Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 97 of 295
Found at i:28762073 original size:8 final size:8
Alignment explanation
Indices: 28762039--28762090 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
28762029 TAGTGATGTG
*
28762039 AATAATAA
1 AATATTAA
*
28762047 AGTATATAA
1 AATAT-TAA
28762056 AATA-TAA
1 AATATTAA
28762063 AATATTAA
1 AATATTAA
*
28762071 AATATCAA
1 AATATTAA
*
28762079 AATATTAG
1 AATATTAA
28762087 AATA
1 AATA
28762091 ATAATAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 23 0.64
9 6 0.17
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:28762080 original size:16 final size:15
Alignment explanation
Indices: 28762043--28762090 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
28762033 GATGTGAATA
*
28762043 ATAAAGTATATAAAAT
1 ATAAAATAT-TAAAAT
28762059 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
28762074 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
28762090 A
1 A
28762091 ATAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:28762301 original size:22 final size:24
Alignment explanation
Indices: 28762242--28762337 Score: 81
Period size: 25 Copynumber: 4.0 Consensus size: 24
28762232 GTGATAATAT
* *
28762242 TAAAAATATGTACATAATATAGTG
1 TAAAAATATATACATAATATAATG
*
28762266 TAAAAAATACATACATAATATAAT-
1 T-AAAAATATATACATAATATAATG
*
28762290 T-AAAATATATACATAAGATAACATG
1 TAAAAATATATACATAATAT-A-ATG
* *
28762315 TAGAAAAAATATATATAA-ATAAT
1 TA-AAAATATATACATAATATAAT
28762338 ATAGTATTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
22 16 0.27
23 1 0.02
24 6 0.10
25 21 0.36
26 2 0.03
27 13 0.22
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.30
Consensus pattern (24 bp):
TAAAAATATATACATAATATAATG
Found at i:28762321 original size:27 final size:28
Alignment explanation
Indices: 28762291--28762362 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
28762281 TAATATAATT
28762291 AAAATATATACATAAGATAACAT-GTA-G
1 AAAATATATACATAA-ATAACATAGTATG
* * * *
28762318 AAAAAATATATATAAATAATATAGTATT
1 AAAATATATACATAAATAACATAGTATG
28762346 AAAGATATATACATAAA
1 AAA-ATATATACATAAA
28762363 ATAGTATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 6 0.17
27 16 0.44
28 3 0.08
29 11 0.31
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (28 bp):
AAAATATATACATAAATAACATAGTATG
Found at i:28762361 original size:25 final size:25
Alignment explanation
Indices: 28762239--28762454 Score: 96
Period size: 23 Copynumber: 8.9 Consensus size: 25
28762229 TACGTGATAA
* *
28762239 TATTAAAAATATGTACATAATATAG
1 TATTAAAGATATATACATAATATAG
* * * *
28762264 TGTAAAAAATACATACATAATATA-
1 TATTAAAGATATATACATAATATAG
*
28762288 -ATTAAA-ATATATACATAAGATAACATG
1 TATTAAAGATATATACAT-A-AT-ATA-G
** * *
28762315 TAGAAAAAATATATATAAATAATATAG
1 T--ATTAAAGATATATACATAATATAG
*
28762342 TATTAAAGATATATACATAAAATAG
1 TATTAAAGATATATACATAATATAG
* *
28762367 TA-T-AATATATATACGTAATATAG
1 TATTAAAGATATATACATAATATAG
* * *
28762390 AATT-TAGA-ATATACCTAATATA-
1 TATTAAAGATATATACATAATATAG
* * * *
28762412 T-TAAAAGA-ATGTATATAATATAA
1 TATTAAAGATATATACATAATATAG
*
28762435 TATT-AAGAAATATA-ATAATA
1 TATTAAAGATATATACATAATA
28762455 ACAAAAAAAA
Statistics
Matches: 145, Mismatches: 32, Indels: 30
0.70 0.15 0.14
Matches are distributed among these distances:
21 1 0.01
22 23 0.16
23 47 0.32
24 11 0.08
25 43 0.30
27 2 0.01
28 2 0.01
29 2 0.01
30 5 0.03
31 9 0.06
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (25 bp):
TATTAAAGATATATACATAATATAG
Found at i:28762746 original size:16 final size:16
Alignment explanation
Indices: 28762708--28762746 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28762698 ATCTTCAAAA
*
28762708 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
28762724 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
28762740 AATAACT
1 AAAAACT
28762747 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:28763011 original size:30 final size:30
Alignment explanation
Indices: 28762921--28763019 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
28762911 TAGGTACAAG
*
28762921 TGGTGGTGGAGTAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* * *
28762951 AGGTAGTGAAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
28762981 TGGTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
28763011 TGGTGGTGG
1 TGGTGGTGG
28763020 CAAAGGCTAG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.18, C:0.05, G:0.48, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:28765320 original size:29 final size:29
Alignment explanation
Indices: 28765241--28765312 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
28765231 AACAGAAATG
* * *
28765241 TCCAACCAAAACACACCAGTATTATATAA
1 TCCATCCAAAACACACCAGAATAATATAA
*
28765270 TCC-TCCCAAACACACCAGAATAATATAA
1 TCCATCCAAAACACACCAGAATAATATAA
28765298 TCCATCCAAAACACA
1 TCCATCCAAAACACA
28765313 ATAGAATAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 24 0.65
29 13 0.35
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.18
Consensus pattern (29 bp):
TCCATCCAAAACACACCAGAATAATATAA
Found at i:28765383 original size:13 final size:13
Alignment explanation
Indices: 28765365--28765390 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28765355 ATAAACATCA
28765365 ACATCTCCAAATC
1 ACATCTCCAAATC
28765378 ACATCTCCAAATC
1 ACATCTCCAAATC
28765391 CCTTCTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
ACATCTCCAAATC
Found at i:28765495 original size:17 final size:17
Alignment explanation
Indices: 28765473--28765511 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28765463 TTTTTTTATT
*
28765473 TCAATTTCATTTCCATA
1 TCAATTTCAATTCCATA
*
28765490 TCAATTTCAATTCCATT
1 TCAATTTCAATTCCATA
28765507 TCAAT
1 TCAAT
28765512 ATACAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (17 bp):
TCAATTTCAATTCCATA
Found at i:28765497 original size:23 final size:24
Alignment explanation
Indices: 28765470--28765518 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
28765460 ACTTTTTTTT
* *
28765470 ATTTCAATTTCATTTCCATAT-CA
1 ATTTCAATTCCATTTCAATATACA
28765493 ATTTCAATTCCATTTCAATATACA
1 ATTTCAATTCCATTTCAATATACA
28765517 AT
1 AT
28765519 CAATTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTCAATTCCATTTCAATATACA
Found at i:28766768 original size:17 final size:16
Alignment explanation
Indices: 28766744--28766781 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
28766734 TTTATTCACT
28766744 AATATAAT-ATCAATTA
1 AATATAATAATCAA-TA
28766760 AATAGTAATAATCAATA
1 AATA-TAATAATCAATA
28766777 AATAT
1 AATAT
28766782 CTTTTACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 10 0.50
18 5 0.25
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (16 bp):
AATATAATAATCAATA
Found at i:28767997 original size:18 final size:18
Alignment explanation
Indices: 28767958--28767993 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28767948 CATGTTGTCA
28767958 GCCCGTGTGAACCCACAC
1 GCCCGTGTGAACCCACAC
*
28767976 GCCCGTGTG-GCCCACAC
1 GCCCGTGTGAACCCACAC
28767993 G
1 G
28767994 GCCCAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.17, C:0.44, G:0.28, T:0.11
Consensus pattern (18 bp):
GCCCGTGTGAACCCACAC
Found at i:28772814 original size:15 final size:16
Alignment explanation
Indices: 28772782--28772816 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
28772772 TAAATATTTT
28772782 TTATAAAGATTATATA
1 TTATAAAGATTATATA
*
28772798 TTATAAAG-TTTTATA
1 TTATAAAGATTATATA
28772813 TTAT
1 TTAT
28772817 TTTTATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
TTATAAAGATTATATA
Found at i:28773541 original size:19 final size:18
Alignment explanation
Indices: 28773517--28773559 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
28773507 TTAGAAATTA
28773517 TTTTTATCA-TACTAATAAT
1 TTTTTAT-AGTACTAAT-AT
*
28773536 TTTTTATAGTATTAATAT
1 TTTTTATAGTACTAATAT
28773554 TTTTTA
1 TTTTTA
28773560 AAAATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTATAGTACTAATAT
Found at i:28777839 original size:26 final size:26
Alignment explanation
Indices: 28777807--28777914 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
28777797 TGAAATGCCC
* *
28777807 ATCATGGAACATTTACTTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28777833 ATTATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
28777859 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28777885 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28777911 ATCA
1 ATCA
28777915 ATTTGTATCA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28784714 original size:26 final size:26
Alignment explanation
Indices: 28784683--28784790 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28784673 TGAAATGCCC
* *
28784683 ATCATGAAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28784709 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28784735 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28784761 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28784787 ATCA
1 ATCA
28784791 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28788361 original size:12 final size:12
Alignment explanation
Indices: 28788344--28788372 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
28788334 TGCTTCCGTA
28788344 TTTAATTTTATT
1 TTTAATTTTATT
28788356 TTTAA-TTTATT
1 TTTAATTTTATT
28788367 TTTAAT
1 TTTAAT
28788373 AATTTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTAATTTTATT
Found at i:28791373 original size:25 final size:25
Alignment explanation
Indices: 28791326--28791373 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28791316 TTCCATGTAC
* * * *
28791326 TTATACTTATTTCGTTTATCTATCG
1 TTATAATTATTTCATATAACTATCG
28791351 TTATAATTATTTCATATAACTAT
1 TTATAATTATTTCATATAACTAT
28791374 TTTGTACATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (25 bp):
TTATAATTATTTCATATAACTATCG
Found at i:28791834 original size:46 final size:46
Alignment explanation
Indices: 28791524--28791832 Score: 433
Period size: 46 Copynumber: 6.7 Consensus size: 46
28791514 TTATCTTTGA
* * * * *
28791524 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGT
*
28791570 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
28791616 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * **
28791662 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * *
28791708 CATGTTGTCATGGTATCTTTCAACCATGG-CCTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * ** *
28791753 CAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
28791799 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA
28791833 CATATTTCAT
Statistics
Matches: 233, Mismatches: 28, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
45 42 0.18
46 191 0.82
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
Found at i:28791840 original size:137 final size:138
Alignment explanation
Indices: 28791524--28791833 Score: 469
Period size: 137 Copynumber: 2.3 Consensus size: 138
28791514 TTATCTTTGA
* * * * *
28791524 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT
1 CATGATGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTT
* * * **
28791589 TCAACCATGGTCTTATTCTTTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA
66 TCAACCATGGTCCTATTCTTTTCATGTCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACA
*
28791654 TTTCATGT
131 TTTCATAT
* * * *
28791662 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGTCATGGTATCTT
1 CATGATGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTT
28791727 TCAACCATGG-CCTATTCTTTTCATGTCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACA
66 TCAACCATGGTCCTATTCTTTTCATGTCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACA
28791791 TTTCATAT
131 TTTCATAT
*
28791799 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC
1 CATGATGCCATGGTATCTTTCAACCATGGTCTTAC
28791834 ATATTTCATT
Statistics
Matches: 154, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
137 88 0.57
138 66 0.43
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (138 bp):
CATGATGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTT
TCAACCATGGTCCTATTCTTTTCATGTCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACA
TTTCATAT
Found at i:28794210 original size:15 final size:15
Alignment explanation
Indices: 28794182--28794215 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28794172 GGATTGAATG
28794182 TTGTAAATGTTATGA
1 TTGTAAATGTTATGA
28794197 TTGTGAAATG-TATGA
1 TTGT-AAATGTTATGA
28794212 TTGT
1 TTGT
28794216 CTGACAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (15 bp):
TTGTAAATGTTATGA
Found at i:28794524 original size:25 final size:24
Alignment explanation
Indices: 28794482--28794539 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
28794472 TACAAATGCA
*
28794482 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTGTGAGCGTCCTGATAT-G
* * *
28794507 GCTCTTTGTTAGCTTCCTGGTATG
1 GCTCTTTGTGAGCGTCCTGATATG
28794531 GCTCGTTTG
1 GCTC-TTTG
28794540 AACATCCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.41
Consensus pattern (24 bp):
GCTCTTTGTGAGCGTCCTGATATG
Found at i:28801701 original size:25 final size:25
Alignment explanation
Indices: 28801673--28801720 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28801663 GACTACCACA
28801673 GCTCTTTGTGAGCATCCTGATATAG
1 GCTCTTTGTGAGCATCCTGATATAG
* *
28801698 GCTCTTTTTGAGCCTCCTGATAT
1 GCTCTTTGTGAGCATCCTGATAT
28801721 CGCTCGCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
GCTCTTTGTGAGCATCCTGATATAG
Found at i:28810391 original size:6 final size:6
Alignment explanation
Indices: 28810374--28810407 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
28810364 GAAAACAAAT
28810374 GGGAGAA GGGAGA GGGAGA GGGAGA GGGAGA GGG
1 GGGAG-A GGGAGA GGGAGA GGGAGA GGGAGA GGG
28810408 GAAGGAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:28816174 original size:34 final size:34
Alignment explanation
Indices: 28816131--28816203 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
28816121 GTAATACTAA
*
28816131 CATTCTTTCTTCGGAATATTATAAAGTTAAATAG
1 CATTCTTTCTTCGAAATATTATAAAGTTAAATAG
28816165 CATTCTTTCTTCGAAATATTATAAAGTTAAATAG
1 CATTCTTTCTTCGAAATATTATAAAGTTAAATAG
28816199 CATTC
1 CATTC
28816204 AACAAATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (34 bp):
CATTCTTTCTTCGAAATATTATAAAGTTAAATAG
Found at i:28817892 original size:126 final size:126
Alignment explanation
Indices: 28817762--28817995 Score: 281
Period size: 130 Copynumber: 1.8 Consensus size: 126
28817752 TATCGAATTT
* *
28817762 CCAAATACACAACATTGCCTCATTTTAA-TTTGAGAAAACATGGATGAAATTTCAAAAGGATATT
1 CCAAACACAAAACATTGCCTCATTTTAATTTTGA-AAAACATGGATGAAATTTCAAAAGGATATT
** * * * *
28817826 TTGTATTTTAGTCGAATGGAAAATCGAAGCCCAGCACGATTGGTCACGACCTCCCAAACCCC
65 CCGCATTTTAGTCGAACGAAAAATCGAAACCCAGCACGATTGGTCACGACCTCCCAAACCCC
** * * *
28817888 CCAAACACAAAATGTTGCCTCGTTTTAATTTTTTTTTAAAAACATGGATGGAATTTCAAAAGGAT
1 CCAAACACAAAACATTGCCTCATTTTAA----TTTTGAAAAACATGGATGAAATTTCAAAAGGAT
* *
28817953 ATTCCGCATTTTAGTTGAACGAAAAATTGAAACCCAGCACGAT
62 ATTCCGCATTTTAGTCGAACGAAAAATCGAAACCCAGCACGAT
28817996 AAGGCACGAT
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
126 23 0.26
130 61 0.69
131 4 0.05
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (126 bp):
CCAAACACAAAACATTGCCTCATTTTAATTTTGAAAAACATGGATGAAATTTCAAAAGGATATTC
CGCATTTTAGTCGAACGAAAAATCGAAACCCAGCACGATTGGTCACGACCTCCCAAACCCC
Found at i:28818177 original size:21 final size:23
Alignment explanation
Indices: 28818130--28818183 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
28818120 CATTCAAGAT
**
28818130 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
28818153 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
28818174 AAAAT-ATATA
1 AAAATAATATA
28818184 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:28818416 original size:25 final size:23
Alignment explanation
Indices: 28818361--28818416 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
28818351 ATAATAATGA
*
28818361 AAATAATAATAGTATATAAATAG
1 AAATAATAATAGTATAGAAATAG
*
28818384 AAAT-ATAATAGTAGTAGAAATAT
1 AAATAATAATAGTA-TAGAAATAG
28818407 AAATAGATAA
1 AAATA-ATAA
28818417 ATAAAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.32
23 15 0.54
25 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (23 bp):
AAATAATAATAGTATAGAAATAG
Found at i:28818427 original size:14 final size:13
Alignment explanation
Indices: 28818401--28818439 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
28818391 ATAGTAGTAG
28818401 AAATATAAATAGAT
1 AAATA-AAATAGAT
28818415 AAATAAAATTAGAT
1 AAATAAAA-TAGAT
28818429 AAATAATAATA
1 AAATAA-AATA
28818440 ATATTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.13
14 18 0.78
15 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (13 bp):
AAATAAAATAGAT
Found at i:28818446 original size:20 final size:22
Alignment explanation
Indices: 28818405--28818447 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
28818395 TAGTAGAAAT
28818405 ATAAATAGATAAATAAAATTAG
1 ATAAATAGATAAATAAAATTAG
*
28818427 ATAAATA-AT-AATAATATTAG
1 ATAAATAGATAAATAAAATTAG
28818447 A
1 A
28818448 ATAAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 2 0.10
22 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
ATAAATAGATAAATAAAATTAG
Found at i:28818734 original size:17 final size:17
Alignment explanation
Indices: 28818712--28818753 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
28818702 TTTTAGGGCC
*
28818712 AAAATTAAGAATAATGA
1 AAAATTAAGAATAACGA
28818729 AAAATTAAGAATAACGA
1 AAAATTAAGAATAACGA
*
28818746 AAACTTAA
1 AAAATTAA
28818754 TTGCAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (17 bp):
AAAATTAAGAATAACGA
Found at i:28819492 original size:45 final size:43
Alignment explanation
Indices: 28819441--28819536 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 43
28819431 GGAACTTAAA
* * * *
28819441 GGAGATAAAATCTAGTAATCTTCAGTCTGCTCCACTACTGCTTAG
1 GGAGATAAAATCT-GTAATCTTCAGCCTACTCCAC-ACTACTCAG
* *
28819486 GGAGATAAGATCTGTAATTTTCAGCCTACTCCACACTACTCAG
1 GGAGATAAAATCTGTAATCTTCAGCCTACTCCACACTACTCAG
28819529 GGAGATAA
1 GGAGATAA
28819537 GGCTCACTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 15 0.33
44 18 0.40
45 12 0.27
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (43 bp):
GGAGATAAAATCTGTAATCTTCAGCCTACTCCACACTACTCAG
Found at i:28819658 original size:43 final size:44
Alignment explanation
Indices: 28819564--28819668 Score: 142
Period size: 43 Copynumber: 2.4 Consensus size: 44
28819554 CTGCTCCGCT
* * *
28819564 ACTGCTTAGGGAGATAAGATATGTAATTTTCAACTTGTTTCCCT
1 ACTGCTTAGGGAGATAAGATATCTAATATTCAACTTGTTTCCCC
* *
28819608 ACTGCTTAGGGAGATAAGATTTCTAA-ATTCAGCTTGTTTCCCC
1 ACTGCTTAGGGAGATAAGATATCTAATATTCAACTTGTTTCCCC
28819651 ACTGCTTAGAGG-GATAAG
1 ACTGCTTAG-GGAGATAAG
28819669 GTTCACCGTC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
43 29 0.53
44 26 0.47
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (44 bp):
ACTGCTTAGGGAGATAAGATATCTAATATTCAACTTGTTTCCCC
Found at i:28819667 original size:131 final size:131
Alignment explanation
Indices: 28819475--28819749 Score: 347
Period size: 131 Copynumber: 2.1 Consensus size: 131
28819465 GTCTGCTCCA
* *
28819475 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTACTCCACACTACTCAGGGAGATAAGGC
1 CTACTGCTTAGGGAGATAAGATCTCTAATATTCAGCCTACTCCACACTACTCAGGGAGATAAGGC
* * * * *
28819540 TCACTGTTTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATATGTAATTTTCAACTTGTTTC
66 TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCAACCTGTTAC
28819605 C
131 C
* * ** * * *
28819606 CTACTGCTTAGGGAGATAAGATTTCTAA-ATTCAGCTTGTTTCCCCACTGCTTAGAGG-GATAAG
1 CTACTGCTTAGGGAGATAAGATCTCTAATATTCAGCCT-ACTCCACACTACTCAG-GGAGATAAG
* * * *
28819669 GTTCACCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTT
64 GCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCAACCTGTT
28819734 ACC
129 ACC
*
28819737 TTACTGCTTAGGG
1 CTACTGCTTAGGG
28819750 GTTAAGGCTT
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
130 7 0.06
131 114 0.93
132 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (131 bp):
CTACTGCTTAGGGAGATAAGATCTCTAATATTCAGCCTACTCCACACTACTCAGGGAGATAAGGC
TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCAACCTGTTAC
C
Found at i:28819697 original size:87 final size:88
Alignment explanation
Indices: 28819606--28820228 Score: 702
Period size: 87 Copynumber: 7.2 Consensus size: 88
28819596 ACTTGTTTCC
* * * * * * *
28819606 CTACTGCTTAGGGAGATAAGATTTCTAA-ATTCAGCTTGTTTCCCCACTGCTTAGAGGGATAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGAGGGTTAAGG
* *
28819670 -TTCACCGTCTTCGATCTGTTCCA
66 CTT-ACCCTCTTCGATCTGCTCCA
*
28819693 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCTTACTGCTTAG-GGGTTAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGAGGGTTAAGG
28819757 CTTACCCTCTTCGATCTGCTCCA
66 CTTACCCTCTTCGATCTGCTCCA
* * * *
28819780 CTACTGCTTAGAGAGATAATATCTGTAATTTTCAGCCTATTACCCTACTACTTA-AGGGCTTAAG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGAGGG-TTAAG
* *
28819844 GCTCACCCTCTTCGATCTACTCCA
65 GCTTACCCTCTTCGATCTGCTCCA
* *
28819868 CTACTGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGAGGGTTAAGG
* ** *
28819933 CTTGCTATCTTCAATCTGCTCCA
66 CTTACCCTCTTCGATCTGCTCCA
* *
28819956 CTACTGTTTA-GG-GATAAGATCTGTAATTTTCTAGCCTATTACCCTACTGCTTAGAGGGTTAAG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTC-AGCCTGTTACCCTACTGCTTAGAGGGTTAAG
** *
28820019 GCTTACTGTCTTCGATTTGCTCCA
65 GCTTACCCTCTTCGATCTGCTCCA
* * *
28820043 CTACTGTTTAGGG-G---AGATCTGT-ATTTTCCAGCCTGTTACCTTACTGCTTAGGGGGTTAAG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTT-CAGCCTGTTACCCTACTGCTTAGAGGGTTAAG
* **
28820103 GCTTGCTGTCTTCGATCTGCTCCA
65 GCTTACCCTCTTCGATCTGCTCCA
* *
28820127 CTACTGTTTAGGG-G---AGATCTGT-ATTTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTT-CAGCCTGTTACCCTACTGCTTAGAGGGTTAAG
* ** *
28820187 GCTTGCTGTCTTTGATCTGCTCCA
65 GCTTACCCTCTTCGATCTGCTCCA
* * *
28820211 TTATTGTTTAGGGGAGAT
1 CTACTGCTTA-GGGAGAT
28820229 CTGTATTTTT
Statistics
Matches: 480, Mismatches: 44, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
84 145 0.30
85 12 0.03
86 20 0.04
87 164 0.34
88 136 0.28
89 3 0.01
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (88 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGAGGGTTAAGG
CTTACCCTCTTCGATCTGCTCCA
Found at i:28819858 original size:175 final size:173
Alignment explanation
Indices: 28819651--28820228 Score: 742
Period size: 175 Copynumber: 3.3 Consensus size: 173
28819641 TTGTTTCCCC
* * *
28819651 ACTGCTTAGAGGGATAAGGTTCACCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATC
1 ACTGCTTA-AGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC
* **
28819716 TGTAATTTTCAGCCTGTTACCTTACTGCTTA-GGGGTTAAGGCTTACCCTCTTCGATCTGCTCCA
65 TGTAATTTTCAGCCTGTTACCTTACTGCTTAGGGGGTTAAGGCTTGCTATCTTCGATCTGCTCCA
* *
28819780 CTACTGCTTAGAGAGATAATATCTGTAATTTTCAGCCTATTACCCT
130 CTACTGTTTAG-G-GATAAGATCTGTAATTTTCAGCCTATTACCCT
* * * *
28819826 ACTACTTAAGGGCTTAAGGCTCACCCTCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATC
1 ACTGCTTAAGGG-TTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC
* *
28819891 TGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGCTATCTTCAATCTGCTCCA
65 TGTAATTTTCAGCCTGTTACCTTACTGCTTAGGGGGTTAAGGCTTGCTATCTTCGATCTGCTCCA
28819956 CTACTGTTTAGGGATAAGATCTGTAATTTTCTAGCCTATTACCCT
130 CTACTGTTTAGGGATAAGATCTGTAATTTTC-AGCCTATTACCCT
* * * *
28820001 ACTGCTTAGAGGGTTAAGGCTTACTGTCTTCGATTTGCTCCACTACTGTTTAGGG-G---AGATC
1 ACTGCTTA-AGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC
*
28820062 TGT-ATTTTCCAGCCTGTTACCTTACTGCTTAGGGGGTTAAGGCTTGCTGTCTTCGATCTGCTCC
65 TGTAATTTT-CAGCCTGTTACCTTACTGCTTAGGGGGTTAAGGCTTGCTATCTTCGATCTGCTCC
* *
28820126 ACTACTGTTTAGGG--GAGATCTGT-ATTTTCCAGCCTGTTACCCT
129 ACTACTGTTTAGGGATAAGATCTGTAATTTT-CAGCCTATTACCCT
* ** * * * * *
28820169 ACTGCTTAGGGGGTTAAGGCTTGCTGTCTTTGATCTGCTCCATTATTGTTTAGGGGAGAT
1 ACTGCTTA-AGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTA-GGGAGAT
28820229 CTGTATTTTT
Statistics
Matches: 360, Mismatches: 33, Indels: 23
0.87 0.08 0.06
Matches are distributed among these distances:
168 63 0.17
169 12 0.03
170 6 0.02
171 74 0.21
174 23 0.06
175 139 0.39
176 43 0.12
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (173 bp):
ACTGCTTAAGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
GTAATTTTCAGCCTGTTACCTTACTGCTTAGGGGGTTAAGGCTTGCTATCTTCGATCTGCTCCAC
TACTGTTTAGGGATAAGATCTGTAATTTTCAGCCTATTACCCT
Found at i:28820124 original size:84 final size:85
Alignment explanation
Indices: 28819635--28820241 Score: 697
Period size: 84 Copynumber: 7.1 Consensus size: 85
28819625 GATTTCTAAA
* * * * * * *
28819635 TTCAGCTTGTTTCCCCACTGCTTAGAGGGATAAGG-TTCACCGTCTTCGATCTGTTCCACTACTG
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTT-ACTGTCTTCGATCTGCTCCACTACTG
*
28819699 CTTAGGGAGATAAGATCTGTAATT
65 TTTAGGGAG---AGATCTGTAATT
* ** *
28819723 TTCAGCCTGTTACCTTACTGCTTA-GGGGTTAAGGCTTACCCTCTTCGATCTGCTCCACTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGT
* *
28819787 TTAGAGAGATAATATCTGTAATT
66 TTAG-G-GA-GAGATCTGTAATT
* * * * * ** * *
28819810 TTCAGCCTATTACCCTACTACTTAAGGGCTTAAGGCTCACCCTCTTCGATCTACTCCACTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGT
*
28819875 TTAGAGAGATAAGATCTGTAATT
66 TTAG-G-GA-GAGATCTGTAATT
* * *
28819898 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGCTATCTTCAATCTGCTCCACTACTGT
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGT
*
28819963 TTAGGGATAAGATCTGTAATT
66 TTAGGGA-GAGATCTGTAATT
* * *
28819984 TTCTAGCCTATTACCCTACTGCTTAGAGGGTTAAGGCTTACTGTCTTCGATTTGCTCCACTACTG
1 TTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTG
28820049 TTTAGGG-GAGATCTGT-ATT
65 TTTAGGGAGAGATCTGTAATT
* *
28820068 TTCCAGCCTGTTACCTTACTGCTTAGGGGGTTAAGGCTTGCTGTCTTCGATCTGCTCCACTACTG
1 TT-CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTG
28820133 TTTAGGG-GAGATCTGT-ATT
65 TTTAGGGAGAGATCTGTAATT
* * * *
28820152 TTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGCTGTCTTTGATCTGCTCCATTATTG
1 TT-CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTG
*
28820217 TTTAGGG-GAGATCTGTATTT
65 TTTAGGGAGAGATCTGTAATT
28820237 TTCAG
1 TTCAG
28820242 TCTGCTCCAT
Statistics
Matches: 466, Mismatches: 45, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
84 160 0.34
85 13 0.03
86 19 0.04
87 132 0.28
88 140 0.30
89 2 0.00
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (85 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGT
TTAGGGAGAGATCTGTAATT
Found at i:28820178 original size:40 final size:40
Alignment explanation
Indices: 28820043--28820180 Score: 111
Period size: 40 Copynumber: 3.4 Consensus size: 40
28820033 ATTTGCTCCA
*
28820043 CTACTGTTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
1 CTACTGCTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
* * * * * * *
28820083 TTACTGCTTAGGGG-GTTAAGGCTTGCTGTCTTCGA-TCTGCT-CC
1 CTACTGCTTAGGGGAG---A-TC-TG-TATTTTCCAGCCTGTTACC
*
28820126 ACTACTGTTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
1 -CTACTGCTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
28820167 CTACTGCTTAGGGG
1 CTACTGCTTAGGGG
28820181 GTTAAGGCTT
Statistics
Matches: 71, Mismatches: 17, Indels: 20
0.66 0.16 0.19
Matches are distributed among these distances:
39 7 0.10
40 31 0.44
41 3 0.04
42 2 0.03
43 3 0.04
44 18 0.25
45 7 0.10
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.36
Consensus pattern (40 bp):
CTACTGCTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
Found at i:28820513 original size:134 final size:134
Alignment explanation
Indices: 28820375--28820629 Score: 302
Period size: 134 Copynumber: 1.9 Consensus size: 134
28820365 GCCATTTTCG
*
28820375 ATCTGCTCCATAGCCGATACATAGAGATAAGATCTGT-AATTCTCAG-TCTGCTCCATAGCCGAT
1 ATCTGCTCCATAGCCAATACATAGAGATAAGA-CTGTCAATT-TCAGATCTGCTCCATAGCCGAT
* * *
28820438 TCATGGAGTTAAGACCTACAATTTTCAACCTGC-TCTCTTGCTACTTCA-GAGAGATAAGGCTGG
64 ACATGGAGATAAGACCTACAATTTTCAACCTGCTTC-CTTGCTACCTCAGGA-AGATAAGGCTGG
28820501 TGGCTAAA
127 TGGCTAAA
** * * * **
28820509 ATCTGCTCTGTAGCCAATACATGGAGATAAGACTTTCCATTTTTGATCTGCTCCATAGCCGATAC
1 ATCTGCTCCATAGCCAATACATAGAGATAAGACTGTCAATTTCAGATCTGCTCCATAGCCGATAC
* ** **
28820574 ATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
66 ATGGAGATAAGACCTACAATTTTCAACCTGCTTCCTTGCTACCTCAGGAAGATAAG
28820630 ACTTGTATCT
Statistics
Matches: 101, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
133 5 0.05
134 92 0.91
135 4 0.04
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (134 bp):
ATCTGCTCCATAGCCAATACATAGAGATAAGACTGTCAATTTCAGATCTGCTCCATAGCCGATAC
ATGGAGATAAGACCTACAATTTTCAACCTGCTTCCTTGCTACCTCAGGAAGATAAGGCTGGTGGC
TAAA
Found at i:28820596 original size:45 final size:44
Alignment explanation
Indices: 28820329--28820605 Score: 166
Period size: 45 Copynumber: 6.2 Consensus size: 44
28820319 TGGTAGCTAA
* * * **
28820329 AATCTGCTCCATAGCTGAGACATGGAGATAGGACTCGCCATTTTC
1 AATCTGCTCCATAGCCGATACATGGAGATAAGACT-GTAATTTTC
* * *
28820374 GATCTGCTCCATAGCCGATACATAGAGATAAGATCTGTAATTCTC
1 AATCTGCTCCATAGCCGATACATGGAGATAAGA-CTGTAATTTTC
* * * **
28820419 AGTCTGCTCCATAGCCGATTCATGGAGTTAAGACCTACAATTTTC
1 AATCTGCTCCATAGCCGATACATGGAGATAAGA-CTGTAATTTTC
* * * * * *** **
28820464 AACCTGCTCTC-TTG-CTACTTCA-GAGAGATAAGGCTGGT-GGCTAA
1 AATCTGCTC-CATAGCCGA-TACATG-GAGATAAGACT-GTAATTTTC
** * * * *
28820508 AATCTGCTCTGTAGCCAATACATGGAGATAAGACTTTCCATTTTT
1 AATCTGCTCCATAGCCGATACATGGAGATAAGACTGT-AATTTTC
*
28820553 GATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTC
1 AATCTGCTCCATAGCCGATACATGGAGATAAGA-CTGTAATTTTC
*
28820598 AGTCTGCT
1 AATCTGCT
28820606 TCCTTGCTAC
Statistics
Matches: 170, Mismatches: 51, Indels: 22
0.70 0.21 0.09
Matches are distributed among these distances:
43 1 0.01
44 29 0.17
45 134 0.79
46 6 0.04
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCATAGCCGATACATGGAGATAAGACTGTAATTTTC
Found at i:28820716 original size:178 final size:177
Alignment explanation
Indices: 28820225--28820896 Score: 886
Period size: 178 Copynumber: 3.8 Consensus size: 177
28820215 TGTTTAGGGG
* * *
28820225 AGATCTGTATTTTTCAGTCTGCTCCATAGCTGA-TACATGAAGATAAGACCTGTAATTTTCAACC
1 AGATCTGTAATTTTCAGTCTGCTCCATAGCT-ACT-CAGGAAGATAAGACTTGT-ATTTTCAACC
* * * * * * *
28820289 TGTTCTCCTGCTAGCTCAGAGAGATAAGGTTGGTAGCTAAAATCTGCTCCATAGCTGAGACATGG
63 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGG
* * *
28820354 AGATAGGACTCGCCATTTTCGATCTGCTCCATAGCCGATACATAGAGATA
128 AGATAAGACTCGCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
* * * * ***
28820404 AGATCTGTAATTCTCAGTCTGCTCCATAGCCGATTCATGG-AGTTAAGACCTACAATTTTCAACC
1 AGATCTGTAATTTTCAGTCTGCTCCATAG-CTACTCA-GGAAGATAAGA-CTTGTATTTTCAACC
* ** *
28820468 TGCTCTCTTGCTACTTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCTGTAGCCAATACATGG
63 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGG
**
28820533 AGATAAGACTTTCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
128 AGATAAGACTCGCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
*
28820583 AGATCTGTAATTTTCAGTCTGCTTCC-TTGCTACCTCAGGAAGATAAGACTTGTATCTTT-AACC
1 AGATCTGTAATTTTCAGTCTGC-TCCATAGCTA-CTCAGGAAGATAAGACTTGTAT-TTTCAACC
28820646 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGG
63 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGG
* *
28820711 AGATAAGACTCGCCATTTTTTATCTGCTCCATAGTCGATACATGGAGATA
128 AGATAAGACTCGCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
* * * * * *
28820761 AGATTTGTAATTTTTAGTCTGCTTCC-TTGCTACCTTAGGAAGATAAGACTTGTATCTTCAACTT
1 AGATCTGTAATTTTCAGTCTGC-TCCATAGCTA-CTCAGGAAGATAAGACTTGTATTTTCAACCT
*
28820825 GCTCTCTTGCTACCTCAGAAAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGA
64 GCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGA
28820890 GATAAGA
129 GATAAGA
28820897 TCTGTAATTT
Statistics
Matches: 437, Mismatches: 47, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
177 2 0.00
178 246 0.56
179 182 0.42
180 7 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (177 bp):
AGATCTGTAATTTTCAGTCTGCTCCATAGCTACTCAGGAAGATAAGACTTGTATTTTCAACCTGC
TCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGA
TAAGACTCGCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
Found at i:28820774 original size:45 final size:44
Alignment explanation
Indices: 28820687--28820783 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
28820677 GGTGGCTAAA
*
28820687 ATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTTT
1 ATCTGCTCCATAGCCGATACATGGAGATAAGACTCG-CAATTTTT
* * * *
28820732 ATCTGCTCCATAGTCGATACATGGAGATAAGATTTGTAATTTTT
1 ATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCAATTTTT
28820776 AGTCTGCT
1 A-TCTGCT
28820784 TCCTTGCTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 7 0.15
45 39 0.85
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (44 bp):
ATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCAATTTTT
Found at i:28827092 original size:126 final size:127
Alignment explanation
Indices: 28826949--28827191 Score: 308
Period size: 130 Copynumber: 1.9 Consensus size: 127
28826939 TATCTAATTT
*
28826949 CCAAATACAAAACATTGCCTCATTTTAA-TTTGAGAAAACATGGATGAAATTTCAAAAGGATATT
1 CCAAACACAAAACATTGCCTCATTTTAATTTTGAGAAAACATGGATGAAATTTCAAAAGGATATT
* * * * * *
28827013 CTGTATTTTAGTAGAATGGAAAATCGAAGCCCAGCACGATTGGACACGACCTCCCAAACCCC
66 CCGCATTTTAGTAGAACGAAAAATCGAAACCCAGCACGATAGGACACGACCTCCCAAACCCC
* * ****
28827075 CCAAACACAAAATATTGCCTCGTTTTAATTTTTTTTTTTAAACATGGATGAAATTTCAAAAGGAT
1 CCAAACACAAAACATTGCCTCATTTTAA---TTTTGAGAAAACATGGATGAAATTTCAAAAGGAT
* * *
28827140 ATTCCGCATTTTAGTTGAACGAAAAATTGAAACCCAGCACGATAGGGCACGA
63 ATTCCGCATTTTAGTAGAACGAAAAATCGAAACCCAGCACGATAGGACACGA
28827192 TTCCTCGAAC
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
126 25 0.26
130 72 0.74
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (127 bp):
CCAAACACAAAACATTGCCTCATTTTAATTTTGAGAAAACATGGATGAAATTTCAAAAGGATATT
CCGCATTTTAGTAGAACGAAAAATCGAAACCCAGCACGATAGGACACGACCTCCCAAACCCC
Found at i:28827362 original size:21 final size:23
Alignment explanation
Indices: 28827315--28827368 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
28827305 CATTCAAGAT
**
28827315 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
28827338 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
28827359 AAAAT-ATATA
1 AAAATAATATA
28827369 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:28827421 original size:51 final size:49
Alignment explanation
Indices: 28827341--28827438 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 49
28827331 CTCTTTAAAA
*
28827341 ATAATATATAAACAATTCAAAATATATAATGTGTAAAAAAGTTTGAAATAC
1 ATAATATATAAACAATTCAAAATAAATAATGTGT-AAAAA-TTTGAAATAC
*
28827392 ATAATATATGAAA-ATATT-AAAGTAAATAATGTGTAAAAATTTGAAAT
1 ATAATATAT-AAACA-ATTCAAAATAAATAATGTGTAAAAATTTGAAAT
28827439 GAGCGTTGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
49 8 0.19
50 5 0.12
51 24 0.56
52 6 0.14
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (49 bp):
ATAATATATAAACAATTCAAAATAAATAATGTGTAAAAATTTGAAATAC
Found at i:28827610 original size:14 final size:13
Alignment explanation
Indices: 28827561--28827659 Score: 55
Period size: 14 Copynumber: 7.2 Consensus size: 13
28827551 ATTAGTATAT
28827561 AAATAGA-AATATA
1 AAATAGATAA-ATA
*
28827574 ATAATAGTAGAAATA
1 A-AATAG-ATAAATA
28827589 CAAATAGATAAATA
1 -AAATAGATAAATA
28827603 AAATTAGATAAATA
1 AAA-TAGATAAATA
*
28827617 ATAATA-TTAGAATA
1 A-AATAGATA-AATA
28827631 AGAA-A-ATAAATA
1 A-AATAGATAAATA
28827643 TAAATAGA-AACATA
1 -AAATAGATAA-ATA
28827657 AAA
1 AAA
28827660 ATAATAGCAA
Statistics
Matches: 71, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
12 6 0.08
13 16 0.23
14 35 0.49
15 11 0.15
16 3 0.04
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (13 bp):
AAATAGATAAATA
Found at i:28827666 original size:17 final size:17
Alignment explanation
Indices: 28827590--28827663 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 17
28827580 GTAGAAATAC
*
28827590 AAATAGATAAATAAAATT
1 AAATAGA-AAATAAAAAT
* * *
28827608 AGATA-AATAATAATATT
1 AAATAGAA-AATAAAAAT
*
28827625 AGAATAAGAAAATAAATAT
1 A-AAT-AGAAAATAAAAAT
28827644 AAATAGAAACATAAAAAT
1 AAATAGAAA-ATAAAAAT
28827662 AA
1 AA
28827664 TAGCAATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
16 1 0.02
17 15 0.34
18 18 0.41
19 8 0.18
20 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.24
Consensus pattern (17 bp):
AAATAGAAAATAAAAAT
Found at i:28827917 original size:17 final size:17
Alignment explanation
Indices: 28827895--28827936 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
28827885 TTTTAGAGCC
*
28827895 AAAATTAAGAATAATGA
1 AAAATTAAGAATAACGA
28827912 AAAATTAAGAATAACGA
1 AAAATTAAGAATAACGA
*
28827929 AAACTTAA
1 AAAATTAA
28827937 TTGCAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (17 bp):
AAAATTAAGAATAACGA
Found at i:28830741 original size:6 final size:6
Alignment explanation
Indices: 28830726--28830760 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
28830716 CTAAAAAATT
* *
28830726 CTACTA CTACTC CTACTC CTACTC TTACTC CTACT
1 CTACTC CTACTC CTACTC CTACTC CTACTC CTACT
28830761 TAAGATAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.37
Consensus pattern (6 bp):
CTACTC
Found at i:28832205 original size:36 final size:36
Alignment explanation
Indices: 28832161--28832235 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
28832151 TGCTATTTTC
*
28832161 TTTTATTATTATAAAAACCCTAAAACTTCCCTTTAT
1 TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
28832197 TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
1 TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
28832233 TTT
1 TTT
28832236 AACTTTGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (36 bp):
TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
Found at i:28840091 original size:18 final size:17
Alignment explanation
Indices: 28840059--28840099 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
28840049 TAATGTTAAC
*
28840059 ATTTATTATTAAAATAA
1 ATTTATAATTAAAATAA
28840076 ATTTATAATATAAAATAA
1 ATTTATAAT-TAAAATAA
28840094 ATTTAT
1 ATTTAT
28840100 TAAAATAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTATAATTAAAATAA
Found at i:28840103 original size:14 final size:15
Alignment explanation
Indices: 28840064--28840107 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
28840054 TTAACATTTA
28840064 TTATTAAAATAAATT
1 TTATTAAAATAAATT
28840079 TATAATATAAAATAAA-T
1 T-T-AT-TAAAATAAATT
28840096 TTATTAAAATAA
1 TTATTAAAATAA
28840108 TCATTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.31
15 3 0.12
16 2 0.08
17 4 0.15
18 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTATTAAAATAAATT
Found at i:28843120 original size:25 final size:25
Alignment explanation
Indices: 28843090--28843139 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
28843080 CTAGAAAGTA
*
28843090 TGACTTGAGAATGTATAGGTGATTT
1 TGACTTGAGAATGTATAAGTGATTT
28843115 TGACTTGAGAATGTATAAGTGATTT
1 TGACTTGAGAATGTATAAGTGATTT
28843140 AACATAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.26, T:0.40
Consensus pattern (25 bp):
TGACTTGAGAATGTATAAGTGATTT
Found at i:28847547 original size:7 final size:7
Alignment explanation
Indices: 28847535--28847563 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28847525 TTAAAAAAGA
28847535 TTTTATT
1 TTTTATT
28847542 TTTTATT
1 TTTTATT
28847549 TTTTATT
1 TTTTATT
28847556 TTTTATT
1 TTTTATT
28847563 T
1 T
28847564 ATATAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTATT
Found at i:28849707 original size:3 final size:3
Alignment explanation
Indices: 28849699--28849730 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28849689 TACTTCATTG
28849699 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28849731 TATTTGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28851399 original size:16 final size:15
Alignment explanation
Indices: 28851378--28851425 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
28851368 ATTTTGAATA
28851378 TTATTTAATATTATTT
1 TTATTT-ATATTATTT
* *
28851394 TTATTTATGTAATTT
1 TTATTTATATTATTT
*
28851409 TTATTTTATAATATTT
1 TTA-TTTATATTATTT
28851425 T
1 T
28851426 ATAACAGCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATTTATATTATTT
Found at i:28860230 original size:126 final size:125
Alignment explanation
Indices: 28859750--28860266 Score: 522
Period size: 126 Copynumber: 4.1 Consensus size: 125
28859740 GGCCAATCAA
* * * *
28859750 GAACTACTGTAGAAAAAGAGCATCCACATGGGAGCTTTTTTTAATAATTTTACTGACAGTGCATC
1 GAACTACTATAGAAAAA-AGCATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATC
* * * *
28859815 CTACTTGAAGCGTTTTTGACACTTTTTTTC-CAGAACCATCTTCTCAAAATTATTTTTCTAG
65 CTGCTTGAAGCGTTTTTGACA-TTATTTTCTCAGAACTATCTTCTCAAAATTATTTTTTTAG
* ** ** * * *
28859876 GAACTAGTATAGAAAAAAAAATCCACATAAGAGCTTTTTTCAGTAATTTTGCTAACAATACATCC
1 GAACTACTATAGAAAAAAGCATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATCC
* * * * * * *
28859941 TGCTTGAAGTGTTTTTGACACTATTTT-TTAGAACTGTCTTCTCAAAATTATATTTTCAA
66 TGCTTGAAGCGTTTTTGACATTATTTTCTCAGAACTATCTTCTCAAAATTATTTTTTTAG
* * * * * * *
28860000 GAACTACTATAGGAAAAAGCGTCCAC--GTGAGTTTTTTTTAGTAATTTTACTGACACTGCATCC
1 GAACTACTATAGAAAAAAGCATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATCC
* * * * * * *
28860063 CGCTTGAAGCATTTTTTACATTATTTTTTCAAAATTGTCTTCTCAAAATTATTTTTTTAG
66 TGCTTGAAGCGTTTTTGACATTATTTTCTCAGAACTATCTTCTCAAAATTATTTTTTTAG
* ** * * * *
28860123 GAACTACTGTAGAAAAAGAGTGTCCACGTGGGAGCTTCTTTCAGTAATTTTGCTAACAGTGTATC
1 GAACTACTATAGAAAAA-AGCATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATC
* * *
28860188 CTGCTTAAAGCGTTTTTGACATTATCTTCTCAGAACTATCTTCTCAAAATTAATTTTTCTA-
65 CTGCTTGAAGCGTTTTTGACATTATTTTCTCAGAACTATCTTCTCAAAATT-ATTTTTTTAG
* *
28860249 AAACTACTACAGAAAAAA
1 GAACTACTATAGAAAAAA
28860267 AAAAACAAAA
Statistics
Matches: 314, Mismatches: 71, Indels: 13
0.79 0.18 0.03
Matches are distributed among these distances:
122 51 0.16
123 41 0.13
124 58 0.18
125 57 0.18
126 99 0.32
127 8 0.03
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (125 bp):
GAACTACTATAGAAAAAAGCATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATCC
TGCTTGAAGCGTTTTTGACATTATTTTCTCAGAACTATCTTCTCAAAATTATTTTTTTAG
Found at i:28860398 original size:34 final size:33
Alignment explanation
Indices: 28860353--28860482 Score: 133
Period size: 34 Copynumber: 3.9 Consensus size: 33
28860343 TAAACACAAA
* *
28860353 AATTATTTTAAAAAAACTAAACCCTAATTTAATC
1 AATT-TTTTAAAAAATCTAAACCCTAATTTAATT
*
28860387 AATTTTCTTAAAAACTCTAAACCCTAATTTAATT
1 AATTTT-TTAAAAAATCTAAACCCTAATTTAATT
** *
28860421 AATTTATTT-AAAACCCTTAAAACCTAATTTAATT
1 AATTT-TTTAAAAAATC-TAAACCCTAATTTAATT
28860455 AA---TTTAAAAAACTCTAAACCCTAATTTA
1 AATTTTTTAAAAAA-TCTAAACCCTAATTTA
28860483 TTTTTTAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
30 3 0.04
31 17 0.20
32 1 0.01
33 8 0.10
34 53 0.64
35 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (33 bp):
AATTTTTTAAAAAATCTAAACCCTAATTTAATT
Found at i:28860453 original size:30 final size:30
Alignment explanation
Indices: 28860363--28860506 Score: 107
Period size: 30 Copynumber: 4.6 Consensus size: 30
28860353 AATTATTTTA
28860363 AAAAAAC-TAAACCCTAATTTAATCAATT-TTCT
1 AAAAAACTTAAACCCTAATTTAAT---TTATT-T
*
28860395 TAAAAACTCTAAACCCTAATTTAATTAATTTATTT
1 AAAAAACT-TAAACCCTAA--T--TTAATTTATTT
** * *
28860430 AAAACCCTTAAAACCTAATTTAATTAATTT
1 AAAAAACTTAAACCCTAATTTAATTTATTT
28860460 AAAAAACTCTAAACCCTAATTT-ATTT-TTT
1 AAAAAACT-TAAACCCTAATTTAATTTATTT
**
28860489 AAAATTCTTAAACCCTAA
1 AAAAAACTTAAACCCTAA
28860507 ATAAATAAAC
Statistics
Matches: 92, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
28 10 0.11
29 9 0.10
30 19 0.21
31 12 0.13
32 7 0.08
34 19 0.21
35 8 0.09
36 3 0.03
38 5 0.05
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAAAACTTAAACCCTAATTTAATTTATTT
Found at i:28860555 original size:8 final size:8
Alignment explanation
Indices: 28860542--28860578 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
28860532 ACAGAACATT
28860542 AACCCTAC
1 AACCCTAC
*
28860550 AACCCTAA
1 AACCCTAC
28860558 AACCCT--
1 AACCCTAC
28860564 AACCCTAC
1 AACCCTAC
28860572 AACCCTA
1 AACCCTA
28860579 GGCACTAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.41, C:0.46, G:0.00, T:0.14
Consensus pattern (8 bp):
AACCCTAC
Found at i:28864760 original size:15 final size:15
Alignment explanation
Indices: 28864739--28864782 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28864729 CAATTTTAAT
* *
28864739 AAAATGTGATTTTTT
1 AAAATGTGATTGTTG
* *
28864754 TAAATGTAATTGTTG
1 AAAATGTGATTGTTG
28864769 AAAATGTGATTGTT
1 AAAATGTGATTGTT
28864783 ATATTGCTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (15 bp):
AAAATGTGATTGTTG
Found at i:28868455 original size:21 final size:22
Alignment explanation
Indices: 28868431--28868474 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28868421 TTAAATCAGT
*
28868431 TTTAATTTAAGAGTTT-GTTTA
1 TTTAATTAAAGAGTTTAGTTTA
*
28868452 TTTAATTAAAGTGTTTAGTTTA
1 TTTAATTAAAGAGTTTAGTTTA
28868474 T
1 T
28868475 ACTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (22 bp):
TTTAATTAAAGAGTTTAGTTTA
Found at i:28872792 original size:10 final size:9
Alignment explanation
Indices: 28872779--28872849 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
28872769 TAAAAAATGG
28872779 AAAAATATAA
1 AAAAAT-TAA
28872789 AAAAATTTACA
1 AAAAA-TTA-A
28872800 AAAAATTAA
1 AAAAATTAA
* *
28872809 AAAATTTCA
1 AAAAATTAA
*
28872818 AAAAATTATTT
1 AAAAATTA--A
*
28872829 AAAAATTAC
1 AAAAATTAA
*
28872838 AAACATTAA
1 AAAAATTAA
28872847 AAA
1 AAA
28872850 CTGATCCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
9 24 0.49
10 10 0.20
11 15 0.31
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATTAA
Found at i:28872803 original size:21 final size:20
Alignment explanation
Indices: 28872779--28872823 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
28872769 TAAAAAATGG
28872779 AAAAATATAAAAAAATTTACA
1 AAAAATAT-AAAAAATTTACA
28872800 AAAAAT-TAAAAAATTT-CA
1 AAAAATATAAAAAATTTACA
28872818 AAAAAT
1 AAAAAT
28872824 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.33
19 9 0.38
20 1 0.04
21 6 0.25
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATATAAAAAATTTACA
Found at i:28872810 original size:18 final size:18
Alignment explanation
Indices: 28872788--28872825 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28872778 GAAAAATATA
28872788 AAAAAATTTACAAAAAATT
1 AAAAAATTT-CAAAAAATT
28872807 AAAAAATTTCAAAAAATT
1 AAAAAATTTCAAAAAATT
28872825 A
1 A
28872826 TTTAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAATTTCAAAAAATT
Found at i:28873044 original size:20 final size:18
Alignment explanation
Indices: 28873021--28873080 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 18
28873011 TTTTTAATAT
28873021 TTTTTAATAATTTTAGTAAA
1 TTTTTAATAATTTTA-T-AA
*
28873041 TTTTTATATATTTTTATAA
1 TTTTTA-ATAATTTTATAA
* *
28873060 -TTTT-GTAATTTTATAC
1 TTTTTAATAATTTTATAA
28873076 TTTTT
1 TTTTT
28873081 TTTCTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 9 0.26
17 4 0.12
18 4 0.12
19 2 0.06
20 7 0.21
21 8 0.24
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTTAATAATTTTATAA
Found at i:28873045 original size:11 final size:10
Alignment explanation
Indices: 28873006--28873063 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
28872996 GTAAAAATAT
28873006 TAAATTTTT-
1 TAAATTTTTA
28873015 TAATATTTTT-
1 TAA-ATTTTTA
*
28873025 TAATAATTTTA
1 TAA-ATTTTTA
28873036 GTAAATTTTTA
1 -TAAATTTTTA
*
28873047 TATATTTTTA
1 TAAATTTTTA
28873057 T-AATTTT
1 TAAATTTT
28873064 GTAATTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 8 0.19
10 25 0.60
11 6 0.14
12 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TAAATTTTTA
Found at i:28873061 original size:19 final size:18
Alignment explanation
Indices: 28873011--28873112 Score: 57
Period size: 20 Copynumber: 5.4 Consensus size: 18
28873001 AATATTAAAT
28873011 TTTTTAATATTTTTTAATAA
1 TTTTTAATA-TTTTT-ATAA
28873031 TTTTAGTAA-ATTTTTATATA
1 TTTT--TAATATTTTTATA-A
* *
28873051 TTTTT-ATAATTTTGTAA
1 TTTTTAATATTTTTATAA
* * *
28873068 TTTTATACT-TTTTTTTCTA
1 TTTT-TAATATTTTTAT-AA
*
28873087 TTTTTAATCATTTTTGTAA
1 TTTTTAAT-ATTTTTATAA
28873106 TTTTTAA
1 TTTTTAA
28873113 ATAACTCTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 19
0.70 0.10 0.21
Matches are distributed among these distances:
17 6 0.09
18 17 0.27
19 17 0.27
20 20 0.31
21 1 0.02
22 3 0.05
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTAATATTTTTATAA
Found at i:28875908 original size:14 final size:14
Alignment explanation
Indices: 28875889--28875915 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28875879 TTGTTTTTAT
28875889 ATATATGTATATAG
1 ATATATGTATATAG
28875903 ATATATGTATATA
1 ATATATGTATATA
28875916 TATAGTAATT
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:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
ATATATGTATATAG
Found at i:28876103 original size:23 final size:23
Alignment explanation
Indices: 28876062--28876110 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
28876052 TTGTTACACC
*
28876062 TTTTACTATTATTACTATTGTAT
1 TTTTACTATTATTACTATTATAT
**
28876085 TTTTACTATTATTGTTATTATAT
1 TTTTACTATTATTACTATTATAT
28876108 TTT
1 TTT
28876111 CCTCTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTACTATTATTACTATTATAT
Found at i:28876325 original size:3 final size:3
Alignment explanation
Indices: 28876317--28876442 Score: 55
Period size: 3 Copynumber: 42.7 Consensus size: 3
28876307 TGTATTTACC
* * * *
28876317 ATT ATT ATT ACT ATT ATT -TT CATT -TT -TT ATT ACT ATT ACT AAT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
28876360 ATC ATT CTT -TT ATT ATT TTCT ATT ATT ATT ATC ACT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
28876405 ATA AAT ATT AAT A-C ACTT ATT ATT ATT TTT ATT ATT AT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT AT
28876443 CATCAATATT
Statistics
Matches: 89, Mismatches: 27, Indels: 14
0.68 0.21 0.11
Matches are distributed among these distances:
2 9 0.10
3 75 0.84
4 5 0.06
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:28876348 original size:28 final size:29
Alignment explanation
Indices: 28876317--28876388 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 29
28876307 TGTATTTACC
*
28876317 ATTATTATTACTATTATTTTCATT-TTTT
1 ATTATTATTACTATTATTATCATTCTTTT
*
28876345 ATTACTATTACTA--A-TATCATTCTTTT
1 ATTATTATTACTATTATTATCATTCTTTT
28876371 ATTATT-TT-CTATTATTAT
1 ATTATTATTACTATTATTAT
28876389 TATCACTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 3 0.08
25 8 0.22
26 11 0.30
27 3 0.08
28 12 0.32
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTATTATTACTATTATTATCATTCTTTT
Found at i:28882462 original size:27 final size:26
Alignment explanation
Indices: 28882425--28882539 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
28882415 AGCATGGCTG
* *
28882425 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
28882451 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
28882479 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * * *
28882506 CCAGATCAGATATTTGTCGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
28882533 CCAGAAC
1 CCAGAAC
28882540 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
26 5 0.06
27 57 0.72
28 17 0.22
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28882484 original size:54 final size:54
Alignment explanation
Indices: 28882425--28882539 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
28882415 AGCATGGCTG
* *
28882425 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTCGCAGAGCCA
* * * *
28882479 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTCGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTCGCAGAGCCA
28882533 CCAGAAC
1 CCAGAAC
28882540 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTCGCAGAGCCA
Found at i:28884194 original size:26 final size:26
Alignment explanation
Indices: 28884158--28884267 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
28884148 CATGAAATTC
28884158 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28884184 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28884210 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
28884236 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
28884262 TTATCA
1 TTATCA
28884268 ATTTGTACCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28893362 original size:25 final size:25
Alignment explanation
Indices: 28893334--28893412 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 25
28893324 TATTTCTATA
28893334 TTATTATCATTATTATTATTATTTG
1 TTATTATCATTATTATTATTATTTG
*
28893359 TTATT-TAATATATTATTATTGTATTT-
1 TTATTATCAT-TATTATTA-T-TATTTG
* *
28893385 TTATTACCATCA-TATTATTATATTG
1 TTATTATCATTATTATTATTAT-TTG
28893410 TTA
1 TTA
28893413 CACCTTTTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
23 3 0.07
24 6 0.14
25 21 0.48
26 7 0.16
27 7 0.16
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (25 bp):
TTATTATCATTATTATTATTATTTG
Found at i:28893682 original size:3 final size:3
Alignment explanation
Indices: 28893674--28893874 Score: 83
Period size: 3 Copynumber: 68.0 Consensus size: 3
28893664 TGTATTTACC
* * * *
28893674 ATT ATT ATT ACT ATT ATT -TT CATT -TT -TT ATT ACT ATT ACT AAT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
* ** * * * *
28893717 ATC ATT CCT -TT ATT ATT TTCT ATT ATT ATT ATC ACT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
28893762 ATA AAT ATT AAT ACT CTT ATT ATT ATT ATT ATT ATT ATT ATC AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** ** * * * *
28893810 A-T AGTT -TT ACC ACC ACT ATT ATC ATT ATCG A-C ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
28893854 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
28893875 GTTTTCATCA
Statistics
Matches: 146, Mismatches: 42, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
2 12 0.08
3 128 0.88
4 6 0.04
ACGTcount: A:0.33, C:0.10, G:0.01, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:28895814 original size:17 final size:17
Alignment explanation
Indices: 28895792--28895825 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28895782 ATCCACTAAT
*
28895792 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
28895809 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
28895826 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:28900453 original size:17 final size:17
Alignment explanation
Indices: 28900431--28900464 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28900421 ATCCACTAAT
*
28900431 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
28900448 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
28900465 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:28902920 original size:56 final size:56
Alignment explanation
Indices: 28902834--28902945 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
28902824 AAAATAAATG
28902834 TTGAAATAACTTAAATGATTGCTTAGAATCAAACTTCACAGGA-GAAGTGGTGCCTA
1 TTGAAATAACTTAAATGATTGCTTAGAATCAAACTTCACA-GATGAAGTGGTGCCTA
*
28902890 TTGAAATTACTTAAATGATTGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
1 TTGAAATAACTTAAATGATTGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
28902946 AGGTGGTGGG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 2 0.04
56 52 0.96
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (56 bp):
TTGAAATAACTTAAATGATTGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
Found at i:28908154 original size:20 final size:19
Alignment explanation
Indices: 28908122--28908172 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
28908112 ATATTTGCAT
*
28908122 AAAAATAAT-AAAATAGAAG
1 AAAAA-AATAAAAAGAGAAG
*
28908141 AAAAAAAGTAAAAAGAGAAT
1 AAAAAAA-TAAAAAGAGAAG
*
28908161 AGAAAAATAAAA
1 AAAAAAATAAAA
28908173 TGTAATTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
20 14 0.52
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAAAATAAAAAGAGAAG
Found at i:28913510 original size:49 final size:49
Alignment explanation
Indices: 28913421--28913529 Score: 132
Period size: 49 Copynumber: 2.2 Consensus size: 49
28913411 GCCGTGTGTT
*
28913421 AGACTGTGTGGCCAGGTCGTGTGTGGCACACAGTCATGTGAAACTT-TAC
1 AGACAGTGTGGCCAGGTCGTGTGTGGCACACAGTCATGTGAAA-TTGTAC
* * * * *
28913470 AGACCGTGTTGCCAGGTTGTGTGTGGCACAC-GGCTGTGTGAAATTGTAC
1 AGACAGTGTGGCCAGGTCGTGTGTGGCACACAGTC-ATGTGAAATTGTAC
28913519 AGACAGTGTGG
1 AGACAGTGTGG
28913530 AGCACATGGA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
48 4 0.08
49 47 0.92
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (49 bp):
AGACAGTGTGGCCAGGTCGTGTGTGGCACACAGTCATGTGAAATTGTAC
Found at i:28914090 original size:25 final size:25
Alignment explanation
Indices: 28914062--28914134 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
28914052 TATATGGTAT
* * *
28914062 GATAAAATATGCTATGTTATGATTC
1 GATAAAACATGATATGTTAAGATTC
*
28914087 GATATAACATGATATGTTAAGATTC
1 GATAAAACATGATATGTTAAGATTC
* ** * *
28914112 AATATGATATGATACGTTAAGAT
1 GATAAAACATGATATGTTAAGAT
28914135 ATGATTTGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (25 bp):
GATAAAACATGATATGTTAAGATTC
Found at i:28914961 original size:12 final size:12
Alignment explanation
Indices: 28914944--28914973 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28914934 AAATCACTCT
28914944 ATATTTTGATAA
1 ATATTTTGATAA
28914956 ATATTTTGATAA
1 ATATTTTGATAA
*
28914968 AAATTT
1 ATATTT
28914974 AAAACTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATTTTGATAA
Found at i:28916706 original size:51 final size:51
Alignment explanation
Indices: 28916629--28916827 Score: 285
Period size: 51 Copynumber: 3.9 Consensus size: 51
28916619 CGGATACACG
* * * *
28916629 GTGGCTTTCACATAGTACCACCCTTGTAG-CTAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAAA
*
28916680 GTGGCCTTCGCATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
28916731 GTGGCCTTCACATAGTACCACA-TATGTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACT-TGTGTCCAAAGCTATTATATTCACAAA
* * * *
28916782 GTGGCCTTCATATAGTACCACAATTGTGTCCAAGGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTC
28916828 CTAAGGTTCA
Statistics
Matches: 136, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
50 2 0.01
51 133 0.98
52 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
Found at i:28916921 original size:28 final size:26
Alignment explanation
Indices: 28916851--28916965 Score: 130
Period size: 24 Copynumber: 4.4 Consensus size: 26
28916841 GGGAAATTTC
*
28916851 TCACTTAGCGCAATGCCATGAACTTTATT
1 TCACTTA--GCAATGCCATGGAC-TTATT
28916880 TCACTTAG--ATGCCATGGACTTATT
1 TCACTTAGCAATGCCATGGACTTATT
*
28916904 TCATTTAGCATATTGCCATGGACTTATT
1 TCACTTAGCA-A-TGCCATGGACTTATT
*
28916932 TCACTTAG--ATGCCATGGTCTTATT
1 TCACTTAGCAATGCCATGGACTTATT
28916956 TCACTTAGCA
1 TCACTTAGCA
28916966 CAATGTCATA
Statistics
Matches: 76, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
24 34 0.45
25 11 0.14
27 2 0.03
28 22 0.29
29 7 0.09
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (26 bp):
TCACTTAGCAATGCCATGGACTTATT
Found at i:28916938 original size:52 final size:53
Alignment explanation
Indices: 28916864--28916965 Score: 170
Period size: 52 Copynumber: 1.9 Consensus size: 53
28916854 CTTAGCGCAA
*
28916864 TGCCATGAACTTTATTTCACTTAGATGCCATGGACTTATTTCATTTAGCATAT
1 TGCCATGAACTTTATTTCACTTAGATGCCATGGACTTATTTCACTTAGCATAT
* *
28916917 TGCCATGGAC-TTATTTCACTTAGATGCCATGGTCTTATTTCACTTAGCA
1 TGCCATGAACTTTATTTCACTTAGATGCCATGGACTTATTTCACTTAGCA
28916966 CAATGTCATA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 37 0.80
53 9 0.20
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (53 bp):
TGCCATGAACTTTATTTCACTTAGATGCCATGGACTTATTTCACTTAGCATAT
Found at i:28931743 original size:15 final size:16
Alignment explanation
Indices: 28931720--28931756 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
28931710 GAATTTAATC
28931720 AAAAA-CAC-ATCAAT
1 AAAAATCACAATCAAT
28931734 AAAAATCACAAATCAAT
1 AAAAATCAC-AATCAAT
28931751 AAAAAT
1 AAAAAT
28931757 TCATTCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 3 0.15
17 12 0.60
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATCACAATCAAT
Found at i:28933612 original size:20 final size:20
Alignment explanation
Indices: 28933587--28933653 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
28933577 AATAATGATA
28933587 TAAAAATAATAGGAGGCCTG
1 TAAAAATAATAGGAGGCCTG
** * * *
28933607 TAAAAATCAA-ACAAATG-ATA
1 TAAAAAT-AATA-GGAGGCCTG
28933627 TAAAAATAATAGGAGGCCTG
1 TAAAAATAATAGGAGGCCTG
28933647 TAAAAAT
1 TAAAAAT
28933654 CAAACAAAAC
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 4 0.12
20 25 0.76
21 4 0.12
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.21
Consensus pattern (20 bp):
TAAAAATAATAGGAGGCCTG
Found at i:28933626 original size:40 final size:40
Alignment explanation
Indices: 28933580--28933661 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
28933570 AATCAAGAAT
28933580 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
1 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
28933620 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
1 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
28933660 AA
1 AA
28933662 ACTAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (40 bp):
AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
Found at i:28933857 original size:18 final size:19
Alignment explanation
Indices: 28933819--28933872 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
28933809 AGAATAAAAC
28933819 AAATAAATGATAATAAG-A
1 AAATAAATGATAATAAGAA
*
28933837 AAATAAATGA-AATAAATAA
1 AAATAAATGATAAT-AAGAA
*
28933856 AAATAAAAGAATAATAA
1 AAATAAATG-ATAATAA
28933873 TTAAGAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
19 9 0.30
20 3 0.10
21 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (19 bp):
AAATAAATGATAATAAGAA
Found at i:28933881 original size:27 final size:25
Alignment explanation
Indices: 28933850--28933922 Score: 64
Period size: 27 Copynumber: 2.9 Consensus size: 25
28933840 TAAATGAAAT
28933850 AAATAAAAATAAAAGAATAATAATTA
1 AAATAAAAATAAAAGAATAATAA-TA
*
28933876 AGAATAATAAA-CAAAGAATGAA-AATA
1 A-AATAA-AAATAAAAGAAT-AATAATA
*
28933902 AAAT-AAAATAAAATAA-AATAA
1 AAATAAAAATAAAAGAATAATAA
28933923 AAAGTGGAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
22 2 0.05
23 5 0.13
24 6 0.15
25 3 0.08
26 4 0.10
27 14 0.36
28 5 0.13
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.19
Consensus pattern (25 bp):
AAATAAAAATAAAAGAATAATAATA
Found at i:28933906 original size:5 final size:5
Alignment explanation
Indices: 28933896--28933924 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28933886 ACAAAGAATG
28933896 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
28933925 AGTGGAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:28949447 original size:38 final size:38
Alignment explanation
Indices: 28949402--28949498 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 38
28949392 GGATTAAAGA
*
28949402 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGATAAAT
* **
28949440 CCCGCAGGCTTCGTGCTAGTATTATATCCGGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGATAAAT
** * *
28949478 CCTACAGGCCTAGTGCTGGTA
1 CCCGCAGGCTTCGTGCTGGTA
28949499 TTATATTCGG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.27
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGATAAAT
Found at i:28949500 original size:38 final size:38
Alignment explanation
Indices: 28949414--28949509 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
28949404 CGCAGGCTTC
** * * * *
28949414 GTGCTGGTAAAATATCCGGGTTAAATCCCGCAGGCTTC
1 GTGCTGGTATTATATCCGGGATAAATCCCACAGGCCTA
* *
28949452 GTGCTAGTATTATATCCGGGATAAATCCTACAGGCCTA
1 GTGCTGGTATTATATCCGGGATAAATCCCACAGGCCTA
*
28949490 GTGCTGGTATTATATTCGGG
1 GTGCTGGTATTATATCCGGG
28949510 CCTTTGTGCC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (38 bp):
GTGCTGGTATTATATCCGGGATAAATCCCACAGGCCTA
Found at i:28949548 original size:43 final size:43
Alignment explanation
Indices: 28949502--28949742 Score: 383
Period size: 43 Copynumber: 5.6 Consensus size: 43
28949492 GCTGGTATTA
* * *
28949502 TATTCGGGCCTTTGTGCCTAGCAGGCTTCGTGTCGGTGATGTA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
** *
28949545 TATTCGGGCCTTCGTAACTAGCAGGCTTTGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
28949588 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * *
28949631 TATTTGGGCCTTCGTGCCTAGCAAGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
28949674 TATTCGAGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28949717 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
28949743 GTAATGCCAG
Statistics
Matches: 181, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 181 1.00
ACGTcount: A:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:28954209 original size:26 final size:26
Alignment explanation
Indices: 28954179--28954286 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
28954169 TGAAATTCCC
28954179 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28954205 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28954231 ATCATGAAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28954257 ATCATGGAACATTTACCTAACACATT
1 ATCATGGAACATTTACCTAACCCATT
28954283 ATCA
1 ATCA
28954287 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28957103 original size:28 final size:28
Alignment explanation
Indices: 28957071--28957141 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
28957061 AGGGAAGTAT
**
28957071 GCCAAGGGCTATCTTAGGTGGAATGTCC
1 GCCAAGGGCTATCTTAGGTCAAATGTCC
* **
28957099 GCCAAAGGCTATCTTAGGTCAAATGTTT
1 GCCAAGGGCTATCTTAGGTCAAATGTCC
*
28957127 GCCAAGGACTATCTT
1 GCCAAGGGCTATCTT
28957142 GAAGACATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (28 bp):
GCCAAGGGCTATCTTAGGTCAAATGTCC
Found at i:28968724 original size:25 final size:25
Alignment explanation
Indices: 28968696--28968747 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28968686 CCGACACTAG
28968696 ATCAATACTAAATTCAACTTCTCTA
1 ATCAATACTAAATTCAACTTCTCTA
28968721 ATCAATACTAAATTCAACTTCTCTA
1 ATCAATACTAAATTCAACTTCTCTA
28968746 AT
1 AT
28968748 AGGAGGCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (25 bp):
ATCAATACTAAATTCAACTTCTCTA
Found at i:28975168 original size:10 final size:10
Alignment explanation
Indices: 28975142--28975174 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
28975132 TAAAGCAGGC
*
28975142 AAAGAACAAA
1 AAAGAAAAAA
28975152 AAA-AAAAAA
1 AAAGAAAAAA
28975161 AAAGAAAAAA
1 AAAGAAAAAA
28975171 AAAG
1 AAAG
28975175 GGCAAATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:28977410 original size:18 final size:19
Alignment explanation
Indices: 28977382--28977418 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
28977372 ATTAAATTAA
28977382 TTGATTGAATCGATCTAAT
1 TTGATTGAATCGATCTAAT
28977401 TTGATT-AATCGATCTAAT
1 TTGATTGAATCGATCTAAT
28977419 CAATCGGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (19 bp):
TTGATTGAATCGATCTAAT
Found at i:28979505 original size:30 final size:30
Alignment explanation
Indices: 28979469--28979530 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
28979459 CTTAACAAGT
*
28979469 AAATGCCTCTAAGATAATAA-ACAAATTAAC
1 AAATGCCTCTAAAATAATAATA-AAATTAAC
*
28979499 AAATGCCTTTAAAATAATAATAAAATTAAC
1 AAATGCCTCTAAAATAATAATAAAATTAAC
28979529 AA
1 AA
28979531 GAAAATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAATAAAATTAAC
Found at i:28979580 original size:14 final size:14
Alignment explanation
Indices: 28979561--28979591 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28979551 ATCCAAAAAA
28979561 TAACAATAAAATAG
1 TAACAATAAAATAG
*
28979575 TAACAATATAATAG
1 TAACAATAAAATAG
28979589 TAA
1 TAA
28979592 AATGGTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (14 bp):
TAACAATAAAATAG
Found at i:28986821 original size:19 final size:20
Alignment explanation
Indices: 28986799--28986855 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
28986789 GAAAAGTTTA
28986799 TAAATAAATAATAATAATT-
1 TAAATAAATAATAATAATTG
*
28986818 TAAATATAATTA-AAT-ATTG
1 TAAATA-AATAATAATAATTG
*
28986837 TAAATAAATATTAATAATT
1 TAAATAAATAATAATAATT
28986856 ATCGAGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.19
19 18 0.58
20 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAATAAATAATAATAATTG
Found at i:28993693 original size:106 final size:106
Alignment explanation
Indices: 28993503--28993715 Score: 381
Period size: 106 Copynumber: 2.0 Consensus size: 106
28993493 AGCTTTCAAT
* *
28993503 AAAATGCTTTAAATTTTATAATTGTTCTATGGATAGTTTCTTCAGTTATCGACTGATAATTACAA
1 AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
* * *
28993568 GAGACCTTTATGCCGATCATGCATGTGTCTTGCATTAACCA
66 GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
28993609 AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
1 AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
28993674 GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
66 GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
28993715 A
1 A
28993716 CTTGATCTAC
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (106 bp):
AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
Found at i:29011467 original size:20 final size:20
Alignment explanation
Indices: 29011442--29011480 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29011432 TAAAGAACAC
29011442 GGGTGTGTCCCAATGCACAT
1 GGGTGTGTCCCAATGCACAT
29011462 GGGTGTGTCCCAATGCACA
1 GGGTGTGTCCCAATGCACA
29011481 CGGTCATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (20 bp):
GGGTGTGTCCCAATGCACAT
Found at i:29011490 original size:22 final size:20
Alignment explanation
Indices: 29011438--29011483 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
29011428 AGGGTAAAGA
*
29011438 ACACGGGTGTGTCCCAATGC
1 ACACGGATGTGTCCCAATGC
* *
29011458 ACATGGGTGTGTCCCAATGC
1 ACACGGATGTGTCCCAATGC
29011478 ACACGG
1 ACACGG
29011484 TCATGTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.30, T:0.20
Consensus pattern (20 bp):
ACACGGATGTGTCCCAATGC
Found at i:29014094 original size:23 final size:21
Alignment explanation
Indices: 29014067--29014109 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
29014057 TATTAATAAC
*
29014067 AATATTTAATAAATTTGAAAATG
1 AATATTT-ATAAAATT-AAAATG
29014090 AATATTTATAAAATTAAAAT
1 AATATTTATAAAATTAAAAT
29014110 ATGCGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AATATTTATAAAATTAAAATG
Found at i:29016014 original size:28 final size:28
Alignment explanation
Indices: 29015974--29016027 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
29015964 ACACAGAGAG
29015974 TAGAACACAGAAAACACTCAAGTTCAAC
1 TAGAACACAGAAAACACTCAAGTTCAAC
*
29016002 TAGAACATAGAAAACACTCAAGTTCA
1 TAGAACACAGAAAACACTCAAGTTCA
29016028 GCCATCAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (28 bp):
TAGAACACAGAAAACACTCAAGTTCAAC
Found at i:29017136 original size:161 final size:161
Alignment explanation
Indices: 29016870--29017463 Score: 1046
Period size: 161 Copynumber: 3.7 Consensus size: 161
29016860 ACGACCATCA
* * *
29016870 CAGTGTTGGTCAACTTAAAGAGCTCATCAAAGAAGCTATAAAAAGACCAATTTTAAAGTGTTGAT
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTAT-AAAAGACCAATTTGAAAGTATTGAT
* *
29016935 CCACTTTCATATACATACTCAAATCCATACACACAAATGATTGATCGTCCAATATACAAGTTGCC
65 CCACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCC
29017000 AAAGATCTTTAACCAACAATCAATGAAGTTTT
130 AAAGATCTTTAACCAACAATCAATGAAGTTTT
29017032 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
*
29017097 CACTTTCATATACATACTCAAATCCATACACACAAATGATTGATCGTCCAATGTACAAGTTGCCA
66 CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
29017162 AAGATCTTTAACCAACAATCAATGAAGTTTT
131 AAGATCTTTAACCAACAATCAATGAAGTTTT
*
29017193 CAGTCTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
*
29017258 CACTTTCATATACATACTCAAATCCATACACACGAAGGATTGATCGTCCAATGTACAAGTTGCCA
66 CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
29017323 AAGATCTTTAACCAACAATCAATGAAGTTTT
131 AAGATCTTTAACCAACAATCAATGAAGTTTT
* * * *
29017354 CAGTGTTGGTCAACTCAAAGGGATCATCAAAGAAGCTATAAAACACCAATTTGAAAGTGTTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
*
29017419 CACCTTT-ATATACATACTCAAAGCCATACACACAAAGGATTGATC
66 CA-CTTTCATATACATACTCAAATCCATACACACAAAGGATTGATC
29017464 ATCTGATAAA
Statistics
Matches: 417, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
161 375 0.90
162 42 0.10
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (161 bp):
CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
AAGATCTTTAACCAACAATCAATGAAGTTTT
Found at i:29019345 original size:32 final size:32
Alignment explanation
Indices: 29019283--29019346 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
29019273 TAATTAATAG
* * *
29019283 TTATAACTTTTGAACTACTTATAATTTTTTAA
1 TTATAACTATTAAACTACTTATAATATTTTAA
*
29019315 TTATAACTATTAAATTA-TTATAAATATTTTAA
1 TTATAACTATTAAACTACTTAT-AATATTTTAA
29019347 AAATTTTACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (32 bp):
TTATAACTATTAAACTACTTATAATATTTTAA
Found at i:29021846 original size:33 final size:35
Alignment explanation
Indices: 29021751--29021847 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
29021741 TTAATATTTT
*
29021751 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
29021786 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
29021819 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
29021848 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:29024309 original size:6 final size:6
Alignment explanation
Indices: 29024298--29024334 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
29024288 AAAATTTATA
* *
29024298 AATGTC AATGTC AAGGTC AATGTC AATATC AATGTC A
1 AATGTC AATGTC AATGTC AATGTC AATGTC AATGTC A
29024335 TAAATGATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (6 bp):
AATGTC
Found at i:29027914 original size:39 final size:39
Alignment explanation
Indices: 29027871--29028023 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
29027861 CTGGACATAT
* *
29027871 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGTTATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
29027910 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
* *
29027949 TTCCAACACGTAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
* *
29027988 TTCCAGCACGTAGCCTGTGGACCCTAAGTCCGGATA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATA
29028024 AACATCGCTG
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 108 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:29027916 original size:78 final size:78
Alignment explanation
Indices: 29027823--29028021 Score: 228
Period size: 78 Copynumber: 2.6 Consensus size: 78
29027813 AAATTTAAAC
* * * * * *
29027823 CCGGTATAATACCAGCTCGAAGCCTGTGGGA-CTTTAG-CCTGGACATATTTCCAGCACATAGCC
1 CCGGTATAATTCCAGCACGAAGCCTGTGGGACCCTAAGTCC-GGACATAATTCCAACACATAGCC
*
29027886 TGCGGACCTTAAGT
65 TGCGGACCCTAAGT
* * *
29027900 CCGGTTATAATTCCAGCAC-ATAGCCTG-CGGACCCTAAGTCCGGATATAATTCCAACACGTAGC
1 CCGG-TATAATTCCAGCACGA-AGCCTGTGGGACCCTAAGTCCGGACATAATTCCAACACATAGC
29027963 CTGCGGACCCTAAGT
64 CTGCGGACCCTAAGT
*
29027978 CCGGATATAATTCCAGCACGTAGCCTGT-GGACCCTAAGTCCGGA
1 CCGG-TATAATTCCAGCACGAAGCCTGTGGGACCCTAAGTCCGGA
29028022 TAAACATCGC
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
77 8 0.08
78 94 0.90
79 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (78 bp):
CCGGTATAATTCCAGCACGAAGCCTGTGGGACCCTAAGTCCGGACATAATTCCAACACATAGCCT
GCGGACCCTAAGT
Found at i:29035636 original size:39 final size:39
Alignment explanation
Indices: 29035545--29035745 Score: 244
Period size: 39 Copynumber: 5.2 Consensus size: 39
29035535 AAATTTAAAC
* * * * *
29035545 CCGG-TATAATACCAGCTCGAAGCTTGCAGGA-CTTTAGC
1 CCGGATATAATTCCAGCACGTAGCTTGC-GGACCTTAAGT
* *
29035583 CCGGACATATTTCCAGCACGTAGCTTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
* * * *
29035622 CCGGTTATAATTCCAGCACATAGCCTGCTGACCTTAAGT
1 CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
*
29035661 CCGGATATAATTCCAGCACGTAGCTTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
* *
29035700 CCGGATATAATTCCAGCACGTAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
*
29035739 CCAGATA
1 CCGGATA
29035746 AACATCGCTG
Statistics
Matches: 141, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
38 7 0.05
39 134 0.95
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
Found at i:29053498 original size:17 final size:18
Alignment explanation
Indices: 29053466--29053501 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
29053456 TTGGGCCAGG
*
29053466 ATGGGCCATGTGGGCCCA
1 ATGGGCCATATGGGCCCA
29053484 ATGGGCC-TATGGGCCCA
1 ATGGGCCATATGGGCCCA
29053501 A
1 A
29053502 GTGGATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.17
Consensus pattern (18 bp):
ATGGGCCATATGGGCCCA
Found at i:29053684 original size:27 final size:26
Alignment explanation
Indices: 29053635--29053733 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 26
29053625 TTTGGTTTAC
29053635 AAAATTACTG-AATA-CCCTCAATTAGT
1 AAAATTACTGAAATACCCCT-AATT-GT
* *
29053661 AAAATTACCGAAATACCCCTAATTTTT
1 AAAATTACTGAAATACCCCTAA-TTGT
* * *
29053688 GAAATTACTGAAATACCCTCGACTTGT
1 AAAATTACTGAAATACCC-CTAATTGT
29053715 AAAATTA-TAGAAATACCCC
1 AAAATTACT-GAAATACCCC
29053734 AAATACCCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
26 11 0.18
27 41 0.68
28 8 0.13
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (26 bp):
AAAATTACTGAAATACCCCTAATTGT
Found at i:29053738 original size:36 final size:36
Alignment explanation
Indices: 29053698--29053768 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
29053688 GAAATTACTG
*
29053698 AAATACCCTCGACTTGTAAAATTA-TAGAAATACCCC
1 AAATACCCTCGACTTGAAAAATTACT-GAAATACCCC
* *
29053734 AAATACCCTTGATTTGAAAAATTACTGAAATACCC
1 AAATACCCTCGACTTGAAAAATTACTGAAATACCC
29053769 TTGATTTGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (36 bp):
AAATACCCTCGACTTGAAAAATTACTGAAATACCCC
Done.