Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 143 of 168
Found at i:42174003 original size:17 final size:17
Alignment explanation
Indices: 42173981--42174017 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
42173971 AAAGATTTGA
42173981 TTTTTCTTTTCT-TTTCC
1 TTTTTCTTTT-TATTTCC
42173998 TTTTTCTTTTTATTTCC
1 TTTTTCTTTTTATTTCC
42174015 TTT
1 TTT
42174018 GAAGTGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTTATTTCC
Found at i:42174588 original size:26 final size:25
Alignment explanation
Indices: 42174545--42174593 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
42174535 TGTTTTAAGC
*
42174545 ACTTTTTTTTTCTTTTTATGTTTTTA
1 ACTTTTTTTTTCTCTTTAT-TTTTTA
42174571 ACTTTCTTTTTT-TCTTTATTTTT
1 ACTTT-TTTTTTCTCTTTATTTTT
42174594 CATTTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 11 0.52
27 6 0.29
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (25 bp):
ACTTTTTTTTTCTCTTTATTTTTTA
Found at i:42177845 original size:18 final size:16
Alignment explanation
Indices: 42177819--42177888 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 16
42177809 TCCTTTCTCC
42177819 TTTCTTTCTTTCCCTT
1 TTTCTTTCTTTCCCTT
*
42177835 TTTCTTATTCTTT-CCTC
1 TTTC-T-TTCTTTCCCTT
42177852 TTTCTTT-TTTCTCC--
1 TTTCTTTCTTTC-CCTT
42177866 TTTCTTTCTTTCCCTT
1 TTTCTTTCTTTCCCTT
42177882 TTTCTTT
1 TTTCTTT
42177889 TTCTTTCCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
14 12 0.26
15 6 0.13
16 14 0.30
17 8 0.17
18 6 0.13
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTCTTTCTTTCCCTT
Found at i:42177872 original size:47 final size:47
Alignment explanation
Indices: 42177803--42177906 Score: 181
Period size: 47 Copynumber: 2.2 Consensus size: 47
42177793 CCTAGCCTTG
**
42177803 TCTTTCTCCTTTCTCCTTTCTTTCTTTCCCTTTTTCTTATTCTTTCC
1 TCTTTCTTTTTTCTCCTTTCTTTCTTTCCCTTTTTCTTATTCTTTCC
*
42177850 TCTTTCTTTTTTCTCCTTTCTTTCTTTCCCTTTTTCTTTTTCTTTCC
1 TCTTTCTTTTTTCTCCTTTCTTTCTTTCCCTTTTTCTTATTCTTTCC
42177897 TCTTTCTTTT
1 TCTTTCTTTT
42177907 CTGTTTCGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (47 bp):
TCTTTCTTTTTTCTCCTTTCTTTCTTTCCCTTTTTCTTATTCTTTCC
Found at i:42177888 original size:6 final size:6
Alignment explanation
Indices: 42177879--42177961 Score: 62
Period size: 6 Copynumber: 13.5 Consensus size: 6
42177869 CTTTCTTTCC
* * *
42177879 CTTTTT CTTTTT C-TTTC CTCTTT C-TTTT CTGTTT CGTTTTT GCTTTGTCT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT -CTTT-T-T
* * *
42177929 CTTTTT CTATTT CTTTTT CTTTAT CTTTAT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTT
42177962 ATTTATTCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
5 8 0.13
6 39 0.63
7 8 0.13
8 6 0.10
9 1 0.02
ACGTcount: A:0.04, C:0.20, G:0.05, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:42177891 original size:18 final size:17
Alignment explanation
Indices: 42177823--42177906 Score: 79
Period size: 17 Copynumber: 5.1 Consensus size: 17
42177813 TTCTCCTTTC
*
42177823 TTTCTTTCCCTTTTTCTT
1 TTTCTTT-CCTCTTTCTT
*
42177841 ATTCTTTCCTCTTTCTT
1 TTTCTTTCCTCTTTCTT
*
42177858 TTT-TCT-C-CTTTC--
1 TTTCTTTCCTCTTTCTT
*
42177870 TTTCTTTCCCTTTTTCTT
1 TTTCTTT-CCTCTTTCTT
42177888 TTTCTTTCCTCTTTCTT
1 TTTCTTTCCTCTTTCTT
42177905 TT
1 TT
42177907 CTGTTTCGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 5 0.09
15 2 0.04
16 6 0.11
17 22 0.42
18 13 0.25
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTCTTTCCTCTTTCTT
Found at i:42177891 original size:22 final size:22
Alignment explanation
Indices: 42177819--42177895 Score: 91
Period size: 22 Copynumber: 3.4 Consensus size: 22
42177809 TCCTTTCTCC
42177819 TTTCTTTCTTTCCCTTTTTCTT
1 TTTCTTTCTTTCCCTTTTTCTT
* * * *
42177841 ATTCTTTCCTCTTTCTTTTTTCTCC
1 TTTCTTT-CT-TTCCCTTTTTCT-T
42177866 TTTCTTTCTTTCCCTTTTTCTT
1 TTTCTTTCTTTCCCTTTTTCTT
42177888 TTTCTTTC
1 TTTCTTTC
42177896 CTCTTTCTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 14 0.32
23 12 0.27
24 12 0.27
25 6 0.14
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTCTTTCTTTCCCTTTTTCTT
Found at i:42177900 original size:29 final size:28
Alignment explanation
Indices: 42177842--42177919 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
42177832 CTTTTTCTTA
42177842 TTCTTTCCTCTTTCTTTTTTCTCCTTTCT
1 TTCTTTCCTCTTTCTTTTTTCTCC-TTCT
* *
42177871 TTCTTTCCCTTTTTCTTTTTCTTTCC-TCT
1 TTCTTT-CCTCTTTCTTTTT-TCTCCTTCT
* * *
42177900 TTCTTTTCTGTTTCGTTTTT
1 TTCTTTCCTCTTTCTTTTTT
42177920 GCTTTGTCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
27 1 0.02
28 10 0.24
29 15 0.36
30 12 0.29
31 4 0.10
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.71
Consensus pattern (28 bp):
TTCTTTCCTCTTTCTTTTTTCTCCTTCT
Found at i:42178611 original size:6 final size:6
Alignment explanation
Indices: 42178602--42178685 Score: 73
Period size: 6 Copynumber: 13.5 Consensus size: 6
42178592 CTTTCTTTCC
*
42178602 CTTTTT CTTTTT C-TTTC CTTTTT C-TTTT CTTGTTT CTTTTTT GCTTTGTCT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTT-TTT C-TTTTT -CTTT-T-T
* * *
42178653 CTTTTT CTATTT CTATTT CTTTAT CTTTTT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTT
42178686 ATTTATTTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
5 9 0.14
6 36 0.55
7 11 0.17
8 8 0.12
9 1 0.02
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.74
Consensus pattern (6 bp):
CTTTTT
Found at i:42178614 original size:22 final size:23
Alignment explanation
Indices: 42178589--42178640 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
42178579 TCCTTTCTCC
42178589 TTTCTTT-CTTTCCCTTTTTCTT-
1 TTTCTTTCCTTTCCC-TTTTCTTG
**
42178611 TTTCTTTCCTTTTTCTTTTCTTG
1 TTTCTTTCCTTTCCCTTTTCTTG
42178634 TTTCTTT
1 TTTCTTT
42178641 TTTGCTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTCTTTCCTTTCCCTTTTCTTG
Found at i:42178629 original size:16 final size:17
Alignment explanation
Indices: 42178589--42178632 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
42178579 TCCTTTCTCC
42178589 TTTC-TTTCTTTCCCTT
1 TTTCTTTTCTTTCCCTT
42178605 TTTCTTTTTCTTT-CCTT
1 TTTC-TTTTCTTTCCCTT
42178622 TTTCTTTTCTT
1 TTTCTTTTCTT
42178633 GTTTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.42
17 8 0.31
18 7 0.27
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTCTTTTCTTTCCCTT
Found at i:42178692 original size:23 final size:23
Alignment explanation
Indices: 42178652--42178716 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
42178642 TTGCTTTGTC
*
42178652 TCTTTTTC-TATTTCTATTTCTTTA
1 TCTTTTTCTTA-TT-TATTTATTTA
42178676 TCTTTTTCTTATTTATTTATTTA
1 TCTTTTTCTTATTTATTTATTTA
* *
42178699 TACCTTCT-TTATTTATTT
1 T-CTTTTTCTTATTTATTT
42178717 GTTTTATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 20 0.56
24 14 0.39
25 2 0.06
ACGTcount: A:0.15, C:0.14, G:0.00, T:0.71
Consensus pattern (23 bp):
TCTTTTTCTTATTTATTTATTTA
Found at i:42181017 original size:21 final size:21
Alignment explanation
Indices: 42180993--42181043 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
42180983 TCTAATTAAA
42180993 AAAGAAGCTGAATGGAAAAAG
1 AAAGAAGCTGAATGGAAAAAG
42181014 AAAGAAGCTGAATGGAAAAAG
1 AAAGAAGCTGAATGGAAAAAG
*
42181035 AGAGAAGCT
1 AAAGAAGCT
42181044 TTGTTGCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.55, C:0.06, G:0.29, T:0.10
Consensus pattern (21 bp):
AAAGAAGCTGAATGGAAAAAG
Found at i:42198265 original size:17 final size:18
Alignment explanation
Indices: 42198243--42198293 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
42198233 TCAATTTTAA
42198243 TAAAAATATAAAAAAAT-
1 TAAAAATATAAAAAAATC
* *
42198260 TAAAAATTTATAAAAATC
1 TAAAAATATAAAAAAATC
42198278 GTAAAAATATAAAAAA
1 -TAAAAATATAAAAAA
42198294 TTGTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 15 0.54
19 13 0.46
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
TAAAAATATAAAAAAATC
Found at i:42198269 original size:28 final size:28
Alignment explanation
Indices: 42198242--42198295 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
42198232 TTCAATTTTA
*
42198242 ATAAAAAT-ATAAAAAAATTAAAAATTT
1 ATAAAAATCATAAAAAAATAAAAAATTT
* *
42198269 ATAAAAATCGTAAAAATATAAAAAATT
1 ATAAAAATCATAAAAAAATAAAAAATT
42198296 GTAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (28 bp):
ATAAAAATCATAAAAAAATAAAAAATTT
Found at i:42198287 original size:36 final size:38
Alignment explanation
Indices: 42198242--42198322 Score: 121
Period size: 36 Copynumber: 2.2 Consensus size: 38
42198232 TTCAATTTTA
42198242 ATAAAAATATAAAAAAAT-TAAAAATTTAT-AAAAATC
1 ATAAAAATATAAAAAAATGTAAAAATTTATGAAAAATC
* * *
42198278 GTAAAAATATAAAAAATTGTAAAATTTTATGAAAAATC
1 ATAAAAATATAAAAAAATGTAAAAATTTATGAAAAATC
42198316 ATAAAAA
1 ATAAAAA
42198323 AATTAACGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 16 0.41
37 10 0.26
38 13 0.33
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (38 bp):
ATAAAAATATAAAAAAATGTAAAAATTTATGAAAAATC
Found at i:42198301 original size:17 final size:17
Alignment explanation
Indices: 42198245--42198302 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
42198235 AATTTTAATA
*
42198245 AAAATATAAAAAAATT-A
1 AAAATAT-AAAAAATTGT
* *
42198262 AAAATTTATAAAAATCGT
1 AAAATATA-AAAAATTGT
42198280 AAAAATATAAAAAATTGT
1 -AAAATATAAAAAATTGT
42198298 AAAAT
1 AAAAT
42198303 TTTATGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 1 0.03
17 17 0.52
18 8 0.24
19 7 0.21
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAATATAAAAAATTGT
Found at i:42198488 original size:9 final size:9
Alignment explanation
Indices: 42198474--42198570 Score: 76
Period size: 9 Copynumber: 10.6 Consensus size: 9
42198464 AACTTATAAA
42198474 ATTTTATAT
1 ATTTTATAT
42198483 ATTTTATAT
1 ATTTTATAT
42198492 ATTTT-TAT
1 ATTTTATAT
42198500 ATTTCTATAT
1 ATTT-TATAT
42198510 ATTTTATA-
1 ATTTTATAT
*
42198518 ATTTT-TTT
1 ATTTTATAT
*
42198526 CGATTTTTATAAA
1 --A-TTTTAT-AT
*
42198539 ATTTTACAT
1 ATTTTATAT
*
42198548 ATTTTTTAT
1 ATTTTATAT
42198557 ATTTT-TACT
1 ATTTTATA-T
42198566 ATTTT
1 ATTTT
42198571 TGTATTTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
7 1 0.01
8 14 0.19
9 38 0.53
10 13 0.18
11 5 0.07
12 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (9 bp):
ATTTTATAT
Found at i:42198571 original size:18 final size:18
Alignment explanation
Indices: 42198475--42198580 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 18
42198465 ACTTATAAAA
42198475 TTTTATATATTTTA-TATAT
1 TTTTATAT-TTTTACTAT-T
* *
42198494 TTTTATATTTCTA-TATA
1 TTTTATATTTTTACTATT
* *
42198511 TTTTATAATTTTTTTCGATT
1 TTTTAT-A-TTTTTACTATT
* *
42198531 TTTATAAAATTTTACATATT
1 TTT-TATATTTTTAC-TATT
42198551 TTTTATATTTTTACTATT
1 TTTTATATTTTTACTATT
42198569 TTTGTAT-TTTTT
1 TTT-TATATTTTT
42198581 TCTAATTTTA
Statistics
Matches: 69, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
17 6 0.09
18 20 0.29
19 29 0.42
20 12 0.17
21 2 0.03
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTATATTTTTACTATT
Found at i:42198579 original size:9 final size:9
Alignment explanation
Indices: 42198475--42198581 Score: 60
Period size: 9 Copynumber: 11.4 Consensus size: 9
42198465 ACTTATAAAA
*
42198475 TTTTATATA
1 TTTTATATT
42198484 TTTTATATAT
1 TTTTATAT-T
42198494 TTTTATA-T
1 TTTTATATT
* *
42198502 TTCTATATA
1 TTTTATATT
42198511 TTTTATAATT
1 TTTTAT-ATT
42198521 TTTT-TCGATT
1 TTTTAT--ATT
*
42198531 TTTATAAAATT
1 TTT-T-ATATT
**
42198542 TTACATATT
1 TTTTATATT
42198551 TTTTATA-T
1 TTTTATATT
42198559 TTTTACTATT
1 TTTTA-TATT
42198569 TTTGTAT-TT
1 TTT-TATATT
42198578 TTTT
1 TTTT
42198582 CTAATTTTAA
Statistics
Matches: 76, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
8 14 0.18
9 30 0.39
10 24 0.32
11 8 0.11
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTATATT
Found at i:42198589 original size:18 final size:19
Alignment explanation
Indices: 42198548--42198589 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
42198538 AATTTTACAT
*
42198548 ATTTTTTATATTTTTACTA
1 ATTTTGTATATTTTTACTA
* *
42198567 TTTTTGTAT-TTTTTTCTA
1 ATTTTGTATATTTTTACTA
42198585 ATTTT
1 ATTTT
42198590 AATAAATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (19 bp):
ATTTTGTATATTTTTACTA
Found at i:42198678 original size:21 final size:20
Alignment explanation
Indices: 42198646--42198687 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
42198636 TATAGCTTTT
*
42198646 ATTTATTTTAATTTTTTATA
1 ATTTATTTTAATTTTTAATA
*
42198666 ATTTTTTTCTAATTTTTAATA
1 ATTTATTT-TAATTTTTAATA
42198687 A
1 A
42198688 AAGTAGGGGC
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:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTATTTTAATTTTTAATA
Found at i:42207281 original size:11 final size:11
Alignment explanation
Indices: 42207265--42207289 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42207255 ATTAATCATT
42207265 TCTCAATTTCC
1 TCTCAATTTCC
42207276 TCTCAATTTCC
1 TCTCAATTTCC
42207287 TCT
1 TCT
42207290 TAAATTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:42207300 original size:11 final size:12
Alignment explanation
Indices: 42207269--42207305 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
42207259 ATCATTTCTC
*
42207269 AATTTCCTC-TC
1 AATTTCCTCTTA
42207280 AATTTCCTCTTA
1 AATTTCCTCTTA
42207292 AATTT-CTCTTA
1 AATTTCCTCTTA
42207303 AAT
1 AAT
42207306 CCCTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTTCCTCTTA
Found at i:42209627 original size:49 final size:49
Alignment explanation
Indices: 42209574--42209691 Score: 200
Period size: 49 Copynumber: 2.4 Consensus size: 49
42209564 TATATTAATG
* *
42209574 TAATAAAAAACGAAATAGTTTAATTTGAATATTTTGATATTATTTGATA
1 TAATAAAATACAAAATAGTTTAATTTGAATATTTTGATATTATTTGATA
* *
42209623 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATG
1 TAATAAAATACAAAATAGTTTAATTTGAATATTTTGATATTATTTGATA
42209672 TAATAAAATACAAAATAGTT
1 TAATAAAATACAAAATAGTT
42209692 AATATTCTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (49 bp):
TAATAAAATACAAAATAGTTTAATTTGAATATTTTGATATTATTTGATA
Found at i:42213012 original size:125 final size:125
Alignment explanation
Indices: 42212790--42213202 Score: 628
Period size: 125 Copynumber: 3.3 Consensus size: 125
42212780 CCCACACATG
* * * **
42212790 CTACTGTAGCAAAAGTGCGTCCACGTGGGAGCTATTTAAAAAATTCTTCTGATAAAGCATCCTAT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
42212855 TTGAAGCGTTTTTTATACTATTTGATCAGAAACGTTAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTAAACTCGAAATTATTTTTTCAGGAC
* *
42212915 CTACTGTAGCAAAAGCGCGTCCATGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
*
42212980 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTAAACTCGAAATTATTTTTTCAGGAC
* * * * *
42213040 CTACTGTAGTAAAAGCACGTCCACGTGGGAGCGATTTCAGAAATTCTTTTTATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * *
42213105 TTGAAGTGTTTTTTATACTATTTGCTCAAAAACGTAAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTAAACTCGAAATTATTTTTTCAGGAC
* ** *
42213165 CTACTGTATCAAAAATGGGTCCACGTGGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
42213203 CTTAATAAAT
Statistics
Matches: 263, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 263 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTAAACTCGAAATTATTTTTTCAGGAC
Found at i:42216212 original size:17 final size:17
Alignment explanation
Indices: 42216190--42216225 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42216180 TAAAGTGTTC
42216190 TAATTACATCTTTAAAT
1 TAATTACATCTTTAAAT
*
42216207 TAATTACATTTTTAAAT
1 TAATTACATCTTTAAAT
42216224 TA
1 TA
42216226 TCGATGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTACATCTTTAAAT
Found at i:42216349 original size:18 final size:19
Alignment explanation
Indices: 42216313--42216348 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
42216303 GCATAATTTT
42216313 TAAAAGTAAAAGCTAAAAA
1 TAAAAGTAAAAGCTAAAAA
42216332 TAAAA-TAAAA-CTAAAAA
1 TAAAAGTAAAAGCTAAAAA
42216349 AAGGACTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 5 0.29
19 5 0.29
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (19 bp):
TAAAAGTAAAAGCTAAAAA
Found at i:42217032 original size:23 final size:23
Alignment explanation
Indices: 42216982--42217051 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
42216972 TCAAAATTTT
*
42216982 ATAATATATTTAAAAATAAAATAG
1 ATAATATATTTAAAAATAAAA-AA
42217006 ATAATATATTTAAAAATAAAAAA
1 ATAATATATTTAAAAATAAAAAA
* * *
42217029 ATAATTTTTTTAAAAATATAAAA
1 ATAATATATTTAAAAATAAAAAA
42217052 TTTCACATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 21 0.50
24 21 0.50
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (23 bp):
ATAATATATTTAAAAATAAAAAA
Found at i:42229369 original size:16 final size:18
Alignment explanation
Indices: 42229334--42229371 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42229324 ATCCTTATTT
*
42229334 AAATAAAATACAGTAGTA
1 AAATAAAATACAGAAGTA
42229352 AAATAAAATA-A-AAGTA
1 AAATAAAATACAGAAGTA
42229368 AAAT
1 AAAT
42229372 TCCTATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAGAAGTA
Found at i:42230828 original size:22 final size:24
Alignment explanation
Indices: 42230798--42230847 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42230788 TTAAAAGGTC
42230798 TTTTCTTTAGC-TG-TTGTTTTTT
1 TTTTCTTTAGCTTGATTGTTTTTT
* *
42230820 TTTTTTTTATCTTGATTGTTTTTT
1 TTTTCTTTAGCTTGATTGTTTTTT
42230844 TTTT
1 TTTT
42230848 AGGCCTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
23 2 0.08
24 13 0.54
ACGTcount: A:0.06, C:0.06, G:0.10, T:0.78
Consensus pattern (24 bp):
TTTTCTTTAGCTTGATTGTTTTTT
Found at i:42233015 original size:23 final size:25
Alignment explanation
Indices: 42232985--42233035 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
42232975 AAGTGATTAA
42232985 ATAATAA-TCCA-AACAAATTAAAT
1 ATAATAATTCCACAACAAATTAAAT
* *
42233008 ATAATAATTTCACAACAATTTAAAT
1 ATAATAATTCCACAACAAATTAAAT
42233033 ATA
1 ATA
42233036 CCTAATAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.29
24 3 0.12
25 14 0.58
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (25 bp):
ATAATAATTCCACAACAAATTAAAT
Found at i:42233906 original size:11 final size:11
Alignment explanation
Indices: 42233890--42233919 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42233880 GTAAAAAGGC
*
42233890 AGAAATAGCAG
1 AGAAATAGAAG
42233901 AGAAATAGAAG
1 AGAAATAGAAG
42233912 AGAAATAG
1 AGAAATAG
42233920 TAGCAAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.27, T:0.10
Consensus pattern (11 bp):
AGAAATAGAAG
Found at i:42234419 original size:33 final size:33
Alignment explanation
Indices: 42234361--42234466 Score: 158
Period size: 33 Copynumber: 3.2 Consensus size: 33
42234351 TAGAGTCGTT
* * * *
42234361 GCCGGAGACCGGCGGCCGTCATGACAGTGACTC
1 GCCGGAGACTGGTGGACGTCGTGACAGTGACTC
42234394 GCCGGAGACTGGTGGACGTCGTGACAGTGACTC
1 GCCGGAGACTGGTGGACGTCGTGACAGTGACTC
**
42234427 GCCGGAGACTGGTGGATATCGTGACAGTGACTC
1 GCCGGAGACTGGTGGACGTCGTGACAGTGACTC
42234460 GCCGGAG
1 GCCGGAG
42234467 CCAAGGCCGG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.19, C:0.26, G:0.39, T:0.16
Consensus pattern (33 bp):
GCCGGAGACTGGTGGACGTCGTGACAGTGACTC
Found at i:42243341 original size:23 final size:23
Alignment explanation
Indices: 42243297--42243341 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
42243287 TCTTATTTTG
* *
42243297 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
42243320 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
42243342 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:42243775 original size:22 final size:22
Alignment explanation
Indices: 42243750--42243796 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
42243740 CTTATTTTTT
42243750 TTTACATATTAAAATATGTATA
1 TTTACATATTAAAATATGTATA
* * * *
42243772 TTTATATATTTATATATTTATA
1 TTTACATATTAAAATATGTATA
42243794 TTT
1 TTT
42243797 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTACATATTAAAATATGTATA
Found at i:42243779 original size:8 final size:8
Alignment explanation
Indices: 42243768--42243794 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
42243758 TTAAAATATG
42243768 TATATTTA
1 TATATTTA
42243776 TATATTTA
1 TATATTTA
42243784 TATATTTA
1 TATATTTA
42243792 TAT
1 TAT
42243795 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATATTTA
Found at i:42243859 original size:23 final size:23
Alignment explanation
Indices: 42243817--42243860 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42243807 ATAATTCACA
* * *
42243817 TACATATATATTTTTCTTATATG
1 TACATATATATATATATTATATG
42243840 TACATATATATATATATTATA
1 TACATATATATATATATTATA
42243861 ATTTTTATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TACATATATATATATATTATATG
Found at i:42244045 original size:3 final size:3
Alignment explanation
Indices: 42244039--42244085 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
42244029 CATCATCATC
42244039 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
42244086 GGTTCTTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:42244918 original size:19 final size:20
Alignment explanation
Indices: 42244874--42244918 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
42244864 TGCCTTTTTT
*
42244874 TGCATT-CATTTCATTCATC
1 TGCATTACATTTCATTCATA
*
42244893 TGTATTACATTTCA-TCATA
1 TGCATTACATTTCATTCATA
42244912 TGCATTA
1 TGCATTA
42244919 AATTCTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TGCATTACATTTCATTCATA
Found at i:42251140 original size:16 final size:16
Alignment explanation
Indices: 42251119--42251149 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42251109 TGCCTCTTTC
42251119 ACCTCTTCATGTCATA
1 ACCTCTTCATGTCATA
*
42251135 ACCTCTTCTTGTCAT
1 ACCTCTTCATGTCAT
42251150 GACTTTTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.32, G:0.06, T:0.42
Consensus pattern (16 bp):
ACCTCTTCATGTCATA
Found at i:42253069 original size:44 final size:44
Alignment explanation
Indices: 42252992--42253306 Score: 220
Period size: 44 Copynumber: 7.2 Consensus size: 44
42252982 GCAGTGGAGT
* * * *
42252992 AGATACAAATCTTACCTCCCTGAAGTTGCAGTGGAACAAATTGA
1 AGATACAAATATGATCTCCCTGAAGTTGCAGTGGAACAGATTGA
* * * * *
42253036 AGATGCAAATATGATTTCCCTGAAATTGTAGTGGAACAGATTAA
1 AGATACAAATATGATCTCCCTGAAGTTGCAGTGGAACAGATTGA
* ** *
42253080 AGCTACAAATATGATCTCTTTGAAGTTGCAGTGGAGCAGATTGA
1 AGATACAAATATGATCTCCCTGAAGTTGCAGTGGAACAGATTGA
** * * * * * * *
42253124 AGA-ATTAATCTTATCTCTCTAAAGTTGCAGTAGAGCATATTGA
1 AGATACAAATATGATCTCCCTGAAGTTGCAGTGGAACAGATTGA
* * * * * * * *
42253167 AGCTACAAATCTAATCTCCATAAAGTTACAGTGGAGCAGATTAA
1 AGATACAAATATGATCTCCCTGAAGTTGCAGTGGAACAGATTGA
* * * * * *
42253211 AGTTACGAATCTTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAA
1 AGATACAAATATGATCTCCCTGAAGTTGCAGTGGAACAG-ATTGA
* * * * * *
42253255 AGCTATAAATCTCATTTCCCTGAAGTTCCAGTGGAACAGATTGA
1 AGATACAAATATGATCTCCCTGAAGTTGCAGTGGAACAGATTGA
*
42253299 AGCTACAA
1 AGATACAA
42253307 GTTACAAATC
Statistics
Matches: 216, Mismatches: 52, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
43 35 0.16
44 180 0.83
45 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (44 bp):
AGATACAAATATGATCTCCCTGAAGTTGCAGTGGAACAGATTGA
Found at i:42253069 original size:81 final size:81
Alignment explanation
Indices: 42252918--42253070 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 81
42252908 CGTCGTGACG
* * * *
42252918 AATCTTATCTCCCTGAAGTTGCAGTGGAAAAGATTAAAGTCACAAAATTTATCTCCTTGAAGTTG
1 AATCTTACCTCCCTGAAGTTGCAGTGGAAAAGATTAAAGTCACAAAATTGATCTCCCTGAAATTG
42252983 CAGTGGAGTAGATACA
66 CAGTGGAGTAGATACA
* * *
42252999 AATCTTACCTCCCTGAAGTTGCAGTGGAACAA-ATTGAAGAT-GC-AAATATGATTTCCCTGAAA
1 AATCTTACCTCCCTGAAGTTGCAGTGGAA-AAGATTAAAG-TCACAAAAT-TGATCTCCCTGAAA
*
42253061 TTGTAGTGGA
63 TTGCAGTGGA
42253071 ACAGATTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
80 4 0.07
81 54 0.89
82 3 0.05
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (81 bp):
AATCTTACCTCCCTGAAGTTGCAGTGGAAAAGATTAAAGTCACAAAATTGATCTCCCTGAAATTG
CAGTGGAGTAGATACA
Found at i:42253265 original size:88 final size:88
Alignment explanation
Indices: 42252995--42253395 Score: 295
Period size: 88 Copynumber: 4.5 Consensus size: 88
42252985 GTGGAGTAGA
* * * * * * * * * * * *
42252995 TACAAATCTTACCTCCCTGAAGTTGCAGTGGAACAAATTGAAGATGCAAATATGATTTCCCTGAA
1 TACAAATCTAATCTCCATGAAGTTACAGTGGAGCAGATTAAAGTTACAAATCTTATCTCCCTGAA
* * *
42253060 ATTGTAGTGGAACAGATTAAAGC
66 GTTGCAGTGGAGCAGATTAAAGC
* * ** * * * ** * *
42253083 TACAAATATGATCTCTTTGAAGTTGCAGTGGAGCAGATTGAAG-AATTAATCTTATCTCTCTAAA
1 TACAAATCTAATCTCCATGAAGTTACAGTGGAGCAGATTAAAGTTACAAATCTTATCTCCCTGAA
* * *
42253147 GTTGCAGTAGAGCATATTGAAGC
66 GTTGCAGTGGAGCAGATTAAAGC
* *
42253170 TACAAATCTAATCTCCATAAAGTTACAGTGGAGCAGATTAAAGTTACGAATCTTATCTCCCTGAA
1 TACAAATCTAATCTCCATGAAGTTACAGTGGAGCAGATTAAAGTTACAAATCTTATCTCCCTGAA
42253235 GTTGCAGTGGAGC-GAATTAAAGC
66 GTTGCAGTGGAGCAG-ATTAAAGC
* * * * * *
42253258 TATAAATCTCATTTCCCTGAAGTTCCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTAT-T
1 TACAAATCTAATCTCCATGAAGTTACAGTGGAGCAGA-T-----TA-AAGTTACAAATCTTATCT
* *
42253322 CCCTGAAGTTGCAGTGGAGTAGATTGAAGC
59 CCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * * * ** *
42253352 TACTAATCTTATATCCCTGAAGTTGTAGCGGAGCAGATTAAAGT
1 TACAAATCTAATCTCCATGAAGTTACAGTGGAGCAGATTAAAGT
42253396 AGCAATTCCT
Statistics
Matches: 248, Mismatches: 55, Indels: 21
0.77 0.17 0.06
Matches are distributed among these distances:
87 69 0.28
88 103 0.42
89 1 0.00
93 1 0.00
94 58 0.23
95 16 0.06
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (88 bp):
TACAAATCTAATCTCCATGAAGTTACAGTGGAGCAGATTAAAGTTACAAATCTTATCTCCCTGAA
GTTGCAGTGGAGCAGATTAAAGC
Found at i:42253389 original size:94 final size:95
Alignment explanation
Indices: 42253210--42253390 Score: 242
Period size: 94 Copynumber: 1.9 Consensus size: 95
42253200 GAGCAGATTA
* * *
42253210 AAGTTACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAGCTATAAATCTCATTTCCC
1 AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGAGAATTAAAGCTATAAATCTCATATCCC
*
42253275 TGAAGTTCCAGTGGAACAGATTGAAGCTAC
66 TGAAGTTCCAGCGGAACAGATTGAAGCTAC
* *
42253305 AAGTTACAAATCTTAT-TCCCTGAAGTTGCAGTGGAGTAG-ATTGAAGCTACT-AATCTTATATC
1 AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAG-AGAATTAAAGCTA-TAAATCTCATATC
** *
42253367 CCTGAAGTTGTAGCGGAGCAGATT
64 CCTGAAGTTCCAGCGGAACAGATT
42253391 AAAGTAGCAA
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
94 58 0.77
95 17 0.23
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (95 bp):
AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGAGAATTAAAGCTATAAATCTCATATCCC
TGAAGTTCCAGCGGAACAGATTGAAGCTAC
Found at i:42253409 original size:44 final size:44
Alignment explanation
Indices: 42253100--42253410 Score: 145
Period size: 44 Copynumber: 7.0 Consensus size: 44
42253090 ATGATCTCTT
* * * * * * *
42253100 TGAAGTTGCAGTGGAGCAGATTGAAG-AATTAATCTTATCTCTC
1 TGAAGTTGCAGCGGAGCAGATTAAAGCTACTAATCCTATATCCC
* ** * * *
42253143 TAAAGTTGCAGTAGAGCATATTGAAGCTACAAAT-CTA-ATCTCC
1 TGAAGTTGCAGCGGAGCAGATTAAAGCTACTAATCCTATATC-CC
* * * * * * *
42253186 ATAAAGTTACAGTGGAGCAGATTAAAGTTACGAATCTTATCTCCC
1 -TGAAGTTGCAGCGGAGCAGATTAAAGCTACTAATCCTATATCCC
* *
42253231 TGAAGTTGCAGTGGAGC-GAATTAAAGCTA-TAAAT-CTCATTTCCC
1 TGAAGTTGCAGCGGAGCAG-ATTAAAGCTACT-AATCCT-ATATCCC
* * * * *
42253275 TGAAGTTCCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTAT-TCCC
1 TGAAGTTGCAGCGGAGCAGATTAAAGCTAC----T---AATCCTATATCCC
* * * *
42253325 TGAAGTTGCAGTGGAGTAGATTGAAGCTACTAATCTTATATCCC
1 TGAAGTTGCAGCGGAGCAGATTAAAGCTACTAATCCTATATCCC
*
42253369 TGAAGTTGTAGCGGAGCAGATTAAAG-TAGC-AATTCCTATATC
1 TGAAGTTGCAGCGGAGCAGATTAAAGCTA-CTAA-TCCTATATC
42253411 TCTAAAGATG
Statistics
Matches: 213, Mismatches: 35, Indels: 39
0.74 0.12 0.14
Matches are distributed among these distances:
42 2 0.01
43 40 0.19
44 124 0.58
45 5 0.02
46 3 0.01
49 1 0.00
50 31 0.15
51 6 0.03
52 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
TGAAGTTGCAGCGGAGCAGATTAAAGCTACTAATCCTATATCCC
Found at i:42254910 original size:4 final size:4
Alignment explanation
Indices: 42254901--42254934 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
42254891 TTACAAGCTG
* *
42254901 TTTA TTTA TTTA TTTA TCTA TTCA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
42254935 ACCTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:42254994 original size:14 final size:16
Alignment explanation
Indices: 42254971--42255011 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
42254961 TTAATTACTC
42254971 TTTTATTTATG-CATT-
1 TTTTA-TTATGTCATTA
42254986 TTTTATTATTGTCATTA
1 TTTTATTA-TGTCATTA
42255003 TTTTATTAT
1 TTTTATTAT
42255012 TATTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 7 0.30
16 5 0.22
17 8 0.35
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTATTATGTCATTA
Found at i:42255056 original size:24 final size:24
Alignment explanation
Indices: 42255006--42255057 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
42254996 GTCATTATTT
* *
42255006 TATTATTATTTTTTGTTCTTGTTA
1 TATTATTATTTCTTGTTATTGTTA
*
42255030 TATTATTATTTCTT-TTATTTTTGA
1 TATTATTATTTCTTGTTATTGTT-A
42255054 TATT
1 TATT
42255058 TTCATGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.71
Consensus pattern (24 bp):
TATTATTATTTCTTGTTATTGTTA
Found at i:42263190 original size:14 final size:13
Alignment explanation
Indices: 42263171--42263207 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
42263161 CGGCCCGTCC
42263171 ATATTAATTTTTT
1 ATATTAATTTTTT
42263184 AATATT-ATTTTTT
1 -ATATTAATTTTTT
42263197 ATA-TAATTTTT
1 ATATTAATTTTT
42263208 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.05
12 9 0.41
13 7 0.32
14 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATATTAATTTTTT
Found at i:42264060 original size:22 final size:22
Alignment explanation
Indices: 42264032--42264184 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
42264022 TTTATTGTTC
*
42264032 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
42264054 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
42264076 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
42264098 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
42264120 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
42264142 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
42264164 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
42264185 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:42265856 original size:23 final size:23
Alignment explanation
Indices: 42265826--42265873 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
42265816 AACAATAAGT
42265826 ATGATTTATCATCGTTGAAGCAA
1 ATGATTTATCATCGTTGAAGCAA
42265849 ATGATTTATCATCGTTGAAGCAA
1 ATGATTTATCATCGTTGAAGCAA
42265872 AT
1 AT
42265874 TATCTCTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (23 bp):
ATGATTTATCATCGTTGAAGCAA
Found at i:42268268 original size:59 final size:57
Alignment explanation
Indices: 42268171--42268304 Score: 173
Period size: 59 Copynumber: 2.3 Consensus size: 57
42268161 AGATCAGGGG
* *
42268171 CTAACTTGGATAAAAAAATTCAGACCCTAACGTGGGAACAATTGCCAAGTTTA-AGGA
1 CTAACTTGGATAAAAAAATCCAGACCCTAACGTGGGAACAACTGCCAAGTTTAGA-GA
* *
42268228 GTAACTTGGATAAAATAAAGTCCA-AGCCCTAATGTGGGAACAACTGCCAAGTTTAGAGA
1 CTAACTTGGATAAAA-AAA-TCCAGA-CCCTAACGTGGGAACAACTGCCAAGTTTAGAGA
*
42268287 CTAACTTGGAAAAAAAAA
1 CTAACTTGGATAAAAAAA
42268305 ATTCAAACTG
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
57 14 0.21
58 7 0.10
59 45 0.67
60 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (57 bp):
CTAACTTGGATAAAAAAATCCAGACCCTAACGTGGGAACAACTGCCAAGTTTAGAGA
Found at i:42269377 original size:32 final size:32
Alignment explanation
Indices: 42269341--42269446 Score: 108
Period size: 37 Copynumber: 3.2 Consensus size: 32
42269331 TAATATTTTT
*
42269341 AATATAATTATTTTTATATTATATTATATTAAA
1 AATATAATTATTTTTATATTAAATTATATT-AA
*
42269374 ATATGATTAAGTTATTTTTTTATTAAATTATATTTTAA
1 A-AT-A-TAA-TTATTTTTATATTAAATTATA--TTAA
*
42269412 AAT-TAAATA-TTTTATATTAAATTATATTAA
1 AATATAATTATTTTTATATTAAATTATATTAA
42269442 AATAT
1 AATAT
42269447 TTCAAATATT
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
30 7 0.11
31 1 0.02
32 16 0.26
33 3 0.05
34 5 0.08
35 1 0.02
36 3 0.05
37 21 0.34
38 3 0.05
39 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (32 bp):
AATATAATTATTTTTATATTAAATTATATTAA
Found at i:42269432 original size:14 final size:15
Alignment explanation
Indices: 42269403--42269444 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
42269393 TTATTAAATT
42269403 ATATTTTAAAATTAA
1 ATATTTTAAAATTAA
*
42269418 ATATTTT-ATATTAA
1 ATATTTTAAAATTAA
*
42269432 ATTATATTAAAAT
1 A-TATTTTAAAAT
42269445 ATTTCAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.32
15 12 0.55
16 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTTAAAATTAA
Found at i:42275029 original size:26 final size:27
Alignment explanation
Indices: 42275000--42275051 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
42274990 GTCAATAAAT
42275000 AATTT-AAA-AATTATAAAAAAGTTCAA
1 AATTTAAAATAATTAT-AAAAAGTTCAA
42275026 AATTTAAAATAATTATAAAAAGTTCA
1 AATTTAAAATAATTATAAAAAGTTCA
42275052 TAAAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.21
27 13 0.54
28 6 0.25
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (27 bp):
AATTTAAAATAATTATAAAAAGTTCAA
Found at i:42278932 original size:125 final size:126
Alignment explanation
Indices: 42278708--42279241 Score: 745
Period size: 125 Copynumber: 4.3 Consensus size: 126
42278698 ATTTTTGCAG
* *
42278708 TCGCGCCCACGAGTACGCGCTTTTGCTACAGTAGGTCCTGGAA-AAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * **
42278772 TCTGAGCAAATAGTATAAAAAACACTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAAAAGAATTTGTGAAA
* * *
42278833 TCGCGCCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* *** * * * *
42278898 TTTGAGCAAATAGTAT-AAATTTGCTTCTACCAGGATACTTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAAAAGAATTTGTGAAA
* * *
42278958 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-AAAAAAATTATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * * * *
42279022 TCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTATTTGAAAAGAATTTTTAAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAAAAGAATTTGTGAAA
* * *
42279083 TTGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * *
42279148 TCTGAGCTAATAGTAT-AAAATCGCTT-ATACCAGGATGCTTTATGAAAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCA-ACCAGGATGCTATATGAAAAGAATTTGTGAAA
42279208 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
42279242 CATGTTTGGG
Statistics
Matches: 356, Mismatches: 49, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
124 38 0.11
125 245 0.69
126 73 0.21
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (126 bp):
TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAAAAGAATTTGTGAAA
Found at i:42279162 original size:250 final size:250
Alignment explanation
Indices: 42278708--42279241 Score: 879
Period size: 250 Copynumber: 2.1 Consensus size: 250
42278698 ATTTTTGCAG
* * **
42278708 TCGCGCCCACGAGTACGCGCTTTTGCTACAGTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTAAAAAAATAATTTCGAGTTGACGTTT
** *
42278773 CTGAGCAAATAGTATAAAAAACACTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCG
66 CTGAGCAAATAGTATAAAAAACACTTCAAGCAGGATGCTATATGAAAAGAATTTGTAAAATCGCG
*
42278838 CCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTTTGA
131 CCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
* * * *
42278903 GCAAATAGTATAAATTTGCTTCTACCAGGATACTTTATGAGAAGAATTTGTGAAA
196 GCAAATAGTATAAAATCGCTTATACCAGGATACTTTATGAAAAGAATTTGTGAAA
*
42278958 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTAAAAAAATTATTTCGAGTTGACGTTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTAAAAAAATAATTTCGAGTTGACGTTT
** * * *
42279023 CTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTATTTGAAAAGAATTTTTAAAATTGCG
66 CTGAGCAAATAGTATAAAAAACACTTCAAGCAGGATGCTATATGAAAAGAATTTGTAAAATCGCG
*
42279088 CCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
131 CCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
* *
42279153 GCTAATAGTATAAAATCGCTTATACCAGGATGCTTTATGAAAAGAATTTGTGAAA
196 GCAAATAGTATAAAATCGCTTATACCAGGATACTTTATGAAAAGAATTTGTGAAA
42279208 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
42279242 CATGTTTGGG
Statistics
Matches: 263, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
250 263 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (250 bp):
TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTAAAAAAATAATTTCGAGTTGACGTTT
CTGAGCAAATAGTATAAAAAACACTTCAAGCAGGATGCTATATGAAAAGAATTTGTAAAATCGCG
CCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
GCAAATAGTATAAAATCGCTTATACCAGGATACTTTATGAAAAGAATTTGTGAAA
Found at i:42282473 original size:22 final size:22
Alignment explanation
Indices: 42282455--42283763 Score: 438
Period size: 22 Copynumber: 60.6 Consensus size: 22
42282445 TGTTTTAAGA
*
42282455 TTTAGGGGTTTTAAGTTTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42282477 TTTAAGGTTTTTAAGTTTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42282499 TTT-GTGGCTTTTAAGTTTAGGG
1 TTTAG-GGTTTTTAAGTTTAGGG
*** *
42282521 TTTATAATTTTTAAGTTTAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
* *
42282543 TTTATGGTTTTTAAGTTAAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
* *
42282565 -CTA-GGTTTTTAAGGTTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42282585 TTTAGGTTTTTTTAAGTTTAGGG
1 TTTAGG-GTTTTTAAGTTTAGGG
* *
42282608 TTTAGGGTTTTTAGGTTTAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
* * *
42282630 CTT-GTGTTTTTAAGTTAAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
* **
42282651 TTAGAATTAGGGTTATGGTTTTAAAGTTAAGTC
1 -T----TTAGGG---T--TTTT-AAGTTTAGGG
* *
42282684 TTTAGGGTTTGT-GGTTTTTAAGTTTAGG
1 TTTAGGGTTTTTAAG--TTT-AG----GG
42282712 ATTTAGGG-TTTTAAGTTTAGGG
1 -TTTAGGGTTTTTAAGTTTAGGG
**
42282734 TTTAAAG--TTTAGAGTTTTTA-GG
1 TTTAGGGTTTTTA-AG--TTTAGGG
* * *
42282756 TTTAAGG--TTT--G---GGGT
1 TTTAGGGTTTTTAAGTTTAGGG
* * *
42282771 TTG-GGGTTTTTAAGTTAATGG
1 TTTAGGGTTTTTAAGTTTAGGG
* * *
42282792 TTAGA-GTTTTTTAGGTTTAGGG
1 TT-TAGGGTTTTTAAGTTTAGGG
* * *
42282814 TTTAAGGTTTTTAGGTTTAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
* *
42282836 TTTAGAGTTTTTAAGTTTAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
* *
42282858 TTTAGGGTTTTTAGGTTTAGAG
1 TTTAGGGTTTTTAAGTTTAGGG
* *
42282880 TTT-GGTTTTTTTAAGTTAAGGG
1 TTTAGG-GTTTTTAAGTTTAGGG
*
42282902 -TTAGCGTTTTTAA-TTTAAGGG
1 TTTAGGGTTTTTAAGTTT-AGGG
* *
42282923 -TTAGTG-TTTTAAGTTAAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42282943 -TTAGGG---TT-AGTGTTAGTGT
1 TTTAGGGTTTTTAAGT-TTAG-GG
** *
42282962 TTTAAAG---TTAAGATTTTAGTG
1 TTTAGGGTTTTTAAG--TTTAGGG
*
42282983 TTTAGGG-TTTTAAGTTTAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
* *
42283004 -TTAGGGGTTTTATGTTTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42283025 TTT-GTGGTTTTTAAGTTAAGGG
1 TTTAG-GGTTTTTAAGTTTAGGG
*
42283047 -TTAGGG-TTTTAAGTTTAGTG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42283067 TTT--GGTGTTTTAGGTTTAGGG
1 TTTAGGGT-TTTTAAGTTTAGGG
* *
42283088 TTTAGGGTTTTTATGTTTAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
42283110 TTT-GGTGTTTTTAAGTTTAGGG
1 TTTAGG-GTTTTTAAGTTTAGGG
* * *
42283132 TTTATGG-TTTTAGGTTTAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
* * *
42283153 CTTGGGGTTTTTAAGTTAAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
**
42283175 -TTAGCATTTTTAA-TTTAAGGG
1 TTTAGGGTTTTTAAGTTT-AGGG
* *
42283196 -TTAGGGTTTTTAAGTTAAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
* * *
42283217 -TTA-GG--ATTAGGGTTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
*** *
42283235 TTTTTAG--TTTAAGGGTTTATGG
1 TTTAGGGTTTTTAA--GTTTAGGG
** * **
42283257 TTT---GTCAATTAAATTATA-CA
1 TTTAGGGT-TTTTAAGTT-TAGGG
* * * **
42283277 TTTA---ATTATAAATTATA-AA
1 TTTAGGGTTTTTAAGTT-TAGGG
* * * *
42283296 ATTA---TATTTAACTTAAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
* * *
42283315 -TTAGGGTTTTAAAGTTAAGGT
1 TTTAGGGTTTTTAAGTTTAGGG
*
42283336 TTTTGGG--TTTAAGGTTTTTAAGTTTAGGG
1 TTTAGGGTTTTTAA-G--TTT-AG-----GG
* *
42283365 TTTAGTGTTTTTAAGTTTATGG
1 TTTAGGGTTTTTAAGTTTAGGG
42283387 TTT-GTGGTTTTTAAGTTTAGGG
1 TTTAG-GGTTTTTAAGTTTAGGG
** *
42283409 TTTATAGTTTTT-AGATTTAAGG
1 TTTAGGGTTTTTAAG-TTTAGGG
* *
42283431 TTTAGGGTTTTTAAGTTAAGAG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42283453 -TTAGGGTTTTTAGGTTTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42283474 TTT-GGGTTTTTAAGTTTAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42283495 TTTAGGG-TTTTAAGGTTTAGAG
1 TTTAGGGTTTTTAA-GTTTAGGG
*
42283517 -TTAGGG-TTTTAAGTTAAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
** * *
42283537 -TTA--G-AATTAGGATTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
** * *
42283555 CTTTAAAG--TTAAAGTTTTAAGG
1 -TTTAGGGTTTTTAAG-TTTAGGG
* *
42283577 TTTGGGGTTTTTTAAGTTTAGAG
1 TTTAGGG-TTTTTAAGTTTAGGG
*
42283600 TTTAGGGTTTTTAGGTTTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
* *
42283622 TTTATGGTTTTTAAGTTTAGAG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42283644 TTTAGTGTTTTTAAGTTTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
* *
42283666 TTT-GGGTTTTTAAGTTAAAGG
1 TTTAGGGTTTTTAAGTTTAGGG
* *
42283687 -TTAGGGTTTTTAGGTTTAGAG
1 TTTAGGGTTTTTAAGTTTAGGG
42283708 TTT-GGGTTTTTTAAGTTTAGGG
1 TTTAGGG-TTTTTAAGTTTAGGG
* *
42283730 CTTAGGGTTTTTAGGTTTAGGG
1 TTTAGGGTTTTTAAGTTTAGGG
*
42283752 -TTAAGGTTTTTA
1 TTTAGGGTTTTTA
42283764 TGTTAATGGT
Statistics
Matches: 970, Mismatches: 207, Indels: 221
0.69 0.15 0.16
Matches are distributed among these distances:
14 2 0.00
15 3 0.00
16 3 0.00
17 3 0.00
18 28 0.03
19 26 0.03
20 91 0.09
21 269 0.28
22 422 0.44
23 57 0.06
24 9 0.01
25 1 0.00
26 4 0.00
27 6 0.01
28 12 0.01
29 14 0.01
30 2 0.00
31 5 0.01
32 5 0.01
33 8 0.01
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (22 bp):
TTTAGGGTTTTTAAGTTTAGGG
Found at i:42282475 original size:15 final size:16
Alignment explanation
Indices: 42282446--42282476 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42282436 TAAAGTTAAT
42282446 GTTTTAAGATTTAGGG
1 GTTTTAAGATTTAGGG
42282462 GTTTTAAG-TTTAGGG
1 GTTTTAAGATTTAGGG
42282477 TTTAAGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (16 bp):
GTTTTAAGATTTAGGG
Found at i:42282486 original size:14 final size:15
Alignment explanation
Indices: 42282420--42282486 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 15
42282410 TATATTTAAC
*
42282420 TTAAGGGTTAGGGTT
1 TTAAGGTTTAGGGTT
* **
42282435 TTAAAG-TTAATGTT
1 TTAAGGTTTAGGGTT
*
42282449 TTAAGATTTAGGGGTT
1 TTAAGGTTTA-GGGTT
42282465 TTAA-GTTTAGGG-T
1 TTAAGGTTTAGGGTT
42282478 TTAAGGTTT
1 TTAAGGTTT
42282487 TTAAGTTTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
13 5 0.12
14 17 0.41
15 12 0.29
16 7 0.17
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.46
Consensus pattern (15 bp):
TTAAGGTTTAGGGTT
Found at i:42282706 original size:29 final size:29
Alignment explanation
Indices: 42282657--42282722 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
42282647 AGGGTTAGAA
**
42282657 TTAGGG-TTATGGTTTTAAAGTTAAGTCT
1 TTAGGGTTTATGGTTTTAAAGTTAAGGAT
* * *
42282685 TTAGGGTTTGTGGTTTTTAAGTTTAGGAT
1 TTAGGGTTTATGGTTTTAAAGTTAAGGAT
42282714 TTAGGGTTT
1 TTAGGGTTT
42282723 TAAGTTTAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.50
Consensus pattern (29 bp):
TTAGGGTTTATGGTTTTAAAGTTAAGGAT
Found at i:42282730 original size:14 final size:14
Alignment explanation
Indices: 42282713--42282765 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
42282703 AAGTTTAGGA
42282713 TTTAGGGTTTTAAG
1 TTTAGGGTTTTAAG
*
42282727 TTTAGGGTTTAAAG
1 TTTAGGGTTTTAAG
* *
42282741 TTTAGAGTTTTTAGG
1 TTTAG-GGTTTTAAG
*
42282756 TTTAAGGTTT
1 TTTAGGGTTT
42282766 GGGGTTTGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 22 0.69
15 10 0.31
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (14 bp):
TTTAGGGTTTTAAG
Found at i:42282877 original size:15 final size:15
Alignment explanation
Indices: 42282807--42282876 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
42282797 GTTTTTTAGG
42282807 TTTAGGGTTTAAGGTT
1 TTTA-GGTTTAAGGTT
42282823 TTTAGGTTTAAGGTT
1 TTTAGGTTTAAGGTT
** *
42282838 TAGAGTTTTTAA-G-T
1 TTTAG-GTTTAAGGTT
* *
42282852 TTAAGGTTTAGGGTT
1 TTTAGGTTTAAGGTT
42282867 TTTAGGTTTA
1 TTTAGGTTTA
42282877 GAGTTTGGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 4 0.09
14 5 0.12
15 25 0.58
16 9 0.21
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.51
Consensus pattern (15 bp):
TTTAGGTTTAAGGTT
Found at i:42283221 original size:21 final size:21
Alignment explanation
Indices: 42282984--42283763 Score: 270
Period size: 21 Copynumber: 36.6 Consensus size: 21
42282974 ATTTTAGTGT
*
42282984 TTAGGG-TTTTAAGTTTAAGG
1 TTAGGGTTTTTAAGTTTAGGG
* *
42283004 TTAGGGGTTTTATGTTTAGGG
1 TTAGGGTTTTTAAGTTTAGGG
* *
42283025 TTTGTGGTTTTTAAGTTAAGGG
1 TTAG-GGTTTTTAAGTTTAGGG
*
42283047 TTAGGG-TTTTAAGTTTAGTG
1 TTAGGGTTTTTAAGTTTAGGG
* *
42283067 TT-TGGTGTTTTAGGTTTAGGG
1 TTAGGGT-TTTTAAGTTTAGGG
* *
42283088 TTTAGGGTTTTTATGTTTAAGG
1 -TTAGGGTTTTTAAGTTTAGGG
*
42283110 TTTGGTGTTTTTAAGTTTAGGG
1 TTAGG-GTTTTTAAGTTTAGGG
* * *
42283132 TTTATGG-TTTTAGGTTTAAGGC
1 -TTAGGGTTTTTAAGTTT-AGGG
* *
42283154 TTGGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTTAGGG
**
42283175 TTAGCATTTTTAA-TTTAAGGG
1 TTAGGGTTTTTAAGTTT-AGGG
* *
42283196 TTAGGGTTTTTAAGTTAAAGG
1 TTAGGGTTTTTAAGTTTAGGG
* * *
42283217 TTA-GG--ATTAGGGTTAGGG
1 TTAGGGTTTTTAAGTTTAGGG
42283235 TT------TTT-AGTTTAAGGG
1 TTAGGGTTTTTAAGTTT-AGGG
* * ***
42283250 TTTATGGTTTGTCAA--TTAAAT
1 -TTAGGGTTT-TTAAGTTTAGGG
*** * ***
42283271 TATACATTTAATTATAAATTATAAAA
1 T-TAGGGTT--TT-TAAGTT-TAGGG
* * *
42283297 TTA---TATTTAACTTAAGGG
1 TTAGGGTTTTTAAGTTTAGGG
* * *
42283315 TTAGGGTTTTAAAGTTAAGGTT
1 TTAGGGTTTTTAAGTTTAGG-G
* * *
42283337 TTTGGG--TTTAAGGTTTTTAAGT
1 TTAGGGTTTTTAA-G--TTTAGGG
*
42283359 TTAGGGTTTAGTGTTTTTAAGTTTATGG
1 TTA-GG----GT-TTTT-AAGTTTAGGG
*
42283387 TTTGTGGTTTTTAAGTTTAGGG
1 TTAG-GGTTTTTAAGTTTAGGG
** *
42283409 TTTATAGTTTTT-AGATTTAAGGT
1 -TTAGGGTTTTTAAG-TTT-AGGG
* *
42283432 TTAGGGTTTTTAAGTTAAGAG
1 TTAGGGTTTTTAAGTTTAGGG
*
42283453 TTAGGGTTTTTAGGTTTAGGG
1 TTAGGGTTTTTAAGTTTAGGG
* *
42283474 TTTGGGTTTTTAAGTTTAAGGT
1 TTAGGGTTTTTAAGTTT-AGGG
*
42283496 TTAGGG-TTTTAAGGTTTAGAG
1 TTAGGGTTTTTAA-GTTTAGGG
*
42283517 TTAGGG-TTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTTAGGG
** * *
42283537 TTA--G-AATTAGGATTAGGG
1 TTAGGGTTTTTAAGTTTAGGG
** * *
42283555 CTTTAAAG--TTAAAGTTTTAAGGT
1 --TTAGGGTTTTTAAG-TTT-AGGG
* *
42283578 TTGGGGTTTTTTAAGTTTAGAGT
1 TTAGGG-TTTTTAAGTTTAG-GG
*
42283601 TTAGGGTTTTTAGGTTTAGGG
1 TTAGGGTTTTTAAGTTTAGGG
* *
42283622 TTTATGGTTTTTAAGTTTAGAGT
1 -TTAGGGTTTTTAAGTTTAG-GG
*
42283645 TTAGTGTTTTTAAGTTTAGGG
1 TTAGGGTTTTTAAGTTTAGGG
* * *
42283666 TTTGGGTTTTTAAGTTAAAGG
1 TTAGGGTTTTTAAGTTTAGGG
* *
42283687 TTAGGGTTTTTAGGTTTAGAG
1 TTAGGGTTTTTAAGTTTAGGG
*
42283708 TTTGGGTTTTTTAAGTTTAGGG
1 TTAGGG-TTTTTAAGTTTAGGG
*
42283730 CTTAGGGTTTTTAGGTTTAGGG
1 -TTAGGGTTTTTAAGTTTAGGG
*
42283752 TTAAGGTTTTTA
1 TTAGGGTTTTTA
42283764 TGTTAATGGT
Statistics
Matches: 565, Mismatches: 129, Indels: 131
0.68 0.16 0.16
Matches are distributed among these distances:
14 3 0.01
15 6 0.01
16 2 0.00
18 24 0.04
19 7 0.01
20 43 0.08
21 211 0.37
22 191 0.34
23 46 0.08
24 8 0.01
25 3 0.01
26 5 0.01
27 2 0.00
28 8 0.01
30 4 0.01
31 2 0.00
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (21 bp):
TTAGGGTTTTTAAGTTTAGGG
Found at i:42283360 original size:15 final size:15
Alignment explanation
Indices: 42283319--42283367 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
42283309 TAAGGGTTAG
*
42283319 GGTTTTAAAG-TTAA
1 GGTTTTTAAGTTTAA
**
42283333 GGTTTTTGGGTTTAA
1 GGTTTTTAAGTTTAA
*
42283348 GGTTTTTAAGTTTAG
1 GGTTTTTAAGTTTAA
42283363 GGTTT
1 GGTTT
42283368 AGTGTTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 7 0.25
15 21 0.75
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (15 bp):
GGTTTTTAAGTTTAA
Found at i:42283374 original size:29 final size:29
Alignment explanation
Indices: 42283311--42283374 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
42283301 ATTTAACTTA
* *
42283311 AGGG-TTAGGGTTTTAAAGTTAAGGTTTT
1 AGGGTTTAAGGTTTTAAAGTTAAGGGTTT
* * *
42283339 TGGGTTTAAGGTTTTTAAGTTTAGGGTTT
1 AGGGTTTAAGGTTTTAAAGTTAAGGGTTT
*
42283368 AGTGTTT
1 AGGGTTT
42283375 TTAAGTTTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.48
Consensus pattern (29 bp):
AGGGTTTAAGGTTTTAAAGTTAAGGGTTT
Found at i:42283619 original size:15 final size:16
Alignment explanation
Indices: 42283593--42283668 Score: 63
Period size: 15 Copynumber: 5.1 Consensus size: 16
42283583 GTTTTTTAAG
42283593 TTTAGAGTTTAGGGTT
1 TTTAGAGTTTAGGGTT
42283609 TTTAG-GTTTAGGGTT
1 TTTAGAGTTTAGGGTT
* * ** *
42283624 TATGGTTTTTA-AG--
1 TTTAGAGTTTAGGGTT
*
42283637 TTTAGAGTTTAGTGTT
1 TTTAGAGTTTAGGGTT
42283653 TTTA-AGTTTAGGGTT
1 TTTAGAGTTTAGGGTT
42283668 T
1 T
42283669 GGGTTTTTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
13 7 0.15
14 1 0.02
15 25 0.54
16 13 0.28
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (16 bp):
TTTAGAGTTTAGGGTT
Found at i:42283637 original size:235 final size:235
Alignment explanation
Indices: 42283315--42283853 Score: 764
Period size: 235 Copynumber: 2.3 Consensus size: 235
42283305 AACTTAAGGG
** * * *
42283315 TTAGGGTTTTAAAGTTAAGGTTTTTGGGTTTAAGGTTTTTAAGTTTAGGGTTTAGTGTTTTTAAG
1 TTAGGGTTTTAAAGTTAAGGTTTTAAGGTTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAGG
* * *
42283380 TTTATGGTTTGTGGTTTTTAAGTTTAGGGTTTA-TAGTTTTT-AGATTTAAGGTTTAGGGTTTTT
66 TTTAGGGTTTATGGTTTTTAAGTTTAGAGTTTAGT-GTTTTTAAG-TTTAAGGTTT-GGGTTTTT
* *
42283443 AAGTT-AAGAGTTAGGGTTTTTAGGTTTAGGGTTTGGG-TTTTTAAGTTTAAGGTTTAGGGTTTT
128 AAGTTAAAG-GTTAGGGTTTTTAGGTTTAGAGTTTGGGTTTTTTAAGTTTAAGGCTTAGGGTTTT
42283506 AAGGTTTAGAGTT-AGGGTTTTAAGTTAAGGGTTAGAATTAGGA
192 AAGGTTTAGAGTTAAGGGTTTTAAGTTAAGGGTTAGAATTAGGA
* * * *
42283549 TTAGGGCTTTAAAGTTAAAGTTTTAAGGTTTGGGGTTTTTTAAGTTTAGAGTTTAGGGTTTTTAG
1 TTAGGGTTTTAAAGTTAAGGTTTTAAGGTTTAGGG-TTTTTAAGTTTAGGGTTTAGGGTTTTTAG
*
42283614 GTTTAGGGTTTATGGTTTTTAAGTTTAGAGTTTAGTGTTTTTAAGTTTAGGGTTTGGGTTTTTAA
65 GTTTAGGGTTTATGGTTTTTAAGTTTAGAGTTTAGTGTTTTTAAGTTTAAGGTTTGGGTTTTTAA
* *
42283679 GTTAAAGGTTAGGGTTTTTAGGTTTAGAGTTTGGGTTTTTTAAGTTTAGGGCTTAGGGTTTTTAG
130 GTTAAAGGTTAGGGTTTTTAGGTTTAGAGTTTGGGTTTTTTAAGTTTAAGGCTTAGGGTTTTAAG
* * * * *
42283744 GTTTAGGGTTAAGGTTTTTATGTTAATGGTTAGAATTAGGG
195 GTTTAGAGTTAAGGGTTTTAAGTTAAGGGTTAGAATTAGGA
* * * *
42283785 TTAGGATTTTAAAGTTAAGGTTATATGGTTTAGGGTTTTTAGGTTTAGGGTTTAGGGTTTTTAGG
1 TTAGGGTTTTAAAGTTAAGGTTTTAAGGTTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAGG
42283850 TTTA
66 TTTA
42283854 AAGTTTTTAA
Statistics
Matches: 269, Mismatches: 30, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
234 69 0.26
235 142 0.53
236 58 0.22
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (235 bp):
TTAGGGTTTTAAAGTTAAGGTTTTAAGGTTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAGG
TTTAGGGTTTATGGTTTTTAAGTTTAGAGTTTAGTGTTTTTAAGTTTAAGGTTTGGGTTTTTAAG
TTAAAGGTTAGGGTTTTTAGGTTTAGAGTTTGGGTTTTTTAAGTTTAAGGCTTAGGGTTTTAAGG
TTTAGAGTTAAGGGTTTTAAGTTAAGGGTTAGAATTAGGA
Found at i:42283769 original size:86 final size:86
Alignment explanation
Indices: 42283585--42283776 Score: 251
Period size: 86 Copynumber: 2.2 Consensus size: 86
42283575 GGTTTGGGGT
* * * * * *
42283585 TTTTTAAGTTTAGAGTTTAGGGTTTTTAGGTTTAGGGTTTATGGTTTTTAAGTTTAGAGTTTAGT
1 TTTTTAAG-TTAAAGGTTAGGGTTTTTAGGTTTAGAGTTTAGGGTTTTTAAGTTTAGAGCTTAGG
**
42283650 GTTTTTAAGTTTAGGGTTTGGG
65 GTTTTTAAGTTTAGGGTTAAGG
*
42283672 TTTTTAAGTTAAAGGTTAGGGTTTTTAGGTTTAGAGTTT-GGGTTTTTTAAGTTTAGGGCTTAGG
1 TTTTTAAGTTAAAGGTTAGGGTTTTTAGGTTTAGAGTTTAGGG-TTTTTAAGTTTAGAGCTTAGG
*
42283736 GTTTTTAGGTTTAGGGTTAAGG
65 GTTTTTAAGTTTAGGGTTAAGG
* *
42283758 TTTTTATGTTAATGGTTAG
1 TTTTTAAGTTAAAGGTTAG
42283777 AATTAGGGTT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
85 2 0.02
86 82 0.89
87 8 0.09
ACGTcount: A:0.19, C:0.01, G:0.29, T:0.51
Consensus pattern (86 bp):
TTTTTAAGTTAAAGGTTAGGGTTTTTAGGTTTAGAGTTTAGGGTTTTTAAGTTTAGAGCTTAGGG
TTTTTAAGTTTAGGGTTAAGG
Found at i:42283802 original size:33 final size:32
Alignment explanation
Indices: 42283746--42283807 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
42283736 GTTTTTAGGT
* *
42283746 TTAGGGTTAAGGTTTTTATGTTAATGGTTAGAA
1 TTAGGGTTAAGGTTTTAAAGTTAA-GGTTAGAA
42283779 TTAGGGTT-AGGATTTTAAAGTTAAGGTTA
1 TTAGGGTTAAGG-TTTTAAAGTTAAGGTTA
42283808 TATGGTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (32 bp):
TTAGGGTTAAGGTTTTAAAGTTAAGGTTAGAA
Found at i:42283837 original size:22 final size:22
Alignment explanation
Indices: 42283802--42283853 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
42283792 TTTAAAGTTA
*
42283802 AGGTTATATGGTTTAGGGTTTTT
1 AGGTT-TAGGGTTTAGGGTTTTT
42283825 AGGTTTAGGGTTTAGGGTTTTT
1 AGGTTTAGGGTTTAGGGTTTTT
42283847 AGGTTTA
1 AGGTTTA
42283854 AAGTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (22 bp):
AGGTTTAGGGTTTAGGGTTTTT
Found at i:42283859 original size:22 final size:22
Alignment explanation
Indices: 42283812--42283859 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
42283802 AGGTTATATG
**
42283812 GTTTAGGGTTTTTAGGTTTAGG
1 GTTTAGGGTTTTTAGGTTTAAA
42283834 GTTTAGGGTTTTTAGGTTTAAA
1 GTTTAGGGTTTTTAGGTTTAAA
42283856 GTTT
1 GTTT
42283860 TTAAGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (22 bp):
GTTTAGGGTTTTTAGGTTTAAA
Found at i:42283860 original size:37 final size:37
Alignment explanation
Indices: 42283819--42283890 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
42283809 ATGGTTTAGG
* *
42283819 GTTTTTAGGTTTAGGGTTTAGGG-TTTTTAGGTTTAAA
1 GTTTTTAAGTTAAGGG-TTAGGGTTTTTTAGGTTTAAA
*
42283856 GTTTTTAAGTTAATGGTTAGGGTTTTTTAGGTTTA
1 GTTTTTAAGTTAAGGGTTAGGGTTTTTTAGGTTTA
42283891 CGGTTTAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 6 0.19
37 25 0.81
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (37 bp):
GTTTTTAAGTTAAGGGTTAGGGTTTTTTAGGTTTAAA
Found at i:42283882 original size:22 final size:23
Alignment explanation
Indices: 42283857--42283905 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
42283847 AGGTTTAAAG
*
42283857 TTTTTAAGTTAATGG-TTAGGGT
1 TTTTTAAGTTAACGGTTTAGGGT
* *
42283879 TTTTTAGGTTTACGGTTTAGGGT
1 TTTTTAAGTTAACGGTTTAGGGT
42283902 TTTT
1 TTTT
42283906 AGGTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.16, C:0.02, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTTTAAGTTAACGGTTTAGGGT
Found at i:42283896 original size:59 final size:61
Alignment explanation
Indices: 42283799--42283914 Score: 193
Period size: 59 Copynumber: 1.9 Consensus size: 61
42283789 GATTTTAAAG
*
42283799 TTAAGGTTATATGGTTTAGGGTTTTTAGGTTTAGGGTTTAGGGTTTTTAGGTTTAAAGTTT
1 TTAAGGTTATATGGTTTAGGGTTTTTAGGTTTACGGTTTAGGGTTTTTAGGTTTAAAGTTT
42283860 TTAA-GTTA-ATGG-TTAGGGTTTTTTAGGTTTACGGTTTAGGGTTTTTAGGTTTAAA
1 TTAAGGTTATATGGTTTAGGG-TTTTTAGGTTTACGGTTTAGGGTTTTTAGGTTTAAA
42283915 ATTTGGGGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
58 6 0.11
59 39 0.74
60 4 0.08
61 4 0.08
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.50
Consensus pattern (61 bp):
TTAAGGTTATATGGTTTAGGGTTTTTAGGTTTACGGTTTAGGGTTTTTAGGTTTAAAGTTT
Found at i:42283906 original size:22 final size:22
Alignment explanation
Indices: 42283879--42283971 Score: 98
Period size: 22 Copynumber: 4.3 Consensus size: 22
42283869 TGGTTAGGGT
*
42283879 TTTTTAGGTTTACGGTTTAGGG
1 TTTTTAGGTTTAAGGTTTAGGG
** *
42283901 TTTTTAGGTTTAAAATTTGGGG
1 TTTTTAGGTTTAAGGTTTAGGG
* *
42283923 TTTTTAAGTTTAAGGTTTAAGG
1 TTTTTAGGTTTAAGGTTTAGGG
* * *
42283945 TTTTTATGTTTAGGGTTT-GGT
1 TTTTTAGGTTTAAGGTTTAGGG
42283966 TTTTTA
1 TTTTTA
42283972 AATTAAGGGT
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
21 7 0.12
22 51 0.88
ACGTcount: A:0.18, C:0.01, G:0.26, T:0.55
Consensus pattern (22 bp):
TTTTTAGGTTTAAGGTTTAGGG
Found at i:42283964 original size:44 final size:44
Alignment explanation
Indices: 42283847--42284005 Score: 130
Period size: 44 Copynumber: 3.7 Consensus size: 44
42283837 TAGGGTTTTT
* * *
42283847 AGGTTTAAAGTTTTTAAG-TTAATGGTTAGGGTTTTTTAGGTTTA
1 AGGTTTAAGGTTTTTAAGTTTAA-GGTTTGGGTTTTTTAAGTTTA
* * * ** *
42283891 CGGTTTAGGGTTTTTAGGTTTAAAATTTGGGGTTTTTAAGTTTA
1 AGGTTTAAGGTTTTTAAGTTTAAGGTTTGGGTTTTTTAAGTTTA
* * *
42283935 AGGTTTAAGGTTTTTATGTTTAGGGTTT-GGTTTTTTAA-ATTA
1 AGGTTTAAGGTTTTTAAGTTTAAGGTTTGGGTTTTTTAAGTTTA
* * *
42283977 AGGGTTATCGG-TTTTAA-TTTAAGGGTTGG
1 AGGTTTA-AGGTTTTTAAGTTTAAGGTTTGG
42284006 TTAGTGTTTT
Statistics
Matches: 90, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 8 0.09
42 15 0.17
43 11 0.12
44 52 0.58
45 4 0.04
ACGTcount: A:0.22, C:0.01, G:0.27, T:0.50
Consensus pattern (44 bp):
AGGTTTAAGGTTTTTAAGTTTAAGGTTTGGGTTTTTTAAGTTTA
Found at i:42284097 original size:21 final size:21
Alignment explanation
Indices: 42284073--42284123 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
42284063 GGGTTTTAGG
42284073 GTTTTAAGTGTAGAGTTTACT
1 GTTTTAAGTGTAGAGTTTACT
* * * **
42284094 GTTTTAGGTTTAGGGTTTGTT
1 GTTTTAAGTGTAGAGTTTACT
42284115 GTTTTAAGT
1 GTTTTAAGT
42284124 TAAAGGTTAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.02, G:0.27, T:0.53
Consensus pattern (21 bp):
GTTTTAAGTGTAGAGTTTACT
Found at i:42284162 original size:22 final size:22
Alignment explanation
Indices: 42284059--42284259 Score: 114
Period size: 22 Copynumber: 9.4 Consensus size: 22
42284049 AAGTTAAGGT
* * *
42284059 TTTAGGGTTTTAGGGTTTTAAG
1 TTTAGGGTTTGATGTTTTTAAG
* * *
42284081 TGTAGAGTTT-ACTG-TTTTAGG
1 TTTAGGGTTTGA-TGTTTTTAAG
*
42284102 TTTAGGGTTTGTTG-TTTTAAG
1 TTTAGGGTTTGATGTTTTTAAG
* * * * *
42284123 TTAAAGG-TT-AGGGTTTTAGG
1 TTTAGGGTTTGATGTTTTTAAG
42284143 TTTAGGGTTTGATGTTTTTAAG
1 TTTAGGGTTTGATGTTTTTAAG
* * *
42284165 TTTAAGGTTT-AGGGTTTTTAGG
1 TTTAGGGTTTGA-TGTTTTTAAG
*
42284187 TTTAGGGTTTGGTGTTTTTAAG
1 TTTAGGGTTTGATGTTTTTAAG
* * * *
42284209 TTAAGGGTTAG-CGCTTTTAA-
1 TTTAGGGTTTGATGTTTTTAAG
*
42284229 TTTAAGGGTTAGA-GTTTTTAAG
1 TTT-AGGGTTTGATGTTTTTAAG
*
42284251 TTAAGGGTT
1 TTTAGGGTT
42284260 AGGATTAGGG
Statistics
Matches: 137, Mismatches: 32, Indels: 21
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.01
20 15 0.11
21 59 0.43
22 62 0.45
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (22 bp):
TTTAGGGTTTGATGTTTTTAAG
Found at i:42284162 original size:42 final size:42
Alignment explanation
Indices: 42284094--42284262 Score: 209
Period size: 42 Copynumber: 4.0 Consensus size: 42
42284084 AGAGTTTACT
*
42284094 GTTTTAGGTTTAGGGTTTGTTG-TTTTAAGTTAAAGGTTAGG
1 GTTTTAGGTTTAGGGTTTGATGTTTTTAAGTTAAAGGTTAGG
*
42284135 GTTTTAGGTTTAGGGTTTGATGTTTTTAAGTTTAAGGTTTAGG
1 GTTTTAGGTTTAGGGTTTGATGTTTTTAAGTTAAAGG-TTAGG
* *
42284178 GTTTTTAGGTTTAGGGTTTGGTGTTTTTAAGTTAAGGGTTAGCG
1 G-TTTTAGGTTTAGGGTTTGATGTTTTTAAGTTAAAGGTTAG-G
* * * *
42284222 CTTTTA-ATTTAAGGGTTAGA-GTTTTTAAGTTAAGGGTTAGG
1 GTTTTAGGTTT-AGGGTTTGATGTTTTTAAGTTAAAGGTTAGG
42284263 ATTAGGGTTA
Statistics
Matches: 114, Mismatches: 9, Indels: 10
0.86 0.07 0.08
Matches are distributed among these distances:
41 22 0.19
42 36 0.32
43 22 0.19
44 34 0.30
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (42 bp):
GTTTTAGGTTTAGGGTTTGATGTTTTTAAGTTAAAGGTTAGG
Found at i:42284228 original size:21 final size:21
Alignment explanation
Indices: 42284116--42284261 Score: 132
Period size: 21 Copynumber: 6.9 Consensus size: 21
42284106 GGGTTTGTTG
* *
42284116 TTTTAAGTTAAAGGTTAG-GG
1 TTTTAAGTTAAGGGTTAGTGT
* * *
42284136 TTTTAGGTTTAGGGTTTGATGT
1 TTTTAAGTTAAGGGTTAG-TGT
* *
42284158 TTTTAAGTTTAAGGTTTAGGGT
1 TTTTAAG-TTAAGGGTTAGTGT
* * *
42284180 TTTTAGGTTTAGGGTTTGGTGT
1 TTTTAAGTTAAGGG-TTAGTGT
* *
42284202 TTTTAAGTTAAGGGTTAGCGC
1 TTTTAAGTTAAGGGTTAGTGT
* *
42284223 TTTTAATTTAAGGGTTAGAGT
1 TTTTAAGTTAAGGGTTAGTGT
42284244 TTTTAAGTTAAGGGTTAG
1 TTTTAAGTTAAGGGTTAG
42284262 GATTAGGGTT
Statistics
Matches: 98, Mismatches: 24, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
20 14 0.14
21 44 0.45
22 32 0.33
23 8 0.08
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.47
Consensus pattern (21 bp):
TTTTAAGTTAAGGGTTAGTGT
Found at i:42284497 original size:21 final size:21
Alignment explanation
Indices: 42284473--42284518 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42284463 TTGTCCAGCT
*
42284473 TCCGGCGGCGG-TTGTGGTTCC
1 TCCGGCGG-GGATTCTGGTTCC
*
42284494 TCCGGCGGGGATTCTGGTTCT
1 TCCGGCGGGGATTCTGGTTCC
42284515 TCCG
1 TCCG
42284519 ATAGGGCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.02, C:0.28, G:0.39, T:0.30
Consensus pattern (21 bp):
TCCGGCGGGGATTCTGGTTCC
Found at i:42286698 original size:22 final size:22
Alignment explanation
Indices: 42286664--42286756 Score: 60
Period size: 22 Copynumber: 3.9 Consensus size: 22
42286654 ATTTAAAAAT
* *
42286664 AGGAATTTAAGAGAAATTTAAA
1 AGGAAATTGAGAGAAATTTAAA
*
42286686 AGGAAATTGAGAGCTAATTGAGATTAAA
1 AGGAAATTGAGAG--AA---A-TTTAAA
* * *
42286714 TATGAATTTGAGAGAAATTTAGA
1 -AGGAAATTGAGAGAAATTTAAA
42286737 AGGAAATTGAGAGGAAATTT
1 AGGAAATTGAGA-GAAATTT
42286757 GAGAGAGGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
22 21 0.39
23 11 0.20
24 3 0.06
27 3 0.06
28 5 0.09
29 11 0.20
ACGTcount: A:0.47, C:0.01, G:0.24, T:0.28
Consensus pattern (22 bp):
AGGAAATTGAGAGAAATTTAAA
Found at i:42293852 original size:3 final size:3
Alignment explanation
Indices: 42293844--42293887 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
42293834 TCAAAACCAA
42293844 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42293888 AGAATAAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42294168 original size:16 final size:16
Alignment explanation
Indices: 42294147--42294180 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42294137 TACTTAAAAG
42294147 TTAAAACTAATTATTA
1 TTAAAACTAATTATTA
* *
42294163 TTAAAATTAATTGTTA
1 TTAAAACTAATTATTA
42294179 TT
1 TT
42294181 GAATTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAAACTAATTATTA
Found at i:42294281 original size:25 final size:25
Alignment explanation
Indices: 42294251--42294298 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
42294241 AAGATTACTT
42294251 ATTTGAATTTAATTACAAACAATTA
1 ATTTGAATTTAATTACAAACAATTA
42294276 ATTTGAATTTAATTACAAACAAT
1 ATTTGAATTTAATTACAAACAAT
42294299 CAAATCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTGAATTTAATTACAAACAATTA
Found at i:42295685 original size:29 final size:29
Alignment explanation
Indices: 42295648--42295743 Score: 93
Period size: 38 Copynumber: 3.0 Consensus size: 29
42295638 CACAACCATT
*
42295648 AACAGCATTAACAGCAAAATCAAAATCAG
1 AACACCATTAACAGCAAAATCAAAATCAG
42295677 AACACCATTAACAGCATTAACAGCAAAATCAAAATCAG
1 AACACCA-T--------TAACAGCAAAATCAAAATCAG
42295715 AACACCATTAACAGCAAAAATCAAAATCA
1 AACACCATTAACAGC-AAAATCAAAATCA
42295744 CAACCAACAT
Statistics
Matches: 56, Mismatches: 1, Indels: 19
0.74 0.01 0.25
Matches are distributed among these distances:
29 13 0.23
30 14 0.25
37 1 0.02
38 28 0.50
ACGTcount: A:0.55, C:0.23, G:0.07, T:0.15
Consensus pattern (29 bp):
AACACCATTAACAGCAAAATCAAAATCAG
Found at i:42295693 original size:38 final size:38
Alignment explanation
Indices: 42295611--42295730 Score: 181
Period size: 38 Copynumber: 3.2 Consensus size: 38
42295601 ACATTAACAG
* * * *
42295611 AACACCATTAACAGCAAAAATAAAAAACA-CA-ACCATT
1 AACAGCATTAACAGC-AAAATCAAAATCAGAACACCATT
42295648 AACAGCATTAACAGCAAAATCAAAATCAGAACACCATT
1 AACAGCATTAACAGCAAAATCAAAATCAGAACACCATT
42295686 AACAGCATTAACAGCAAAATCAAAATCAGAACACCATT
1 AACAGCATTAACAGCAAAATCAAAATCAGAACACCATT
42295724 AACAGCA
1 AACAGCA
42295731 AAAATCAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
36 11 0.14
37 15 0.19
38 51 0.66
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (38 bp):
AACAGCATTAACAGCAAAATCAAAATCAGAACACCATT
Found at i:42295737 original size:30 final size:29
Alignment explanation
Indices: 42295686--42295743 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
42295676 GAACACCATT
*
42295686 AACAGCATTAACAGCAAAATCAAAATCAG
1 AACACCATTAACAGCAAAATCAAAATCAG
42295715 AACACCATTAACAGCAAAAATCAAAATCA
1 AACACCATTAACAGC-AAAATCAAAATCA
42295744 CAACCAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.57, C:0.22, G:0.07, T:0.14
Consensus pattern (29 bp):
AACACCATTAACAGCAAAATCAAAATCAG
Found at i:42299875 original size:9 final size:9
Alignment explanation
Indices: 42299861--42299891 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42299851 GTTAAACGAA
42299861 TCGAGTTAT
1 TCGAGTTAT
*
42299870 TCGAGTTAA
1 TCGAGTTAT
42299879 TCGAGTTAT
1 TCGAGTTAT
42299888 TCGA
1 TCGA
42299892 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:42299962 original size:9 final size:9
Alignment explanation
Indices: 42299945--42299981 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42299935 TGAGTTTTCG
42299945 AATTCGAAT
1 AATTCGAAT
*
42299954 AACTCGAAT
1 AATTCGAAT
42299963 AATTCGAAT
1 AATTCGAAT
42299972 AATTCGAAT
1 AATTCGAAT
42299981 A
1 A
42299982 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42301656 original size:2 final size:2
Alignment explanation
Indices: 42301649--42301682 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42301639 TAATATAGTG
42301649 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
42301683 AATAAAGAGA
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):
TA
Found at i:42308236 original size:36 final size:35
Alignment explanation
Indices: 42308158--42308243 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 35
42308148 CGGCACAAGT
* *
42308158 GTATATA-TATTATAAATATTTAAATTTAAAATATA
1 GTATATATTATTAT-AATATTAAAACTTAAAATATA
42308193 -TATTATATTATTATAATATTAAAACTTAAAAGT-TAA
1 GTA-TATATTATTATAATATTAAAACTTAAAA-TAT-A
42308229 GTATATATTATTATA
1 GTATATATTATTATA
42308244 TTATAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
34 2 0.05
35 20 0.45
36 20 0.45
37 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (35 bp):
GTATATATTATTATAATATTAAAACTTAAAATATA
Found at i:42308312 original size:5 final size:5
Alignment explanation
Indices: 42308254--42308323 Score: 52
Period size: 5 Copynumber: 13.4 Consensus size: 5
42308244 TTATAATAAT
* * * *
42308254 AAAGAA AAAGA GAAAGA GAAAGA AACGA AACGA AACAGA GAAGG AAAG-
1 AAAG-A AAAGA -AAAGA -AAAGA AAAGA AAAGA AA-AGA AAAGA AAAGA
*
42308302 AAAGA AAAGA AAAAA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AA
42308324 GAAGGAGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
4 4 0.07
5 32 0.59
6 18 0.33
ACGTcount: A:0.73, C:0.04, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:42308630 original size:18 final size:19
Alignment explanation
Indices: 42308601--42308636 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42308591 TGTGAAAATT
*
42308601 TGAAATTTAGGGATTTAAG
1 TGAAATTTAGGGAGTTAAG
42308620 TGAAA-TTAGGGAGTTAA
1 TGAAATTTAGGGAGTTAA
42308637 ATATAGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGGGAGTTAAG
Found at i:42309261 original size:40 final size:40
Alignment explanation
Indices: 42309141--42309274 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 40
42309131 ACTTCGACTT
*
42309141 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATT-ATCC
* * * * *
42309182 GATGAGGCATTGGGTGCCAA--T-TTACTTCGGTTTAACC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
*
42309219 GATGAGACACTGGGTGTCAATTTATTACTTCGAATTATCC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
* *
42309259 GATGAGGCACTAGGTG
1 GATGAGACACTGGGTG
42309275 ATAAACTGGT
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
37 19 0.25
38 11 0.14
39 2 0.03
40 27 0.36
41 17 0.22
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
Found at i:42314081 original size:20 final size:20
Alignment explanation
Indices: 42314040--42314092 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
42314030 TACTTATAGC
*
42314040 ATAAATTATATATAAAATAA
1 ATAAATTCTATATAAAATAA
*
42314060 ATAAATTCTATATATACA-AA
1 ATAAATTCTATATA-AAATAA
42314080 ATAATATTCTATA
1 ATAA-ATTCTATA
42314093 AAATATCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAATTCTATATAAAATAA
Found at i:42314169 original size:20 final size:21
Alignment explanation
Indices: 42314125--42314170 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42314115 AAAAATATAT
** *
42314125 ATATAAAATGAATTAAGAGAA
1 ATATAAAAAAAATAAAGAGAA
42314146 ATATAAAAAAAATAAAGA-AA
1 ATATAAAAAAAATAAAGAGAA
42314166 ATATA
1 ATATA
42314171 CATATATATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.22
Consensus pattern (21 bp):
ATATAAAAAAAATAAAGAGAA
Found at i:42316197 original size:108 final size:106
Alignment explanation
Indices: 42315936--42316255 Score: 388
Period size: 106 Copynumber: 3.0 Consensus size: 106
42315926 AAGTTAAGAG
* * *
42315936 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAATCCAGCACGTTAGGGTACGTTCTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAAT
** * * ** *
42316001 TTCCAAATACAAAACATTGCCTCATTTTGAAATTTCGAAAG
66 TTCCAAACGCAAAATATTGCCTAATTTTGAAATTTAAAAAA
* * * * * * *
42316042 GGTATTCGACTATTTGGTCAAACGAGTAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGATT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAAT
**
42316107 TTCCAAACGTGAAATATTGCCTAATTTTGAAAGTTTAAAAAA
66 TTCCAAACGCAAAATATTGCCTAATTTTGAAA-TTTAAAAAA
* *
42316149 GATATTTGGCTATTTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGCTTTCTTGAA
1 GATATTTGGCTA-TTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAA
* * * *
42316214 TTTCCAAACGCAAAATATTTCCTTACTTTGAAACTTTTAAAA
65 TTTCCAAACGCAAAATATTGCCTAATTTTGAAA-TTTAAAAA
42316256 GAATATTAAT
Statistics
Matches: 177, Mismatches: 35, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
106 81 0.46
107 15 0.08
108 81 0.46
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (106 bp):
GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAAT
TTCCAAACGCAAAATATTGCCTAATTTTGAAATTTAAAAAA
Found at i:42316421 original size:44 final size:45
Alignment explanation
Indices: 42316350--42316447 Score: 146
Period size: 44 Copynumber: 2.2 Consensus size: 45
42316340 TAAATCAATG
*
42316350 ACATACAAAATAACAACATATAGAAGCAAAT-AAAATAAAAAAAT
1 ACATACAAAATAACAACACATAGAAGCAAATAAAAATAAAAAAAT
* *
42316394 ACATACAAAATAACAATACATATAAGCAAATAAAAATAAAAAAAT
1 ACATACAAAATAACAACACATAGAAGCAAATAAAAATAAAAAAAT
*
42316439 AAATA-AAAA
1 ACATACAAAA
42316448 GGGTACTCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 32 0.65
45 17 0.35
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.16
Consensus pattern (45 bp):
ACATACAAAATAACAACACATAGAAGCAAATAAAAATAAAAAAAT
Found at i:42316428 original size:25 final size:23
Alignment explanation
Indices: 42316356--42316439 Score: 59
Period size: 25 Copynumber: 3.6 Consensus size: 23
42316346 AATGACATAC
*
42316356 AAAATAACAACATATAGAAGCAAAT
1 AAAATAACAA-A-ATATAAGCAAAT
* *
42316381 AAAATAA-AAAA-AT-A-CATAC
1 AAAATAACAAAATATAAGCAAAT
42316400 AAAATAACAATACATATAAGCAAAT
1 AAAATAACAA-A-ATATAAGCAAAT
*
42316425 AAAAATAAAAAAATA
1 -AAAATAACAAAATA
42316440 AATAAAAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
19 10 0.22
20 3 0.07
21 2 0.04
22 2 0.04
23 3 0.07
24 6 0.13
25 11 0.24
26 9 0.20
ACGTcount: A:0.70, C:0.10, G:0.04, T:0.17
Consensus pattern (23 bp):
AAAATAACAAAATATAAGCAAAT
Found at i:42316744 original size:27 final size:27
Alignment explanation
Indices: 42316693--42316746 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
42316683 GATTATAGAA
*
42316693 GAAATATAAAAGTATGTATACATATAT
1 GAAATATAAAAGTATGTATAAATATAT
42316720 GAAA-ATAAAA-TATGTACGTAAATATAT
1 GAAATATAAAAGTATGTA--TAAATATAT
42316747 AGATGTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 6 0.25
26 6 0.25
27 12 0.50
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.31
Consensus pattern (27 bp):
GAAATATAAAAGTATGTATAAATATAT
Found at i:42316834 original size:2 final size:2
Alignment explanation
Indices: 42316787--42316814 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42316777 AATGTATAAG
42316787 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
42316815 AAACGCATGT
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):
TA
Found at i:42319554 original size:3 final size:3
Alignment explanation
Indices: 42319548--42319644 Score: 108
Period size: 3 Copynumber: 31.7 Consensus size: 3
42319538 ATATAAAAAA
* * * *
42319548 AAT AAT AAC AAT AAT ATT AAT GAAT -AT AAT AAT AAT AAG AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
42319593 AA- AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AACT AATT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T
42319640 AAT AA
1 AAT AA
42319645 AGTTGCTAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
2 3 0.04
3 68 0.84
4 10 0.12
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:42328182 original size:5 final size:5
Alignment explanation
Indices: 42328172--42328203 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
42328162 TTTAATGTTT
*
42328172 TAATA TAATA TAATA TAATA TGATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TA
42328204 TGTGCATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:42340804 original size:30 final size:32
Alignment explanation
Indices: 42340759--42340823 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
42340749 TTTTTAGAAC
* *
42340759 TTTTATTAGATCCCTC-AAAAATATTGGAAAT
1 TTTTATTAGAACCCTCTAAAAATATTGAAAAT
*
42340790 TTTTATTA-AACCCTCTAAAAATTTTGAAAAT
1 TTTTATTAGAACCCTCTAAAAATATTGAAAAT
42340821 TTT
1 TTT
42340824 AGTTCAACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.43
Consensus pattern (32 bp):
TTTTATTAGAACCCTCTAAAAATATTGAAAAT
Found at i:42340824 original size:30 final size:31
Alignment explanation
Indices: 42340759--42340824 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
42340749 TTTTTAGAAC
* *
42340759 TTTTATTAGATCCCTCAAAAATATTGGAAAT
1 TTTTATTAGAACCCTCAAAAATATTGGAAAA
*
42340790 TTTTATTA-AACCCTCTAAAAAT-TTTGAAAA
1 TTTTATTAGAACCCTC-AAAAATATTGGAAAA
42340820 TTTTA
1 TTTTA
42340825 GTTCAACCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (31 bp):
TTTTATTAGAACCCTCAAAAATATTGGAAAA
Found at i:42350494 original size:12 final size:12
Alignment explanation
Indices: 42350479--42350511 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42350469 GAAACCGGAG
42350479 GAGAAGAAAGAA
1 GAGAAGAAAGAA
*
42350491 GAGAAGAAGGAA
1 GAGAAGAAAGAA
42350503 GAGAA-AAAG
1 GAGAAGAAAG
42350512 CCACCCAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (12 bp):
GAGAAGAAAGAA
Found at i:42351117 original size:21 final size:20
Alignment explanation
Indices: 42351093--42351138 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
42351083 GGTTCCGCCT
42351093 AAGAAAGATGACGGCGGTGAG
1 AAGAAAGA-GACGGCGGTGAG
42351114 AAG-AA-AGACGGCGGTGAG
1 AAGAAAGAGACGGCGGTGAG
42351132 AAGAAAG
1 AAGAAAG
42351139 TCACCGACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 15 0.65
19 3 0.13
20 2 0.09
21 3 0.13
ACGTcount: A:0.43, C:0.09, G:0.41, T:0.07
Consensus pattern (20 bp):
AAGAAAGAGACGGCGGTGAG
Found at i:42351123 original size:18 final size:18
Alignment explanation
Indices: 42351102--42351138 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42351092 TAAGAAAGAT
42351102 GACGGCGGTGAGAAGAAA
1 GACGGCGGTGAGAAGAAA
42351120 GACGGCGGTGAGAAGAAA
1 GACGGCGGTGAGAAGAAA
42351138 G
1 G
42351139 TCACCGACGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.46, T:0.05
Consensus pattern (18 bp):
GACGGCGGTGAGAAGAAA
Found at i:42351452 original size:33 final size:33
Alignment explanation
Indices: 42351376--42351454 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
42351366 CAGGGGTACA
* *
42351376 TGAATCAAGGCTATATGTCTCATCCTGGGTATG
1 TGAATCAAGGGTATATGTCTCACCCTGGGTATG
*
42351409 CGAATCAAGGGTATATGTCTCACCCTGGGTATG
1 TGAATCAAGGGTATATGTCTCACCCTGGGTATG
42351442 TGAATCAAGGGTA
1 TGAATCAAGGGTA
42351455 CATGGTGGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (33 bp):
TGAATCAAGGGTATATGTCTCACCCTGGGTATG
Found at i:42356475 original size:25 final size:25
Alignment explanation
Indices: 42356447--42356509 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
42356437 ATTATATATT
*
42356447 AAATATATATTTTTTATTTTTAATC
1 AAATATATATTTTTCATTTTTAATC
42356472 AAATATATATTTTTCATTTTTAATC
1 AAATATATATTTTTCATTTTTAATC
42356497 AAATATATATTTT
1 AAATATATATTTT
42356510 ATATATATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATATATATTTTTCATTTTTAATC
Found at i:42356484 original size:23 final size:23
Alignment explanation
Indices: 42356451--42356530 Score: 99
Period size: 25 Copynumber: 3.4 Consensus size: 23
42356441 TATATTAAAT
*
42356451 ATATATTTTTTATTTTTAATCAA
1 ATATATATTTTATTTTTAATCAA
42356474 ATATATATTTTTCATTTTTAATCAA
1 ATATATA-TTTT-ATTTTTAATCAA
* * *
42356499 ATATATATTTTATATAT-ATTAA
1 ATATATATTTTATTTTTAATCAA
42356521 ATATATATTT
1 ATATATATTT
42356531 AATATGGGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
22 14 0.27
23 10 0.20
24 8 0.16
25 19 0.37
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATATATTTTATTTTTAATCAA
Found at i:42356515 original size:11 final size:11
Alignment explanation
Indices: 42356498--42356535 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
42356488 TTTTTAATCA
42356498 AATATATATTT
1 AATATATATTT
* *
42356509 TATATATATTA
1 AATATATATTT
42356520 AATATATATTT
1 AATATATATTT
42356531 AATAT
1 AATAT
42356536 GGGTCGGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:42356708 original size:2 final size:2
Alignment explanation
Indices: 42356701--42356746 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
42356691 TTCGAATGAA
*
42356701 AT AT AT AT AT AT AA 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
42356743 AT AT
1 AT AT
42356747 TATTGTTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42360566 original size:4 final size:4
Alignment explanation
Indices: 42360557--42360586 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
42360547 CCATTCTCTT
42360557 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
42360587 ATTCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:42361668 original size:14 final size:15
Alignment explanation
Indices: 42361651--42361688 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
42361641 AAATCTATAT
42361651 ATTTTAATTT-CTAA
1 ATTTTAATTTACTAA
* *
42361665 ATTTTAATTTATTAT
1 ATTTTAATTTACTAA
42361680 ATTTTAATT
1 ATTTTAATT
42361689 ACTGTATCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTAATTTACTAA
Found at i:42361687 original size:15 final size:14
Alignment explanation
Indices: 42361648--42361688 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
42361638 TTTAAATCTA
42361648 TATATTTTAATTTC
1 TATATTTTAATTTC
* *
42361662 TAAATTTTAATTTAT
1 TATATTTTAATTT-C
42361677 TATATTTTAATT
1 TATATTTTAATT
42361689 ACTGTATCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATTTTAATTTC
Found at i:42364194 original size:14 final size:14
Alignment explanation
Indices: 42364177--42364205 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42364167 TTTTCATATA
42364177 TTTATTTTTCAGTT
1 TTTATTTTTCAGTT
42364191 TTTATTTTTCAGTT
1 TTTATTTTTCAGTT
42364205 T
1 T
42364206 ATTTTGCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTATTTTTCAGTT
Done.