849 AAAATTTT
1 AAAATTTT
41526857 TTTGAGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
9 9 0.35
13 17 0.65
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (13 bp):
AAAATTTTATGTT
Found at i:41526839 original size:22 final size:22
Alignment explanation
Indices: 41526813--41526856 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41526803 ATTTTAAAGA
41526813 AAAAATTTTATGTTAAAATTTT
1 AAAAATTTTATGTTAAAATTTT
41526835 AAAAATTTTATGTTAAAATTTT
1 AAAAATTTTATGTTAAAATTTT
41526857 TTTGAGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
AAAAATTTTATGTTAAAATTTT
Found at i:41531469 original size:28 final size:28
Alignment explanation
Indices: 41531417--41531470 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
41531407 ATTAAGATTC
* **
41531417 AATTGATGGTACATATTTACCTTTAAAA
1 AATTGATGATACATATTTAAATTTAAAA
*
41531445 AATTGATTATACATATTTAAATTTAA
1 AATTGATGATACATATTTAAATTTAA
41531471 CTGAAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (28 bp):
AATTGATGATACATATTTAAATTTAAAA
Found at i:41542224 original size:13 final size:13
Alignment explanation
Indices: 41542206--41542230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41542196 AGTTCTTTAT
41542206 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
41542219 TGCTTTTGAGAA
1 TGCTTTTGAGAA
41542231 ATTTGAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:41543195 original size:11 final size:11
Alignment explanation
Indices: 41543179--41543204 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41543169 CAAGAAATAC
41543179 CAGCAAATCAA
1 CAGCAAATCAA
41543190 CAGCAAATCAA
1 CAGCAAATCAA
41543201 CAGC
1 CAGC
41543205 TTCAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.31, G:0.12, T:0.08
Consensus pattern (11 bp):
CAGCAAATCAA
Found at i:41543255 original size:19 final size:19
Alignment explanation
Indices: 41543209--41543257 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
41543199 AACAGCTTCA
* *
41543209 AAATATTAAACAGAAGAGG
1 AAATATAAAACAGAAGAAG
*
41543228 AACTAATAAAACAGAAGAAG
1 AAAT-ATAAAACAGAAGAAG
41543248 AAATATAAAA
1 AAATATAAAA
41543258 GAAACTCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.65, C:0.06, G:0.14, T:0.14
Consensus pattern (19 bp):
AAATATAAAACAGAAGAAG
Found at i:41551354 original size:13 final size:13
Alignment explanation
Indices: 41551336--41551363 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41551326 GCAATCGTTA
41551336 TAGAATACATGGT
1 TAGAATACATGGT
41551349 TAGAATACATGGT
1 TAGAATACATGGT
41551362 TA
1 TA
41551364 ATGGTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (13 bp):
TAGAATACATGGT
Found at i:41554281 original size:3 final size:3
Alignment explanation
Indices: 41554273--41554298 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41554263 TTCTTTTCGT
41554273 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
41554299 TTCATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41569458 original size:18 final size:18
Alignment explanation
Indices: 41569435--41569471 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
41569425 AAGTGGCATG
41569435 CTGCTTTGACAAAGTTTC
1 CTGCTTTGACAAAGTTTC
41569453 CTGCTTTGACAAAGTTTC
1 CTGCTTTGACAAAGTTTC
41569471 C
1 C
41569472 AACTTCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (18 bp):
CTGCTTTGACAAAGTTTC
Found at i:41573939 original size:17 final size:18
Alignment explanation
Indices: 41573917--41573951 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41573907 ATGTTTTGGA
41573917 TCCTTATT-TATTTATGT
1 TCCTTATTATATTTATGT
*
41573934 TCCTTATTATTTTTATGT
1 TCCTTATTATATTTATGT
41573952 ACAATGTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (18 bp):
TCCTTATTATATTTATGT
Found at i:41586327 original size:13 final size:13
Alignment explanation
Indices: 41586305--41586340 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
41586295 GGGTATAGTT
*
41586305 ATATATTAAAAAA
1 ATATAGTAAAAAA
41586318 ATATAGT-AAAAA
1 ATATAGTAAAAAA
41586330 ATATAGTAAAA
1 ATATAGTAAAA
41586341 TATTAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (13 bp):
ATATAGTAAAAAA
Found at i:41586443 original size:3 final size:3
Alignment explanation
Indices: 41586435--41586475 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
41586425 CAAATATTAA
*
41586435 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATG ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
41586476 GTTTGTCAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:41594965 original size:3 final size:3
Alignment explanation
Indices: 41594945--41595080 Score: 229
Period size: 3 Copynumber: 45.7 Consensus size: 3
41594935 GTCTGTTAAT
* * *
41594945 TAA TAA TGA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41594993 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
41595041 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
41595081 GCTGTAAGTC
Statistics
Matches: 128, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
2 2 0.02
3 126 0.98
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:41596088 original size:27 final size:28
Alignment explanation
Indices: 41596058--41596112 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
41596048 CAAAAAAGTT
*
41596058 TTTTAAAAA-ATTAAAAA-ATTCATAAAA
1 TTTTAAAAAGATAAAAAATATTC-TAAAA
41596085 TTTTAAAAAGATAAAAAATATTCTAAAA
1 TTTTAAAAAGATAAAAAATATTCTAAAA
41596113 AATTAGACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 9 0.36
28 12 0.48
29 4 0.16
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (28 bp):
TTTTAAAAAGATAAAAAATATTCTAAAA
Found at i:41612350 original size:16 final size:17
Alignment explanation
Indices: 41612317--41612352 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
41612307 GTGTATAATT
41612317 AAATTAATACTACAAATC
1 AAATTAATAC-ACAAATC
41612335 AAATTAATAC-CAAATC
1 AAATTAATACACAAATC
41612351 AA
1 AA
41612353 TCAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATTAATACACAAATC
Found at i:41612617 original size:22 final size:21
Alignment explanation
Indices: 41612585--41612628 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
41612575 AACAAGACTT
* *
41612585 TATTTTTATTTTAAAATATAA
1 TATTTTTATTTAAAAAAATAA
41612606 TATTTTTAATTTAAAAAAATAA
1 TATTTTT-ATTTAAAAAAATAA
41612628 T
1 T
41612629 TTTCAACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTTATTTAAAAAAATAA
Found at i:41620991 original size:6 final size:6
Alignment explanation
Indices: 41620980--41621023 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
41620970 TGAGAAGAGG
*
41620980 AGAAAA AGAAAA AGAAAA AGAAAA TA-AAGAA ATAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA -AGAA-AA AGAAAA AGAAAA A
41621024 TTAAATTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AGAAAA
Found at i:41625453 original size:20 final size:20
Alignment explanation
Indices: 41625428--41625484 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
41625418 TACCTTTTGT
* * *
41625428 AAATTATCAAATTTCTTACA
1 AAATTACCAAATATCTTAAA
*
41625448 AAATTACCGAATATCTTAAA
1 AAATTACCAAATATCTTAAA
*
41625468 AAATTACTAAAT-TCTTA
1 AAATTACCAAATATCTTA
41625485 TAATATTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATTACCAAATATCTTAAA
Found at i:41627729 original size:19 final size:19
Alignment explanation
Indices: 41627705--41627743 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41627695 AATAATTAAC
* * *
41627705 TTTATATTTCATATAATTT
1 TTTATAATTAATAAAATTT
41627724 TTTATAATTAATAAAATTT
1 TTTATAATTAATAAAATTT
41627743 T
1 T
41627744 ATAATGTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATAATTAATAAAATTT
Found at i:41636489 original size:7 final size:7
Alignment explanation
Indices: 41636477--41636502 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41636467 TTTAGTGATT
41636477 TATTTTC
1 TATTTTC
41636484 TATTTTC
1 TATTTTC
41636491 TATTTTC
1 TATTTTC
41636498 TATTT
1 TATTT
41636503 GCAGGGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTTC
Found at i:41637781 original size:20 final size:21
Alignment explanation
Indices: 41637739--41637781 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
41637729 TTGAGAGTGG
**
41637739 ATATTTTTAATTTAATTTTAA
1 ATATTTTTAATTTAATTAAAA
41637760 ATATTTTT-ATTTAATTAAAA
1 ATATTTTTAATTTAATTAAAA
41637780 AT
1 AT
41637782 GTCGCATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTTTTAATTTAATTAAAA
Found at i:41647109 original size:9 final size:9
Alignment explanation
Indices: 41647097--41647175 Score: 88
Period size: 9 Copynumber: 8.8 Consensus size: 9
41647087 AAAAATTAAC
41647097 CGAATTACT
1 CGAATTACT
*
41647106 CGAATTACC
1 CGAATTACT
*
41647115 CGAATTAAT
1 CGAATTACT
*
41647124 CGAATTATT
1 CGAATTACT
41647133 CGAATTACT
1 CGAATTACT
*
41647142 CGAATTATT
1 CGAATTACT
* *
41647151 TGAATTACC
1 CGAATTACT
41647160 CGAATTAAC-
1 CGAATT-ACT
41647169 CGAATTA
1 CGAATTA
41647176 TCCTAATTGA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
8 1 0.02
9 56 0.95
10 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (9 bp):
CGAATTACT
Found at i:41647117 original size:18 final size:18
Alignment explanation
Indices: 41647090--41647175 Score: 100
Period size: 18 Copynumber: 4.8 Consensus size: 18
41647080 TTTGGTTAAA
41647090 AATTAACCGAATTACTCG
1 AATTAACCGAATTACTCG
* *
41647108 AATTACCCGAATTAATCG
1 AATTAACCGAATTACTCG
**
41647126 AATTATTCGAATTACTCG
1 AATTAACCGAATTACTCG
*** *
41647144 AATTATTTGAATTACCCG
1 AATTAACCGAATTACTCG
41647162 AATTAACCGAATTA
1 AATTAACCGAATTA
41647176 TCCTAATTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (18 bp):
AATTAACCGAATTACTCG
Found at i:41647128 original size:27 final size:27
Alignment explanation
Indices: 41647090--41647175 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 27
41647080 TTTGGTTAAA
*
41647090 AATTAACCGAATTACTCGAATTACCCG
1 AATTAATCGAATTACTCGAATTACCCG
* *
41647117 AATTAATCGAATTATTCGAATTACTCG
1 AATTAATCGAATTACTCGAATTACCCG
* * * *
41647144 AATTATTTGAATTACCCGAATTAACCG
1 AATTAATCGAATTACTCGAATTACCCG
41647171 AATTA
1 AATTA
41647176 TCCTAATTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (27 bp):
AATTAATCGAATTACTCGAATTACCCG
Found at i:41647309 original size:13 final size:13
Alignment explanation
Indices: 41647291--41647325 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
41647281 TATGATTGGG
41647291 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
41647304 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
*
41647317 TTGTGTTGG
1 TTGGGTTGG
41647326 ATTGAATACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.11, C:0.00, G:0.46, T:0.43
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:41653067 original size:35 final size:35
Alignment explanation
Indices: 41653021--41653092 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
41653011 GTGAAATTTT
41653021 TTACTACATAAGTATCATGATATTAATAATCAATG
1 TTACTACATAAGTATCATGATATTAATAATCAATG
41653056 TTACTACATAAGTATCATGATATTAATAATCAATG
1 TTACTACATAAGTATCATGATATTAATAATCAATG
41653091 TT
1 TT
41653093 GGGATGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (35 bp):
TTACTACATAAGTATCATGATATTAATAATCAATG
Found at i:41655369 original size:13 final size:12
Alignment explanation
Indices: 41655337--41655370 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
41655327 AAAAGAGGAA
41655337 AGAAAAGAAAAG
1 AGAAAAGAAAAG
*
41655349 AGATAAGAAACAG
1 AGAAAAGAAA-AG
41655362 AGAAAAGAA
1 AGAAAAGAA
41655371 GGAAAATCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.71, C:0.03, G:0.24, T:0.03
Consensus pattern (12 bp):
AGAAAAGAAAAG
Found at i:41675017 original size:62 final size:62
Alignment explanation
Indices: 41674930--41675773 Score: 1634
Period size: 62 Copynumber: 13.6 Consensus size: 62
41674920 ACAAACAACA
*
41674930 AAATAAAATAAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAGACACAAAAATAAAT
1 AAAT-AAAT-AAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
*
41674994 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAGACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
*
41675056 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAGACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
*
41675118 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAGACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675180 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675242 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675304 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675366 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675428 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675490 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675552 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675614 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675676 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
41675738 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAA
1 AAATAAATAAATAAACAAAAATGCAAGAACAGAAAA
41675774 AATTTGGAGT
Statistics
Matches: 779, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
62 771 0.99
63 4 0.01
64 4 0.01
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.11
Consensus pattern (62 bp):
AAATAAATAAATAAACAAAAATGCAAGAACAGAAAAGGTAGAAAACAAACACAAAAATAAAT
Found at i:41676111 original size:15 final size:15
Alignment explanation
Indices: 41676075--41676124 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
41676065 CTTGGGCATT
**
41676075 GGTTTGGGCTG-AAG
1 GGTTTGGGCTGTTCG
41676089 GGTATTGGGCTGTTCG
1 GGT-TTGGGCTGTTCG
*
41676105 GGTTTGGGCTATTCG
1 GGTTTGGGCTGTTCG
41676120 GGTTT
1 GGTTT
41676125 TGCTAGTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.10
15 24 0.77
16 4 0.13
ACGTcount: A:0.08, C:0.10, G:0.44, T:0.38
Consensus pattern (15 bp):
GGTTTGGGCTGTTCG
Found at i:41676720 original size:107 final size:107
Alignment explanation
Indices: 41676527--41676731 Score: 315
Period size: 107 Copynumber: 1.9 Consensus size: 107
41676517 TGCCATTGTT
41676527 GATTATGAAGAAGAACTAGATTGTAAAGTTTAATTGTTAGTTTTGTACATAAGAACTAAAATGTA
1 GATTATGAAGAAGAACTAGATTGTAAAGTTTAATTGTTAGTTTTGTACATAAGAACTAAAATGTA
*
41676592 TAAATGGTGAAATTTCAGTGAAATTTCAGTAATCTAAGCTTA
66 TAAATGATGAAATTTCAGTGAAATTTCAGTAATCTAAGCTTA
* * * *
41676634 GATTATGGAA-AAGGACTAGATTGTAAAGTTTAATTGTTAGTTTTGTGCTTAAGGACTAAAATGT
1 GATTAT-GAAGAAGAACTAGATTGTAAAGTTTAATTGTTAGTTTTGTACATAAGAACTAAAATGT
* *
41676698 ATAAATGATGAAA-TTGAGGTGAAATTTTAGTAAT
65 ATAAATGATGAAATTTCA-GTGAAATTTCAGTAAT
41676732 AATAGACAGT
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
106 3 0.03
107 83 0.93
108 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (107 bp):
GATTATGAAGAAGAACTAGATTGTAAAGTTTAATTGTTAGTTTTGTACATAAGAACTAAAATGTA
TAAATGATGAAATTTCAGTGAAATTTCAGTAATCTAAGCTTA
Found at i:41677775 original size:3 final size:3
Alignment explanation
Indices: 41677767--41677809 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
41677757 AAAATTCACC
41677767 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
41677810 GATTTGCCAT
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:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:41681150 original size:2 final size:2
Alignment explanation
Indices: 41681143--41681219 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
41681133 CGTAAATGAG
41681143 AT AT AT AT 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 AT AT AT AT
41681185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41681220 CAAAAAAGCA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41701192 original size:99 final size:99
Alignment explanation
Indices: 41701016--41701214 Score: 362
Period size: 99 Copynumber: 2.0 Consensus size: 99
41701006 TCCGGGGCTT
41701016 TGGCACCAAAAATGCAGATCTCAGTTATTTAACTTTCTTGGTAATTTATAAATTAGTTGCAGAAC
1 TGGCACCAAAAATGCAGATCTCAGTTATTTAACTTTCTTGGTAATTTATAAATTAGTTGCAGAAC
41701081 ATTGTTGCGAACTTGGTCATTGTATTTGTCTCCC
66 ATTGTTGCGAACTTGGTCATTGTATTTGTCTCCC
*
41701115 TGGCACCAAAAATGCAGATCTCAGTTATTTAACTTTCTTGGTAATTTATAATTTAGTTGCAGAAC
1 TGGCACCAAAAATGCAGATCTCAGTTATTTAACTTTCTTGGTAATTTATAAATTAGTTGCAGAAC
* * *
41701180 ATTTTTGGGAACTTGGTCATTGTATTTGTGTCCC
66 ATTGTTGCGAACTTGGTCATTGTATTTGTCTCCC
41701214 T
1 T
41701215 ACCAATATAT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 96 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (99 bp):
TGGCACCAAAAATGCAGATCTCAGTTATTTAACTTTCTTGGTAATTTATAAATTAGTTGCAGAAC
ATTGTTGCGAACTTGGTCATTGTATTTGTCTCCC
Found at i:41704694 original size:19 final size:20
Alignment explanation
Indices: 41704651--41704703 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
41704641 TATATTTTTG
**
41704651 TTTATATATTATTTTTTAATA
1 TTTATATATT-TTTTGAAATA
41704672 TTTATATATTTTTTGAAAT-
1 TTTATATATTTTTTGAAATA
*
41704691 TTTATGTATTTTT
1 TTTATATATTTTT
41704704 ATTTTGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 7 0.24
21 10 0.34
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (20 bp):
TTTATATATTTTTTGAAATA
Found at i:41712283 original size:145 final size:146
Alignment explanation
Indices: 41712037--41712327 Score: 575
Period size: 145 Copynumber: 2.0 Consensus size: 146
41712027 AAATTTATTT
41712037 TGATAAAATGAACTTTATTTTATGATTTTTGAATATTATTTGACAAAATTTCAAAATCTTTTCAT
1 TGATAAAATGAACTTTATTTTATGATTTTTGAATATTATTTGACAAAATTTCAAAATCTTTTCAT
41712102 AAATATTTAAAAATAATAATCTTTCAAGAACTTTTAAATTATTTCATTATTTTAAATATGAATAT
66 AAATATTTAAAAATAATAATCTTTCAAGAACTTTTAAATTATTTCATTATTTTAAATATGAATAT
41712167 TTA-TTTTATATCATA
131 TTATTTTTATATCATA
41712182 TGATAAAATGAACTTTATTTTATGATTTTTGAATATTATTTGACAAAATTTCAAAATCTTTTCAT
1 TGATAAAATGAACTTTATTTTATGATTTTTGAATATTATTTGACAAAATTTCAAAATCTTTTCAT
41712247 AAATATTTAAAAATAATAATCTTTCAAGAACTTTTAAATTATTTCATTATTTTAAATATGAATAT
66 AAATATTTAAAAATAATAATCTTTCAAGAACTTTTAAATTATTTCATTATTTTAAATATGAATAT
41712312 TTATTTTTATATCATA
131 TTATTTTTATATCATA
41712328 AAGTGTTAAA
Statistics
Matches: 145, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
145 133 0.92
146 12 0.08
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (146 bp):
TGATAAAATGAACTTTATTTTATGATTTTTGAATATTATTTGACAAAATTTCAAAATCTTTTCAT
AAATATTTAAAAATAATAATCTTTCAAGAACTTTTAAATTATTTCATTATTTTAAATATGAATAT
TTATTTTTATATCATA
Found at i:41712591 original size:22 final size:21
Alignment explanation
Indices: 41712544--41712596 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
41712534 TGTACAAAAT
** *
41712544 AAAAAAAAATTAAAGATTTTT
1 AAAAAAAAATTAAAGAAATTG
*
41712565 CAAAAAAAATTAAAAGAAATTG
1 AAAAAAAAATT-AAAGAAATTG
41712587 AAAAAGAAAA
1 AAAAA-AAAA
41712597 GAGAGGAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 10 0.40
22 11 0.44
23 4 0.16
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (21 bp):
AAAAAAAAATTAAAGAAATTG
Found at i:41716345 original size:11 final size:11
Alignment explanation
Indices: 41716327--41716367 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41716317 ATAATAACAA
41716327 CAAAATAATAG
1 CAAAATAATAG
*
41716338 CAACATAATAG
1 CAAAATAATAG
* *
41716349 TAAAATAGTAG
1 CAAAATAATAG
41716360 CAAAATAA
1 CAAAATAA
41716368 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:41717344 original size:28 final size:28
Alignment explanation
Indices: 41717300--41717353 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
41717290 TAACATCATA
* *
41717300 AACTTATGGATTGATTACTTGAATTTAGT
1 AACTTATGGATTAATTAATT-AATTTAGT
41717329 AACTTAT-GATTAATTAATTAATTTA
1 AACTTATGGATTAATTAATTAATTTA
41717354 ATTTGATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 10 0.43
29 7 0.30
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (28 bp):
AACTTATGGATTAATTAATTAATTTAGT
Found at i:41717749 original size:2 final size:2
Alignment explanation
Indices: 41717742--41717806 Score: 98
Period size: 2 Copynumber: 33.0 Consensus size: 2
41717732 GGTACGTAGT
41717742 TA 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 TA
*
41717784 TA TGA TA T- TA AA TA TA -A TA TA TA
1 TA T-A TA TA TA TA TA TA TA TA TA TA
41717807 AATTATAACT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 2 0.03
2 54 0.93
3 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:41722024 original size:12 final size:12
Alignment explanation
Indices: 41721969--41722030 Score: 88
Period size: 12 Copynumber: 5.2 Consensus size: 12
41721959 TTTGAACCTT
*
41721969 TGCTTCTATCAC
1 TGCTTCTATCGC
*
41721981 TGCTTCTATCAC
1 TGCTTCTATCGC
41721993 TGCTTCTATCGC
1 TGCTTCTATCGC
*
41722005 TGCTTCTCTCGC
1 TGCTTCTATCGC
*
41722017 TGCTTCTCTCGC
1 TGCTTCTATCGC
41722029 TG
1 TG
41722031 TAGCCTCTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.08, C:0.35, G:0.15, T:0.42
Consensus pattern (12 bp):
TGCTTCTATCGC
Found at i:41722057 original size:21 final size:21
Alignment explanation
Indices: 41722019--41722059 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41722009 TCTCTCGCTG
* *
41722019 CTTCTCTCGCTGTAGCCTCTA
1 CTTCCCTCGCTGCAGCCTCTA
*
41722040 CTTCCCTCGCTGCCGCCTCT
1 CTTCCCTCGCTGCAGCCTCT
41722060 GCTTTAAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.46, G:0.15, T:0.34
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCTA
Found at i:41728593 original size:13 final size:15
Alignment explanation
Indices: 41728574--41728614 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
41728564 CATATAAGTT
41728574 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
41728588 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
41728602 TTATGTAAGTTAT
1 -TATGTAAGTTAT
41728615 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:41728609 original size:16 final size:16
Alignment explanation
Indices: 41728573--41728651 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
41728563 ACATATAAGT
41728573 TTATGTAAGTTATG-A
1 TTATGTAAGTTATGTA
41728588 --ATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
41728602 TTATGTAAGTTATTTAAA
1 TTATGTAAGTTATGT--A
* *
41728620 TTATTTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
41728636 TTAAGTAAGTCATGTA
1 TTATGTAAGTTATGTA
41728652 GGCTATGTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 12 0.24
14 1 0.02
16 25 0.49
18 13 0.25
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:41728773 original size:23 final size:24
Alignment explanation
Indices: 41728720--41728774 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
41728710 AAATTTTAAT
*
41728720 AAATATATATTAAAACTGTATATA
1 AAATATATATCAAAACTGTATATA
*
41728744 AATATATATATCAAAGA-TGT-TTTA
1 AA-ATATATATCAAA-ACTGTATATA
41728768 AAATATA
1 AAATATA
41728775 ACTTTGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 7 0.26
25 14 0.52
26 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (24 bp):
AAATATATATCAAAACTGTATATA
Found at i:41733302 original size:14 final size:14
Alignment explanation
Indices: 41733283--41733350 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
41733273 ATGACCGTTG
41733283 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
41733297 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
41733312 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
41733325 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
41733338 AAACCTTAAATCT
1 AAACCCTAAATCT
41733351 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:41733306 original size:15 final size:15
Alignment explanation
Indices: 41733286--41733323 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
41733276 ACCGTTGAAA
41733286 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
41733301 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
41733316 CCCTAAAT
1 CCCTAAAT
41733324 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:41733776 original size:41 final size:40
Alignment explanation
Indices: 41733712--41733910 Score: 137
Period size: 41 Copynumber: 4.9 Consensus size: 40
41733702 TTTTGTTACT
* * *
41733712 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTAAATGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGTAGA-GC
* * * * *
41733753 ATTAGCGGCGCTTAGATATAAACGTCGCTAAAGGCCAGAGA
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGG-TAGAGC
* * * * * * * *
41733794 ATTAGTGGCACTCAGATAAATACGCCACTAAAGATCCGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGT-AGAGC
* * * *
41733835 ATTAGCGGCGCTTAGACAAAAACGCCGCTAACGGCCATAGG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGG-TAGAGC
* * * * *
41733876 ATTAGTGACGCTCAAATAAAAACGCCGCTAAAGGT
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGT
41733911 TTAAAAATCG
Statistics
Matches: 117, Mismatches: 38, Indels: 7
0.72 0.23 0.04
Matches are distributed among these distances:
41 115 0.98
42 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (40 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGTAGAGC
Found at i:41733849 original size:82 final size:82
Alignment explanation
Indices: 41733751--41733908 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 82
41733741 AAAGGTAAAT
* * * * * *
41733751 GCATTAGCGGCGCTTAGATATAAACGTCGCTAAAGGCCAGAGAATTAGTGGCACTCAGATAAATA
1 GCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAGAATTAGTGACACTCAAATAAAAA
41733816 CGCCACTAAAGATCCGA
66 CGCCACTAAAGATCCGA
* * * *
41733833 GCATTAGCGGCGCTTAGACAAAAACGCCGCTAACGGCCATAGGATTAGTGACGCTCAAATAAAAA
1 GCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAGAATTAGTGACACTCAAATAAAAA
*
41733898 CGCCGCTAAAG
66 CGCCACTAAAG
41733909 GTTTAAAAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (82 bp):
GCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAGAATTAGTGACACTCAAATAAAAA
CGCCACTAAAGATCCGA
Found at i:41734497 original size:31 final size:29
Alignment explanation
Indices: 41734459--41734535 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
41734449 TTAACGGCTC
* *
41734459 AGTGACTAAAATGTTACAACATGATAACATA
1 AGTGACTAAAATGTAAC-ACATCA-AACATA
* **
41734490 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACATCAAACATA
41734519 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
41734536 TTGAACCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACATCAAACATA
Found at i:41742065 original size:15 final size:14
Alignment explanation
Indices: 41742042--41742087 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
41742032 ATAATTTAAA
*
41742042 TTCAGTACTTAAATT
1 TTCAATACTT-AATT
41742057 TTCAATACTTAATAT
1 TTCAATACTTAAT-T
*
41742072 TTCAACACTTAATT
1 TTCAATACTTAATT
41742086 TT
1 TT
41742088 TTTTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 6 0.21
15 22 0.79
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (14 bp):
TTCAATACTTAATT
Found at i:41748078 original size:159 final size:160
Alignment explanation
Indices: 41747789--41748110 Score: 637
Period size: 159 Copynumber: 2.0 Consensus size: 160
41747779 ATTGTTTTTA
41747789 TTTTAAGAAGGTTAAAAATTAATGCTTTCCATTTTGCTTTTAGAATTTCTTTGGAAAAAAATTCA
1 TTTTAAGAAGGTTAAAAATTAATGCTTTCCATTTTGCTTTTAGAATTTCTTTGGAAAAAAATTCA
41747854 TTTCAATTTATGTTTATTTACTTTAAAAAATTTGCCAATATCTAAAAAGAATTTATTAATATTTG
66 TTTCAATTTATGTTTATTTACTTTAAAAAATTTGCCAATATCTAAAAAGAATTTATTAATATTTG
41747919 AAAATTAAAATATTTTTA-TAATTTTATAT
131 AAAATTAAAATATTTTTATTAATTTTATAT
41747948 TTTTAAGAAGGTTAAAAATTAATGCTTTCCATTTTGCTTTTAGAATTTCTTTGGAAAAAAATTCA
1 TTTTAAGAAGGTTAAAAATTAATGCTTTCCATTTTGCTTTTAGAATTTCTTTGGAAAAAAATTCA
41748013 TTTCAATTTATGTTTATTTACTTTAAAAAATTTGCCAATATCTAAAAAGAATTTATTAATATTTG
66 TTTCAATTTATGTTTATTTACTTTAAAAAATTTGCCAATATCTAAAAAGAATTTATTAATATTTG
41748078 AAAATTAAAATATTTTTATTAATTTTATAT
131 AAAATTAAAATATTTTTATTAATTTTATAT
41748108 TTT
1 TTT
41748111 CATTAAAAAT
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 148 0.91
160 14 0.09
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (160 bp):
TTTTAAGAAGGTTAAAAATTAATGCTTTCCATTTTGCTTTTAGAATTTCTTTGGAAAAAAATTCA
TTTCAATTTATGTTTATTTACTTTAAAAAATTTGCCAATATCTAAAAAGAATTTATTAATATTTG
AAAATTAAAATATTTTTATTAATTTTATAT
Found at i:41750344 original size:6 final size:6
Alignment explanation
Indices: 41750328--41750357 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
41750318 TTTAATTACA
41750328 ATAATAT ATAAAT ATAAAT ATAAAT ATAAA
1 ATAA-AT ATAAAT ATAAAT ATAAAT ATAAA
41750358 ATTATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:41751671 original size:19 final size:19
Alignment explanation
Indices: 41751647--41751690 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
41751637 TAAAAGCAAC
41751647 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
41751666 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
41751685 ACAACA
1 ACAACA
41751691 AAAATAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.27, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:41753994 original size:13 final size:14
Alignment explanation
Indices: 41753975--41754008 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
41753965 GTGGAGGACC
41753975 GGAGGTGGATCGGT
1 GGAGGTGGATCGGT
*
41753989 -GAGGTGGATTGGT
1 GGAGGTGGATCGGT
41754002 GGAGGTG
1 GGAGGTG
41754009 AAGGTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.15, C:0.03, G:0.59, T:0.24
Consensus pattern (14 bp):
GGAGGTGGATCGGT
Found at i:41754177 original size:29 final size:30
Alignment explanation
Indices: 41754123--41754179 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
41754113 GTATTACTAT
41754123 TAGTGTATTTTAAAAATAAAAAAATATATG
1 TAGTGTATTTTAAAAATAAAAAAATATATG
41754153 TAGTGTATTTTAAAAAT-AAAAAATATA
1 TAGTGTATTTTAAAAATAAAAAAATATA
41754180 GTTTATATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (30 bp):
TAGTGTATTTTAAAAATAAAAAAATATATG
Found at i:41754933 original size:19 final size:19
Alignment explanation
Indices: 41754909--41754950 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
41754899 GGTAGGAAGG
*
41754909 AAACAAAATAAG-GAAAAA
1 AAACAAAAGAAGAGAAAAA
41754927 TAAACAAAAGAAGAGAAAAA
1 -AAACAAAAGAAGAGAAAAA
41754947 AAAC
1 AAAC
41754951 TAGCTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.76, C:0.07, G:0.12, T:0.05
Consensus pattern (19 bp):
AAACAAAAGAAGAGAAAAA
Found at i:41763267 original size:20 final size:20
Alignment explanation
Indices: 41763239--41763282 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
41763229 CTATAAGAAT
*
41763239 AAAACAAAAAAATTAAATTA
1 AAAACAAAAAAATTAAAATA
* *
41763259 AAAATAAAAATATTAAAATA
1 AAAACAAAAAAATTAAAATA
41763279 AAAA
1 AAAA
41763283 AATGGCTAAA
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:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAACAAAAAAATTAAAATA
Found at i:41766110 original size:19 final size:19
Alignment explanation
Indices: 41766086--41766162 Score: 127
Period size: 19 Copynumber: 3.9 Consensus size: 19
41766076 AATTTTTGAG
41766086 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
41766105 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
41766124 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41766143 GATATATGCAATCTTAGATA
1 G--ATATGCAATCTTAGATA
41766163 GTTCTTTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 37 0.69
21 17 0.31
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41766332 original size:98 final size:98
Alignment explanation
Indices: 41766163--41767632 Score: 2940
Period size: 98 Copynumber: 15.0 Consensus size: 98
41766153 ATCTTAGATA
41766163 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41766228 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41766261 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41766326 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41766359 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41766424 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41766457 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41766522 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41766555 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41766620 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41766653 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41766718 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41766751 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41766816 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41766849 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41766914 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41766947 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41767012 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41767045 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41767110 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41767143 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41767208 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41767241 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41767306 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41767339 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41767404 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41767437 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41767502 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41767535 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
1 GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
41767600 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
66 GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
41767633 ATTGTTTAAA
Statistics
Matches: 1372, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 1372 1.00
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.35
Consensus pattern (98 bp):
GTTCTTTTAAAGAAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATT
GGGTGTGATTTCTTAAATCTTGGATAAGTGGAT
Found at i:41771284 original size:13 final size:13
Alignment explanation
Indices: 41771266--41771294 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
41771256 TAAAAGTGAT
41771266 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
41771279 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
41771292 AAA
1 AAA
41771295 GAAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:41771294 original size:11 final size:11
Alignment explanation
Indices: 41771267--41771310 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
41771257 AAAAGTGATA
41771267 AAAAGAAAAAG
1 AAAAGAAAAAG
41771278 AAAAAAGAAAAAG
1 --AAAAGAAAAAG
*
41771291 AAAAGAAAAAT
1 AAAAGAAAAAG
41771302 AAAAGAAAA
1 AAAAGAAAA
41771311 TGGAGAGGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:41772358 original size:44 final size:45
Alignment explanation
Indices: 41772308--41772899 Score: 544
Period size: 44 Copynumber: 13.4 Consensus size: 45
41772298 GTAGAGACAA
* *
41772308 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * * * *
41772352 AGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAGGAT
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * ** *
41772397 -GCAGATCTTGTCTTCCCATACTGGAGGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * * * *
41772441 ATCAGATCTTGTCTTCATGTATTGG-CGTGAACTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * * * *
41772485 AGCAGGTCCTGTCTACCTATATTGGTAG-GAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * * * *
41772529 -GCAGATCTTATCTT-CTCATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCT-ATATTGGTCGTGAAGTAGATCGAAGAT
* *
41772573 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * * * *
41772617 AGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAGGAT
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * ** *
41772662 -GCAGATCTTGTCTTCCCATACTGGAGGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * * * *
41772706 ATCAGATCTTGTCTTCATGTATTGG-CGTGAACTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * * * *
41772750 AGCAGGTCCTGTCTACCTATATTGGTAG-GAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* * * * *
41772794 -GCAGATCTTATCTT-CTCATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCT-ATATTGGTCGTGAAGTAGATCGAAGAT
* * *
41772838 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAAAT
1 AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
* *
41772882 AGCAGGTCCTGTCTTCCT
1 AGCAGATCTTGTCTTCCT
41772900 GCACTAGTAA
Statistics
Matches: 430, Mismatches: 104, Indels: 28
0.77 0.19 0.05
Matches are distributed among these distances:
42 4 0.01
43 36 0.08
44 282 0.66
45 106 0.25
46 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (45 bp):
AGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGAT
Found at i:41772586 original size:132 final size:133
Alignment explanation
Indices: 41772306--41772895 Score: 970
Period size: 132 Copynumber: 4.5 Consensus size: 133
41772296 AAGTAGAGAC
* * *
41772306 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTACCTA
* * *
41772371 TATTGGTAGCGAAGTGGATCGAGGATGCAGATCTTGTCTTCCCATACTGGAGGTGAAGTAGATCG
66 TATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATACTGGAGGCGAAGTAGATCG
41772436 AAG
131 AAG
* *
41772439 AAATCAGATCTTGTCTTCATGTATTGGCGTGAACTAGATCAAAGATAGCAGGTCCTGTCTACCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTACCTA
* *
41772504 TATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTATCTTCTCATACTGGTGGCGAAGTAGATCG
66 TATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATACTGGAGGCGAAGTAGATCG
41772568 AAG
131 AAG
* * *
41772571 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTACCTA
* * *
41772636 TATTGGTAGCGAAGTGGATCGAGGATGCAGATCTTGTCTTCCCATACTGGAGGTGAAGTAGATCG
66 TATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATACTGGAGGCGAAGTAGATCG
41772701 AAG
131 AAG
* *
41772704 AAATCAGATCTTGTCTTCATGTATTGGCGTGAACTAGATCAAAGATAGCAGGTCCTGTCTACCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTACCTA
* *
41772769 TATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTATCTTCTCATACTGGTGGCGAAGTAGATCG
66 TATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATACTGGAGGCGAAGTAGATCG
41772833 AAG
131 AAG
41772836 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAA-ATAGCAGGTCCTGTCT
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-AAAGATAGCAGGTCCTGTCT
41772896 TCCTGCACTA
Statistics
Matches: 423, Mismatches: 32, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
132 229 0.54
133 194 0.46
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (133 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTACCTA
TATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATACTGGAGGCGAAGTAGATCG
AAG
Found at i:41772779 original size:265 final size:265
Alignment explanation
Indices: 41772306--41772899 Score: 1170
Period size: 265 Copynumber: 2.2 Consensus size: 265
41772296 AAGTAGAGAC
41772306 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
41772371 TATTGGTAGCGAAGTGGATCGAGGATGCAGATCTTGTCTTCCCATACTGGAGGTGAAGTAGATCG
66 TATTGGTAGCGAAGTGGATCGAGGATGCAGATCTTGTCTTCCCATACTGGAGGTGAAGTAGATCG
41772436 AAGAAATCAGATCTTGTCTTCATGTATTGGCGTGAACTAGATCAAAGATAGCAGGTCCTGTCTAC
131 AAGAAATCAGATCTTGTCTTCATGTATTGGCGTGAACTAGATCAAAGATAGCAGGTCCTGTCTAC
41772501 CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCTCATACTGGTGGCGAAGTAGAT
196 CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCTCATACTGGTGGCGAAGTAGAT
41772566 CGAAG
261 CGAAG
41772571 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
41772636 TATTGGTAGCGAAGTGGATCGAGGATGCAGATCTTGTCTTCCCATACTGGAGGTGAAGTAGATCG
66 TATTGGTAGCGAAGTGGATCGAGGATGCAGATCTTGTCTTCCCATACTGGAGGTGAAGTAGATCG
41772701 AAGAAATCAGATCTTGTCTTCATGTATTGGCGTGAACTAGATCAAAGATAGCAGGTCCTGTCTAC
131 AAGAAATCAGATCTTGTCTTCATGTATTGGCGTGAACTAGATCAAAGATAGCAGGTCCTGTCTAC
41772766 CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCTCATACTGGTGGCGAAGTAGAT
196 CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCTCATACTGGTGGCGAAGTAGAT
41772831 CGAAG
261 CGAAG
* *
41772836 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGGTCCTGTCTTCCT
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCT
41772900 GCACTAGTAA
Statistics
Matches: 327, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
265 327 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (265 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTA
TATTGGTAGCGAAGTGGATCGAGGATGCAGATCTTGTCTTCCCATACTGGAGGTGAAGTAGATCG
AAGAAATCAGATCTTGTCTTCATGTATTGGCGTGAACTAGATCAAAGATAGCAGGTCCTGTCTAC
CTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCTCATACTGGTGGCGAAGTAGAT
CGAAG
Found at i:41773110 original size:44 final size:44
Alignment explanation
Indices: 41773062--41773255 Score: 139
Period size: 44 Copynumber: 4.4 Consensus size: 44
41773052 CTGGGCAACT
*
41773062 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
1 GTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
* * * * * * **
41773106 GTGGAGCAGATTGAGGATTGCGGATTTTACCTCCCT--GTGGTTACA
1 GTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG-T--A
* * * * **
41773151 GTGGAGTACATTGAAGCTAGT-A-AT-TCTA-CTTCCCTAGGCAACA
1 GTGGAGTAGATTGAAGAT-TTCAGATCT-TATC-TCCCTAAGCAGTA
*
41773194 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
1 GTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
*
41773238 GTGGAGTAGATCGAAGAT
1 GTGGAGTAGATTGAAGAT
41773256 GGTGGATTTT
Statistics
Matches: 109, Mismatches: 29, Indels: 24
0.67 0.18 0.15
Matches are distributed among these distances:
42 3 0.03
43 20 0.18
44 68 0.62
45 17 0.16
46 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (44 bp):
GTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
Found at i:41773144 original size:132 final size:132
Alignment explanation
Indices: 41772907--41773361 Score: 698
Period size: 132 Copynumber: 3.4 Consensus size: 132
41772897 CCTGCACTAG
*
41772907 TAATTCTACTTCCCAGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
1 TAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
* *
41772972 TAGTGGAGTAGATCGAAGATGGCGGGTTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
66 TAGTGGAGTAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
41773037 AA
131 AA
*
41773039 TAATTCTACTTCCCTGGGCAACTGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
1 TAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
* * * * *
41773104 TAGTGGAGCAGATTGAGGATTGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCT
66 TAGTGGAGTAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
*
41773169 AG
131 AA
*
41773171 TAATTCTACTTCCCTAGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
1 TAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
* * *
41773236 TAGTGGAGTAGATCGAAGATGGTGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGTC
66 TAGTGGAGTAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
41773301 AA
131 AA
* * ** * *
41773303 TAATCCTA-TCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTAAG-TCTTATCTCCCT
1 TAATTCTACT-TCCCTGGGCAACAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT
41773362 GCAGTTGTAG
Statistics
Matches: 293, Mismatches: 28, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
131 1 0.00
132 289 0.99
133 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (132 bp):
TAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
TAGTGGAGTAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
AA
Found at i:41773655 original size:21 final size:19
Alignment explanation
Indices: 41773590--41773678 Score: 151
Period size: 19 Copynumber: 4.6 Consensus size: 19
41773580 AATTTTTGAG
41773590 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
41773609 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
41773628 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41773647 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
41773668 GATATGCAATC
1 GATATGCAATC
41773679 NNNNNNNNNN
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
19 47 0.71
21 19 0.29
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41773665 original size:40 final size:38
Alignment explanation
Indices: 41773590--41773678 Score: 151
Period size: 40 Copynumber: 2.3 Consensus size: 38
41773580 AATTTTTGAG
41773590 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
*
41773628 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCCTAGATAT
41773668 GATATGCAATC
1 GATATGCAATC
41773679 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 20 0.42
40 28 0.58
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
Found at i:41774543 original size:9 final size:9
Alignment explanation
Indices: 41774531--41774555 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41774521 GATGATGTAT
41774531 TTATTATTG
1 TTATTATTG
41774540 TTATTATTG
1 TTATTATTG
41774549 TTATTAT
1 TTATTAT
41774556 AGCATTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:41774963 original size:97 final size:97
Alignment explanation
Indices: 41774832--41775024 Score: 316
Period size: 97 Copynumber: 2.0 Consensus size: 97
41774822 TTAAAATAAT
* *
41774832 AAAGGAAATATTCAGAGTTTGTGATTTTAAAGGAAT-TGTGCCCTAACGTATTGGGTGTGATTTC
1 AAAGGAAATATTCAGAGTTTGAGATTCTAAAGGAATCT-TGCCCTAACGTATTGGGTGTGATTTC
* *
41774896 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
65 TTAAAGCTTGGATAAGTGAATGTTCTTTTAAAG
* *
41774929 AAAGGAAATATTCCGAGTTTGAGATTCTAGAGGAATCTTGCCCTAACGTATTGGGTGTGATTTCT
1 AAAGGAAATATTCAGAGTTTGAGATTCTAAAGGAATCTTGCCCTAACGTATTGGGTGTGATTTCT
41774994 TAAAGCTTGGATAAGTGAATGTTCTTTTAAA
66 TAAAGCTTGGATAAGTGAATGTTCTTTTAAA
41775025 CTTTTATTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
97 88 0.99
98 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (97 bp):
AAAGGAAATATTCAGAGTTTGAGATTCTAAAGGAATCTTGCCCTAACGTATTGGGTGTGATTTCT
TAAAGCTTGGATAAGTGAATGTTCTTTTAAAG
Found at i:41787994 original size:20 final size:20
Alignment explanation
Indices: 41787938--41787993 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
41787928 CAAATTTAAT
* *
41787938 TAAAAATTAATTTAAATGAA
1 TAAAATTTAATTTAAAAGAA
41787958 T-AAATTTAAGTTTAAAAGAA
1 TAAAATTTAA-TTTAAAAGAA
41787978 TAAAATTTAA-TTAAAA
1 TAAAATTTAATTTAAAA
41787994 ATAATTAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 13 0.41
20 11 0.34
21 8 0.25
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAAATTTAATTTAAAAGAA
Found at i:41788002 original size:21 final size:19
Alignment explanation
Indices: 41787938--41787998 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 19
41787928 CAAATTTAAT
* *
41787938 TAAAAATTAATTTAAATGAA
1 TAAAATTTAATTAAAAT-AA
*
41787958 T-AAATTTAAGTTTAAAAGAA
1 TAAAATTTAA--TTAAAATAA
41787978 TAAAATTTAATTAAAAATAA
1 TAAAATTTAATT-AAAATAA
41787998 T
1 T
41787999 TAAAGAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 9 0.27
20 11 0.33
21 13 0.39
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
TAAAATTTAATTAAAATAA
Found at i:41788053 original size:29 final size:28
Alignment explanation
Indices: 41787990--41788055 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
41787980 AAATTTAATT
**
41787990 AAAAATAATTAAAGAAATAAACTAAGTA
1 AAAAATAATTAAAGAAATAAAAAAAGTA
* * *
41788018 AAGAAATATTTCAAGAAATAAAAAAATTTA
1 AA-AAATAATTAAAGAAATAAAAAAA-GTA
41788048 AAAAATAA
1 AAAAATAA
41788056 ACCATAGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.07
29 24 0.80
30 4 0.13
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (28 bp):
AAAAATAATTAAAGAAATAAAAAAAGTA
Found at i:41788093 original size:134 final size:136
Alignment explanation
Indices: 41787930--41788190 Score: 386
Period size: 134 Copynumber: 1.9 Consensus size: 136
41787920 TCGATAATCA
* * *
41787930 AATTTAATTAAAAATTAATTTAAATGAATAAATTTAAGTTTAAAAGAATAAAATTTAATT-AAA-
1 AATTTAATTAAAAATTAATATAAAGGAATAAATTTAAATTTAAAAGAATAAAATTTAATTAAAAG
* * * *
41787993 AATAATTAAAGAA-ATAAACTAAGTAAAGAAATATTTCAAGAAA-TAAAAAAATTTAAAAAATAA
66 AATAATTAAAGAATA-AAACTAAATAAAGAAATATTTAAAGAAACAAAAAAAAATTAAAAAATAA
41788056 ACCATAG
130 ACCATAG
*
41788063 AATTTAATTAAAATATTAATATAAAGGAATAAATTTAAATTTAAAAGATTAAAATTTAATTAAAA
1 AATTTAATTAAAA-ATTAATATAAAGGAATAAATTTAAATTTAAAAGAATAAAATTTAATT--AA
41788128 AAGAATAATTAAAGAATAAAACTAAATAAAGAAATATTTAAAGAAACAAAAAAAAATTAAAAA
63 AAGAATAATTAAAGAATAAAACTAAATAAAGAAATATTTAAAGAAACAAAAAAAAATTAAAAA
41788191 CTTGATTGGC
Statistics
Matches: 113, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
133 13 0.12
134 43 0.38
137 3 0.03
138 39 0.35
139 15 0.13
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (136 bp):
AATTTAATTAAAAATTAATATAAAGGAATAAATTTAAATTTAAAAGAATAAAATTTAATTAAAAG
AATAATTAAAGAATAAAACTAAATAAAGAAATATTTAAAGAAACAAAAAAAAATTAAAAAATAAA
CCATAG
Found at i:41788123 original size:20 final size:20
Alignment explanation
Indices: 41788069--41788127 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
41788059 ATAGAATTTA
* *
41788069 ATTAAAATATTAATATAAAGG
1 ATTAAAAT-TTAATTTAAAAG
*
41788090 AAT-AAATTTAAATTTAAAAG
1 ATTAAAATTT-AATTTAAAAG
41788110 ATTAAAATTTAA-TTAAAA
1 ATTAAAATTTAATTTAAAA
41788128 AAGAATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 8 0.25
20 16 0.50
21 8 0.25
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTAAAATTTAATTTAAAAG
Found at i:41794425 original size:20 final size:18
Alignment explanation
Indices: 41794400--41794447 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
41794390 TTTATTTCAA
41794400 TTTTCTTTCTTGCACTTTCT
1 TTTTCTTTCTTG-A-TTTCT
41794420 TTTTCTTGT-TTGATTTCT
1 TTTTCTT-TCTTGATTTCT
41794438 TTTT-TTTCTT
1 TTTTCTTTCTT
41794448 CTCTCAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 4 0.15
18 9 0.35
19 1 0.04
20 10 0.38
21 1 0.04
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.73
Consensus pattern (18 bp):
TTTTCTTTCTTGATTTCT
Found at i:41800564 original size:3 final size:3
Alignment explanation
Indices: 41800556--41800580 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41800546 AGTCAAAATA
41800556 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
41800581 AGAAATTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:41802529 original size:25 final size:25
Alignment explanation
Indices: 41802498--41802548 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
41802488 TTTGTTTAGT
41802498 CCATTCAATTGACTCTAACGATGTC
1 CCATTCAATTGACTCTAACGATGTC
41802523 CCATTCAATTGACTCTAACGATGTC
1 CCATTCAATTGACTCTAACGATGTC
41802548 C
1 C
41802549 TAAATTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.31
Consensus pattern (25 bp):
CCATTCAATTGACTCTAACGATGTC
Found at i:41804782 original size:11 final size:11
Alignment explanation
Indices: 41804766--41804790 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41804756 ACATGGCATA
41804766 AATGATGTCAT
1 AATGATGTCAT
41804777 AATGATGTCAT
1 AATGATGTCAT
41804788 AAT
1 AAT
41804791 CTAATTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
AATGATGTCAT
Found at i:41807023 original size:17 final size:17
Alignment explanation
Indices: 41806969--41807049 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 17
41806959 NNNNNTCTAC
41806969 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
41806986 TAAATTTCACATT-TTATAT
1 T--ATTT-ATATTATTAAAT
41807005 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
*
41807022 TATTTAGTCA-TATTGAA-
1 TATTTA-T-ATTATTAAAT
41807039 TATTTATATTA
1 TATTTATATTA
41807050 AAATTGAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 22 0.42
18 7 0.13
19 11 0.21
20 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:41807653 original size:7 final size:7
Alignment explanation
Indices: 41807641--41807666 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41807631 TAGTCGATTG
41807641 GTATTTA
1 GTATTTA
41807648 GTATTTA
1 GTATTTA
41807655 GTATTTA
1 GTATTTA
41807662 GTATT
1 GTATT
41807667 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:41808344 original size:18 final size:18
Alignment explanation
Indices: 41808317--41808356 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41808307 CAGGTGCGTT
* *
41808317 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
41808335 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
41808353 TCCT
1 TCCT
41808357 TTTCCAAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:41808918 original size:27 final size:27
Alignment explanation
Indices: 41808898--41808971 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 27
41808888 TTAATTGACA
41808898 AACCCTAAACCCTTAACTTAAAAACCAT
1 AACCCT-AACCCTTAACTTAAAAACCAT
41808926 AACCCTAACCCTTAACTTAAAAACCCACT
1 AACCCTAACCCTTAACTTAAAAA-CCA-T
*
41808955 AACCCTAAACCCCTAAC
1 AACCCT-AACCCTTAAC
41808972 CCTAATCCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 17 0.40
28 9 0.21
29 7 0.17
30 9 0.21
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (27 bp):
AACCCTAACCCTTAACTTAAAAACCAT
Found at i:41808987 original size:26 final size:26
Alignment explanation
Indices: 41808953--41809002 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
41808943 TAAAAACCCA
41808953 CTAACCCTAAACCCCTAACCCTAATC
1 CTAACCCTAAACCCCTAACCCTAATC
*
41808979 CTAACCCTAAACCCTTAACCCTAA
1 CTAACCCTAAACCCCTAACCCTAA
41809003 ACCCTAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.20
Consensus pattern (26 bp):
CTAACCCTAAACCCCTAACCCTAATC
Found at i:41809007 original size:14 final size:14
Alignment explanation
Indices: 41808898--41809007 Score: 86
Period size: 14 Copynumber: 7.9 Consensus size: 14
41808888 TTAATTGACA
41808898 AACCCTAAACCCTT
1 AACCCTAAACCCTT
* * *
41808912 AA-CTTAAAAACCAT
1 AACCCT-AAACCCTT
41808926 AACCCT-AACCCTT
1 AACCCTAAACCCTT
* *
41808939 AA-CTTAAAAACCCACT
1 AACCCT--AAACCC-TT
*
41808955 AACCCTAAACCCCT
1 AACCCTAAACCCTT
*
41808969 AACCCT-AATCC-T
1 AACCCTAAACCCTT
41808981 AACCCTAAACCCTT
1 AACCCTAAACCCTT
41808995 AACCCTAAACCCT
1 AACCCTAAACCCT
41809008 AAAGCCTAAC
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
12 9 0.12
13 17 0.22
14 32 0.42
15 13 0.17
16 3 0.04
17 2 0.03
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCCTAAACCCTT
Found at i:41809010 original size:7 final size:7
Alignment explanation
Indices: 41808955--41809016 Score: 67
Period size: 7 Copynumber: 9.1 Consensus size: 7
41808945 AAAACCCACT
41808955 AACCCTA
1 AACCCTA
41808962 AACCCCT-
1 AA-CCCTA
41808969 AACCCT-
1 AACCCTA
*
41808975 AATCCT-
1 AACCCTA
41808981 AACCCTA
1 AACCCTA
*
41808988 AACCCTT
1 AACCCTA
41808995 AACCCTA
1 AACCCTA
41809002 AACCCTA
1 AACCCTA
*
41809009 AAGCCTA
1 AACCCTA
41809016 A
1 A
41809017 CCTTTAACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
6 14 0.29
7 30 0.62
8 4 0.08
ACGTcount: A:0.39, C:0.42, G:0.02, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:41809059 original size:22 final size:22
Alignment explanation
Indices: 41809020--41809076 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
41809010 AGCCTAACCT
*
41809020 TTAACTT-AAAACCTTAAACT-
1 TTAACTTAAAAACCATAAACTC
41809040 TGTAACTTAAAAACCATAAACTC
1 T-TAACTTAAAAACCATAAACTC
41809063 TTAACTTAAAAACC
1 TTAACTTAAAAACC
41809077 CTAACCTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 1 0.03
21 6 0.18
22 25 0.76
23 1 0.03
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (22 bp):
TTAACTTAAAAACCATAAACTC
Found at i:41811037 original size:335 final size:335
Alignment explanation
Indices: 41810425--41811095 Score: 1137
Period size: 335 Copynumber: 2.0 Consensus size: 335
41810415 AATGGCTTGT
* * * *
41810425 AGTATGGAAATGTGTCTCGGCATCGCTTAAAGGTCCAAAACAGGCATTTGAACACTTAGTATCCA
1 AGTATGGAAATGCGTCACAGCATCGCTTAAAGGTCCAAAACAGGCATTTGAACACTTAGCATCCA
* *
41810490 CGTAGCAATCGGCCGTTATAGTACGCATGTTCCGTTTCAAGGTCTGTGATGGCACCTGGGATATA
66 CGTAGCAATCGGCCGTTATAGTACGCATGTTCCGTTTCAAGGTCTGTGATAGCACCTGGAATATA
41810555 TCTCTCTAGCACTTGACACCACTGCCATATTTCATTATATGAAGCGTCCCACCCACTATGCATCT
131 TCTCTCTAGCACTTGACACCACTGCCATATTTCATTATATGAAGCGTCCCACCCACTATGCATCT
41810620 TCTCCAACGCCTTCTGCTTAGCTATCCAAGCATTGCGGTAAGAGGGCGTGTACCCCATTTGGCTA
196 TCTCCAACGCCTTCTGCTTAGCTATCCAAGCATTGCGGTAAGAGGGCGTGTACCCCATTTGGCTA
*
41810685 CGAATATTGGCAATTAAGACCGGCACTGAAGTCTTG-GGATCTGCCTTCACCGTGGGTAGTATCA
261 CGAATATTGGCAATTAAGACCGGCACTGAAGTCCTGAGG-TCTGCCTTCACCGTGGGTAGTATCA
*
41810749 AGCTAGCTAAC
325 AGCTAACTAAC
* * * *
41810760 AGTATGGAAATGCGTCACAGCATTGCTTAAAGGTCCAAAATAGGCGTTTGAACACTTGGCATCCA
1 AGTATGGAAATGCGTCACAGCATCGCTTAAAGGTCCAAAACAGGCATTTGAACACTTAGCATCCA
* * * * * *
41810825 TGTAGCAATCGGCTGTTGTAGTACGTATGTTCCGTTTCAAGGTCTGTGATAGCATCTGGAATGTA
66 CGTAGCAATCGGCCGTTATAGTACGCATGTTCCGTTTCAAGGTCTGTGATAGCACCTGGAATATA
41810890 TCTCTCTAGCACTTGACACCACTGCCATATTTCATTATATGAAGCGTCCCACCCACTATGCATCT
131 TCTCTCTAGCACTTGACACCACTGCCATATTTCATTATATGAAGCGTCCCACCCACTATGCATCT
*
41810955 TCTCCAACGCCTTCTGCTTAGCTATCCAAGCCTTGCGGTAAGAGGGCGTGTACCCCATTTGGCTA
196 TCTCCAACGCCTTCTGCTTAGCTATCCAAGCATTGCGGTAAGAGGGCGTGTACCCCATTTGGCTA
* *
41811020 CGAATATTGGTAATTAAGACCGGCATTGAAGTCCTGAGGTCTGCCTTCACCGTGGGTAGTATCAA
261 CGAATATTGGCAATTAAGACCGGCACTGAAGTCCTGAGGTCTGCCTTCACCGTGGGTAGTATCAA
41811085 GCTAACTAAC
326 GCTAACTAAC
41811095 A
1 A
41811096 TAGCTGAATC
Statistics
Matches: 314, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
335 312 0.99
336 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (335 bp):
AGTATGGAAATGCGTCACAGCATCGCTTAAAGGTCCAAAACAGGCATTTGAACACTTAGCATCCA
CGTAGCAATCGGCCGTTATAGTACGCATGTTCCGTTTCAAGGTCTGTGATAGCACCTGGAATATA
TCTCTCTAGCACTTGACACCACTGCCATATTTCATTATATGAAGCGTCCCACCCACTATGCATCT
TCTCCAACGCCTTCTGCTTAGCTATCCAAGCATTGCGGTAAGAGGGCGTGTACCCCATTTGGCTA
CGAATATTGGCAATTAAGACCGGCACTGAAGTCCTGAGGTCTGCCTTCACCGTGGGTAGTATCAA
GCTAACTAAC
Found at i:41812697 original size:124 final size:124
Alignment explanation
Indices: 41812455--41812771 Score: 440
Period size: 125 Copynumber: 2.5 Consensus size: 124
41812445 CCCAAACATG
* * *
41812455 CTACTGTAGCAAAAAGCGCGTCCACGTGGGAGCGATTTCACAAATTCTTCTGATAAAGCATCCTG
1 CTACTGTAGC-AAAAGCGTGTCCACG-AGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTG
* * * *
41812520 CTTGAAGCATTTTTATACTATTTGTTCAGAAACATCAACTCGAAATTATTTTTTCCAG-GC
64 CTTGAAGCATTTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTTTTACAGAAC
* *
41812580 CTACTGTAGCAAAAGCGTGTCCACGAGGTCGAGATTTCACAAATTCTTCTTATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGTGTCCACGAGG-CGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
* *
41812645 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTA-TTTTTACAGAAC
65 TTGAAGC-ATTTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTTTTACAGAAC
* * * *
41812705 CTACTGTAGCAAAAGCGTGTACACGTCGGCGCGACTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGTGTCCACG-AGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
41812770 TT
65 TT
41812772 TAATTTTATC
Statistics
Matches: 171, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
123 2 0.01
124 62 0.36
125 105 0.61
126 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGTGTCCACGAGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGCT
TGAAGCATTTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTTTTACAGAAC
Found at i:41812934 original size:21 final size:22
Alignment explanation
Indices: 41812896--41812936 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
41812886 TTAAAAATCT
* *
41812896 TAAAAACCTTAAACCCTAACCC
1 TAAAAACCTAAAAACCTAACCC
41812918 TAAAAACC-AAAAACCTAAC
1 TAAAAACCTAAAAACCTAAC
41812937 ATGGGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.15
Consensus pattern (22 bp):
TAAAAACCTAAAAACCTAACCC
Found at i:41816439 original size:9 final size:9
Alignment explanation
Indices: 41816425--41816469 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
41816415 TTTTAGAATA
41816425 TTTTTAATT
1 TTTTTAATT
41816434 TTTTTATATT
1 TTTTTA-ATT
*
41816444 TTTTAGAATT
1 TTTT-TAATT
*
41816454 TTTATAATT
1 TTTTTAATT
41816463 TTTTTAA
1 TTTTTAA
41816470 AATATAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 16 0.53
10 13 0.43
11 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTAATT
Found at i:41816451 original size:29 final size:30
Alignment explanation
Indices: 41816410--41816468 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
41816400 GTCTCAAAAT
41816410 TATTATTTTAGAATATTTT-TAATTTTTTTA
1 TATTATTTTAGAAT-TTTTATAATTTTTTTA
41816440 TATT-TTTTAGAATTTTTATAATTTTTTTA
1 TATTATTTTAGAATTTTTATAATTTTTTTA
41816469 AAATATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.14
29 20 0.71
30 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (30 bp):
TATTATTTTAGAATTTTTATAATTTTTTTA
Found at i:41816508 original size:19 final size:20
Alignment explanation
Indices: 41816484--41816526 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
41816474 TAAATTTTGA
*
41816484 AATTTTT-ATAAATATTTTC
1 AATTTTTGAAAAATATTTTC
*
41816503 AATTTTTGAAAAATATTTTG
1 AATTTTTGAAAAATATTTTC
41816523 AATT
1 AATT
41816527 ATTTTGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (20 bp):
AATTTTTGAAAAATATTTTC
Found at i:41816509 original size:20 final size:20
Alignment explanation
Indices: 41816462--41816531 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
41816452 TTTTTATAAT
*
41816462 TTTTTTAAAATATAAATTTTGAA
1 TTTTTTAAAA-AT--ATTTTCAA
* *
41816485 ATTTTTATAAATATTTTCAA
1 TTTTTTAAAAATATTTTCAA
* *
41816505 TTTTTGAAAAATATTTTGAA
1 TTTTTTAAAAATATTTTCAA
41816525 TTATTTT
1 TT-TTTT
41816532 GTAATTTTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 25 0.66
21 3 0.08
22 2 0.05
23 8 0.21
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTTAAAAATATTTTCAA
Found at i:41819791 original size:18 final size:18
Alignment explanation
Indices: 41819770--41819804 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41819760 AATTTAGCCA
* *
41819770 TTTTTATTTTTATTTTTG
1 TTTTTAGTTTAATTTTTG
41819788 TTTTTAGTTTAATTTTT
1 TTTTTAGTTTAATTTTT
41819805 ACATTCTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTTAGTTTAATTTTTG
Found at i:41822666 original size:237 final size:237
Alignment explanation
Indices: 41822251--41822725 Score: 880
Period size: 237 Copynumber: 2.0 Consensus size: 237
41822241 AAGCGACGCC
* *
41822251 ATGATGAGCATGTGGATGGAATGAACCAATTCAAGGTTAAAGATAAGGTACTACTAGATAAAATA
1 ATGATGAGCATGTGGATGGAACGAACCAATTCAAGGTTAAAGATAAGGTACTACTAGATAAAACA
41822316 GATCCATGTATTGCCACTTTAGAGCTGGATGCAAACAAATCAAAATCTTTTACAATACTGAACGT
66 GATCCATGTATTGCCACTTTAGAGCTGGATGCAAACAAATCAAAATCTTTTACAATACTGAACGT
*
41822381 CTTTCTATACGGTACAATCGAGTTAACTAATTCTGAACTTGACACATTTAAGGTAAATATTACTC
131 CTTTCTATACGATACAATCGAGTTAACTAATTCTGAACTTGACACATTTAAGGTAAATATTACTC
41822446 GACTTAAACCTTATTTTGATCATAGAATTGATAACAAGAAAG
196 GACTTAAACCTTATTTTGATCATAGAATTGATAACAAGAAAG
*
41822488 ATGATGAGCATGTGGATGGAACGAACCAATTCAAGGTTAAAGATAAGGTACTACTAGATAAAACG
1 ATGATGAGCATGTGGATGGAACGAACCAATTCAAGGTTAAAGATAAGGTACTACTAGATAAAACA
*
41822553 GATCCATGTATTGCCACTTTAGAGCTGGATGTAAACAAATCAAAATCTTTTACAATACTGAACGT
66 GATCCATGTATTGCCACTTTAGAGCTGGATGCAAACAAATCAAAATCTTTTACAATACTGAACGT
41822618 CTTTCTATACGATACAATCGAGTTAA-TGAATTCTGAACTTGACACATTTAAGGTAAATATTACT
131 CTTTCTATACGATACAATCGAGTTAACT-AATTCTGAACTTGACACATTTAAGGTAAATATTACT
*
41822682 CGACTTAAACCTTATTTTGATCATAGAATTGATAACGAGAAAG
195 CGACTTAAACCTTATTTTGATCATAGAATTGATAACAAGAAAG
41822725 A
1 A
41822726 GGAGCTTTGG
Statistics
Matches: 231, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
236 1 0.00
237 230 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (237 bp):
ATGATGAGCATGTGGATGGAACGAACCAATTCAAGGTTAAAGATAAGGTACTACTAGATAAAACA
GATCCATGTATTGCCACTTTAGAGCTGGATGCAAACAAATCAAAATCTTTTACAATACTGAACGT
CTTTCTATACGATACAATCGAGTTAACTAATTCTGAACTTGACACATTTAAGGTAAATATTACTC
GACTTAAACCTTATTTTGATCATAGAATTGATAACAAGAAAG
Found at i:41823885 original size:15 final size:16
Alignment explanation
Indices: 41823865--41823904 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
41823855 TGCTTATTAC
*
41823865 TTTATTTTAGTTTCT-
1 TTTATTTTAGTATCTA
41823880 TTTATTTTAGTATCTA
1 TTTATTTTAGTATCTA
41823896 TATTATTTT
1 T-TTATTTT
41823905 TCTTGTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 1 0.05
17 7 0.32
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTATTTTAGTATCTA
Found at i:41829208 original size:16 final size:16
Alignment explanation
Indices: 41829176--41829222 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
41829166 AAAATGTTAG
* *
41829176 AAAGATGAAAAATTAA
1 AAAGATAAAAAAATAA
*
41829192 AAGGATAAAAAAATAA
1 AAAGATAAAAAAATAA
*
41829208 AAAGATAGAAAAATA
1 AAAGATAAAAAAATA
41829223 TAATTTTTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (16 bp):
AAAGATAAAAAAATAA
Found at i:41834523 original size:41 final size:41
Alignment explanation
Indices: 41834458--41834594 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
41834448 GGCACTAACG
* * * *
41834458 GAAAAATGCCACAATAGGTAAAGCAGTAGCAGCGTTTATGA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCAGCGTTTATGA
* * *
41834499 GAAAAACGCTGCAAAAGGTCAAGCATTAGCGGCGTTTATGA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCAGCGTTTATGA
* * * *
41834540 GAAAAACGCCGCAAAAGGTCAAGCATTAG-TG-GTGCTATAA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCAGCGT-TTATGA
41834580 GAAAAACGCCGCAAA
1 GAAAAACGCCGCAAA
41834595 GTATCATTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 2 0.02
40 20 0.24
41 62 0.74
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
GAAAAACGCCGCAAAAGGTCAAGCAGTAGCAGCGTTTATGA
Found at i:41834704 original size:21 final size:21
Alignment explanation
Indices: 41834679--41834721 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
41834669 CCCTTTTTTC
41834679 CCCTAAAAATT-TTCCCTAAAT
1 CCCT-AAAATTATTCCCTAAAT
*
41834700 CCCTAAATTTATTCCCTAAAT
1 CCCTAAAATTATTCCCTAAAT
41834721 C
1 C
41834722 AAAATCCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (21 bp):
CCCTAAAATTATTCCCTAAAT
Found at i:41834818 original size:27 final size:27
Alignment explanation
Indices: 41834747--41834820 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
41834737 TCCCCGGCCA
* *
41834747 TCTGTTGCATCGCCGTCAACTGTCCCC
1 TCTGTTGCATCGCCGTCGACTATCCCC
* *
41834774 TCTGCTGCATCACCGTCGACTATCCCC
1 TCTGTTGCATCGCCGTCGACTATCCCC
41834801 TCTGTTGCATCGCCGTCGAC
1 TCTGTTGCATCGCCGTCGAC
41834821 ACTCCTCTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.12, C:0.41, G:0.19, T:0.28
Consensus pattern (27 bp):
TCTGTTGCATCGCCGTCGACTATCCCC
Found at i:41835891 original size:22 final size:22
Alignment explanation
Indices: 41835866--41835909 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41835856 TGTGCTGCTG
*
41835866 TTTGCAATTTTTGGATT-ATTTA
1 TTTGCAAATTTT-GATTAATTTA
*
41835888 TTTGTAAATTTTGATTAATTTA
1 TTTGCAAATTTTGATTAATTTA
41835910 ATTATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.59
Consensus pattern (22 bp):
TTTGCAAATTTTGATTAATTTA
Found at i:41837217 original size:22 final size:22
Alignment explanation
Indices: 41837192--41837235 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41837182 TGTGCTGTTG
*
41837192 TTTGCAATTTTTTGATT-ATTTA
1 TTTGCAA-ATTTTGATTAATTTA
*
41837214 TTTGTAAATTTTGATTAATTTA
1 TTTGCAAATTTTGATTAATTTA
41837236 ATCAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTGCAAATTTTGATTAATTTA
Found at i:41839587 original size:9 final size:9
Alignment explanation
Indices: 41839573--41839639 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
41839563 AAACTTTGGA
41839573 ACATAACTT
1 ACATAACTT
41839582 ACATAA--T
1 ACATAACTT
*
41839589 ACATAA-AT
1 ACATAACTT
* * *
41839597 ATATATCAT
1 ACATAACTT
*
41839606 ATCATAAATT
1 A-CATAACTT
*
41839616 ACATAAATT
1 ACATAACTT
41839625 ACATAACTT
1 ACATAACTT
41839634 ACATAA
1 ACATAA
41839640 TGGTTTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
7 7 0.15
8 5 0.10
9 31 0.65
10 5 0.10
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (9 bp):
ACATAACTT
Found at i:41840897 original size:6 final size:6
Alignment explanation
Indices: 41840881--41840912 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
41840871 AAATGGAAAC
41840881 TAAAA- TAAAAT TAAAAT TAAAAT T-AAAT TAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAA
41840913 GAGGGCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAAAT
Found at i:41842747 original size:17 final size:17
Alignment explanation
Indices: 41842727--41842759 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41842717 TTTAATTAGA
*
41842727 TAAATTATTTTTTCAAT
1 TAAATAATTTTTTCAAT
41842744 TAAATAATTTTTTCAA
1 TAAATAATTTTTTCAA
41842760 CCTAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATAATTTTTTCAAT
Found at i:41843734 original size:24 final size:24
Alignment explanation
Indices: 41843644--41843735 Score: 75
Period size: 23 Copynumber: 3.9 Consensus size: 24
41843634 AAGCAGCAAT
*
41843644 TTGGACAGCA-CT-TATACACAAAA
1 TTGGACAGCATATATATAC-CAAAA
* * *
41843667 TTTGACGGCATGTATATA-CAAAA
1 TTGGACAGCATATATATACCAAAA
* *
41843690 TTGGACAGCATTTGT-TCACCAAAA
1 TTGGACAGCATATATAT-ACCAAAA
*
41843714 TTGGGCAGCATATATATACCAA
1 TTGGACAGCATATATATACCAA
41843736 TTTTAGACCA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
22 1 0.02
23 25 0.46
24 23 0.43
25 5 0.09
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (24 bp):
TTGGACAGCATATATATACCAAAA
Found at i:41844358 original size:28 final size:28
Alignment explanation
Indices: 41844318--41844555 Score: 449
Period size: 28 Copynumber: 8.5 Consensus size: 28
41844308 NNNNNNNNNN
* *
41844318 TCGCACACTTAGTGCTTTGCCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41844346 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41844374 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41844402 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41844430 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41844458 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41844486 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
41844514 TCGCACACTTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGCTTTACAATTAAAC
41844542 TCGCACACTTAGTG
1 TCGCACACTTAGTG
41844556 TCGAAAGTCA
Statistics
Matches: 207, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 207 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Done.