Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008755.1 Hibiscus syriacus cultivar Beakdansim tig00111847_pilon, whole genome shotgun sequence
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: 3030620
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1308591 original size:30 final size:30
Alignment explanation
Indices: 1308555--1308747 Score: 368
Period size: 30 Copynumber: 6.4 Consensus size: 30
1308545 CCCAAAGGAC
*
1308555 CTATCCAGAGGTCATAAAGATCCTAGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1308585 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1308615 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1308645 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1308675 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1308705 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1308735 CTGTCCAGAGGTC
1 CTATCCAGAGGTC
1308748 CCGAATAACC
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 161 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1308764 original size:90 final size:90
Alignment explanation
Indices: 1308555--1308772 Score: 346
Period size: 90 Copynumber: 2.4 Consensus size: 90
1308545 CCCAAAGGAC
* *
1308555 CTATCCAGAGGTCATAAAGATCCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1308620 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* * *
1308645 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1308710 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* * * *
1308735 CTGTCCAGAGGTCCCGAATAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGAACCTAGGT-AACTATCCA
1308773 TATGTTCCTT
Statistics
Matches: 119, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 110 0.92
91 9 0.08
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (90 bp):
CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCATAAAGATCCTCGGTAA
Found at i:1308956 original size:4 final size:4
Alignment explanation
Indices: 1308947--1310642 Score: 3198
Period size: 4 Copynumber: 424.2 Consensus size: 4
1308937 ATATAACCAT
1308947 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1308995 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309043 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309091 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309139 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309187 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309235 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309283 TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309329 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309377 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309425 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309473 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309521 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309569 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309617 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309665 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309713 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309761 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309809 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309857 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309905 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309953 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310001 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
1310049 TACA TACA TACA TACA TACA TACA TACA TACA TACG TACG TACG TACG
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * * * * * * *
1310097 TACG TACG TACG TACG TACG TACG TACC TACG TACG TACG TACC TACG
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
1310145 TACG TACA TACTA TACG TACG TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TAC-A TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310194 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310242 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310290 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310338 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310386 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310434 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310482 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310530 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310578 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1310626 TACA TACA TACA TACA T
1 TACA TACA TACA TACA T
1310643 GTCATCATTT
Statistics
Matches: 1681, Mismatches: 8, Indels: 6
0.99 0.00 0.00
Matches are distributed among these distances:
2 2 0.00
4 1675 1.00
5 4 0.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:1311613 original size:64 final size:63
Alignment explanation
Indices: 1311545--1311663 Score: 157
Period size: 64 Copynumber: 1.9 Consensus size: 63
1311535 GTACCCGTGC
* *
1311545 ATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGGGATGCATCGATGCACTCCTTTTGT
1 ATCGATGCACAAATCACATTCGATGTTTTCATTTTAAGAGG-TGCATCGATGCACTCCTTTTGT
* *** * *
1311609 ATCGATGCACCAATTGTATTCGTTGTTTTCATTTTAATAGGTGCATCGATGCACT
1 ATCGATGCACAAATCACATTCGATGTTTTCATTTTAAGAGGTGCATCGATGCACT
1311664 TCCTATGCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 14 0.30
64 33 0.70
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (63 bp):
ATCGATGCACAAATCACATTCGATGTTTTCATTTTAAGAGGTGCATCGATGCACTCCTTTTGT
Found at i:1312765 original size:22 final size:21
Alignment explanation
Indices: 1312737--1312789 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1312727 ATTTAACATT
1312737 TTTTATTTTTTTTTAAATAAAA
1 TTTTATTTTTTTTT-AATAAAA
* * *
1312759 TTTTATTCGTTTTTTCATTAAA
1 TTTTATT-TTTTTTTAATAAAA
1312781 TTTTATTTT
1 TTTTATTTT
1312790 ATTATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 19 0.73
23 6 0.23
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTATTTTTTTTTAATAAAA
Found at i:1312893 original size:21 final size:21
Alignment explanation
Indices: 1312855--1312894 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1312845 AAAGTTTAAG
*
1312855 ATTTTCTTCATCTTATTTTTT
1 ATTTTCTTAATCTTATTTTTT
*
1312876 ATTTTCTTAAT-TTAATTTT
1 ATTTTCTTAATCTTATTTTT
1312895 CTTTCTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTCTTAATCTTATTTTTT
Found at i:1317277 original size:6 final size:6
Alignment explanation
Indices: 1317266--1317297 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1317256 TTTTAATCTC
*
1317266 CACCAT CACCAT TACCAT CACCAT CACCAT CA
1 CACCAT CACCAT CACCAT CACCAT CACCAT CA
1317298 TCTGCCATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (6 bp):
CACCAT
Found at i:1318709 original size:29 final size:27
Alignment explanation
Indices: 1318676--1318778 Score: 80
Period size: 31 Copynumber: 3.4 Consensus size: 27
1318666 TTAACATATT
1318676 AAATATATTTTACTGTTATTTTAATGTAAA
1 AAATATATTTTACT-TTATTTTAAT-T-AA
* *
1318706 AATATATATTTTATCTTTATCTTCACTTAA
1 AA-ATATATTTTA-CTTTAT-TTTAATTAA
* *
1318736 AAATATATTTTATTTGTATCTTAATTTTTAA
1 AAATATATTTTACTT-TATTTTAA---TTAA
1318767 AAATATATTTTA
1 AAATATATTTTA
1318779 AAAATATATT
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
28 4 0.07
29 13 0.22
30 6 0.10
31 31 0.52
32 6 0.10
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (27 bp):
AAATATATTTTACTTTATTTTAATTAA
Found at i:1318713 original size:31 final size:31
Alignment explanation
Indices: 1318678--1318743 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
1318668 AACATATTAA
*
1318678 ATATATTTTA-CTGTTAT-TTTAATGTAAAAAT
1 ATATATTTTATCT-TTATCTTCAAT-TAAAAAT
*
1318709 ATATATTTTATCTTTATCTTCACTTAAAAAT
1 ATATATTTTATCTTTATCTTCAATTAAAAAT
1318740 ATAT
1 ATAT
1318744 TTTATTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.52
Consensus pattern (31 bp):
ATATATTTTATCTTTATCTTCAATTAAAAAT
Found at i:1318779 original size:13 final size:13
Alignment explanation
Indices: 1318761--1318788 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1318751 GTATCTTAAT
1318761 TTTTAAAAATATA
1 TTTTAAAAATATA
1318774 TTTTAAAAATATA
1 TTTTAAAAATATA
1318787 TT
1 TT
1318789 AACTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAATATA
Found at i:1321246 original size:39 final size:41
Alignment explanation
Indices: 1321147--1321246 Score: 129
Period size: 41 Copynumber: 2.5 Consensus size: 41
1321137 TGCATGTGTA
1321147 TCTTGTCAATAGTTAAGAAAGATGTGTATATAGAGTATATGG
1 TCTTGTCAATAGTTAAGAAAGATGTGTATATAGAG-ATATGG
1321189 T-TTGTCAATAGTTAAGAAAGATGTGTATGCAT-G-G-TAT-G
1 TCTTGTCAATAGTTAAGAAAGATGTGTAT--ATAGAGATATGG
*
1321227 TCTTGTCAATAGTTCAGAAA
1 TCTTGTCAATAGTTAAGAAA
1321247 AATTCTAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
38 2 0.04
39 20 0.37
41 28 0.52
42 2 0.04
43 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (41 bp):
TCTTGTCAATAGTTAAGAAAGATGTGTATATAGAGATATGG
Found at i:1322174 original size:15 final size:16
Alignment explanation
Indices: 1322146--1322176 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1322136 ATTCACCGGT
1322146 TCAATTACTAAAAAAA
1 TCAATTACTAAAAAAA
1322162 TCAATTA-TAAAAAAA
1 TCAATTACTAAAAAAA
1322177 GTACTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
TCAATTACTAAAAAAA
Found at i:1326596 original size:3 final size:3
Alignment explanation
Indices: 1326579--1326640 Score: 99
Period size: 3 Copynumber: 20.7 Consensus size: 3
1326569 TGAGTTTACA
*
1326579 TAT TGAT TA- TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1326624 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1326641 CTACTACTAC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1326645 original size:3 final size:3
Alignment explanation
Indices: 1326639--1326665 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1326629 TTATTATTAT
1326639 TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC
1326666 AAATAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:1332408 original size:12 final size:12
Alignment explanation
Indices: 1332371--1332433 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
1332361 ATCTGATACT
1332371 TGACATGGATTC
1 TGACATGGATTC
*
1332383 TGATAT-GATATC
1 TGACATGGAT-TC
1332395 TGACATGGATTC
1 TGACATGGATTC
* *
1332407 TGATAT-GATAC
1 TGACATGGATTC
*
1332418 TTGACTTGGATTC
1 -TGACATGGATTC
1332431 TGA
1 TGA
1332434 TCTGATACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:1332487 original size:24 final size:24
Alignment explanation
Indices: 1332356--1332470 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
1332346 TCGATTTGAT
*
1332356 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
1332380 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
*
1332404 TTCTGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* * *
1332428 TTCTGATCTGATACTTGACCTAGA
1 TTCTGATATGATACTTGACATGGA
*
1332452 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
1332471 GTGAATTATG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:1332693 original size:2 final size:2
Alignment explanation
Indices: 1332686--1332710 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1332676 CGGATGGGGG
1332686 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
1332711 GTTTTAAAAG
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:1334602 original size:21 final size:21
Alignment explanation
Indices: 1334576--1334629 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1334566 AAATGATCAG
1334576 TTTGACCGGTTTTGTAACCCA
1 TTTGACCGGTTTTGTAACCCA
*
1334597 TTTGACCGGTTTTGTAACCTA
1 TTTGACCGGTTTTGTAACCCA
*
1334618 TTTGACAGGTTT
1 TTTGACCGGTTT
1334630 GACCGGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (21 bp):
TTTGACCGGTTTTGTAACCCA
Found at i:1337103 original size:12 final size:12
Alignment explanation
Indices: 1337066--1337104 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1337056 ATCTGATACT
1337066 TGACATGGATTC
1 TGACATGGATTC
*
1337078 TGATAT-GATATC
1 TGACATGGAT-TC
1337090 TGACATGGATTC
1 TGACATGGATTC
1337102 TGA
1 TGA
1337105 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:1337182 original size:24 final size:24
Alignment explanation
Indices: 1337051--1337165 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
1337041 TTGATTTGAT
*
1337051 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
1337075 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
1337099 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
*
1337123 TTCTAATATGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
*
1337147 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
1337166 GTGAATTATG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:1341744 original size:42 final size:41
Alignment explanation
Indices: 1341659--1341765 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 41
1341649 CCTGAAGGTC
* * * *
1341659 TTATGGATGGCTCGAAGGACTTA-TCATCTTTCTCGAAAGAT
1 TTAT-GATGGCCCGAAGGACTTACCCATCATGCTCGAAAGAT
*
1341700 TTATAGATGGCCCGAAGGATTTACCCATCATGCTCGAAAGAT
1 TTAT-GATGGCCCGAAGGACTTACCCATCATGCTCGAAAGAT
1341742 TTAGTGATGGCCCGAAGGACTTAC
1 TTA-TGATGGCCCGAAGGACTTAC
1341766 ATGTCAAGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
41 20 0.35
42 36 0.63
43 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (41 bp):
TTATGATGGCCCGAAGGACTTACCCATCATGCTCGAAAGAT
Found at i:1342027 original size:42 final size:42
Alignment explanation
Indices: 1341947--1342046 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
1341937 TGGATGACTT
* *
1341947 GAAGGACTTA-TCATCTTGCTCGAAAGACTTATAGATGGCCC
1 GAAGGACTTACGCATCATGCTCGAAAGACTTATAGATGGCCC
* *
1341988 GAAGGACTTACGCATCATGCTCGAAAGATTTACTA-ATGGCTC
1 GAAGGACTTACGCATCATGCTCGAAAGACTTA-TAGATGGCCC
1342030 GAAGGACTTACGCATCA
1 GAAGGACTTACGCATCA
1342047 AGAAACCCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 10 0.19
42 41 0.77
43 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (42 bp):
GAAGGACTTACGCATCATGCTCGAAAGACTTATAGATGGCCC
Found at i:1342040 original size:20 final size:20
Alignment explanation
Indices: 1341964--1342040 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
1341954 TTATCATCTT
1341964 GCTCGAAAGACTTA-TAGATG
1 GCTCGAAAGACTTACTA-ATG
* * *
1341984 GCCCGAAGGACTTACGCATCAT-
1 GCTCGAAAGACTTA--C-TAATG
*
1342006 GCTCGAAAGATTTACTAATG
1 GCTCGAAAGACTTACTAATG
*
1342026 GCTCGAAGGACTTAC
1 GCTCGAAAGACTTAC
1342041 GCATCAAGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
19 3 0.07
20 26 0.60
22 11 0.26
23 2 0.05
24 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (20 bp):
GCTCGAAAGACTTACTAATG
Found at i:1342143 original size:275 final size:272
Alignment explanation
Indices: 1341638--1342469 Score: 1105
Period size: 275 Copynumber: 3.0 Consensus size: 272
1341628 GGAAATGTTA
* * * * *
1341638 AAAACACCCTTCCTGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTTCTCGAAAGATTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTA
* * *
1341703 TAGATGGCCCGAAGGATTTACCCATCATGCTCGAAAGATTTAGTGATGGCCCGAAGGACTTACAT
66 TAGATGGCCCGAAGGATTTACGCATCATGCTCGAAAGATTTACTGATGG-CCGAAGGACTTACAC
* ** *
1341768 GTCAAGAAAAACTTGAAAATCAAGCTTAGTTTCTCAGTTGTCAAGGAACCCCTAAAAATTAGGCT
130 ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCT-AAAATTAGGCT
*
1341833 TAGATTCCTTTTAAAAACTCTTTGGAGATAATCATCAAGAAACCCCTAAAAATCAGGCTTAGTTT
194 TAGCTTCCTTTTAAAAACTCTTTGGAGATAATCATCAAGAAACCCCTAAAAATCAGGCTTAGTTT
1341898 CTAAAAACTCATTTG
259 CTAAAAA-TCATTTG
* *
1341913 AAAACATCCTACCCGAAGGTCTTATGGATGACTTGAAGGACTTATCATCTTGCTCGAAAGACTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTA
* * *
1341978 TAGATGGCCCGAAGGACTTACGCATCATGCTCGAAAGATTTACTAATGGCTCGAAGGACTTACGC
66 TAGATGGCCCGAAGGATTTACGCATCATGCTCGAAAGATTTACTGATGGC-CGAAGGACTTACAC
*
1342043 ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTTAAGCT
130 ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAA-TTAGGCT
* *
1342108 TAGCTTCCTTTTAAAAACTCTTT-GATGATAATCATCAAGAAACCCTTGAAAATCAGGCTTAGTT
194 TAGCTTCCTTTTAAAAACTCTTTGGA-GATAATCATCAAGAAACCCCTAAAAATCAGGCTTAGTT
* *
1342172 TTTAAAAAATCATTTA
258 TCT-AAAAATCATTTG
*** * * * *
1342188 AAAACAT-CTGGGTCGAA-GTCTTATGGTTGGCCCGAATGACTTATCATCTTGCTCAAAAGACTT
1 AAAACATCCT-ACCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTT
** * * * * * *
1342251 ATAGATTACCCGAAGGATTTAAGTACCATGCTTGAAAGACTTACTGATGGCCTGAAGGACTTACT
65 ATAGATGGCCCGAAGGATTTACGCATCATGCTCGAAAGATTTACTGATGGCC-GAAGGACTTACA
* * *
1342316 CATCAAGAAACCCTTGAAAATTAAGCTTGGTTTCTTAGTTGTCATCAAGAAACCCCTAAAATTAG
129 CATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTG---TCAAGGAACCCCTAAAATTAG
* * * * * *
1342381 GATTAACTT-CTTTTAAAAACTCTTTGGAGATAATCATCAAGAAATCCCTAAAAATTAGACTTAT
191 GCTTAGCTTCCTTTTAAAAACTCTTTGGAGATAATCATCAAGAAACCCCTAAAAATCAGGCTTAG
1342445 TTTCTAAAAATCATTTG
256 TTTCTAAAAATCATTTG
1342462 AAAACATC
1 AAAACATC
1342470 AAGAAACCCC
Statistics
Matches: 490, Mismatches: 56, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
273 1 0.00
274 159 0.32
275 297 0.61
276 17 0.03
277 16 0.03
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (272 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTA
TAGATGGCCCGAAGGATTTACGCATCATGCTCGAAAGATTTACTGATGGCCGAAGGACTTACACA
TCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTAGGCTTA
GCTTCCTTTTAAAAACTCTTTGGAGATAATCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCT
AAAAATCATTTG
Found at i:1342474 original size:51 final size:54
Alignment explanation
Indices: 1342357--1342525 Score: 179
Period size: 51 Copynumber: 3.1 Consensus size: 54
1342347 TTCTTAGTTG
* * *
1342357 TCATCAAGAAACCCCT-AAAATTAGGA-TTAACTTCTTTTAAAAACTCTTTGGAGATAA
1 TCATCAAGAAACCCCTAAAAATTA-GACTT-ACTTCTTCTAAAAATTCATT-GA-A-AA
*
1342414 TCATCAAGAAATCCCTAAAAATTAGACTTA-TT-TTCTAAAAA-TCATTTGAAAA
1 TCATCAAGAAACCCCTAAAAATTAGACTTACTTCTTCTAAAAATTCA-TTGAAAA
* *
1342466 -CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGAAAA
1 TCATCAAGAAACCCCTAAAAATTAGACTTA-CTTCTTCTAAAAATTCATTGAAAA
1342520 TCATCA
1 TCATCA
1342526 TCAATAAACC
Statistics
Matches: 98, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
51 27 0.28
52 2 0.02
53 3 0.03
54 19 0.19
55 18 0.18
56 2 0.02
57 18 0.18
58 9 0.09
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (54 bp):
TCATCAAGAAACCCCTAAAAATTAGACTTACTTCTTCTAAAAATTCATTGAAAA
Found at i:1342544 original size:58 final size:56
Alignment explanation
Indices: 1342357--1342568 Score: 188
Period size: 58 Copynumber: 3.8 Consensus size: 56
1342347 TTCTTAGTTG
* * * * *
1342357 TCATCAAGAAACCCCT-AAAATTAGGATTAACTTCTTTTAAAAACTCTTTGGAGATAA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATT-GAAAT-A
* * *
1342414 TCATCAAGAAATCCCTAAAAATTAGACTTA--TT-TTCTAAAAA-TCATTTGAAA-A
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCA-TTGAAATA
1342466 -CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGAAAATCA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTG-AAAT-A
* * * * * * *
1342523 TCATCAATAAACCCTTGAAAATCAAGCTTAGTTTC-TTTAACAATTC
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTC
1342569 TTTTTGAAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
51 27 0.21
52 1 0.01
53 2 0.02
54 16 0.12
55 16 0.12
56 2 0.02
57 26 0.20
58 39 0.30
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (56 bp):
TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGAAATA
Found at i:1342558 original size:109 final size:108
Alignment explanation
Indices: 1342358--1342558 Score: 262
Period size: 109 Copynumber: 1.9 Consensus size: 108
1342348 TCTTAGTTGT
* * *
1342358 CATCAAGAAACCCCTAAAATTAGGATTAACTTCTTTTAAAAACTCTTTGGAGATAATCATCAAGA
1 CATCAAGAAACCCCTAAAATTAGGATTAACTTCTTTTAAAAACTCATTGAAAATAATCATCAAGA
* *
1342423 AATCCCTAAAAATTAGACTTATTTTCTAAAAATCATTTGAAAA
66 AATCCCTAAAAATAAGACTTAGTTTCTAAAAATCATTTGAAAA
* * * * *
1342466 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGAAAATCATCATCAAT
1 CATCAAGAAACCCCT-AAAATTAGGATTAACTTCTTTTAAAAACTCATTGAAAATAATCATCAAG
*
1342531 AAA-CCCTTGAAAATCAAG-CTTAGTTTCT
65 AAATCCC-TAAAAAT-AAGACTTAGTTTCT
1342559 TTAACAATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
108 18 0.23
109 59 0.75
110 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (108 bp):
CATCAAGAAACCCCTAAAATTAGGATTAACTTCTTTTAAAAACTCATTGAAAATAATCATCAAGA
AATCCCTAAAAATAAGACTTAGTTTCTAAAAATCATTTGAAAA
Found at i:1344529 original size:4 final size:4
Alignment explanation
Indices: 1344520--1344595 Score: 70
Period size: 4 Copynumber: 19.2 Consensus size: 4
1344510 TTTTATTGGT
*
1344520 TTTC TTTC TTTC TTT- TTTC TTTC TTTC TTTTCC TTTTC CTT- TTTC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C -TTTC TTTC TTTC TTTC
* *
1344568 TTT- TTTC TTTT TTTC TTTT TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1344596 CTTTTTTATG
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
3 11 0.18
4 41 0.67
5 4 0.07
6 5 0.08
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:1344539 original size:15 final size:14
Alignment explanation
Indices: 1344519--1344602 Score: 69
Period size: 15 Copynumber: 5.5 Consensus size: 14
1344509 TTTTTATTGG
*
1344519 TTTTCTTTCTTTCT
1 TTTTTTTTCTTTCT
1344533 TTTTTCTTTCTTTCT
1 TTTTT-TTTCTTTCT
*
1344548 TTTCCTTTTCCTTTTTCT
1 TTT--TTTT--TCTTTCT
*
1344566 TTTTTTTTCTTTTTT
1 TTTTTTTTC-TTTCT
1344581 TCTTTTTTTCTTTCT
1 T-TTTTTTTCTTTCT
*
1344596 CTTTTTT
1 TTTTTTT
1344603 ATGTATTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.19
15 21 0.37
16 14 0.25
17 2 0.04
18 9 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTTCTTTCT
Found at i:1344557 original size:26 final size:26
Alignment explanation
Indices: 1344528--1344601 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
1344518 GTTTTCTTTC
1344528 TTTCTTTTTTCTTTCTTTCTTT-TCCT
1 TTTCTTTTTTCTTTCTTT-TTTCTCCT
* **
1344554 TTTCCTTTTTCTTT-TTTTTTCTTTT
1 TTTCTTTTTTCTTTCTTTTTTCTCCT
1344579 TTTCTTTTTTTCTTTCTCTTTTT
1 TTTC-TTTTTTCTTTCT-TTTTT
1344602 TATGTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 3 0.08
25 9 0.22
26 22 0.55
27 1 0.03
28 5 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTCTTTTTTCTTTCTTTTTTCTCCT
Found at i:1344566 original size:18 final size:18
Alignment explanation
Indices: 1344524--1344601 Score: 61
Period size: 18 Copynumber: 4.2 Consensus size: 18
1344514 ATTGGTTTTC
*
1344524 TTTC-TTTCTTTTTTCTTT
1 TTTCTTTTCTTTTCTC-TT
1344542 CTTTCTTTTCCTTTTC-CTT
1 -TTTCTTTT-CTTTTCTCTT
* *
1344561 TTTCTTTTTTTTTCTTTT
1 TTTCTTTTCTTTTCTCTT
*
1344579 TTTCTTTTTTTCTTTCTCTT
1 TTTC-TTTTCT-TTTCTCTT
1344599 TTT
1 TTT
1344602 TATGTATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
17 5 0.10
18 14 0.28
19 12 0.24
20 14 0.28
21 5 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTCTTTTCTTTTCTCTT
Found at i:1349539 original size:15 final size:17
Alignment explanation
Indices: 1349509--1349541 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1349499 ATATACTTTG
1349509 ATTAATATAGTTATAAT
1 ATTAATATAGTTATAAT
1349526 ATTAA-ATA-TTATAAT
1 ATTAATATAGTTATAAT
1349541 A
1 A
1349542 GGATTATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTAATATAGTTATAAT
Found at i:1349601 original size:15 final size:14
Alignment explanation
Indices: 1349576--1349609 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
1349566 ATTATTTAGT
1349576 AATTATTTAAATTA
1 AATTATTTAAATTA
1349590 AATTATTTTAAATTA
1 AATTA-TTTAAATTA
1349605 AATTA
1 AATTA
1349610 AATATAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTATTTAAATTA
Found at i:1356525 original size:96 final size:96
Alignment explanation
Indices: 1356344--1356749 Score: 532
Period size: 96 Copynumber: 4.2 Consensus size: 96
1356334 TAAGTCATCC
* * *
1356344 TCAAACTTCACGGAAGAGTAGTGAAGCAGAAAGCAGGAGCCA-AATAAAATTCAGTTTTCATGGA
1 TCAAAATTCACGGAAGAGTAGTGAAGCAGAAAGCAGGAACCATAATAAAATTCAGTTTTCACGGA
* * *
1356408 AGAGTTGTGGAATGAATTTTTCAGCAAAGTA
66 AGAGTAGTGGAACGGATTTTTCAGCAAAGTA
* * * * *
1356439 TCAAAATTCACAGAAGAGCATTGAAGCATAAAGCAGGAACCATAATAAAATTCATTTTTCACGGA
1 TCAAAATTCACGGAAGAGTAGTGAAGCAGAAAGCAGGAACCATAATAAAATTCAGTTTTCACGGA
* * *
1356504 AGAGTGGTCGAACGGATTTTTCAGCAAGGTA
66 AGAGTAGTGGAACGGATTTTTCAGCAAAGTA
* *
1356535 T-AAAACTTCACGGAAGAGTAGTGAAGTAGAAAGCAGGAACCAGAATAAAATTCAGTTTTCACGG
1 TCAAAA-TTCACGGAAGAGTAGTGAAGCAGAAAGCAGGAACCATAATAAAATTCAGTTTTCACGG
* *
1356599 AAGAGTAGTGGAACAGATTTTTCAGCAAAGTG
65 AAGAGTAGTGGAACGGATTTTTCAGCAAAGTA
* * *
1356631 TCAAACTTCACGGAA-ATGTAGTGAAGCAGAAAGCAAGAACCATGATAAAATTCAGTTTTCACGG
1 TCAAAATTCACGGAAGA-GTAGTGAAGCAGAAAGCAGGAACCATAATAAAATTCAGTTTTCACGG
1356695 AAGAGTAGTGGAAC-GATTTTTCAGCAAAGTA
65 AAGAGTAGTGGAACGGATTTTTCAGCAAAGTA
* * * *
1356726 TGAGAACTTCATGGAAAAGTAGTG
1 TCA-AAATTCACGGAAGAGTAGTG
1356750 GAGTAATCCA
Statistics
Matches: 272, Mismatches: 33, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
95 59 0.22
96 209 0.77
97 4 0.01
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (96 bp):
TCAAAATTCACGGAAGAGTAGTGAAGCAGAAAGCAGGAACCATAATAAAATTCAGTTTTCACGGA
AGAGTAGTGGAACGGATTTTTCAGCAAAGTA
Found at i:1358451 original size:15 final size:17
Alignment explanation
Indices: 1358421--1358453 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1358411 ATATACTTTG
1358421 ATTAATATAGTTATAAT
1 ATTAATATAGTTATAAT
1358438 ATTAA-ATA-TTATAAT
1 ATTAATATAGTTATAAT
1358453 A
1 A
1358454 GGATTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTAATATAGTTATAAT
Found at i:1359773 original size:33 final size:32
Alignment explanation
Indices: 1359736--1359798 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1359726 TACCCATAAA
* *
1359736 TACATAAAATACATAAAAAAAAGAGGCAATATT
1 TACAT-AAACACATAAAAAAAAGAGGAAATATT
* *
1359769 TACATCAACACATATAAAAAAGAGGAAATA
1 TACATAAACACATAAAAAAAAGAGGAAATA
1359799 ACCAAAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.60, C:0.11, G:0.10, T:0.19
Consensus pattern (32 bp):
TACATAAACACATAAAAAAAAGAGGAAATATT
Found at i:1366122 original size:124 final size:122
Alignment explanation
Indices: 1365973--1366814 Score: 754
Period size: 124 Copynumber: 6.9 Consensus size: 122
1365963 TATTATTCAT
*
1365973 GACTCCC-AGTAGAGTCTATCTTTGACTTCCTTATGAAGAGAAGTCAACCTTTGTTATTTACGAC
1 GACTCCCTAGTAGAGTCTATCTTTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATTT-CGAC
* ** * *
1366037 TCACTCCCAGTATAGTCAATCTTAAACTTTCTTGCGAAGAGAAGACAACCCATGTTTTA
65 TCACTCCCAGTAGAGTCAATCTTTGA-TTTCTCGCGAAGAGAAGTCAACCCATGTTTTA
* **
1366096 GACTCCCTAGTAGAGTCTATCTTTGACTTCCTCATGAAGAAAAGTCAACCCATG-T-TTT--A--
1 GACTCCCTAGTAGAGTCTATCTTTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATTTCGACT
* * * ** ** * *
1366155 GACTCCCGGTAGAGTCTATCTTTGACTTTCTCATGAAGAGAAGTCAACCTTTTTTATTTTC
66 CACTCCCAGTAGAGTCAATCTTTGA-TTTCTCGCGAAGAGAAGTCAACC---CATGTTTTA
* * * * * ** **
1366216 GACTCACTCCCAATATAGTCAATCTTTGACTTTCTCGCGAAGAGAAGTCAACCCATGTT-TTT-G
1 GACT--C-CCTAGTAGAGTCTATCTTTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATTTCG
* * *
1366279 ACT--C-CCCAGTAGAGTCTATCTTTGATTTCCTCGTGAAGAGAAGTCAACCCAGGTTTTA
63 ACTCACTCCCAGTAGAGTCAATCTTTGATTT-CTCGCGAAGAGAAGTCAACCCATGTTTTA
* * * * ** * *
1366337 GACTCCCTATTAGAGTATGTCATTGACTTCCTTGTGAAAAGAAGGCAACCTTTGTTATTTCCGAC
1 GACTCCCTAGTAGAGTCTATCTTTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATTT-CGAC
* * *
1366402 TCACTCCTAGTAGAGTCAATCTTTAAATTCCTCGCGAAGAGAAGTCAACCCATGTTTTA
65 TCACTCCCAGTAGAGTCAATCTTT-GATTTCTCGCGAAGAGAAGTCAACCCATGTTTTA
* * * *
1366461 GACTCCCCATTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTTAC
1 GACTCCCTAGTAGAGTCTATCTTTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATTTC-GAC
* * * * * * *
1366526 TCTCTCCCAGTATAGTTAATCTTTGACTTCCTCGTGAAGAAAAGTTAACCCATGTTTTA
65 TCACTCCCAGTAGAGTCAATCTTTGA-TTTCTCGCGAAGAGAAGTCAACCCATGTTTTA
* * * *
1366585 AACT-CCTCAGTAGAGTATATCTTTGAATTCCTCATGAAGAGAAGTCAACCTTTGTTATTTCTAA
1 GACTCCCT-AGTAGAGTCTATCTTTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATTTC-GA
* * * *
1366649 CTCACTACCAGTAGAGTCAATCCTTT-ATTTCCTCGCGAAAAGAAGTAAACTCATGTTTTA
64 CTCACTCCCAGTAGAGTCAAT-CTTTGATTT-CTCGCGAAGAGAAGTCAACCCATGTTTTA
* * * * *
1366709 GACTCCCTAGTAGAGCCAATCCTTGACTTCCTCATGAACAGAAGTCAACCTATG----TTC-A-T
1 GACTCCCTAGTAGAGTCTATCTTTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATTTCGACT
* *
1366768 GACTCCCAGTAGAGTCAAT-TCTTGATTTCCTCGCGAAGAAAAGTCAA
66 CACTCCCAGTAGAGTCAATCT-TTGATTT-CTCGCGAAGAGAAGTCAA
1366815 TATTCCAGAT
Statistics
Matches: 593, Mismatches: 99, Indels: 60
0.79 0.13 0.08
Matches are distributed among these distances:
115 1 0.00
116 2 0.00
117 77 0.13
118 38 0.06
119 5 0.01
120 12 0.02
121 12 0.02
122 4 0.01
123 59 0.10
124 371 0.63
125 12 0.02
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (122 bp):
GACTCCCTAGTAGAGTCTATCTTTGACTTCCTCATGAAGAGAAGTCAACCTTTGTTATTTCGACT
CACTCCCAGTAGAGTCAATCTTTGATTTCTCGCGAAGAGAAGTCAACCCATGTTTTA
Found at i:1366135 original size:59 final size:59
Alignment explanation
Indices: 1365973--1366814 Score: 611
Period size: 59 Copynumber: 13.8 Consensus size: 59
1365963 TATTATTCAT
** **
1365973 GACT-CCCAGTAGAGTCTATCTTTGACTTCCTTATGAAGAGAAGTCAACCTTTGTTATTTA
1 GACTCCCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATG-T-TTTA
* * ** * * * *
1366033 CGACTCACTCCCAGTATAGTCAATCTTAAACTTTCTTGCGAAGAGAAGACAACCCATGTTTTA
1 -GACT--C-CCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATGTTTTA
* * *
1366096 GACTCCCTAGTAGAGTCTATCTTTGACTTCCTCATGAAGAAAAGTCAACCCATGTTTTA
1 GACTCCCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATGTTTTA
* * * ** * *
1366155 GACT-CCCGGTAGAGTCTATCTTTGACTTTCTCATGAAGAGAAGTCAACCTTTTTTATTTTC
1 GACTCCCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACC---CATGTTTTA
* * * * * *
1366216 GACTCACTCCCAATATAGTCAATCTTTGACTTTCTCGCGAAGAGAAGTCAACCCATGTTTTT
1 GACT--C-CCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATGTTTTA
* *
1366278 GACTCCCCAGTAGAGTCTATCTTTGATTTCCTCGTGAAGAGAAGTCAACCCAGGTTTTA
1 GACTCCCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATGTTTTA
* * * * * * * * ** *
1366337 GACTCCCTATTAGAGTATGTCATTGACTTCCTTGTGAAAAGAAGGCAACCTTTGTTATTTCC
1 GACTCCCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATG-T-TTT-A
* * * *
1366399 GACTCACTCCTAGTAGAGTCAATCTTTAAATTCCTCGCGAAGAGAAGTCAACCCATGTTTTA
1 GACTC-C-CC-AGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATGTTTTA
* **
1366461 GACTCCCCATTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTTA
1 GACTCCCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATG----TT-TTA
** * * *
1366525 CTCTCTCCCAGTATAGT-TAATCTTTGACTTCCTCGTGAAGAAAAGTTAACCCATGTTTTA
1 GACTC-CCCAGTAGAGTCT-ATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATGTTTTA
* * * * * **
1366585 AACTCCTCAGTAGAGTATATCTTTGAATTCCTCATGAAGAGAAGTCAACCTTTGTTATTTCTA
1 GACTCCCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATG---TTT-TA
* * * * * *
1366648 -ACTCACTACCAGTAGAGTCAATCCTTT-ATTTCCTCGCGAAAAGAAGTAAACTCATGTTTTA
1 GACTC-C--CCAGTAGAGTCTAT-CTTTGACTTCCTCGTGAAGAGAAGTCAACCCATGTTTTA
* * * * * * * *
1366709 GACTCCCTAGTAGAGCCAATCCTTGACTTCCTCATGAACAGAAGTCAACCTATG-TTCA
1 GACTCCCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATGTTTTA
* * * *
1366767 TGACT-CCCAGTAGAGTCAAT-TCTTGATTTCCTCGCGAAGAAAAGTCAA
1 -GACTCCCCAGTAGAGTCTATCT-TTGACTTCCTCGTGAAGAGAAGTCAA
1366815 TATTCCAGAT
Statistics
Matches: 614, Mismatches: 130, Indels: 77
0.75 0.16 0.09
Matches are distributed among these distances:
58 81 0.13
59 251 0.41
60 12 0.02
61 22 0.04
62 37 0.06
63 13 0.02
64 10 0.02
65 184 0.30
66 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (59 bp):
GACTCCCCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCATGTTTTA
Found at i:1366284 original size:182 final size:182
Alignment explanation
Indices: 1365973--1366510 Score: 806
Period size: 182 Copynumber: 3.0 Consensus size: 182
1365963 TATTATTCAT
1365973 GACTCCCAGTAGAGTCTATCTTTGACTTCCTTATGAAGAGAAGTCAACCTTTGTTATTTACGACT
1 GACTCCCAGTAGAGTCTATCTTTGACTTCCTTATGAAGAGAAGTCAACCTTTGTTATTTACGACT
* * *
1366038 CACTCCCAGTATAGTCAATCTTAAACTTTCTTGCGAAGAGAAGACAACCCATGTTTTAGACTCCC
66 CACTCCCAGTATAGTCAATCTTTAACTTTCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCCC
* * * *
1366103 TAGTAGAGTCTATCTTTGACTTCCTCATGAAGAAAAGTCAACCCATGTTTTA
131 CAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCAGGTTTTA
* * * * *
1366155 GACTCCCGGTAGAGTCTATCTTTGACTTTCTCATGAAGAGAAGTCAACCTTTTTTATTTTCGACT
1 GACTCCCAGTAGAGTCTATCTTTGACTTCCTTATGAAGAGAAGTCAACCTTTGTTATTTACGACT
* * *
1366220 CACTCCCAATATAGTCAATCTTTGACTTTCTCGCGAAGAGAAGTCAACCCATGTTTTTGACTCCC
66 CACTCCCAGTATAGTCAATCTTTAACTTTCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCCC
*
1366285 CAGTAGAGTCTATCTTTGATTTCCTCGTGAAGAGAAGTCAACCCAGGTTTTA
131 CAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCAGGTTTTA
* * * * * * * *
1366337 GACTCCCTATTAGAGTATGTCATTGACTTCCTTGTGAAAAGAAGGCAACCTTTGTTATTTCCGAC
1 GACTCCC-AGTAGAGTCTATCTTTGACTTCCTTATGAAGAGAAGTCAACCTTTGTTATTTACGAC
* * * *
1366402 TCACTCCTAGTAGAGTCAATCTTTAAATTCCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCC
65 TCACTCCCAGTATAGTCAATCTTTAACTTTCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCC
*
1366467 CCATTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACC
130 CCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACC
1366511 TTTGTTATTT
Statistics
Matches: 318, Mismatches: 37, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
182 173 0.54
183 145 0.46
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (182 bp):
GACTCCCAGTAGAGTCTATCTTTGACTTCCTTATGAAGAGAAGTCAACCTTTGTTATTTACGACT
CACTCCCAGTATAGTCAATCTTTAACTTTCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCCC
CAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCCAGGTTTTA
Found at i:1366599 original size:183 final size:177
Alignment explanation
Indices: 1365975--1366814 Score: 639
Period size: 183 Copynumber: 4.6 Consensus size: 177
1365965 TTATTCATGA
** *
1365975 CTCCCAGTAGAGTCT-ATCTTTGACTTCCTTATGAAGAGAAGTCAACCTTTGTTATTTACGACTC
1 CTCCCAGTAGAGT-TAATCTTTGACTTCCTCGTGAAGAAAAGTCAACCTTTG-T-TTT-CGACTC
* * * *
1366039 ACTCCCAGTATAGTCAATC-TTAAACTTTCTTGCGAAGAGAAGACAACCCATGTTTTAGACTCCC
62 ACT-CCAGTAGAGTCAATCTTTAAA-TTCCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCCC
* * * **
1366103 TAGTAGAGTCTATCTTTGACTTCCTCATGAAGAAAAGTCAACCCATGTTTTAGA
125 CAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAA-CCATGTTTTACT
* * * * *
1366157 CTCCCGGTAGAGTCT-ATCTTTGACTTTCTCATGAAGAGAAGTCAACCTTTTTTATTTTCGACTC
1 CTCCCAGTAGAGT-TAATCTTTGACTTCCTCGTGAAGAAAAGTCAACC---TTTGTTTTCGACTC
* * * * * *
1366221 ACTCCCAATATAGTCAATCTTTGACTTTCTCGCGAAGAGAAGTCAACCCATGTTTTTGACTCCCC
62 ACT-CCAGTAGAGTCAATCTTTAAATTCCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCCCC
* * **
1366286 AGTAGAGTCTATCTTTGATTTCCTCGTGAAGAGAAGTCAACCCAGGTTTTAGA
126 AGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAA-CCATGTTTTACT
* * * * *
1366339 CTCCCTATTAGAG-TATGTCATTGACTTCCTTGTGAA-AAGAAGGCAACCTTTGTTATTTCCGAC
1 CTCCC-AGTAGAGTTA-ATCTTTGACTTCCTCGTGAAGAA-AAGTCAACCTTTG-T-TTT-CGAC
1366402 TCACTCCTAGTAGAGTCAATCTTTAAATTCCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCC
60 TCACTCC-AGTAGAGTCAATCTTTAAATTCCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCC
* *
1366467 CCATTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTTACTCT
124 CCAGTAGAGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACC-ATG----TT-TTA--CT
* * ** **
1366529 CTCCCAGTATAGTTAATCTTTGACTTCCTCGTGAAGAAAAGTTAACCCATGTTTTAAACTC-CT-
1 CTCCCAGTAGAGTTAATCTTTGACTTCCTCGTGAAGAAAAGTCAACCTTTGTTTTCGACTCACTC
* ** **
1366592 CAGTAGAGT-ATATCTTTGAATTCCTCATGAAGAGAAGTCAACCTTTGTTATTTCTA-ACTCACT
66 CAGTAGAGTCA-ATCTTTAAATTCCTCGCGAAGAGAAGTCAACCCATG---TTT-TAGACTC-C-
* * * * * **
1366655 ACCAGTAGAGTCAATCCTTT-ATTTCCTCGCGAAAAGAAGTAAACTCATGTTTTAGA
124 -CCAGTAGAGTCTAT-CTTTGACTTCCTCGTGAAGAGAAGTCAAC-CATGTTTTACT
** * * * * * *
1366711 CTCCCTAGTAGAGCCAATCCTTGACTTCCTCATGAACAGAAGTCAACCTATG--TTC-A-TGACT
1 CTCCC-AGTAGAGTTAATCTTTGACTTCCTCGTGAAGAAAAGTCAACCTTTGTTTTCGACTCACT
* * *
1366772 CCCAGTAGAGTCAAT-TCTTGATTTCCTCGCGAAGAAAAGTCAA
65 -CCAGTAGAGTCAATCT-TTAAATTCCTCGCGAAGAGAAGTCAA
1366815 TATTCCAGAT
Statistics
Matches: 543, Mismatches: 77, Indels: 76
0.78 0.11 0.11
Matches are distributed among these distances:
179 1 0.00
180 6 0.01
181 5 0.01
182 205 0.38
183 212 0.39
184 5 0.01
185 7 0.01
186 11 0.02
187 8 0.01
188 4 0.01
189 65 0.12
190 14 0.03
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (177 bp):
CTCCCAGTAGAGTTAATCTTTGACTTCCTCGTGAAGAAAAGTCAACCTTTGTTTTCGACTCACTC
CAGTAGAGTCAATCTTTAAATTCCTCGCGAAGAGAAGTCAACCCATGTTTTAGACTCCCCAGTAG
AGTCTATCTTTGACTTCCTCGTGAAGAGAAGTCAACCATGTTTTACT
Found at i:1367100 original size:3 final size:3
Alignment explanation
Indices: 1367087--1367126 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1367077 TTCATTATAA
* *
1367087 TAT TA- TAT TAT TAT TAG TAC TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1367127 CAAATAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1372148 original size:25 final size:25
Alignment explanation
Indices: 1372120--1372241 Score: 71
Period size: 24 Copynumber: 5.2 Consensus size: 25
1372110 TTGTCTATCC
*
1372120 CATTTTACATACAATGCAAAATCTT
1 CATTTTACATACAATGCAATATCTT
* * * * *
1372145 CA-TTTGCA-ACCAT-TATTATC-C
1 CATTTTACATACAATGCAATATCTT
* *
1372166 CATTTGACATACAATGCAAAATCTT
1 CATTTTACATACAATGCAATATCTT
* * * * *
1372191 CA-TTTGCA-ACCAT-TATTATC-C
1 CATTTTACATACAATGCAATATCTT
1372212 CATTTTACATACAATGCAATATCTT
1 CATTTTACATACAATGCAATATCTT
1372237 CATTT
1 CATTT
1372242 GCAACCATTA
Statistics
Matches: 64, Mismatches: 25, Indels: 16
0.61 0.24 0.15
Matches are distributed among these distances:
21 4 0.06
22 17 0.27
23 16 0.25
24 18 0.28
25 9 0.14
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (25 bp):
CATTTTACATACAATGCAATATCTT
Found at i:1372168 original size:46 final size:46
Alignment explanation
Indices: 1372115--1372255 Score: 264
Period size: 46 Copynumber: 3.1 Consensus size: 46
1372105 ATATTTTGTC
1372115 TATCCCATTTTACATACAATGCAAAATCTTCATTTGCAACCATTAT
1 TATCCCATTTTACATACAATGCAAAATCTTCATTTGCAACCATTAT
*
1372161 TATCCCATTTGACATACAATGCAAAATCTTCATTTGCAACCATTAT
1 TATCCCATTTTACATACAATGCAAAATCTTCATTTGCAACCATTAT
*
1372207 TATCCCATTTTACATACAATGCAATATCTTCATTTGCAACCATTAT
1 TATCCCATTTTACATACAATGCAAAATCTTCATTTGCAACCATTAT
1372253 TAT
1 TAT
1372256 TGTCGATACG
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 92 1.00
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (46 bp):
TATCCCATTTTACATACAATGCAAAATCTTCATTTGCAACCATTAT
Found at i:1372171 original size:21 final size:21
Alignment explanation
Indices: 1372145--1372216 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
1372135 GCAAAATCTT
1372145 CATTTGCAACCATTATTATCC
1 CATTTGCAACCATTATTATCC
* * ** *
1372166 CATTTGACATACAATGCAAAATCTT
1 CATTTG-CA-ACCAT-TATTATC-C
1372191 CATTTGCAACCATTATTATCC
1 CATTTGCAACCATTATTATCC
1372212 CATTT
1 CATTT
1372217 TACATACAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 11 0.30
22 6 0.16
23 8 0.22
24 6 0.16
25 6 0.16
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (21 bp):
CATTTGCAACCATTATTATCC
Found at i:1376017 original size:19 final size:19
Alignment explanation
Indices: 1375993--1376055 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
1375983 TACATGGTTA
1375993 GTTTTTATATTATTTTTAT
1 GTTTTTATATTATTTTTAT
* *
1376012 GTTTTTA-ATTAGATATTAT
1 GTTTTTATATTA-TTTTTAT
*
1376031 ATTTTTATATTTAATTTTTAT
1 GTTTTTATA-TT-ATTTTTAT
1376052 GTTT
1 GTTT
1376056 AATGTTATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.12
19 18 0.53
20 1 0.03
21 10 0.29
22 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.68
Consensus pattern (19 bp):
GTTTTTATATTATTTTTAT
Found at i:1376047 original size:13 final size:13
Alignment explanation
Indices: 1376031--1376073 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1376021 TAGATATTAT
1376031 ATTTTTATATTTA
1 ATTTTTATATTTA
*
1376044 ATTTTTATGTTTA
1 ATTTTTATATTTA
* *
1376057 ATGTTATATTTTTA
1 AT-TTTTATATTTA
1376071 ATT
1 ATT
1376074 GAATATTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (13 bp):
ATTTTTATATTTA
Found at i:1376082 original size:19 final size:18
Alignment explanation
Indices: 1375994--1376087 Score: 54
Period size: 19 Copynumber: 5.2 Consensus size: 18
1375984 ACATGGTTAG
* * *
1375994 TTTTTATATTATTTTTATG
1 TTTTTA-ATTAATATTATA
1376013 TTTTTAATTAGATATTATA
1 TTTTTAATTA-ATATTATA
1376032 TTTTT-A-T-AT-TTA-A
1 TTTTTAATTAATATTATA
* *
1376045 TTTTTATGTTTAATGTTATA
1 TTTTTA--ATTAATATTATA
*
1376065 TTTTTAATTGAATATTATG
1 TTTTTAATT-AATATTATA
1376084 TTTT
1 TTTT
1376088 AATGTTATGT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
13 6 0.10
14 3 0.05
15 2 0.03
17 2 0.03
18 9 0.15
19 30 0.51
20 7 0.12
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTTAATTAATATTATA
Found at i:1376094 original size:32 final size:33
Alignment explanation
Indices: 1376027--1376106 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 33
1376017 TAATTAGATA
* *
1376027 TTATATTTTTATATTTAATTTTTATGTTTAATG
1 TTATATTTTTATATTGAATTATTATGTTTAATG
1376060 TTATATTTTTA-ATTGAA-TATTATGTTTTAATG
1 TTATATTTTTATATTGAATTATTATG-TTTAATG
*
1376092 TTATGTTTTTATATT
1 TTATATTTTTATATT
1376107 TATGTTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 6 0.14
32 22 0.52
33 14 0.33
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (33 bp):
TTATATTTTTATATTGAATTATTATGTTTAATG
Found at i:1376097 original size:13 final size:13
Alignment explanation
Indices: 1376079--1376121 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
1376069 TAATTGAATA
1376079 TTATGTTTTAATG
1 TTATGTTTTAATG
1376092 TTATGTTTTTATAT-
1 TTATG-TTTTA-ATG
1376106 TTATG-TTTAATG
1 TTATGTTTTAATG
1376118 TTAT
1 TTAT
1376122 CTAGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.07
12 8 0.30
13 5 0.19
14 10 0.37
15 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (13 bp):
TTATGTTTTAATG
Found at i:1376106 original size:26 final size:26
Alignment explanation
Indices: 1376076--1376211 Score: 93
Period size: 26 Copynumber: 5.3 Consensus size: 26
1376066 TTTTAATTGA
*
1376076 ATATTATGTTTTAATGTTATGTTTTT
1 ATATTATGTTTTAATATTATGTTTTT
* * **
1376102 ATATTTATG-TTTAATGTTATCTAGTT
1 ATA-TTATGTTTTAATATTATGTTTTT
* *
1376128 -T-TTATGTTTTTATATTATG-TTTA
1 ATATTATGTTTTAATATTATGTTTTT
*
1376151 ATGTTTAATGTTTCT-ATATTATGTTTTT
1 AT-ATT-ATGTTT-TAATATTATGTTTTT
* * * *
1376179 GTATGATATTTTAATTTTATGTTTTT
1 ATATTATGTTTTAATATTATGTTTTT
1376205 ATATTAT
1 ATATTAT
1376212 TTTCGCTGTC
Statistics
Matches: 84, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
23 6 0.07
24 10 0.12
25 2 0.02
26 41 0.49
27 20 0.24
28 5 0.06
ACGTcount: A:0.24, C:0.01, G:0.10, T:0.64
Consensus pattern (26 bp):
ATATTATGTTTTAATATTATGTTTTT
Found at i:1376147 original size:13 final size:13
Alignment explanation
Indices: 1376076--1376211 Score: 82
Period size: 13 Copynumber: 10.5 Consensus size: 13
1376066 TTTTAATTGA
*
1376076 ATATTATGTTTTA
1 ATATTATGTTTTT
*
1376089 ATGTTATGTTTTT
1 ATATTATGTTTTT
*
1376102 ATATTTATG-TTTA
1 ATA-TTATGTTTTT
* * **
1376115 ATGTTATCTAGTT
1 ATATTATGTTTTT
1376128 -T-TTATGTTTTT
1 ATATTATGTTTTT
*
1376139 ATATTATG-TTTA
1 ATATTATGTTTTT
* *
1376151 ATGTTTAATGTTTCT
1 AT-ATT-ATGTTTTT
1376166 ATATTATGTTTTT
1 ATATTATGTTTTT
* * * *
1376179 GTATGATATTTTA
1 ATATTATGTTTTT
*
1376192 ATTTTATGTTTTT
1 ATATTATGTTTTT
1376205 ATATTAT
1 ATATTAT
1376212 TTTCGCTGTC
Statistics
Matches: 88, Mismatches: 28, Indels: 14
0.68 0.22 0.11
Matches are distributed among these distances:
11 7 0.08
12 11 0.12
13 56 0.64
14 10 0.11
15 4 0.05
ACGTcount: A:0.24, C:0.01, G:0.10, T:0.64
Consensus pattern (13 bp):
ATATTATGTTTTT
Found at i:1376155 original size:43 final size:39
Alignment explanation
Indices: 1376100--1376211 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 39
1376090 TGTTATGTTT
*
1376100 TTATATTTATGTTTAATGTTATCTAGTTTTTATGTTTTTATA
1 TTATATTTATGTTTAATGTT-TCTA--TATTATGTTTTTATA
* *
1376142 TTATGTTTAATGTTTAATGTTTCTATATTATGTTTTTGTA
1 TTATATTT-ATGTTTAATGTTTCTATATTATGTTTTTATA
* *
1376182 TGATATTTTAAT-TTT-ATGTTTTTATATTAT
1 TTATA-TTT-ATGTTTAATGTTTCTATATTAT
1376212 TTTCGCTGTC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
39 14 0.23
40 19 0.31
41 6 0.10
42 11 0.18
43 12 0.19
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (39 bp):
TTATATTTATGTTTAATGTTTCTATATTATGTTTTTATA
Found at i:1376729 original size:26 final size:25
Alignment explanation
Indices: 1376695--1376759 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
1376685 AAAGGAATAA
* *
1376695 AAATAAAGACAAATATAAAATAAGAT
1 AAATAAAGAAAAAAATAAAATAA-AT
* *
1376721 AAATGAAGAAAAAAATACAATAAAT
1 AAATAAAGAAAAAAATAAAATAAAT
*
1376746 AAACAAA-AAAAAAA
1 AAATAAAGAAAAAAA
1376760 GCGAAGAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 7 0.21
25 7 0.21
26 19 0.58
ACGTcount: A:0.75, C:0.05, G:0.06, T:0.14
Consensus pattern (25 bp):
AAATAAAGAAAAAAATAAAATAAAT
Found at i:1376736 original size:21 final size:21
Alignment explanation
Indices: 1376711--1376756 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1376701 AGACAAATAT
* *
1376711 AAAATA-AGATAAATGAAGAAA
1 AAAATACA-ATAAATAAACAAA
1376732 AAAATACAATAAATAAACAAA
1 AAAATACAATAAATAAACAAA
1376753 AAAA
1 AAAA
1376757 AAAGCGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (21 bp):
AAAATACAATAAATAAACAAA
Found at i:1376798 original size:2 final size:2
Alignment explanation
Indices: 1376793--1376817 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1376783 CAAATAAAGT
1376793 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
1376818 TAGCTTGTAA
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:1376951 original size:33 final size:33
Alignment explanation
Indices: 1376904--1376989 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
1376894 AATAAAATGT
* *
1376904 TAAAAAATGAAAAAAATATGGTAAAATAA-AT-AA
1 TAAAAAAAGAAAAAAA-ATAG-AAAATAACATAAA
*
1376937 TAATAACAAGAAAAAAAATAGAAAATAACATAAA
1 TAA-AAAAAGAAAAAAAATAGAAAATAACATAAA
*
1376971 TAAAAAAAGAATAAAAATA
1 TAAAAAAAGAAAAAAAATA
1376990 ATAAAGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
32 7 0.16
33 22 0.49
34 16 0.36
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (33 bp):
TAAAAAAAGAAAAAAAATAGAAAATAACATAAA
Found at i:1376963 original size:25 final size:24
Alignment explanation
Indices: 1376928--1377006 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 24
1376918 AATATGGTAA
1376928 AATAAATAATAATAACAAGAAAAAA-
1 AATAAA-AATAATAA-AAGAAAAAAG
1376953 AATAGAAAATAACATAAATA-AAAAAAG
1 AATA-AAAAT-A-ATAAA-AGAAAAAAG
*
1376980 AATAAAAATAAT-AAAGAAAAAAT
1 AATAAAAATAATAAAAGAAAAAAG
1377003 AATA
1 AATA
1377007 CATATGTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
22 1 0.02
23 12 0.26
24 2 0.04
25 8 0.17
26 15 0.32
27 9 0.19
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (24 bp):
AATAAAAATAATAAAAGAAAAAAG
Found at i:1378113 original size:17 final size:17
Alignment explanation
Indices: 1378071--1378104 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1378061 TATATTATGT
1378071 AATATAGTT-TATAATAA
1 AATATA-TTATATAATAA
1378088 AATATATTATATAATAA
1 AATATATTATATAATAA
1378105 TATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AATATATTATATAATAA
Found at i:1380057 original size:17 final size:18
Alignment explanation
Indices: 1380035--1380076 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1380025 CCCTAAACAT
1380035 TTTTCTCTTT-TTTTTTA
1 TTTTCTCTTTCTTTTTTA
*
1380052 TTTTCT-TTTCTTTTTTC
1 TTTTCTCTTTCTTTTTTA
1380069 TTTT-TCTT
1 TTTTCTCTT
1380077 CTTCGATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTCTCTTTCTTTTTTA
Found at i:1382344 original size:99 final size:99
Alignment explanation
Indices: 1382231--1382409 Score: 279
Period size: 99 Copynumber: 1.8 Consensus size: 99
1382221 TATAAATACC
* * *
1382231 TTTATCAGGTTAGCTGAATCTTATCCATAAGGCTGAGGCGTTTAACCAATTGC-CTTAGAGGGAC
1 TTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGAGGCGTTTAACCAATTGCTC-TAGAGGGAC
1382295 AACTCAAGCTTTATTGCATATATATTATAATCACT
65 AACTCAAGCTTTATTGCATATATATTATAATCACT
* *
1382330 TTTATTAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACA
1 TTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACA
* *
1382395 ATTCAAGTTTTATTG
66 ACTCAAGCTTTATTG
1382410 TGTACATATA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 71 0.99
100 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (99 bp):
TTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACA
ACTCAAGCTTTATTGCATATATATTATAATCACT
Found at i:1386675 original size:10 final size:10
Alignment explanation
Indices: 1386654--1386691 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
1386644 AAGAAATAAA
1386654 ATAAATATAT
1 ATAAATATAT
1386664 ATATACATATAT
1 ATA-A-ATATAT
1386676 ATAAATATAT
1 ATAAATATAT
1386686 A-AAATA
1 ATAAATA
1386692 AAATGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 5 0.19
10 10 0.38
11 2 0.08
12 9 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAAATATAT
Found at i:1387228 original size:23 final size:24
Alignment explanation
Indices: 1387195--1387239 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1387185 CGGCGCAAAT
* *
1387195 TTTTTTTTTTAT-TTTTAAAAACC
1 TTTTTTCTTTATCTCTTAAAAACC
1387218 TTTTTTCTTTATCTCTTAAAAA
1 TTTTTTCTTTATCTCTTAAAAA
1387240 ATCCAAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTTTCTTTATCTCTTAAAAACC
Found at i:1387904 original size:17 final size:17
Alignment explanation
Indices: 1387872--1387905 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1387862 TATATTATGT
* *
1387872 AATATATTTTATAATAA
1 AATATATTATACAATAA
1387889 AATATATTATACAATAA
1 AATATATTATACAATAA
1387906 TATTAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATATTATACAATAA
Found at i:1388741 original size:3 final size:3
Alignment explanation
Indices: 1388733--1388758 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1388723 AATTGAAACA
1388733 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1388759 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1388791 original size:20 final size:20
Alignment explanation
Indices: 1388756--1389025 Score: 74
Period size: 20 Copynumber: 13.5 Consensus size: 20
1388746 TTATTATTAT
1388756 TATATATATAT-A-TATATA
1 TATATATATATAACTATATA
1388774 TATATATATATAACTATATA
1 TATATATATATAACTATATA
1388794 GT-T-TAT-TGATAA-TAGTATA
1 -TATATATAT-ATAACTA-TATA
*
1388813 TAAACTATATATAAAC-A-ATA
1 TATA-TATATAT-AACTATATA
* * *
1388833 TATACTA-ACTTTTACTATATG
1 TATA-TATA-TATAACTATATA
* * *
1388854 TAAACTATATAT-ATTATGTA
1 TATA-TATATATAACTATATA
* * *
1388874 -ATTTACATATGAACTATATG
1 TATATATATAT-AACTATATA
*
1388894 TATAAACTATATAAACTATATA
1 TATATA-TATAT-AACTATATA
*
1388916 GT-T-TATGTATGAACTATATA
1 -TATATATATAT-AACTATATA
*
1388936 TATAGTTTATTAATGAACTATATA
1 TATA-TATA-T-AT-AACTATATA
* * *
1388960 AACTATTTATAT-AGTATATA
1 TA-TATATATATAACTATATA
* *
1388980 CTACATATAT-GAAC--TATA
1 -TATATATATATAACTATATA
1388998 TATATATATA-AACTATATA
1 TATATATATATAACTATATA
1389017 TAT-TATATA
1 TATATATATA
1389026 GTTTACATAT
Statistics
Matches: 187, Mismatches: 34, Indels: 62
0.66 0.12 0.22
Matches are distributed among these distances:
17 11 0.06
18 31 0.17
19 24 0.13
20 56 0.30
21 21 0.11
22 22 0.12
23 3 0.02
24 17 0.09
25 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (20 bp):
TATATATATATAACTATATA
Found at i:1388793 original size:2 final size:2
Alignment explanation
Indices: 1388756--1388785 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1388746 TTATTATTAT
1388756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1388786 ACTATATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1388927 original size:42 final size:42
Alignment explanation
Indices: 1388846--1388939 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
1388836 ACTAACTTTT
* * *
1388846 ACTATATG--TAAACTATATATATTATGTAATTTACATATGA
1 ACTATATGTATAAACTATATAAACTATATAATTTACATATGA
* **
1388886 ACTATATGTATAAACTATATAAACTATATAGTTTATGTATGA
1 ACTATATGTATAAACTATATAAACTATATAATTTACATATGA
*
1388928 ACTATATATATA
1 ACTATATGTATA
1388940 GTTTATTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 8 0.18
42 37 0.82
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (42 bp):
ACTATATGTATAAACTATATAAACTATATAATTTACATATGA
Found at i:1388964 original size:33 final size:31
Alignment explanation
Indices: 1388927--1389007 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
1388917 TTTATGTATG
*
1388927 AACTATATATATAGTTTATTAATGA-ACTATATA
1 AACTATATATATAGTATA-TAAT-ACA-TATATA
* * *
1388960 AACTATTTATATAGTATATACTACATATATG
1 AACTATATATATAGTATATAATACATATATA
1388991 AACTATATATATA-TATA
1 AACTATATATATAGTATA
1389008 AACTATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 4 0.10
31 18 0.43
32 4 0.10
33 16 0.38
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (31 bp):
AACTATATATATAGTATATAATACATATATA
Found at i:1389010 original size:48 final size:46
Alignment explanation
Indices: 1388954--1389066 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 46
1388944 ATTAATGAAC
*
1388954 TATATAAACTATTTATATAGTATATACTACATATATGAACTATATATA
1 TATATAAACTA--TATATAGTATATACTACACATATGAACTATATATA
* * **
1389002 TATATAAACTATATATATTATATAGTTTACATATGAAC--TATATA
1 TATATAAACTATATATAGTATATACTACACATATGAACTATATATA
1389046 TA-A-AAACTATATATATGTATA
1 TATATAAACTATATATA-GTATA
1389067 AACATATATA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
42 12 0.21
43 5 0.09
44 8 0.14
46 22 0.38
48 11 0.19
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (46 bp):
TATATAAACTATATATAGTATATACTACACATATGAACTATATATA
Found at i:1389014 original size:13 final size:13
Alignment explanation
Indices: 1388998--1389061 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
1388988 ATGAACTATA
1388998 TATATATATAAAC
1 TATATATATAAAC
*
1389011 TATATATATTATATAG
1 TATATATA-TA-A-AC
* * *
1389027 TTTACATATGAAC
1 TATATATATAAAC
*
1389040 TATATATAAAAAC
1 TATATATATAAAC
1389053 TATATATAT
1 TATATATAT
1389062 GTATAAACAT
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
13 26 0.68
14 3 0.08
15 2 0.05
16 7 0.18
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:1393338 original size:14 final size:14
Alignment explanation
Indices: 1393319--1393348 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1393309 TGGTTGTTGC
*
1393319 TGCCTGTTGGATGT
1 TGCCTGTTGAATGT
1393333 TGCCTGTTGAATGT
1 TGCCTGTTGAATGT
1393347 TG
1 TG
1393349 TTGCCTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.33, T:0.43
Consensus pattern (14 bp):
TGCCTGTTGAATGT
Found at i:1395976 original size:3 final size:3
Alignment explanation
Indices: 1395955--1396006 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
1395945 TGTCTGCTCC
* * * *
1395955 TGA TGA CGA CGA TGG TGA TGA TGG TGGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA T-GA TGA TGA TGA TGA TGA TGA
1396001 TGA TGA
1 TGA TGA
1396007 CAACAGTGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.29
Consensus pattern (3 bp):
TGA
Found at i:1399617 original size:46 final size:46
Alignment explanation
Indices: 1399548--1399684 Score: 134
Period size: 49 Copynumber: 2.9 Consensus size: 46
1399538 ATTTTTTGTA
*
1399548 TTTTCATTTATG-CATCCTTTCATATCCATTATGCACTGTTTACA-T
1 TTTTCCTTTATGACATCCTTTCATA-CCATTATGCACTGTTTACATT
* * * *
1399593 TTTTCCTTTATGACATCCATTCATACCAATTATACATTATTGTACATT
1 TTTTCCTTTATGACATCCTTTCATACC-ATTATGCACTGTT-TACATT
* * * *
1399641 TTTTATCTATATGATATCCTTTCATACCACTTATGCACCGTTTA
1 TTTT-CCTTTATGACATCCTTTCATACCA-TTATGCACTGTTTA
1399685 TATCCAAATG
Statistics
Matches: 73, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
45 13 0.18
46 21 0.29
47 4 0.05
48 8 0.11
49 27 0.37
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.47
Consensus pattern (46 bp):
TTTTCCTTTATGACATCCTTTCATACCATTATGCACTGTTTACATT
Found at i:1399925 original size:65 final size:65
Alignment explanation
Indices: 1399812--1399937 Score: 207
Period size: 65 Copynumber: 1.9 Consensus size: 65
1399802 TCAACGGTCT
* * * *
1399812 TTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTCCCAATTGCACAGCTAGGCCATTAGTC
1 TTAACCGTTCATCTAACTGGCAAAATTGACACCTTTCTCCCAAATGCACAACTAGGCCATTAGTC
*
1399877 TTAACCGTTCATCTAACTGGCAAAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATT
1 TTAACCGTTCATCTAACTGGCAAAATTGACACCTTTCTCCCAAATGCACAACTAGGCCATT
1399938 TATCTTTTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (65 bp):
TTAACCGTTCATCTAACTGGCAAAATTGACACCTTTCTCCCAAATGCACAACTAGGCCATTAGTC
Found at i:1400013 original size:81 final size:81
Alignment explanation
Indices: 1399877--1400418 Score: 762
Period size: 81 Copynumber: 6.7 Consensus size: 81
1399867 GCCATTAGTC
* *
1399877 TTAACCGTTCATCTAACTGGCAAAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTTATC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATC
1399942 TTTTACTCAACGGTCT
66 TTTTACTCAACGGTCT
* * * *
1399958 TTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCATAGCTAGGCTATTTATC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATC
* *
1400023 TTTTACTCAATGGTTT
66 TTTTACTCAACGGTCT
* * * * * *
1400039 TTAACCGCTCATCTAATTGGCATAATTGACACATTTATGCCAAATGCACGGCTAGGTCATTTATC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATC
1400104 TTTTACTCAACGGTCT
66 TTTTACTCAACGGTCT
* * *
1400120 TTAACC-TTTATCTAACTGGCATAATTGACACCTTTCTCCCAAATGCACACCTAGGCCATTTATC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATC
1400184 TTTTACTCAACGGTCT
66 TTTTACTCAACGGTCT
* * * ** * * *
1400200 TTAACCATTTATCTAACTGGCATAATTGATACCTTTCTGTTAAATACACAGATATGCCATTTATC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATC
*
1400265 TTTTACTCAACGATCT
66 TTTTACTCAACGGTCT
** * * * *
1400281 TTAACTATTCATCTAACTGGCATAATTGGCACCTTTCTGCCAAATTCATAGCTTGGCCATTTATC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATC
1400346 TTTTACTCAACGGTCT
66 TTTTACTCAACGGTCT
* * *
1400362 TTAACCGTTCATCTAACTGACATAATTGACACCTTTCTTCCAATTGCACAGCTAGGC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGC
1400419 ATCAAAGGCA
Statistics
Matches: 401, Mismatches: 59, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
80 71 0.18
81 330 0.82
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (81 bp):
TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATC
TTTTACTCAACGGTCT
Found at i:1400324 original size:242 final size:243
Alignment explanation
Indices: 1399877--1400418 Score: 762
Period size: 242 Copynumber: 2.2 Consensus size: 243
1399867 GCCATTAGTC
* *
1399877 TTAACCGTTCATCTAACTGGCAAAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTTATC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTCCCAAATGCACAACTAGGCCATTTATC
** * *
1399942 TTTTACTCAACGGTCTTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCAT
66 TTTTACTCAACGGTCTTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTACCAAATACAC
* * * * * * *
1400007 AGCTAGGCTATTTATCTTTTACTCAATGGTTTTTAACCGCTCATCTAATTGGCATAATTGACACA
131 AGATAGGCCATTTATCTTTTACTCAACGATCTTTAACCACTCATCTAACTGGCATAATTGACACA
* *
1400072 TTTATGCCAAATGCACGGCTAGGTCATTTATCTTTTACTCAACGGTCT
196 TTTATGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCT
* *
1400120 TTAACC-TTTATCTAACTGGCATAATTGACACCTTTCTCCCAAATGCACACCTAGGCCATTTATC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTCCCAAATGCACAACTAGGCCATTTATC
* * ***
1400184 TTTTACTCAACGGTCTTTAACCATTTATCTAACTGGCATAATTGATACCTTTCTGTTAAATACAC
66 TTTTACTCAACGGTCTTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTACCAAATACAC
* * * * *
1400249 AGATATGCCATTTATCTTTTACTCAACGATCTTTAACTATTCATCTAACTGGCATAATTGGCACC
131 AGATAGGCCATTTATCTTTTACTCAACGATCTTTAACCACTCATCTAACTGGCATAATTGACACA
* * * *
1400314 TTTCTGCCAAATTCATAGCTTGGCCATTTATCTTTTACTCAACGGTCT
196 TTTATGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCT
* * * *
1400362 TTAACCGTTCATCTAACTGACATAATTGACACCTTTCTTCCAATTGCACAGCTAGGC
1 TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTCCCAAATGCACAACTAGGC
1400419 ATCAAAGGCA
Statistics
Matches: 262, Mismatches: 36, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
242 211 0.81
243 51 0.19
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (243 bp):
TTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTCCCAAATGCACAACTAGGCCATTTATC
TTTTACTCAACGGTCTTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTACCAAATACAC
AGATAGGCCATTTATCTTTTACTCAACGATCTTTAACCACTCATCTAACTGGCATAATTGACACA
TTTATGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCT
Found at i:1400486 original size:68 final size:67
Alignment explanation
Indices: 1400369--1400552 Score: 260
Period size: 68 Copynumber: 2.7 Consensus size: 67
1400359 TCTTTAACCG
* * *
1400369 TTCATCTAACTGACATAATTGACACCTTTCTTCCAATTGCACAGCTAGGCATCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTT-CAAATGCACAGTTAGGCATCAAAGGCACTTAG
1400434 CCT
65 CCT
* * * *
1400437 TTCCTCTAATTGGCATAATTGAAACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCT-TCAAATGCACAGTTAGGCATCAAAGGCACTTAG
1400502 CCT
65 CCT
* *
1400505 TTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCAGAGTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCT-TCAAATGCACAGTTAG
1400553 ACTATTAATT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
68 101 0.99
69 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (67 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTTCAAATGCACAGTTAGGCATCAAAGGCACTTAGC
CT
Found at i:1400832 original size:53 final size:55
Alignment explanation
Indices: 1400770--1400911 Score: 200
Period size: 55 Copynumber: 2.6 Consensus size: 55
1400760 ATATTTCCCC
* * * * *
1400770 TACGGAAATTCATACACTTAGT-TTAATTT-TGTAG-TTTGCACACATAGTGGCCT
1 TACGAAAATTCATACACTTAGTATGAATTTCT-TAGTTTTGCACACAAAGTGCCCA
*
1400823 TACGAAAATTTATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
1 TACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
1400878 TACGAAAATTCATACACTTAGTATGAATTTCTTA
1 TACGAAAATTCATACACTTAGTATGAATTTCTTA
1400912 ACTTTTTGCA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
53 20 0.25
54 9 0.11
55 50 0.63
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (55 bp):
TACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
Found at i:1401342 original size:20 final size:20
Alignment explanation
Indices: 1401317--1401370 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1401307 TATGTGATCA
*
1401317 ATGGTATCGATATCATCCTC
1 ATGGTATCGATATCACCCTC
1401337 ATGGTATCGATACTC-CCCTC
1 ATGGTATCGATA-TCACCCTC
*
1401357 TTGGTATCGA-ATCA
1 ATGGTATCGATATCA
1401371 ATCATATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.07
19 1 0.03
20 25 0.83
21 2 0.07
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (20 bp):
ATGGTATCGATATCACCCTC
Found at i:1401767 original size:20 final size:20
Alignment explanation
Indices: 1401742--1401794 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1401732 TATGTGATCA
*
1401742 ATGGTATCGATA-TCATCCTC
1 ATGGTATCGATACTC-CCCTC
1401762 ATGGTATCGATACTCCCCTC
1 ATGGTATCGATACTCCCCTC
*
1401782 TTGGTATCGATAC
1 ATGGTATCGATAC
1401795 CACTTGAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (20 bp):
ATGGTATCGATACTCCCCTC
Found at i:1404591 original size:16 final size:17
Alignment explanation
Indices: 1404560--1404591 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1404550 TTCTCTATGA
1404560 TTTCTTATTGCTTGATG
1 TTTCTTATTGCTTGATG
1404577 TTTCTTATT-CTTGAT
1 TTTCTTATTGCTTGAT
1404592 CAATGGCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTCTTATTGCTTGATG
Found at i:1407550 original size:21 final size:23
Alignment explanation
Indices: 1407501--1407552 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1407491 ATTCCCCTGT
1407501 GGGGGGAAATCGGTTCCCCTTCAA
1 GGGGGG-AATCGGTTCCCCTTCAA
* *
1407525 AGGGGGAATCGGTT-GCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
1407546 GGGGGGA
1 GGGGGGA
1407553 TTGATTCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 10 0.40
22 2 0.08
23 8 0.32
24 5 0.20
ACGTcount: A:0.21, C:0.19, G:0.42, T:0.17
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:1412405 original size:16 final size:17
Alignment explanation
Indices: 1412374--1412405 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1412364 TTCTCTATGA
1412374 TTTCTTATTGCTTGATG
1 TTTCTTATTGCTTGATG
1412391 TTTCTTATT-CTTGAT
1 TTTCTTATTGCTTGAT
1412406 CAATGGCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTCTTATTGCTTGATG
Found at i:1415277 original size:63 final size:65
Alignment explanation
Indices: 1415166--1415293 Score: 226
Period size: 63 Copynumber: 2.0 Consensus size: 65
1415156 ATCATCTGGC
1415166 GCAGAGATCTCGGTCATCACCAACACACATCAACAAACCAACTACATTAGAAATCCTAGTTCAAA
1 GCAGAGATCTCGGTCATCACCAACACACATCAACAAACCAACTACATTAG-AATCCTAGTTCAAA
1415231 T
65 T
1415232 GCAGAGATCTCGGTCATCACC-A-A-ACATCAACAAACCAACTACATTAGAATCCTAGTTCAAAT
1 GCAGAGATCTCGGTCATCACCAACACACATCAACAAACCAACTACATTAGAATCCTAGTTCAAAT
1415294 AGGATACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
62 15 0.24
63 24 0.39
64 1 0.02
65 1 0.02
66 21 0.34
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (65 bp):
GCAGAGATCTCGGTCATCACCAACACACATCAACAAACCAACTACATTAGAATCCTAGTTCAAAT
Found at i:1417143 original size:39 final size:39
Alignment explanation
Indices: 1417089--1417165 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
1417079 TATTTATGTA
1417089 TTTTATTGTACTAACTTTTTGCATGTGTTTGTTTTTTTT
1 TTTTATTGTACTAACTTTTTGCATGTGTTTGTTTTTTTT
1417128 TTTTATTGTACTAACTTTTTGCATGTGTTTGTTTTTTT
1 TTTTATTGTACTAACTTTTTGCATGTGTTTGTTTTTTT
1417166 AGCATTTGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.66
Consensus pattern (39 bp):
TTTTATTGTACTAACTTTTTGCATGTGTTTGTTTTTTTT
Found at i:1427612 original size:106 final size:106
Alignment explanation
Indices: 1427453--1427813 Score: 516
Period size: 106 Copynumber: 3.4 Consensus size: 106
1427443 ACGAATAGGC
*
1427453 TTCCCAATTTCAGAGCCAATTTCAACTTCACGATGAAGGATATTGGACCCAAGACAACACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACCCAAGACAACACAAGCT
* *
1427518 CAACTTCACGACGAAGGGGCGGGTGACTGTCAACAAATAAT
66 CAACTTCACGACGAAGGGGCGGCTGACTGTCAACAAACAAT
*
1427559 TTCCCAATTTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACCCAAGACAACACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACCCAAGACAACACAAGCT
*
1427624 CAACTTCACGACGAAGGGGCGGCTGACTGTCAACACACAAT
66 CAACTTCACGACGAAGGGGCGGCTGACTGTCAACAAACAAT
* * * * * * *
1427665 TT--C-A-TTCATAGTCAATTTCAACTTCACAACGAAGAATATTAGACTCAAGACAGCACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACCCAAGACAACACAAGCT
* *
1427726 CAACTTCACGGCGAAGAGGCGGCTGACTGTCAACAAACAAT
66 CAACTTCACGACGAAGGGGCGGCTGACTGTCAACAAACAAT
* * * *
1427767 TTCCCAGTTCCAGAACCAATTTCAACTTCACGGC-AGAGGATATTGGA
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACGACGA-AGGATATTGGA
1427814 TTCAGAACAA
Statistics
Matches: 225, Mismatches: 25, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
102 89 0.40
103 1 0.00
104 2 0.01
105 1 0.00
106 132 0.59
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (106 bp):
TTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACCCAAGACAACACAAGCT
CAACTTCACGACGAAGGGGCGGCTGACTGTCAACAAACAAT
Found at i:1441496 original size:19 final size:19
Alignment explanation
Indices: 1441469--1441513 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1441459 TGCAATAAAA
*
1441469 GACATTGTAAAACATATAG
1 GACACTGTAAAACATATAG
1441488 GACACTGTAAAACATATAG
1 GACACTGTAAAACATATAG
1441507 GACACTG
1 GACACTG
1441514 CAACAAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (19 bp):
GACACTGTAAAACATATAG
Found at i:1441523 original size:21 final size:19
Alignment explanation
Indices: 1441477--1441526 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
1441467 AAGACATTGT
*
1441477 AAAACATATAGGACACTGT
1 AAAACATATAGGACACTGA
1441496 AAAACATATAGGACACTGCA
1 AAAACATATAGGACACTG-A
1441516 ACAAACATATA
1 A-AAACATATA
1441527 TACCAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 18 0.64
20 1 0.04
21 9 0.32
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (19 bp):
AAAACATATAGGACACTGA
Found at i:1448180 original size:23 final size:24
Alignment explanation
Indices: 1448140--1448185 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1448130 CTATAAAATA
*
1448140 ATTTTTTATAATTCTAAA-TTAAG
1 ATTTTTTATAATTATAAAGTTAAG
*
1448163 ATTTTTTATATTTATAAAGTTAA
1 ATTTTTTATAATTATAAAGTTAA
1448186 ATAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTTTTATAATTATAAAGTTAAG
Found at i:1454402 original size:2 final size:2
Alignment explanation
Indices: 1454395--1454422 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1454385 GTTTCACTTA
1454395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1454423 TTGTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1455991 original size:15 final size:15
Alignment explanation
Indices: 1455971--1455999 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1455961 CAGACTGAAC
1455971 AAATATTTTATTTTA
1 AAATATTTTATTTTA
1455986 AAATATTTTATTTT
1 AAATATTTTATTTT
1456000 TCACGCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATATTTTATTTTA
Found at i:1457359 original size:25 final size:24
Alignment explanation
Indices: 1457331--1457401 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 24
1457321 TTAAATTCAT
1457331 AATATTTATATATATTAACTTAAAA
1 AATATTT-TATATATTAACTTAAAA
1457356 AATATTTT-TATATTAACTTATTAAA
1 AATATTTTATATATTAACTTA--AAA
*
1457381 TATATTTTAT-TATTAACTTAA
1 AATATTTTATATATTAACTTAA
1457402 TTTAAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
23 13 0.31
24 1 0.02
25 27 0.64
26 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
AATATTTTATATATTAACTTAAAA
Found at i:1457371 original size:23 final size:23
Alignment explanation
Indices: 1457331--1457401 Score: 88
Period size: 23 Copynumber: 2.9 Consensus size: 23
1457321 TTAAATTCAT
1457331 AATATTTATATATATTAACTTAAAA
1 AATATTT-T-TATATTAACTTAAAA
**
1457356 AATATTTTTATATTAACTTATTA
1 AATATTTTTATATTAACTTAAAA
1457379 AATATATTTTATTATTAACTTAA
1 AATAT-TTTTA-TATTAACTTAA
1457402 TTTAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 18 0.44
24 6 0.15
25 17 0.41
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTTTTATATTAACTTAAAA
Found at i:1457393 original size:27 final size:27
Alignment explanation
Indices: 1457331--1457418 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 27
1457321 TTAAATTCAT
1457331 AATA-TTTATATATATTAACTTA--AAA
1 AATATTTTAT-TATATTAACTTATTAAA
1457356 AATA-TTT-TTATATTAACTTATTAAA
1 AATATTTTATTATATTAACTTATTAAA
*
1457381 TATATTTTA-T-TATTAACTTAATTTAAA
1 AATATTTTATTATATTAACTT-A-TTAAA
1457408 AATATTTTATT
1 AATATTTTATT
1457419 TTAAATTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
23 12 0.22
24 1 0.02
25 22 0.41
26 5 0.09
27 13 0.24
28 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATTTTATTATATTAACTTATTAAA
Found at i:1457439 original size:27 final size:27
Alignment explanation
Indices: 1457332--1457444 Score: 98
Period size: 27 Copynumber: 4.3 Consensus size: 27
1457322 TAAATTCATA
*
1457332 ATATTTATATATATTAACTTAA--AAAAT
1 ATATTT-TAT-TATTAACTTAATTTAAAT
1457359 AT-TTTTA-TATTAACTT-A-TTAAAT
1 ATATTTTATTATTAACTTAATTTAAAT
*
1457382 ATATTTTATTATTAACTTAATTTAAAA
1 ATATTTTATTATTAACTTAATTTAAAT
* *
1457409 ATATTTTATT-TTAAATTTTCATTT-AAT
1 ATATTTTATTATT-AA-CTTAATTTAAAT
1457436 ATATTTTAT
1 ATATTTTAT
1457445 GTGAAAATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
22 1 0.01
23 15 0.20
24 5 0.07
25 11 0.15
26 6 0.08
27 30 0.41
28 6 0.08
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATTTTATTATTAACTTAATTTAAAT
Found at i:1460759 original size:172 final size:171
Alignment explanation
Indices: 1460452--1460794 Score: 476
Period size: 172 Copynumber: 2.0 Consensus size: 171
1460442 GTTTAAAACT
* * *
1460452 GAAAATGTTATGATCATATATAAGAAATATGGTTGTGCTCAATAATGTCATGGCTCAATAATAAA
1 GAAAATGTTATGATCATATATAAGAAATACGGTTCTACTCAATAATGTCATGGCTCAATAATAAA
* * * * *
1460517 AAAAGGTTATAATCTGGAATGTTAATACTTTTAATAATAAAACATGTTGCGACGATAATGTTATC
66 AAAAAGTTATAATCTGGAATATTAATACTTTCAATAATAAAACAGGTTGCGACGAAAATGTTATC
*
1460582 AGAGTTTAAGCTGATGGAG-CGTTAGATTAT-CACAGTATAAG
131 AGAGTTTAAGCTGACGGAGTC-TTAGATTATCCA-AGTATAAG
* * *
1460623 GAAAATGTTATGATTATATATAAGAAATACGGTTACTAC-CAATAATGTCTTGGTTCAATAATAA
1 GAAAATGTTATGATCATATATAAGAAATACGGTT-CTACTCAATAATGTCATGGCTCAATAAT-A
* * *
1460687 AAAAAAAGTTGTAATCTGGAATATTAATACTTTCAATAATAAAATAGGTTGCGCCGAAAATGTTA
64 AAAAAAAGTTATAATCTGGAATATTAATACTTTCAATAATAAAACAGGTTGCGACGAAAATGTTA
* *
1460752 TCAGAGTTTAAGTTGACGGAGTCTTGGATTATCCAAGTATAAG
129 TCAGAGTTTAAGCTGACGGAGTCTTAGATTATCCAAGTATAAG
1460795 TAAATAATTT
Statistics
Matches: 151, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
171 53 0.35
172 95 0.63
173 3 0.02
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (171 bp):
GAAAATGTTATGATCATATATAAGAAATACGGTTCTACTCAATAATGTCATGGCTCAATAATAAA
AAAAAGTTATAATCTGGAATATTAATACTTTCAATAATAAAACAGGTTGCGACGAAAATGTTATC
AGAGTTTAAGCTGACGGAGTCTTAGATTATCCAAGTATAAG
Found at i:1461189 original size:185 final size:186
Alignment explanation
Indices: 1460623--1461426 Score: 911
Period size: 185 Copynumber: 4.3 Consensus size: 186
1460613 ACAGTATAAG
* * ** *
1460623 GAAAATGTTATGATTATATATAAGAAATACGGTTACTACCAATAATGTCTTGGTTCAATAATAAA
1 GAAAATGTTATGATCATATATAAGAAATACGGTTGCGCCCAATAATGTCATGGTTCAATAAT--A
* * * * *
1460688 AAAAAAGTTGTAATCTGGAATATTAATACTTTCAATAATAAAATAGGTTGCGCCGAAAATGTTAT
64 AAAAAGGTTGTAATCTGGAATGTTAATACTTTTAACAATAAAATAGGTTGCGCCGAAAATATTAT
* * * * * * *
1460753 CAGAGTTTAAGTTGACGGAGTCTTGGATTAT-CCAAGTATAAGTAAATAATTTTGAAACT
129 CAAAGTTTAAGCTGATGGAG-CTTGAATTATCCCAA-TATAAGAAAATAAGTTTAAAACT
* * *
1460812 GAAAATGTCATGAACATATATATATAATAAATACGGTTGCGCCCAATAATGTCATGGTTCAATAA
1 GAAAATGTTATG---AT-CATATATAAGAAATACGGTTGCGCCCAATAATGTCATGGTTCAATAA
* * * * * * * * *
1460877 TAAAAAAAGGTTGTAACCTGAAATGTTAATATTTTTAACAATTAAGTATGATGTGCCAAAAATAT
62 T-AAAAAAGGTTGTAATCTGGAATGTTAATACTTTTAACAATAAAATAGGTTGCGCCGAAAATAT
* * *
1460942 TATCATAGTTTAAGCTGATGGAGCATTGAATTATCCTAGTATAAGAAAATAAGTTTAAAACT
126 TATCAAAGTTTAAGCTGATGGAGC-TTGAATTATCCCAATATAAGAAAATAAGTTTAAAACT
* * *
1461004 GAAAATGCTATGATCATATATAAGAAATACGATTGCGCCCAATAATGTCATGGTTCAATTATAAA
1 GAAAATGTTATGATCATATATAAGAAATACGGTTGCGCCCAATAATGTCATGGTTCAATAATAAA
* * *
1461069 AAA-GTTGTAATATGGAATGTTAATATTTTTAACAATAAAGTA-GTTGCGCCGAAAATATTATCA
66 AAAGGTTGTAATCTGGAATGTTAATACTTTTAACAATAAAATAGGTTGCGCCGAAAATATTATCA
*
1461132 AAGTTTAAGCTGATGGAGCGTTGAATTATCCCAATATAAACAAAATAAG-TTAAAACT
131 AAGTTTAAGCTGATGGAGC-TTGAATTATCCCAATAT-AAGAAAATAAGTTTAAAACT
* * *
1461189 GAAAATGTTATG-TCATATATAAGAAATATGGTTGCGCCCAATAATGTCATAGCTCAATAATAAA
1 GAAAATGTTATGATCATATATAAGAAATACGGTTGCGCCCAATAATGTCATGGTTCAATAATAAA
* * * *
1461253 AAAGGTTGTAATCTAGAATGTTAATACTTTTAATAATAAAATAGGTTACGCCGAAAATGTTATCA
66 AAAGGTTGTAATCTGGAATGTTAATACTTTTAACAATAAAATAGGTTGCGCCGAAAATATTATCA
* * * *** *
1461318 AATTTTAAGCGGAT-GAGGCCTTGGAA-GATTTGAGTATAAGAAAATAAGTTTAAAACT
131 AAGTTTAAGCTGATGGA-G-CTT-GAATTATCCCAATATAAGAAAATAAGTTTAAAACT
* * * *
1461375 GCAAATATTATGAACATATATAAGAAATACGGTTGCGCCCATTAATGTCATG
1 GAAAATGTTATGATCATATATAAGAAATACGGTTGCGCCCAATAATGTCATG
1461427 AGTTACTAAG
Statistics
Matches: 527, Mismatches: 74, Indels: 30
0.84 0.12 0.05
Matches are distributed among these distances:
184 50 0.09
185 116 0.22
186 103 0.20
187 45 0.09
188 44 0.08
189 13 0.02
191 1 0.00
192 110 0.21
193 45 0.09
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (186 bp):
GAAAATGTTATGATCATATATAAGAAATACGGTTGCGCCCAATAATGTCATGGTTCAATAATAAA
AAAGGTTGTAATCTGGAATGTTAATACTTTTAACAATAAAATAGGTTGCGCCGAAAATATTATCA
AAGTTTAAGCTGATGGAGCTTGAATTATCCCAATATAAGAAAATAAGTTTAAAACT
Found at i:1461369 original size:371 final size:377
Alignment explanation
Indices: 1460623--1461426 Score: 968
Period size: 371 Copynumber: 2.1 Consensus size: 377
1460613 ACAGTATAAG
* * ** *
1460623 GAAAATGTTATGATTATATATAAGAAATACGGTTACTACCAATAATGTCTTGGTTCAATAATAAA
1 GAAAATGTTATGATCATATATAAGAAATACGGTTGCGCCCAATAATGTCATGGTTCAAT-ATAAA
* * *
1460688 AAAAAAGTTGTAATCTGGAATATTAATACTTTCAATAATAAAATAGGTTGCGCCGAAAATGTTAT
65 AAAAAAGTTGTAATATGGAATATTAATACTTTCAACAATAAAATAGGTTGCGCCGAAAATATTAT
* * * ** * *
1460753 CAGAGTTTAAGTTGACGGAGTCTTGGATTATCCAAGTATAAGTAAATAATTTTGAAACTGAAAAT
130 CAAAGTTTAAGCTGACGGAGTCTTGAATTATCCAAGTATAACAAAATAATGTTAAAACTGAAAAT
* * * *
1460818 GTCATGAACATATATATATAATAAATACGGTTGCGCCCAATAATGTCATGGTTCAATAATAAAAA
195 GTCATG---ATACATATATAAGAAATACGGTTGCGCCCAATAATGTCATAGCTCAATAATAAAAA
* * * * ** *
1460883 AAGGTTGTAACCTGAAATGTTAATATTTTTAACAATTAAGTATGATGTGCCAAAAATATTATCAT
257 AAGGTTGTAACCTGAAATGTTAATACTTTTAACAATAAAATAGGATACGCCAAAAATATTATCAA
* *
1460948 AGTTTAAGCTGATGGAGCATTGAATTATCCTAGTATAAGAAAATAAGTTTAAAACT
322 AGTTTAAGCGGATGGAGCATTGAATGATCCTAGTATAAGAAAATAAGTTTAAAACT
* * *
1461004 GAAAATGCTATGATCATATATAAGAAATACGATTGCGCCCAATAATGTCATGGTTCAAT-T-ATA
1 GAAAATGTTATGATCATATATAAGAAATACGGTTGCGCCCAATAATGTCATGGTTCAATATAAAA
* * * *
1461067 AAAAAGTTGTAATATGGAATGTTAATATTTTTAACAATAAAGTA-GTTGCGCCGAAAATATTATC
66 AAAAAGTTGTAATATGGAATATTAATACTTTCAACAATAAAATAGGTTGCGCCGAAAATATTATC
*
1461131 AAAGTTTAAGCTGATGGAG-CGTTGAATTATCCCAA-TATAAACAAAATAA-GTTAAAACTGAAA
131 AAAGTTTAAGCTGACGGAGTC-TTGAATTAT-CCAAGTAT-AACAAAATAATGTTAAAACTGAAA
* *
1461193 ATGTTATG-T-CATATATAAGAAATATGGTTGCGCCCAATAATGTCATAGCTCAATAAT-AAAAA
193 ATGTCATGATACATATATAAGAAATACGGTTGCGCCCAATAATGTCATAGCTCAATAATAAAAAA
* * * * *
1461255 AGGTTGTAATCT-AGAATGTTAATACTTTTAATAATAAAATAGGTTACGCCGAAAATGTTATCAA
258 AGGTTGTAACCTGA-AATGTTAATACTTTTAACAATAAAATAGGATACGCCAAAAATATTATCAA
* * *
1461319 ATTTTAAGCGGAT-GAGGCCTTGGAA-GAT-TTGAGTATAAGAAAATAAGTTTAAAACT
322 AGTTTAAGCGGATGGA-GCATT-GAATGATCCT-AGTATAAGAAAATAAGTTTAAAACT
* * * *
1461375 GCAAATATTATGAACATATATAAGAAATACGGTTGCGCCCATTAATGTCATG
1 GAAAATGTTATGATCATATATAAGAAATACGGTTGCGCCCAATAATGTCATG
1461427 AGTTACTAAG
Statistics
Matches: 364, Mismatches: 52, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
370 4 0.01
371 143 0.39
372 46 0.13
373 1 0.00
376 1 0.00
377 64 0.18
378 52 0.14
379 1 0.00
381 52 0.14
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (377 bp):
GAAAATGTTATGATCATATATAAGAAATACGGTTGCGCCCAATAATGTCATGGTTCAATATAAAA
AAAAAGTTGTAATATGGAATATTAATACTTTCAACAATAAAATAGGTTGCGCCGAAAATATTATC
AAAGTTTAAGCTGACGGAGTCTTGAATTATCCAAGTATAACAAAATAATGTTAAAACTGAAAATG
TCATGATACATATATAAGAAATACGGTTGCGCCCAATAATGTCATAGCTCAATAATAAAAAAAGG
TTGTAACCTGAAATGTTAATACTTTTAACAATAAAATAGGATACGCCAAAAATATTATCAAAGTT
TAAGCGGATGGAGCATTGAATGATCCTAGTATAAGAAAATAAGTTTAAAACT
Found at i:1463838 original size:25 final size:25
Alignment explanation
Indices: 1463821--1463867 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1463811 CTTGATTATT
*
1463821 CTGAA-CCATATGTAACTTGAGTTA
1 CTGAATCCATATGCAACTTGAGTTA
*
1463845 CTGAATTCATATGCAACTTGAGT
1 CTGAATCCATATGCAACTTGAGT
1463868 GAAGAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (25 bp):
CTGAATCCATATGCAACTTGAGTTA
Found at i:1465861 original size:100 final size:98
Alignment explanation
Indices: 1465423--1465861 Score: 385
Period size: 100 Copynumber: 4.4 Consensus size: 98
1465413 ATTATAACCA
* * * *
1465423 AAACGGTTGACAATATAAGAAGGAGCTACCTGTATTGTTATAAATATTACCCTTTTTTTATCTTA
1 AAACGGTTGACAATATAA-AAGGCGCTACCTGTA-TGTTATAAATA-TAACCTTGTTTTGTCTTA
* *
1465488 CATAAGCATAATGAAAATGGTTTCACACATATAACTT
63 CATAACCCTAATGAAAAT-GTTTCACACATATAACTT
* * * * *
1465525 AAACGGTTGACAATATAAGAAGGCGATATACATGT-TGTTATAAATTTAGACCTTCTTTT-T-GT
1 AAACGGTTGACAATATAA-AAGGCG--CTACCTGTATGTTATAAATATA-ACCTTGTTTTGTCTT
***** * * *
1465587 ACATTGTATTAATAAAAAATGTTTCGA-ATATATAACAT
62 ACATAACCCTAAT-GAAAATGTTTC-ACACATATAACTT
* * * * *
1465625 AAACGATTGACACTATAAAAGGTGCTACC----T-TTATAAATATAACCTTGTTTTGTTTTGCAT
1 AAACGGTTGACAATATAAAAGGCGCTACCTGTATGTTATAAATATAACCTTGTTTTGTCTTACAT
* * *
1465685 AACTCTAATGAACATGTTTCGCACATATAACTT
66 AACCCTAATGAAAATGTTTCACACATATAACTT
* * * *
1465718 AAACGGTTGACACTATAAAAGGCTCTATCTTTATTGTTATAAATATAATCC-TGTTTTGTCTTAC
1 AAACGGTTGACAATATAAAAGGCGCTACCTGTA-TGTTATAAATATAA-CCTTGTTTTGTCTTAC
1465782 ATAACCCTAATGAAATATGTTTCACACATATAACTT
64 ATAACCCTAATGAAA-ATGTTTCACACATATAACTT
* *
1465818 AAACGGTTGACAATATAAAAAGCGCTACCTGTAATGTTTTAAAT
1 AAACGGTTGACAATATAAAAGGCGCTACCTGT-ATGTTATAAAT
1465862 TTAAACATGT
Statistics
Matches: 271, Mismatches: 49, Indels: 36
0.76 0.14 0.10
Matches are distributed among these distances:
92 9 0.03
93 54 0.20
94 9 0.03
97 3 0.01
98 1 0.00
99 41 0.15
100 96 0.35
101 10 0.04
102 42 0.15
104 6 0.02
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (98 bp):
AAACGGTTGACAATATAAAAGGCGCTACCTGTATGTTATAAATATAACCTTGTTTTGTCTTACAT
AACCCTAATGAAAATGTTTCACACATATAACTT
Found at i:1465904 original size:100 final size:100
Alignment explanation
Indices: 1465700--1465912 Score: 221
Period size: 100 Copynumber: 2.1 Consensus size: 100
1465690 TAATGAACAT
* * * * * * *
1465700 GTTTCGCACATATAACTTAAACGGTTGACACTATAAAAGGCTCTATCTTTATTGTTATAAATATA
1 GTTTCACACATATAACTTAAACGGTTGACAATATAAAAAGCGCTACCTGTAATGTTATAAATATA
* * * * * * * *
1465765 ATCCTGTTTTGTCTTACATAACCCTAATGAAATAT
66 AACATGTTTTCTATAACAGAACCCTAATGAAAAAA
* *
1465800 GTTTCACACATATAACTTAAACGGTTGACAATATAAAAAGCGCTACCTGTAATGTTTTAAATTTA
1 GTTTCACACATATAACTTAAACGGTTGACAATATAAAAAGCGCTACCTGTAATGTTATAAATATA
** *
1465865 AACATGTTTTCTATAACAGATTCTTAAT-AATAAAA
66 AACATGTTTTCTATAACAGAACCCTAATGAA-AAAA
*
1465900 GTTTCAAACATAT
1 GTTTCACACATAT
1465913 TCAAATATTT
Statistics
Matches: 91, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
99 2 0.02
100 89 0.98
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (100 bp):
GTTTCACACATATAACTTAAACGGTTGACAATATAAAAAGCGCTACCTGTAATGTTATAAATATA
AACATGTTTTCTATAACAGAACCCTAATGAAAAAA
Found at i:1470991 original size:296 final size:296
Alignment explanation
Indices: 1470228--1471111 Score: 1234
Period size: 296 Copynumber: 3.0 Consensus size: 296
1470218 TTCATTTCAC
*
1470228 CAATTTTCTTTTCAACCGATCCAAACAACTCTTTCACTTCTACCCTCAATTTACTTACTTCCTTA
1 CAATTTTCTTTTCAACCGATCCAAACAACTCTTTCACTTCTACCCTCAATTTACTCACTTCCTTA
* * * * * * * ***** *
1470293 ACCGCCACACCCCTTCTCAGTTCCTCCAGCCAATTAACAAAAAAAAAATTCAA-AGTCACCAATA
66 ACTGTCACACCCCTTTTTAGTTCATCCAACCCATTAAC--AAATTTTTTTCAAGA-TCACCAACA
* * * *
1470357 GAACTCTTCATCCCCTCAATTTCACCCCTTATTTTATCAACTTATTCCACTACTCCAATAAATTT
128 GAACACTTCATCCCCTCAATTTCACCCCTTATTTTATCAACTTCTTCCACCACTCCAACAAATTT
* * ** *
1470422 TGCATTACTTTTCTCCACAAACTCCATTCTATCATACTTTTGGGTCTCAAATTCTTCCTCTATCC
193 TGCATTACTTTTCTCCACAAACTCTATTCAATCATACTTTTGGGTCTCAAACGCTTCCTCCATCC
*
1470487 TCACTTGTCTTTCATGAACCTCAAAAACACTTCTACCCT
258 TCACTTGTCTTTCATGAACCTCAGAAACACTTCTACCCT
* * *
1470526 CAAATTTTCTTTTCAACCGATCCAAACAACTATTTCCCTTCTACCATCAATTTACTCACTTCCTT
1 C-AATTTTCTTTTCAACCGATCCAAACAACTCTTTCACTTCTACCCTCAATTTACTCACTTCCTT
* * * * * *
1470591 AA-TCGTTATACCCCTTTTTAATTCATCTATCCCATTAACAAATTTTTTTAAAGATCACCAACAG
65 AACT-GTCACACCCCTTTTTAGTTCATCCAACCCATTAACAAATTTTTTTCAAGATCACCAACAG
*
1470655 AACACTTCATCCCCTCAATTTCACCTCTTATTTTATCAACTTCTTCCACCACTCCAACAAATTTT
129 AACACTTCATCCCCTCAATTTCACCCCTTATTTTATCAACTTCTTCCACCACTCCAACAAATTTT
* *
1470720 GCATTAATTTTCTCCACAAACTCTATTCAATCATACTTTTGGGTCGCAAACGCTTCCTCCATCCT
194 GCATTACTTTTCTCCACAAACTCTATTCAATCATACTTTTGGGTCTCAAACGCTTCCTCCATCCT
*
1470785 CACTTGTCTTTCATGAACCTCAGAAACACTTCTACCGT
259 CACTTGTCTTTCATGAACCTCAGAAACACTTCTACCCT
* * *
1470823 CAATTTTCTTTTCAACCGATCCAAACAACTCTTTTATTTCTACCCTCAATTTACTGACTTCCTTA
1 CAATTTTCTTTTCAACCGATCCAAACAACTCTTTCACTTCTACCCTCAATTTACTCACTTCCTTA
* * *
1470888 ACTGTCGCACCCCTTTTTAGTTCATCCAACCCATTAACAATTTTTTTTCAAGATCACCAACATAA
66 ACTGTCACACCCCTTTTTAGTTCATCCAACCCATTAACAAATTTTTTTCAAGATCACCAACAGAA
* * *
1470953 CACTTTATCCCCTCAATTTCACCCCTT-TTTTAATCAACTTCTTCAACCACTCCAACAAATGTTG
131 CACTTCATCCCCTCAATTTCACCCCTTATTTT-ATCAACTTCTTCCACCACTCCAACAAATTTTG
* * **
1471017 CAATACTTTTCTCCAAAAACTCTATTCCGTCATACTTTTGGGTCTCAAACGCTTCCTCCATCCTC
195 CATTACTTTTCTCCACAAACTCTATTCAATCATACTTTTGGGTCTCAAACGCTTCCTCCATCCTC
*
1471082 ACTTGTCTTTTATGAACCTCAGAAACACTT
260 ACTTGTCTTTCATGAACCTCAGAAACACTT
1471112 TGTTTGATTT
Statistics
Matches: 519, Mismatches: 62, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
295 4 0.01
296 255 0.49
297 172 0.33
298 2 0.00
299 86 0.17
ACGTcount: A:0.28, C:0.31, G:0.05, T:0.36
Consensus pattern (296 bp):
CAATTTTCTTTTCAACCGATCCAAACAACTCTTTCACTTCTACCCTCAATTTACTCACTTCCTTA
ACTGTCACACCCCTTTTTAGTTCATCCAACCCATTAACAAATTTTTTTCAAGATCACCAACAGAA
CACTTCATCCCCTCAATTTCACCCCTTATTTTATCAACTTCTTCCACCACTCCAACAAATTTTGC
ATTACTTTTCTCCACAAACTCTATTCAATCATACTTTTGGGTCTCAAACGCTTCCTCCATCCTCA
CTTGTCTTTCATGAACCTCAGAAACACTTCTACCCT
Found at i:1473247 original size:17 final size:17
Alignment explanation
Indices: 1473216--1473261 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1473206 TTTGATATTA
*
1473216 TTTTTTATTAAATAAT-
1 TTTTTTAATAAATAATC
1473232 TTTTTTAATAATATAATC
1 TTTTTTAATAA-ATAATC
1473250 TTTTTT-ATAAAT
1 TTTTTTAATAAAT
1473262 TTAAAAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 12 0.44
17 9 0.33
18 6 0.22
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTTAATAAATAATC
Found at i:1474625 original size:18 final size:18
Alignment explanation
Indices: 1474602--1474637 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1474592 GCTCAGCGGT
*
1474602 TCAACGAGATATTCCCCA
1 TCAACGAGAAATTCCCCA
*
1474620 TCAACGTGAAATTCCCCA
1 TCAACGAGAAATTCCCCA
1474638 GTGTGCTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.22
Consensus pattern (18 bp):
TCAACGAGAAATTCCCCA
Found at i:1475043 original size:18 final size:17
Alignment explanation
Indices: 1475022--1475060 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1475012 CAATTCATAT
1475022 AAATAAAAAATATATTTA
1 AAATAAAAAATA-ATTTA
* *
1475040 AAATATAAGATAATTTA
1 AAATAAAAAATAATTTA
1475057 AAAT
1 AAAT
1475061 TTTTAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAATAAAAAATAATTTA
Found at i:1475277 original size:60 final size:59
Alignment explanation
Indices: 1475188--1475302 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
1475178 AAGTACATAG
* *
1475188 ATGGTCCTCAACTATAAGACATTGTTTTGTTGAGTCATCCGATTATTAAAAGTTATGAA
1 ATGGTCCTCAACTATAAGACATTGCTTTGTTGAGTCATCCGACTATTAAAAGTTATGAA
* ** * * *
1475247 ATGGTCTCTCAACTATAGGGTATTGCTTTGTTTATTCATTCGACTATTAAAAGTTA
1 ATGGTC-CTCAACTATAAGACATTGCTTTGTTGAGTCATCCGACTATTAAAAGTTA
1475303 CAAACTTGTC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 6 0.13
60 41 0.87
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.40
Consensus pattern (59 bp):
ATGGTCCTCAACTATAAGACATTGCTTTGTTGAGTCATCCGACTATTAAAAGTTATGAA
Found at i:1481122 original size:14 final size:15
Alignment explanation
Indices: 1481103--1481137 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1481093 AAATATTAGA
1481103 ATTATTTAT-TTAAT
1 ATTATTTATGTTAAT
1481117 ATTATTTATGTTAAT
1 ATTATTTATGTTAAT
1481132 ATTATT
1 ATTATT
1481138 ATTAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
ATTATTTATGTTAAT
Found at i:1481222 original size:24 final size:26
Alignment explanation
Indices: 1481170--1481222 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
1481160 AATTTTATAA
**
1481170 ATTAAAATATTAAGATTATTATATTTT
1 ATTAAAATA-TAAGATTATTATAACTT
1481197 ATTAAAATA-AA-ATTATTATAACTT
1 ATTAAAATATAAGATTATTATAACTT
1481221 AT
1 AT
1481223 AATTATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.54
25 2 0.08
27 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTAAAATATAAGATTATTATAACTT
Found at i:1481227 original size:27 final size:27
Alignment explanation
Indices: 1481164--1481227 Score: 62
Period size: 27 Copynumber: 2.3 Consensus size: 27
1481154 ATCTATAATT
1481164 TTATAAATTAAAATATTAAGATTATTATA
1 TTAT-AATTAAAATA-TAAGATTATTATA
*
1481193 TT-TTATTAAAATA-AA-ATTATTATAA
1 TTATAATTAAAATATAAGATTATTAT-A
1481218 CTTATAATTA
1 -TTATAATTA
1481228 TAATTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
24 8 0.27
25 3 0.10
26 2 0.07
27 14 0.47
28 1 0.03
29 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
TTATAATTAAAATATAAGATTATTATA
Found at i:1481271 original size:37 final size:36
Alignment explanation
Indices: 1481230--1481324 Score: 100
Period size: 39 Copynumber: 2.5 Consensus size: 36
1481220 TATAATTATA
*
1481230 ATTTATTAAAATAATAATAATAAATTATTATTTATTT
1 ATTTATTAAAATAATAATAATAAATT-TTATTTAATT
* * * *
1481267 ATTTATTAAAACAATGATATTATTAATTTTTTTTAATT
1 ATTTATTAAAATAAT-A-ATAATAAATTTTATTTAATT
*
1481305 ATTATATTAAAATAAAAATA
1 ATT-TATTAAAATAATAATA
1481325 TTTTGTTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
37 16 0.34
38 13 0.28
39 18 0.38
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (36 bp):
ATTTATTAAAATAATAATAATAAATTTTATTTAATT
Found at i:1481483 original size:43 final size:47
Alignment explanation
Indices: 1481423--1481516 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 47
1481413 AATAATTTAT
1481423 TATACATTATGAAAATAA-AAGTACAATATTATAT-ATTAT-AAT-AA
1 TATACATTATGAAAATAAGAA-TACAATATTATATAATTATCAATAAA
1481467 TATAC-TTAT-AACAATAAGAATACAATATTATATAATTATCAATAAA
1 TATACATTATGAA-AATAAGAATACAATATTATATAATTATCAATAAA
1481513 TATA
1 TATA
1481517 ATTTAATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
42 2 0.04
43 22 0.49
44 12 0.27
45 3 0.07
46 6 0.13
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.36
Consensus pattern (47 bp):
TATACATTATGAAAATAAGAATACAATATTATATAATTATCAATAAA
Found at i:1481523 original size:21 final size:21
Alignment explanation
Indices: 1481485--1481534 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1481475 TAACAATAAG
* *
1481485 AATACAATATTATATAATTATC
1 AATA-AATATAATATAATAATC
* *
1481507 AATAAATATAATTTAATAATT
1 AATAAATATAATATAATAATC
1481528 AATAAAT
1 AATAAAT
1481535 TTATTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAAATATAATATAATAATC
Found at i:1485483 original size:18 final size:19
Alignment explanation
Indices: 1485460--1485502 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1485450 TTTAACAATT
* *
1485460 AATTTT-AAAAGTCAATAA
1 AATTTTCAAAAATAAATAA
*
1485478 AATTTTCAAAAATAAATGA
1 AATTTTCAAAAATAAATAA
1485497 AATTTT
1 AATTTT
1485503 TAAATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (19 bp):
AATTTTCAAAAATAAATAA
Found at i:1486712 original size:50 final size:50
Alignment explanation
Indices: 1486649--1486751 Score: 134
Period size: 50 Copynumber: 2.1 Consensus size: 50
1486639 ATCTACATAA
* * * *
1486649 TTACATCGGTGTAAGTATGTGTTAACTGTTACACTTTTTATTTTATTTAC
1 TTACACCGGTGTAAATATGTGTTAACTGTTACACTTTTTAGTTTATTCAC
* * * *
1486699 TTACACCGTTGTAAATATGTGTTAAGTGTTACCCTTTTTGGTTTATTCAC
1 TTACACCGGTGTAAATATGTGTTAACTGTTACACTTTTTAGTTTATTCAC
1486749 TTA
1 TTA
1486752 TGTATTAAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.49
Consensus pattern (50 bp):
TTACACCGGTGTAAATATGTGTTAACTGTTACACTTTTTAGTTTATTCAC
Found at i:1501296 original size:45 final size:45
Alignment explanation
Indices: 1501228--1501662 Score: 692
Period size: 45 Copynumber: 9.6 Consensus size: 45
1501218 ATTATTCATT
*
1501228 ATTTTCATTTAT-AGCATCCTTTCATGCCTCTAATGCACCGTTATGC
1 ATTTT-ATTTATGA-CATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1501274 ATTTTATTTATGACATCATTTCATGTCTTTAATGCACCGTTATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1501319 ATTTTATTTATGGCATCCTTCCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1501364 ATTTTATTTATGACATCCTTTAATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1501409 ATTTTAGTTATGACATCCTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
1501454 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
* * **
1501499 ATTTTATTTATGGCATTCTTTCATGCCTTCGATGCACCGTTATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
1501544 ATTTTATTTATGGCATCCTTTAATGCCTTTAATGCACCGTTATGT
1 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1501589 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1501634 ATTTTATTTATGGCATCCTTTCATGCCTT
1 ATTTTATTTATGACATCCTTTCATGCCTT
1501663 AAACATACAT
Statistics
Matches: 362, Mismatches: 26, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
45 356 0.98
46 6 0.02
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (45 bp):
ATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:1506058 original size:20 final size:20
Alignment explanation
Indices: 1506033--1506073 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1506023 CAAATCCTAA
1506033 GTCTCCACGAAATCGTCTTG
1 GTCTCCACGAAATCGTCTTG
1506053 GTCTCCACGAAATCGTCTTG
1 GTCTCCACGAAATCGTCTTG
1506073 G
1 G
1506074 GCTCTACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (20 bp):
GTCTCCACGAAATCGTCTTG
Found at i:1506247 original size:18 final size:19
Alignment explanation
Indices: 1506207--1506247 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1506197 CTTTATGGGT
*
1506207 TTTATTCCAAATTTGTTTA
1 TTTATTCCAAATTTGTATA
*
1506226 -TTATTCTAAATTT-TATA
1 TTTATTCCAAATTTGTATA
1506243 TTTAT
1 TTTAT
1506248 AAAAGAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTATTCCAAATTTGTATA
Found at i:1516104 original size:81 final size:81
Alignment explanation
Indices: 1515969--1516380 Score: 479
Period size: 81 Copynumber: 5.1 Consensus size: 81
1515959 ATGTTTTAAA
* * * *
1515969 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAATGTGTCAATTATGCCAGTTGGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1516034 GTTAAATACCTTTGAT
66 GTTAAATACCTTTGAG
** * *
1516050 TAAAAGATTAATAACCTAGTTGTGCATTTGACAAAAAGGTGTTAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1516115 GTTAAATATCTTTTAG
66 GTTAAATACCTTTGAG
* * * *
1516131 TAAAAGATTAATGGCCTAGTTGTTCATTTGACAAAAATGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1516196 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* ** *
1516212 TAAAAGATTAATGGCCTAGCTGTGCATTTGA-AAGAAAGGTGTCAATCATGTAAGTTAGATAAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAA-AAAGGTGTCAATTATGCCAGTTAGATGAAA
* *
1516276 GGCTAAATGCCTTTGAG
65 GGTTAAATACCTTTGAG
* * * * * * * * *
1516293 TTAAAGATTAAAT-GTCTAACTGTGCATTTGGCAAAAAGGTGCCAATCATACAAGTTAAATGAAA
1 TAAAAGATT-AATGGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAA
** *
1516357 GACTAAATGCCTTTG-G
65 GGTTAAATACCTTTGAG
1516373 CTAAAAGA
1 -TAAAAGA
1516381 CTAAATGCTT
Statistics
Matches: 287, Mismatches: 40, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
80 3 0.01
81 279 0.97
82 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:1523920 original size:23 final size:23
Alignment explanation
Indices: 1523893--1523948 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1523883 GGAGCCGAGC
*
1523893 TGGAGCATGGGCGTGGGTAACAG
1 TGGAGCATGGACGTGGGTAACAG
* * *
1523916 TGGAGAAAGGACGTGGGTGACAG
1 TGGAGCATGGACGTGGGTAACAG
*
1523939 TCGAGCATGG
1 TGGAGCATGG
1523949 TGCTTCACAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.46, T:0.16
Consensus pattern (23 bp):
TGGAGCATGGACGTGGGTAACAG
Found at i:1524237 original size:16 final size:18
Alignment explanation
Indices: 1524216--1524268 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
1524206 ATATTAATAC
* *
1524216 TAATAATAATTATAATTTA
1 TAATAATAATAATTA-TTA
1524235 TAATAATAATAATTATTA
1 TAATAATAATAATTATTA
*
1524253 TAATAA-AATATTTATT
1 TAATAATAATAATTATT
1524269 TCCCAGACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 9 0.29
18 9 0.29
19 13 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATAATAATAATTATTA
Done.