Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1422
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: 293460
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
File 2 of 3
Found at i:146536 original size:20 final size:20
Alignment explanation
Indices: 146511--146581 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
146501 ACCCTGATGC
*
146511 ATCGATACATTTTTCAATAT
1 ATCGATACATTTTTCAATGT
* * *
146531 ATCGATACATGTATGAATGT
1 ATCGATACATTTTTCAATGT
* * *
146551 ATCGATATATTCTACAATGT
1 ATCGATACATTTTTCAATGT
146571 ATCGATACATT
1 ATCGATACATT
146582 ATGTCTTTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (20 bp):
ATCGATACATTTTTCAATGT
Found at i:147529 original size:22 final size:23
Alignment explanation
Indices: 147498--147550 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
147488 TTTGACCATT
147498 CATTTTTTTTATTATGTTTCATG
1 CATTTTTTTTATTATGTTTCATG
147521 CATTTTTTTTATTATGTTTCATG
1 CATTTTTTTTATTATGTTTCATG
147544 CATTTTT
1 CATTTTT
147551 AACATGTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.09, G:0.08, T:0.66
Consensus pattern (23 bp):
CATTTTTTTTATTATGTTTCATG
Found at i:147557 original size:20 final size:21
Alignment explanation
Indices: 147502--147557 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 21
147492 ACCATTCATT
**
147502 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
147523 TTTTTTTTATTATGTTTCATGCA
1 --TTTTTTAACATGTTTCATGCA
147546 -TTTTTAACATGT
1 TTTTTTAACATGT
147558 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 10 0.32
23 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:150610 original size:2 final size:2
Alignment explanation
Indices: 150603--150635 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
150593 TTATTAGGCA
150603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
150636 AAACGTCATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:155633 original size:2 final size:2
Alignment explanation
Indices: 155626--155659 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
155616 CTAATTAGGA
155626 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
155660 TAAAAAAAAC
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:158577 original size:16 final size:16
Alignment explanation
Indices: 158558--158591 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
158548 TTTAACATTA
158558 AATAAAT-ATTAAATAT
1 AATAAATAATT-AATAT
158574 AATAAATAATTAATAT
1 AATAAATAATTAATAT
158590 AA
1 AA
158592 ATATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAATAATTAATAT
Found at i:159152 original size:14 final size:14
Alignment explanation
Indices: 159129--159177 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
159119 TATTACTGTA
*
159129 AAAAAAATTTAGTT
1 AAAAAAATTTAATT
*
159143 AAAAATATTTAAATT
1 AAAAAAATTT-AATT
*
159158 AAAAAAATTGTATTT
1 AAAAAAATT-TAATT
159173 AAAAA
1 AAAAA
159178 GTGTCGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 9 0.31
15 19 0.66
16 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (14 bp):
AAAAAAATTTAATT
Found at i:161465 original size:20 final size:19
Alignment explanation
Indices: 161440--161511 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 19
161430 ATTAAATTAA
161440 TTTTATTTATTTTTATAATT
1 TTTTATTTATTTTTAT-ATT
* *
161460 TTTTATATA-ATTTATATT
1 TTTTATTTATTTTTATATT
*
161478 TATTTAATTTAATTATTATATT
1 T-TTT-ATTT-ATTTTTATATT
161500 TTATT-TTTATTT
1 TT-TTATTTATTT
161512 ATGTAAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
18 4 0.10
19 11 0.27
20 14 0.34
21 2 0.05
22 10 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATTTATTTTTATATT
Found at i:161483 original size:29 final size:31
Alignment explanation
Indices: 161437--161513 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 31
161427 AAAATTAAAT
*
161437 TAATTT-TATTTATTTTTATAATTT-TTTA-TA
1 TAATTTATATTTA--TTTATAATTTAATTATTA
161467 TAATTTATATTTA-TT-TAATTTAATTATTA
1 TAATTTATATTTATTTATAATTTAATTATTA
* *
161496 TATTTTATTTTTATTTAT
1 TAATTTATATTTATTTAT
161514 GTAAATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 6 0.15
28 5 0.13
29 13 0.33
30 8 0.21
31 7 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (31 bp):
TAATTTATATTTATTTATAATTTAATTATTA
Found at i:161520 original size:29 final size:29
Alignment explanation
Indices: 161465--161523 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
161455 TAATTTTTTA
*
161465 TATAATTTATATTTATTTAATTTAATTAT
1 TATAATTTATATTTATTTAATTAAATTAT
* *
161494 TATATTTTATTTTTATTT-ATGTAAATTAT
1 TATAATTTATATTTATTTAAT-TAAATTAT
161523 T
1 T
161524 TATGTTGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (29 bp):
TATAATTTATATTTATTTAATTAAATTAT
Found at i:161805 original size:12 final size:12
Alignment explanation
Indices: 161788--161812 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
161778 ATATATAAAG
161788 ATTCTCTTGTAT
1 ATTCTCTTGTAT
161800 ATTCTCTTGTAT
1 ATTCTCTTGTAT
161812 A
1 A
161813 AAAACAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (12 bp):
ATTCTCTTGTAT
Found at i:162485 original size:26 final size:24
Alignment explanation
Indices: 162456--162505 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
162446 ATTAAAACAA
* *
162456 AATAAATTTTTAAATAATTATAAAAT
1 AATAAA-TCTTAAA-AAATATAAAAT
162482 AATAAATCTTAAAAAATATAAAAT
1 AATAAATCTTAAAAAATATAAAAT
162506 TATCGCTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 6 0.27
26 6 0.27
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AATAAATCTTAAAAAATATAAAAT
Found at i:162612 original size:19 final size:19
Alignment explanation
Indices: 162573--162613 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
162563 ATATTATAAT
162573 ATTTGAATAAATTATTTTA
1 ATTTGAATAAATTATTTTA
162592 ATTT-AATAATATT-TTTATA
1 ATTTGAATAA-ATTATTT-TA
162611 ATT
1 ATT
162614 AATTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTGAATAAATTATTTTA
Found at i:166001 original size:3 final size:3
Alignment explanation
Indices: 165993--166030 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
165983 TGAAAAGCAA
165993 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
166031 TATTAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:167638 original size:2 final size:2
Alignment explanation
Indices: 167631--167669 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
167621 CAGGTGAACT
167631 TA TA TA 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 TA TA TA T
167670 CAATTTAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:168000 original size:17 final size:17
Alignment explanation
Indices: 167980--168017 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
167970 ATATATTTAA
*
167980 TATATTTTTTAAAAAAT
1 TATATTATTTAAAAAAT
*
167997 TATA-TATTTAAAAGAT
1 TATATTATTTAAAAAAT
168013 TATAT
1 TATAT
168018 CTTGTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATATTATTTAAAAAAT
Found at i:168008 original size:16 final size:16
Alignment explanation
Indices: 167987--168017 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
167977 TAATATATTT
167987 TTTAAAAAATTATATA
1 TTTAAAAAATTATATA
*
168003 TTTAAAAGATTATAT
1 TTTAAAAAATTATAT
168018 CTTGTATTTA
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:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTAAAAAATTATATA
Found at i:169899 original size:13 final size:14
Alignment explanation
Indices: 169879--169920 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
169869 TTATTTGTGT
169879 ATTTTTT-TAGAATA
1 ATTTTTTATA-AATA
169893 ATTTTTTATAAATA
1 ATTTTTTATAAATA
*
169907 ATTTTTTAAAAATA
1 ATTTTTTATAAATA
169921 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 24 0.92
15 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
ATTTTTTATAAATA
Found at i:170583 original size:13 final size:13
Alignment explanation
Indices: 170563--170596 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
170553 TGATAAAAAT
170563 ATAT-AAAATAAA
1 ATATCAAAATAAA
170575 ATATCAAAATAAA
1 ATATCAAAATAAA
*
170588 ATCTCAAAA
1 ATATCAAAA
170597 GATTGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (13 bp):
ATATCAAAATAAA
Found at i:170741 original size:18 final size:18
Alignment explanation
Indices: 170715--170757 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
170705 TGAGATATTT
*
170715 TAATATTTTATATAAAAA
1 TAATATTTTATAAAAAAA
* *
170733 TAATTTTTTTTAAAAAAA
1 TAATATTTTATAAAAAAA
170751 TAATATT
1 TAATATT
170758 AGTATTAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATATTTTATAAAAAAA
Found at i:171471 original size:5 final size:5
Alignment explanation
Indices: 171445--171502 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
171435 TTTATATAAA
** * *
171445 AATAT AATAT TTTA- AATTT AATAT AATAT AAAAT AATAT AAATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT
171495 AATTAT AA
1 AA-TAT AA
171503 AAAATTTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
4 1 0.02
5 31 0.74
6 10 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:171479 original size:26 final size:26
Alignment explanation
Indices: 171426--171513 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 26
171416 ATCATTAACT
* * *
171426 TAATTAAAATTT-ATATAAAAATATAA
1 TAATTTAAATTTAATAT-AATATAAAA
*
171452 TATTTTAAATTTAATATAATATAAAA
1 TAATTTAAATTTAATATAATATAAAA
* *
171478 TAATATAAATATAATATAATTATAAAA
1 TAATTTAAATTTAATATAA-TATAAAA
171505 -AATTTAAAT
1 TAATTTAAAT
171514 AAAAATCTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
26 41 0.79
27 11 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TAATTTAAATTTAATATAATATAAAA
Found at i:171493 original size:11 final size:11
Alignment explanation
Indices: 171464--171502 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
171454 TTTTAAATTT
171464 AATATAATATA
1 AATATAATATA
171475 AA-ATAATATA
1 AATATAATATA
171485 AATATAATATA
1 AATATAATATA
*
171496 ATTATAA
1 AATATAA
171503 AAAATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATAATATA
Found at i:171913 original size:21 final size:21
Alignment explanation
Indices: 171888--171927 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
171878 TATAAAAAAT
171888 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
171909 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
171928 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:172656 original size:15 final size:16
Alignment explanation
Indices: 172633--172674 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
172623 CATAGTTTGA
172633 TTTTTATTT-TA-ATT
1 TTTTTATTTATATATT
172647 TTTTTAATTTATATATT
1 TTTTT-ATTTATATATT
172664 TTTTATATTTA
1 TTTT-TATTTA
172675 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.21
15 4 0.17
16 2 0.08
17 12 0.50
18 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATTTATATATT
Found at i:172679 original size:15 final size:15
Alignment explanation
Indices: 172633--172679 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
172623 CATAGTTTGA
*
172633 TTTTTAT-TTTAATT
1 TTTTTATATTTAAAT
172647 TTTTTA-ATTTATATAT
1 TTTTTATATTTA-A-AT
172663 TTTTTATATTTAAAT
1 TTTTTATATTTAAAT
172678 TT
1 TT
172680 AAAATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.36
15 5 0.18
16 8 0.29
17 5 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTATATTTAAAT
Found at i:172686 original size:22 final size:23
Alignment explanation
Indices: 172652--172709 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
172642 TAATTTTTTT
* *
172652 AATTTATATATTTTTTA-TATTTA
1 AATTTA-AAATTTTTTATTATATA
172675 AATTTAAAATTTTTTATTATATA
1 AATTTAAAATTTTTTATTATATA
*
172698 AA-TAAAAATTTT
1 AATTTAAAATTTT
172710 AATTAAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTTAAAATTTTTTATTATATA
Found at i:176228 original size:20 final size:22
Alignment explanation
Indices: 176203--176261 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
176193 TAAAATCGAA
*
176203 TTATATTAGTT-ATTTTAA-AT
1 TTATATTAGTTAAATTTAATAT
*
176223 TTATATTAATTAAATTTAATAT
1 TTATATTAGTTAAATTTAATAT
*
176245 TTAAATTAGTTTAAATT
1 TTATATTAG-TTAAATT
176262 CGAATCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 10 0.31
21 6 0.19
22 9 0.28
23 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TTATATTAGTTAAATTTAATAT
Found at i:176700 original size:17 final size:18
Alignment explanation
Indices: 176645--176703 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
176635 ATTACACATA
176645 TTATATTCATATTTAATAT
1 TTATATT-ATATTTAATAT
**
176664 TT-TAAAATATTTAATAAT
1 TTATATTATATTTAAT-AT
176682 TTATATTATATTT-ATAT
1 TTATATTATATTTAATAT
176699 TTATA
1 TTATA
176704 CTAATGCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 16 0.47
18 8 0.24
19 10 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATTATATTTAATAT
Found at i:182030 original size:97 final size:97
Alignment explanation
Indices: 181774--182069 Score: 452
Period size: 97 Copynumber: 3.1 Consensus size: 97
181764 CTCTAACTCT
181774 ATTCCTCCGAGGAGATACTTCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACT
1 ATTCCTCCGAGGAGATACTTCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACT
* * * *
181839 TAAATTATCATCATCGGGGATACTCCAACCCC
66 CAAATTGTCATTATCGGGGACACTCCAACCCC
*
181871 ATTCCTCCGAGG-GATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACT
1 ATTCCTCCGAGGAGATACTTCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACT
*
181935 CAAATTGTCATTATCGGGGACATTCCAACCCC
66 CAAATTGTCATTATCGGGGACACTCCAACCCC
* * *
181967 ATTCTTCCAAGGAGATACTTCAACCCCACTTTTAAACACATCAAAAG-TTAAATCTTATTCTCAC
1 ATTCCTCCGAGGAGATACTTCAACCCCGCTTTTAAACACATC-AAAGTTTAAATCTTATTCTCAC
* * * *
182031 TCAAGTTGTCATTATCGGAGAGACTCCAACCCG
65 TCAAATTGTCATTATCGGGGACACTCCAACCCC
182064 ATTCCT
1 ATTCCT
182070 TTGAGTGGAT
Statistics
Matches: 181, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
96 88 0.49
97 89 0.49
98 4 0.02
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.30
Consensus pattern (97 bp):
ATTCCTCCGAGGAGATACTTCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACT
CAAATTGTCATTATCGGGGACACTCCAACCCC
Found at i:186765 original size:30 final size:29
Alignment explanation
Indices: 186731--186790 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
186721 CGAAAAAGTC
186731 AAAA-GCAAAAACACAAAAAAATAAAAAGAA
1 AAAAGGCAAAAACA-AAAAAAA-AAAAAGAA
* *
186761 AAAAGTGCAAAAGCAAAATAAAAAAAAGAA
1 AAAAG-GCAAAAACAAAAAAAAAAAAAGAA
186791 CAACAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 12 0.46
31 6 0.23
32 8 0.31
ACGTcount: A:0.77, C:0.08, G:0.10, T:0.05
Consensus pattern (29 bp):
AAAAGGCAAAAACAAAAAAAAAAAAAGAA
Found at i:187567 original size:19 final size:19
Alignment explanation
Indices: 187543--187598 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
187533 TTTCAACGAT
187543 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
187562 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
187576 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
187594 TTGTA
1 TTGTA
187599 ATGTATGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 11 0.35
15 2 0.06
17 2 0.06
19 16 0.52
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:187581 original size:13 final size:13
Alignment explanation
Indices: 187563--187587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187553 ACATAAGTGT
187563 TGTATCGATACAA
1 TGTATCGATACAA
187576 TGTATCGATACA
1 TGTATCGATACA
187588 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:187740 original size:52 final size:52
Alignment explanation
Indices: 187678--187806 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
187668 CACTGATCTT
* *
187678 TGTATTGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
*
187730 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
187782 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
187807 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
Found at i:191497 original size:20 final size:20
Alignment explanation
Indices: 191469--191543 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
191459 TTTTACCCAG
191469 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
191489 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
191509 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
191529 ATGTATCGATACATT
1 ATGTATCGATACATT
191544 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:191529 original size:40 final size:39
Alignment explanation
Indices: 191469--191546 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
191459 TTTTACCCAG
*
191469 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
191509 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
191547 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:209147 original size:13 final size:13
Alignment explanation
Indices: 209129--209158 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
209119 GGCGTCCTCC
209129 ACAAAAAAAAAAA
1 ACAAAAAAAAAAA
209142 ACAAAAAAAAAAA
1 ACAAAAAAAAAAA
209155 ACAA
1 ACAA
209159 CAATAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
ACAAAAAAAAAAA
Found at i:209170 original size:16 final size:16
Alignment explanation
Indices: 209131--209161 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
209121 CGTCCTCCAC
209131 AAAAAAAAAAAACAAA
1 AAAAAAAAAAAACAAA
*
209147 AAAAAAAAACAACAA
1 AAAAAAAAAAAACAA
209162 TAACAAAAAG
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:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAACAAA
Found at i:210667 original size:30 final size:29
Alignment explanation
Indices: 210594--210928 Score: 447
Period size: 27 Copynumber: 11.7 Consensus size: 29
210584 AGACATTCCT
* *
210594 CACCCTTTTCAAAAGCCCATAAATCAGTGG
1 CACCC-TTTCCAAAGCCCACAAATCAGTGG
*
210624 CAACC-TT-CAAAGCCCACAAATCAGTGG
1 CACCCTTTCCAAAGCCCACAAATCAGTGG
210651 CACCCTTTTCCAAAGCCCACAAATCAGTGG
1 CACCC-TTTCCAAAGCCCACAAATCAGTGG
210681 CACCCTTTCCAAAGCCCACAAATCAGTGG
1 CACCCTTTCCAAAGCCCACAAATCAGTGG
*
210710 CAACC-TT-CAAAGCCCACAAATCAGTGG
1 CACCCTTTCCAAAGCCCACAAATCAGTGG
210737 CACCCTTTTCCAAAGCCCACAAATCAGTGG
1 CACCC-TTTCCAAAGCCCACAAATCAGTGG
*
210767 CAACC-TT-CAAAGCCCACAAATCAGTGG
1 CACCCTTTCCAAAGCCCACAAATCAGTGG
*
210794 CACCCTTTTCCGAAGCCCACAAATCAGTGG
1 CACCC-TTTCCAAAGCCCACAAATCAGTGG
*
210824 CAACCTTT--AAAGCCCACAAATCAGTGG
1 CACCCTTTCCAAAGCCCACAAATCAGTGG
* *
210851 CACCCTTTTCCAAAGCTCACAAATTAGTGG
1 CACCC-TTTCCAAAGCCCACAAATCAGTGG
*
210881 CAACC-TT-CAAAGCCCACAAATCAGTGG
1 CACCCTTTCCAAAGCCCACAAATCAGTGG
*
210908 CACCATTTTCCAAAGCCCACA
1 CACC-CTTTCCAAAGCCCACA
210929 GGCCAGCGGC
Statistics
Matches: 271, Mismatches: 19, Indels: 30
0.85 0.06 0.09
Matches are distributed among these distances:
27 113 0.42
28 11 0.04
29 39 0.14
30 108 0.40
ACGTcount: A:0.33, C:0.34, G:0.14, T:0.19
Consensus pattern (29 bp):
CACCCTTTCCAAAGCCCACAAATCAGTGG
Found at i:210682 original size:57 final size:56
Alignment explanation
Indices: 210605--210957 Score: 503
Period size: 57 Copynumber: 6.2 Consensus size: 56
210595 ACCCTTTTCA
* * *
210605 AAAGCCCATAAATCAGTGGCAACC-TT-CAAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAATCAGTGGCACCCTTTCCAAAGCCCACAAATCAGTGGCAACC--TT-C
210662 AAAGCCCACAAATCAGTGGCACCCTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCACCCTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
210718 AAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCACCC-TTTCCAAAGCCCACAAATCAGTGGCAACCTTC
* *
210775 AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAATCAGTGGCAACCTTT
1 AAAGCCCACAAATCAGTGGCACCC-TTTCCAAAGCCCACAAATCAGTGGCAACCTTC
* *
210832 AAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCTCACAAATTAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCACCC-TTTCCAAAGCCCACAAATCAGTGGCAACCTTC
* *** *
210889 AAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACAGGCCAGCGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCACC-CTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
*
210946 TAAAGTCCACAA
1 -AAAGCCCACAA
210958 CTGCGTGGCA
Statistics
Matches: 274, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
56 25 0.09
57 213 0.78
58 12 0.04
59 24 0.09
ACGTcount: A:0.33, C:0.34, G:0.15, T:0.18
Consensus pattern (56 bp):
AAAGCCCACAAATCAGTGGCACCCTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
Found at i:211063 original size:71 final size:70
Alignment explanation
Indices: 210941--211114 Score: 203
Period size: 71 Copynumber: 2.5 Consensus size: 70
210931 CCAGCGGCAA
* * ** *
210941 CCTTCTAAAGTCCACAACTGC-GTGGCACT-TTTCTTCTTTTTAAAGCCCACAACTGTGCGGCGC
1 CCTTTTAAAGTCCACAACT-CTGTGGCACTCTTT-TTCCTTTTAAAGCCCACAACTCCGCGGCAC
211004 TCTTTTT
64 TCTTTTT
* * *
211011 CCTTTTTAAAGCCCACAACTCTGTGGACACTCTTTTTCCTTTT-AAGCTCACAACTCCGTGGCAC
1 CC-TTTTAAAGTCCACAACTCTGTGG-CACTCTTTTTCCTTTTAAAGCCCACAACTCCGCGGCAC
211075 TCTTTTT
64 TCTTTTT
*
211082 CCTTTT-AAGTCCACAACTCTGTGGCACCCTTTT
1 CCTTTTAAAGTCCACAACTCTGTGGCACTCTTTT
211115 AAGCCCACAA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
68 8 0.09
69 17 0.19
70 7 0.08
71 44 0.49
72 11 0.12
73 3 0.03
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (70 bp):
CCTTTTAAAGTCCACAACTCTGTGGCACTCTTTTTCCTTTTAAAGCCCACAACTCCGCGGCACTC
TTTTT
Found at i:211081 original size:34 final size:35
Alignment explanation
Indices: 210941--211114 Score: 194
Period size: 35 Copynumber: 5.0 Consensus size: 35
210931 CCAGCGGCAA
* *
210941 CCTTCTAAAGTCCACAACTGC-GTGGCACT-TTTCTT
1 CCTTTTAAAGCCCACAACT-CTGTGGCACTCTTT-TT
* * * *
210976 CTTTTTAAAGCCCACAACTGTGCGGCGCTCTTTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
211011 CCTTTTTAAAGCCCACAACTCTGTGGACACTCTTTTT
1 CC-TTTTAAAGCCCACAACTCTGTGG-CACTCTTTTT
* *
211048 CCTTTT-AAGCTCACAACTCCGTGGCACTCTTTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
* *
211082 CCTTTT-AAGTCCACAACTCTGTGGCACCCTTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
211115 AAGCCCACAA
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
34 39 0.33
35 41 0.34
36 28 0.24
37 11 0.09
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (35 bp):
CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
Found at i:211135 original size:27 final size:27
Alignment explanation
Indices: 211082--211157 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
211072 CACTCTTTTT
* * *
211082 CCTTTTAAGTCCACAACTCTGTGGCA-C
1 CCTTTTAAGCCCACAAGT-TGTAGCACC
211109 CCTTTTAAGCCCACAAGTTGGTAGCACC
1 CCTTTTAAGCCCACAAGTT-GTAGCACC
*
211137 CCTTTTCAAAACCCACAAGTT
1 CCTTTT--AAGCCCACAAGTT
211158 AGTGGCAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.02
27 21 0.51
28 7 0.17
30 12 0.29
ACGTcount: A:0.26, C:0.33, G:0.13, T:0.28
Consensus pattern (27 bp):
CCTTTTAAGCCCACAAGTTGTAGCACC
Found at i:211197 original size:28 final size:29
Alignment explanation
Indices: 211115--211220 Score: 96
Period size: 30 Copynumber: 3.6 Consensus size: 29
211105 GCACCCTTTT
*
211115 AAGCC-CACAAGTTGGTAGCACCCCTTTTCAA
1 AAGCCACACAAGTTGGT-GCA-ACC-TTTCAA
*
211146 AA-CC-CACAAGTTAGTGGCAACC-TTCAA
1 AAGCCACACAAGTTGGT-GCAACCTTTCAA
*
211173 AAG-CACAGAAGTTGGTGCAACCCTTTCAA
1 AAGCCACACAAGTTGGTGCAA-CCTTTCAA
211202 AAGCCCACACAAGTTGGTG
1 AAG-CCACACAAGTTGGTG
211221 GCATCTTCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
27 12 0.19
28 11 0.17
29 10 0.16
30 15 0.24
31 15 0.24
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (29 bp):
AAGCCACACAAGTTGGTGCAACCTTTCAA
Found at i:211348 original size:49 final size:49
Alignment explanation
Indices: 211227--211518 Score: 431
Period size: 49 Copynumber: 5.9 Consensus size: 49
211217 GGTGGCATCT
*
211227 TCTTCTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCAGCCTTTTCA
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CC--TTCA
* *
211280 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* *
211329 TCTTTAAGTCCAATATCGCTGACCTTGAATCAGCATATTGGCACCTTTA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * ** *
211378 CCTTTAAGTCCAATGTCGCTAACCTTGAATCAGCATATTGGCACCTTTA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * *
211427 CCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
211476 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
211519 TCTTTAACAT
Statistics
Matches: 224, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
49 182 0.81
51 2 0.01
52 36 0.16
53 4 0.02
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
Found at i:211381 original size:27 final size:27
Alignment explanation
Indices: 211350--211430 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
211340 AATATCGCTG
211350 ACCTTGAATCAGCATATTGGCACCTTT
1 ACCTTGAATCAGCATATTGGCACCTTT
* * * *
211377 ACCTTTAAGTC--CA-A-TGTC-GC-TA
1 ACCTTGAA-TCAGCATATTGGCACCTTT
211399 ACCTTGAATCAGCATATTGGCACCTTT
1 ACCTTGAATCAGCATATTGGCACCTTT
211426 ACCTT
1 ACCTT
211431 TAAGTCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
21 2 0.05
22 8 0.21
23 3 0.08
24 4 0.10
25 4 0.10
26 3 0.08
27 13 0.33
28 2 0.05
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (27 bp):
ACCTTGAATCAGCATATTGGCACCTTT
Found at i:211502 original size:147 final size:150
Alignment explanation
Indices: 211232--211524 Score: 484
Period size: 147 Copynumber: 2.0 Consensus size: 150
211222 CATCTTCTTC
** *
211232 TAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCAGCCTTTTCATCTTTAAGTCCAATGTC
1 TAAGTCCAATATCACTAACCTTGAATCAGCATATTGGCAGCCTTTTCACCTTTAAGTCCAATGTC
*
211297 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGACCTTGAATCAG
66 GCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGACCTTGAATCAG
211362 CATATTGGCACCTTTACCTT
131 CATATTGGCACCTTTACCTT
* *
211382 TAAGTCCAATGTCGCTAACCTTGAATCAGCATATTGGCA-CC-TTT-ACCTTTAAGTCCAATGTC
1 TAAGTCCAATATCACTAACCTTGAATCAGCATATTGGCAGCCTTTTCACCTTTAAGTCCAATGTC
* *
211444 GCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
66 GCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGACCTTGAATCAG
*
211509 CATATTGGCATCTTTA
131 CATATTGGCACCTTTA
211525 ACATTCCTAA
Statistics
Matches: 134, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
147 94 0.70
148 3 0.02
149 2 0.01
150 35 0.26
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (150 bp):
TAAGTCCAATATCACTAACCTTGAATCAGCATATTGGCAGCCTTTTCACCTTTAAGTCCAATGTC
GCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGACCTTGAATCAG
CATATTGGCACCTTTACCTT
Found at i:212372 original size:32 final size:32
Alignment explanation
Indices: 212336--212406 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
212326 TTCAACGATT
212336 TGTATCGATACAAAAGTGTTGTATCGATACAA
1 TGTATCGATACAAAAGTGTTGTATCGATACAA
* * *
212368 TGTATCGATACATATGTTTTGTATCGATACAA
1 TGTATCGATACAAAAGTGTTGTATCGATACAA
212400 TGTATCG
1 TGTATCG
212407 TTACGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAAGTGTTGTATCGATACAA
Found at i:212373 original size:13 final size:14
Alignment explanation
Indices: 212355--212384 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
212345 ACAAAAGTGT
212355 TGTATCGATACA-A
1 TGTATCGATACATA
212368 TGTATCGATACATA
1 TGTATCGATACATA
212382 TGT
1 TGT
212385 TTTGTATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (14 bp):
TGTATCGATACATA
Found at i:212547 original size:52 final size:52
Alignment explanation
Indices: 212483--212611 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
212473 ACACTGATCT
*
212483 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
*
212535 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
212587 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
212612 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAA
Found at i:216635 original size:28 final size:28
Alignment explanation
Indices: 216542--217271 Score: 718
Period size: 28 Copynumber: 25.2 Consensus size: 28
216532 AGTCCATGAT
*
216542 TCAGTGGCATTCCTTTTTAAAGCCCACAAG
1 TCAGTGGCA-TCC-TTTCAAAGCCCACAAG
216572 TCAGTGGCATCCTTTCAAAAGCCCACAAG
1 TCAGTGGCATCCTTTC-AAAGCCCACAAG
* *
216601 TCAGTGGCATCCTTTCAAAACTCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * *
216629 TCAGTGGTATCCTTTCAAAGCCTATAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
216657 TTAGTGGCATCCTTTCTAAAG-CCATAAG
1 TCAGTGGCATCCTTTC-AAAGCCCACAAG
*
216685 TCAGTGGCATCCTTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
216713 TAAGTGGTATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
*
216741 TCAGTGGCATCCTTTCAAAGTCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
216769 TCAGTGACATCTTTTCAAAAGCCCACAAG
1 TCAGTGGCATCCTTTC-AAAGCCCACAAG
* * *
216798 TTAGTGGCATCTTTTTTTTCAAAGCCCACAAC
1 TCAGTGGCATC----CTTTCAAAGCCCACAAG
* * *
216830 TCCGTGGCACCCTTTCAAAG-CTACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
*
216857 TCAGTGGCATCCTTTCAAAGCCTACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
216885 TCAGTGGCATCTTTTCAAAGCCTACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * *
216913 TCAGTGGTA-CGCTTTTAAAGCCCACACAAA
1 TCAGTGGCATC-CTTTCAAAG-CC-CACAAG
*
216943 TC-GATGGCGT-CTTTCCAAAGCCCACAAG
1 TCAG-TGGCATCCTTT-CAAAGCCCACAAG
** *
216971 TCAGTGGCATTTTTTTTAAAGCCCACAAG
1 TCAGTGGCA-TCCTTTCAAAGCCCACAAG
*
217000 TCAGTGGCATCCTTTCAAAAGCCTACAAG
1 TCAGTGGCATCCTTTC-AAAGCCCACAAG
* *
217029 TCAGTAGCATCCTTTCAAAACCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
*
217057 TTAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
217085 TCAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
217113 TTAGTGACATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * * * * *
217141 TTAGCGACATCTTCTTTTTCAAAACTCACAAC
1 TCAGTGGCATC--C--TTTCAAAGCCCACAAG
*
217173 TCCA-TGGCA-CCATTTCAAAGCTCACAAG
1 T-CAGTGGCATCC-TTTCAAAGCCCACAAG
*
217201 TCAGTGGCACCCTTCTCTAAAGCCTACACAAG
1 TCAGTGGCATCCTT-TC-AAAGCC--CACAAG
* *
217233 TCGGTGGCAACCCTTTCCAAAGTCCACACAAG
1 TCAGTGGC-ATCCTTT-CAAAG-CC-CACAAG
*
217265 TCGGTGG
1 TCAGTGG
217272 AAACCCCTTT
Statistics
Matches: 597, Mismatches: 70, Indels: 64
0.82 0.10 0.09
Matches are distributed among these distances:
27 30 0.05
28 334 0.56
29 118 0.20
30 31 0.05
31 1 0.00
32 68 0.11
33 15 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (28 bp):
TCAGTGGCATCCTTTCAAAGCCCACAAG
Found at i:216914 original size:172 final size:173
Alignment explanation
Indices: 216542--217271 Score: 779
Period size: 172 Copynumber: 4.2 Consensus size: 173
216532 AGTCCATGAT
*
216542 TCAGTGGCATTCCTTTTTAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAGTG
1 TCAGTGGCA-TCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTC-AAAGCCCACAAGTCAGTG
* * * * * * * * *
216607 GCATCCTTTCAAAA-CTCACAAGTCAGTGGTATC----CTTTCAAAGCCTATAAGTTAGTGGCAT
63 ACATCCTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTTTTCAAAGCCCACAACTCAGTGGCAC
* * * *
216667 CCTTTCTAAAGCCATAAGTCAGTGGCATCCTTTCAAAGCCCATAAG
128 CCTTTCAAAAGCTACAAGTCAGTGGCATCCTTTCAAAGCCCACAAG
* * *
216713 TAAGTGGTATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGACA
1 TCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGACA
* * *
216778 TCTTTTCAAAAGCCCACAAGTTAGTGGCATCTTTTTTTTCAAAGCCCACAACTCCGTGGCACCCT
66 TCCTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTTTTCAAAGCCCACAACTCAGTGGCACCCT
*
216843 TTC-AAAGCTACAAGTCAGTGGCATCCTTTCAAAGCCTACAAG
131 TTCAAAAGCTACAAGTCAGTGGCATCCTTTCAAAGCCCACAAG
* * * * *
216885 TCAGTGGCATCTTTTCAAAGCCTACAAGTCAGTGGTA-CGCTTTTAAAGCCCACACAAATC-GAT
1 TCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAG-CC-CACAAGTCAG-T
* * * *
216948 GGCGT-CTTTCCAAAGCCCACAAGTCAGTGGCA--TTTTTTTT-AAAGCCCACAAGTCAGTGGCA
62 GACATCCTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTTTTCAAAGCCCACAACTCAGTGGCA
* * *
217009 TCCTTTCAAAAGCCTACAAGTCAGTAGCATCCTTTCAAAACCCACAAG
127 CCCTTTCAAAAG-CTACAAGTCAGTGGCATCCTTTCAAAGCCCACAAG
* *
217057 TTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGACA
1 TCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGACA
* * * * * * *
217122 TCCTTTC-AAAGCCCACAAGTTAGCGACATCTTCTTTTTCAAAACTCACAACTCCA-TGGCACCA
66 TCCTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTTTTCAAAGCCCACAACT-CAGTGGCACCC
*
217185 TTTC-AAAGCTCACAAGTCAGTGGCACCCTTCTCTAAAGCCTACACAAG
130 TTTCAAAAGCT-ACAAGTCAGTGGCATCCTT-TC-AAAGCC--CACAAG
* * *
217233 TCGGTGGCAACCCTTTCCAAAGTCCACACAAGTCGGTGG
1 TCAGTGGC-ATCCTTT-CAAAG-CC-CACAAGTCAGTGG
217272 AAACCCCTTT
Statistics
Matches: 468, Mismatches: 64, Indels: 45
0.81 0.11 0.08
Matches are distributed among these distances:
168 29 0.06
169 47 0.10
170 56 0.12
171 30 0.06
172 176 0.38
173 75 0.16
174 18 0.04
176 12 0.03
177 6 0.01
178 5 0.01
179 2 0.00
180 12 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (173 bp):
TCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGACA
TCCTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTTTTCAAAGCCCACAACTCAGTGGCACCCT
TTCAAAAGCTACAAGTCAGTGGCATCCTTTCAAAGCCCACAAG
Found at i:217240 original size:32 final size:32
Alignment explanation
Indices: 217195--217277 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 32
217185 TTTCAAAGCT
* *
217195 CACAAGTCAGTGGC-ACCCTTCTCTAAAG-CCTA
1 CACAAGTCGGTGGCAACCCTT-TCCAAAGTCC-A
217227 CACAAGTCGGTGGCAACCCTTTCCAAAGTCCA
1 CACAAGTCGGTGGCAACCCTTTCCAAAGTCCA
*
217259 CACAAGTCGGTGGAAACCC
1 CACAAGTCGGTGGCAACCC
217278 CTTTTAAGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 38 0.83
33 8 0.17
ACGTcount: A:0.29, C:0.34, G:0.19, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCTTTCCAAAGTCCA
Found at i:219039 original size:97 final size:97
Alignment explanation
Indices: 218909--219236 Score: 450
Period size: 97 Copynumber: 3.4 Consensus size: 97
218899 CTATTTATTA
* * * * * *
218909 GGGATACTCTAACCCTATTCCTCCGAGAGGATACTCTAACCCCACTTTTAAACACATCAAAGTTT
1 GGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTT
*
218974 AAATCTTATTCTCACTTAAATTGTCATCATTG
66 AAATCTTATTCTCACTCAAATTGTCATCATTG
*
219006 GGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACTCCGCTTTTAAACACATC-AAG-TT
1 GGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTT
* * *
219069 --ATTTTATTCTCACTCAAATTGTTATCATCG
66 AAATCTTATTCTCACTCAAATTGTCATCATTG
* * * *
219099 GGCATACTCCAACCTCATTCCTCCGAGGGGATGCTCCAACCCCGCTTTTAAACACATCAAAGTTT
1 GGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTT
219164 AAATCTTATTCTCACTCAAATTGTCATCATTG
66 AAATCTTATTCTCACTCAAATTGTCATCATTG
* * * *
219196 GGGACACTCCAACCCGATTCTTCTGA-GGGATACTCTAACCC
1 GGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCC
219237 TGTTTTTCAA
Statistics
Matches: 200, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
93 79 0.40
94 3 0.01
95 4 0.02
96 16 0.08
97 98 0.49
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (97 bp):
GGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTT
AAATCTTATTCTCACTCAAATTGTCATCATTG
Found at i:220245 original size:24 final size:24
Alignment explanation
Indices: 220218--220270 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
220208 ACAATAAAAA
220218 ATGCACTATAATTTTGTAATACTT
1 ATGCACTATAATTTTGTAATACTT
* *
220242 ATGCATTGTAATTTTGTAATACTT
1 ATGCACTATAATTTTGTAATACTT
220266 ATGCA
1 ATGCA
220271 TTATGAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (24 bp):
ATGCACTATAATTTTGTAATACTT
Found at i:220271 original size:24 final size:24
Alignment explanation
Indices: 220226--220272 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
220216 AAATGCACTA
220226 TAATTTTGTAATACTTATGCATTG
1 TAATTTTGTAATACTTATGCATTG
220250 TAATTTTGTAATACTTATGCATT
1 TAATTTTGTAATACTTATGCATT
220273 ATGAGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (24 bp):
TAATTTTGTAATACTTATGCATTG
Found at i:225418 original size:18 final size:19
Alignment explanation
Indices: 225395--225432 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
225385 GGTTTAAATT
225395 ATTTATTTAA-ATTTAAAA
1 ATTTATTTAATATTTAAAA
225413 ATTTATTTAATATTTAAAA
1 ATTTATTTAATATTTAAAA
225432 A
1 A
225433 GATTGAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATTTAATATTTAAAA
Found at i:226579 original size:21 final size:23
Alignment explanation
Indices: 226532--226581 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
226522 TAAATTAAAA
*
226532 TTTTATTTTTAATATTTATAATT
1 TTTTATTTTTAATATTTACAATT
*
226555 TTTTATTTTTAA-A-TTACAGTT
1 TTTTATTTTTAATATTTACAATT
226576 TTTTAT
1 TTTTAT
226582 AAAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 1 0.04
23 12 0.48
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTATTTTTAATATTTACAATT
Found at i:227005 original size:20 final size:19
Alignment explanation
Indices: 226964--227038 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
226954 AAAATATAAA
226964 AAAATAAATTA-AAAATAATT
1 AAAA-AAATTATAAAA-AATT
* *
226984 AAGAAAATTTTTAAAAAATT
1 AA-AAAAATTATAAAAAATT
227004 AAAAAAATTATAAAAAATT
1 AAAAAAATTATAAAAAATT
*
227023 -ATAAAATTA-AAAAAAT
1 AAAAAAATTATAAAAAAT
227039 AATTTAAGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.15
18 8 0.17
19 15 0.31
20 12 0.25
21 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (19 bp):
AAAAAAATTATAAAAAATT
Found at i:227007 original size:8 final size:8
Alignment explanation
Indices: 226994--227036 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
226984 AAGAAAATTT
226994 TTAAAAAA
1 TTAAAAAA
227002 TTAAAAAAA
1 TT-AAAAAA
227011 TTATAAAAAA
1 -T-TAAAAAA
*
227021 TTATAAAA
1 TTAAAAAA
227029 TTAAAAAA
1 TTAAAAAA
227037 ATAATTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 15 0.50
9 7 0.23
10 7 0.23
11 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TTAAAAAA
Found at i:227008 original size:9 final size:9
Alignment explanation
Indices: 226964--227038 Score: 71
Period size: 10 Copynumber: 7.9 Consensus size: 9
226954 AAAATATAAA
226964 AAAATAAATT
1 AAAA-AAATT
226974 AAAAATAATT
1 AAAAA-AATT
*
226984 AAGAAAATTTT
1 AA-AAAA-ATT
*
226995 TAAAAAATT
1 AAAAAAATT
227004 AAAAAAATT
1 AAAAAAATT
227013 ATAAAAAATT
1 A-AAAAAATT
*
227023 -ATAAAATT
1 AAAAAAATT
227031 AAAAAAAT
1 AAAAAAAT
227039 AATTTAAGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
8 7 0.13
9 18 0.33
10 23 0.43
11 6 0.11
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAAAAATT
Found at i:227019 original size:29 final size:27
Alignment explanation
Indices: 226969--227038 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
226959 ATAAAAAAAT
*
226969 AAATTAAAAATAATTAAGAAAATTTTTAAA
1 AAATTAAAAA-AATTAAGAAAA--ATTAAA
*
226999 AAATTAAAAAAATTATA-AAAAATTATA
1 AAATTAAAAAAATTA-AGAAAAATTAAA
227026 AAATTAAAAAAAT
1 AAATTAAAAAAAT
227039 AATTTAAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 17 0.46
29 9 0.24
30 11 0.30
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (27 bp):
AAATTAAAAAAATTAAGAAAAATTAAA
Found at i:227533 original size:15 final size:16
Alignment explanation
Indices: 227498--227540 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
227488 CTGGTCCAAA
227498 ATAATATATATTTTAAAT
1 ATAATA-ATA-TTTAAAT
227516 ATAATAATATTT-AAT
1 ATAATAATATTTAAAT
*
227531 ATAATTATAT
1 ATAATAATAT
227541 AAATATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 12 0.50
16 3 0.12
17 3 0.12
18 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAATAATATTTAAAT
Found at i:227535 original size:5 final size:5
Alignment explanation
Indices: 227513--227583 Score: 50
Period size: 5 Copynumber: 15.4 Consensus size: 5
227503 ATATATTTTA
* *
227513 AATAT AATA- ATATTT AATAT AAT-T -ATAT AAATAT TATAT AA-A- AATA-
1 AATAT AATAT A-ATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT
227559 AATAT AATAT AATAT AA-AT -ATAT AA
1 AATAT AATAT AATAT AATAT AATAT AA
227584 ATATTTTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
3 5 0.09
4 13 0.25
5 30 0.57
6 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:227539 original size:21 final size:21
Alignment explanation
Indices: 227497--227652 Score: 62
Period size: 21 Copynumber: 7.6 Consensus size: 21
227487 ACTGGTCCAA
* * *
227497 AATAATATATATTTTAAATAT
1 AATAATATTTAATATAAATAT
*
227518 AATAATATTTAATATAATTAT
1 AATAATATTTAATATAAATAT
*
227539 -ATAA-ATATT-ATATAAAAAT
1 AATAATAT-TTAATATAAATAT
*
227558 AA-ATATAATATAATATAAATAT
1 AATA-AT-ATTTAATATAAATAT
227580 -ATAAATATTT--TA-AAAT-T
1 AAT-AATATTTAATATAAATAT
* * * *
227597 TATATTATATAAATTATTAATAT
1 AATAATAT-TTAA-TATAAATAT
* *
227620 ATTAAAATTTAA-ATAAATAT
1 AATAATATTTAATATAAATAT
*
227640 AAAAATATATTAA
1 AATAATAT-TTAA
227653 ACACAAGTAT
Statistics
Matches: 98, Mismatches: 21, Indels: 32
0.65 0.14 0.21
Matches are distributed among these distances:
17 5 0.05
18 7 0.07
19 13 0.13
20 20 0.20
21 28 0.29
22 19 0.19
23 6 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAATATTTAATATAAATAT
Found at i:227559 original size:17 final size:16
Alignment explanation
Indices: 227539--227580 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
227529 ATATAATTAT
*
227539 ATAAATATTATATAAAA
1 ATAAATATAATAT-AAA
*
227556 ATAAATATAATATAAT
1 ATAAATATAATATAAA
227572 ATAAATATA
1 ATAAATATA
227581 TAAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAATATAATATAAA
Found at i:227625 original size:32 final size:33
Alignment explanation
Indices: 227565--227648 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
227555 AATAAATATA
*
227565 ATATAATATAAATATATAAATATTTTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
* *
227598 ATATTATATAAAT-TATTAATATATTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
* *
227630 AAATAAATATAAAAATATA
1 ATAT-AATATAAATATATA
227649 TTAAACACAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 20 0.48
33 19 0.45
34 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATTAAAATTT
Found at i:227642 original size:17 final size:17
Alignment explanation
Indices: 227496--227643 Score: 51
Period size: 16 Copynumber: 8.8 Consensus size: 17
227486 AACTGGTCCA
* *
227496 AAAT-AATATATATTTT
1 AAATAAATATAAAATTT
* *
227512 AAATATA-ATAATATTT
1 AAATAAATATAAAATTT
*
227528 AATATAATTATATAAATATT
1 AA-ATAAATATA-AAAT-TT
* * *
227548 ATATAAAAAT-AAATAT
1 AAATAAATATAAAATTT
*
227564 -AATATAATATAAATATAT
1 AAATA-AATATAAA-ATTT
* *
227582 AAAT-ATTTTAAAATTT
1 AAATAAATATAAAATTT
* *
227598 ATAT-TATAT-AAATTAT
1 AAATAAATATAAAATT-T
* *
227614 TAATATAT-TAAAATTT
1 AAATAAATATAAAATTT
227630 AAATAAATATAAAA
1 AAATAAATATAAAA
227644 ATATATTAAA
Statistics
Matches: 95, Mismatches: 24, Indels: 25
0.66 0.17 0.17
Matches are distributed among these distances:
15 8 0.08
16 36 0.38
17 29 0.31
18 7 0.07
19 12 0.13
20 3 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATATAAAATTT
Found at i:227868 original size:27 final size:27
Alignment explanation
Indices: 227838--227892 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
227828 TTTATTTTTA
227838 TTAAAATTTAAATAATTAAAATA-TAAT
1 TTAAAATTTAAAT-ATTAAAATATTAAT
* *
227865 TTAAAATTTTAATATTAAATTATTAAT
1 TTAAAATTTAAATATTAAAATATTAAT
227892 T
1 T
227893 ATATAAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAAATTTAAATATTAAAATATTAAT
Found at i:233226 original size:11 final size:11
Alignment explanation
Indices: 233210--233235 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
233200 TCCCTTCTTA
233210 CAAATCAAGAC
1 CAAATCAAGAC
233221 CAAATCAAGAC
1 CAAATCAAGAC
233232 CAAA
1 CAAA
233236 AAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.27, G:0.08, T:0.08
Consensus pattern (11 bp):
CAAATCAAGAC
Found at i:234624 original size:20 final size:20
Alignment explanation
Indices: 234599--234638 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
234589 ATGATATAAG
234599 CTTCTTGATAATAATACAAA
1 CTTCTTGATAATAATACAAA
**
234619 CTTCTTGATGGTAATACAAA
1 CTTCTTGATAATAATACAAA
234639 ACTTGTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
CTTCTTGATAATAATACAAA
Found at i:235223 original size:38 final size:34
Alignment explanation
Indices: 235174--235247 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
235164 ACAACTTCTC
*
235174 ATTATCCTATATTGTGACTCTCTATCTATGCAGATATT
1 ATTATCCTATATTGTG---C-CTATCTATGCACATATT
*
235212 ATTATCTTATATTGTGCCTATCTATGCACATATT
1 ATTATCCTATATTGTGCCTATCTATGCACATATT
235246 AT
1 AT
235248 CATATGCCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 18 0.53
35 1 0.03
38 15 0.44
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.46
Consensus pattern (34 bp):
ATTATCCTATATTGTGCCTATCTATGCACATATT
Found at i:236021 original size:43 final size:43
Alignment explanation
Indices: 235959--236041 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
235949 AAAATGAAGG
* *
235959 AGATTATGCTATAGCTTTTCTGAGGAAATTGGGACAGCTCAGA
1 AGATTATACTATAGCTTTTCTAAGGAAATTGGGACAGCTCAGA
* * *
236002 AGATTATACTGTAGTTTTTCTAAGGAAATTGGTACAGCTC
1 AGATTATACTATAGCTTTTCTAAGGAAATTGGGACAGCTC
236042 CAATGTCAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (43 bp):
AGATTATACTATAGCTTTTCTAAGGAAATTGGGACAGCTCAGA
Found at i:236989 original size:3 final size:3
Alignment explanation
Indices: 236981--237012 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
236971 AGATTACATT
236981 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
237013 TATTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:237017 original size:3 final size:3
Alignment explanation
Indices: 237011--237046 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
237001 AATAATAATA
237011 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
237047 TTTGTGGCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:237698 original size:14 final size:15
Alignment explanation
Indices: 237669--237701 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
237659 TATTTAATTG
237669 AATAAAATCAAAATCA
1 AATAAAAT-AAAATCA
237685 AATAAAAT-AAATCA
1 AATAAAATAAAATCA
237699 AAT
1 AAT
237702 GATTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAAAATAAAATCA
Found at i:238522 original size:2 final size:2
Alignment explanation
Indices: 238468--238512 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
238458 TGAACTCGTG
238468 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
238510 TA T
1 TA T
238513 TGGTATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:238681 original size:2 final size:2
Alignment explanation
Indices: 238676--238709 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
238666 ATTCAAAATC
238676 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
238710 TGCTGGAACA
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:239597 original size:6 final size:6
Alignment explanation
Indices: 239586--239626 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
239576 AAAGGACATA
*
239586 TATATC TATATC TATATC TATA-- TATATA TATATC -ATATC TA
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TA
239627 AAGTATTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
4 4 0.13
5 5 0.16
6 22 0.71
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATC
Found at i:239784 original size:2 final size:2
Alignment explanation
Indices: 239779--239803 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
239769 GTGTGTGTGT
239779 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
239804 TTAAAGGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:242957 original size:19 final size:18
Alignment explanation
Indices: 242924--242963 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
242914 ACACAATTAT
242924 AATATAATAAAATATATA
1 AATATAATAAAATATATA
242942 AATATAATATAAATATATA
1 AATATAATA-AAATATATA
242961 AAT
1 AAT
242964 TATCAAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAATAAAATATATA
Found at i:243039 original size:12 final size:12
Alignment explanation
Indices: 243022--243048 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
243012 TATATGCATG
243022 TTGTATTTGGGA
1 TTGTATTTGGGA
243034 TTGTATTTGGGA
1 TTGTATTTGGGA
243046 TTG
1 TTG
243049 GCAGCCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (12 bp):
TTGTATTTGGGA
Found at i:243247 original size:2 final size:2
Alignment explanation
Indices: 243240--243267 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
243230 CATTTGTATT
243240 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
243268 AAGTTTTAAT
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:243565 original size:28 final size:28
Alignment explanation
Indices: 243529--243585 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
243519 TTTAAAATAT
*
243529 ATTTATTAAAAATAATTTTTTATTTTAAA
1 ATTTATTAAAAATAATTTTTT-TTTAAAA
*
243558 ATTT-TTAATAATAATTTTTTTTTAAAA
1 ATTTATTAAAAATAATTTTTTTTTAAAA
243585 A
1 A
243586 AATAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 7 0.27
28 15 0.58
29 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTATTAAAAATAATTTTTTTTTAAAA
Found at i:243586 original size:28 final size:29
Alignment explanation
Indices: 243518--243586 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 29
243508 ATAAACATAA
243518 TTTTAAAATATATTTATTAAAAATAATTTTT
1 TTTTAAAA-A-ATTTATTAAAAATAATTTTT
* *
243549 TATTT-TAAAATTT-TTAATAATAATTTTT
1 T-TTTAAAAAATTTATTAAAAATAATTTTT
243577 TTTTAAAAAA
1 TTTTAAAAAA
243587 ATAATTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 3 0.09
28 19 0.58
29 4 0.12
30 1 0.03
31 3 0.09
32 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTTAAAAAATTTATTAAAAATAATTTTT
Found at i:244028 original size:29 final size:29
Alignment explanation
Indices: 243983--244051 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
243973 CTATGATTTA
* * **
243983 TAAAAATT-TTAAATTTTAAATTTAAT-T
1 TAAAAATTATTTATTTTTAAATAAAATAT
*
244010 TAAAATATTATTTATTTTTTAATAAAATAT
1 TAAAA-ATTATTTATTTTTAAATAAAATAT
244040 TAAAAATTATTT
1 TAAAAATTATTT
244052 TTATAATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 5 0.15
28 3 0.09
29 20 0.59
30 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TAAAAATTATTTATTTTTAAATAAAATAT
Found at i:244072 original size:25 final size:25
Alignment explanation
Indices: 244015--244072 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
244005 TAATTTAAAA
*
244015 TATTATTTATTTTTTAATAAAATAT
1 TATTAATTATTTTTTAATAAAATAT
** *
244040 TAAAAATTATTTTTATAATAATAT-T
1 TATTAATTATTTTT-TAATAAAATAT
244065 TATTAATT
1 TATTAATT
244073 TTAAATATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTAATTATTTTTTAATAAAATAT
Found at i:244105 original size:21 final size:21
Alignment explanation
Indices: 244067--244117 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 21
244057 ATAATATTTA
244067 TTAATTTTAAATATTTATTAT
1 TTAATTTTAAATATTTATTAT
*
244088 TTAATTTT---TAATTATTAT
1 TTAATTTTAAATATTTATTAT
*
244106 TTTATTTTAAAT
1 TTAATTTTAAAT
244118 CAAATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 16 0.64
21 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTAATTTTAAATATTTATTAT
Found at i:244589 original size:3 final size:3
Alignment explanation
Indices: 244581--244607 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
244571 TTAAATTCGT
244581 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
244608 TCAAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:245072 original size:16 final size:16
Alignment explanation
Indices: 245053--245087 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
245043 TTTAAAATAA
245053 TAAAAAACCCATAAAC
1 TAAAAAACCCATAAAC
* *
245069 TAAAAAACTCGTAAAC
1 TAAAAAACCCATAAAC
245085 TAA
1 TAA
245088 CCTAATAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (16 bp):
TAAAAAACCCATAAAC
Found at i:245592 original size:15 final size:16
Alignment explanation
Indices: 245564--245594 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
245554 AACATTTTTA
245564 AAATTTTATAATTATT
1 AAATTTTATAATTATT
245580 AAATTTT-TAATTATT
1 AAATTTTATAATTATT
245595 TATTTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTTATAATTATT
Found at i:246654 original size:13 final size:13
Alignment explanation
Indices: 246607--246651 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
246597 AATTTAGTGG
*
246607 AAAAATTGTGTTT
1 AAAAATTGTGATT
246620 AAAAATTGTGA-T
1 AAAAATTGTGATT
246632 AAAAATT-TGATT
1 AAAAATTGTGATT
246644 CAAAAATT
1 -AAAAATT
246652 TGAAGTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 3 0.10
12 9 0.31
13 17 0.59
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (13 bp):
AAAAATTGTGATT
Found at i:247215 original size:14 final size:15
Alignment explanation
Indices: 247192--247225 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
247182 AATTATATTT
*
247192 ATAAATAATAAT-AA
1 ATAAAAAATAATAAA
247206 ATAAAAAATAATAAA
1 ATAAAAAATAATAAA
247221 ATAAA
1 ATAAA
247226 TCTTTACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAAAAATAATAAA
Found at i:247564 original size:23 final size:23
Alignment explanation
Indices: 247520--247579 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
247510 GATGATTATG
*
247520 AATATAATATAATTAAATAATAA-
1 AATATAATATAA-AAAATAATAAT
*
247543 AATTATAATTTAAAAAATAATAAT
1 AA-TATAATATAAAAAATAATAAT
247567 AATATAATATAAA
1 AATATAATATAAA
247580 TATATGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 21 0.66
24 11 0.34
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AATATAATATAAAAAATAATAAT
Found at i:247633 original size:32 final size:33
Alignment explanation
Indices: 247568--247651 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 33
247558 AATAATAATA
*
247568 ATATAATATAAATATATGAATATTTTAAAATTT
1 ATATAAAATAAATATATGAATATTTTAAAATTT
*
247601 ATATAAAATAAAT-TATTAAT-TTATTAAAATTT
1 ATATAAAATAAATATATGAATATT-TTAAAATTT
247633 ATATAAATATAAAATATAT
1 ATATAAA-AT-AAATATAT
247652 AAAATATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
31 2 0.04
32 22 0.49
33 14 0.31
34 4 0.09
35 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (33 bp):
ATATAAAATAAATATATGAATATTTTAAAATTT
Found at i:247643 original size:8 final size:8
Alignment explanation
Indices: 247632--247704 Score: 73
Period size: 8 Copynumber: 9.1 Consensus size: 8
247622 TATTAAAATT
247632 TATATAAA
1 TATATAAA
247640 TATA-AAA
1 TATATAAA
247647 TATATAAA
1 TATATAAA
247655 -ATAT-AA
1 TATATAAA
247661 T-TATAATA
1 TATATAA-A
*
247669 TATAAAAA
1 TATATAAA
247677 TATATAAATA
1 TATAT-AA-A
247687 TGATATAAA
1 T-ATATAAA
247696 TATATAAA
1 TATATAAA
247704 T
1 T
247705 TATTAAGCCT
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
6 5 0.09
7 12 0.22
8 22 0.40
9 8 0.15
10 4 0.07
11 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (8 bp):
TATATAAA
Found at i:247665 original size:22 final size:21
Alignment explanation
Indices: 247633--247704 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
247623 ATTAAAATTT
247633 ATATAAATATAAAATATATAAA
1 ATATAAATATAAAATATA-AAA
* *
247655 ATATAATTATAATATATAAAA
1 ATATAAATATAAAATATAAAA
** *
247676 ATATATAA-ATATGATATAAAT
1 ATATA-AATATAAAATATAAAA
247697 ATATAAAT
1 ATATAAAT
247705 TATTAAGCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
20 2 0.05
21 23 0.55
22 17 0.40
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (21 bp):
ATATAAATATAAAATATAAAA
Found at i:247673 original size:29 final size:28
Alignment explanation
Indices: 247633--247703 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
247623 ATTAAAATTT
247633 ATATAA-ATAT-AAAATATATAAAATATA
1 ATATAATATATAAAAATATAT-AAATATA
*
247660 ATTATAATATATAAAAATATATAAATATG
1 A-TATAATATATAAAAATATATAAATATA
247689 ATATAAATATATAAA
1 ATAT-AATATATAAA
247704 TTATTAAGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
27 1 0.03
28 8 0.21
29 21 0.54
30 9 0.23
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (28 bp):
ATATAATATATAAAAATATATAAATATA
Found at i:247677 original size:47 final size:49
Alignment explanation
Indices: 247600--247703 Score: 135
Period size: 47 Copynumber: 2.2 Consensus size: 49
247590 TTTTAAAATT
* * *
247600 TATATAAAATAAATTATTAATTTATTAAAATTTATATAA-AT-ATA-AAA
1 TATATAAAATAAATTATTAATATATAAAAATATATA-AATATGATATAAA
247647 TATATAAAATATAATTA-TAATATATAAAAATATATAAATATGATATAAA
1 TATATAAAATA-AATTATTAATATATAAAAATATATAAATATGATATAAA
247696 TATATAAA
1 TATATAAA
247704 TTATTAAGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
46 2 0.04
47 29 0.58
48 8 0.16
49 11 0.22
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (49 bp):
TATATAAAATAAATTATTAATATATAAAAATATATAAATATGATATAAA
Found at i:247694 original size:11 final size:10
Alignment explanation
Indices: 247627--247701 Score: 65
Period size: 9 Copynumber: 7.9 Consensus size: 10
247617 TAATTTATTA
*
247627 AAATTTATAT
1 AAATATATAT
247637 -AA-ATATA-
1 AAATATATAT
247644 AAATATATA-
1 AAATATATAT
247653 AAATATA-ATT
1 AAATATATA-T
247663 ATAATATATA-
1 A-AATATATAT
247673 AAA-ATATAT
1 AAATATATAT
247682 AAATATGATAT
1 AAATAT-ATAT
247693 AAATATATA
1 AAATATATA
247702 AATTATTAAG
Statistics
Matches: 55, Mismatches: 1, Indels: 18
0.74 0.01 0.24
Matches are distributed among these distances:
8 12 0.22
9 19 0.35
10 7 0.13
11 16 0.29
12 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (10 bp):
AAATATATAT
Found at i:248791 original size:19 final size:20
Alignment explanation
Indices: 248769--248816 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
248759 TTTTCTTCCA
248769 AAATATTTTCTTTT-CAC-AT
1 AAATATTTT-TTTTCCACTAT
248788 AAAT-TTTTTTTTCCACTAT
1 AAATATTTTTTTTCCACTAT
*
248807 ACATATTTTT
1 AAATATTTTT
248817 AATTTCTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.16
18 7 0.28
19 9 0.36
20 5 0.20
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATATTTTTTTTCCACTAT
Found at i:249359 original size:2 final size:2
Alignment explanation
Indices: 249352--249382 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
249342 AAAGATATTA
249352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
249383 CATACACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:251364 original size:2 final size:2
Alignment explanation
Indices: 251357--251386 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
251347 TGGATTGCTG
251357 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
251387 TGAAATTCAA
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):
AT
Found at i:254171 original size:3 final size:3
Alignment explanation
Indices: 254163--254206 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
254153 TATTAAAAAC
254163 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
254207 TACATAAATA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:255069 original size:18 final size:18
Alignment explanation
Indices: 255048--255082 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
255038 GGTACATAAT
255048 ATATAAAATATATAATTA
1 ATATAAAATATATAATTA
* *
255066 ATATATATTATATAATT
1 ATATAAAATATATAATT
255083 GTAAAATAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAAAATATATAATTA
Found at i:255703 original size:4 final size:4
Alignment explanation
Indices: 255694--255721 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
255684 GTCAGAGACC
255694 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
255722 TAATTTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:257508 original size:8 final size:8
Alignment explanation
Indices: 257497--257702 Score: 67
Period size: 8 Copynumber: 26.1 Consensus size: 8
257487 AGATTTAAGA
257497 ATTTATAT
1 ATTTATAT
257505 A-TT-TAT
1 ATTTATAT
257511 ATTTATAT
1 ATTTATAT
257519 ATTT-TATT
1 ATTTATA-T
257527 ATGTTATAAAT
1 AT-TTAT--AT
257538 AAATTTA-AT
1 --ATTTATAT
257547 AATTTATAT
1 -ATTTATAT
257556 A-TT-TAT
1 ATTTATAT
257562 ATTTATAT
1 ATTTATAT
257570 ATTT-TATT
1 ATTTATA-T
257578 ATGTTATA-
1 AT-TTATAT
257586 A-TTATAT
1 ATTTATAT
* *
257593 -TTAAAAT
1 ATTTATAT
257600 ATTT-TAT
1 ATTTATAT
257607 ATTTATAT
1 ATTTATAT
257615 AAATTTTAATAT
1 --A-TTT-ATAT
*
257627 ATTAATA-
1 ATTTATAT
*
257634 ATTTATTT
1 ATTTATAT
257642 ATATTAT-T
1 AT-TTATAT
257650 -TTTAT-T
1 ATTTATAT
257656 ATATTATAT
1 AT-TTATAT
257665 -TTTA-AT
1 ATTTATAT
257671 -TTT-T-T
1 ATTTATAT
257676 ACTTTATATT
1 A-TTTATA-T
257686 ACTTT-TAT
1 A-TTTATAT
257694 ATTTATAT
1 ATTTATAT
257702 A
1 A
257703 ATATAATTAT
Statistics
Matches: 156, Mismatches: 7, Indels: 70
0.67 0.03 0.30
Matches are distributed among these distances:
5 1 0.01
6 23 0.15
7 38 0.24
8 52 0.33
9 17 0.11
10 11 0.07
11 4 0.03
12 8 0.05
13 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (8 bp):
ATTTATAT
Found at i:257544 original size:51 final size:50
Alignment explanation
Indices: 257482--257614 Score: 203
Period size: 51 Copynumber: 2.6 Consensus size: 50
257472 GTACTTAATG
*
257482 TAAATAGATTTAAGAATTTATATATTTATATTTATATATTTTATTATGTTA
1 TAAATAAATTTAA-AATTTATATATTTATATTTATATATTTTATTATGTTA
257533 TAAATAAATTTAATAATTTATATATTTATATTTATATATTTTATTATGTTA
1 TAAATAAATTTAA-AATTTATATATTTATATTTATATATTTTATTATGTTA
* * *
257584 TAATTATATTTAAAATATTTTATATTTATAT
1 TAAATAAATTTAAAAT-TTATATATTTATAT
257615 AAATTTTAAT
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 3 0.04
51 73 0.96
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (50 bp):
TAAATAAATTTAAAATTTATATATTTATATTTATATATTTTATTATGTTA
Found at i:257634 original size:18 final size:17
Alignment explanation
Indices: 257506--257703 Score: 72
Period size: 18 Copynumber: 11.9 Consensus size: 17
257496 AATTTATATA
257506 TTTATATTTATAT--AT
1 TTTATATTTATATAAAT
257521 TTTATTATGTTATAAATAAAT
1 TTTA-TAT-TTAT--ATAAAT
*
257542 TTAATAATTTATAT--A-
1 TTTAT-ATTTATATAAAT
257557 TTTATATTTATAT--AT
1 TTTATATTTATATAAAT
*
257572 TTTATTATGT-TAT-AA-
1 TTTA-TATTTATATAAAT
257587 -TTATATTTA-A-AATAT
1 TTTATATTTATATAA-AT
257602 TTTATATTTATATAAAT
1 TTTATATTTATATAAAT
257619 TTTAATATATTA-AT-AA-
1 TTT-ATAT-TTATATAAAT
* *
257635 -TT-TATTTATATTATT
1 TTTATATTTATATAAAT
*
257650 TTTATTATATTATATTTTAAT
1 TTTA-TAT-TTATA--TAAAT
* * *
257671 TTTTTACTTTATATTACT
1 TTTATA-TTTATATAAAT
257689 TTTATATTTATATAA
1 TTTATATTTATATAA
257704 TATAATTATG
Statistics
Matches: 144, Mismatches: 10, Indels: 56
0.69 0.05 0.27
Matches are distributed among these distances:
12 3 0.02
13 11 0.08
14 14 0.10
15 17 0.12
16 20 0.14
17 20 0.14
18 22 0.15
19 10 0.07
20 12 0.08
21 15 0.10
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (17 bp):
TTTATATTTATATAAAT
Found at i:257653 original size:78 final size:79
Alignment explanation
Indices: 257502--257663 Score: 192
Period size: 78 Copynumber: 2.1 Consensus size: 79
257492 TAAGAATTTA
* * *
257502 TATATTTATATTTATATATTTTATTATGTTATAAATAAATTTAATAATTTATATATTTATATTTA
1 TATAATTATATTTAAATATTTTATTATGTTAT-AATAAATTTAATAATTAATATATTTATATTTA
*
257567 TATATTTTATTATGT
65 TATATTTTATTATAT
257582 TATAATTATATTTAAAATATTTTA-TAT-TTAT-ATAAATTTTAATATATTAATA-A-TT-TATT
1 TATAATTATATTT-AAATATTTTATTATGTTATAATAAA-TTTAATA-ATTAATATATTTATATT
257641 TATATTATTTTTATTATAT
63 TATA-TA-TTTTATTATAT
257660 TATA
1 TATA
257664 TTTTAATTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
76 8 0.11
77 9 0.12
78 22 0.30
79 10 0.14
80 15 0.21
81 9 0.12
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (79 bp):
TATAATTATATTTAAATATTTTATTATGTTATAATAAATTTAATAATTAATATATTTATATTTAT
ATATTTTATTATAT
Found at i:257710 original size:39 final size:38
Alignment explanation
Indices: 257635--257710 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 38
257625 ATATTAATAA
* *
257635 TTTATTTATATTATTTTTATTATATTATATTTTAATTT
1 TTTATTTATATTATTTTTATTATATTATAATATAATTT
257673 TTTACTTTATATTACTTTTATATT-TA-TATAATATAATT
1 TTTA-TTTATATTA-TTTT-TATTATATTATAATATAATT
257711 ATGTCATGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
38 4 0.12
39 19 0.58
40 6 0.18
41 4 0.12
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (38 bp):
TTTATTTATATTATTTTTATTATATTATAATATAATTT
Found at i:257880 original size:22 final size:21
Alignment explanation
Indices: 257852--257894 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
257842 TATATTAAAA
257852 ATATATTTT-TATATTAATATTT
1 ATATATTTTATA-ATTAA-ATTT
257874 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
257895 TAAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 14 0.70
23 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:257896 original size:22 final size:22
Alignment explanation
Indices: 257852--257894 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
257842 TATATTAAAA
257852 ATATATTTTTATATTAATATTT
1 ATATATTTTTATATTAATATTT
257874 ATATA-TTTTATAATTAA-ATTT
1 ATATATTTTTAT-ATTAATATTT
257895 TAAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATATTTTTATATTAATATTT
Found at i:258642 original size:24 final size:24
Alignment explanation
Indices: 258589--258654 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
258579 TAAATTCTTC
* * *
258589 ATCTTTAATTTA-CATTCAATTAA
1 ATCTTTAATTTATAATTTAAATAA
*
258612 ATTTTTAATTTATAATTTAAATAA
1 ATCTTTAATTTATAATTTAAATAA
258636 ATCTTTAATCTT-TAATTTA
1 ATCTTTAAT-TTATAATTTA
258655 TACTTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 11 0.31
24 23 0.64
25 2 0.06
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (24 bp):
ATCTTTAATTTATAATTTAAATAA
Found at i:258652 original size:31 final size:32
Alignment explanation
Indices: 258615--258676 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
258605 CAATTAAATT
*
258615 TTTAATTTATAATT-TAAATAAATCTTTAATC
1 TTTAATTTATAATTAAAAATAAATCTTTAATC
* *
258646 TTTAATTTATACTTAAAAATAAATTTTTAAT
1 TTTAATTTATAATTAAAAATAAATCTTTAAT
258677 ACAAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (32 bp):
TTTAATTTATAATTAAAAATAAATCTTTAATC
Found at i:258732 original size:30 final size:30
Alignment explanation
Indices: 258696--258758 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
258686 TTTTTCATTT
* *
258696 AAAATAAATATTTATTTACATACAAAT-TAA
1 AAAATAAATACTTATTTA-ATAAAAATATAA
258726 AAAATAAATACTTATTTAATAAAAATATAA
1 AAAATAAATACTTATTTAATAAAAATATAA
258756 AAA
1 AAA
258759 TTTAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAATAAATACTTATTTAATAAAAATATAA
Found at i:258881 original size:3 final size:3
Alignment explanation
Indices: 258873--258904 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
258863 CCAATTTCTT
258873 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
258905 CAATAATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:259167 original size:26 final size:27
Alignment explanation
Indices: 259138--259213 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 27
259128 GATATTTATG
259138 ATATATATTTGATTATATATGAAAAAAT
1 ATATATATTTGATTATATAT-AAAAAAT
*
259166 ATA-ATCTTTTGA--ATATATAAAAAAT
1 ATATAT-ATTTGATTATATATAAAAAAT
259191 ATAAATATATTTGTATTATATAT
1 AT--ATATATTTG-ATTATATAT
259214 TTATATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
25 9 0.23
26 6 0.15
27 7 0.18
28 11 0.28
30 6 0.15
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (27 bp):
ATATATATTTGATTATATATAAAAAAT
Found at i:259177 original size:28 final size:29
Alignment explanation
Indices: 259140--259213 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 29
259130 TATTTATGAT
259140 ATATATTTGATTATATATGAAAAAATAT-A
1 ATATATTTGATTATATAT-AAAAAATATAA
*
259169 ATCT-TTTGA--ATATATAAAAAATATAA
1 ATATATTTGATTATATATAAAAAATATAA
259195 ATATATTTGTATTATATAT
1 ATATATTTG-ATTATATAT
259214 TTATATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 9 0.24
26 10 0.26
27 4 0.11
28 6 0.16
29 3 0.08
30 6 0.16
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (29 bp):
ATATATTTGATTATATATAAAAAATATAA
Found at i:259509 original size:6 final size:6
Alignment explanation
Indices: 259500--259524 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
259490 ATAATAATAA
259500 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
259525 TATAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Done.