Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold500
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: 2046043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1382047 original size:15 final size:16
Alignment explanation
Indices: 1382027--1382058 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1382017 CATAAAATTA
1382027 TTTTCTTTCTTT-TTT
1 TTTTCTTTCTTTCTTT
1382042 TTTTCTTTCTTTCTTT
1 TTTTCTTTCTTTCTTT
1382058 T
1 T
1382059 CAGCAAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTCTTTCTTT
Found at i:1382076 original size:1 final size:1
Alignment explanation
Indices: 1382070--1382096 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1382060 AGCAAAACGT
1382070 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1382097 GAGGACGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1382227 original size:6 final size:6
Alignment explanation
Indices: 1382207--1382240 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1382197 ACTTATTTTC
1382207 TATTAA T-TT-A TATTAA TATTAA TATTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
1382241 ATTCTTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 2 0.08
5 4 0.15
6 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAA
Found at i:1382239 original size:18 final size:16
Alignment explanation
Indices: 1382207--1382240 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
1382197 ACTTATTTTC
1382207 TATTAATTTATATTAA
1 TATTAATTTATATTAA
1382223 TATTAATATTAATATTAA
1 TATTAAT-TT-ATATTAA
1382241 ATTCTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTAATTTATATTAA
Found at i:1382525 original size:12 final size:12
Alignment explanation
Indices: 1382508--1382551 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1382498 GTTTTTTCGG
1382508 TTTTAAATATAT
1 TTTTAAATATAT
1382520 TTTT-AATATATT
1 TTTTAAATATA-T
1382532 TTATTAAATATAT
1 TT-TTAAATATAT
*
1382545 ATTTAAA
1 TTTTAAA
1382552 AAATTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 6 0.21
12 12 0.43
13 4 0.14
14 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTAAATATAT
Found at i:1382557 original size:25 final size:25
Alignment explanation
Indices: 1382510--1382557 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1382500 TTTTTCGGTT
* * *
1382510 TTAAATATATTTTTAATATATTTTA
1 TTAAATATATATTTAAAAAATTTTA
1382535 TTAAATATATATTTAAAAAATTT
1 TTAAATATATATTTAAAAAATTT
1382558 AAATATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAAATATATATTTAAAAAATTTTA
Found at i:1383126 original size:17 final size:17
Alignment explanation
Indices: 1383106--1383155 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
1383096 ATATTAATTA
1383106 TATAAATATAAATATAT
1 TATAAATATAAATATAT
1383123 TATAAATTATTAAATATAT
1 TATAAA-TA-TAAATATAT
*
1383142 CA-AAATATAAATAT
1 TATAAATATAAATAT
1383156 GAATACAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.23
17 8 0.27
18 5 0.17
19 10 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TATAAATATAAATATAT
Found at i:1383136 original size:25 final size:25
Alignment explanation
Indices: 1383093--1383140 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1383083 TCGTATATTT
*
1383093 TATATATTAATTATATAAATATAAA
1 TATATATAAATTATATAAATATAAA
1383118 TATATTATAAATTAT-TAAATATA
1 TATA-TATAAATTATATAAATATA
1383141 TCAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATATATAAATTATATAAATATAAA
Found at i:1383462 original size:2 final size:2
Alignment explanation
Indices: 1383455--1383481 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1383445 ACCGAGCTAT
1383455 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1383482 GAAAGTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1390245 original size:8 final size:7
Alignment explanation
Indices: 1390227--1390259 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
1390217 TCATGTTTGG
1390227 TTTTTTA
1 TTTTTTA
1390234 TTTTTTA
1 TTTTTTA
1390241 TTTTTTA
1 TTTTTTA
1390248 TTTTTTCA
1 TTTTTT-A
1390256 TTTT
1 TTTT
1390260 AATCTTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:1393734 original size:19 final size:19
Alignment explanation
Indices: 1393693--1393734 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1393683 CTTTACAACG
* *
1393693 GTCGTTAAAGAAGTTCTGG
1 GTCGTTAAAGAAGCTCTGA
1393712 GTCGTTAAAGAAGACT-TGA
1 GTCGTTAAAGAAG-CTCTGA
1393731 GTCG
1 GTCG
1393735 GGACAAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.29
Consensus pattern (19 bp):
GTCGTTAAAGAAGCTCTGA
Found at i:1398299 original size:21 final size:21
Alignment explanation
Indices: 1398274--1398313 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1398264 CCATTCTCAC
1398274 CAAAGCTTCCATTTTTATCTT
1 CAAAGCTTCCATTTTTATCTT
*
1398295 CAAAGCTTCCGTTTTTATC
1 CAAAGCTTCCATTTTTATC
1398314 AACCAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (21 bp):
CAAAGCTTCCATTTTTATCTT
Found at i:1398320 original size:22 final size:21
Alignment explanation
Indices: 1398270--1398330 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1398260 AACCCCATTC
1398270 TCACCAAAGCTTCCATTTTTA
1 TCACCAAAGCTTCCATTTTTA
** *
1398291 TCTTCAAAGCTTCCGTTTTTA
1 TCACCAAAGCTTCCATTTTTA
* *
1398312 TCAACCAAACCCTCCATTT
1 TC-ACCAAAGCTTCCATTT
1398331 CAGCTTTCTC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.38
Consensus pattern (21 bp):
TCACCAAAGCTTCCATTTTTA
Found at i:1405551 original size:25 final size:24
Alignment explanation
Indices: 1405505--1405553 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1405495 ATTCAGAGAA
* **
1405505 AAATATATTTTAATATTTATATTT
1 AAATATATTTAAATATAAATATTT
1405529 AAATATATATTAAATATAAATATTT
1 AAATATAT-TTAAATATAAATATTT
1405554 TAAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATATATTTAAATATAAATATTT
Found at i:1407155 original size:12 final size:13
Alignment explanation
Indices: 1407138--1407174 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1407128 GTTTGGCTCC
*
1407138 AATATATATCT-T
1 AATATATATATAT
1407150 AATATATATATAT
1 AATATATATATAT
1407163 -ATATATATATAT
1 AATATATATATAT
1407175 GTGTGTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 22 0.96
13 1 0.04
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
AATATATATATAT
Found at i:1409452 original size:19 final size:19
Alignment explanation
Indices: 1409430--1409482 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
1409420 AAATAATATT
1409430 AATATAATTATATAAATAA
1 AATATAATTATATAAATAA
* * *
1409449 AATATAAATATTTAAAATAT
1 AATATAATTATAT-AAATAA
*
1409469 ATTATAATTA-ATAA
1 AATATAATTATATAA
1409483 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 2 0.07
19 12 0.44
20 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATAATTATATAAATAA
Found at i:1409475 original size:31 final size:33
Alignment explanation
Indices: 1409411--1409535 Score: 92
Period size: 32 Copynumber: 4.0 Consensus size: 33
1409401 AAATCTTTTT
* *
1409411 TTATAAAT--TAA-ATAATATTAATATAAT-TA
1 TTATAAATAATAATATAAAATTTATATAATATA
1409440 -TATAAATAA-AATATAAATATTTA-A-AATATA
1 TTATAAATAATAATATAAA-ATTTATATAATATA
* *
1409470 TTATAATTAATAATTTAAAATTTATATAATATAA
1 TTATAAATAATAATATAAAATTTATATAATAT-A
*
1409504 CTTATTAAT--TAAT-TAAAATTTATATAAATATA
1 -TTATAAATAATAATATAAAATTTATAT-AATATA
1409536 AAATATTTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
28 7 0.09
29 5 0.06
30 7 0.09
31 17 0.22
32 21 0.27
33 14 0.18
34 1 0.01
35 6 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (33 bp):
TTATAAATAATAATATAAAATTTATATAATATA
Found at i:1409501 original size:33 final size:32
Alignment explanation
Indices: 1409431--1409535 Score: 98
Period size: 32 Copynumber: 3.4 Consensus size: 32
1409421 AATAATATTA
* *
1409431 ATATAAT-TATATAAATAA-AATATAAATATTT
1 ATATAATATATATAATTAATAATTTAAA-ATTT
1409462 A-A-AATATATTATAATTAATAATTTAAAATTT
1 ATATAATATA-TATAATTAATAATTTAAAATTT
*
1409493 ATATAATATA-ACTTATTAATTAA-TTAAAATTT
1 ATATAATATATA-TAATTAA-TAATTTAAAATTT
1409525 ATATAA-ATATA
1 ATATAATATATA
1409536 AAATATTTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
29 3 0.05
30 3 0.05
31 18 0.29
32 30 0.48
33 9 0.14
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAATATATATAATTAATAATTTAAAATTT
Found at i:1409520 original size:32 final size:33
Alignment explanation
Indices: 1409475--1409536 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1409465 ATATATTATA
1409475 ATTAATAATTTAAAATTTATAT-AATATAACTT
1 ATTAATAATTTAAAATTTATATAAATATAACTT
1409507 ATTAATTAA-TTAAAATTTATATAAATATAA
1 ATTAA-TAATTTAAAATTTATATAAATATAA
1409537 AATATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
ATTAATAATTTAAAATTTATATAAATATAACTT
Found at i:1409539 original size:17 final size:16
Alignment explanation
Indices: 1409479--1409539 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
1409469 ATTATAATTA
*
1409479 ATAATTTAAAATTTAT
1 ATAATATAAAATTTAT
**
1409495 ATAATATAACTTATTA-
1 ATAATATAAAAT-TTAT
1409511 ATTAAT-TAAAATTTAT
1 A-TAATATAAAATTTAT
1409527 ATAAATATAAAAT
1 AT-AATATAAAAT
1409540 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
15 4 0.11
16 18 0.51
17 13 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATATAAAATTTAT
Found at i:1409549 original size:11 final size:13
Alignment explanation
Indices: 1409532--1409564 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
1409522 TTTATATAAA
1409532 TATAAAATATT-T
1 TATAAAATATTAT
1409544 TA-AAAATATTAT
1 TATAAAATATTAT
1409556 TATAAAATA
1 TATAAAATA
1409565 CATAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 5 0.26
13 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATAAAATATTAT
Found at i:1416736 original size:26 final size:25
Alignment explanation
Indices: 1416707--1416759 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
1416697 TCTCATATTA
*
1416707 AATTAAATTTAGATAATTTATTTGAT
1 AATTAAATTTAAATAATTTATTT-AT
*
1416733 AATTTAATTTAAATAATTTATTTAT
1 AATTAAATTTAAATAATTTATTTAT
1416758 AA
1 AA
1416760 AATAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
AATTAAATTTAAATAATTTATTTAT
Found at i:1416755 original size:13 final size:13
Alignment explanation
Indices: 1416713--1416756 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
1416703 ATTAAATTAA
1416713 ATTTAGATAATTT
1 ATTTAGATAATTT
1416726 ATTT-GATAATTT
1 ATTTAGATAATTT
*
1416738 AATTTAAATAATTT
1 -ATTTAGATAATTT
1416752 ATTTA
1 ATTTA
1416757 TAAAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 8 0.29
13 13 0.46
14 7 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (13 bp):
ATTTAGATAATTT
Found at i:1417905 original size:28 final size:27
Alignment explanation
Indices: 1417849--1417967 Score: 89
Period size: 28 Copynumber: 4.2 Consensus size: 27
1417839 ATACAAGCAC
* * * * *
1417849 AATATAAAAAAATAATTAAAAAATATA
1 AATATATATAAATAATTAAATATTTTA
1417876 AATATGATATAAATAATTAAATATTTTA
1 AATAT-ATATAAATAATTAAATATTTTA
*
1417904 AATTATATATAACATGAAATATTAATATATTTA
1 AA-TATATATAA-AT--AAT-TAAATAT-TTTA
*
1417937 AATTTATATAAAT-A-TATAATATTTTA
1 AATATATATAAATAATTA-AATATTTTA
1417963 AATAT
1 AATAT
1417968 TATTAAAATA
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
26 9 0.12
27 10 0.13
28 26 0.35
29 5 0.07
31 5 0.07
32 14 0.19
33 6 0.08
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (27 bp):
AATATATATAAATAATTAAATATTTTA
Found at i:1417958 original size:27 final size:26
Alignment explanation
Indices: 1417920--1417980 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
1417910 ATATAACATG
1417920 AAATAT-TAATATATTTAAAT-TTATAT
1 AAATATATAATAT-TTTAAATATTAT-T
1417946 AAATATATAATATTTTAAATATTATT
1 AAATATATAATATTTTAAATATTATT
1417972 AAA-ATATAA
1 AAATATATAA
1417981 AAAAATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
25 6 0.18
26 17 0.52
27 10 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATATATAATATTTTAAATATTATT
Found at i:1417960 original size:25 final size:25
Alignment explanation
Indices: 1417920--1417980 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 25
1417910 ATATAACATG
1417920 AAATATTAATATATTTAAAT-TTATATA
1 AAATA-TAATAT-TTTAAATATTAT-TA
1417947 AATATATAATATTTTAAATATTATTA
1 AA-ATATAATATTTTAAATATTATTA
1417973 AAATATAA
1 AAATATAA
1417981 AAAAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 6 0.19
26 11 0.34
27 12 0.38
28 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATATAATATTTTAAATATTATTA
Found at i:1429621 original size:29 final size:31
Alignment explanation
Indices: 1429571--1429629 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1429561 GTTAGAAAGT
1429571 TTATTTTAATATTTAAAATTATAA-TAAAAA
1 TTATTTTAATATTTAAAATTATAACTAAAAA
*
1429601 TTATTTT-ATA-TTAATATTTATAACTAAAA
1 TTATTTTAATATTTAA-AATTATAACTAAAA
1429630 TGTAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 10 0.38
30 12 0.46
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
TTATTTTAATATTTAAAATTATAACTAAAAA
Found at i:1430494 original size:9 final size:9
Alignment explanation
Indices: 1430474--1430506 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1430464 CCCCCCCCCC
1430474 CTTTTCTTTT
1 CTTTT-TTTT
1430484 CTTTTTTTT
1 CTTTTTTTT
1430493 CTTTTTTTT
1 CTTTTTTTT
1430502 -TTTTT
1 CTTTTT
1430507 CATATTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:1430494 original size:14 final size:14
Alignment explanation
Indices: 1430475--1430507 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1430465 CCCCCCCCCC
1430475 TTTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
*
1430489 TTTTCTTTTTTTTT
1 TTTTCTTTTCTTTT
1430503 TTTTC
1 TTTTC
1430508 ATATTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTCTTTTCTTTT
Found at i:1437272 original size:5 final size:5
Alignment explanation
Indices: 1437262--1437293 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1437252 GCAATCATGA
1437262 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1437294 GATGCCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1440154 original size:50 final size:50
Alignment explanation
Indices: 1440065--1440211 Score: 131
Period size: 48 Copynumber: 2.9 Consensus size: 50
1440055 ATTGATGAAC
* *
1440065 TTATAGAAAGAATTAAA-ATATATATATATTTATATATTTTATTATAATATTATG
1 TTATA-AAA-AATTAAATATATTTAAATATTTA-A-ATTTTATTATAAT-TTATG
* ** * *
1440119 TT-TAAAATATTTTATATTTTTAAATTTTTAAATTTTA--ATAATTTATG
1 TTATAAAAAATTAAATATATTTAAATATTTAAATTTTATTATAATTTATG
* * *
1440166 TTATAAAAAATTAAATATATTTATATATTTATATTATATTATAATT
1 TTATAAAAAATTAAATATATTTAAATATTTAAATTTTATTATAATT
1440212 ATATTTTTTG
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
47 7 0.09
48 32 0.43
50 12 0.16
51 5 0.07
52 14 0.19
53 2 0.03
54 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (50 bp):
TTATAAAAAATTAAATATATTTAAATATTTAAATTTTATTATAATTTATG
Found at i:1440161 original size:17 final size:16
Alignment explanation
Indices: 1440119--1440162 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1440109 TAATATTATG
*
1440119 TTTAAAATATTTTATAT
1 TTTAAAAT-TTTTAAAT
*
1440136 TTTTAAATTTTTAAAT
1 TTTAAAATTTTTAAAT
1440152 TTTAATAATTT
1 TTTAA-AATTT
1440163 ATGTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTTTTAAAT
Found at i:1442510 original size:3 final size:3
Alignment explanation
Indices: 1442504--1442560 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
1442494 ACCCCCTTTG
1442504 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1442552 CTT CTT CTT
1 CTT CTT CTT
1442561 AGTTTACGAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:1456288 original size:2 final size:2
Alignment explanation
Indices: 1456283--1456314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1456273 AAAAGATAGC
1456283 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1456315 AGCTTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1467797 original size:351 final size:351
Alignment explanation
Indices: 1467154--1467860 Score: 1387
Period size: 351 Copynumber: 2.0 Consensus size: 351
1467144 GATGCCATTT
1467154 TTTCTTGTGCAGTTTCTTGATTGTCAATATATACAGGGCTGGAATAATCAGTAAATGTTTAAACA
1 TTTCTTGTGCAGTTTCTTGATTGTCAATATATACAGGGCTGGAATAATCAGTAAATGTTTAAACA
1467219 GTACCAGATTGCAACACATGGCACTTCAAGTTCGAAAGTTGAAATAACAAAGCTGGAATTATCAA
66 GTACCAGATTGCAACACATGGCACTTCAAGTTCGAAAGTTGAAATAACAAAGCTGGAATTATCAA
1467284 TATATTTAACATTCATATTGGCATACAGCTATCCAGATTAATCTATTCTTTTGCCAGAGATGGCA
131 TATATTTAACATTCATATTGGCATACAGCTATCCAGATTAATCTATTCTTTTGCCAGAGATGGCA
1467349 ATTGGTACTTTTCTCAGCATTGTTTTACGTTGGCTAATGATAACATCATAGAACCTAATCATTCT
196 ATTGGTACTTTTCTCAGCATTGTTTTACGTTGGCTAATGATAACATCATAGAACCTAATCATTCT
*
1467414 TCATACTCCGCTTCCTCCTCATAGTCTTCCTCATCGTCAGCAGTGGCATCCTGGTACTGCTGATA
261 TCATACTCCGCTTCCTCCTCATAGTCTTCCTCATCGTCAGCAGTAGCATCCTGGTACTGCTGATA
1467479 CTCTGAGACCAGATCGTTCATGTTGC
326 CTCTGAGACCAGATCGTTCATGTTGC
1467505 TTTCTTGTGCAGTTTCTTGATTGTCAATATATACAGGGCTGGAATAATCAGTAAATGTTTAAACA
1 TTTCTTGTGCAGTTTCTTGATTGTCAATATATACAGGGCTGGAATAATCAGTAAATGTTTAAACA
* *
1467570 GTACCAGATTGCAACATATGGCGCTTCAAGTTCGAAAGTTGAAATAACAAAGCTGGAATTATCAA
66 GTACCAGATTGCAACACATGGCACTTCAAGTTCGAAAGTTGAAATAACAAAGCTGGAATTATCAA
1467635 TATATTTAACATTCATATTGGCATACAGCTATCCAGATTAATCTATTCTTTTGCCAGAGATGGCA
131 TATATTTAACATTCATATTGGCATACAGCTATCCAGATTAATCTATTCTTTTGCCAGAGATGGCA
1467700 ATTGGTACTTTTCTCAGCATTGTTTTACGTTGGCTAATGATAACATCATAGAACCTAATCATTCT
196 ATTGGTACTTTTCTCAGCATTGTTTTACGTTGGCTAATGATAACATCATAGAACCTAATCATTCT
1467765 TCATACTCCGCTTCCTCCTCATAGTCTTCCTCATCGTCAGCAGTAGCATCCTGGTACTGCTGATA
261 TCATACTCCGCTTCCTCCTCATAGTCTTCCTCATCGTCAGCAGTAGCATCCTGGTACTGCTGATA
1467830 CTCTGAGACCAGATCGTTCATGTTGC
326 CTCTGAGACCAGATCGTTCATGTTGC
1467856 TTTCT
1 TTTCT
1467861 GCCTCTGTGA
Statistics
Matches: 353, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
351 353 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (351 bp):
TTTCTTGTGCAGTTTCTTGATTGTCAATATATACAGGGCTGGAATAATCAGTAAATGTTTAAACA
GTACCAGATTGCAACACATGGCACTTCAAGTTCGAAAGTTGAAATAACAAAGCTGGAATTATCAA
TATATTTAACATTCATATTGGCATACAGCTATCCAGATTAATCTATTCTTTTGCCAGAGATGGCA
ATTGGTACTTTTCTCAGCATTGTTTTACGTTGGCTAATGATAACATCATAGAACCTAATCATTCT
TCATACTCCGCTTCCTCCTCATAGTCTTCCTCATCGTCAGCAGTAGCATCCTGGTACTGCTGATA
CTCTGAGACCAGATCGTTCATGTTGC
Found at i:1480505 original size:2 final size:2
Alignment explanation
Indices: 1480498--1480542 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1480488 CCACACTTTC
* * *
1480498 TA TA TA TA TA TA TA TA TA TA TT TC TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1480540 TA T
1 TA T
1480543 TATTTTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1480521 original size:24 final size:24
Alignment explanation
Indices: 1480494--1480543 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1480484 TCTGCCACAC
*
1480494 TTTCTATATATATATATATATATA
1 TTTCTACATATATATATATATATA
1480518 TTTCTACATATATATATATATATA
1 TTTCTACATATATATATATATATA
1480542 TT
1 TT
1480544 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTCTACATATATATATATATATA
Found at i:1487017 original size:48 final size:48
Alignment explanation
Indices: 1486953--1487050 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
1486943 GTCTTTTATG
*
1486953 TTGCCAGGTGATTTGAGTTTCTTTGTATATATTGTTATTGAATGTTAA
1 TTGCCAGGTGATTTGAGTTTCTTTATATATATTGTTATTGAATGTTAA
* *
1487001 TTGCCAGGTGATTTGAGTTTCTTTATATTTATTTTTATTGAATGTTAA
1 TTGCCAGGTGATTTGAGTTTCTTTATATATATTGTTATTGAATGTTAA
1487049 TT
1 TT
1487051 AAATATATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.22, C:0.06, G:0.18, T:0.53
Consensus pattern (48 bp):
TTGCCAGGTGATTTGAGTTTCTTTATATATATTGTTATTGAATGTTAA
Found at i:1500048 original size:2 final size:2
Alignment explanation
Indices: 1500043--1500072 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1500033 TTTGTGTGTG
1500043 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
1500073 CACACACTTC
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:1503690 original size:18 final size:18
Alignment explanation
Indices: 1503663--1503724 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
1503653 AAAAATATAT
1503663 TTTTAATTAATTAAATTA
1 TTTTAATTAATTAAATTA
* *
1503681 TTTTATTTAATTAAATTT
1 TTTTAATTAATTAAATTA
*
1503699 TTTTAAAATAAATATAAATTA
1 TTTT--AATTAAT-TAAATTA
1503720 TTTTA
1 TTTTA
1503725 TTTTTAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 20 0.56
19 1 0.03
20 5 0.14
21 10 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAATTAATTAAATTA
Found at i:1504092 original size:17 final size:17
Alignment explanation
Indices: 1504040--1504100 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 17
1504030 CATATATCTA
1504040 TATATAAATATTTTAAAAT
1 TATATAAA-A-TTTAAAAT
1504059 T-TATAAAATTT-AAAT
1 TATATAAAATTTAAAAT
1504074 TAT-TAAAATATTAAAAT
1 TATATAAAAT-TTAAAAT
1504091 TAATATAAAA
1 T-ATATAAAA
1504101 ATTTTATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.30
16 6 0.16
17 6 0.16
18 8 0.22
19 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATAAAATTTAAAAT
Found at i:1504374 original size:27 final size:27
Alignment explanation
Indices: 1504344--1504402 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1504334 TAATAATTAA
* *
1504344 TATATTCATATTATATTTATAA-TATTT
1 TATATT-ATAATATATTAATAATTATTT
*
1504371 TATATTTTAATATATTAATAATTATTT
1 TATATTATAATATATTAATAATTATTT
1504398 TATAT
1 TATAT
1504403 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TATATTATAATATATTAATAATTATTT
Found at i:1504383 original size:15 final size:16
Alignment explanation
Indices: 1504354--1504383 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1504344 TATATTCATA
1504354 TTATATTTATAATATT
1 TTATATTTATAATATT
1504370 TTATATTT-TAATAT
1 TTATATTTATAATAT
1504384 ATTAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTTATAATATT
Found at i:1504628 original size:3 final size:3
Alignment explanation
Indices: 1504620--1504648 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1504610 ATTGAATGTG
1504620 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1504649 TTGTAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1505155 original size:26 final size:28
Alignment explanation
Indices: 1505093--1505157 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 28
1505083 TTTTATATTT
* *
1505093 TTAA-ATATAATATAAAAATATAACATA
1 TTAATATAAAATATAAAAAAATAACATA
*
1505120 TT--TATTAAATATAAAAAAATAA-A-A
1 TTAATATAAAATATAAAAAAATAACATA
1505144 TTAATATAAAATAT
1 TTAATATAAAATAT
1505158 GTAATACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 25 0.81
27 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
TTAATATAAAATATAAAAAAATAACATA
Found at i:1514905 original size:11 final size:10
Alignment explanation
Indices: 1514887--1514970 Score: 68
Period size: 9 Copynumber: 8.2 Consensus size: 10
1514877 TAAAATTATG
1514887 ATATAAAAAT
1 ATATAAAAAT
1514897 ATGATAAAAA-
1 AT-ATAAAAAT
*
1514907 ATATAAATAT
1 ATATAAAAAT
1514917 A-ATAAAAAT
1 ATATAAAAAT
1514926 AT-T-AAAAT
1 ATATAAAAAT
1514934 ATATTAAAATTTAT
1 ATA-TAAAA---AT
*
1514948 ATAATATAAAT
1 AT-ATAAAAAT
1514959 ATATAAAAAT
1 ATATAAAAAT
1514969 AT
1 AT
1514971 TTTAAAAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
8 7 0.12
9 15 0.25
10 15 0.25
11 14 0.23
14 8 0.13
15 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:1514931 original size:18 final size:19
Alignment explanation
Indices: 1514887--1514956 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
1514877 TAAAATTATG
*
1514887 ATATAAAAATATGATAAAAA
1 ATAT-AAAATATAATAAAAA
1514907 ATAT-AAATATAAT-AAAA
1 ATATAAAATATAATAAAAA
* *
1514924 ATATTAAAATATATTAAAAT
1 ATA-TAAAATATAATAAAAA
* *
1514944 TTATATAATATAA
1 ATATAAAATATAA
1514957 ATATATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 7 0.17
18 9 0.22
19 16 0.39
20 9 0.22
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (19 bp):
ATATAAAATATAATAAAAA
Found at i:1514939 original size:10 final size:10
Alignment explanation
Indices: 1514911--1514977 Score: 55
Period size: 10 Copynumber: 6.3 Consensus size: 10
1514901 TAAAAAATAT
*
1514911 AAATATAATA
1 AAATATATTA
1514921 AAA-ATATTA
1 AAATATATTA
1514930 AAATATATTA
1 AAATATATTA
1514940 AAATTTATATAATA
1 AAA--TATAT--TA
*
1514954 TAAATATATAA
1 -AAATATATTA
*
1514965 AAATATTTTA
1 AAATATATTA
1514975 AAA
1 AAA
1514978 AATCACAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
9 8 0.17
10 23 0.49
11 1 0.02
12 5 0.11
13 5 0.11
14 2 0.04
15 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATATATTA
Found at i:1514959 original size:33 final size:35
Alignment explanation
Indices: 1514869--1514977 Score: 105
Period size: 35 Copynumber: 3.0 Consensus size: 35
1514859 TAAAATGTGA
*
1514869 TTATATAATAAAATTATGATATAAAAATATGATAAAAAAT
1 TTATATAATAAAA--AT-ATATAAAAATAT-AT-TAAAAT
*
1514909 ATAAATATAATAAAAATAT-T-AAAATATATTAAAAT
1 -T-TATATAATAAAAATATATAAAAATATATTAAAAT
* *
1514944 TTATATAATATAAATATATAAAAATATTTTAAAA
1 TTATATAATAAAAATATATAAAAATATATTAAAA
1514978 AATCACAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
33 14 0.23
34 2 0.03
35 18 0.30
36 2 0.03
37 7 0.12
38 1 0.02
39 2 0.03
40 2 0.03
41 1 0.02
42 11 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (35 bp):
TTATATAATAAAAATATATAAAAATATATTAAAAT
Found at i:1515386 original size:2 final size:2
Alignment explanation
Indices: 1515379--1515413 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1515369 TCCGTTTGGA
1515379 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1515414 GTAAAATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1519515 original size:21 final size:22
Alignment explanation
Indices: 1519491--1519533 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1519481 TTATGAATTT
*
1519491 TAATATAAAAAT-TATGAAAAA
1 TAATATAAAAATATATAAAAAA
* *
1519512 TAATTTTAAAATATATAAAAAA
1 TAATATAAAAATATATAAAAAA
1519534 AATTGAGACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATATAAAAATATATAAAAAA
Found at i:1519537 original size:21 final size:21
Alignment explanation
Indices: 1519498--1519537 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1519488 TTTTAATATA
*
1519498 AAAATTATGAAAAATAATTTT
1 AAAATTATGAAAAAAAATTTT
1519519 AAAATATAT-AAAAAAAATT
1 AAAAT-TATGAAAAAAAATT
1519538 GAGACATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATTATGAAAAAAAATTTT
Found at i:1521455 original size:2 final size:2
Alignment explanation
Indices: 1521448--1521477 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1521438 AGGGGAGGGG
1521448 GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1521478 GGAGCAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1522851 original size:21 final size:21
Alignment explanation
Indices: 1522839--1522878 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1522829 AGGTTTTCTC
1522839 TTGATGCAGCAAGGATGTCGT
1 TTGATGCAGCAAGGATGTCGT
1522860 TTGATGCAGCAAGGATGTC
1 TTGATGCAGCAAGGATGTC
1522879 CTGTGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (21 bp):
TTGATGCAGCAAGGATGTCGT
Found at i:1522885 original size:21 final size:21
Alignment explanation
Indices: 1522840--1522886 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1522830 GGTTTTCTCT
* *
1522840 TGATGCAGCAAGGATGTCGTT
1 TGATGCAGCAAGGATGTCCTG
1522861 TGATGCAGCAAGGATGTCCTG
1 TGATGCAGCAAGGATGTCCTG
1522882 TGATG
1 TGATG
1522887 ATCCAAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (21 bp):
TGATGCAGCAAGGATGTCCTG
Found at i:1540861 original size:2 final size:2
Alignment explanation
Indices: 1540849--1540895 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1540839 CCAATAGCTT
*
1540849 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1540891 TA TA T
1 TA TA T
1540896 TTAACTCAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1546676 original size:2 final size:2
Alignment explanation
Indices: 1546669--1546698 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1546659 TTTCATCATC
1546669 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
1546699 AAAGAAAAAA
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:1548723 original size:2 final size:2
Alignment explanation
Indices: 1548716--1548763 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1548706 TCTTGAAGTT
*
1548716 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1548758 T- TA TA T
1 TA TA TA T
1548764 GAAGACAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1549722 original size:2 final size:2
Alignment explanation
Indices: 1549717--1549756 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1549707 TGGTGTGTTC
1549717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1549757 TATTTTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1549769 original size:20 final size:20
Alignment explanation
Indices: 1549722--1549869 Score: 57
Period size: 20 Copynumber: 7.5 Consensus size: 20
1549712 TGTTCATATA
*
1549722 TATATATATATATATATATATAT
1 TATATATATAT-TAT-TTTA-AT
1549745 ATATATATATATTATTTTAAT
1 -TATATATATATTATTTTAAT
* *
1549766 TATA-ATTAAAATATTTTATAT
1 TATATA-TATATTATTTTA-AT
1549787 T-TATATA-A--ATTTTAA-
1 TATATATATATTATTTTAAT
* *
1549802 AATATATAT-TTATATTATAT
1 TATATATATATTATTTTA-AT
* * *
1549822 TATAT-TTTAAATATTTTATT
1 TATATATAT-ATTATTTTAAT
*
1549842 TATAT-TATATTCA-TATAAT
1 TATATATATATT-ATTTTAAT
1549861 TATA-ATATA
1 TATATATATA
1549870 AGAGATGTAC
Statistics
Matches: 97, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
16 7 0.07
17 6 0.06
18 5 0.05
19 19 0.20
20 31 0.32
21 12 0.12
22 3 0.03
23 3 0.03
24 11 0.11
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATATATTATTTTAAT
Found at i:1549814 original size:30 final size:28
Alignment explanation
Indices: 1549717--1549851 Score: 94
Period size: 30 Copynumber: 4.7 Consensus size: 28
1549707 TGGTGTGTTC
* * * *
1549717 ATATATATATATA-TATATATA-TATAT
1 ATATATATTTATATTATATAAATTTTAA
* * * *
1549743 ATATATATATATATTATTTTAATTATAA
1 ATATATATTTATATTATATAAATTTTAA
* *
1549771 TTAAAATATTTTATATTTATATAAATTTTAAA
1 AT-ATATA-TTTATA-TTATATAAATTTT-AA
*
1549803 ATATATATTTATATTATATTATATTTTAA
1 ATATATATTTATATTATA-TAAATTTTAA
*
1549832 ATATTTTATTTATATTATAT
1 ATA-TATATTTATATTATAT
1549852 TCATATAATT
Statistics
Matches: 87, Mismatches: 14, Indels: 13
0.76 0.12 0.11
Matches are distributed among these distances:
26 13 0.15
27 5 0.06
28 5 0.06
29 15 0.17
30 32 0.37
31 14 0.16
32 3 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATATATTTATATTATATAAATTTTAA
Found at i:1549851 original size:25 final size:25
Alignment explanation
Indices: 1549751--1549852 Score: 82
Period size: 25 Copynumber: 3.8 Consensus size: 25
1549741 ATATATATAT
* * *
1549751 ATATATTAT-TTTAATTATAATTAAA
1 ATATTTTATATTT-ATTATATTTTAA
*
1549776 ATATTTTATATTTATATAAATTTTAAAA
1 ATATTTTATATTTAT-TATATTTT--AA
1549804 TATATATTTATATTATATTATATTTTAA
1 -ATAT-TTTATATT-TATTATATTTTAA
1549832 ATATTTTAT-TTATATTATATT
1 ATATTTTATATT-TATTATATT
1549853 CATATAATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
25 22 0.34
26 13 0.20
27 4 0.06
28 4 0.06
29 4 0.06
30 15 0.23
31 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTTTATATTTATTATATTTTAA
Found at i:1554270 original size:23 final size:22
Alignment explanation
Indices: 1554224--1554270 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1554214 TTAAAATTTA
* **
1554224 AATATAAATTTATTAATTTTTT
1 AATAAAAATTTATTAATTAATT
1554246 AATAAAAATTATATTAATTAATT
1 AATAAAAATT-TATTAATTAATT
1554269 AA
1 AA
1554271 ATTTAACCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAAAAATTTATTAATTAATT
Found at i:1554337 original size:18 final size:18
Alignment explanation
Indices: 1554310--1554367 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
1554300 TTTTGCTGCT
*
1554310 AATTAAATTAATTAATTG
1 AATTATATTAATTAATTG
*
1554328 AATTATATTAATTAATTA
1 AATTATATTAATTAATTG
1554346 AATTATATTAATTAATTG
1 AATTATATTAATTAATTG
1554364 AATT
1 AATT
1554368 TAACCCTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
AATTATATTAATTAATTG
Found at i:1554367 original size:9 final size:8
Alignment explanation
Indices: 1554309--1554367 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 8
1554299 TTTTTGCTGC
1554309 TAATTAAAT
1 TAATT-AAT
1554318 TAATTAAT
1 TAATTAAT
1554326 TGAATTATAT
1 T-AATTA-AT
1554336 TAATTAAT
1 TAATTAAT
1554344 TAAATTATAT
1 T-AATTA-AT
1554354 TAATTAAT
1 TAATTAAT
1554362 TGAATT
1 T-AATT
1554368 TAACCCTGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
8 10 0.22
9 29 0.64
10 6 0.13
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (8 bp):
TAATTAAT
Found at i:1554814 original size:13 final size:15
Alignment explanation
Indices: 1554754--1554816 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 15
1554744 GATAGATGTG
1554754 ATTAT-ATATATATAT
1 ATTATAATATA-ATAT
* *
1554769 ATTAAAGATTATGATAT
1 ATTATA-A-TATAATAT
1554786 AATTATAATATAATAT
1 -ATTATAATATAATAT
1554802 ATTA-AAT-TAATAT
1 ATTATAATATAATAT
1554815 AT
1 AT
1554817 AATATCGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
13 8 0.20
14 3 0.08
15 8 0.20
16 7 0.17
17 6 0.15
18 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
ATTATAATATAATAT
Found at i:1557685 original size:2 final size:2
Alignment explanation
Indices: 1557678--1557707 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1557668 GGCTTTATTT
1557678 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
1557708 AAATATGTGT
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:1565197 original size:23 final size:26
Alignment explanation
Indices: 1565162--1565215 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
1565152 TTTTAATATA
*
1565162 TTAATAAATTATA-TTATAT-AAATT
1 TTAATAAAATATATTTATATCAAATT
*
1565186 TTAA-AAAATATATTTATATCATATT
1 TTAATAAAATATATTTATATCAAATT
1565211 TTAAT
1 TTAAT
1565216 TAATTTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 7 0.28
24 10 0.40
25 8 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAATAAAATATATTTATATCAAATT
Found at i:1570791 original size:17 final size:19
Alignment explanation
Indices: 1570761--1570798 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1570751 GTATTGAGAT
*
1570761 TATATTTAATAAACGATAA
1 TATATTTAATAAACGAAAA
1570780 TATATTT-A-AAACGAAAA
1 TATATTTAATAAACGAAAA
1570797 TA
1 TA
1570799 AAAATTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
TATATTTAATAAACGAAAA
Found at i:1571413 original size:18 final size:18
Alignment explanation
Indices: 1571392--1571442 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
1571382 AAAATTTTTA
*
1571392 TAATATAAATTATTTACT
1 TAATATAAATTATTTAAT
*
1571410 TAATA-AAATT-TATAAT
1 TAATATAAATTATTTAAT
* *
1571426 AAATATAAAATATTTAA
1 TAATATAAATTATTTAA
1571443 ATATGATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 8 0.31
17 9 0.35
18 9 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATAAATTATTTAAT
Found at i:1571462 original size:8 final size:9
Alignment explanation
Indices: 1571412--1571472 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
1571402 TATTTACTTA
*
1571412 ATAAAATTT
1 ATAAAATAT
1571421 ATAATAA-AT
1 ATAA-AATAT
1571430 ATAAAATAT
1 ATAAAATAT
*
1571439 TTAAATATGATT
1 ATAAA-AT-A-T
1571451 ATAAAATA-
1 ATAAAATAT
1571459 ATAAAATAT
1 ATAAAATAT
1571468 ATAAA
1 ATAAA
1571473 TTATCAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
8 10 0.23
9 20 0.47
10 5 0.12
11 3 0.07
12 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (9 bp):
ATAAAATAT
Found at i:1571781 original size:21 final size:20
Alignment explanation
Indices: 1571755--1571796 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1571745 AATTAATTAA
*
1571755 TATATTATTTTATGATAAAAT
1 TATATTATATTAT-ATAAAAT
*
1571776 TATATTATATTATATTAAAT
1 TATATTATATTATATAAAAT
1571796 T
1 T
1571797 TAATAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATATTATATTATATAAAAT
Found at i:1574044 original size:4 final size:4
Alignment explanation
Indices: 1574035--1574066 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
1574025 CTATCAAGAG
1574035 TTTA TTTA TTTA TTTA TTTA TTTA TATTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTT
1574067 TTTTTGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1576996 original size:1 final size:1
Alignment explanation
Indices: 1576985--1577018 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
1576975 CACACACATT
*
1576985 AAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1577019 GGTCGCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1587866 original size:22 final size:21
Alignment explanation
Indices: 1587841--1587884 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1587831 ACAAATATTA
1587841 AAATATAAATTTTTAATAAATT
1 AAATATAAATTTTTAA-AAATT
* *
1587863 AAATATTATTTTTTAAAAATT
1 AAATATAAATTTTTAAAAATT
1587884 A
1 A
1587885 TTATATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATATAAATTTTTAAAAATT
Found at i:1603208 original size:49 final size:53
Alignment explanation
Indices: 1603143--1603253 Score: 142
Period size: 49 Copynumber: 2.2 Consensus size: 53
1603133 TTTATATAAT
* *
1603143 TATATATTTTATTATATT-A-TAATTATATT-TA-AAATATTTTA-TATTTTTA
1 TATATATTTTAATATATTAATTAATTATATTATATAAA-ATTTAATTATTTTTA
*
1603192 TATATATTTTAATATATTAATTATTTATATTATATAAAATTTAATTATTTTTA
1 TATATATTTTAATATATTAATTAATTATATTATATAAAATTTAATTATTTTTA
1603245 TATTATATT
1 TA-TATATT
1603254 CAAATTAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
49 17 0.32
50 1 0.02
51 9 0.17
52 7 0.13
53 13 0.25
54 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (53 bp):
TATATATTTTAATATATTAATTAATTATATTATATAAAATTTAATTATTTTTA
Found at i:1603235 original size:32 final size:31
Alignment explanation
Indices: 1603139--1603253 Score: 94
Period size: 32 Copynumber: 3.7 Consensus size: 31
1603129 GAAGTTTATA
* * *
1603139 TAATTATATATTTTATTATATTATAATTATATT
1 TAATTAT-TATTATATTATATTAT-ATAAAATT
* * *
1603172 TAAAATATT-TTATATT-T-TTATATATATTT
1 T-AATTATTATTATATTATATTATATAAAATT
1603201 TAATATATTAATTAT-TTATATTATATAAAATT
1 TAAT-TATT-ATTATATTATATTATATAAAATT
*
1603233 TAATTATTTTTATATTATATT
1 TAATTATTATTATATTATATT
1603254 CAAATTAAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
28 2 0.03
29 9 0.14
30 10 0.15
31 17 0.26
32 20 0.31
33 2 0.03
34 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TAATTATTATTATATTATATTATATAAAATT
Found at i:1603261 original size:26 final size:26
Alignment explanation
Indices: 1603184--1603261 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
1603174 AAATATTTTA
*
1603184 TATTTTTATATATATTTTAATATATTAAT
1 TATTTTTATAT-TATATTAA-A-ATTAAT
1603213 TA--TTTATATTATA-TAAAATTTAAT
1 TATTTTTATATTATATTAAAA-TTAAT
*
1603237 TATTTTTATATTATATTCAAATTAA
1 TATTTTTATATTATATTAAAATTAA
1603262 ACCTAATGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
23 1 0.02
24 8 0.19
25 3 0.07
26 18 0.42
27 11 0.26
29 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTTTTATATTATATTAAAATTAAT
Found at i:1604337 original size:14 final size:14
Alignment explanation
Indices: 1604301--1604355 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
1604291 TTAAATTATT
*
1604301 ATTTAATTAATAAA
1 ATTTAATTATTAAA
* *
1604315 ATTT-TTTATTTAA
1 ATTTAATTATTAAA
1604328 ATTTAATTA-TAAA
1 ATTTAATTATTAAA
1604341 ATATATAATTATTAA
1 AT-T-TAATTATTAA
1604356 TATAAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 15 0.47
14 8 0.25
15 6 0.19
16 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTAATTATTAAA
Found at i:1609997 original size:14 final size:14
Alignment explanation
Indices: 1609974--1610017 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
1609964 ATTCTCTCCT
1609974 ACTGTGATATTCAC
1 ACTGTGATATTCAC
*
1609988 ACTGTTATATTCAC
1 ACTGTGATATTCAC
1610002 ACTGTGATATTCAC
1 ACTGTGATATTCAC
1610016 AC
1 AC
1610018 CGTTATGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (14 bp):
ACTGTGATATTCAC
Found at i:1610297 original size:354 final size:354
Alignment explanation
Indices: 1609648--1610649 Score: 1995
Period size: 354 Copynumber: 2.8 Consensus size: 354
1609638 TTTCTCTCCT
*
1609648 ACTGTGATATTCACACTGTTATGCATTAAGAAAGAAAAAAAGTTACTTGAACCATTCATATCTGC
1 ACTGTGATATTCACACCGTTATGCATTAAGAAAGAAAAAAAGTTACTTGAACCATTCATATCTGC
1609713 AGAATGCATATGATATATGTAATGGAGCCTGCCCCAAGACTCTGAGTTCCATCGTATGCATTTTG
66 AGAATGCATATGATATATGTAATGGAGCCTGCCCCAAGACTCTGAGTTCCATCGTATGCATTTTG
1609778 CCTTTGTCTATTCCATGGTTATTCTTGCACCAATTAATATACTTCACTTATAATCAAGAGGTTAG
131 CCTTTGTCTATTCCATGGTTATTCTTGCACCAATTAATATACTTCACTTATAATCAAGAGGTTAG
1609843 ACAAAAATTAAGTAGAATGAAGGGAGATCATAGAAAAAGGGATGACCGATTTATTGGTTTTTGGC
196 ACAAAAATTAAGTAGAATGAAGGGAGATCATAGAAAAAGGGATGACCGATTTATTGGTTTTTGGC
1609908 TGTCTGTATGCCGGTGGGTTGTCTAGAGCAGCAGAATGCATATGATATATGTATGCATTCTCTCC
261 TGTCTGTATGCCGGTGGGTTGTCTAGAGCAGCAGAATGCATATGATATATGTATGCATTCTCTCC
1609973 TACTGTGATATTCACACTGTTATATTCAC
326 TACTGTGATATTCACACTGTTATATTCAC
1610002 ACTGTGATATTCACACCGTTATGCATTAAGAAAGAAAAAAAGTTACTTGAACCATTCATATCTGC
1 ACTGTGATATTCACACCGTTATGCATTAAGAAAGAAAAAAAGTTACTTGAACCATTCATATCTGC
1610067 AGAATGCATATGATATATGTAATGGAGCCTGCCCCAAGACTCTGAGTTCCATCGTATGCATTTTG
66 AGAATGCATATGATATATGTAATGGAGCCTGCCCCAAGACTCTGAGTTCCATCGTATGCATTTTG
1610132 CCTTTGTCTATTCCATGGTTATTCTTGCACCAATTAATATACTTCACTTATAATCAAGAGGTTAG
131 CCTTTGTCTATTCCATGGTTATTCTTGCACCAATTAATATACTTCACTTATAATCAAGAGGTTAG
1610197 ACAAAAATTAAGTAGAATGAAGGGAGATCATAGAAAAAGGGATGACCGATTTATTGGTTTTTGGC
196 ACAAAAATTAAGTAGAATGAAGGGAGATCATAGAAAAAGGGATGACCGATTTATTGGTTTTTGGC
1610262 TGTCTGTATGCCGGTGGGTTGTCTAGAGCAGCAGAATGCATATGATATATGTATGCATTCTCTCC
261 TGTCTGTATGCCGGTGGGTTGTCTAGAGCAGCAGAATGCATATGATATATGTATGCATTCTCTCC
1610327 TACTGTGATATTCACACTGTTATATTCAC
326 TACTGTGATATTCACACTGTTATATTCAC
1610356 ACTGTGATATTCACACCGTTATGCATTAAGAAAGAAAAAAAGTTACTTGAACCATTCATATCTGC
1 ACTGTGATATTCACACCGTTATGCATTAAGAAAGAAAAAAAGTTACTTGAACCATTCATATCTGC
1610421 AGAATGCATATGATATATGTAATGGAGCCTGCCCCAAGACTCTGAGTTCCATCGTATGCATTTTG
66 AGAATGCATATGATATATGTAATGGAGCCTGCCCCAAGACTCTGAGTTCCATCGTATGCATTTTG
1610486 CCTTTGTCTATTCCATGGTTATTCTTGCACCAATTAATATACTTCACTTATAATCAAGAGGTTAG
131 CCTTTGTCTATTCCATGGTTATTCTTGCACCAATTAATATACTTCACTTATAATCAAGAGGTTAG
1610551 ACAAAAATTAAGTAGAATGAAGGGAGATCATAGAAAAAGGGATGACCGATTTATTGGTTTTTGGC
196 ACAAAAATTAAGTAGAATGAAGGGAGATCATAGAAAAAGGGATGACCGATTTATTGGTTTTTGGC
1610616 TGTCTGTATGCCGGTGGGTTGTCTAGAGCAGCAG
261 TGTCTGTATGCCGGTGGGTTGTCTAGAGCAGCAG
1610650 GTAGCTGACC
Statistics
Matches: 647, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
354 647 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (354 bp):
ACTGTGATATTCACACCGTTATGCATTAAGAAAGAAAAAAAGTTACTTGAACCATTCATATCTGC
AGAATGCATATGATATATGTAATGGAGCCTGCCCCAAGACTCTGAGTTCCATCGTATGCATTTTG
CCTTTGTCTATTCCATGGTTATTCTTGCACCAATTAATATACTTCACTTATAATCAAGAGGTTAG
ACAAAAATTAAGTAGAATGAAGGGAGATCATAGAAAAAGGGATGACCGATTTATTGGTTTTTGGC
TGTCTGTATGCCGGTGGGTTGTCTAGAGCAGCAGAATGCATATGATATATGTATGCATTCTCTCC
TACTGTGATATTCACACTGTTATATTCAC
Found at i:1610351 original size:14 final size:14
Alignment explanation
Indices: 1610328--1610371 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
1610318 ATTCTCTCCT
1610328 ACTGTGATATTCAC
1 ACTGTGATATTCAC
*
1610342 ACTGTTATATTCAC
1 ACTGTGATATTCAC
1610356 ACTGTGATATTCAC
1 ACTGTGATATTCAC
1610370 AC
1 AC
1610372 CGTTATGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (14 bp):
ACTGTGATATTCAC
Found at i:1610838 original size:2 final size:2
Alignment explanation
Indices: 1610827--1610873 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1610817 CAAAGAGAGA
*
1610827 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1610869 AT AT A
1 AT AT A
1610874 GTAGAAAAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1612329 original size:2 final size:2
Alignment explanation
Indices: 1612322--1612347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1612312 ACATACATAT
1612322 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
1612348 GATATCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1620449 original size:142 final size:144
Alignment explanation
Indices: 1620191--1620454 Score: 469
Period size: 142 Copynumber: 1.8 Consensus size: 144
1620181 AACATGCAAC
* *
1620191 TACAAGAGCTTTGGCATAACAATGCAAGACCCAAGAGGAGCTGCCAACAGTATTTTTCAGTACCT
1 TACAAGAGCTTTGGCATAACAATGCAAGACCCAAGAGGAGCAGCCAACAGTATATTTCAGTACCT
1620256 AAAATTTGGATCAAGTCAAATTAAAACCAACTAAAGGCATATCGAATCTAGAAGCATAACAAGGA
66 AAAATTTGGATCAAGTCAAATTAAAACCAACTAAAGGCATATCGAATCTAGAAGCATAACAAGGA
1620321 AAACAGTATTTCAG
131 AAACAGTATTTCAG
*
1620335 TACAAGAGCTTTGGCATAACAATGCAAGACCCAAGAGGAGCAGCCAGCA-T-TATTTCAGTACCT
1 TACAAGAGCTTTGGCATAACAATGCAAGACCCAAGAGGAGCAGCCAACAGTATATTTCAGTACCT
* *
1620398 AAAATTTGGATCAAGTCAGATTAAAACCAACTAAAGGCATATCGGATCTAGAAGCAT
66 AAAATTTGGATCAAGTCAAATTAAAACCAACTAAAGGCATATCGAATCTAGAAGCAT
1620455 GTACATGACA
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
142 67 0.58
143 1 0.01
144 47 0.41
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (144 bp):
TACAAGAGCTTTGGCATAACAATGCAAGACCCAAGAGGAGCAGCCAACAGTATATTTCAGTACCT
AAAATTTGGATCAAGTCAAATTAAAACCAACTAAAGGCATATCGAATCTAGAAGCATAACAAGGA
AAACAGTATTTCAG
Found at i:1623350 original size:2 final size:2
Alignment explanation
Indices: 1623345--1623382 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
1623335 ATATATATAT
1623345 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG CAG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG
1623383 CACCACGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1632081 original size:34 final size:33
Alignment explanation
Indices: 1632034--1632151 Score: 173
Period size: 34 Copynumber: 3.5 Consensus size: 33
1632024 GGTAAAAACT
*
1632034 ACCATTTAATCAACAATGGTAAGCTACCAAATC
1 ACCATTTAATCAACAATGGTAAACTACCAAATC
* * * *
1632067 TCTCATTTAGTCAACAATGGCAAACCACCAAATC
1 AC-CATTTAATCAACAATGGTAAACTACCAAATC
1632101 ACCCATTTAATCAACAATGGTAAACTACCAAATC
1 A-CCATTTAATCAACAATGGTAAACTACCAAATC
1632135 ACCATTTAATCAACAAT
1 ACCATTTAATCAACAAT
1632152 TCTCCCACTT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
33 17 0.23
34 56 0.76
35 1 0.01
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
ACCATTTAATCAACAATGGTAAACTACCAAATC
Found at i:1633047 original size:33 final size:33
Alignment explanation
Indices: 1633005--1633079 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
1632995 AAGCGTCACA
1633005 AAATCTTCTCCAGATAATTCTTTTGAGAAATCC
1 AAATCTTCTCCAGATAATTCTTTTGAGAAATCC
1633038 AAATCTTCTCCAGATAATTCTTTTGAGAAATCC
1 AAATCTTCTCCAGATAATTCTTTTGAGAAATCC
1633071 AAATCTTCT
1 AAATCTTCT
1633080 TATTATTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.37
Consensus pattern (33 bp):
AAATCTTCTCCAGATAATTCTTTTGAGAAATCC
Found at i:1635431 original size:637 final size:636
Alignment explanation
Indices: 1634210--1635486 Score: 2347
Period size: 637 Copynumber: 2.0 Consensus size: 636
1634200 GGGCATTATA
*
1634210 CAATATATATGCAGGACATCCAAATATGTGGAGATTAGAGTAATCAACTGGCTTACTTGTCCACA
1 CAATACATATGCAGGACATCCAAATATGTGGAGATTAGAGTAATCAACTGGCTTACTTGTCCACA
* *
1634275 TTTCCATTGGAGTCTTCAGTCCAATTGCTGTAGATGGAGCTCGATTTATCACATAACATGTGGTC
66 TTTCCATTGGAGTCTTCAGTCCAATTGCTGTAGATGGAGCCCGATTTATCACATAACATGCGGTC
*
1634340 TTGAGTGCTTCTGCCCAAAACGACTTCGCCAGACCAGCAACTTTCAACATAGCTCTGGTTCTTTC
131 TTGACTGCTTCTGCCCAAAACGACTTCGCCAGACCAGCAACTTTCAACATAGCTCTGGTTCTTTC
* *
1634405 GAGTAGAGTTCTATTCATCCGCTCTGCCACTCCATTCTGTTGCGGTTTGTAAGCCACGCTAAATT
196 GAGTAGAGTTCTATTCATCCACTCTGCCACTCCATTCTGTTGCGGTGTGTAAGCCACGCTAAATT
1634470 GCCTTTTAATGCCTTCATTTTGACAGAAAGCATTAAACTCACCACTCGTGTATTCTCCTCCATTG
261 GCCTTTTAATGCCTTCATTTTGACAGAAAGCATTAAACTCACCACTCGTGTATTCTCCTCCATTG
1634535 TTTGTCCTCAAACACTTGATCTTCTTTCCAGATTCAAGTTCCACCCGTGCTTTGTATACTTTGAA
326 TTTGTCCTCAAACACTTGATCTTCTTTCCAGATTCAAGTTCCACCCGTGCTTTGTATACTTTGAA
* * * *
1634600 AACTATAAATACATCTGCTTTATTTTTTATTGGATACACCCAACATCTTCTGGAGAAATCATCAA
391 AACTATAAACACATCTGCTTTACTTTTGATTGGATACACCCAACATCTTCTGAAGAAATCATCAA
1634665 TAAATGACACAAAGTATTTTGCTCCTCCTAGAGACATAACCGGTGCTTGCCAAACATCTAAATGA
456 TAAATGACACAAAGTATTTTGCTCCTCCTAGAGACATAACCGGTGCTTGCCAAACATCTAAATGA
1634730 ATTAACTCCAGAATGCACTTACTTCTAGCATTAGATGTGCTGAACTTCAATATATTTTGCTTGCT
521 ATTAACTCCAGAATGCACTTACTTCTAGCATTAGATGTGCTGAACTTCAATATATTTTGCTTGCT
*
1634795 TAAAACACAATGCTCACAAAAAGGTAGACTTAGTGTTTTGAGTCCAGGAAG
586 TAAAACACAATGCTCACAAAAAGGTAGACTTACTGTTTTGAGTCCAGGAAG
1634846 TCAATACATATGCAGGACATCCAAATATGTGGAGATTAGAGTAATCAACTGGCTTACTTGTCCAC
1 -CAATACATATGCAGGACATCCAAATATGTGGAGATTAGAGTAATCAACTGGCTTACTTGTCCAC
*
1634911 ATTTCCATTGGAGTCTTCAGTCCAATTGCTGTAGATGGAGCCCGATTTATCACATAGCATGCGGT
65 ATTTCCATTGGAGTCTTCAGTCCAATTGCTGTAGATGGAGCCCGATTTATCACATAACATGCGGT
* ** *
1634976 CTTGACTGCTTTTGCCCAAAACGACTTCGCCAGACCAGCAGTTTTCAGCATAGCTCTGGTTCTTT
130 CTTGACTGCTTCTGCCCAAAACGACTTCGCCAGACCAGCAACTTTCAACATAGCTCTGGTTCTTT
1635041 CGAGTAGAGTTCTATTCATCCACTCTGCCACTCCATTCTGTTGCGGTGTGTAAGCCACGCTAAAT
195 CGAGTAGAGTTCTATTCATCCACTCTGCCACTCCATTCTGTTGCGGTGTGTAAGCCACGCTAAAT
*
1635106 TGCCTTTTAATGCCTTCATTTTGACAGAAAGCATTAAACTCACCACTCGTGTATTTTCCTCCATT
260 TGCCTTTTAATGCCTTCATTTTGACAGAAAGCATTAAACTCACCACTCGTGTATTCTCCTCCATT
*
1635171 GTTTGTCCTTAAACACTTGATCTTCTTTCCAGATTCAAGTTCCACCCGTGCTTTGTATACTTTGA
325 GTTTGTCCTCAAACACTTGATCTTCTTTCCAGATTCAAGTTCCACCCGTGCTTTGTATACTTTGA
* * *
1635236 AAACTGTAAACACATCTGTTTTACTTTTGATTGGATACATCCAACATCTTCTGAAGAAATCATCA
390 AAACTATAAACACATCTGCTTTACTTTTGATTGGATACACCCAACATCTTCTGAAGAAATCATCA
*
1635301 ATAAATGACACAAAGTATTTTGCTCCTCCTAGAGACATAACCGGTGCTTGCCAAACATCTGAATG
455 ATAAATGACACAAAGTATTTTGCTCCTCCTAGAGACATAACCGGTGCTTGCCAAACATCTAAATG
1635366 AATTAACTCCAGAATGCACTTACTTCTAGCATTAGATGTGCTGAACTTCAATATATTTTGCTTGC
520 AATTAACTCCAGAATGCACTTACTTCTAGCATTAGATGTGCTGAACTTCAATATATTTTGCTTGC
1635431 TTAAAACACAATGCTCACAAAAAGGTAGACTTACTGTTTTGAGTCCAGGAAG
585 TTAAAACACAATGCTCACAAAAAGGTAGACTTACTGTTTTGAGTCCAGGAAG
1635483 CAAT
1 CAAT
1635487 CTACTATCAG
Statistics
Matches: 618, Mismatches: 22, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
636 4 0.01
637 614 0.99
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (636 bp):
CAATACATATGCAGGACATCCAAATATGTGGAGATTAGAGTAATCAACTGGCTTACTTGTCCACA
TTTCCATTGGAGTCTTCAGTCCAATTGCTGTAGATGGAGCCCGATTTATCACATAACATGCGGTC
TTGACTGCTTCTGCCCAAAACGACTTCGCCAGACCAGCAACTTTCAACATAGCTCTGGTTCTTTC
GAGTAGAGTTCTATTCATCCACTCTGCCACTCCATTCTGTTGCGGTGTGTAAGCCACGCTAAATT
GCCTTTTAATGCCTTCATTTTGACAGAAAGCATTAAACTCACCACTCGTGTATTCTCCTCCATTG
TTTGTCCTCAAACACTTGATCTTCTTTCCAGATTCAAGTTCCACCCGTGCTTTGTATACTTTGAA
AACTATAAACACATCTGCTTTACTTTTGATTGGATACACCCAACATCTTCTGAAGAAATCATCAA
TAAATGACACAAAGTATTTTGCTCCTCCTAGAGACATAACCGGTGCTTGCCAAACATCTAAATGA
ATTAACTCCAGAATGCACTTACTTCTAGCATTAGATGTGCTGAACTTCAATATATTTTGCTTGCT
TAAAACACAATGCTCACAAAAAGGTAGACTTACTGTTTTGAGTCCAGGAAG
Found at i:1636901 original size:19 final size:19
Alignment explanation
Indices: 1636874--1636955 Score: 110
Period size: 19 Copynumber: 4.3 Consensus size: 19
1636864 TCACGTGTAC
* *
1636874 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1636893 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
* **
1636912 AGTATCAATATACGTGAAT
1 AGTACCCGTATACGTGAAT
*
1636931 AGTACCTGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
1636950 AGTACC
1 AGTACC
1636956 TCAACAACCA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 55 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1637324 original size:34 final size:34
Alignment explanation
Indices: 1637264--1637377 Score: 128
Period size: 34 Copynumber: 3.4 Consensus size: 34
1637254 AAAAACTACT
* * *
1637264 ATTTAATCAACAATGGT-AAGCTATCAAATCTCTC
1 ATTTAATCAACAATGATAAATC-ATCAAATCACTC
* *
1637298 ATTTAGTCAATAATGATAAATCATCAAATCACTC
1 ATTTAATCAACAATGATAAATCATCAAATCACTC
1637332 ATTTAATCAACAATGATAAA-C-TACTAAATCA-TC
1 ATTTAATCAACAATGATAAATCAT-C-AAATCACTC
1637365 ATTTAATCAACAA
1 ATTTAATCAACAA
1637378 AATCTACTAG
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
32 1 0.01
33 17 0.24
34 49 0.70
35 3 0.04
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (34 bp):
ATTTAATCAACAATGATAAATCATCAAATCACTC
Found at i:1637831 original size:2 final size:2
Alignment explanation
Indices: 1637824--1637859 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1637814 TTTTCAATTT
1637824 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1637860 CAAAAAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1646538 original size:2 final size:2
Alignment explanation
Indices: 1646526--1646558 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1646516 AACTACATAC
*
1646526 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1646559 AAAAACCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1646807 original size:14 final size:14
Alignment explanation
Indices: 1646786--1646818 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1646776 ATATACAAAT
1646786 TATA-TATATTAAA
1 TATATTATATTAAA
*
1646799 TATATTATATTAAT
1 TATATTATATTAAA
1646813 TATATT
1 TATATT
1646819 TAAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATATTATATTAAA
Found at i:1655152 original size:15 final size:15
Alignment explanation
Indices: 1655132--1655160 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1655122 CATGGTCCTT
1655132 GATTAGCTTTGCTGG
1 GATTAGCTTTGCTGG
1655147 GATTAGCTTTGCTG
1 GATTAGCTTTGCTG
1655161 TTGTGTCTCA
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:0.14, C:0.14, G:0.31, T:0.41
Consensus pattern (15 bp):
GATTAGCTTTGCTGG
Found at i:1657302 original size:2 final size:2
Alignment explanation
Indices: 1657285--1657325 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1657275 ATCTACTCAA
*
1657285 AT AT TT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1657326 CACAGCTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1661103 original size:2 final size:2
Alignment explanation
Indices: 1661096--1661129 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1661086 AGGTATTCGC
1661096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1661130 CCATGCATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1663239 original size:25 final size:23
Alignment explanation
Indices: 1663197--1663268 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 23
1663187 TTTTTTAATA
1663197 AAATATATATCATATACATACAT
1 AAATATATATCATATACATACAT
*
1663220 AAATATATATCTTCATTACATACAT
1 AAATATATATCAT-A-TACATACAT
** * *
1663245 CTATATATAT-ATATATATATAT
1 AAATATATATCATATACATACAT
1663267 AA
1 AA
1663269 TTTTAAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 7 0.18
23 13 0.33
24 2 0.05
25 17 0.44
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATATATCATATACATACAT
Found at i:1663286 original size:24 final size:24
Alignment explanation
Indices: 1663254--1663311 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
1663244 TCTATATATA
*
1663254 TATATATATATATAAT-TTTAAAAT
1 TATAAATATAT-TAATATTTAAAAT
1663278 TATAAATAT-TTAATATTTAAAAT
1 TATAAATATATTAATATTTAAAAT
*
1663301 TTTAAA-ATATT
1 TATAAATATATT
1663312 CAAAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 6 0.20
23 16 0.53
24 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATAAATATATTAATATTTAAAAT
Found at i:1663340 original size:14 final size:14
Alignment explanation
Indices: 1663306--1663346 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1663296 AAAATTTTAA
*
1663306 AATATTCAA-AAA-
1 AATATTAAATAAAT
*
1663318 AATAATAAATAAAT
1 AATATTAAATAAAT
1663332 AATATTAAATAAAT
1 AATATTAAATAAAT
1663346 A
1 A
1663347 TAATAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 7 0.29
13 3 0.12
14 14 0.58
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
AATATTAAATAAAT
Found at i:1663344 original size:18 final size:18
Alignment explanation
Indices: 1663321--1663356 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1663311 TCAAAAAAAT
1663321 AATAAATA-AATAATATTA
1 AATAAATATAATAA-ATTA
1663339 AATAAATATAATAAATTA
1 AATAAATATAATAAATTA
1663357 TTATTAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATATAATAAATTA
Found at i:1667685 original size:23 final size:23
Alignment explanation
Indices: 1667628--1667706 Score: 56
Period size: 23 Copynumber: 3.5 Consensus size: 23
1667618 TAATTGGTTA
* *
1667628 ATATAATTAATTAATATTTAATAA-
1 ATATAATT-TTTAAAATTTAA-AAT
* *
1667652 ATTTAAATTTTAAAATTTAAAAT
1 ATATAATTTTTAAAATTTAAAAT
* * *
1667675 ATATAATTTTT-TATTTTTAAAT
1 ATATAATTTTTAAAATTTAAAAT
1667697 -TATAATTTTT
1 ATATAATTTTT
1667707 TTAAATAATC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
21 10 0.22
22 10 0.22
23 19 0.42
24 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATAATTTTTAAAATTTAAAAT
Found at i:1667690 original size:21 final size:21
Alignment explanation
Indices: 1667667--1667707 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1667657 AATTTTAAAA
1667667 TTTAAAATATATAATTTTTTAT
1 TTTAAAAT-TATAATTTTTTAT
*
1667689 TTTTAAATTATAATTTTTT
1 TTTAAAATTATAATTTTTT
1667708 TAAATAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAAAATTATAATTTTTTAT
Found at i:1668844 original size:19 final size:20
Alignment explanation
Indices: 1668796--1668844 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
1668786 ATTTTTTTAA
1668796 ATTTTATAAAAATAATTAATTT
1 ATTTTAT-AAAATAATT-ATTT
*
1668818 A-ATT-TAAAATAATT-TTT
1 ATTTTATAAAATAATTATTT
1668835 ATTTTATAAA
1 ATTTTATAAA
1668845 GTTTTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
17 4 0.17
18 2 0.09
19 13 0.57
20 1 0.04
21 2 0.09
22 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTATAAAATAATTATTT
Found at i:1673653 original size:6 final size:6
Alignment explanation
Indices: 1673637--1673665 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1673627 TATCTCATTC
1673637 TTTTG- TTTTGT TTTTGT TTTTGT TTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
1673666 CAGTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTGT
Found at i:1675216 original size:31 final size:29
Alignment explanation
Indices: 1675159--1675216 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1675149 AAGATTATTG
* * *
1675159 TTAAATATGATTTTTTATTTTTAAAATTT
1 TTAAAAATAATTTTTTATTTTAAAAATTT
1675188 TTAAAAATAATTTTTTATCTCTTAAAAAT
1 TTAAAAATAATTTTTTAT-T-TTAAAAAT
1675217 AATTATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 1 0.04
31 7 0.29
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (29 bp):
TTAAAAATAATTTTTTATTTTAAAAATTT
Found at i:1680247 original size:19 final size:19
Alignment explanation
Indices: 1680223--1680261 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1680213 AAGAAATTAA
1680223 ACAATATACACAGCAATCG
1 ACAATATACACAGCAATCG
1680242 ACAATATACACAGCAATCG
1 ACAATATACACAGCAATCG
1680261 A
1 A
1680262 TCCACAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (19 bp):
ACAATATACACAGCAATCG
Found at i:1681592 original size:2 final size:2
Alignment explanation
Indices: 1681587--1681619 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1681577 ATATATGTTT
1681587 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1681620 CTGCCATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1683064 original size:2 final size:2
Alignment explanation
Indices: 1683059--1683085 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1683049 TGTGTGTGCG
1683059 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1683086 GCTTGGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1689352 original size:34 final size:34
Alignment explanation
Indices: 1689285--1689500 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
1689275 CCGTCTTCAA
* * *
1689285 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1689318 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1689352 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1689385 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1689419 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1689453 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1689487 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1689501 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1689466 original size:68 final size:67
Alignment explanation
Indices: 1689285--1689502 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
1689275 CCGTCTTCAA
* * * * *
1689285 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1689350 AT
66 AT
* * * *
1689352 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1689417 AT
66 AT
* * *
1689419 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
1689484 CAT
65 CAT
1689487 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1689503 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:1693981 original size:34 final size:34
Alignment explanation
Indices: 1693911--1694128 Score: 287
Period size: 34 Copynumber: 6.5 Consensus size: 34
1693901 AAGTGGGAGA
* * *
1693911 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * **
1693944 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGTC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1693978 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1694011 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1694045 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1694079 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1694113 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1694129 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 41 0.25
34 121 0.75
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1694094 original size:68 final size:67
Alignment explanation
Indices: 1693911--1694130 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
1693901 AAGTGGGAGA
* * * * *
1693911 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
*
1693976 TC
66 CC
* * * *
1693978 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1694043 CC
66 CC
* * *
1694045 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
1694110 GCC
65 GCC
1694113 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1694131 GTTTTTACCA
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:1699471 original size:1 final size:1
Alignment explanation
Indices: 1699465--1699555 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
1699455 AAATCTTCAC
* * ** * * * **
1699465 TTTTTTTTTGTTTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
1699530 TTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1699556 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:1699515 original size:32 final size:32
Alignment explanation
Indices: 1699466--1699549 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
1699456 AATCTTCACT
1699466 TTTTTTTTGTTTT-TTTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCC
1699497 TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCC
1699529 TTTTTTTTGTTTTGTTTTTTT
1 TTTTTTTTGTTTTGTTTTTTT
1699550 CTTTTTCCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 13 0.25
32 39 0.75
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.87
Consensus pattern (32 bp):
TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCC
Found at i:1712868 original size:16 final size:17
Alignment explanation
Indices: 1712828--1712869 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1712818 TATAAAAAAT
1712828 ATAA-TTTTTTATTTTA
1 ATAACTTTTTTATTTTA
* *
1712844 ATAATTTTTTTATTTTC
1 ATAACTTTTTTATTTTA
1712861 A-AACTTTTT
1 ATAACTTTTT
1712870 AAAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
ATAACTTTTTTATTTTA
Found at i:1712869 original size:17 final size:17
Alignment explanation
Indices: 1712828--1712859 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1712818 TATAAAAAAT
1712828 ATAA-TTTTTTATTTTA
1 ATAATTTTTTTATTTTA
1712844 ATAATTTTTTTATTTT
1 ATAATTTTTTTATTTT
1712860 CAAACTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
ATAATTTTTTTATTTTA
Found at i:1712908 original size:26 final size:26
Alignment explanation
Indices: 1712865--1712917 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
1712855 ATTTTCAAAC
*
1712865 TTTTTAAAATAATAATAAT-TAATTAA
1 TTTTTAAAAAAATAATAATAT-ATTAA
1712891 TTTTTAAATAAAAT-ATAATATATTAA
1 TTTTTAAA-AAAATAATAATATATTAA
1712917 T
1 T
1712918 ATGAAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTTTAAAAAAATAATAATATATTAA
Found at i:1713007 original size:15 final size:15
Alignment explanation
Indices: 1712987--1713016 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1712977 AAATTAAAGA
1712987 GAAGTTAATATATAT
1 GAAGTTAATATATAT
1713002 GAAGTTAATATATAT
1 GAAGTTAATATATAT
1713017 AAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (15 bp):
GAAGTTAATATATAT
Found at i:1713011 original size:42 final size:41
Alignment explanation
Indices: 1712915--1713021 Score: 148
Period size: 42 Copynumber: 2.6 Consensus size: 41
1712905 ATAATATATT
*
1712915 AATATGAAGTTAATATATATAATTAATTAAAGAGAAGTTTAA
1 AATATGAAGTTAATATATATAA-AAATTAAAGAGAAGTTTAA
*
1712957 AAT-TTAAG-TAATATATATAAAAATTAAAGAGAAG-TTAA
1 AATATGAAGTTAATATATATAAAAATTAAAGAGAAGTTTAA
1712995 TATATATGAAGTTAATATATATAAAAA
1 -A-ATATGAAGTTAATATATATAAAAA
1713022 ATTTAAGTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
38 4 0.07
39 14 0.24
40 14 0.24
41 8 0.14
42 18 0.31
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (41 bp):
AATATGAAGTTAATATATATAAAAATTAAAGAGAAGTTTAA
Done.