Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold174
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: 2085601
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 12 of 15
Found at i:1379897 original size:27 final size:26
Alignment explanation
Indices: 1379815--1379908 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 26
1379805 TTAAATTCGT
* * *
1379815 ATATTTATATTATTTTTTATATATTT
1 ATATTTATATAATTTTTTATAAATTA
* *
1379841 TTATTTATTATATTTATGTTTA-AGATATTAA
1 ATATTTA-TATAATT-T-TTTATA-A-ATT-A
1379872 ATATTTATATAATTTTTTATAAATTA
1 ATATTTATATAATTTTTTATAAATTA
1379898 ATAATTTATAT
1 AT-ATTTATAT
1379909 TATATAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
26 9 0.17
27 16 0.30
28 7 0.13
29 6 0.11
30 9 0.17
31 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
ATATTTATATAATTTTTTATAAATTA
Found at i:1379914 original size:22 final size:24
Alignment explanation
Indices: 1379889--1379933 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1379879 TATAATTTTT
1379889 TATAAA-TTAATA-ATTTATATTA
1 TATAAATTTAATATATTTATATTA
1379911 TATAAATTTTAATATATTTATAT
1 TATAAA-TTTAATATATTTATAT
1379934 ATTCGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TATAAATTTAATATATTTATATTA
Found at i:1379951 original size:25 final size:24
Alignment explanation
Indices: 1379923--1379983 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
1379913 TAAATTTTAA
1379923 TATATTTATATATTCGTATTAT-TTT
1 TATATTTAT-T-TTCGTATTATATTT
*
1379948 TATA-TTATTTTTGTATTATATTT
1 TATATTTATTTTCGTATTATATTT
1379971 TATATCTTATTTT
1 TATAT-TTATTTT
1379984 AATTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 9 0.28
23 8 0.25
24 4 0.12
25 11 0.34
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (24 bp):
TATATTTATTTTCGTATTATATTT
Found at i:1379955 original size:11 final size:11
Alignment explanation
Indices: 1379939--1379975 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1379929 TATATATTCG
1379939 TATTATTTTTA
1 TATTATTTTTA
*
1379950 TATTATTTTTG
1 TATTATTTTTA
1379961 TATTATATTTTA
1 TATTAT-TTTTA
1379973 TAT
1 TAT
1379976 CTTATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:1380106 original size:6 final size:6
Alignment explanation
Indices: 1380095--1380149 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
1380085 AATATCCGTG
* * * * *
1380095 TATTTA TATTTA TATTTT TTTTTA TAATTA TGTTTA -AATTA T-TTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1380141 TATTTA TAT
1 TATTTA TAT
1380150 AAATATTGAC
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
5 7 0.19
6 30 0.81
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:1380195 original size:16 final size:16
Alignment explanation
Indices: 1380149--1380195 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1380139 TATATTTATA
1380149 TAAATATTGACACATT
1 TAAATATTGACACATT
* **
1380165 AATAAT-TTGTGACATT
1 TA-AATATTGACACATT
1380181 TAAATATTGACACAT
1 TAAATATTGACACAT
1380196 ATTTGAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
15 3 0.13
16 17 0.74
17 3 0.13
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (16 bp):
TAAATATTGACACATT
Found at i:1380686 original size:2 final size:2
Alignment explanation
Indices: 1380681--1380716 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1380671 TGTGTGTGTG
1380681 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
1380717 ATCAATCGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1383899 original size:25 final size:22
Alignment explanation
Indices: 1383871--1383940 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 22
1383861 TTTATCGATT
1383871 TAATAATATTAAAATATTATTTTTA
1 TAATAATATT--AATA-TATTTTTA
*
1383896 TAATAATATTTATATATTTTTA
1 TAATAATATTAATATATTTTTA
* *
1383918 TAATTAAATTTTAATAAATTTTT
1 TAA-T-AATATTAATATATTTTT
1383941 TTATTTATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
22 11 0.28
23 4 0.10
24 14 0.36
25 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TAATAATATTAATATATTTTTA
Found at i:1385508 original size:16 final size:18
Alignment explanation
Indices: 1385481--1385514 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1385471 TTCATAATAC
1385481 ATATATATATTAT-TTTT
1 ATATATATATTATATTTT
1385498 ATATA-ATATTATATTTT
1 ATATATATATTATATTTT
1385515 TATTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATATATATTATATTTT
Found at i:1387852 original size:18 final size:18
Alignment explanation
Indices: 1387829--1387866 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1387819 TCAGTGATTG
1387829 CAGATGGATTTGAGCTAT
1 CAGATGGATTTGAGCTAT
1387847 CAGATGGATTTGAGCTAT
1 CAGATGGATTTGAGCTAT
1387865 CA
1 CA
1387867 CCTTTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (18 bp):
CAGATGGATTTGAGCTAT
Found at i:1391118 original size:22 final size:24
Alignment explanation
Indices: 1391093--1391136 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1391083 AATTAATTTT
*
1391093 ATATTTAAAT-TTAAT-TATAAAA
1 ATATGTAAATATTAATATATAAAA
1391115 ATATGTAAATATTAATATATAA
1 ATATGTAAATATTAATATATAA
1391137 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATGTAAATATTAATATATAAAA
Found at i:1391996 original size:78 final size:79
Alignment explanation
Indices: 1391893--1392045 Score: 218
Period size: 78 Copynumber: 1.9 Consensus size: 79
1391883 GGCTCATCCA
* * * * *
1391893 CTGCACCACCAGCACCTCCTTTAACTTCCTTCACTGTCTTCTTTCCTTCCATAAAC-TTGGTTTC
1 CTGCACCACCACCACCACCTTTAACTTCCATCACCGTCGTCTTTCCTTCCATAAACTTTGGTTTC
1391957 ACCGGTTTCTTTGT
66 ACCGGTTTCTTTGT
* *
1391971 CTGCACCACCACCACCACCTTTAACTTTCATCGCCGTCGTCTTTCCTTCCATAAACTTGTTGGTT
1 CTGCACCACCACCACCACCTTTAACTTCCATCACCGTCGTCTTTCCTTCCATAAAC-T-TTGGTT
1392036 TCACCGGTTT
64 TCACCGGTTT
1392046 TCTTGTTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
78 49 0.75
81 16 0.25
ACGTcount: A:0.16, C:0.35, G:0.11, T:0.37
Consensus pattern (79 bp):
CTGCACCACCACCACCACCTTTAACTTCCATCACCGTCGTCTTTCCTTCCATAAACTTTGGTTTC
ACCGGTTTCTTTGT
Found at i:1393034 original size:8 final size:8
Alignment explanation
Indices: 1393006--1393057 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
1392996 TCAAATTTTT
1393006 TAAAGTATA
1 TAAA-TATA
*
1393015 TAATAAATA
1 TAA-ATATA
1393024 TAAATATA
1 TAAATATA
*
1393032 TAAATATTT
1 TAAATA-TA
*
1393041 TAAATGTA
1 TAAATATA
1393049 TAAATATA
1 TAAATATA
1393057 T
1 T
1393058 TTTATGTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 19 0.54
9 15 0.43
10 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (8 bp):
TAAATATA
Found at i:1393038 original size:23 final size:24
Alignment explanation
Indices: 1393012--1393057 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
1393002 TTTTTAAAGT
1393012 ATATAATAAA-TATAAATATATAA
1 ATATAATAAAGTATAAATATATAA
**
1393035 ATATTTTAAATGTATAAATATAT
1 ATATAATAAA-GTATAAATATAT
1393058 TTTATGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
25 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
ATATAATAAAGTATAAATATATAA
Found at i:1393488 original size:20 final size:20
Alignment explanation
Indices: 1393450--1393488 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1393440 AATTTTAATT
* *
1393450 ATTATTTATAAGTATATTTA
1 ATTATTTATAAATAAATTTA
1393470 ATTATTTATAAATAAATTT
1 ATTATTTATAAATAAATTT
1393489 TATAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTATTTATAAATAAATTTA
Found at i:1393716 original size:17 final size:17
Alignment explanation
Indices: 1393696--1393729 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1393686 AAATTAATTT
1393696 AAATAATAAATAATTAA
1 AAATAATAAATAATTAA
* *
1393713 AAATATTTAATAATTAA
1 AAATAATAAATAATTAA
1393730 TTAAAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATAATAAATAATTAA
Found at i:1393723 original size:21 final size:22
Alignment explanation
Indices: 1393699--1393742 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1393689 TTAATTTAAA
1393699 TAATAAATAATTAAAA-ATATT
1 TAATAAATAATTAAAATATATT
*
1393720 TAATAATTAATTAAAATATATT
1 TAATAAATAATTAAAATATATT
1393742 T
1 T
1393743 TATTTAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAAATAATTAAAATATATT
Found at i:1394135 original size:27 final size:27
Alignment explanation
Indices: 1394072--1394153 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 27
1394062 TTTTAAAATA
*
1394072 AATTTTTAATTTATATTTAGTTAAAACTTT
1 AATTTTTAATTTATATTTA---AAAATTTT
1394102 -ATCTTTTAATTTATATTTAAAAATTTT
1 AAT-TTTTAATTTATATTTAAAAATTTT
*
1394129 AATTTTTAATATATA-TTAAATAATT
1 AATTTTTAATTTATATTTAAA-AATT
1394154 ATCGATATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
26 5 0.11
27 22 0.47
28 2 0.04
29 2 0.04
30 16 0.34
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (27 bp):
AATTTTTAATTTATATTTAAAAATTTT
Found at i:1394230 original size:23 final size:22
Alignment explanation
Indices: 1394177--1394237 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1394167 AATATTTCAT
1394177 TTAAAAT-AAAAATTTATTTAA
1 TTAAAATAAAAAATTTATTTAA
* *
1394198 ATATAATAAAAAATTTATTTAA
1 TTAAAATAAAAAATTTATTTAA
*
1394220 TTAAAATTAAATAATTTA
1 TTAAAA-TAAAAAATTTA
1394238 GAGATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 5 0.15
22 18 0.55
23 10 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAATAAAAAATTTATTTAA
Found at i:1394710 original size:26 final size:26
Alignment explanation
Indices: 1394681--1394731 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1394671 AGTGATATTA
* *
1394681 ATATT-ATATTTATTTAATTTATATAC
1 ATATTAATATATA-TTAATTAATATAC
1394707 ATATTAATATATATTAATTAATATA
1 ATATTAATATATATTAATTAATATA
1394732 AAATTTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
ATATTAATATATATTAATTAATATAC
Found at i:1395689 original size:29 final size:29
Alignment explanation
Indices: 1395648--1395743 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
1395638 AAGTAAGAAT
*
1395648 TTATTTAAATATAAATTAAAGTTTATAAC
1 TTATTTATATATAAATTAAAGTTTATAAC
* * *
1395677 TTATTTATCTATAAATTAAATTTTCAAAAC
1 TTATTTATATATAAATTAAAGTTT-ATAAC
* * * * *
1395707 TTATTTTTGTATAAACTTAAAGCTAATGAC
1 TTATTTATATATAAA-TTAAAGTTTATAAC
1395737 TTATTTA
1 TTATTTA
1395744 GATGCAAATT
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 21 0.40
30 26 0.49
31 6 0.11
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (29 bp):
TTATTTATATATAAATTAAAGTTTATAAC
Found at i:1395710 original size:30 final size:29
Alignment explanation
Indices: 1395648--1395728 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
1395638 AAGTAAGAAT
* *
1395648 TTATTTAAATATAAATTAAAGTTTATAAC
1 TTATTTATATATAAATTAAAGTTTAAAAC
* *
1395677 TTATTTATCTATAAATTAAATTTTCAAAAC
1 TTATTTATATATAAATTAAAGTTT-AAAAC
* *
1395707 TTATTTTTGTATAAACTTAAAG
1 TTATTTATATATAAA-TTAAAG
1395729 CTAATGACTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.49
30 17 0.40
31 5 0.12
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (29 bp):
TTATTTATATATAAATTAAAGTTTAAAAC
Found at i:1402056 original size:19 final size:19
Alignment explanation
Indices: 1402034--1402098 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1402024 TTATTATAAA
*
1402034 ATTAAATATTAATTTAATT
1 ATTAAATATTAATTTATTT
* *
1402053 ATTATATTTTAATTTATTT
1 ATTAAATATTAATTTATTT
* * *
1402072 TTTTAATATTTAATTTTTTT
1 ATTAAATA-TTAATTTATTT
1402092 ATTAAAT
1 ATTAAAT
1402099 TAAGTTTTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTAAATATTAATTTATTT
Found at i:1403603 original size:12 final size:12
Alignment explanation
Indices: 1403586--1403619 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1403576 TTGACTTGTG
*
1403586 TTTCTTTTTCTT
1 TTTCTTCTTCTT
1403598 TTTCTTCTTCTT
1 TTTCTTCTTCTT
*
1403610 CTTCTTCTTC
1 TTTCTTCTTC
1403620 AATGGCGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTCTTCTTCTT
Found at i:1411155 original size:21 final size:22
Alignment explanation
Indices: 1411103--1411155 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1411093 AAAATATTTT
1411103 TATTTAAATTTAATTATAAAATA
1 TATTTAAA-TTAATTATAAAATA
**
1411126 TATAAAAATTAATT-TAAAATA
1 TATTTAAATTAATTATAAAATA
*
1411147 TTTTTAAAT
1 TATTTAAAT
1411156 ATTTTTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 13 0.52
22 6 0.24
23 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTTAAATTAATTATAAAATA
Found at i:1411157 original size:10 final size:10
Alignment explanation
Indices: 1411142--1411166 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1411132 AATTAATTTA
1411142 AAATATTTTT
1 AAATATTTTT
1411152 AAATATTTTT
1 AAATATTTTT
1411162 AAATA
1 AAATA
1411167 ATAATTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AAATATTTTT
Found at i:1418473 original size:30 final size:29
Alignment explanation
Indices: 1418433--1418490 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
1418423 TGGAGTTGGT
* *
1418433 ATGATTTAATTTATTAATAATAAAAATTTA
1 ATGATATAATTTAATAA-AATAAAAATTTA
*
1418463 ATGATATAATTTAATAAAATTAAAATTT
1 ATGATATAATTTAATAAAATAAAAATTT
1418491 TTTTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
ATGATATAATTTAATAAAATAAAAATTTA
Found at i:1418993 original size:24 final size:24
Alignment explanation
Indices: 1418948--1418995 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1418938 TTATTATATT
** *
1418948 AAATAAATATTATTTTTTATTAAA
1 AAATAAATATTATTGATAATTAAA
*
1418972 AAATTAATATTATTGATAATTAAA
1 AAATAAATATTATTGATAATTAAA
1418996 TTTAGATGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AAATAAATATTATTGATAATTAAA
Found at i:1419037 original size:15 final size:15
Alignment explanation
Indices: 1419017--1419059 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1419007 ATAAATTTTA
1419017 TTAAA-TAAATATAAT
1 TTAAATTAAAT-TAAT
1419032 TTAAATTAAATTAAT
1 TTAAATTAAATTAAT
*
1419047 TTAATTTAAATTA
1 TTAAATTAAATTA
1419060 TATAAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATTAAATTAAT
Found at i:1419039 original size:20 final size:20
Alignment explanation
Indices: 1419016--1419075 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
1419006 AATAAATTTT
1419016 ATTAAATAAATATAATTTAA
1 ATTAAATAAATATAATTTAA
* *
1419036 ATTAAATTAATTTAATTTAA
1 ATTAAATAAATATAATTTAA
* *
1419056 ATTATATAAATCTAATTTAA
1 ATTAAATAAATATAATTTAA
1419076 TATGGATGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAATAAATATAATTTAA
Found at i:1421636 original size:123 final size:124
Alignment explanation
Indices: 1421414--1421661 Score: 401
Period size: 123 Copynumber: 2.0 Consensus size: 124
1421404 GAAACTCGAT
*
1421414 ATGCCTCCATAAGGCGAGAAACCGACTTCGGAATAGAGGACATATATAAAGTTTACCCTCACAGT
1 ATGCCTCCATAAGGCGAGAAACCGACTTCGGAAAAGAGGACATATATAAAGTTTACCCTCACAGT
*
1421479 CATGGATCCCCATCAAGTTCTACCTAGTTTCAGTACAATGTCTAGATATTGTTCGATTA
66 CATGGATCCCCATCAAGTTCTACCTAGCTTCAGTACAATGTCTAGATATTGTTCGATTA
* * *
1421538 ATGCCTCGATAAGG-GAAGAAACCGACTTTGGAAAAGAGGACATATATAAAG-TTGCCCTCACAG
1 ATGCCTCCATAAGGCG-AGAAACCGACTTCGGAAAAGAGGACATATATAAAGTTTACCCTCACAG
* * *
1421601 TCATGGATCCCCATCAAGTTCTACCTAGCTTCAGTATAATGTCTAGATTTTGTTTGATTA
65 TCATGGATCCCCATCAAGTTCTACCTAGCTTCAGTACAATGTCTAGATATTGTTCGATTA
1421661 A
1 A
1421662 AGGTATATAC
Statistics
Matches: 115, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
123 69 0.60
124 46 0.40
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (124 bp):
ATGCCTCCATAAGGCGAGAAACCGACTTCGGAAAAGAGGACATATATAAAGTTTACCCTCACAGT
CATGGATCCCCATCAAGTTCTACCTAGCTTCAGTACAATGTCTAGATATTGTTCGATTA
Found at i:1425408 original size:3 final size:3
Alignment explanation
Indices: 1425402--1425438 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
1425392 TTTATAATAA
*
1425402 ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
1425439 TAAGCTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1425424 original size:19 final size:19
Alignment explanation
Indices: 1425402--1425440 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1425392 TTTATAATAA
1425402 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATTT
*
1425421 ATTATTATTATTTTTATTT
1 ATTATTATTATTATTATTT
1425440 A
1 A
1425441 AGCTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTATTATTATTATTATTT
Found at i:1425526 original size:12 final size:12
Alignment explanation
Indices: 1425509--1425551 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
1425499 ATAAAATTAT
1425509 TAAAAACTTAAAA
1 TAAAAA-TTAAAA
*
1425522 TAAAATTTAAAA
1 TAAAAATTAAAA
*
1425534 TAATAAAATAAAA
1 TAA-AAATTAAAA
1425547 TAAAA
1 TAAAA
1425552 TAAAAGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAAAATTAAAA
Found at i:1425531 original size:20 final size:21
Alignment explanation
Indices: 1425498--1425548 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
1425488 ATATTAATTT
*
1425498 AATAAAATTATTAAAA-ACTTAA
1 AATAAAA-TATTAAAATA-ATAA
1425520 AATAAAAT-TTAAAATAATAA
1 AATAAAATATTAAAATAATAA
1425540 AATAAAATA
1 AATAAAATA
1425549 AAATAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.65
21 2 0.08
22 7 0.27
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAAAATATTAAAATAATAA
Found at i:1425553 original size:15 final size:16
Alignment explanation
Indices: 1425517--1425556 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1425507 ATTAAAAACT
1425517 TAAAATAAAATTTAAAA
1 TAAAATAAAA-TTAAAA
1425534 T--AATAAAA-TAAAA
1 TAAAATAAAATTAAAA
1425547 TAAAATAAAA
1 TAAAATAAAA
1425557 GATATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 6 0.29
15 14 0.67
17 1 0.05
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAATAAAATTAAAA
Found at i:1425810 original size:22 final size:25
Alignment explanation
Indices: 1425785--1425830 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1425775 AAAAAATCTT
1425785 TTAAAT-AAT-CA-TATTAATAAAG
1 TTAAATAAATCCATTATTAATAAAG
*
1425807 TTAATTAAATCCATTATTAATAAA
1 TTAAATAAATCCATTATTAATAAA
1425831 TAAATTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 3 0.15
24 2 0.10
25 10 0.50
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (25 bp):
TTAAATAAATCCATTATTAATAAAG
Found at i:1426474 original size:23 final size:23
Alignment explanation
Indices: 1426443--1426510 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
1426433 AAATTTTAAA
*
1426443 ATATATATTTATATCATATCATAT
1 ATATATATTTATATAAT-TCATAT
*
1426467 -TATATATTT-TATAATTTATAT
1 ATATATATTTATATAATTCATAT
1426488 ATATTATATTTATATAATT-ATAT
1 ATA-TATATTTATATAATTCATAT
1426511 TTAAAATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 5 0.13
22 7 0.18
23 20 0.51
24 7 0.18
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATATATTTATATAATTCATAT
Found at i:1426520 original size:12 final size:14
Alignment explanation
Indices: 1426362--1426513 Score: 93
Period size: 15 Copynumber: 10.6 Consensus size: 14
1426352 ATAATTTGTA
*
1426362 TATATATATATATAT
1 TATATTTATATA-AT
1426377 TATATTTATAT-AT
1 TATATTTATATAAT
* *
1426390 TTTATCGTATCATAAT
1 TATAT-TTAT-ATAAT
* *
1426406 TATATTTAAAATATTT
1 TATATTT-ATATA-AT
1426422 TATATTTATATAA-
1 TATATTTATATAAT
1426435 -AT-TTTA-A-AAT
1 TATATTTATATAAT
*
1426445 ATATATTTATATCA-
1 -TATATTTATATAAT
*
1426459 TATCATATTATATATTT
1 TAT-AT-TTATATA-AT
1426476 TATAATTTATATATAT
1 TAT-ATTTATATA-AT
1426492 TATATTTATATAAT
1 TATATTTATATAAT
1426506 TATATTTA
1 TATATTTA
1426514 AAATTATTAA
Statistics
Matches: 108, Mismatches: 14, Indels: 31
0.71 0.09 0.20
Matches are distributed among these distances:
9 2 0.02
10 1 0.01
11 4 0.04
12 4 0.04
13 13 0.12
14 16 0.15
15 36 0.33
16 27 0.25
17 5 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (14 bp):
TATATTTATATAAT
Found at i:1427256 original size:3 final size:3
Alignment explanation
Indices: 1427235--1427281 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
1427225 CCATCCTCCT
* *
1427235 TTC TTT TTC TTC CTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1427282 ATTATTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1427286 original size:3 final size:3
Alignment explanation
Indices: 1427280--1427311 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1427270 CTTCTTCTTC
1427280 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1427312 GAGAAATATA
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:1428158 original size:21 final size:22
Alignment explanation
Indices: 1428132--1428228 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 22
1428122 TTATTCGATC
1428132 TTTTATATTCATAT-TTCATAT
1 TTTTATATTCATATATTCATAT
* *
1428153 TTTTAT-TTGATTATATGTTAGTAT
1 TTTTATATTCA-TATAT-TCA-TAT
1428177 AATTTTATA-TCTATATTATTCGAT-T
1 --TTTTATATTC-ATA-TATTC-ATAT
*
1428202 TTTTATATTCATAT-TTTATAT
1 TTTTATATTCATATATTCATAT
1428223 TTTTAT
1 TTTTAT
1428229 TCGATTATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 24
0.67 0.06 0.27
Matches are distributed among these distances:
20 5 0.08
21 18 0.31
22 2 0.03
23 12 0.20
24 5 0.08
25 1 0.02
26 11 0.19
27 5 0.08
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTTATATTCATATATTCATAT
Found at i:1428185 original size:70 final size:70
Alignment explanation
Indices: 1428105--1428241 Score: 229
Period size: 70 Copynumber: 2.0 Consensus size: 70
1428095 AAATTGAAAG
* *
1428105 ATAATCTTATATCTATGTTATTCGATCTTTTATATTCATATTTCATATTTTTATTTGATTATATG
1 ATAATCTTATATCTATATTATTCGATCTTTTATATTCATATTTCATATTTTTATTCGATTATATG
1428170 TTAGT
66 TTAGT
* * *
1428175 ATAATTTTATATCTATATTATTCGATTTTTTATATTCATATTTTATATTTTTATTCGATTATATG
1 ATAATCTTATATCTATATTATTCGATCTTTTATATTCATATTTCATATTTTTATTCGATTATATG
1428240 TT
66 TT
1428242 CAATATGAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.28, C:0.07, G:0.06, T:0.59
Consensus pattern (70 bp):
ATAATCTTATATCTATATTATTCGATCTTTTATATTCATATTTCATATTTTTATTCGATTATATG
TTAGT
Found at i:1429130 original size:2 final size:2
Alignment explanation
Indices: 1429123--1429161 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1429113 CTCCATCACA
1429123 AT AT 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 AT AT A
1429162 AAACTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1431291 original size:21 final size:21
Alignment explanation
Indices: 1431267--1431308 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1431257 AGGTTTGATA
*
1431267 GATTTAATTTAAATATAATTT
1 GATTTAAATTAAATATAATTT
* *
1431288 GATTTAAATTAATTTTAATTT
1 GATTTAAATTAAATATAATTT
1431309 TAAAATATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
GATTTAAATTAAATATAATTT
Found at i:1431292 original size:16 final size:15
Alignment explanation
Indices: 1431268--1431308 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
1431258 GGTTTGATAG
1431268 ATTTAATTTAAATATA
1 ATTTAATTTAAAT-TA
*
1431284 ATTTGATTTAAATTA
1 ATTTAATTTAAATTA
1431299 ATTTTAATTT
1 A-TTTAATTT
1431309 TAAAATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTTAATTTAAATTA
Found at i:1431643 original size:30 final size:30
Alignment explanation
Indices: 1431607--1431663 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1431597 GTTAAAATAA
*
1431607 AATAAAAT-AATTATAATAATAATTTAATTT
1 AATAAAATAAAATATAATAA-AATTTAATTT
*
1431637 AATAAAATAAAATATTATAAAATTTAA
1 AATAAAATAAAATATAATAAAATTTAA
1431664 ATCATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
AATAAAATAAAATATAATAAAATTTAATTT
Found at i:1435821 original size:29 final size:29
Alignment explanation
Indices: 1435779--1435840 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1435769 CATAATTAGG
1435779 CTATTCAGACTAGGAAAATACATTGAACT
1 CTATTCAGACTAGGAAAATACATTGAACT
1435808 CTATTCAGACTAGGAAAATACATTGAACT
1 CTATTCAGACTAGGAAAATACATTGAACT
1435837 CTAT
1 CTAT
1435841 GGAGCTGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (29 bp):
CTATTCAGACTAGGAAAATACATTGAACT
Found at i:1443978 original size:2 final size:2
Alignment explanation
Indices: 1443971--1444013 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1443961 GCTCGGTTTC
1443971 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1444013 G
1 G
1444014 GAATATTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1448877 original size:29 final size:29
Alignment explanation
Indices: 1448818--1448881 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1448808 ATTTTTTAAG
*
1448818 ATAATTATTTTATATATAAATAATAAAAA
1 ATAAATATTTTATATATAAATAATAAAAA
* * *
1448847 ATTAAATATTTT-TATATTAATAATTATAA
1 A-TAAATATTTTATATATAAATAATAAAAA
1448876 ATAAAT
1 ATAAAT
1448882 TTAAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 5 0.17
29 16 0.53
30 9 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
ATAAATATTTTATATATAAATAATAAAAA
Found at i:1453618 original size:14 final size:14
Alignment explanation
Indices: 1453599--1453626 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1453589 GAGATCTGTG
1453599 TATAAATTTAGAGC
1 TATAAATTTAGAGC
1453613 TATAAATTTAGAGC
1 TATAAATTTAGAGC
1453627 CGGTGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
TATAAATTTAGAGC
Found at i:1455208 original size:2 final size:2
Alignment explanation
Indices: 1455201--1455227 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1455191 AGATTGACAC
1455201 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1455228 CCCCTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1455750 original size:19 final size:19
Alignment explanation
Indices: 1455722--1455763 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1455712 AATGATTTGA
1455722 AAAAAAAAAAATA-AGAATT
1 AAAAAAAAAAATAGA-AATT
*
1455741 AAAAATAAAAATAGAAATT
1 AAAAAAAAAAATAGAAATT
1455760 AAAA
1 AAAA
1455764 GATTACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAAAAAAAAATAGAAATT
Found at i:1463453 original size:30 final size:30
Alignment explanation
Indices: 1463417--1463491 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
1463407 GCTATGCATC
1463417 GCCACAGTATTATCCACAATCACAACAAGA
1 GCCACAGTATTATCCACAATCACAACAAGA
* *
1463447 GCCACAGTATTATCCACAGTCACAACCAGA
1 GCCACAGTATTATCCACAATCACAACAAGA
*
1463477 GCCACAGTATCATCC
1 GCCACAGTATTATCC
1463492 TTCTTCACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.17
Consensus pattern (30 bp):
GCCACAGTATTATCCACAATCACAACAAGA
Found at i:1463500 original size:30 final size:30
Alignment explanation
Indices: 1463417--1463512 Score: 122
Period size: 30 Copynumber: 3.2 Consensus size: 30
1463407 GCTATGCATC
* * *
1463417 GCCACAGTATTATCCACAATCACAACAAGA
1 GCCACAGTATCATCCACAGTCACAACCAGA
*
1463447 GCCACAGTATTATCCACAGTCACAACCAGA
1 GCCACAGTATCATCCACAGTCACAACCAGA
* *
1463477 GCCACAGTATCATCCTTC-TTCACAACCAGA
1 GCCACAGTATCATCC-ACAGTCACAACCAGA
1463507 GCCACA
1 GCCACA
1463513 CAGCAGCGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 59 0.98
31 1 0.02
ACGTcount: A:0.36, C:0.34, G:0.11, T:0.18
Consensus pattern (30 bp):
GCCACAGTATCATCCACAGTCACAACCAGA
Found at i:1466624 original size:20 final size:20
Alignment explanation
Indices: 1466601--1466640 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1466591 GGGAAGAATG
*
1466601 TTTATTTTTGAAAGGATTCA
1 TTTATTCTTGAAAGGATTCA
1466621 TTTATTCTTGAAAGGATTCA
1 TTTATTCTTGAAAGGATTCA
1466641 ATTTCTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTATTCTTGAAAGGATTCA
Found at i:1466648 original size:18 final size:19
Alignment explanation
Indices: 1466603--1466651 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1466593 GAAGAATGTT
1466603 TATTT-TTGAAAGGATTCA
1 TATTTCTTGAAAGGATTCA
*
1466621 TTTATTCTTGAAAGGATTCA
1 TAT-TTCTTGAAAGGATTCA
1466641 -ATTTCTTGAAA
1 TATTTCTTGAAA
1466652 ATATTTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.41
19 3 0.11
20 13 0.48
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (19 bp):
TATTTCTTGAAAGGATTCA
Found at i:1471047 original size:41 final size:41
Alignment explanation
Indices: 1470997--1471078 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
1470987 CCCTCCAAGC
1470997 CATTTTTGTTCATACTTTTAAATGCCAGATTCTTCAAGCTA
1 CATTTTTGTTCATACTTTTAAATGCCAGATTCTTCAAGCTA
*
1471038 CATTTTTGTTCATACTTTTAAATGCCAGATTCTTCCAGCTA
1 CATTTTTGTTCATACTTTTAAATGCCAGATTCTTCAAGCTA
1471079 GGTCAAATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.44
Consensus pattern (41 bp):
CATTTTTGTTCATACTTTTAAATGCCAGATTCTTCAAGCTA
Found at i:1474865 original size:40 final size:40
Alignment explanation
Indices: 1474821--1474902 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1474811 TATAAATTTT
1474821 TTATTTTGATCACACAACAATTTTTGAGTTAAATCTATGA
1 TTATTTTGATCACACAACAATTTTTGAGTTAAATCTATGA
1474861 TTATTTTGATCACACAACAATTTTTGAGTTAAATCTATGA
1 TTATTTTGATCACACAACAATTTTTGAGTTAAATCTATGA
1474901 TT
1 TT
1474903 CTCTTACAAT
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:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (40 bp):
TTATTTTGATCACACAACAATTTTTGAGTTAAATCTATGA
Found at i:1475375 original size:2 final size:2
Alignment explanation
Indices: 1475368--1475394 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1475358 CAAACACTAC
1475368 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1475395 GTATGCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1479586 original size:26 final size:26
Alignment explanation
Indices: 1479542--1479596 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1479532 AATTAAAATT
* * *
1479542 TATTTTTATAGTAATATTTATATATA
1 TATTTTTATAATAATATTTAAATAAA
1479568 TATTTTTATAAATAA-ATTTAAATAAA
1 TATTTTTAT-AATAATATTTAAATAAA
1479594 TAT
1 TAT
1479597 AGTTATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTTTTATAATAATATTTAAATAAA
Found at i:1479624 original size:17 final size:16
Alignment explanation
Indices: 1479576--1479637 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
1479566 TATATTTTTA
1479576 TAAATA-AATTTAAA-
1 TAAATATAATTTAAAT
* *
1479590 TAAATATAGTTATTAAT
1 TAAATATAATT-TAAAT
1479607 TAAATAATAATTTAAAT
1 TAAAT-ATAATTTAAAT
1479624 TAAATCA-AATTTAA
1 TAAAT-ATAATTTAA
1479638 GCTAAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 6 0.15
15 3 0.08
16 10 0.26
17 15 0.38
18 5 0.13
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAATATAATTTAAAT
Found at i:1481027 original size:26 final size:27
Alignment explanation
Indices: 1480998--1481049 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1480988 ATATGCTTTT
*
1480998 GAACGT-ATAAA-ATTTATTGTAATTAC
1 GAACGTAATAAATA-TTATTATAATTAC
1481024 GAACGTAATAAATATTATTATAATTA
1 GAACGTAATAAATATTATTATAATTA
1481050 ATTAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 16 0.70
28 1 0.04
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (27 bp):
GAACGTAATAAATATTATTATAATTAC
Found at i:1481042 original size:27 final size:26
Alignment explanation
Indices: 1480998--1481049 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1480988 ATATGCTTTT
*
1480998 GAACGTATAAAATTTATTGTAATTAC
1 GAACGTATAAAATTTATTATAATTAC
1481024 GAACGTA-ATAAATATTATTATAATTA
1 GAACGTATA-AAAT-TTATTATAATTA
1481050 ATTAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 1 0.04
26 11 0.48
27 11 0.48
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (26 bp):
GAACGTATAAAATTTATTATAATTAC
Found at i:1482509 original size:2 final size:2
Alignment explanation
Indices: 1482502--1482526 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1482492 TCTTCTGCAA
1482502 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1482527 GTTTTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1482911 original size:23 final size:22
Alignment explanation
Indices: 1482883--1482946 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 22
1482873 ATTCACATTA
1482883 TTATTTATTAACTAAAAATTATT
1 TTATTTATTAA-TAAAAATTATT
* *
1482906 TTATTTATTTAT-AAAA-TATA
1 TTATTTATTAATAAAAATTATT
*
1482926 TTA-ATATTAATAAAAATTATT
1 TTATTTATTAATAAAAATTATT
1482947 ATTTAAAGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 6 0.18
20 10 0.29
21 7 0.21
22 1 0.03
23 10 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTTATTAATAAAAATTATT
Found at i:1489530 original size:46 final size:45
Alignment explanation
Indices: 1489421--1489530 Score: 118
Period size: 46 Copynumber: 2.4 Consensus size: 45
1489411 AGTAAAACTC
** *
1489421 TATTTATATTATTAT-TTAAAATATATATTATTTTTTATTTTTAA
1 TATTTATATTATTATATTAAAATATATAAAATTTTATATTTTTAA
*
1489465 TAATTTTATATT-TTTTATTAAAATATA-AAAATTTAATATATTTTTAA
1 T-A-TTTATATTATTATATTAAAATATATAAAATTT--TATATTTTTAA
*
1489512 TATTTATATTATAATATTA
1 TATTTATATTATTATATTA
1489531 TTTAAATTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
44 1 0.02
45 17 0.31
46 25 0.46
47 11 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (45 bp):
TATTTATATTATTATATTAAAATATATAAAATTTTATATTTTTAA
Found at i:1489776 original size:35 final size:35
Alignment explanation
Indices: 1489736--1489838 Score: 106
Period size: 35 Copynumber: 2.9 Consensus size: 35
1489726 TATTATATAT
* *
1489736 AATTAAA-AAATAATTTAAATTATTTAAATTTTAA
1 AATTAAATAAATAATTTAAATAAATTAAATTTTAA
*
1489770 ATATTAATATAAA-AA-TTATATCAAA-TAAATTTTAA
1 A-ATTAA-ATAAATAATTTAAAT-AAATTAAATTTTAA
1489805 AATTTAAATAAATAATTTAATATAAATTAAATTT
1 AA-TTAAATAAATAATTTAA-ATAAATTAAATTT
1489839 ATTTAATTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
34 7 0.12
35 27 0.48
36 10 0.18
37 12 0.21
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (35 bp):
AATTAAATAAATAATTTAAATAAATTAAATTTTAA
Found at i:1489783 original size:40 final size:40
Alignment explanation
Indices: 1489708--1489784 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
1489698 ATTTATGATT
* *
1489708 ATTTATATTATATAAATGTATTATATATAATTAAAAAATA
1 ATTTAAATTATATAAATGTATTAAATATAATTAAAAAATA
*
1489748 ATTTAAATTATTTAAAT-T-TTAAATATTAATATAAAAA
1 ATTTAAATTATATAAATGTATTAAATA-TAAT-TAAAAA
1489785 TTATATCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 6 0.19
39 5 0.16
40 21 0.66
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (40 bp):
ATTTAAATTATATAAATGTATTAAATATAATTAAAAAATA
Found at i:1490392 original size:29 final size:29
Alignment explanation
Indices: 1490329--1490412 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
1490319 TATGATATTA
* * *
1490329 TATT-ATATAAAATTTTAAA-ATATTTACG
1 TATTCATATAATA-TTTAAATATTTTTTCG
*
1490357 TATTCATATAATATTTATATTATTTTTTCG
1 TATTCATATAATATTTA-AATATTTTTTCG
* *
1490387 TA-TCATATCATTTTTAAATATTTTTT
1 TATTCATATAATATTTAAATATTTTTT
1490413 ATACAATCAG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 17 0.37
29 20 0.43
30 9 0.20
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (29 bp):
TATTCATATAATATTTAAATATTTTTTCG
Found at i:1490408 original size:28 final size:29
Alignment explanation
Indices: 1490341--1490412 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
1490331 TTATATAAAA
* *
1490341 TTTTAAA-ATATTTACGTATTCATATAAT
1 TTTTAAATATTTTTTCGTATTCATATAAT
* * *
1490369 ATTTATATTATTTTTTCGTA-TCATATCAT
1 TTTTA-AATATTTTTTCGTATTCATATAAT
1490398 TTTTAAATATTTTTT
1 TTTTAAATATTTTTT
1490413 ATACAATCAG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
28 13 0.37
29 13 0.37
30 9 0.26
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTAAATATTTTTTCGTATTCATATAAT
Found at i:1497648 original size:18 final size:18
Alignment explanation
Indices: 1497625--1497660 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1497615 TGCGAGGTTC
1497625 TGCAAATTACTATCAGAA
1 TGCAAATTACTATCAGAA
1497643 TGCAAATTACTATCAGAA
1 TGCAAATTACTATCAGAA
1497661 AACTGTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
TGCAAATTACTATCAGAA
Found at i:1501719 original size:217 final size:222
Alignment explanation
Indices: 1501327--1501762 Score: 650
Period size: 217 Copynumber: 2.0 Consensus size: 222
1501317 TCTTGAAATA
* * *
1501327 TTGGTGTCCAACACATTTTTGGATATAGGTATGGTTTATGAGTATGACCTTCCAAATACAAGGAT
1 TTGGTATCCAACACATTTTTGGAGATAGGTAAGGTTTATGAGTATGACCTTCCAAATACAAGGAT
* * ** * *
1501392 AAATTTAAAAAAATTTGAATATTTCTTGTCAAACATGTATCTGCATCTAGCAATCACACCCAAGT
66 AAACTTAAAAAAATTTGAATATATCTTGTCAAACATAAACCTGCATCCAGCAATCACACCCAAGT
* *
1501457 TCAAGAAACATAGACTAAAATGACTTGAATTACATTTTCCAGACAATTATTAAAAGCAAAATCAA
131 TCAAGAAACACAGACTAAAATGACTTAAATTACATTTTCCAGACAATTATTAAAAGCAAAATCAA
1501522 ATGTTACGAAGGAAGCTAGATTTGATT
196 ATGTTACGAAGGAAGCTAGATTTGATT
* * *
1501549 TTGGTATCCAATACATTTTTGGAGATAGGTAAGGTTTATGAGTATG-GC-T-CAAATACATGGAT
1 TTGGTATCCAACACATTTTTGGAGATAGGTAAGGTTTATGAGTATGACCTTCCAAATACAAGGAT
* *
1501611 AAACTT-AAAAATTTTGAATATATCTTGTCAAACA-AAACCTGCATCCGGCAATCACACCCAAG-
66 AAACTTAAAAAAATTTGAATATATCTTGTCAAACATAAACCTGCATCCAGCAATCACACCCAAGT
* *
1501673 TCTAAGAAACACAGATTAAAATGACTTAAATTACATTTTTCAGACAATTATTAAAAGCAAAATCA
131 TC-AAGAAACACAGACTAAAATGACTTAAATTACATTTTCCAGACAATTATTAAAAGCAAAATCA
*
1501738 AATGTTACGAAGGAAGTTAGATTTG
195 AATGTTACGAAGGAAGCTAGATTTG
1501763 CTGGGCTGTG
Statistics
Matches: 194, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
216 2 0.01
217 105 0.54
218 26 0.13
219 17 0.09
220 1 0.01
221 1 0.01
222 42 0.22
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (222 bp):
TTGGTATCCAACACATTTTTGGAGATAGGTAAGGTTTATGAGTATGACCTTCCAAATACAAGGAT
AAACTTAAAAAAATTTGAATATATCTTGTCAAACATAAACCTGCATCCAGCAATCACACCCAAGT
TCAAGAAACACAGACTAAAATGACTTAAATTACATTTTCCAGACAATTATTAAAAGCAAAATCAA
ATGTTACGAAGGAAGCTAGATTTGATT
Found at i:1513439 original size:25 final size:25
Alignment explanation
Indices: 1513409--1513457 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1513399 ATAGTTAAGC
1513409 ATGTTAAACACTGAAGCAAGGTCCA
1 ATGTTAAACACTGAAGCAAGGTCCA
* *
1513434 ATGTTAAATACTGCAGCAAGGTCC
1 ATGTTAAACACTGAAGCAAGGTCC
1513458 CAGACAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (25 bp):
ATGTTAAACACTGAAGCAAGGTCCA
Found at i:1513844 original size:33 final size:33
Alignment explanation
Indices: 1513807--1513873 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1513797 ATAACCATGG
* *
1513807 TGCTGCTCAAGCACTCATTAGCAATCCTGATGC
1 TGCTGCCCAAGCACTCATCAGCAATCCTGATGC
* * *
1513840 TGCTGCCCAGGCACTCCTCAGCAATCCTGGTGC
1 TGCTGCCCAAGCACTCATCAGCAATCCTGATGC
1513873 T
1 T
1513874 ATTAATCAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.19, C:0.34, G:0.21, T:0.25
Consensus pattern (33 bp):
TGCTGCCCAAGCACTCATCAGCAATCCTGATGC
Found at i:1518215 original size:37 final size:37
Alignment explanation
Indices: 1518143--1518377 Score: 199
Period size: 37 Copynumber: 6.3 Consensus size: 37
1518133 TAAAAATCGA
* *
1518143 TTTC-AACCGTGCCACCAGTTAAAAATAATGGTTTTTG
1 TTTCGAACCGTGCCACC-GGTAAAAATAATAGTTTTTG
** * *
1518180 TTTCGATTCGTGTCACCGGTAAAAATAGT-GATTTTTG
1 TTTCGAACCGTGCCACCGGTAAAAATAATAG-TTTTTG
* * *
1518217 TTTC-AACCCATGCCACTGGTAATAATAATAGTTTTTG
1 TTTCGAA-CCGTGCCACCGGTAAAAATAATAGTTTTTG
* * * * * *
1518254 TTCCGACCCATGCCATCGGTAATAATAATAGTTTTTA
1 TTTCGAACCGTGCCACCGGTAAAAATAATAGTTTTTG
* * * * * *
1518291 TTTTGATCCGTGTCACCGATAAGAATAGT-GATTTTTG
1 TTTCGAACCGTGCCACCGGTAAAAATAATAG-TTTTTG
*
1518328 TTTTGAACCGTGCCACCGGTTAAAAATAATAGTTTTTG
1 TTTCGAACCGTGCCACCGG-TAAAAATAATAGTTTTTG
1518366 TTTCGAACCGTG
1 TTTCGAACCGTG
1518378 TCATCGGATT
Statistics
Matches: 157, Mismatches: 33, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
36 3 0.02
37 117 0.75
38 36 0.23
39 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (37 bp):
TTTCGAACCGTGCCACCGGTAAAAATAATAGTTTTTG
Found at i:1518364 original size:75 final size:75
Alignment explanation
Indices: 1518264--1518407 Score: 193
Period size: 75 Copynumber: 1.9 Consensus size: 75
1518254 TTCCGACCCA
* * * *
1518264 TGCCATCGGTAATAATAATAGTTTTTATTTTGATCCGTGTCA-CCGATAAGAATAGTGA-TTTTT
1 TGCCACCGGTAAAAATAATAGTTTTTATTTCGAACCGTGTCATCCGATAAGAATAGT-ACTTTTT
1518327 GTTTTGAACCG
65 GTTTTGAACCG
* * *
1518338 TGCCACCGGTTAAAAATAATAGTTTTTGTTTCGAACCGTGTCATCGGATTAGAATAGTACTTTTT
1 TGCCACCGG-TAAAAATAATAGTTTTTATTTCGAACCGTGTCATCCGATAAGAATAGTACTTTTT
1518403 GTTTT
65 GTTTT
1518408 AACATATGCC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
74 8 0.13
75 30 0.50
76 22 0.37
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (75 bp):
TGCCACCGGTAAAAATAATAGTTTTTATTTCGAACCGTGTCATCCGATAAGAATAGTACTTTTTG
TTTTGAACCG
Found at i:1518402 original size:38 final size:36
Alignment explanation
Indices: 1518298--1518406 Score: 103
Period size: 38 Copynumber: 2.9 Consensus size: 36
1518288 TTATTTTGAT
* * *
1518298 CCGTGTCACCGATAAGAATAGTGATTTTTGTTTTGAA
1 CCGTGTCACGGATTAGAATAGT-ATTTTTGTTTCGAA
* * *
1518335 CCGTGCCACCGG-TTAAAAATAATAGTTTTTGTTTCGAA
1 CCGTGTCA-CGGATT-AGAATAGTA-TTTTTGTTTCGAA
1518373 CCGTGTCATCGGATTAGAATAGTACTTTTTGTTT
1 CCGTGTCA-CGGATTAGAATAGTA-TTTTTGTTT
1518407 TAACATATGC
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
37 9 0.16
38 46 0.81
39 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (36 bp):
CCGTGTCACGGATTAGAATAGTATTTTTGTTTCGAA
Found at i:1520432 original size:10 final size:9
Alignment explanation
Indices: 1520393--1520424 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
1520383 TTTAAATACA
1520393 TAAATAAATT
1 TAAA-AAATT
1520403 TAAAAAATT
1 TAAAAAATT
1520412 TAAAAAATT
1 TAAAAAATT
1520421 TAAA
1 TAAA
1520425 TATATTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAAATT
Found at i:1520832 original size:2 final size:2
Alignment explanation
Indices: 1520825--1520858 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1520815 ATTCTTTTGT
*
1520825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1520859 ATCTTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1525296 original size:17 final size:17
Alignment explanation
Indices: 1525276--1525329 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
1525266 ACTATATTAC
*
1525276 TTAAATTTAAATATATA
1 TTAAATATAAATATATA
*
1525293 TTAAATATAAAAATATA
1 TTAAATATAAATATATA
* *
1525310 TTTAATATGAATATAT-
1 TTAAATATAAATATATA
1525326 TTAA
1 TTAA
1525330 TTTTTTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
16 3 0.10
17 28 0.90
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAAATATAAATATATA
Found at i:1525791 original size:2 final size:2
Alignment explanation
Indices: 1525780--1525810 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1525770 TATCCTTTTG
1525780 AT AT -T 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
1525811 CAGTTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1526577 original size:2 final size:2
Alignment explanation
Indices: 1526570--1526607 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1526560 AGGCCATGTG
1526570 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
1526608 TTTCCCCTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1535275 original size:15 final size:15
Alignment explanation
Indices: 1535255--1535287 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1535245 GGATATAAAT
1535255 TTTAAATATT-TATTA
1 TTTAAAT-TTGTATTA
1535270 TTTAAATTTGTATTA
1 TTTAAATTTGTATTA
1535285 TTT
1 TTT
1535288 TTATGAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTAAATTTGTATTA
Found at i:1537305 original size:45 final size:45
Alignment explanation
Indices: 1537255--1537390 Score: 175
Period size: 45 Copynumber: 3.0 Consensus size: 45
1537245 TTCGAACTCC
*
1537255 AAAACCCTAAAATGAAATCTTGAAATCTAACGACCAAACA-TGATG
1 AAAACCCTAAAATGAAATCTTGAAATCTAACCACCAAACATTG-TG
*
1537300 AAAACCCTAATATGAAATCTTGAAATCTAACCACCAAACATTGTG
1 AAAACCCTAAAATGAAATCTTGAAATCTAACCACCAAACATTGTG
** * * * **
1537345 AAAGTCTTAAAATGAAATCTTGGATTCTAACCATAAAACATTGTG
1 AAAACCCTAAAATGAAATCTTGAAATCTAACCACCAAACATTGTG
1537390 A
1 A
1537391 TAAGTTTGAG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 78 0.98
46 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (45 bp):
AAAACCCTAAAATGAAATCTTGAAATCTAACCACCAAACATTGTG
Found at i:1538031 original size:12 final size:12
Alignment explanation
Indices: 1537989--1538032 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1537979 GCCATCTCCA
*
1537989 TCACCTTCAAAG
1 TCACCATCAAAG
* *
1538001 TCGCCTTCAAAG
1 TCACCATCAAAG
*
1538013 TCTCCATCAAAG
1 TCACCATCAAAG
1538025 TCACCATC
1 TCACCATC
1538033 TTCTTCCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (12 bp):
TCACCATCAAAG
Found at i:1538777 original size:22 final size:22
Alignment explanation
Indices: 1538734--1538779 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1538724 ATATTAAAAA
* **
1538734 AATTAAAAATTTTAATTGATAT
1 AATTAAAAATTATAATAAATAT
1538756 AATTAAAAATTATAATAAATAT
1 AATTAAAAATTATAATAAATAT
1538778 AA
1 AA
1538780 AAATATGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AATTAAAAATTATAATAAATAT
Found at i:1538975 original size:23 final size:23
Alignment explanation
Indices: 1538929--1538975 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1538919 AAAAATATTA
*
1538929 TAAATTAATCAAATAAATTTATT
1 TAAATTAATCAAATAAATTAATT
*
1538952 TAAATTAAT-TAATAAAATTAATT
1 TAAATTAATCAAAT-AAATTAATT
1538975 T
1 T
1538976 TTATCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAATTAATCAAATAAATTAATT
Found at i:1544564 original size:18 final size:18
Alignment explanation
Indices: 1544541--1544583 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1544531 TTACATAAAT
1544541 TTATAT-ATAATTATTGTA
1 TTATATAAT-ATTATTGTA
*
1544559 TTATATAATATTATTTTA
1 TTATATAATATTATTGTA
1544577 TTA-ATAA
1 TTATATAA
1544584 AAATATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 17 0.74
19 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTATATAATATTATTGTA
Found at i:1544620 original size:25 final size:22
Alignment explanation
Indices: 1544571--1544615 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1544561 ATATAATATT
*
1544571 ATTTTATTAATAAAAATATAAA
1 ATTTTATTAAAAAAAATATAAA
*
1544593 ATTTTATTAAAAATAAATTTAAA
1 ATTTTATTAAAAA-AAATATAAA
1544616 TAATTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTTATTAAAAAAAATATAAA
Found at i:1545141 original size:21 final size:21
Alignment explanation
Indices: 1545112--1545152 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1545102 TATTGAAAAA
**
1545112 TTTAAATTTATTTTTAAAATT
1 TTTAAATTTAAATTTAAAATT
*
1545133 TTTATATTTAAATTTAAAAT
1 TTTAAATTTAAATTTAAAAT
1545153 GAAAAAAATA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAATTTAAATTTAAAATT
Found at i:1545260 original size:20 final size:20
Alignment explanation
Indices: 1545235--1545279 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1545225 TATCAAAAAT
* *
1545235 TAAAAA-TAATCATAAATTTA
1 TAAAAATTAAT-AAAAATATA
1545255 TAAAAATTAATAAAAATATA
1 TAAAAATTAATAAAAATATA
1545275 TAAAA
1 TAAAA
1545280 TTTTTTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAATTAATAAAAATATA
Found at i:1545280 original size:29 final size:29
Alignment explanation
Indices: 1545218--1545282 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
1545208 AATAGATTTT
*
1545218 TAAATTTTATCAAAAATTAAAAATAATCA
1 TAAAATTTATCAAAAATTAAAAATAATCA
*
1545247 T-AAATTTAT-AAAAATTAATAAA-AATATA
1 TAAAATTTATCAAAAATTAA-AAATAAT-CA
1545275 TAAAATTT
1 TAAAATTT
1545283 TTTACTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 12 0.39
28 12 0.39
29 7 0.23
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (29 bp):
TAAAATTTATCAAAAATTAAAAATAATCA
Found at i:1545940 original size:23 final size:22
Alignment explanation
Indices: 1545873--1545940 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
1545863 TAGGAAGTAA
1545873 TTTAAATAAAATTAAATAAAA-T
1 TTTAAA-AAAATTAAATAAAATT
* * *
1545895 ATTAAAAAAATT-AGTACTCAATT
1 TTTAAAAAAATTAAATA--AAATT
1545918 TTTAAAAAAATTAAATTAAAATT
1 TTTAAAAAAATTAAA-TAAAATT
1545941 AATATCATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
20 3 0.09
21 6 0.17
22 7 0.20
23 16 0.46
24 1 0.03
25 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (22 bp):
TTTAAAAAAATTAAATAAAATT
Found at i:1546276 original size:21 final size:22
Alignment explanation
Indices: 1546246--1546299 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
1546236 TTTTAAAAAA
* *
1546246 TAATTGTTAAGATAAT-TTTTT
1 TAATTTTTAAGATAATAATTTT
1546267 TAATTTTTAA-A-AATAATTTT
1 TAATTTTTAAGATAATAATTTT
*
1546287 TATTTTTTAAGAT
1 TAATTTTTAAGAT
1546300 GATTATTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.11
20 14 0.52
21 10 0.37
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TAATTTTTAAGATAATAATTTT
Found at i:1550837 original size:15 final size:15
Alignment explanation
Indices: 1550817--1550860 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1550807 ATTTAAATTT
1550817 TATATTTATTAAATA
1 TATATTTATTAAATA
1550832 TATATTT-TTAAA-A
1 TATATTTATTAAATA
1550845 TA-A-TTATATAAATA
1 TATATTTAT-TAAATA
1550859 TA
1 TA
1550861 AATTAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 7 0.27
14 8 0.31
15 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATTTATTAAATA
Found at i:1556764 original size:50 final size:50
Alignment explanation
Indices: 1556699--1556802 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
1556689 TTTTAATATT
* *
1556699 TTTTAATTTAATTTAATTATATATAAAT-TATTAATTATT-A-ATAAAAATAA
1 TTTTAATTTAATTTAATCATA-A-AAATATA-TAAATATTAATATAAAAATAA
1556749 TTTT-ATTTAAATTTAATCATAAAAATATATAAATATTAATATAAAAATAA
1 TTTTAATTT-AATTTAATCATAAAAATATATAAATATTAATATAAAAATAA
1556799 TTTT
1 TTTT
1556803 TTAATATTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
48 11 0.23
49 8 0.17
50 29 0.60
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (50 bp):
TTTTAATTTAATTTAATCATAAAAATATATAAATATTAATATAAAAATAA
Found at i:1556781 original size:22 final size:22
Alignment explanation
Indices: 1556756--1556797 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1556746 TAATTTTATT
1556756 TAAAT-TTAATCATAAAAATATA
1 TAAATATTAAT-ATAAAAATATA
1556778 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1556798 ATTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1558531 original size:2 final size:2
Alignment explanation
Indices: 1558524--1558548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1558514 CAGAAGAATT
1558524 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1558549 TGCTGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1559376 original size:13 final size:13
Alignment explanation
Indices: 1559360--1559386 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1559350 TTTTTTGAAT
1559360 TTAAATATAATTA
1 TTAAATATAATTA
1559373 TTAAATATAATTA
1 TTAAATATAATTA
1559386 T
1 T
1559387 ATTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATATAATTA
Found at i:1566058 original size:2 final size:2
Alignment explanation
Indices: 1566051--1566076 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1566041 GTTTGTTTAC
1566051 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
1566077 GAATGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1567383 original size:2 final size:2
Alignment explanation
Indices: 1567376--1567402 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1567366 TATCTGCTAA
1567376 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1567403 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1567407 original size:2 final size:2
Alignment explanation
Indices: 1567402--1567432 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1567392 TCTCTCTCTC
*
1567402 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1567433 TAAAAATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1567783 original size:15 final size:14
Alignment explanation
Indices: 1567760--1567802 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1567750 AGTAATTGAG
*
1567760 TTAACTTAATTATAT
1 TTAAATTAATT-TAT
1567775 TTAAATTAATGTTAT
1 TTAAATTAAT-TTAT
1567790 TTAAATTTAATTT
1 TTAAA-TTAATTT
1567803 TATATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (14 bp):
TTAAATTAATTTAT
Found at i:1568982 original size:9 final size:9
Alignment explanation
Indices: 1568970--1568995 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1568960 ATAATTTTTT
1568970 AAATTAAAA
1 AAATTAAAA
1568979 AAATTAAAA
1 AAATTAAAA
1568988 AAATTAAA
1 AAATTAAA
1568996 TATATACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATTAAAA
Found at i:1569372 original size:2 final size:2
Alignment explanation
Indices: 1569367--1569403 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1569357 ATGGAATCAA
*
1569367 AT AT AT AT AT AT AT AT AT AT GT 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 AT A
1569404 GAAAGTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1570226 original size:2 final size:2
Alignment explanation
Indices: 1570219--1570245 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1570209 AACAGCTTGG
1570219 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1570246 GCATGCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1571277 original size:16 final size:15
Alignment explanation
Indices: 1571248--1571277 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1571238 TTACACTGCT
1571248 TTTTTAAAGTAAAAA
1 TTTTTAAAGTAAAAA
*
1571263 TTTTTCAAGTAAAAA
1 TTTTTAAAGTAAAAA
1571278 GTGAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (15 bp):
TTTTTAAAGTAAAAA
Found at i:1571317 original size:20 final size:20
Alignment explanation
Indices: 1571261--1571317 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
1571251 TTAAAGTAAA
* *
1571261 AATTTTTCAAGTAAAAAGTG
1 AATTTTTTAAGTAAAAATTG
*
1571281 AATTTTTTTAGT-AAAATTG
1 AATTTTTTAAGTAAAAATTG
*
1571300 AATTTTTTAATTAAAAAT
1 AATTTTTTAAGTAAAAAT
1571318 AGATATTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (20 bp):
AATTTTTTAAGTAAAAATTG
Found at i:1571966 original size:4 final size:4
Alignment explanation
Indices: 1571957--1571985 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1571947 ATAATTCCCC
1571957 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1571986 TATATATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1573172 original size:22 final size:21
Alignment explanation
Indices: 1573126--1573175 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
1573116 ACATAATTAG
1573126 TAAATAAAAAATAAAATATGAT
1 TAAATAAAAAAT-AAATATGAT
1573148 TAAATAAAAAAT-AATATGAATT
1 TAAATAAAAAATAAATATG-A-T
1573170 TAAATA
1 TAAATA
1573176 TGTTATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.23
21 1 0.04
22 19 0.73
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (21 bp):
TAAATAAAAAATAAATATGAT
Found at i:1573208 original size:32 final size:31
Alignment explanation
Indices: 1573159--1573219 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
1573149 AAATAAAAAA
* *
1573159 TAATATGAATTTAAATATGTTATAATTTATT
1 TAATATAAATTTAAATATGTTAAAATTTATT
*
1573190 TAATATAAATTATTAATATGTTAAAATTTA
1 TAATATAAATT-TAAATATGTTAAAATTTA
1573220 AATAAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (31 bp):
TAATATAAATTTAAATATGTTAAAATTTATT
Found at i:1574282 original size:4 final size:4
Alignment explanation
Indices: 1574257--1574299 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
1574247 GCAAGGAGCT
* *
1574257 ATAA ATAC ATAA ATAC ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1574300 GTACTTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1575307 original size:23 final size:22
Alignment explanation
Indices: 1575281--1575324 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1575271 AAATGTTAAA
1575281 AAATATTTT-TAATTAATATTTAT
1 AAAT-TTTTATAATTAA-ATTTAT
1575304 AAATTTTTATAATTAAATTTA
1 AAATTTTTATAATTAAATTTA
1575325 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATTTTTATAATTAAATTTAT
Found at i:1575880 original size:27 final size:27
Alignment explanation
Indices: 1575844--1575896 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1575834 TCACCATAAG
1575844 TTTTTTTTAATATGATT-AAAATATTT
1 TTTTTTTTAATATGATTAAAAATATTT
1575870 TTTTATTTTAATATGATTAAAAATATT
1 TTTT-TTTTAATATGATTAAAAATATT
1575897 AAAAGAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 4 0.16
27 13 0.52
28 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTTTTTTAATATGATTAAAAATATTT
Found at i:1576629 original size:2 final size:2
Alignment explanation
Indices: 1576622--1576670 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1576612 AAATGGTAGA
1576622 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
1576664 AT AT AT A
1 AT AT AT A
1576671 AAATGGTGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1580275 original size:39 final size:39
Alignment explanation
Indices: 1580231--1580308 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
1580221 CATAGTTTAA
*
1580231 AGCAGTCAATGATTACGGTTTATCATAATGCATCAGTTT
1 AGCAGTCAATGATTACAGTTTATCATAATGCATCAGTTT
1580270 AGCAGTCAATGATTACAGTTTATCATAATGCATCAGTTT
1 AGCAGTCAATGATTACAGTTTATCATAATGCATCAGTTT
1580309 CTTTTGGAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (39 bp):
AGCAGTCAATGATTACAGTTTATCATAATGCATCAGTTT
Found at i:1580289 original size:21 final size:21
Alignment explanation
Indices: 1580231--1580291 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1580221 CATAGTTTAA
*
1580231 AGCAGTCAATGATTACGGTTT
1 AGCAGTCAATGATTACAGTTT
*
1580252 ATCA-T-AATGCA-T-CAGTTT
1 AGCAGTCAATG-ATTACAGTTT
1580270 AGCAGTCAATGATTACAGTTT
1 AGCAGTCAATGATTACAGTTT
1580291 A
1 A
1580292 TCATAATGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
18 8 0.25
19 7 0.22
20 7 0.22
21 10 0.31
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (21 bp):
AGCAGTCAATGATTACAGTTT
Found at i:1580308 original size:18 final size:18
Alignment explanation
Indices: 1580248--1580308 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 18
1580238 AATGATTACG
1580248 GTTTATCATAATGCATCA
1 GTTTATCATAATGCATCA
*
1580266 GTTTAGCAGTCAATG-ATTACA
1 GTTTATCA-T-AATGCA-T-CA
1580287 GTTTATCATAATGCATCA
1 GTTTATCATAATGCATCA
1580305 GTTT
1 GTTT
1580309 CTTTTGGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 13 0.36
19 7 0.19
20 7 0.19
21 9 0.25
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (18 bp):
GTTTATCATAATGCATCA
Found at i:1588846 original size:21 final size:22
Alignment explanation
Indices: 1588822--1588867 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1588812 CCTAAAGTGT
*
1588822 CAATAAAT-AAATAAAATGA-TA
1 CAATAAATCAAACAAAA-GAGTA
1588843 CAATAAATCAAACAAAAGAGTA
1 CAATAAATCAAACAAAAGAGTA
1588865 CAA
1 CAA
1588868 CTCAAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.65, C:0.11, G:0.07, T:0.17
Consensus pattern (22 bp):
CAATAAATCAAACAAAAGAGTA
Done.