Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 11 of 15
Found at i:1395668 original size:2 final size:2
Alignment explanation
Indices: 1395661--1395705 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1395651 TAATGTGTAA
1395661 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1395703 TC T
1 TC T
1395706 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1395728 original size:2 final size:2
Alignment explanation
Indices: 1395723--1395754 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1395713 TATATATATA
1395723 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1395755 CGCGCGCGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1396590 original size:2 final size:2
Alignment explanation
Indices: 1396583--1396615 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1396573 ATCAGCAGGT
1396583 TC TC TC 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 TC TC TC T
1396616 TACACGTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1399875 original size:5 final size:5
Alignment explanation
Indices: 1399860--1399909 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
1399850 ATTTGGATAG
*
1399860 AATTGT AATTT AATTT -TTTT AATTTT AATTT AAATTT AATTT -ATTT
1 AATT-T AATTT AATTT AATTT AA-TTT AATTT -AATTT AATTT AATTT
1399906 AATT
1 AATT
1399910 ACTTAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
4 7 0.18
5 17 0.45
6 14 0.37
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (5 bp):
AATTT
Found at i:1399978 original size:22 final size:22
Alignment explanation
Indices: 1399950--1399995 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1399940 TATTAAAATT
1399950 TATTTTTAT-ATTAAAATTTATA
1 TATTTTTATAATT-AAATTTATA
1399972 TATTTTTATAATTAAATTTATA
1 TATTTTTATAATTAAATTTATA
1399994 TA
1 TA
1399996 AATTAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1400480 original size:3 final size:3
Alignment explanation
Indices: 1400474--1400507 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1400464 TATACTTTTT
1400474 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1400508 AGCATGCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1403040 original size:3 final size:3
Alignment explanation
Indices: 1403026--1403056 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1403016 GAATGGAACA
*
1403026 GAT GAT GGT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1403057 TCAATGGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.39, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1403351 original size:2 final size:2
Alignment explanation
Indices: 1403346--1403370 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1403336 TGTGTGTGTG
1403346 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 T
1403371 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1403375 original size:2 final size:2
Alignment explanation
Indices: 1403370--1403394 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1403360 TCTCTCTCTC
1403370 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
1403395 TAAGTGTGAT
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:1405446 original size:44 final size:42
Alignment explanation
Indices: 1405366--1405450 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 42
1405356 TTTATGTATT
* * *
1405366 AATATTGTATTTATATAATTTTTATATTATAATAATTTTTAA
1 AATATTATATTTATATAATATTGATATTATAATAATTTTTAA
1405408 AATATTATATATTATATAAATATTGATATGT-TAATAATTTTTA
1 AATATTATAT-TTATAT-AATATTGATAT-TATAATAATTTTTA
1405451 TTATATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 9 0.24
43 6 0.16
44 21 0.57
45 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (42 bp):
AATATTATATTTATATAATATTGATATTATAATAATTTTTAA
Found at i:1405453 original size:32 final size:33
Alignment explanation
Indices: 1405404--1405489 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
1405394 ATAATAATTT
* * *
1405404 TTAAAATATTATATATTATATAAATATTGATATG
1 TTAATATATT-TATATTATATAAATATTAATATA
* *
1405438 TTAATA-ATTTTTATTATATAAATTTTAATATA
1 TTAATATATTTATATTATATAAATATTAATATA
*
1405470 TTTATATATTTATATTATAT
1 TTAATATATTTATATTATAT
1405490 TTATCATCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 24 0.55
33 15 0.34
34 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (33 bp):
TTAATATATTTATATTATATAAATATTAATATA
Found at i:1405501 original size:21 final size:18
Alignment explanation
Indices: 1405466--1405519 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
1405456 TAAATTTTAA
1405466 TATATTTATATATTTATAT
1 TATATTTATATATTTAT-T
1405485 TATATTTATCATCATTTATT
1 TATATTTAT-AT-ATTTATT
1405505 TCATA-TTATAT-TTTA
1 T-ATATTTATATATTTA
1405520 ATTTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.12
19 11 0.34
20 8 0.25
21 9 0.28
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTTATATATTTATT
Found at i:1405876 original size:17 final size:18
Alignment explanation
Indices: 1405842--1405892 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
1405832 AAAATTATAT
* *
1405842 TATATAATTATATTTAAA
1 TATATAATTAAATATAAA
1405860 TATAT-ATTAAATATAAA
1 TATATAATTAAATATAAA
* *
1405877 TAT-TAAATAAAAATAA
1 TATATAATTAAATATAA
1405893 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 1 0.04
17 22 0.79
18 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATATAATTAAATATAAA
Found at i:1405881 original size:13 final size:13
Alignment explanation
Indices: 1405855--1405897 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1405845 ATAATTATAT
1405855 TTAAATAT--ATA
1 TTAAATATAAATA
1405866 TTAAATATAAATA
1 TTAAATATAAATA
*
1405879 TTAAATAAAAATAA
1 TTAAATATAAAT-A
1405893 TTAAA
1 TTAAA
1405898 AAATATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 8 0.29
13 14 0.50
14 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:1406196 original size:31 final size:32
Alignment explanation
Indices: 1406141--1406201 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
1406131 TTAAATTATT
*
1406141 ATTTACATAATAAAAATATAATTTTTATTTAA
1 ATTTACATAATAAAAATATAATTTTAATTTAA
*
1406173 ATTTA-ATTATAAAAATA-ATATTTTAATTT
1 ATTTACATAATAAAAATATA-ATTTTAATTT
1406202 TTTTGTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.04
31 20 0.77
32 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (32 bp):
ATTTACATAATAAAAATATAATTTTAATTTAA
Found at i:1406643 original size:17 final size:17
Alignment explanation
Indices: 1406621--1406654 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1406611 ACTCGGATTC
1406621 AAATAAAAGTATTAAAT
1 AAATAAAAGTATTAAAT
1406638 AAATAAAAGTATTAAAT
1 AAATAAAAGTATTAAAT
1406655 GTGGGTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
AAATAAAAGTATTAAAT
Found at i:1407784 original size:21 final size:21
Alignment explanation
Indices: 1407747--1407787 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1407737 ATTTTTTATT
1407747 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
*
1407768 TAAATATTATTTA-AAAATAT
1 TAAAT-TTAATTATAAAATAT
1407788 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1409296 original size:2 final size:2
Alignment explanation
Indices: 1409283--1409319 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1409273 CGGTGGCAGG
*
1409283 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1409320 TATTTCAATC
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1410296 original size:17 final size:18
Alignment explanation
Indices: 1410276--1410309 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1410266 TTTATTATTT
1410276 AAAATAAT-TTTAATTAA
1 AAAATAATCTTTAATTAA
*
1410293 AAAATTATCTTTAATTA
1 AAAATAATCTTTAATTA
1410310 TTAGTAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATAATCTTTAATTAA
Found at i:1410697 original size:28 final size:26
Alignment explanation
Indices: 1410629--1410698 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
1410619 ATTATCACTA
*
1410629 AATTTTTAAATAATA-GTTAATAATT
1 AATTTTAAAATAATATGTTAATAATT
* * *
1410654 AATTTAAATAAAAATATTTTAATAGATT
1 AATTTTAA-AATAATATGTTAATA-ATT
1410682 AATTTTAAAATTAATAT
1 AATTTTAAAA-TAATAT
1410699 ATAATTGAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 6 0.17
26 6 0.17
27 8 0.23
28 15 0.43
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (26 bp):
AATTTTAAAATAATATGTTAATAATT
Found at i:1411231 original size:22 final size:22
Alignment explanation
Indices: 1411206--1411247 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1411196 TATTTTTAAT
1411206 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1411228 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1411248 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1411939 original size:24 final size:25
Alignment explanation
Indices: 1411886--1411941 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
1411876 TTCGAATATT
*
1411886 TATATTATATTATAATTATATTTAA
1 TATATTATATTATAATTAAATTTAA
*
1411911 AATATTATA-TATTAA-TAAATTTAA
1 TATATTATATTA-TAATTAAATTTAA
1411935 TATATTA
1 TATATTA
1411942 ATAGTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTATATTATAATTAAATTTAA
Found at i:1412987 original size:19 final size:18
Alignment explanation
Indices: 1412942--1412990 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
1412932 ATGCAATGTG
1412942 AAATAAATT-TTATTTTT
1 AAATAAATTATTATTTTT
1412959 AAATAGAATTATTATTTTT
1 AAATA-AATTATTATTTTT
*
1412978 AACTCAAATTATT
1 AAAT-AAATTATT
1412991 TTTGGTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 18 0.64
20 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (18 bp):
AAATAAATTATTATTTTT
Found at i:1414704 original size:3 final size:3
Alignment explanation
Indices: 1414696--1414726 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1414686 AAGTAAAACA
1414696 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1414727 CCCAAGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1416198 original size:7 final size:7
Alignment explanation
Indices: 1416186--1416228 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
1416176 CTTTTGTAGT
1416186 ATAAAAA
1 ATAAAAA
1416193 ATAAAAA
1 ATAAAAA
*
1416200 ATAAATA
1 ATAAAAA
*
1416207 A-AAAAT
1 ATAAAAA
1416213 ATAAAAA
1 ATAAAAA
1416220 TATAAAAA
1 -ATAAAAA
1416228 A
1 A
1416229 ATAATAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
ATAAAAA
Found at i:1416207 original size:11 final size:11
Alignment explanation
Indices: 1416191--1416235 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
1416181 GTAGTATAAA
1416191 AAATAAAAAAT
1 AAATAAAAAAT
1416202 AAATAAAAAAT
1 AAATAAAAAAT
1416213 --ATAAAAATAT
1 AAATAAAAA-AT
1416223 AAA-AAAATAAT
1 AAATAAAA-AAT
1416234 AA
1 AA
1416236 GAAGTGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 7 0.23
10 2 0.07
11 19 0.63
12 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:1416209 original size:18 final size:18
Alignment explanation
Indices: 1416186--1416232 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
1416176 CTTTTGTAGT
1416186 ATAAAAAATAAAAAATAA
1 ATAAAAAATAAAAAATAA
*
1416204 ATAAAAAATATAAAAATAT
1 ATAAAAAATA-AAAAATAA
1416223 A-AAAAAATAA
1 ATAAAAAATAA
1416233 TAAGAAGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 18 0.67
19 8 0.30
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
ATAAAAAATAAAAAATAA
Found at i:1416218 original size:8 final size:8
Alignment explanation
Indices: 1416185--1416232 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
1416175 TCTTTTGTAG
1416185 TATAAAAA
1 TATAAAAA
1416193 -ATAAAAA
1 TATAAAAA
1416200 -AT--AAA
1 TATAAAAA
1416205 TA-AAAAA
1 TATAAAAA
1416212 TATAAAAA
1 TATAAAAA
1416220 TATAAAAA
1 TATAAAAA
*
1416228 AATAA
1 TATAA
1416233 TAAGAAGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
5 3 0.09
6 1 0.03
7 14 0.40
8 17 0.49
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
TATAAAAA
Found at i:1417035 original size:2 final size:2
Alignment explanation
Indices: 1417028--1417064 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1417018 TTCTTTTAGA
1417028 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 A
1417065 ATGTCTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1419242 original size:17 final size:19
Alignment explanation
Indices: 1419206--1419259 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 19
1419196 AATTTACGTA
*
1419206 AATATATAATATTTTAAACAT
1 AATATA-AATA-TATAAACAT
1419227 AAT-T-AATATATAAACAT
1 AATATAAATATATAAACAT
1419244 AATATAAATATATAAA
1 AATATAAATATATAAA
1419260 TTTTTAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 11 0.37
18 5 0.17
19 10 0.33
20 1 0.03
21 3 0.10
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATAAATATATAAACAT
Found at i:1420016 original size:19 final size:20
Alignment explanation
Indices: 1419973--1420016 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1419963 TTAAGTGAAA
*
1419973 AAATTTATAATTAATTATTT
1 AAATTTATAATTAATTATGT
* *
1419993 AAATTTATATTTTATTA-GT
1 AAATTTATAATTAATTATGT
1420012 AAATT
1 AAATT
1420017 ATTTTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AAATTTATAATTAATTATGT
Found at i:1420649 original size:38 final size:38
Alignment explanation
Indices: 1420607--1420681 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
1420597 TTAATGTAAG
**
1420607 TAATTTTTAATTATTATTTTGTATAAATAATATTTTAC
1 TAATTTTTAATTATTATTTAATATAAATAATATTTTAC
**
1420645 TAATTTTTAATTATTATTTAATATAAATTTTATTTTA
1 TAATTTTTAATTATTATTTAATATAAATAATATTTTA
1420682 TTATTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (38 bp):
TAATTTTTAATTATTATTTAATATAAATAATATTTTAC
Found at i:1420722 original size:80 final size:85
Alignment explanation
Indices: 1420649--1420810 Score: 199
Period size: 91 Copynumber: 1.9 Consensus size: 85
1420639 TTTTACTAAT
1420649 TTTTAATTATTATT-TAA-TATAA-ATTT-TATTTTATTATTTAATATGTATATAA-ATGTTAAC
1 TTTTAATTATTATTATAATTATAATATTTATATTTTATTATTTAATATGTATATAATATGTTAAC
1420709 ATAAATATAATTTTAATCAA
66 ATAAATATAATTTTAATCAA
*
1420729 TTTTAATTATTATTCAACATAATTATAATTTCATTTATATTTTATTATTTAATATGTATATAATT
1 TTTTAATTATTATT----ATAATTATAA--T-ATTTATATTTTATTATTTAATATGTATATAATA
* *
1420794 TTTTAACGTAAATATAA
59 TGTTAACATAAATATAA
1420811 CTGTTAAGTT
Statistics
Matches: 67, Mismatches: 3, Indels: 12
0.82 0.04 0.15
Matches are distributed among these distances:
80 14 0.21
85 3 0.04
86 5 0.07
90 4 0.06
91 26 0.39
92 15 0.22
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (85 bp):
TTTTAATTATTATTATAATTATAATATTTATATTTTATTATTTAATATGTATATAATATGTTAAC
ATAAATATAATTTTAATCAA
Found at i:1421266 original size:17 final size:17
Alignment explanation
Indices: 1421235--1421277 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1421225 TGTAAAATTA
*
1421235 TATTAATAAATTATT-T
1 TATTTATAAATTATTCT
1421251 TATTTATAAGATTATTCT
1 TATTTATAA-ATTATTCT
1421269 TATTT-TAAA
1 TATTTATAAA
1421278 ATGATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.38
17 9 0.38
18 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTATAAATTATTCT
Found at i:1421968 original size:17 final size:17
Alignment explanation
Indices: 1421948--1421981 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1421938 AGATATTGCT
1421948 ACAAAGATGTGCTGCCA
1 ACAAAGATGTGCTGCCA
1421965 ACAAAGATGTGCTGCCA
1 ACAAAGATGTGCTGCCA
1421982 TTCACAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (17 bp):
ACAAAGATGTGCTGCCA
Found at i:1423884 original size:90 final size:90
Alignment explanation
Indices: 1423731--1423910 Score: 333
Period size: 90 Copynumber: 2.0 Consensus size: 90
1423721 GTACATACTC
* *
1423731 AGACTTGGTTATAACGTATCATCGGAGTAGGATGCATATACATAATTGATCATTATCACTCTCTC
1 AGACTTGGTTATAACGTATCATCCGAGTAGGATGCATATACATAATTGATCAATATCACTCTCTC
*
1423796 AATCAAGTGCAATGTTCTCAACTTT
66 AATCAAGTACAATGTTCTCAACTTT
1423821 AGACTTGGTTATAACGTATCATCCGAGTAGGATGCATATACATAATTGATCAATATCACTCTCTC
1 AGACTTGGTTATAACGTATCATCCGAGTAGGATGCATATACATAATTGATCAATATCACTCTCTC
1423886 AATCAAGTACAATGTTCTCAACTTT
66 AATCAAGTACAATGTTCTCAACTTT
1423911 GATCTAAGAA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (90 bp):
AGACTTGGTTATAACGTATCATCCGAGTAGGATGCATATACATAATTGATCAATATCACTCTCTC
AATCAAGTACAATGTTCTCAACTTT
Found at i:1426149 original size:13 final size:13
Alignment explanation
Indices: 1426118--1426162 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
1426108 TAAAATATAA
1426118 AAAATTA-TTTTT
1 AAAATTATTTTTT
1426130 AATAATTATTTTTT
1 AA-AATTATTTTTT
1426144 AAAATTTATATTTTT
1 AAAA-TTAT-TTTTT
1426159 AAAA
1 AAAA
1426163 AGTTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.07
13 7 0.24
14 11 0.38
15 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:1426163 original size:16 final size:15
Alignment explanation
Indices: 1426123--1426163 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
1426113 TATAAAAAAT
*
1426123 TATTTTTAATAATTA
1 TATTTTTAAAAATTA
*
1426138 T-TTTTTAAAATTTA
1 TATTTTTAAAAATTA
1426152 TATTTTTAAAAA
1 TATTTTTAAAAA
1426164 GTTTTTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTTAAAAATTA
Found at i:1427929 original size:33 final size:34
Alignment explanation
Indices: 1427838--1428013 Score: 266
Period size: 34 Copynumber: 5.1 Consensus size: 34
1427828 TCGACTTATT
1427838 CACCTTCTTCTTTTCAAAGCCCACAACTCCGTGG
1 CACCTTCTTCTTTTCAAAGCCCACAACTCCGTGG
1427872 CACCTTCTTCTTTTCAAAGCCCACAACTCCGTGG
1 CACCTTCTTCTTTTCAAAGCCCACAACTCCGTGG
**
1427906 CACCTTCTTCTTTT-AAAGCCCACAACTTTGTGG
1 CACCTTCTTCTTTTCAAAGCCCACAACTCCGTGG
*
1427939 CACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGG
1 CAC-C-TTCTT-CTTTTCAAAGCCCACAACTCCGTGG
* *
1427976 CACCTTTTTCTTTT-AAAGCCCACAACTCTGTGG
1 CACCTTCTTCTTTTCAAAGCCCACAACTCCGTGG
1428009 CACCT
1 CACCT
1428014 ACAACTTTGT
Statistics
Matches: 132, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
33 43 0.33
34 54 0.41
35 9 0.07
36 6 0.05
37 20 0.15
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.33
Consensus pattern (34 bp):
CACCTTCTTCTTTTCAAAGCCCACAACTCCGTGG
Found at i:1427970 original size:70 final size:70
Alignment explanation
Indices: 1427838--1428157 Score: 358
Period size: 70 Copynumber: 4.3 Consensus size: 70
1427828 TCGACTTATT
* *
1427838 CACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCAC-C-TTCTT-CTTTTCAAAGCCCACAACT
1 CACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACT
1427900 CCGTGG
65 CCGTGG
* **
1427906 CACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTC
1 CACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTC
1427971 CGTGG
66 CGTGG
*
1427976 CACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCTACAACTTTGTGGCACTCTCTTTCCCTT
1 CACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCA-CT----C----T-----T-T-TTT-CCTT
*
1428041 TTTAAAGCCCACAACTCCGTGG
49 TTCAAAGCCCACAACTCCGTGG
*
1428063 CACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACT
1 CACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACT
1428128 CCGTGG
65 CCGTGG
* *
1428134 CACTTTTTTCTTCTAAAGCCCACA
1 CACCTTTTTCTTTTAAAGCCCACA
1428158 CAAGTCGGTG
Statistics
Matches: 220, Mismatches: 11, Indels: 40
0.81 0.04 0.15
Matches are distributed among these distances:
67 20 0.09
68 15 0.07
69 4 0.02
70 70 0.32
71 37 0.17
72 2 0.01
73 1 0.00
74 1 0.00
75 1 0.00
79 2 0.01
83 1 0.00
84 1 0.00
85 1 0.00
86 3 0.01
87 38 0.17
88 23 0.10
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.33
Consensus pattern (70 bp):
CACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTC
CGTGG
Found at i:1428064 original size:37 final size:36
Alignment explanation
Indices: 1428022--1428143 Score: 176
Period size: 37 Copynumber: 3.4 Consensus size: 36
1428012 CTACAACTTT
1428022 GTGGCACTCTCTTTCCCTTTTTAAAGCCCACAACTCC
1 GTGGCACTCT-TTTCCCTTTTTAAAGCCCACAACTCC
* *
1428059 GTGGCAC-CTTTT-TCTGTTTAAAGCCCACAACTCC
1 GTGGCACTCTTTTCCCTTTTTAAAGCCCACAACTCC
*
1428093 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCC
1 GTGGCACTC-TTTTCCCTTTTTAAAGCCCACAACTCC
*
1428130 GTGGCACTTTTTTC
1 GTGGCACTCTTTTC
1428144 TTCTAAAGCC
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
34 27 0.36
35 4 0.05
36 11 0.14
37 34 0.45
ACGTcount: A:0.18, C:0.34, G:0.13, T:0.34
Consensus pattern (36 bp):
GTGGCACTCTTTTCCCTTTTTAAAGCCCACAACTCC
Found at i:1428073 original size:87 final size:88
Alignment explanation
Indices: 1427927--1428099 Score: 303
Period size: 87 Copynumber: 2.0 Consensus size: 88
1427917 TTTAAAGCCC
* *
1427927 ACAACTTTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTA
1 ACAACTTTGTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
*
1427991 AAGCCCACAACTCTGTGGCACCT
66 AAGCCCACAACTCCGTGGCACCT
*
1428014 ACAACTTTGTGGCACTCTCTTTCCCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
1 ACAACTTTGTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
1428079 AAGCCCACAACTCCGTGGCAC
66 AAGCCCACAACTCCGTGGCAC
1428100 TCTTTTTCCC
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 57 0.70
88 24 0.30
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (88 bp):
ACAACTTTGTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
AAGCCCACAACTCCGTGGCACCT
Found at i:1428084 original size:34 final size:33
Alignment explanation
Indices: 1428040--1428157 Score: 173
Period size: 34 Copynumber: 3.4 Consensus size: 33
1428030 CTCTTTCCCT
1428040 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
1428073 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 T-TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--C
*
1428110 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
*
1428144 TTCTAAAGCCCACA
1 TTTTAAAGCCCACA
1428158 CAAGTCGGTG
Statistics
Matches: 78, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
33 11 0.14
34 29 0.37
35 6 0.08
36 8 0.10
37 24 0.31
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (33 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
Found at i:1428119 original size:71 final size:70
Alignment explanation
Indices: 1428022--1428157 Score: 227
Period size: 71 Copynumber: 1.9 Consensus size: 70
1428012 CTACAACTTT
* *
1428022 GTGGCACTCTCTTTCCCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCAC
1 GTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCT-TCTAAAGCCCAC
1428087 AACTCC
65 AACTCC
* *
1428093 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTCTAAAGCCCACA
1 GTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTCTAAAGCCCACA
1428158 CAAGTCGGTG
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
70 12 0.20
71 49 0.80
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (70 bp):
GTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTCTAAAGCCCACA
ACTCC
Found at i:1428236 original size:49 final size:49
Alignment explanation
Indices: 1428178--1428715 Score: 603
Period size: 49 Copynumber: 10.8 Consensus size: 49
1428168 GCAACCCTTC
* *
1428178 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
1428227 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1428276 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
1428325 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
1428374 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * * * *
1428423 TAAGTCCAATGTAGCTGGCCTTGACTTAGCACATTGGCA-TTTCCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-CATCTT
* *
1428472 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
1428520 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1428569 TCAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * * *
1428621 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC----T--TCATCTT
* * * * *
1428677 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
1428716 TCTTTATCAC
Statistics
Matches: 409, Mismatches: 69, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
48 40 0.10
49 286 0.70
51 2 0.00
52 39 0.10
53 2 0.00
55 3 0.01
56 36 0.09
57 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:1428352 original size:98 final size:97
Alignment explanation
Indices: 1428178--1428656 Score: 737
Period size: 98 Copynumber: 4.9 Consensus size: 97
1428168 GCAACCCTTC
* *
1428178 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTCATCTTTAAGTCCAATGTAGCT
1428243 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
65 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
*
1428276 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTCATCTTTAAGTCCAATGTAGCT
1428341 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
65 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
* *
1428374 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC-TTCATCTTTAAGTCCAATGTAGCT
* *
1428439 GGCCTTGACTTAGCACATTGGCA-TTTCCACCAT
65 GGCCTTGACTCAGCACATTGGCACCTT-CACCAT
*
1428472 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC-TTCATCTTTAAGTCCAATGTAGCT
* *
1428536 GGCCTTGACTCAGCACATTGGCACCTTCATCTT
65 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
* * *
1428569 TCAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C--TT-CATCTTTAAGTCCAATGTA
*
1428634 GCTGGCCTTGAATCAGCACATTG
62 GCTGGCCTTGACTCAGCACATTG
1428657 ACATCCTTTT
Statistics
Matches: 355, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
97 92 0.26
98 220 0.62
99 1 0.00
100 3 0.01
101 39 0.11
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (97 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTCATCTTTAAGTCCAATGTAGCTG
GCCTTGACTCAGCACATTGGCACCTTCACCAT
Found at i:1428588 original size:195 final size:196
Alignment explanation
Indices: 1428178--1428656 Score: 766
Period size: 195 Copynumber: 2.4 Consensus size: 196
1428168 GCAACCCTTC
* * *
1428178 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCT
1428243 GGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
66 GGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
1428308 ATTGGCATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCA
131 ATTGGCATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCA
1428373 T
196 T
1428374 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCT
* *
1428439 GGCCTTGACTTAGCACATTGGCA-TTTCCACCATTAAGTCC-ATATAGCTGGCCTTGAATCAGCA
66 GGCCTTGACTCAGCACATTGGCACCTT-CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCA
* * *
1428502 TATTGGCA-CTTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
130 TATTGGCATC-ATCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAC
*
1428566 CTT
194 CAT
* * * *
1428569 TCAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTTT--ATCTTTAAGTCCAATGTA
*
1428634 GCTGGCCTTGAATCAGCACATTG
63 GCTGGCCTTGACTCAGCACATTG
1428657 ACATCCTTTT
Statistics
Matches: 263, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
194 1 0.00
195 122 0.46
196 102 0.39
198 38 0.14
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (196 bp):
TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCT
GGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
ATTGGCATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCA
T
Found at i:1429622 original size:33 final size:33
Alignment explanation
Indices: 1429585--1429651 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1429575 TTCAACGATT
1429585 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1429618 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1429651 T
1 T
1429652 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1429623 original size:13 final size:13
Alignment explanation
Indices: 1429605--1429629 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1429595 CATAAAATGT
1429605 TGTATCGATACAA
1 TGTATCGATACAA
1429618 TGTATCGATACA
1 TGTATCGATACA
1429630 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1429712 original size:13 final size:13
Alignment explanation
Indices: 1429694--1429718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1429684 ATTACTCACA
1429694 TGTATCGATACAT
1 TGTATCGATACAT
1429707 TGTATCGATACA
1 TGTATCGATACA
1429719 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1429855 original size:52 final size:52
Alignment explanation
Indices: 1429727--1429843 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
1429717 CACTGATCTT
*
1429727 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1429779 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1429831 TGTATCGATACAT
1 TGTATCGATACAT
1429844 ACAGATAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1435250 original size:18 final size:18
Alignment explanation
Indices: 1435227--1435261 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1435217 TTTCATGAAA
1435227 GAGAAA-TTAGAAACTTTG
1 GAGAAATTTA-AAACTTTG
1435245 GAGAAATTTAAAACTTT
1 GAGAAATTTAAAACTTT
1435262 CAAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (18 bp):
GAGAAATTTAAAACTTTG
Found at i:1438274 original size:7 final size:7
Alignment explanation
Indices: 1438262--1438305 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
1438252 TATATAATGT
1438262 AAATAAA
1 AAATAAA
1438269 AAATAAA
1 AAATAAA
1438276 AAATAATTA
1 AAATAA--A
1438285 AAATAAA
1 AAATAAA
*
1438292 ATAT-AA
1 AAATAAA
1438298 AAATAAA
1 AAATAAA
1438305 A
1 A
1438306 TAAATTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 5 0.16
7 20 0.62
9 7 0.22
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAATAAA
Found at i:1438302 original size:13 final size:13
Alignment explanation
Indices: 1438262--1438307 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
1438252 TATATAATGT
*
1438262 AAATAAAAAATAA
1 AAATAAAATATAA
*
1438275 AAA-ATAAT-T-A
1 AAATAAAATATAA
1438285 AAATAAAATATAA
1 AAATAAAATATAA
1438298 AAATAAAATA
1 AAATAAAATA
1438308 AATTTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
10 4 0.15
11 5 0.19
12 4 0.15
13 14 0.52
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAAAATATAA
Found at i:1438304 original size:29 final size:29
Alignment explanation
Indices: 1438262--1438328 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1438252 TATATAATGT
1438262 AAATA-AAAAATAAAA-AATAATTAAAATA
1 AAATATAAAAATAAAATAA-AATTAAAATA
* *
1438290 AAATATAAAAATAAAATAAATTTAATATA
1 AAATATAAAAATAAAATAAAATTAAAATA
1438319 AATATATAAA
1 AA-ATATAAA
1438329 GATATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 5 0.15
29 20 0.59
30 9 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (29 bp):
AAATATAAAAATAAAATAAAATTAAAATA
Found at i:1438309 original size:23 final size:23
Alignment explanation
Indices: 1438262--1438309 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1438252 TATATAATGT
*
1438262 AAATAAAAAATAAAAAATAATTA
1 AAATAAAAAATAAAAAATAAATA
*
1438285 AAATAAAATAT-AAAAATAAAATA
1 AAATAAAAAATAAAAAAT-AAATA
1438308 AA
1 AA
1438310 TTTAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (23 bp):
AAATAAAAAATAAAAAATAAATA
Found at i:1438319 original size:11 final size:11
Alignment explanation
Indices: 1438253--1438419 Score: 74
Period size: 11 Copynumber: 14.6 Consensus size: 11
1438243 AATAAAGATT
*
1438253 ATATAATGTAA
1 ATATAATATAA
* *
1438264 ATAAAAAATAAA
1 ATATAATAT-AA
*
1438276 AAATAAT-TAAA
1 ATATAATAT-AA
*
1438287 ATAAAATATAA
1 ATATAATATAA
* *
1438298 AAATAAAATAA
1 ATATAATATAA
*
1438309 ATTTAATATAA
1 ATATAATATAA
1438320 ATAT-ATA-AA
1 ATATAATATAA
* *
1438329 GATATTAAAAATATG
1 -ATA-T-AATATA-A
1438344 ATATAAATATAA
1 ATAT-AATATAA
1438356 ATATAATATAA
1 ATATAATATAA
1438367 ATAT-ATATAA
1 ATATAATATAA
*
1438377 CATTTTAAATATAA
1 -A-TAT-AATATAA
* *
1438391 ATTATTACATAA
1 A-TATAATATAA
1438403 A-ATAATATAA
1 ATATAATATAA
*
1438413 ATGTAAT
1 ATATAAT
1438420 GTCAATATGT
Statistics
Matches: 117, Mismatches: 26, Indels: 26
0.69 0.15 0.15
Matches are distributed among these distances:
9 2 0.02
10 20 0.17
11 53 0.45
12 19 0.16
13 13 0.11
14 10 0.09
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1438322 original size:6 final size:6
Alignment explanation
Indices: 1438285--1438392 Score: 63
Period size: 6 Copynumber: 18.7 Consensus size: 6
1438275 AAAATAATTA
* *
1438285 AAATA- AAATAT AAAAAT AAA-AT AAAT-T TAATAT AAATAT --ATA-
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
* *
1438327 AAGATATT AAAAAT ATGATAT AAATAT AAATAT -AATAT AAATAT --ATAT
1 AA-ATA-T AAATAT A-AATAT AAATAT AAATAT AAATAT AAATAT AAATAT
*
1438375 AACATTTT AAATAT AAAT
1 AA-A-TAT AAATAT AAAT
1438393 TATTACATAA
Statistics
Matches: 80, Mismatches: 9, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
4 7 0.09
5 19 0.24
6 40 0.50
7 8 0.10
8 6 0.08
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (6 bp):
AAATAT
Found at i:1438357 original size:17 final size:17
Alignment explanation
Indices: 1438269--1438371 Score: 69
Period size: 17 Copynumber: 6.4 Consensus size: 17
1438259 TGTAAATAAA
*
1438269 AAATA-AAAAATAAT-T
1 AAATATAAATATAATAT
*
1438284 AAA-ATAAAATATAAAAAT
1 AAATAT-AAATAT-AATAT
*
1438302 AAA-ATAAATTTAATAT
1 AAATATAAATATAATAT
*
1438318 AAATAT--ATA-AAGAT
1 AAATATAAATATAATAT
* * *
1438332 -ATTAAAAATATGATAT
1 AAATATAAATATAATAT
1438348 AAATATAAATATAATAT
1 AAATATAAATATAATAT
1438365 AAATATA
1 AAATATA
1438372 TATAACATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
13 3 0.05
14 5 0.08
15 8 0.12
16 15 0.23
17 29 0.44
18 6 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AAATATAAATATAATAT
Found at i:1440930 original size:27 final size:26
Alignment explanation
Indices: 1440887--1440953 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
1440877 TTTTTACTAT
* *
1440887 ATATATTT-TTATTTTTAATGTAACTA
1 ATAT-TTTATTATTTTTAATATAAATA
1440913 AT-TTTTAATTATTATTTAATATAAATA
1 ATATTTT-ATTATT-TTTAATATAAATA
1440940 ATATTTTATTATTT
1 ATATTTTATTATTT
1440954 AATATGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
24 3 0.09
25 1 0.03
26 8 0.23
27 19 0.54
28 4 0.11
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (26 bp):
ATATTTTATTATTTTTAATATAAATA
Found at i:1441116 original size:91 final size:92
Alignment explanation
Indices: 1440944--1441116 Score: 276
Period size: 91 Copynumber: 1.9 Consensus size: 92
1440934 TAAATAATAT
* *
1440944 TTTATTATTTAATATGTATATCAATTTTTAGCATAAATATAATTTTAATCAATTTTAATTATTAT
1 TTTATTATTTAATATGTATATCAATTTTTAACATAAATATAATTTTAATCAATTTCAATTATTAT
* *
1441009 TCAACATAAGTGTAATTTCATTTATAG
66 TCAACATAAATATAATTTCATTTATAG
*
1441036 TTTATTATTTAATATTTATAT-AATTTTTAACATAAATATAATTTTAATCAATTTCAATTATTAT
1 TTTATTATTTAATATGTATATCAATTTTTAACATAAATATAATTTTAATCAATTTCAATTATTAT
**
1441100 TCTGCATAAATATAATT
66 TCAACATAAATATAATT
1441117 CTTAAGTATT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 54 0.73
92 20 0.27
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.51
Consensus pattern (92 bp):
TTTATTATTTAATATGTATATCAATTTTTAACATAAATATAATTTTAATCAATTTCAATTATTAT
TCAACATAAATATAATTTCATTTATAG
Found at i:1441829 original size:51 final size:51
Alignment explanation
Indices: 1441768--1441864 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
1441758 AACACGATTA
* *
1441768 AAATGGTCACAATGTGTCGTAATTTTATTAGACCTCAAAAAGAATATAATT
1 AAATGATCACAATGTGTCGTAATCTTATTAGACCTCAAAAAGAATATAATT
* *
1441819 AAATGATCACAATGTGTCGTAATCTTATTGGATCTCAAAAAGAATA
1 AAATGATCACAATGTGTCGTAATCTTATTAGACCTCAAAAAGAATA
1441865 CTGTACTGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (51 bp):
AAATGATCACAATGTGTCGTAATCTTATTAGACCTCAAAAAGAATATAATT
Found at i:1442996 original size:16 final size:16
Alignment explanation
Indices: 1442959--1442998 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
1442949 ATTTAAATTT
*
1442959 AATTATAAAATATATA
1 AATTTTAAAATATATA
1442975 AA-TTTAAAATATATA
1 AATTTTAAAATATATA
1442990 AATTTTAAA
1 AATTTTAAA
1442999 TCTTTCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTTAAAATATATA
Found at i:1442998 original size:22 final size:21
Alignment explanation
Indices: 1442948--1442999 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1442938 ATAATATTTT
*
1442948 TATTTAAATTTAATTATAAAA
1 TATTTAAATTTAAATATAAAA
*
1442969 TATATAAATTTAAAATATATAAA
1 TATTTAAATTT-AAATATA-AAA
1442992 T-TTTAAAT
1 TATTTAAAT
1443000 CTTTCTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 10 0.38
22 12 0.46
23 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTAAATTTAAATATAAAA
Found at i:1444956 original size:18 final size:18
Alignment explanation
Indices: 1444913--1444961 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
1444903 TTAAACCAAA
*
1444913 AATAATTTGAGTTAAAAAT
1 AATAATTT-ATTTAAAAAT
1444932 AATAATTCTATTTAAAAAT
1 AATAATT-TATTTAAAAAT
1444951 AA-AATTTATTT
1 AATAATTTATTT
1444962 CACATTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 18 0.64
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (18 bp):
AATAATTTATTTAAAAAT
Found at i:1445519 original size:44 final size:45
Alignment explanation
Indices: 1445451--1445538 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 45
1445441 TCATAAAATC
1445451 AAAGATTTTCCAGTCTTCAACAATTGTTGAGAATGAAGGGCTACG
1 AAAGATTTTCCAGTCTTCAACAATTGTTGAGAATGAAGGGCTACG
*
1445496 AAAGATTTT-CAGTCTTCAGCAATTGTTGAGAATGAAGGGCTAC
1 AAAGATTTTCCAGTCTTCAACAATTGTTGAGAATGAAGGGCTAC
1445539 TAAACCCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 33 0.79
45 9 0.21
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (45 bp):
AAAGATTTTCCAGTCTTCAACAATTGTTGAGAATGAAGGGCTACG
Found at i:1445989 original size:11 final size:10
Alignment explanation
Indices: 1445945--1446034 Score: 60
Period size: 11 Copynumber: 8.6 Consensus size: 10
1445935 TAAATACGAG
1445945 ATAATTATATT
1 ATAA-TATATT
*
1445956 A-AATA-AAT
1 ATAATATATT
*
1445964 ATAATATAAT
1 ATAATATATT
1445974 ATAATATATT
1 ATAATATATT
1445984 ATTAATATATT
1 A-TAATATATT
*
1445995 A-AATGTATT
1 ATAATATATT
1446004 AATATATAATATT
1 -ATA-AT-ATATT
*
1446017 TTAAATATAATT
1 AT-AATAT-ATT
1446029 ATAATA
1 ATAATA
1446035 CGATATGAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
8 3 0.05
9 13 0.20
10 16 0.25
11 18 0.28
12 9 0.14
13 5 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (10 bp):
ATAATATATT
Found at i:1446005 original size:17 final size:16
Alignment explanation
Indices: 1445970--1446010 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1445960 AAATATAATA
* *
1445970 TAATATAATATATTAT
1 TAATATATTAAATTAT
1445986 TAATATATTAAATGTAT
1 TAATATATTAAAT-TAT
1446003 TAATATAT
1 TAATATAT
1446011 AATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TAATATATTAAATTAT
Found at i:1446689 original size:22 final size:22
Alignment explanation
Indices: 1446664--1446705 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1446654 ATTAAAATAT
1446664 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1446686 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1446706 AATAAAATAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1450374 original size:17 final size:17
Alignment explanation
Indices: 1450333--1450378 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1450323 TTTAGAATTA
*
1450333 AATTTAAATAAAAATATT
1 AATTTAAAT-TAAATATT
1450351 --TTATAAATTAAATATT
1 AATT-TAAATTAAATATT
1450367 AATTTAAATTAA
1 AATTTAAATTAA
1450379 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 9 0.38
17 13 0.54
18 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTAAATTAAATATT
Found at i:1450375 original size:28 final size:27
Alignment explanation
Indices: 1450304--1450384 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 27
1450294 TAAAATATTT
* * *
1450304 TTAAATAAT-ATTTATATATTTTAGAA
1 TTAAATATTAATTTAAATATTTTAAAA
**
1450330 TTAAAT-TTAAATAAAAATATTTTATAAA
1 TTAAATATT-AATTTAAATATTTTA-AAA
*
1450358 TTAAATATTAATTTAAATTAATTTAAA
1 TTAAATATTAATTTAAA-TATTTTAAA
1450385 TAAAAAATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
25 1 0.02
26 6 0.14
27 11 0.26
28 16 0.38
29 8 0.19
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
TTAAATATTAATTTAAATATTTTAAAA
Found at i:1452274 original size:13 final size:13
Alignment explanation
Indices: 1452246--1452288 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1452236 TTTCATATTT
*
1452246 TTTAATTATTTTTA
1 TTTAA-TATTTATA
1452260 TTTAATATTTATA
1 TTTAATATTTATA
1452273 TTTAATA--TATA
1 TTTAATATTTATA
1452284 TTTAA
1 TTTAA
1452289 ATATAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 9 0.32
13 14 0.50
14 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:1452721 original size:32 final size:33
Alignment explanation
Indices: 1452653--1452725 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
1452643 AATTATGTAA
* * *
1452653 ATATAATATAAATATATAAATATATTAAAATTT
1 ATATAATAAAAATATATAAACATATCAAAATTT
* *
1452686 ATATAATAAAAAT-TATTAACATATCAATATTT
1 ATATAATAAAAATATATAAACATATCAAAATTT
1452718 ATATAATA
1 ATATAATA
1452726 TATAATATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 23 0.66
33 12 0.34
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (33 bp):
ATATAATAAAAATATATAAACATATCAAAATTT
Found at i:1452760 original size:20 final size:21
Alignment explanation
Indices: 1452720--1452773 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
1452710 CAATATTTAT
* *
1452720 ATAATATATAATATTTTAAAA
1 ATAATATATAATATATAAAAA
1452741 ATAAT-TATAATATAT-AAAA
1 ATAATATATAATATATAAAAA
*
1452760 ATTATATA-AATATA
1 ATAATATATAATATA
1452774 ATATTAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 14 0.47
20 11 0.37
21 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATATATAATATATAAAAA
Found at i:1454785 original size:2 final size:2
Alignment explanation
Indices: 1454780--1454821 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1454770 ATATATATAT
* *
1454780 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG TG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1454822 TGACACACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.50, T:0.05
Consensus pattern (2 bp):
AG
Found at i:1455113 original size:12 final size:12
Alignment explanation
Indices: 1455096--1455126 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1455086 CCACCATTGA
*
1455096 CATCATCATCGT
1 CATCATCATCGC
1455108 CATCATCATCGC
1 CATCATCATCGC
1455120 CATCATC
1 CATCATC
1455127 TGTTCTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.39, G:0.06, T:0.29
Consensus pattern (12 bp):
CATCATCATCGC
Found at i:1456253 original size:14 final size:15
Alignment explanation
Indices: 1456234--1456262 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1456224 TATAATATAT
1456234 AATTAAAAAT-TAAA
1 AATTAAAAATATAAA
1456248 AATTAAAAATATAAA
1 AATTAAAAATATAAA
1456263 TAATAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATTAAAAATATAAA
Found at i:1456662 original size:21 final size:18
Alignment explanation
Indices: 1456630--1456684 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 18
1456620 ATTTATTTAA
*
1456630 ATATAAATATAAAAATAT
1 ATATAAAAATAAAAATAT
*
1456648 AATTTTTAAAAATAAAAATAT
1 -A--TATAAAAATAAAAATAT
1456669 ATATAAAAATAAAAAT
1 ATATAAAAATAAAAAT
1456685 TTTAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 14 0.45
19 1 0.03
20 1 0.03
21 15 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAAAAATAAAAATAT
Found at i:1456702 original size:33 final size:33
Alignment explanation
Indices: 1456627--1456690 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1456617 AATATTTATT
* * * *
1456627 TAAATATAAATATAAAAATATAATTTTTAAAAA
1 TAAAAATATATATAAAAATAAAAATTTTAAAAA
1456660 TAAAAATATATATAAAAATAAAAATTTTAAA
1 TAAAAATATATATAAAAATAAAAATTTTAAA
1456691 TATTATCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (33 bp):
TAAAAATATATATAAAAATAAAAATTTTAAAAA
Found at i:1457508 original size:3 final size:3
Alignment explanation
Indices: 1457500--1457527 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1457490 TTTGCATGCT
1457500 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1457528 GTATAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1461713 original size:91 final size:90
Alignment explanation
Indices: 1461616--1461812 Score: 310
Period size: 91 Copynumber: 2.2 Consensus size: 90
1461606 ATTATATTTT
*
1461616 TATTAAATAAT-AATATATAAATGAAATTATATTTAT-TCAGAATAATAATTGAAATTGATTAAA
1 TATTAAATAATAAAT-TATAAATGAAATTATACTTATGT-AGAATAATAATTGAAATTGATTAAA
1461679 ATTATATTTATGTTAAAAATT-ATATACA
64 ATTATATTTATGTTAAAAATTGATAT--A
*
1461707 TATTAAATAATAAATTATAAATGAAATTATACTTATGTTGAATAATAATTGAAATTGATTAAAAT
1 TATTAAATAATAAATTATAAATGAAATTATACTTATGTAGAATAATAATTGAAATTGATTAAAAT
1461772 TATATTTATGTTAAAAATTGATATA
66 TATATTTATGTTAAAAATTGATATA
1461797 TATTAAATAATCAAAT
1 TATTAAATAAT-AAAT
1461813 ATTATTTATA
Statistics
Matches: 100, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
90 12 0.12
91 80 0.80
92 8 0.08
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (90 bp):
TATTAAATAATAAATTATAAATGAAATTATACTTATGTAGAATAATAATTGAAATTGATTAAAAT
TATATTTATGTTAAAAATTGATATA
Found at i:1461868 original size:26 final size:26
Alignment explanation
Indices: 1461833--1461895 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
1461823 TTAAATAATA
* *
1461833 ATTAAAAATAAGTAAATATTATTTAT
1 ATTAAAAATAAGTAAAAATTAGTTAT
* *
1461859 ATTAAGAATAATTAAAAATTAGTTAT
1 ATTAAAAATAAGTAAAAATTAGTTAT
1461885 ATTAAAAATAA
1 ATTAAAAATAA
1461896 AAAATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (26 bp):
ATTAAAAATAAGTAAAAATTAGTTAT
Found at i:1461876 original size:36 final size:37
Alignment explanation
Indices: 1461801--1461877 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1461791 GATATATATT
*
1461801 AAATAATCAAATATTATTTATATTAAATAATAATTAA
1 AAATAATCAAATATTATTTATATTAAAGAATAATTAA
1461838 AAATAAGT-AAATATTATTTATATT-AAGAATAATTAA
1 AAATAA-TCAAATATTATTTATATTAAAGAATAATTAA
1461874 AAAT
1 AAAT
1461878 TAGTTATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 15 0.39
37 22 0.58
38 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (37 bp):
AAATAATCAAATATTATTTATATTAAAGAATAATTAA
Found at i:1461907 original size:26 final size:26
Alignment explanation
Indices: 1461833--1461907 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
1461823 TTAAATAATA
*
1461833 ATTAAAAATAAGT-AAATATTATTTAT
1 ATTAAAAATAA-TAAAATATTAGTTAT
*
1461859 ATTAAGAATAATTAAAA-ATTAGTTAT
1 ATTAAAAATAA-TAAAATATTAGTTAT
1461885 ATTAAAAATAA-AAAATATATAGT
1 ATTAAAAATAATAAAATAT-TAGT
1461908 AAAAAATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 4 0.10
25 2 0.05
26 33 0.79
27 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.37
Consensus pattern (26 bp):
ATTAAAAATAATAAAATATTAGTTAT
Found at i:1463251 original size:17 final size:19
Alignment explanation
Indices: 1463218--1463271 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 19
1463208 AATTTAAAAA
1463218 TTTATATATTTATATTATG
1 TTTATATATTTATATTATG
1463237 TTTATATA-TTA-ATTATG
1 TTTATATATTTATATTATG
*
1463254 TTTAAAATATTATATATT
1 TTT-ATATATT-TATATT
1463272 CACATAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.30
18 7 0.23
19 9 0.30
20 2 0.07
21 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTATATATTTATATTATG
Found at i:1464377 original size:11 final size:11
Alignment explanation
Indices: 1464317--1464489 Score: 72
Period size: 11 Copynumber: 15.3 Consensus size: 11
1464307 ATTGACATTG
1464317 TATTTATATTA
1 TATTTATATTA
* *
1464328 T-TTTATGTAA
1 TATTTATATTA
1464338 TAATTTATATTTAA
1 T-ATTTATA-TT-A
* *
1464352 AATGTTAT-GTA
1 TAT-TTATATTA
1464363 TATTTATATTA
1 TATTTATATTA
1464374 TATTTATATTA
1 TATTTATATTA
*
1464385 TTTTTATATTTA
1 TATTTATA-TTA
* *
1464397 TATCATATTTTTAA
1 TAT-TTA-TATT-A
*
1464411 CATCTT-TA-TA
1 TAT-TTATATTA
1464421 TATTTATATTA
1 TATTTATATTA
* * *
1464432 AATTAATTTTA
1 TATTTATATTA
1464443 -ATTTTATATCT-
1 TA-TTTATAT-TA
1464454 TATTT-TAATTA
1 TATTTAT-ATTA
* *
1464465 TTTTTATATTT
1 TATTTATATTA
1464476 TATTTATATTA
1 TATTTATATTA
1464487 TAT
1 TAT
1464490 CATTTTTATT
Statistics
Matches: 119, Mismatches: 25, Indels: 36
0.66 0.14 0.20
Matches are distributed among these distances:
9 2 0.02
10 20 0.17
11 64 0.54
12 15 0.13
13 7 0.06
14 11 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTATATTA
Found at i:1464397 original size:28 final size:28
Alignment explanation
Indices: 1464317--1464498 Score: 105
Period size: 28 Copynumber: 6.6 Consensus size: 28
1464307 ATTGACATTG
* * *
1464317 TATTTATATTATTTTATGTAATAAT-TTA
1 TATTTATATTATTTT-TATATTTATATTA
* * * *
1464345 TATTTAAAATGTTATGTATATTTATATTA
1 TATTTATATTATT-TTTATATTTATATTA
*
1464374 TATTTATATTATTTTTATATTTATATCA
1 TATTTATATTATTTTTATATTTATATTA
* ** *
1464402 TATTTTTAACATCTTTATA--TAT-TTA
1 TATTTATATTATTTTTATATTTATATTA
* *
1464427 TA-TTAAATTAATTTTA-ATTTTATATCT-
1 TATTTATATTATTTTTATA-TTTATAT-TA
1464454 TATTT-TAATTATTTTTATATTT-TATT-
1 TATTTAT-ATTATTTTTATATTTATATTA
*
1464480 TATATTATATCATTTTTAT
1 TAT-TTATATTATTTTTAT
1464499 TATATCTAAA
Statistics
Matches: 116, Mismatches: 26, Indels: 25
0.69 0.16 0.15
Matches are distributed among these distances:
23 1 0.01
24 8 0.07
25 4 0.03
26 10 0.09
27 18 0.16
28 60 0.52
29 15 0.13
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (28 bp):
TATTTATATTATTTTTATATTTATATTA
Found at i:1464471 original size:52 final size:53
Alignment explanation
Indices: 1464367--1464486 Score: 135
Period size: 52 Copynumber: 2.3 Consensus size: 53
1464357 TATGTATATT
*
1464367 TATA-TTATATTTATATT-ATTTTTATATTTATATCATATTTTTAACATCTTTA
1 TATATTTATA-TTATATTAATTTTAATATTTATATCATATTTTTAACATCTTTA
* * * *
1464419 TATATTTATATTAAATTAATTTTAAT-TTTATATCTTA-TTTTAATTATTTTTA
1 TATATTTATATTATATTAATTTTAATATTTATATCATATTTTTAA-CATCTTTA
1464471 TAT-TTTAT-TTATATTA
1 TATATTTATATTATATTA
1464487 TATCATTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
50 7 0.12
51 11 0.19
52 29 0.49
53 12 0.20
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (53 bp):
TATATTTATATTATATTAATTTTAATATTTATATCATATTTTTAACATCTTTA
Found at i:1468666 original size:90 final size:90
Alignment explanation
Indices: 1468513--1468692 Score: 326
Period size: 90 Copynumber: 2.0 Consensus size: 90
1468503 TTCTTCGATC
* *
1468513 AAAGTTGAGAACATTGTACTTGATTGAGAGAGTGATATTGATCAATTATGTATATGCATCCTAC-
1 AAAGTTGAGAACATTGCACTTGATTGAGAGAGTGATAATGATCAATTATGTATATGCATCCTACT
1468577 TCGGATGATACGTTATAACCAAGTCT
66 TC-GATGATACGTTATAACCAAGTCT
1468603 AAAGTTGAGAACATTGCACTTGATTGAGAGAGTGATAATGATCAATTATGTATATGCATCCTACT
1 AAAGTTGAGAACATTGCACTTGATTGAGAGAGTGATAATGATCAATTATGTATATGCATCCTACT
1468668 TCGATGATACGTTATAACCAAGTCT
66 TCGATGATACGTTATAACCAAGTCT
1468693 GAGTATGTAT
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
90 85 0.98
91 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (90 bp):
AAAGTTGAGAACATTGCACTTGATTGAGAGAGTGATAATGATCAATTATGTATATGCATCCTACT
TCGATGATACGTTATAACCAAGTCT
Found at i:1471713 original size:16 final size:15
Alignment explanation
Indices: 1471667--1471720 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1471657 ATTTATATAC
*
1471667 ATATTAAATAATAA-A
1 ATATTTAATAA-AATA
1471682 ATATTTAATAAAATA
1 ATATTTAATAAAATA
*
1471697 ATATTTATATTAAATA
1 ATATTTA-ATAAAATA
*
1471713 ATAATTAA
1 ATATTTAA
1471721 AAATTAGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.06
15 19 0.56
16 13 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTTAATAAAATA
Found at i:1471743 original size:38 final size:38
Alignment explanation
Indices: 1471667--1471764 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
1471657 ATTTATATAC
* *
1471667 ATATTAAATAATAA--AATATTTAATAAAATAATATTT
1 ATATTAAATAATAATTAAAAATTAATAAAATAATATTT
* * *
1471703 ATATTAAATAATAATTAAAAATTAGTGAAATATTATTT
1 ATATTAAATAATAATTAAAAATTAATAAAATAATATTT
*
1471741 ATACTAAATAATAATTAAAAATTA
1 ATATTAAATAATAATTAAAAATTA
1471765 CTTATATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 14 0.26
38 40 0.74
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (38 bp):
ATATTAAATAATAATTAAAAATTAATAAAATAATATTT
Found at i:1472286 original size:19 final size:17
Alignment explanation
Indices: 1472251--1472292 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1472241 TGTTAACAAC
1472251 ATTT-AAAAAATATTTA
1 ATTTAAAAAAATATTTA
1472267 ATTTAAAAATAATAATTTA
1 ATTTAAAAA-AAT-ATTTA
1472286 ATATTAA
1 AT-TTAA
1472293 TTATATTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 4 0.18
18 3 0.14
19 7 0.32
20 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAAAAATATTTA
Found at i:1474235 original size:6 final size:6
Alignment explanation
Indices: 1474212--1474334 Score: 75
Period size: 6 Copynumber: 21.5 Consensus size: 6
1474202 TTATGTAATA
* * * *
1474212 ATTTAT ATTTAA AATTAT ATTTAT ATTTAT ATGATAT TTTTAAT ATTT-T
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT-TTAT ATTT-AT ATTTAT
* * *
1474261 -TATAT ATTTAT A--TAA ATTTAT -TTTAT TTTTAT ATTT-T ATTT-T
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
* *
1474303 AATTATT TTTTAT ATTT-T ATTTAT A-TTAT ATT
1 ATTTA-T ATTTAT ATTTAT ATTTAT ATTTAT ATT
1474335 ATGCTTATTA
Statistics
Matches: 89, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
4 5 0.06
5 26 0.29
6 45 0.51
7 13 0.15
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:1474286 original size:51 final size:52
Alignment explanation
Indices: 1474212--1474334 Score: 137
Period size: 51 Copynumber: 2.4 Consensus size: 52
1474202 TTATGTAATA
1474212 ATTTATATTTAAAATTATATTTATATTTATATGATATTTTTAA-TATTTTTATAT
1 ATTTATA-TTAAAATTATATTTATATTTATATGATA-TTTTAATTATTTTT-TAT
* * **
1474266 ATTTATA-TAAATTTAT-TTTATTTTTATATTTTATTTTAATTATTTTTTAT
1 ATTTATATTAAAATTATATTTATATTTATATGATATTTTAATTATTTTTTAT
* *
1474316 ATTT-TATTTATATTATATT
1 ATTTATATTAAAATTATATT
1474335 ATGCTTATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
49 2 0.03
50 19 0.32
51 23 0.39
52 8 0.14
54 7 0.12
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (52 bp):
ATTTATATTAAAATTATATTTATATTTATATGATATTTTAATTATTTTTTAT
Found at i:1474297 original size:13 final size:13
Alignment explanation
Indices: 1474279--1474324 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
1474269 TATATAAATT
1474279 TATTTTATTTTTA
1 TATTTTATTTTTA
1474292 TATTTTA-TTTTA
1 TATTTTATTTTTA
*
1474304 -ATTAT-TTTTTA
1 TATTTTATTTTTA
1474315 TATTTTATTT
1 TATTTTATTT
1474325 ATATTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 9 0.32
12 9 0.32
13 10 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTTTA
Found at i:1474303 original size:23 final size:23
Alignment explanation
Indices: 1474277--1474334 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1474267 TTTATATAAA
1474277 TTTATTTTATTTTTATATTTTAT
1 TTTATTTTATTTTTATATTTTAT
*
1474300 TTTA-ATTATTTTTTATATTTTAT
1 TTTATTTTA-TTTTTATATTTTAT
*
1474323 TTATATTATATT
1 TT-TATTTTATT
1474335 ATGCTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.10
23 20 0.69
24 4 0.14
25 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTATTTTATTTTTATATTTTAT
Found at i:1476637 original size:19 final size:18
Alignment explanation
Indices: 1476588--1476645 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
1476578 ACTGCCAGTT
1476588 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
*
1476607 TCCATTTATCGATACAATG
1 T-CATGTATCGATACAATG
1476626 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
1476645 T
1 T
1476646 ATCGATACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.54
20 15 0.43
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:1476647 original size:13 final size:13
Alignment explanation
Indices: 1476629--1476655 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1476619 TACAATGATC
1476629 ATGTATCGATACA
1 ATGTATCGATACA
1476642 ATGTATCGATACA
1 ATGTATCGATACA
1476655 A
1 A
1476656 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1476671 original size:33 final size:32
Alignment explanation
Indices: 1476613--1476674 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
1476603 ATTGTCCATT
* *
1476613 TATCGATACAATGATCATGTATCGATACAATG
1 TATCGATACAAAGATAATGTATCGATACAATG
1476645 TATCGATACAAAGCATAATGTATCGATACA
1 TATCGATACAAAG-ATAATGTATCGATACA
1476675 TTTGGGTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (32 bp):
TATCGATACAAAGATAATGTATCGATACAATG
Found at i:1476914 original size:21 final size:19
Alignment explanation
Indices: 1476890--1476928 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1476880 TAAGTGAGTA
1476890 AAACTTATTTACTGATTTTAC
1 AAACTT-TTTACTG-TTTTAC
*
1476911 AAACTTTTTTCTGTTTTA
1 AAACTTTTTACTGTTTTA
1476929 TTCAATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (19 bp):
AAACTTTTTACTGTTTTAC
Found at i:1478838 original size:13 final size:13
Alignment explanation
Indices: 1478820--1478846 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1478810 TTAGTAATCC
1478820 ATGTATCGATACA
1 ATGTATCGATACA
1478833 ATGTATCGATACA
1 ATGTATCGATACA
1478846 A
1 A
1478847 GGAATGTTGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1485053 original size:13 final size:13
Alignment explanation
Indices: 1485035--1485065 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1485025 ACAATTCATC
1485035 ATGTATCGATATA
1 ATGTATCGATATA
1485048 ATGTATCGATATA
1 ATGTATCGATATA
1485061 ATGTA
1 ATGTA
1485066 CCATGTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:1504590 original size:60 final size:58
Alignment explanation
Indices: 1504403--1506285 Score: 477
Period size: 60 Copynumber: 31.9 Consensus size: 58
1504393 GTAACACTCG
*
1504403 TTTAGTCCTCAAAGA-ACAGAACGCA-TTTTTT-AAAGCTCACACAAGTTGATGGCACCA
1 TTTAGTCCTCAAAGAGA-AG-ACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCACCA
* * *
1504460 GTTTAGTCTTCAAAGAGCAAGACGCCTTTTTTCTTTTAAAAGCTCACACAAGTTGGTGACACTCA
1 -TTTAGTCCTCAAAGAG-AAGACG-C--ATTT-TTTTAAAAGCTCACACAAGTTGGTGGCAC-CA
* *
1504525 TTTAGTCCTCAAAGAGAATGACGCATTTTTTTAAAAGCTCACATAAGTTGGTAGCACCA
1 TTTAGTCCTCAAAGAGAA-GACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCACCA
* * * * * *
1504584 TGTTAGTCCTTAAAGAGTAGGACGCCTTTTTTCAAAAGCCCATACAAGTTGGTGGCACCCA
1 T-TTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCA
* * * *
1504645 TTTAATCATCAAAGAGCAGGACGCATTTTTTTAAAAGC-CTACACAAGTTGGTGGTGC-CCG
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCTC-ACACAAGTTGGT-G-GCACCA
* * * *
1504705 TTTAGTCCTCAAAGAGCAAGATGCCTTTTTTTAAAAGCACACACAAGTTGGTGGCACCCG
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCA
* ** * * *
1504765 TTTAGTCCTCAAAGAGCATGACGTTTTTTTTTAAAAG-TC-CATAAAGTTAGTGGCACTCG
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCTCACA-CAAGTTGGTGGCAC-CA
* * * *
1504824 TTTTGTCCTCAAAGAGTAAGACGCCTTTTTTTAAAAG-TCCACACAAGTCGATGG---CA
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCT-CACACAAGTTGGTGGCACCA
* * * ** * **** * * *
1504880 TTT-CT-TTCTAAGCCCAATATCGC-TGACCTT-GAA--TCAGCAC-A----CTGGCACCC
1 TTTAGTCCTCAAAG-AGAAGA-CGCATTTTTTTAAAAGCTCA-CACAAGTTGGTGGCACCA
* * ** * *** * * *
1504930 TTACATGT--T-TAAGCCCAACGTCGC-TAGCCTTGAATTAGCCCACACAAGTTGGTGGCACCCA
1 TT-TA-GTCCTCAAAG-AGAA-GACGCAT-TTTTTTAA-AAGCTCACACAAGTTGGTGGCA-CCA
* * * * *
1504991 TTTAGTCTTCAAAGAGCAGGACATC-TTTTTTTAAAAGCACACACAAGTTGGTGACACCTA
1 TTTAGTCCTCAAAGAG-AAGAC-GCATTTTTTTAAAAGCTCACACAAGTTGGTGGCACC-A
* * * * * *
1505051 TTGAGTCCTCAAAGAGCATGACG-TTTTTTTTAAAAGCTCACACAAATTGGTAGCACCCTG
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CC-A
* * * *
1505111 TTTAGTCCTCAAAGAGCAGGACGTC-TTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCG
1 TTTAGTCCTCAAAGAG-AAGACG-CATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCA
* * * * *
1505171 TTTAGTCCT-AAAAAGACAGGACACCTTTTTTTAAAAG-TCCACACAAGTCGATGG---CA
1 TTTAGTCCTCAAAGAGA-A-GACGCATTTTTTTAAAAGCT-CACACAAGTTGGTGGCACCA
* * * ** * **** * * * *
1505227 TTT-CT-TTCTAAGCCTAATATCGC-TGACCTT-GAA--TCATCAC-A----CTAGCACCC
1 TTTAGTCCTCAAAG-AGAAGA-CGCATTTTTTTAAAAGCTCA-CACAAGTTGGTGGCACCA
* * ** * ** * * * * *
1505277 TTATCA-TGCT-TAAGCCCAATGTCGC-TAGCTTTGAATTAGCCCACACAAATTGGTGGCACCCG
1 TT-T-AGTCCTCAAAG-AGAA-GACGCAT-TTTTTTAA-AAGCTCACACAAGTTGGTGGCA-CCA
* * * *
1505339 TTTAGTCTTCAAAGGGCAAGACG--TTTTTTTAAAAGCACACACAAGTTGGTGGCACCCG
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCA
* * * * *
1505397 TTTAGTCCTCAAAGAGCAGAACGCCTTTTTTTAAAAAGCCCACACAAGTTGGTAGCACCTG
1 TTTAGTCCTCAAAGAGAAG-ACGCATTTTTTT-AAAAGCTCACACAAGTTGGTGGCACC-A
* * * * * *
1505458 TTTAGTCCTCAAAGAGTAGGATGCCTTTTTTCAAAAGCCCATACAAGTTGGTAGGCACCCA
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCTCACACAAGTTGGT-GGCA-CCA
* * *
1505519 TTTAGTCCTCAAAGAGTAGGACGCATTTTTTCAAAAGCAT-ACACAAATTGGTGGCACCTA
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGC-TCACACAAGTTGGTGGCACC-A
* * * * *
1505579 TTTCGTCCTCAAAGAGCATGACGC-TTTTTTTGAAAG-TCCACACAAGTTAGTGGCACTCG
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCT-CACACAAGTTGGTGGCAC-CA
* * *
1505638 TTTAGTCCTCAAAGAGCAAGACGTC-GTTTTTTAAAAG-TCCACACAAGTCGATGG-A--A
1 TTTAGTCCTCAAAGAG-AAGACG-CATTTTTTTAAAAGCT-CACACAAGTTGGTGGCACCA
* * * ** * * *** * * * ** * **
1505694 TTT-CT-TTCTAAGCCCAATATC-AATGACCTTGAATCAGCACACTGACACCTT--T-ACA-TG
1 TTTAGTCCTCAAAG-AGAAGA-CGCAT-TTTTTTAA-AAGCTCAC--ACAAGTTGGTGGCACCA
* * * *** * *
1505751 TTTAAG-CC-CAATGTCGCTAG-C-C-TTGAATT---AGCCCACACAAGTTGGTGGCACCCG
1 TTT-AGTCCTCAAAG-AG-AAGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCA
* * * *
1505805 TTTAGTCCTCAAAGAGTAGGACATC-TTTTTTTAAAAGCACACACAAGTTGGTGCCACCCA
1 TTTAGTCCTCAAAGAG-AAGAC-GCATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCA
* * * * * * *
1505865 TTTAGTCCTCAAAAAGCAGGACGCCTTTTTTTAAAAGCCCATACAAGTTGGTAGCACCTG
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCACC-A
* * * *
1505925 TTTAGTCCTCAAAGAGTATGACGTC-TTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCG
1 TTTAGTCCTCAAAGAG-AAGACG-CATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCA
* * * * * *
1505985 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGTACCCG
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCA
* * * ** **
1506045 TTTAGTCCCCAAAGAGCATGACGTC-TTTTTTTAAAAGCCCGTACAAGTTGGTGGCACTTG
1 TTTAGTCCTCAAAGAG-AAGACG-CATTTTTTTAAAAGCTCACACAAGTTGGTGGCAC-CA
* * * * *
1506105 TTTAGTCCTCAAAGAGCAGGACTCCTTTTTTTAAAAG-TCCACACAAGTTGGTGACACTA
1 TTTAGTCCTCAAAGAG-AAGACGCATTTTTTTAAAAGCT-CACACAAGTTGGTGGCACCA
* * * * *
1506164 GTTTAGTCCTTAAAGA-ACGAGATGCTTTTTTCTTTTAAAG-TCCACACAAGTTGGTGGCACCCG
1 -TTTAGTCCTCAAAGAGA--AGACGC-ATTTT-TTTAAAAGCT-CACACAAGTTGGTGGCA-CCA
* * * * *
1506227 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTTTTTTCAAAGCCCACATAAGTTGGTGGCA
1 TTTAGTCCTCAAAGAG-AAGACG-C--ATTTTTTTAAAAGCTCACACAAGTTGGTGGCA
1506286 ACTCTCTTAT
Statistics
Matches: 1400, Mismatches: 280, Indels: 285
0.71 0.14 0.15
Matches are distributed among these distances:
47 5 0.00
49 5 0.00
50 6 0.00
51 27 0.02
52 27 0.02
53 10 0.01
54 33 0.02
55 26 0.02
56 26 0.02
57 15 0.01
58 72 0.05
59 154 0.11
60 679 0.49
61 169 0.12
62 64 0.05
63 32 0.02
64 48 0.03
65 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (58 bp):
TTTAGTCCTCAAAGAGAAGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCACCA
Found at i:1504680 original size:120 final size:119
Alignment explanation
Indices: 1504403--1506285 Score: 823
Period size: 120 Copynumber: 16.0 Consensus size: 119
1504393 GTAACACTCG
* * *
1504403 TTTAGTCCTCAAAGAACAGAACGCA-TTTTTT-AAAGCTCACACAAGTTGATGGCACCAGTTTAG
1 TTTAGTCCTCAAAGAGCAGGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCACCA-TTTAG
* * * *
1504466 TCTTCAAAGAGCAAGACGCCTTTTTTCTTTTAAAAGCTCACACAAGTTGGTGACACTCA
65 TCCTCAAAGAGCAAGACGCCTTTTTTC----AAAAGCCCACACAAGTTGGTGGCACCCA
* * * *
1504525 TTTAGTCCTCAAAGAGAATGACGCATTTTTTTAAAAGCTCACATAAGTTGGTAGCACCATGTTAG
1 TTTAGTCCTCAAAGAGCAGGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCACCAT-TTAG
* * * *
1504590 TCCTTAAAGAGTAGGACGCCTTTTTTCAAAAGCCCATACAAGTTGGTGGCACCCA
65 TCCTCAAAGAGCAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
* * *
1504645 TTTAATCATCAAAGAGCAGGACGCATTTTTTTAAAAGC-CTACACAAGTTGGTGGTGC-CCGTTT
1 TTTAGTCCTCAAAGAGCAGGACGCATTTTTTTAAAAGCTC-ACACAAGTTGGT-G-GCACCATTT
* * * *
1504708 AGTCCTCAAAGAGCAAGATGCCTTTTTTTAAAAGCACACACAAGTTGGTGGCACCCG
63 AGTCCTCAAAGAGCAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
* ** * * * *
1504765 TTTAGTCCTCAAAGAGCATGACGTTTTTTTTTAAAAG-TC-CATAAAGTTAGTGGCACTCGTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCATTTTTTTAAAAGCTCACA-CAAGTTGGTGGCAC-CATTTA
* * * * *
1504828 GTCCTCAAAGAGTAAGACGCCTTTTTTTAAAAGTCCACACAAGTCGATGG----CA
64 GTCCTCAAAGAGCAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
* * * ** ** **** * * * *
1504880 TTT-CT-TTCTAAGCCCAATATCGC-TGACCTT-GAA--TCAGCAC-A----CTGGCACCCTTAC
1 TTTAGTCCTCAAAGAGCAGGA-CGCATTTTTTTAAAAGCTCA-CACAAGTTGGTGGCACCATT-T
* ** * *** * *
1504934 ATGT--T-TAAGCCCAACGTCG-CTAGCCTTGAATTAGCCCACACAAGTTGGTGGCACCCA
63 A-GTCCTCAAAGAGCAA-GACGCCT-TTTTTCAA-AAGCCCACACAAGTTGGTGGCACCCA
* * * * *
1504991 TTTAGTCTTCAAAGAGCAGGACATC-TTTTTTTAAAAGCACACACAAGTTGGTGACACCTATTGA
1 TTTAGTCCTCAAAGAGCAGGAC-GCATTTTTTTAAAAGCTCACACAAGTTGGTGGCACC-ATTTA
* * * * * * *
1505055 GTCCTCAAAGAGCATGACG-TTTTTTTTAAAAGCTCACACAAATTGGTAGCACCCTG
64 GTCCTCAAAGAGCAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCC-A
* * *
1505111 TTTAGTCCTCAAAGAGCAGGACGTC-TTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCGTTTA
1 TTTAGTCCTCAAAGAGCAGGACG-CATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCATTTA
* * * * * * * ** *
1505175 GTCCT-AAAAAGACAGGACACCTTTTTTTAAAAGTCCACACAAGTCGATGGCATTTCT
64 GTCCTCAAAGAG-CAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCA-CCCA
** * * * * *
1505232 TTCTAAG-CCT-AATATCGC-TGAC-C------TT-GAA--TCATCAC-A----CTAGCACCCTT
1 TT-T-AGTCCTCAA-AGAGCAGGACGCATTTTTTTAAAAGCTCA-CACAAGTTGGTGGCACCATT
* * ** * ** * * * *
1505279 ATCA-TGCT-TAAGCCCAATGTCG-CTAGCTTTGAATTAGCCCACACAAATTGGTGGCACCCG
62 -T-AGTCCTCAAAGAGCAA-GACGCCT-TTTTTCAA-AAGCCCACACAAGTTGGTGGCACCCA
* * * * *
1505339 TTTAGTCTTCAAAGGGCAAGACG--TTTTTTTAAAAGCACACACAAGTTGGTGGCACCCGTTTAG
1 TTTAGTCCTCAAAGAGCAGGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCATTTAG
* * **
1505402 TCCTCAAAGAGC-AGAACGCCTTTTTTTAAAAAGCCCACACAAGTTGGTAGCACCTG
65 TCCTCAAAGAGCAAG-ACGCC-TTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
* * * * * *
1505458 TTTAGTCCTCAAAGAGTAGGATGCCTTTTTTCAAAAGCCCATACAAGTTGGTAGGCACCCATTTA
1 TTTAGTCCTCAAAGAGCAGGACGCATTTTTTTAAAAGCTCACACAAGTTGGT-GGCA-CCATTTA
* * * ** * *
1505523 GTCCTCAAAGAGTAGGACGCATTTTTTCAAAAGCATACACAAATTGGTGGCACCTA
64 GTCCTCAAAGAGCAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
* * * * *
1505579 TTTCGTCCTCAAAGAGCATGACGC-TTTTTTTGAAAG-TCCACACAAGTTAGTGGCACTCGTTTA
1 TTTAGTCCTCAAAGAGCAGGACGCATTTTTTTAAAAGCT-CACACAAGTTGGTGGCAC-CATTTA
* * * *
1505642 GTCCTCAAAGAGCAAGACGTCGTTTTTT-AAAAGTCCACACAAGTCGATGG-A---A
64 GTCCTCAAAGAGCAAGACG-CCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
* * * ** ** * **** * * *
1505694 TTT-CT-TTCTAAGCCCAATATC-AATGACCTT-GAA--TCAGCAC-A----CTGACACC-TTTA
1 TTTAGTCCTCAAAGAGCAGGA-CGCATTTTTTTAAAAGCTCA-CACAAGTTGGTGGCACCATTTA
* * ** ** * *** * * *
1505747 CAT-GTTTAAGCCCAATGTCG-CTAGCCTTGAATTAGCCCACACAAGTTGGTGGCACCCG
64 -GTCCTCAAAGAGCAA-GACGCCT-TTTTTCAA-AAGCCCACACAAGTTGGTGGCACCCA
* * * *
1505805 TTTAGTCCTCAAAGAGTAGGACATC-TTTTTTTAAAAGCACACACAAGTTGGTGCCACCCATTTA
1 TTTAGTCCTCAAAGAGCAGGAC-GCATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCATTTA
* * * * * **
1505869 GTCCTCAAAAAGCAGGACGCCTTTTTTTAAAAGCCCATACAAGTTGGTAGCACCTG
64 GTCCTCAAAGAGCAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
* * * * *
1505925 TTTAGTCCTCAAAGAGTATGACGTC-TTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCGTTTA
1 TTTAGTCCTCAAAGAGCAGGACG-CATTTTTTTAAAAGCTCACACAAGTTGGTGGCA-CCATTTA
* * *
1505989 GTCCTCAAAGAGCAGGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGTACCCG
64 GTCCTCAAAGAGCAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
* * * ** **
1506045 TTTAGTCCCCAAAGAGCATGACGTC-TTTTTTTAAAAGCCCGTACAAGTTGGTGGCACTTGTTTA
1 TTTAGTCCTCAAAGAGCAGGACG-CATTTTTTTAAAAGCTCACACAAGTTGGTGGCAC-CATTTA
* * * * * *
1506109 GTCCTCAAAGAGCAGGACTCCTTTTTTTAAAAGTCCACACAAGTTGGTGACA-CTA
64 GTCCTCAAAGAGCAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
* * * * * *
1506164 GTTTAGTCCTTAAAGAAC-GAGATGCTTTTTTCTTTTAAAG-TCCACACAAGTTGGTGGCACCCG
1 -TTTAGTCCTCAAAGAGCAG-GACGC-ATTTT-TTTAAAAGCT-CACACAAGTTGGTGGCA-CCA
* *
1506227 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTTTTTTC-AAAGCCCACATAAGTTGGTGGCA
60 TTTAGTCCTCAAAGAGCAAGACGCC----TTTTTTCAAAAGCCCACACAAGTTGGTGGCA
1506286 ACTCTCTTAT
Statistics
Matches: 1319, Mismatches: 319, Indels: 243
0.70 0.17 0.13
Matches are distributed among these distances:
104 1 0.00
105 22 0.02
106 32 0.02
107 68 0.05
108 21 0.02
111 17 0.01
112 15 0.01
113 50 0.04
114 16 0.01
115 17 0.01
116 6 0.00
117 2 0.00
118 8 0.01
119 182 0.14
120 522 0.40
121 132 0.10
122 121 0.09
123 11 0.01
124 50 0.04
125 20 0.02
126 6 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (119 bp):
TTTAGTCCTCAAAGAGCAGGACGCATTTTTTTAAAAGCTCACACAAGTTGGTGGCACCATTTAGT
CCTCAAAGAGCAAGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCA
Found at i:1504755 original size:180 final size:179
Alignment explanation
Indices: 1504401--1506258 Score: 716
Period size: 180 Copynumber: 10.5 Consensus size: 179
1504391 ACGTAACACT
* * * * *
1504401 CGTTTAGTCCTCAAAGAACAGAACGCATTTTTT-AAAGCTCACACAAGTTGATGGCA-CCAGTTT
1 CGTTTAGTCCTCAAAGAGCAGGACGCATTTTTTAAAAGCCCATACAAGTTGGTGGCACCCA-TTT
* * *
1504464 AGTCTTCAAAGAGCAAGACGCCTTTTTTCTTTTAAAAG-CTCACACAAGTTGGTGACACTCATTT
65 AGTCATCAAAGAGCAAGACG-C--ATTT-TTTTAAAAGCCT-ACACAAGTTGGTGACACCCATTT
* *
1504528 AGTCCTCAAAGAGAATGACGCATTTTTTTAAAAGCTCACATAAGTTGGTAGCA-C
125 AGTCCTCAAAGAGAATGACGCATTTTTTTAAAAGCACACACAAGTTGGTAGCACC
* * * *
1504582 CATGTTAGTCCTTAAAGAGTAGGACGCCTTTTTTCAAAAGCCCATACAAGTTGGTGGCACCCATT
1 CGT-TTAGTCCTCAAAGAGCAGGACGCATTTTTT-AAAAGCCCATACAAGTTGGTGGCACCCATT
* * *** *
1504647 TAATCATCAAAGAGCAGGACGCATTTTTTTAAAAGCCTACACAAGTTGGTGGTGCCCGTTTAGTC
64 TAGTCATCAAAGAGCAAGACGCATTTTTTTAAAAGCCTACACAAGTTGGTGACACCCATTTAGTC
* * *
1504712 CTCAAAGAGCAA-GATGCCTTTTTTTAAAAGCACACACAAGTTGGTGGCACC
129 CTCAAAGAG-AATGACGCATTTTTTTAAAAGCACACACAAGTTGGTAGCACC
* ** * * * *
1504763 CGTTTAGTCCTCAAAGAGCATGACGTTTTTTTTTAAAAGTCCATA-AAGTTAGTGGCACTCGTTT
1 CGTTTAGTCCTCAAAGAGCAGGACG-CATTTTTTAAAAGCCCATACAAGTTGGTGGCACCCATTT
* * * * * * * *
1504827 TGTCCTCAAAGAGTAAGACGCCTTTTTTTAAAAGTCC-ACACAAGTCGATG----GCATTT-CT-
65 AGTCATCAAAGAGCAAGACGCATTTTTTTAAAAG-CCTACACAAGTTGGTGACACCCATTTAGTC
* * ** **** * *
1504885 TTCTAAGCCCAAT-ATCGC-TGACCTT-GAATCAGCACAC----T-G--GCACC
129 CTCAAAG-AGAATGA-CGCATTTTTTTAAAAGCA-CACACAAGTTGGTAGCACC
* * ** * * *** * * *
1504929 C-TTACATGT--T-TAAGCCCAACGTCGCTAGCCTTGAATTAGCCCACACAAGTTGGTGGCACCC
1 CGTT-TA-GTCCTCAAAGAGC-AGGACGC-ATTTTTTAA-AAGCCCATACAAGTTGGTGGCACCC
* * * *
1504990 ATTTAGTCTTCAAAGAGCAGGACATC-TTTTTTTAAAAGCAC-ACACAAGTTGGTGACACCTATT
61 ATTTAGTCATCAAAGAGCAAGAC-GCATTTTTTTAAAAGC-CTACACAAGTTGGTGACACCCATT
* * * * *
1505053 GAGTCCTCAAAGAGCATGACG-TTTTTTTTAAAAGCTCACACAAATTGGTAGCACC
124 TAGTCCTCAAAGAGAATGACGCATTTTTTTAAAAGCACACACAAGTTGGTAGCACC
* *
1505108 CTGTTTAGTCCTCAAAGAGCAGGACGTC-TTTTTTCAAAAGCCCACACAAGTTGGTGGCACCCGT
1 C-GTTTAGTCCTCAAAGAGCAGGACG-CATTTTTT-AAAAGCCCATACAAGTTGGTGGCACCCAT
* * * * * * * *
1505172 TTAGTCCT-AAAAAGACAGGACACCTTTTTTTAAAAGTCC-ACACAAGTCGATG----GCATTT-
63 TTAGTCATCAAAGAG-CAAGACGCATTTTTTTAAAAG-CCTACACAAGTTGGTGACACCCATTTA
* * * ** **** * *
1505230 CT-TTCTAAGCCTAAT-ATCGC-TGACCTT-GAATCATCACAC-------TAGCACC
126 GTCCTCAAAG-AGAATGA-CGCATTTTTTTAAAAGCA-CACACAAGTTGGTAGCACC
* * ** * * ** * * * *
1505276 C--TTA-TCATGCTTAAGCCCAATGTCGCTAGCTTTGAATTAGCCCACACAAATTGGTGGCACCC
1 CGTTTAGTCCT-C-AAAGAGC-AGGACGC-ATTTTTTAA-AAGCCCATACAAGTTGGTGGCACCC
* * * * *
1505338 GTTTAGTCTTCAAAGGGCAAGACG--TTTTTTTAAAAGCAC-ACACAAGTTGGTGGCACCCGTTT
61 ATTTAGTCATCAAAGAGCAAGACGCATTTTTTTAAAAGC-CTACACAAGTTGGTGACACCCATTT
* * *
1505400 AGTCCTCAAAGAGCA-GAACGCCTTTTTTTAAAAAGCCCACACAAGTTGGTAGCACC
125 AGTCCTCAAAGAGAATG-ACGCATTTTTTT-AAAAGCACACACAAGTTGGTAGCACC
* * * *
1505456 TGTTTAGTCCTCAAAGAGTAGGATGCCTTTTTTCAAAAGCCCATACAAGTTGGTAGGCACCCATT
1 CGTTTAGTCCTCAAAGAGCAGGACGCATTTTTT-AAAAGCCCATACAAGTTGGT-GGCACCCATT
* * * * * * * * *
1505521 TAGTCCTCAAAGAGTAGGACGCATTTTTTCAAAAGCATACACAAATTGGTGGCACCTATTTCGTC
64 TAGTCATCAAAGAGCAAGACGCATTTTTTTAAAAGCCTACACAAGTTGGTGACACCCATTTAGTC
* * * * *
1505586 CTCAAAGAGCATGACGC-TTTTTTTGAAAGTC-CACACAAGTTAGTGGCACT
129 CTCAAAGAGAATGACGCATTTTTTTAAAAG-CACACACAAGTTGGTAGCACC
* * * * * *
1505636 CGTTTAGTCCTCAAAGAGCAAGACGTCGTTTTTTAAAAGTCCACACAAGTCGATGG-A---ATTT
1 CGTTTAGTCCTCAAAGAGCAGGACG-CATTTTTTAAAAGCCCATACAAGTTGGTGGCACCCATTT
* * * ** * * *** * *
1505697 -CT-TTCTAAGCCCAATATC-AATGACCTTGAATCAG-C-ACAC-------TGACA-CC-TTTAC
65 AGTCATCAAAGAGCAAGA-CGCAT-TTTTTTAA-AAGCCTACACAAGTTGGTGACACCCATTTA-
* * ** ** * *** * * * *
1505748 AT-GTTTAAGCCCAATGTCGC-TAGCCTTGAATTAGCCCACACAAGTTGGTGGCACC
126 GTCCTCAAAG-AGAATGACGCAT-TTTTTTAA-AAGCACACACAAGTTGGTAGCACC
* * * * * *
1505803 CGTTTAGTCCTCAAAGAGTAGGACATCTTTTTTTAAAAGCACACACAAGTTGGTGCCACCCATTT
1 CGTTTAGTCCTCAAAGAGCAGGAC-GCATTTTTTAAAAGCCCATACAAGTTGGTGGCACCCATTT
* * * * * * **
1505868 AGTCCTCAAAAAGCAGGACGCCTTTTTTTAAAAGCCCATACAAGTTGGT-AGCACCTGTTTAGTC
65 AGTCATCAAAGAGCAAGACGCATTTTTTTAAAAGCCTACACAAGTTGGTGA-CACCCATTTAGTC
* * * *
1505932 CTCAAAGAGTATGACGTC-TTTTTTCAAAAGCCCACACAAGTTGGTGGCACC
129 CTCAAAGAGAATGACG-CATTTTTTTAAAAGCACACACAAGTTGGTAGCACC
* * * *
1505983 CGTTTAGTCCTCAAAGAGCAGGACGCCTTTTTTCAAAAGCCCACACAAGTTGGTGGTACCCGTTT
1 CGTTTAGTCCTCAAAGAGCAGGACGCATTTTTT-AAAAGCCCATACAAGTTGGTGGCACCCATTT
** * *** * ***
1506048 AGTCCCCAAAGAGCATGACGTC-TTTTTTTAAAAGCCCGTACAAGTTGGTGGCACTTGTTTAGTC
65 AGTCATCAAAGAGCAAGACG-CATTTTTTTAAAAGCCTACACAAGTTGGTGACACCCATTTAGTC
* * * * *
1506112 CTCAAAGAGCAGGACTCCTTTTTTTAAAAGTC-CACACAAGTTGGT-GACACT
129 CTCAAAGAGAATGACGCATTTTTTTAAAAG-CACACACAAGTTGGTAG-CACC
* * * * * * * * *
1506163 AGTTTAGTCCTTAAAGAAC-GAGATGCTTTTTTCTTTTAAAGTCCACACAAGTTGGTGGCACCCG
1 CGTTTAGTCCTCAAAGAGCAG-GACGC--ATTT-TTTAAAAGCCCATACAAGTTGGTGGCACCCA
* * *
1506227 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTTT
62 TTTAGTCATCAAAGAGCAAGACGCATTTTTTT
1506259 TTTCAAAGCC
Statistics
Matches: 1245, Mismatches: 303, Indels: 257
0.69 0.17 0.14
Matches are distributed among these distances:
164 14 0.01
165 25 0.02
166 51 0.04
167 128 0.10
168 51 0.04
169 5 0.00
170 4 0.00
171 14 0.01
172 33 0.03
173 54 0.04
174 21 0.02
175 23 0.02
176 4 0.00
177 1 0.00
178 1 0.00
179 100 0.08
180 455 0.37
181 60 0.05
182 150 0.12
183 8 0.01
184 40 0.03
185 3 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (179 bp):
CGTTTAGTCCTCAAAGAGCAGGACGCATTTTTTAAAAGCCCATACAAGTTGGTGGCACCCATTTA
GTCATCAAAGAGCAAGACGCATTTTTTTAAAAGCCTACACAAGTTGGTGACACCCATTTAGTCCT
CAAAGAGAATGACGCATTTTTTTAAAAGCACACACAAGTTGGTAGCACC
Found at i:1505428 original size:347 final size:346
Alignment explanation
Indices: 1504620--1505555 Score: 1296
Period size: 346 Copynumber: 2.7 Consensus size: 346
1504610 TTTTTTCAAA
* * *
1504620 AGCCCATACAAGTTGGTGGCACCCATTTAATCATCAAAGAGCAGGACGCATTTTTTTAAAAGC-C
1 AGCCCACACAAGTTGGTGGCACCCATTTAGTCTTCAAAGAGCAGGACG--TTTTTTTAAAAGCAC
** *
1504684 TACACAAGTTGGTGGTGCCCGTTTAGTCCTCAAAGAGCA-AGATGCCTTTTTTTAAAAGCACACA
64 -ACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGA-ACGCCTTTTTTTAAAAGCACACA
* * * * *
1504748 CAAGTTGGTGGCACCC-GTTTAGTCCTCAAAGAGCATGACGTTTTTTTTTAAAAGTCCATA-AAG
127 CAAGTTGGTAGCACCCTGTTTAGTCCTCAAAGAGCAGGACGTCTTTTTTCAAAAGCCCATACAAG
* * * * *
1504811 TTAGTGGCACTCGTTTTGTCCTCAAAGAGTAAGACGCCTTTTTTTAAAAGTCCACACAAGTCGAT
192 TTGGTGGCACCCGTTTAGTCCTCAAAAAGTAAGACACCTTTTTTTAAAAGTCCACACAAGTCGAT
* *
1504876 GGCATTTCTTTCTAAGCCCAATATCGCTGACCTTGAATCAGCACACTGGCACCCTTACATGTTTA
257 GGCATTTCTTTCTAAGCCCAATATCGCTGACCTTGAATCAGCACACTAGCACCCTTACATGCTTA
1504941 AGCCCAACGTCGCTAGCCTTGAATT
322 AGCCCAACGTCGCTAGCCTTGAATT
*
1504966 AGCCCACACAAGTTGGTGGCACCCATTTAGTCTTCAAAGAGCAGGACATCTTTTTTTAAAAGCAC
1 AGCCCACACAAGTTGGTGGCACCCATTTAGTCTTCAAAGAGCAGGAC--GTTTTTTTAAAAGCAC
* ** * * *
1505031 ACACAAGTTGGTGACACCTATTGAGTCCTCAAAGAGCATG-ACG-TTTTTTTTAAAAGCTCACAC
64 ACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCA-GAACGCCTTTTTTTAAAAGCACACAC
* *
1505094 AAATTGGTAGCACCCTGTTTAGTCCTCAAAGAGCAGGACGTCTTTTTTCAAAAGCCCACACAAGT
128 AAGTTGGTAGCACCCTGTTTAGTCCTCAAAGAGCAGGACGTCTTTTTTCAAAAGCCCATACAAGT
1505159 TGGTGGCACCCGTTTAGTCCT-AAAAAG-ACAGGACACCTTTTTTTAAAAGTCCACACAAGTCGA
193 TGGTGGCACCCGTTTAGTCCTCAAAAAGTA-A-GACACCTTTTTTTAAAAGTCCACACAAGTCGA
* *
1505222 TGGCATTTCTTTCTAAGCCTAATATCGCTGACCTTGAATCATCACACTAGCACCCTTATCATGCT
256 TGGCATTTCTTTCTAAGCCCAATATCGCTGACCTTGAATCAGCACACTAGCACCCTTA-CATGCT
* *
1505287 TAAGCCCAATGTCGCTAGCTTTGAATT
320 TAAGCCCAACGTCGCTAGCCTTGAATT
* * * *
1505314 AGCCCACACAAATTGGTGGCACCCGTTTAGTCTTCAAAGGGCAAGACGTTTTTTTAAAAGCACAC
1 AGCCCACACAAGTTGGTGGCACCCATTTAGTCTTCAAAGAGCAGGACGTTTTTTTAAAAGCACAC
*
1505379 ACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACGCCTTTTTTTAAAAAGCCCACACAA
66 ACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACGCCTTTTTTT-AAAAGCACACACAA
* * *
1505444 GTTGGTAGCA-CCTGTTTAGTCCTCAAAGAGTAGGATGCCTTTTTTCAAAAGCCCATACAAGTTG
130 GTTGGTAGCACCCTGTTTAGTCCTCAAAGAGCAGGACGTCTTTTTTCAAAAGCCCATACAAGTTG
* * * * * *
1505508 GTAGGCACCCATTTAGTCCTCAAAGAGTAGGACGCATTTTTTCAAAAG
195 GT-GGCACCCGTTTAGTCCTCAAAAAGTAAGACACCTTTTTTTAAAAG
1505556 CATACACAAA
Statistics
Matches: 521, Mismatches: 53, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
345 33 0.06
346 188 0.36
347 168 0.32
348 126 0.24
349 5 0.01
350 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (346 bp):
AGCCCACACAAGTTGGTGGCACCCATTTAGTCTTCAAAGAGCAGGACGTTTTTTTAAAAGCACAC
ACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACGCCTTTTTTTAAAAGCACACACAAG
TTGGTAGCACCCTGTTTAGTCCTCAAAGAGCAGGACGTCTTTTTTCAAAAGCCCATACAAGTTGG
TGGCACCCGTTTAGTCCTCAAAAAGTAAGACACCTTTTTTTAAAAGTCCACACAAGTCGATGGCA
TTTCTTTCTAAGCCCAATATCGCTGACCTTGAATCAGCACACTAGCACCCTTACATGCTTAAGCC
CAACGTCGCTAGCCTTGAATT
Found at i:1505461 original size:61 final size:59
Alignment explanation
Indices: 1505314--1506285 Score: 679
Period size: 60 Copynumber: 16.4 Consensus size: 59
1505304 GCTTTGAATT
* * *
1505314 AGCCCACACAAATTGGTGGCACCCGTTTAGTCTTCAAAGGGCA-AGACG-TTTTTTTAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGA-ACGCTTTTTTTAAA
*
1505372 AGCACACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACGCCTTTTTTTAAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACG-CTTTTTTT-AAA
* * * * * *
1505433 AGCCCACACAAGTTGGTAGCACCTGTTTAGTCCTCAAAGAGTAGGATGCCTTTTTTCAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACG-CTTTTTTTAAA
* * * * *
1505493 AGCCCATACAAGTTGGTAGGCACCCATTTAGTCCTCAAAGAGTAGGACGCATTTTTTCAAA
1 AGCCCACACAAGTTGGT-GGCACCCGTTTAGTCCTCAAAGAGCAGAACGC-TTTTTTTAAA
** * ** * *
1505554 AGCATACACAAATTGGTGGCACCTATTTCGTCCTCAAAGAGCATG-ACGCTTTTTTTGAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCA-GAACGCTTTTTTTAAA
* * * *
1505613 AGTCCACACAAGTTAGTGGCACTCGTTTAGTCCTCAAAGAGCA-AGACGTCGTTTTTTAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGA-ACG-CTTTTTTTAAA
* * * * ** * * * * *
1505673 AGTCCACACAAGTCGATGGAATTTCTTTCTAAG-CC-C-AATATCA-ATGAC-C----TTGAATC
1 AGCCCACACAAGTTGGTGGCA-CCCGTT-T-AGTCCTCAAAGAGCAGA--ACGCTTTTTTTAA-A
* ** ** * * ***
1505729 AGCACACTGACACCTT--T---ACATGTTTAAG-CC-CAATGTCGCTAG--C-CTTGAATT---
1 AGCCCAC--ACAAGTTGGTGGCACCCGTTT-AGTCCTCAAAG-AGC-AGAACGCTTTTTTTAAA
* * *
1505780 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGTAGGACATCTTTTTTTAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAAC-GCTTTTTTTAAA
* * * * *
1505840 AGCACACACAAGTTGGTGCCACCCATTTAGTCCTCAAAAAGCAGGACGCCTTTTTTTAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACG-CTTTTTTTAAA
* * * * *
1505900 AGCCCATACAAGTTGGTAGCACCTGTTTAGTCCTCAAAGAGTATG-ACGTCTTTTTTCAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCA-GAACG-CTTTTTTTAAA
* *
1505960 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGGACGCCTTTTTTCAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACG-CTTTTTTTAAA
* *
1506020 AGCCCACACAAGTTGGTGGTACCCGTTTAGTCCCCAAAGAGCATG-ACGTCTTTTTTTAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCA-GAACG-CTTTTTTTAAA
** ** * *
1506080 AGCCCGTACAAGTTGGTGGCACTTGTTTAGTCCTCAAAGAGCAGGACTCCTTTTTTTAAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAAC-GCTTTTTTTAAA
* * ** * * * *
1506140 AGTCCACACAAGTTGGTGACACTAGTTTAGTCCTTAAAGAAC-GAGATGCTTTTTTCTTTTAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGA-ACGC--TTTT-TTTAAA
* * *
1506202 AGTCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGGACGCCTTTTTTTTTTCAA
1 AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACG-C---TTTTTTTAAA
*
1506265 AGCCCACATAAGTTGGTGGCA
1 AGCCCACACAAGTTGGTGGCA
1506286 ACTCTCTTAT
Statistics
Matches: 737, Mismatches: 125, Indels: 99
0.77 0.13 0.10
Matches are distributed among these distances:
49 5 0.01
51 16 0.02
52 3 0.00
53 6 0.01
54 10 0.01
55 10 0.01
56 6 0.01
57 5 0.01
58 46 0.06
59 51 0.07
60 380 0.52
61 118 0.16
62 47 0.06
63 28 0.04
64 6 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (59 bp):
AGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGAACGCTTTTTTTAAA
Found at i:1505622 original size:467 final size:465
Alignment explanation
Indices: 1504966--1506152 Score: 1682
Period size: 467 Copynumber: 2.5 Consensus size: 465
1504956 GCCTTGAATT
* ** * * * * *
1504966 AGCCCACACAAGTTGGTGGCACCCATTTAGTCTTCAAAGAGCAGGACATCTTTTTTTAAAAGCAC
1 AGCCCACACAAGTTGGTAGCACCTGTTTAGTCCTCAAAGAGTAGGACGTCTTTTTTCAAAAGCCC
* * * * * *
1505031 ACACAAGTTGGTGACACCTATTGAGTCCTCAAAGAGCATGACG-TTTTTTTTAAAAGCTCACACA
66 ACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGACGCATTTTTTCAAAAGCT-ACACA
* * *
1505095 AATTGGTAGCACCCTGTTTAGTCCTCAAAGAGCAGGACGTCTTTTTTCAAAAGCCCACACAAGTT
130 AATTGGTGGCA-CCTGTTTAGTCCTCAAAGAGCATGACGTCTTTTTTTAAAAGCCCACACAAGTT
* *
1505160 GGTGGCACCCGTTTAGTCCT-AAAAAGACAGGACACCTTTTTTTAAAAGTCCACACAAGTCGATG
194 GGTGGCACTCGTTTAGTCCTCAAAGAG-CAGGACACCTTTTTTTAAAAGTCCACACAAGTCGATG
* * ** *
1505224 GCATTTCTTTCTAAGCCTAATATCGCTGACCTTGAATCATCACACT-AGCACCCTTATCATGCTT
258 GAATTTCTTTCTAAGCCCAATATCAATGACCTTGAATCAGCACACTGA-CACCCTTA-CATGCTT
* *
1505288 AAGCCCAATGTCGCTAGCTTTGAATTAGCCCACACAAATTGGTGGCACCCGTTTAGTCTTCAAAG
321 AAGCCCAATGTCGCTAGCCTTGAATTAGCCCACACAAATTGGTGGCACCCGTTTAGTCCTCAAAG
* * * * *
1505353 GGCAAGAC-GTTTTTTTAAAAGCACACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGA
386 AGCAAGACACTTTTTTTAAAAGCACACACAAGTTGGTGCCACCCATTTAGTCCTCAAAAAGCAGA
1505417 ACGCCTTTTTTTAAAA
451 ACGCCTTTTTTT-AAA
* *
1505433 AGCCCACACAAGTTGGTAGCACCTGTTTAGTCCTCAAAGAGTAGGATGCCTTTTTTCAAAAGCCC
1 AGCCCACACAAGTTGGTAGCACCTGTTTAGTCCTCAAAGAGTAGGACGTCTTTTTTCAAAAGCCC
* *
1505498 ATACAAGTTGGTAGGCACCCATTTAGTCCTCAAAGAGTAGGACGCATTTTTTCAAAAGCATACAC
66 ACACAAGTTGGT-GGCACCCATTTAGTCCTCAAAGAGCAGGACGCATTTTTTCAAAAGC-TACAC
* * * *
1505563 AAATTGGTGGCACCTATTTCGTCCTCAAAGAGCATGACG-CTTTTTTTGAAAGTCCACACAAGTT
129 AAATTGGTGGCACCTGTTTAGTCCTCAAAGAGCATGACGTCTTTTTTTAAAAGCCCACACAAGTT
* * ** *
1505627 AGTGGCACTCGTTTAGTCCTCAAAGAGCAAGACGTCGTTTTTTAAAAGTCCACACAAGTCGATGG
194 GGTGGCACTCGTTTAGTCCTCAAAGAGCAGGACACCTTTTTTTAAAAGTCCACACAAGTCGATGG
* *
1505692 AATTTCTTTCTAAGCCCAATATCAATGACCTTGAATCAGCACACTGACACCTTTACATGTTTAAG
259 AATTTCTTTCTAAGCCCAATATCAATGACCTTGAATCAGCACACTGACACCCTTACATGCTTAAG
* *
1505757 CCCAATGTCGCTAGCCTTGAATTAGCCCACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGT
324 CCCAATGTCGCTAGCCTTGAATTAGCCCACACAAATTGGTGGCACCCGTTTAGTCCTCAAAGAGC
* *
1505822 AGGACATCTTTTTTTAAAAGCACACACAAGTTGGTGCCACCCATTTAGTCCTCAAAAAGCAGGAC
389 AAGACA-CTTTTTTTAAAAGCACACACAAGTTGGTGCCACCCATTTAGTCCTCAAAAAGCAGAAC
1505887 GCCTTTTTTTAAA
453 GCCTTTTTTTAAA
* *
1505900 AGCCCATACAAGTTGGTAGCACCTGTTTAGTCCTCAAAGAGTATGACGTCTTTTTTCAAAAGCCC
1 AGCCCACACAAGTTGGTAGCACCTGTTTAGTCCTCAAAGAGTAGGACGTCTTTTTTCAAAAGCCC
* * *
1505965 ACACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGGACGCCTTTTTTCAAAAGCCCACACA
66 ACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGACGCATTTTTTCAAAAG-CTACACA
* * * * **
1506030 AGTTGGTGGTACCCGTTTAGTCCCCAAAGAGCATGACGTCTTTTTTTAAAAGCCCGTACAAGTTG
130 AATTGGTGGCACCTGTTTAGTCCTCAAAGAGCATGACGTCTTTTTTTAAAAGCCCACACAAGTTG
* *
1506095 GTGGCACTTGTTTAGTCCTCAAAGAGCAGGACTCCTTTTTTTAAAAGTCCACACAAGT
195 GTGGCACTCGTTTAGTCCTCAAAGAGCAGGACACCTTTTTTTAAAAGTCCACACAAGT
1506153 TGGTGACACT
Statistics
Matches: 636, Mismatches: 75, Indels: 18
0.87 0.10 0.02
Matches are distributed among these distances:
466 152 0.24
467 337 0.53
468 119 0.19
469 27 0.04
470 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (465 bp):
AGCCCACACAAGTTGGTAGCACCTGTTTAGTCCTCAAAGAGTAGGACGTCTTTTTTCAAAAGCCC
ACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGACGCATTTTTTCAAAAGCTACACAA
ATTGGTGGCACCTGTTTAGTCCTCAAAGAGCATGACGTCTTTTTTTAAAAGCCCACACAAGTTGG
TGGCACTCGTTTAGTCCTCAAAGAGCAGGACACCTTTTTTTAAAAGTCCACACAAGTCGATGGAA
TTTCTTTCTAAGCCCAATATCAATGACCTTGAATCAGCACACTGACACCCTTACATGCTTAAGCC
CAATGTCGCTAGCCTTGAATTAGCCCACACAAATTGGTGGCACCCGTTTAGTCCTCAAAGAGCAA
GACACTTTTTTTAAAAGCACACACAAGTTGGTGCCACCCATTTAGTCCTCAAAAAGCAGAACGCC
TTTTTTTAAA
Found at i:1512009 original size:79 final size:80
Alignment explanation
Indices: 1511894--1512048 Score: 199
Period size: 79 Copynumber: 1.9 Consensus size: 80
1511884 ATATTTCCCG
* * * *
1511894 ATGAGAAATTTAATATTTTGGAGATAATAACGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCT
1 ATGAGAAATTCAATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGCT
1511959 GGAGTATCCCTAATT
66 GGAGTATCCCTAATT
* * *
1511974 ATGAGAAA-TCAATATTTTGG-GAATAA-AGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGG
1 ATGAGAAATTCAATATTTTGGAG-ATAATA-ACGGGGTTGGAGTATCCCCTCGAAAATAACGGGG
*
1512036 TTGGAGTATCCCT
64 CTGGAGTATCCCT
1512049 GATGAAATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
78 2 0.03
79 55 0.85
80 8 0.12
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (80 bp):
ATGAGAAATTCAATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGCT
GGAGTATCCCTAATT
Found at i:1512043 original size:28 final size:28
Alignment explanation
Indices: 1512003--1512074 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
1511993 GGAATAAAGC
*
1512003 CGGGGTTGGAGTATCCCCTCG-GAAGTAA
1 CGGGGTTGGAGTATCCCCT-GAGAAATAA
1512031 CGGGGTTGGAGTAT-CCCTGATGAAATAA
1 CGGGGTTGGAGTATCCCCTGA-GAAATAA
*
1512059 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1512075 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.03
27 4 0.10
28 33 0.85
29 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTGAGAAATAA
Found at i:1512133 original size:53 final size:52
Alignment explanation
Indices: 1512063--1512192 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 52
1512053 AAATAACGAG
* * * **
1512063 GTTGGAGTATCCTCGATTGTGA-AAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAATATCCCCGATTGTGAGAAAATTAGTG--TTTTCAAAATAAAATCGGA
*
1512116 GTTGGAATATCCCCGATTAT-AGAAAATTAGTGTTTTCAAAATAAAATCGGA
1 GTTGGAATATCCCCGATTGTGAGAAAATTAGTGTTTTCAAAATAAAATCGGA
1512167 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAATATCCCCGATTGT-GAGAA
1512193 TTGAGAAACT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
51 36 0.54
52 1 0.01
53 30 0.45
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (52 bp):
GTTGGAATATCCCCGATTGTGAGAAAATTAGTGTTTTCAAAATAAAATCGGA
Found at i:1514230 original size:28 final size:28
Alignment explanation
Indices: 1514169--1514250 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1514159 TTTTGGAGAT
* *
1514169 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-ATCCC-CGATGA
*
1514197 AGTAACGAGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCCCGATGA
*
1514225 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCCCGAT
1514251 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 41 0.87
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCCCGATGA
Found at i:1514294 original size:52 final size:50
Alignment explanation
Indices: 1514233--1514402 Score: 187
Period size: 52 Copynumber: 3.3 Consensus size: 50
1514223 GAAATAACGA
* *
1514233 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAATCG
* * * * *
1514284 GTGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCG
1 G-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAATCG
*** * *
1514336 GAGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAGTCG
1 G-GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCG
1514387 AGGTTGGAGTATCCCC
1 -GGTTGGAGTATCCCC
1514403 TCGGAAATAA
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
51 36 0.37
52 52 0.53
53 10 0.10
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCG
Found at i:1514422 original size:28 final size:27
Alignment explanation
Indices: 1514388--1514459 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1514378 ATAAAGTCGA
**
1514388 GGTTGGAGTATCCCCTCGGAAATAACGG
1 GGTTGGAGTATCCCCGAGG-AATAACGG
* *
1514416 GGTTGGAGTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCCCGAGGAATAACGG
*
1514443 GGTTGGAGTGTCCCCGA
1 GGTTGGAGTATCCCCGA
1514460 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.24
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGAGGAATAACGG
Found at i:1514541 original size:211 final size:211
Alignment explanation
Indices: 1514177--1514566 Score: 604
Period size: 211 Copynumber: 1.8 Consensus size: 211
1514167 ATAATAACGG
* * *
1514177 GGTTGGAGTGTTCCCTCGGAAGTAACGAGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* *
1514242 ATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATTAAA
66 ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
** *
1514307 GGAAAATTGGTGTTTTGAAAATAAAACCGGAGTTGGAGTATCCCCGATTATGAAAAATCAATATT
131 GGAAAATTAATGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAATATT
1514372 TTAGAAATAAAGTCGA
196 TTAGAAATAAAGTCGA
* * *
1514388 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGT
1 GGTTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* *
1514452 GTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
66 ATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
* * *
1514517 TA-GAAAATTAATGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATT
129 AAGGAAAATTAATGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATT
1514567 GTGGAGAATT
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
210 28 0.17
211 94 0.58
212 39 0.24
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (211 bp):
GGTTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
GGAAAATTAATGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAATATT
TTAGAAATAAAGTCGA
Found at i:1516942 original size:13 final size:13
Alignment explanation
Indices: 1516924--1516949 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1516914 ACAAAGATCC
1516924 ATGTATCGATACA
1 ATGTATCGATACA
1516937 ATGTATCGATACA
1 ATGTATCGATACA
1516950 CAGAAAAATG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1516945 original size:33 final size:33
Alignment explanation
Indices: 1516903--1516969 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1516893 AAAATTTCCA
***
1516903 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1516936 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1516969 A
1 A
1516970 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1517010 original size:13 final size:13
Alignment explanation
Indices: 1516992--1517016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1516982 TAGCTAATTA
1516992 TGTATCGATACAT
1 TGTATCGATACAT
1517005 TGTATCGATACA
1 TGTATCGATACA
1517017 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1518636 original size:20 final size:20
Alignment explanation
Indices: 1518609--1518663 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1518599 TAAAATTTCC
*
1518609 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
1518629 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
1518649 AAATGTATCGATACA
1 AAATGTATCGATACA
1518664 TTTCCTTAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:1518707 original size:19 final size:18
Alignment explanation
Indices: 1518683--1518750 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
1518673 CAGTAGCTAA
1518683 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
*
1518702 TTATGTATGGATAC--A-
1 TTATGTATCGATACAAAC
1518717 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
1518734 TTATGTATTGATACAAA
1 TTATGTATCGATACAAA
1518751 TTGTTGAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
13 10 0.25
14 1 0.03
16 2 0.05
18 4 0.10
19 23 0.57
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Done.