Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold334
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: 475332
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 1 of 3
Found at i:5330 original size:2 final size:2
Alignment explanation
Indices: 5323--5355 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5313 AAACAAATTG
5323 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5356 GTAAATGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9503 original size:13 final size:15
Alignment explanation
Indices: 9481--9522 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
9471 CAAAGATCAG
*
9481 TGTATTGATACA-A-
1 TGTATCGATACATAT
9494 TGTATCGATACATTAT
1 TGTATCGATACA-TAT
9510 TGTATCGATACAT
1 TGTATCGATACAT
9523 TTGAGTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 11 0.44
15 2 0.08
16 12 0.48
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (15 bp):
TGTATCGATACATAT
Found at i:9536 original size:21 final size:19
Alignment explanation
Indices: 9492--9545 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
9482 GTATTGATAC
9492 AATGTATCGATACA-TTAT
1 AATGTATCGATACATTTAT
9510 --TGTATCGATACATTTGAGT
1 AATGTATCGATACATTT-A-T
9529 AATGTATCGATACATTT
1 AATGTATCGATACATTT
9546 TCTTAGAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 12 0.39
17 2 0.06
18 1 0.03
19 1 0.03
21 15 0.48
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (19 bp):
AATGTATCGATACATTTAT
Found at i:9599 original size:19 final size:18
Alignment explanation
Indices: 9575--9635 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
9565 CGATACATTA
9575 TATCGATACAAAACTTATG
1 TATCGATAC-AAACTTATG
9594 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
9607 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
9626 TATCGATACA
1 TATCGATACA
9636 TTGTATCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
16 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (18 bp):
TATCGATACAAACTTATG
Found at i:9611 original size:32 final size:32
Alignment explanation
Indices: 9565--9646 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
9555 AGCTTCATAG
*
9565 CGATACATTATATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
9597 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
9629 CGATACATTGTATCGATA
1 CGATACATTGTATCGATA
9647 TAAATCGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:9642 original size:13 final size:13
Alignment explanation
Indices: 9592--9646 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
9582 ACAAAACTTA
9592 TGTATCGATACAT
1 TGTATCGATACAT
9605 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
9623 ATGTATCGATACAT
1 -TGTATCGATACAT
9637 TGTATCGATA
1 TGTATCGATA
9647 TAAATCGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 19 0.53
14 1 0.03
16 6 0.17
18 1 0.03
19 9 0.25
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11007 original size:337 final size:332
Alignment explanation
Indices: 10447--11109 Score: 976
Period size: 337 Copynumber: 2.0 Consensus size: 332
10437 TAGAATATAA
* *
10447 AAAAAAAGTTTCAAAATAAATTGATTGTGAAAAAAAATGAAATTAATATGGAAATATTTTATAAA
1 AAAAAAAGTTTCAAAATAAATTGATTATGAAAAAAAATGAAATTAATATGGAAAGATTTTATAAA
*
10512 CTTTTATTTCCTATCATTTCAATTAAATATGGTAGAATAAAAATATGAAAAGTTATTTTTATATT
66 CTTTTATTTCCTATCATTTCAATTAAATATGGTAGAATAAAAACATGAAAAGTTATTTTTATATT
*
10577 TTAAATATTTATTTTCAAATCATACCTCGTAAAATATGGAAAAAAAACTAATATAATAAAGTTTC
131 TTAAATATTTATTTTCAAATCATACCTCGTAAAATATGAAAAAAAAACTAATATAATAAAGTTTC
* * *
10642 ATATTTTATTTTTTATTACTAGTAACTTTTGCAAAATTAATACTTGCT-AAATATTGAAATTAAT
196 ATATTTTATTTTTTATTAATAGTAACTTTTGAAAAATTAATACTTG-TAAAACATTGAAATTAAT
* *
10706 TAATATGAAATTTTCATATTTTTCTTTTTATTTAAACTAATTTATTTAAAAACATTTAATATGGA
260 TAATATGAAATTGTCATATTTTTCTTTTTATTTAAACTAATTCATTT-AAAACATTTAATAT-GA
10771 AATATTTTAT
323 AATATTTTAT
* * *
10781 AAAAAAAGTTTCAACATAAATTGATTATG-AGAAAATTGAAATTAATATGGAAAGATTTTATAAA
1 AAAAAAAGTTTCAAAATAAATTGATTATGAAAAAAAATGAAATTAATATGGAAAGATTTTATAAA
* * * *
10845 CTTTT-TTT-TTGTCTTTTCAATTAAA-ATTGGTTGAATAAAAACATGAAAAGTTTATTTTTATA
66 CTTTTATTTCCTATCATTTCAATTAAATA-TGGTAGAATAAAAACATGAAAAG-TTATTTTTATA
** * *
10907 TTTTAAATATTTATTTTCAAATCAATAGTTTGTGAAATATGAAAAATATTAAAACTAATATAATA
129 TTTTAAATATTTATTTTCAAATC-ATACCTCGTAAAATATG-AAAA-A--AAAACTAATATAATA
* * * *
10972 AAGTTTCATATTTTATTTTTTGTTAATATTAACTTTTTAAAAATTAATGCTTGTAAAACATTGAA
189 AAGTTTCATATTTTATTTTTTATTAATAGTAACTTTTGAAAAATTAATACTTGTAAAACATTGAA
*
11037 ATTAATTAATATGAAATTGTCATATTTTTCTTTTTATTTAAACTAATTCATTTAAAGCATTTAAT
254 ATTAATTAATATGAAATTGTCATATTTTTCTTTTTATTTAAACTAATTCATTTAAAACATTTAAT
11102 ATGAAATA
319 ATGAAATA
11110 GGTTTTCTAA
Statistics
Matches: 296, Mismatches: 25, Indels: 15
0.88 0.07 0.04
Matches are distributed among these distances:
330 1 0.00
331 35 0.12
332 37 0.12
333 50 0.17
334 30 0.10
335 7 0.02
336 14 0.05
337 122 0.41
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (332 bp):
AAAAAAAGTTTCAAAATAAATTGATTATGAAAAAAAATGAAATTAATATGGAAAGATTTTATAAA
CTTTTATTTCCTATCATTTCAATTAAATATGGTAGAATAAAAACATGAAAAGTTATTTTTATATT
TTAAATATTTATTTTCAAATCATACCTCGTAAAATATGAAAAAAAAACTAATATAATAAAGTTTC
ATATTTTATTTTTTATTAATAGTAACTTTTGAAAAATTAATACTTGTAAAACATTGAAATTAATT
AATATGAAATTGTCATATTTTTCTTTTTATTTAAACTAATTCATTTAAAACATTTAATATGAAAT
ATTTTAT
Found at i:16806 original size:12 final size:12
Alignment explanation
Indices: 16789--16817 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
16779 TTCACAGTAG
16789 TAGGCTTAATTT
1 TAGGCTTAATTT
16801 TAGGCTTAATTT
1 TAGGCTTAATTT
16813 TAGGC
1 TAGGC
16818 CATAACAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (12 bp):
TAGGCTTAATTT
Found at i:21707 original size:39 final size:39
Alignment explanation
Indices: 21656--21734 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
21646 CCTATAGGGG
* * *
21656 AAAGAAAGAAGCTATCACCAAACTAGGAAATACCCTATT
1 AAAGAAAAAAGCTATCAACAAACTAGGAAAGACCCTATT
*
21695 AAAGAAAAAAGCTATCAACAAACTAGGAAAGACCTTATT
1 AAAGAAAAAAGCTATCAACAAACTAGGAAAGACCCTATT
21734 A
1 A
21735 GGTTATTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.52, C:0.18, G:0.13, T:0.18
Consensus pattern (39 bp):
AAAGAAAAAAGCTATCAACAAACTAGGAAAGACCCTATT
Found at i:25306 original size:33 final size:33
Alignment explanation
Indices: 25264--25333 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
25254 AATAAATCTA
* **
25264 ATCTAATCTAATCTATTTAACTTGTTTATCATG
1 ATCTAATCTAATATAGATAACTTGTTTATCATG
* *
25297 ATCTAATCTAATATAGATGACTTGTTTATCCTG
1 ATCTAATCTAATATAGATAACTTGTTTATCATG
25330 ATCT
1 ATCT
25334 TGATAAGATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.46
Consensus pattern (33 bp):
ATCTAATCTAATATAGATAACTTGTTTATCATG
Found at i:29649 original size:32 final size:33
Alignment explanation
Indices: 29579--29649 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
29569 ATTTTAAATA
* *
29579 AATCTAATTTAATCTATTTAACTTCTTTATCAT
1 AATCTTATATAATCTATTTAACTTCTTTATCAT
* * * *
29612 GATCTTATATAATCT-TTTGACTTGTTTATCCT
1 AATCTTATATAATCTATTTAACTTCTTTATCAT
29644 AATCTT
1 AATCTT
29650 GATAAGATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.52
Consensus pattern (33 bp):
AATCTTATATAATCTATTTAACTTCTTTATCAT
Found at i:35316 original size:29 final size:29
Alignment explanation
Indices: 35283--35344 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
35273 ACAAATATTA
* *
35283 ATATTATAAAATTTAT-ATATATATAAAAT
1 ATATTAAAAAAATTATAATATA-ATAAAAT
35312 ATATTAAAAAAATTATAATATAATAAAAT
1 ATATTAAAAAAATTATAATATAATAAAAT
35341 ATAT
1 ATAT
35345 AAATATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
ATATTAAAAAAATTATAATATAATAAAAT
Found at i:35338 original size:46 final size:48
Alignment explanation
Indices: 35258--35351 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 48
35248 GATATAATTT
* * * *
35258 TAAAATATATATAATACAAATATTAATATTATAAAATTTATATATATA
1 TAAAATATATATAATAAAAATATTAATATAATAAAATATATAAATATA
35306 TAAAATATAT-TAA-AAAAAT-TATAATATAATAAAATATATAAATATA
1 TAAAATATATATAATAAAAATAT-TAATATAATAAAATATATAAATATA
35352 ATACGAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 1 0.02
46 27 0.66
47 3 0.07
48 10 0.24
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (48 bp):
TAAAATATATATAATAAAAATATTAATATAATAAAATATATAAATATA
Found at i:35395 original size:2 final size:2
Alignment explanation
Indices: 35388--35419 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35378 AAATTTTTAG
35388 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
35420 GTAGCTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35933 original size:2 final size:2
Alignment explanation
Indices: 35926--35950 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35916 TATGCCACAA
35926 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 A
35951 ATAAAATTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36575 original size:31 final size:33
Alignment explanation
Indices: 36498--36583 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 33
36488 TATACTTTTA
* *
36498 TTTGATTAAATTTTACAATTAGACTTTTAATTTT
1 TTTGATTAAATTTTGCCATTAGACTTTTAA-TTT
* *
36532 TTTTATTGAATTTTGCCATTCA-A-TTTTAA-TT
1 TTTGATTAAATTTTGCCATT-AGACTTTTAATTT
*
36563 TTTGATTAAATTTTGTCATTA
1 TTTGATTAAATTTTGCCATTA
36584 AACAATCATT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
30 1 0.02
31 19 0.43
33 6 0.14
34 17 0.39
35 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (33 bp):
TTTGATTAAATTTTGCCATTAGACTTTTAATTT
Found at i:37655 original size:2 final size:2
Alignment explanation
Indices: 37648--37674 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37638 ACATCTAGAA
37648 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 A
37675 GATAAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45070 original size:15 final size:15
Alignment explanation
Indices: 45050--45080 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
45040 TTCATATTGA
45050 TGGTAATTGTTAATC
1 TGGTAATTGTTAATC
45065 TGGTAATTGTTAATC
1 TGGTAATTGTTAATC
45080 T
1 T
45081 TTATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (15 bp):
TGGTAATTGTTAATC
Found at i:54417 original size:22 final size:22
Alignment explanation
Indices: 54389--54430 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54379 TTCTTTTATG
* *
54389 AAAAAAGAAAAGAAAGGAAAGA
1 AAAAAAGAAAACAAAAGAAAGA
54411 AAAAAAGAAAACAAAAGAAA
1 AAAAAAGAAAACAAAAGAAA
54431 TAAGGGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAACAAAAGAAAGA
Found at i:54517 original size:69 final size:69
Alignment explanation
Indices: 54464--54623 Score: 195
Period size: 69 Copynumber: 2.4 Consensus size: 69
54454 TCGTATATTT
* *
54464 ATAATGTATTTGTAT-T-ACTTTT-ATATATTTAAAATATAATAAATTTATAAAATTTTTTACTC
1 ATAATGTATTTGTATCTAAATTTTGATACATTTAAAATATAATAAATTTATAAAATTTTTTACTC
54526 ATTA
66 ATTA
* * * * *
54530 ATAATTTATTTTTATCTAAATTTTGATACGTTTAAAATATTATAAATTTATATAATTTTTTACAT
1 ATAATGTATTTGTATCTAAATTTTGATACATTTAAAATATAATAAATTTATAAAATTTTTTAC-T
54595 -ATTA
65 CATTA
* *
54599 ATAATTTATTT-TATATAAATTTTGA
1 ATAATGTATTTGTATCTAAATTTTGA
54624 CACGTTCACA
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
66 13 0.16
67 1 0.01
68 18 0.22
69 49 0.60
70 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (69 bp):
ATAATGTATTTGTATCTAAATTTTGATACATTTAAAATATAATAAATTTATAAAATTTTTTACTC
ATTA
Found at i:54551 original size:34 final size:34
Alignment explanation
Indices: 54507--54621 Score: 107
Period size: 34 Copynumber: 3.4 Consensus size: 34
54497 ATATAATAAA
54507 TTTATA-AAATTTTTTAC-TCATTAATAATTTATT
1 TTTATATAAATTTTTTACAT-ATTAATAATTTATT
* * * *
54540 TTTATCTAAATTTTGATACGT-TTAA-AATATTATAAA
1 TTTATATAAATTTT-TTACATATTAATAAT-TTAT--T
54576 TTTATAT-AATTTTTTACATATTAATAATTTA-T
1 TTTATATAAATTTTTTACATATTAATAATTTATT
54608 TTTATATAAATTTT
1 TTTATATAAATTTT
54622 GACACGTTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
32 7 0.11
33 14 0.21
34 19 0.29
35 16 0.24
36 10 0.15
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (34 bp):
TTTATATAAATTTTTTACATATTAATAATTTATT
Found at i:54629 original size:68 final size:69
Alignment explanation
Indices: 54491--54629 Score: 219
Period size: 69 Copynumber: 2.0 Consensus size: 69
54481 CTTTTATATA
*
54491 TTTAAAATATAATAAATTTATAAAATTTTTTACTCATTAATAATTTATTTTTATCTAAATTTTGA
1 TTTAAAATATAATAAATTTATAAAATTTTTTACTCATTAATAATTTATTTTTATATAAATTTTGA
*
54556 TACG
66 CACG
* *
54560 TTTAAAATATTATAAATTTATATAATTTTTTACAT-ATTAATAATTTA-TTTTATATAAATTTTG
1 TTTAAAATATAATAAATTTATAAAATTTTTTAC-TCATTAATAATTTATTTTTATATAAATTTTG
54623 ACACG
65 ACACG
54628 TT
1 TT
54630 CACATATTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
68 21 0.32
69 43 0.66
70 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (69 bp):
TTTAAAATATAATAAATTTATAAAATTTTTTACTCATTAATAATTTATTTTTATATAAATTTTGA
CACG
Found at i:54768 original size:108 final size:109
Alignment explanation
Indices: 54559--54779 Score: 239
Period size: 108 Copynumber: 2.0 Consensus size: 109
54549 ATTTTGATAC
* * *
54559 GTTTAAAATATTATAAATTTATATAATTTTTTACATATTAATAATTTATTTTATATAAATTTTGA
1 GTTTAAAATATTATAAATTTATATAAATTTTTACATATTAAAAATTCATTTTATATAAATTTTGA
* * * * *
54624 CACGTTCACATATTCATGTCTTATTTATGTTATTTTCTTAT-AT
66 CACATTCACATATTCATATCATATTCATGTTATTTTCATATCAT
* * * * *
54667 GTTTAAAGTATTATAAGTTTGTATAAATTTTTACATGTTAAAAATTCGTTTTAT-TAAATTTTGA
1 GTTTAAAATATTATAAATTTATATAAATTTTTACATATTAAAAATTCATTTTATATAAATTTTGA
* * *** * *
54731 TATATTCGTGTATTTATATCATGTTCATGTTATTTTTCATATCAT
66 CACATTCACATATTCATATCATATTCATGTTA-TTTTCATATCAT
54776 GTTT
1 GTTT
54780 TAATTATTTT
Statistics
Matches: 91, Mismatches: 20, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
107 31 0.34
108 54 0.59
109 6 0.07
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (109 bp):
GTTTAAAATATTATAAATTTATATAAATTTTTACATATTAAAAATTCATTTTATATAAATTTTGA
CACATTCACATATTCATATCATATTCATGTTATTTTCATATCAT
Found at i:55180 original size:26 final size:26
Alignment explanation
Indices: 55151--55201 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
55141 TCATTCTATA
*
55151 TTTT-AAATAATTTATCATAATAATTT
1 TTTTAAAATAATTTATC-TAAAAATTT
*
55177 TTTTAAAATTATTTATCTAAAAATT
1 TTTTAAAATAATTTATCTAAAAATT
55202 GAATCATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTAAAATAATTTATCTAAAAATTT
Found at i:55401 original size:29 final size:29
Alignment explanation
Indices: 55359--55415 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
55349 GGTCTGGAAT
* *
55359 AATTTTGTAATAAAAATCAAATTGAAGGC
1 AATTTTATAATAAAAACCAAATTGAAGGC
55388 AATTTTATAATAAAAACCAAATTGAAGG
1 AATTTTATAATAAAAACCAAATTGAAGG
55416 ATCATGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (29 bp):
AATTTTATAATAAAAACCAAATTGAAGGC
Found at i:56442 original size:16 final size:14
Alignment explanation
Indices: 56421--56463 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
56411 AATAAATTAA
56421 ATTTATATATTTATGT
1 ATTTATAT-TTTAT-T
56437 ATTTATATTATTA-T
1 ATTTATATT-TTATT
56451 ATTTATATTTTAT
1 ATTTATATTTTAT
56464 AATAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 10 0.40
15 1 0.04
16 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
ATTTATATTTTATT
Found at i:57028 original size:40 final size:41
Alignment explanation
Indices: 56980--57058 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 41
56970 CATCTACTTA
*
56980 AAATAAAACTTTAATAAAAAGAGTTAAAAA-TAATTAAACT
1 AAATAAAACTTTAATAAAAAAAGTTAAAAAGTAATTAAACT
57020 AAATAAAACTTTAATAAAAAAAGTTAAAAAGTAATTAAA
1 AAATAAAACTTTAATAAAAAAAGTTAAAAAGTAATTAAA
57059 TTATACTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 29 0.78
41 8 0.22
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.27
Consensus pattern (41 bp):
AAATAAAACTTTAATAAAAAAAGTTAAAAAGTAATTAAACT
Found at i:59031 original size:3 final size:3
Alignment explanation
Indices: 59023--59063 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
59013 TTCAGTGAGG
59023 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
59064 TGGTTTTGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:61918 original size:3 final size:3
Alignment explanation
Indices: 61910--61959 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
61900 TCAAAAGCTG
61910 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61958 TA
1 TA
61960 TGCCACGGTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:67892 original size:2 final size:2
Alignment explanation
Indices: 67885--67916 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
67875 AGATCTAACA
67885 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
67917 TTGCTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71895 original size:33 final size:33
Alignment explanation
Indices: 71850--71924 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
71840 AATAAATCTA
*
71850 ATCTAATATAATTTGTATGATTTGTTTACCATG
1 ATCTAATATAATTTGTATGACTTGTTTACCATG
* * *
71883 ATCTAATCTAATTTGTTTGACTTGTTTATCATG
1 ATCTAATATAATTTGTATGACTTGTTTACCATG
71916 ATCCTAATA
1 AT-CTAATA
71925 AACTAAAGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 31 0.86
34 5 0.14
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (33 bp):
ATCTAATATAATTTGTATGACTTGTTTACCATG
Found at i:77573 original size:19 final size:21
Alignment explanation
Indices: 77530--77581 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
77520 TTCAATAATT
77530 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAATAGTAAA
*
77551 TGTATCGATACATA-AGT-AA
1 TGTATCGATACAAATAGTAAA
77570 TGTATCGATACA
1 TGTATCGATACA
77582 GTATATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAAATAGTAAA
Found at i:77652 original size:13 final size:13
Alignment explanation
Indices: 77634--77659 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
77624 ATTTATAGAA
77634 TGTATCGATACAT
1 TGTATCGATACAT
77647 TGTATCGATACAT
1 TGTATCGATACAT
77660 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:80146 original size:51 final size:50
Alignment explanation
Indices: 80021--80188 Score: 151
Period size: 51 Copynumber: 3.3 Consensus size: 50
80011 TTCATCTCGA
* * * * * *
80021 GGATACTCCAATCCCG-GTTTCATTTCCAAGACATCAATTTTTTCTTAATCGG
1 GGATACTCCAA-CCCGACTTT-ATTTCTAAAACACCAA-TTTCTCATAATCGG
* * *
80073 GGATACTCAAACTCCGATTTTATTTCTAAAACACCCATTT-TCCATAATCGG
1 GGATACTCCAAC-CCGACTTTATTTCTAAAACACCAATTTCT-CATAATCGG
* **
80124 GGATACTCCAACCCTGACTTTATTTCTAAAATATTAATTTCTCATAATCGG
1 GGATACTCCAACCC-GACTTTATTTCTAAAACACCAATTTCTCATAATCGG
*
80175 GGATATTCCAACCC
1 GGATACTCCAACCC
80189 CGTTATTTTC
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
50 3 0.03
51 65 0.67
52 26 0.27
53 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (50 bp):
GGATACTCCAACCCGACTTTATTTCTAAAACACCAATTTCTCATAATCGG
Found at i:80212 original size:79 final size:79
Alignment explanation
Indices: 80122--80375 Score: 289
Period size: 79 Copynumber: 3.2 Consensus size: 79
80112 TTCCATAATC
* * * * *
80122 GGGGATACTCCAACCCTGACTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATATTCCAAC
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAACATAAATTTTTCATAATCGGGGATACTCCAAC
80187 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* * *
80201 GGGGATACTCCAA-CCTCAGTTTTATTTCTAAAACATAAATTTTTCATAATCGGGAATGCTCCAA
1 GGGGATACTCCAACCCTGA-TTTTATTTCTAAAACATAAATTTTTCATAATCGGGGATACTCCAA
* * * * *
80265 TCTCATTATTTCCAA
65 CCCCGTTATTTTCGA
* ** *
80280 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAACATAAATTTTTCATAATCGGGGATACTCCAAC
*
80345 TCCGATTATTTCATCGA
66 CCCG-TTATTT--TCGA
80362 --GGATACTCCAACCC
1 GGGGATACTCCAACCC
80376 CGTTATTTTC
Statistics
Matches: 144, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
78 4 0.03
79 115 0.80
80 23 0.16
82 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCTGATTTTATTTCTAAAACATAAATTTTTCATAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:80393 original size:28 final size:28
Alignment explanation
Indices: 80330--80431 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 28
80320 TTTTCACAAT
* *
80330 CGGGGATACTCCAACTCCGATTA-TTTCAT
1 CGGGGATACTCCAACCCCG-TTATTTTC-G
*
80359 CGAGGATACTCCAACCCCGTTATTTTCG
1 CGGGGATACTCCAACCCCGTTATTTTCG
* *
80387 CGGGGATACTCCAACTCCGTTATTTTTG
1 CGGGGATACTCCAACCCCGTTATTTTCG
*
80415 AGGGGATACTCCAACCC
1 CGGGGATACTCCAACCC
80432 AGATTTTATT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 43 0.67
29 21 0.33
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (28 bp):
CGGGGATACTCCAACCCCGTTATTTTCG
Found at i:80476 original size:79 final size:79
Alignment explanation
Indices: 80389--80557 Score: 234
Period size: 79 Copynumber: 2.1 Consensus size: 79
80379 TATTTTCGCG
***
80389 GGGATACTCCAACTCC-GTTATTTTTGAGGGGATACTCCAACCCAGATTTTATTTTCAAAACACC
1 GGGATACTCCAAC-CCTGTTATTTCCAAGGGGATACTCCAACCCAGATTTTATTTTCAAAACA-C
* *
80453 T-ATTTTCTATAATTA
64 TGATTTTCCATAATCA
* *
80468 GGGATACTCCAACCCTGTTATTTCCAAGGGTATACTCCAACCCCGATTTTATTTTCAAAACACTG
1 GGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCAGATTTTATTTTCAAAACACTG
80533 ATTTTCCATAATCA
66 ATTTTCCATAATCA
*
80547 GGGGTACTCCA
1 GGGATACTCCA
80558 GCCCCGTCGT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 4 0.05
79 76 0.95
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (79 bp):
GGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCAGATTTTATTTTCAAAACACTG
ATTTTCCATAATCA
Found at i:81951 original size:16 final size:17
Alignment explanation
Indices: 81912--81953 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
81902 TATAAAGTAT
*
81912 TTACTTTTTTTAGGAACA
1 TTACTTTTTTTA-GAAAA
*
81930 TAACTTTTTTT-GAAAA
1 TTACTTTTTTTAGAAAA
81946 TTACTTTT
1 TTACTTTT
81954 CACAATTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.55
Consensus pattern (17 bp):
TTACTTTTTTTAGAAAA
Found at i:83422 original size:16 final size:17
Alignment explanation
Indices: 83384--83429 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
83374 ATTTTCAACT
* *
83384 AAAATATAATTATATTA
1 AAAATATTATAATATTA
*
83401 ATAATATTATAAT-TTA
1 AAAATATTATAATATTA
83417 AAAATATTA-AATA
1 AAAATATTATAATA
83430 AATAATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.12
16 11 0.46
17 10 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATATTATAATATTA
Found at i:83440 original size:25 final size:25
Alignment explanation
Indices: 83395--83442 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
83385 AAATATAATT
*
83395 ATATTAATAATATTATAATTTAAAA
1 ATATTAATAATATAATAATTTAAAA
*
83420 ATATTAAATAA-ATAATTATTTAA
1 ATATT-AATAATATAATAATTTAA
83443 TTAAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATTAATAATATAATAATTTAAAA
Found at i:83444 original size:30 final size:30
Alignment explanation
Indices: 83383--83457 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
83373 AATTTTCAAC
* *
83383 TAAAATATAATTATATTAATAATATTATAATT
1 TAAAATAT-ATTAAATAAATAATATTATAA-T
83415 TAAAA-ATATTAAATAAATAATTATT-TAAT
1 TAAAATATATTAAATAAATAA-TATTATAAT
*
83444 TAAAATTTATTAAA
1 TAAAATATATTAAA
83458 AATTGAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 6 0.16
30 21 0.55
31 6 0.16
32 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TAAAATATATTAAATAAATAATATTATAAT
Found at i:84547 original size:2 final size:2
Alignment explanation
Indices: 84540--84574 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
84530 ATAAATTAAA
*
84540 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
84575 CACACACGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84547 original size:38 final size:39
Alignment explanation
Indices: 84474--84552 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
84464 CATTGCATTC
* *
84474 TAATTTTATTTAATTTTTATAAAATAACTATTATAT-TA
1 TAATTTTATTTAATTTTAATAAAATAAATATTATATCTA
* *
84512 TAATTTTATTTTATTTTAATAAATTAAA-ATATATATCTA
1 TAATTTTATTTAATTTTAATAAAATAAATAT-TATATCTA
84551 TA
1 TA
84553 TATATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 2 0.06
38 29 0.83
39 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (39 bp):
TAATTTTATTTAATTTTAATAAAATAAATATTATATCTA
Found at i:87163 original size:3 final size:3
Alignment explanation
Indices: 87155--87192 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
87145 TTTAAAAATT
87155 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
87193 TTTTGCATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:87874 original size:30 final size:30
Alignment explanation
Indices: 87817--87911 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
87807 TCGTGTATTT
* *
87817 AATTTATTTTCATGA-AATTT-GATTTATGC
1 AATTTATTTTC-TTACAATTTAAATTTATGC
*
87846 AATTTATTTT-TTAGCAATTTAAATTTATGA
1 AATTTATTTTCTTA-CAATTTAAATTTATGC
*
87876 AATTTATTTTCTTATAATTTAAATTTATGC
1 AATTTATTTTCTTACAATTTAAATTTATGC
87906 AATTTA
1 AATTTA
87912 GATTATGCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.04
29 15 0.26
30 37 0.65
31 3 0.05
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (30 bp):
AATTTATTTTCTTACAATTTAAATTTATGC
Found at i:87879 original size:15 final size:15
Alignment explanation
Indices: 87861--87925 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 15
87851 ATTTTTTAGC
87861 AATTTAAATTTATGA
1 AATTTAAATTTATGA
* * *
87876 AATTT-ATTTTCTTA
1 AATTTAAATTTATGA
*
87890 TAATTTAAATTTATGC
1 -AATTTAAATTTATGA
* *
87906 AATTTAGA-TTATGC
1 AATTTAAATTTATGA
87920 AATTTA
1 AATTTA
87926 TTTTCCTACA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
14 18 0.45
15 17 0.43
16 5 0.12
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (15 bp):
AATTTAAATTTATGA
Found at i:87918 original size:44 final size:45
Alignment explanation
Indices: 87855--87955 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 45
87845 CAATTTATTT
* *
87855 TTTA-GCAATTTAAATTTATGAAATTTATTTTCTTATAATTTAAA
1 TTTATGCAATTTAAATTTATGAAATTTATTTTCCTACAATTTAAA
* *
87899 TTTATGCAATTTAGA-TTATGCAATTTATTTTCCTACAATTTAAA
1 TTTATGCAATTTAAATTTATGAAATTTATTTTCCTACAATTTAAA
*
87943 TTTATGCACTTTA
1 TTTATGCAATTTA
87956 CTTTTACTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 42 0.82
45 9 0.18
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (45 bp):
TTTATGCAATTTAAATTTATGAAATTTATTTTCCTACAATTTAAA
Found at i:87950 original size:30 final size:30
Alignment explanation
Indices: 87905--87990 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
87895 TAAATTTATG
* *
87905 CAATTTAGA-TTATGCAATTTATTTTCCTA
1 CAATTTAAATTTATGCAATTTATTTTACTA
* *
87934 CAATTTAAATTTATGCACTTTACTTTTACTG
1 CAATTTAAATTTATGCAATTTA-TTTTACTA
* * *
87965 CAATTT-AATCTATACATTTTATTTTA
1 CAATTTAAATTTATGCAATTTATTTTA
87991 TTGAATATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 13 0.27
30 23 0.48
31 12 0.25
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (30 bp):
CAATTTAAATTTATGCAATTTATTTTACTA
Found at i:87955 original size:15 final size:15
Alignment explanation
Indices: 87838--87972 Score: 82
Period size: 15 Copynumber: 9.0 Consensus size: 15
87828 ATGAAATTTG
87838 ATTTATGCAATTT-A
1 ATTTATGCAATTTAA
* *
87852 TTTTTTAGCAATTTAA
1 ATTTAT-GCAATTTAA
* *
87868 ATTTATGAAATTTATT
1 ATTTATGCAATTTA-A
*
87884 TTCTTAT--AATTTAA
1 AT-TTATGCAATTTAA
*
87898 ATTTATGCAATTTAG
1 ATTTATGCAATTTAA
87913 A-TTATGCAATTT-A
1 ATTTATGCAATTTAA
* * *
87926 TTTTCCTACAATTTAA
1 ATTT-ATGCAATTTAA
* *
87942 ATTTATGCACTTTAC
1 ATTTATGCAATTTAA
*
87957 TTTTACTGCAATTTAA
1 ATTTA-TGCAATTTAA
87973 TCTATACATT
Statistics
Matches: 89, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
13 4 0.04
14 18 0.20
15 45 0.51
16 18 0.20
17 4 0.04
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (15 bp):
ATTTATGCAATTTAA
Found at i:88347 original size:14 final size:14
Alignment explanation
Indices: 88328--88356 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
88318 CTTTCATGCA
88328 ATTTATCCTTTGCC
1 ATTTATCCTTTGCC
88342 ATTTATCCTTTGCC
1 ATTTATCCTTTGCC
88356 A
1 A
88357 CACAAACTTT
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:0.17, C:0.28, G:0.07, T:0.48
Consensus pattern (14 bp):
ATTTATCCTTTGCC
Found at i:91146 original size:19 final size:20
Alignment explanation
Indices: 91122--91174 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
91112 ACATTATGCT
***
91122 TTGTATCGATACAT-GTTTA
1 TTGTATCGATACATGGACAA
*
91141 TTGTATCGATATATGGACAA
1 TTGTATCGATACATGGACAA
91161 TTGTATCGATACAT
1 TTGTATCGATACAT
91175 AAAACTGGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:91233 original size:20 final size:19
Alignment explanation
Indices: 91204--91257 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
91194 CTACCACTAT
*
91204 TTGTACCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
91224 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGA-GAA
91244 TTGTATCGATACAT
1 TTGTATCGATACAT
91258 TGCTTCTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:92441 original size:15 final size:15
Alignment explanation
Indices: 92418--92447 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
92408 CACTGGAGTT
*
92418 TTACCATAAAAAATA
1 TTACAATAAAAAATA
92433 TTACAATAAAAAATA
1 TTACAATAAAAAATA
92448 AAAGATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (15 bp):
TTACAATAAAAAATA
Found at i:93442 original size:16 final size:16
Alignment explanation
Indices: 93423--93498 Score: 71
Period size: 16 Copynumber: 4.8 Consensus size: 16
93413 GAATTTAGGT
93423 TCGTTCGGGTTCAGGC
1 TCGTTCGGGTTCAGGC
*
93439 TCGTTTGGGTTCAGGC
1 TCGTTCGGGTTCAGGC
** * **
93455 TTATTCGAGTTTGGGC
1 TCGTTCGGGTTCAGGC
*
93471 TCGTTCGGGTTCAAGC
1 TCGTTCGGGTTCAGGC
* *
93487 TTGTTCGAGTTC
1 TCGTTCGGGTTC
93499 GAGCTCGTAC
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.20, G:0.33, T:0.38
Consensus pattern (16 bp):
TCGTTCGGGTTCAGGC
Found at i:93481 original size:32 final size:32
Alignment explanation
Indices: 93426--93506 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
93416 TTTAGGTTCG
* * * *
93426 TTCGGGTTCAGGCTCGTTTGGGTTCAGGCTTA
1 TTCGAGTTCGGGCTCGTTCGGGTTCAAGCTTA
* *
93458 TTCGAGTTTGGGCTCGTTCGGGTTCAAGCTTG
1 TTCGAGTTCGGGCTCGTTCGGGTTCAAGCTTA
*
93490 TTCGAGTTCGAGCTCGT
1 TTCGAGTTCGGGCTCGT
93507 ACAGGCTCGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.10, C:0.20, G:0.33, T:0.37
Consensus pattern (32 bp):
TTCGAGTTCGGGCTCGTTCGGGTTCAAGCTTA
Found at i:93753 original size:18 final size:17
Alignment explanation
Indices: 93699--93761 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 17
93689 TAATATATTT
*
93699 AATT-ATTTATTTATTGA
1 AATTAATTTATTTA-TAA
93716 AATCTATATTTATTTATAA
1 AAT-TA-ATTTATTTATAA
93735 AATTAATTTATTATATAA
1 AATTAATTTATT-TATAA
93753 AATTAATTT
1 AATTAATTT
93762 TTCAAATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
17 10 0.24
18 17 0.41
19 5 0.12
20 9 0.22
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTAATTTATTTATAA
Found at i:93770 original size:18 final size:18
Alignment explanation
Indices: 93731--93770 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
93721 ATATTTATTT
*
93731 ATAAAATTAATTTATTAT
1 ATAAAATTAATTTATTAA
93749 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTATT-AA
93767 ATAA
1 ATAA
93771 TTTCTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTATTAA
Found at i:93947 original size:22 final size:20
Alignment explanation
Indices: 93909--93949 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
93899 CACCTAATTA
*
93909 ATATTTAAAAATTTTAAAAT
1 ATATTTAAAAATATTAAAAT
93929 ATATTTAATAAAATATTAAAA
1 ATATTT-A-AAAATATTAAAA
93950 ACTCATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATTTAAAAATATTAAAAT
Found at i:94033 original size:13 final size:13
Alignment explanation
Indices: 94015--94039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
94005 AACTCAATTA
94015 AAATAAAAAAATG
1 AAATAAAAAAATG
94028 AAATAAAAAAAT
1 AAATAAAAAAAT
94040 CCCAAATCTT
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAATAAAAAAATG
Found at i:95794 original size:20 final size:19
Alignment explanation
Indices: 95769--95827 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
95759 CAGGCCACCA
95769 TTTCTTTCATTTTTTTTCTT
1 TTTCTTT-ATTTTTTTTCTT
* *
95789 TTTCTTTTTTTTTTTTGTT
1 TTTCTTTATTTTTTTTCTT
*
95808 TTTGTTT-TTTTGTTTT-TT
1 TTTCTTTATTTT-TTTTCTT
95826 TT
1 TT
95828 GTATTTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.23
19 20 0.57
20 7 0.20
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (19 bp):
TTTCTTTATTTTTTTTCTT
Found at i:95796 original size:14 final size:13
Alignment explanation
Indices: 95779--95827 Score: 71
Period size: 14 Copynumber: 3.6 Consensus size: 13
95769 TTTCTTTCAT
*
95779 TTTTTTTCTTTTTC
1 TTTTTTT-TTTTTG
95793 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
95806 TTTTTGTTTTTTTG
1 TTTTT-TTTTTTTG
95820 TTTTTTTT
1 TTTTTTTT
95828 GTATTTTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 13 0.39
14 20 0.61
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:95802 original size:19 final size:19
Alignment explanation
Indices: 95778--95824 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
95768 ATTTCTTTCA
95778 TTTTTTTTCTTTTTCTTTT
1 TTTTTTTTCTTTTTCTTTT
* *
95797 TTTTTTTTGTTTTTGTTTT
1 TTTTTTTTCTTTTTCTTTT
95816 TTTGTTTTT
1 TTT-TTTTT
95825 TTTGTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.89
Consensus pattern (19 bp):
TTTTTTTTCTTTTTCTTTT
Found at i:95835 original size:1 final size:1
Alignment explanation
Indices: 95778--95827 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
95768 ATTTCTTTCA
* * * * *
95778 TTTTTTTTCTTTTTCTTTTTTTTTTTTGTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
95828 GTATTTTTCA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:96048 original size:16 final size:15
Alignment explanation
Indices: 96021--96050 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
96011 ATGTTAACTT
96021 TATATTCTATTCTAC
1 TATATTCTATTCTAC
96036 TATATTACTATTCTA
1 TATATT-CTATTCTA
96051 AGTACAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:96594 original size:16 final size:15
Alignment explanation
Indices: 96555--96676 Score: 57
Period size: 16 Copynumber: 7.6 Consensus size: 15
96545 TGGGTTCTCC
96555 CGAGTTCGAGTTCTTT
1 CGAGTTCGAGTT-TTT
96571 CG-GATTCGAGTTTTAT
1 CGAG-TTCGAGTTTT-T
* *
96587 CGAGTTCGAACTTTCT
1 CGAGTTCG-AGTTTTT
* *
96603 CGAGTTCGAACTATTT
1 CGAGTTCG-AGTTTTT
* *
96619 CGGGTTCGAATAATTTT
1 CGAGTTCGAGT--TTTT
** *
96636 TAAATTCGAGTTTTAT
1 CGAGTTCGAGTTTT-T
* *
96652 CGAGTTCGAACTTTCT
1 CGAGTTCG-AGTTTTT
96668 CGAGTTCGA
1 CGAGTTCGA
96677 ACTATTTCGG
Statistics
Matches: 81, Mismatches: 17, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
15 9 0.11
16 54 0.67
17 18 0.22
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (15 bp):
CGAGTTCGAGTTTTT
Found at i:96649 original size:65 final size:65
Alignment explanation
Indices: 96574--96713 Score: 280
Period size: 65 Copynumber: 2.2 Consensus size: 65
96564 GTTCTTTCGG
96574 ATTCGAGTTTTATCGAGTTCGAACTTTCTCGAGTTCGAACTATTTCGGGTTCGAATAATTTTTAA
1 ATTCGAGTTTTATCGAGTTCGAACTTTCTCGAGTTCGAACTATTTCGGGTTCGAATAATTTTTAA
96639 ATTCGAGTTTTATCGAGTTCGAACTTTCTCGAGTTCGAACTATTTCGGGTTCGAATAATTTTTAA
1 ATTCGAGTTTTATCGAGTTCGAACTTTCTCGAGTTCGAACTATTTCGGGTTCGAATAATTTTTAA
96704 ATTCGAGTTT
1 ATTCGAGTTT
96714 CTGACTTTTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 75 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (65 bp):
ATTCGAGTTTTATCGAGTTCGAACTTTCTCGAGTTCGAACTATTTCGGGTTCGAATAATTTTTAA
Found at i:96677 original size:16 final size:16
Alignment explanation
Indices: 96651--96693 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
96641 TCGAGTTTTA
96651 TCGAGTTCGAACT-TT
1 TCGAGTTCGAACTATT
96666 CTCGAGTTCGAACTATT
1 -TCGAGTTCGAACTATT
*
96683 TCGGGTTCGAA
1 TCGAGTTCGAA
96694 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.92
17 2 0.08
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (16 bp):
TCGAGTTCGAACTATT
Found at i:104038 original size:38 final size:34
Alignment explanation
Indices: 103993--104090 Score: 90
Period size: 37 Copynumber: 2.7 Consensus size: 34
103983 ATAACATTAT
103993 TAAAATATTATTTTAAATATTTTATTATAA-AATTTAAA
1 TAAAATATT-TTTT-AATA-TTTA--ATAATAATTTAAA
*
104031 TAAAATATTTTTTATTATTTAATAATAATTTAAA
1 TAAAATATTTTTTAATATTTAATAATAATTTAAA
* *
104065 TAACAAAATTTTATTTAAAATTTAAT
1 TAA-AATA-TTT-TTTAATATTTAAT
104091 TCTTATAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
33 4 0.08
34 11 0.21
35 7 0.13
36 6 0.12
37 15 0.29
38 9 0.17
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (34 bp):
TAAAATATTTTTTAATATTTAATAATAATTTAAA
Found at i:104088 original size:37 final size:33
Alignment explanation
Indices: 104019--104090 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
104009 ATATTTTATT
* **
104019 ATAAAATTTAAATAAAATATTTTTTATTATTTA
1 ATAAAATTTAAATAAAAAATTTTTTAAAATTTA
104052 ATAATAATTTAAATAACAAAATTTTATTTAAAATTTA
1 ATAA-AATTTAAATAA-AAAA-TTT-TTTAAAATTTA
104089 AT
1 AT
104091 TCTTATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 4 0.12
34 11 0.34
35 3 0.09
36 3 0.09
37 11 0.34
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (33 bp):
ATAAAATTTAAATAAAAAATTTTTTAAAATTTA
Found at i:110037 original size:16 final size:18
Alignment explanation
Indices: 110018--110062 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
110008 ATGATATATA
110018 AAAATATA-ATT-ATAAT
1 AAAATATATATTAATAAT
110034 AAAA-ATATATTAATAATT
1 AAAATATATATTAATAA-T
*
110052 AAATTATATAT
1 AAAATATATAT
110063 AAAAATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 3 0.12
16 7 0.29
17 4 0.17
18 4 0.17
19 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATATATTAATAAT
Found at i:110049 original size:17 final size:16
Alignment explanation
Indices: 109994--110064 Score: 63
Period size: 17 Copynumber: 4.3 Consensus size: 16
109984 TAATTTTAAA
* *
109994 TATAATATAATTATAT
1 TATAATAAAAATATAT
*
110010 GATATATAAAAATATAAT
1 TATA-ATAAAAATAT-AT
110028 TATAATAAAAATATAT
1 TATAATAAAAATATAT
* *
110044 TAATAATTAAATTATA-
1 T-ATAATAAAAATATAT
110060 TATAA
1 TATAA
110065 AAATCATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
15 4 0.09
16 7 0.15
17 30 0.65
18 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
TATAATAAAAATATAT
Found at i:110066 original size:28 final size:29
Alignment explanation
Indices: 110025--110110 Score: 101
Period size: 28 Copynumber: 3.1 Consensus size: 29
110015 ATAAAAATAT
110025 AATTATA-ATAAAAATATATTAATA-ATTA
1 AATTATATAT-AAAATATATTAATATATTA
110053 AATTATATATAAAA-ATCATTAATATATTA
1 AATTATATATAAAATAT-ATTAATATATTA
* *
110082 AATTTTATAT-AAATATA-TAATATTTTA
1 AATTATATATAAAATATATTAATATATTA
110109 AA
1 AA
110111 AATAATTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
27 13 0.25
28 22 0.42
29 17 0.33
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
AATTATATATAAAATATATTAATATATTA
Found at i:110081 original size:29 final size:28
Alignment explanation
Indices: 110025--110110 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 28
110015 ATAAAAATAT
110025 AATTATA-ATAAAAATATATTAATA-ATTA
1 AATTATATAT-AAAA-ATATTAATATATTA
110053 AATTATATATAAAAATCATTAATATATTA
1 AATTATATATAAAAAT-ATTAATATATTA
* * *
110082 AATTTTATATAAATATA-TAATATTTTA
1 AATTATATATAAAAATATTAATATATTA
110109 AA
1 AA
110111 AATAATTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 13 0.25
28 19 0.37
29 20 0.38
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTATATATAAAAATATTAATATATTA
Found at i:110102 original size:27 final size:28
Alignment explanation
Indices: 110025--110110 Score: 104
Period size: 27 Copynumber: 3.1 Consensus size: 28
110015 ATAAAAATAT
*
110025 AATTATAATAAAAATATATTAATA-ATTA
1 AATTAT-ATATAAATATATTAATATATTA
*
110053 AATTATATATAAAAATCATTAATATATTA
1 AATTATATATAAATAT-ATTAATATATTA
* *
110082 AATTTTATATAAATATA-TAATATTTTA
1 AATTATATATAAATATATTAATATATTA
110109 AA
1 AA
110111 AATAATTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 19 0.37
28 14 0.27
29 18 0.35
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTATATATAAATATATTAATATATTA
Found at i:110521 original size:6 final size:6
Alignment explanation
Indices: 110503--110544 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
110493 GCTTATTTTT
* *
110503 AAATAA AATTAA AAAT-A AAATAA AAATTAA AAATAA ACATAA
1 AAATAA AAATAA AAATAA AAATAA AAA-TAA AAATAA AAATAA
110545 CACTCTCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:110530 original size:18 final size:18
Alignment explanation
Indices: 110503--110544 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
110493 GCTTATTTTT
110503 AAAT-AAAATTAAAAATA
1 AAATAAAAATTAAAAATA
110520 AAATAAAAATTAAAAATA
1 AAATAAAAATTAAAAATA
110538 AACATAA
1 AA-ATAA
110545 CACTCTCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 4 0.17
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATAAAAATTAAAAATA
Found at i:112925 original size:14 final size:15
Alignment explanation
Indices: 112895--112926 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
112885 TTGGCCATCA
112895 CTTTCTTTTCTTTCC
1 CTTTCTTTTCTTTCC
112910 CTTTCTTTTC-TTCC
1 CTTTCTTTTCTTTCC
112924 CTT
1 CTT
112927 CCATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTTCTTTTCTTTCC
Found at i:123217 original size:51 final size:50
Alignment explanation
Indices: 123162--123274 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 50
123152 TGATTACATC
* *
123162 TATCGATACATTGA-ATAATGTGTTGATACATCTGGGTA-AAATACCCAGATG
1 TATCGATACATTGATA-AATATATTGATACAT-TGGGTAGAAA-ACCCAGATG
* * * * *
123213 TATCGATAGAATGATAAATATATTGATACATTTGGTAGAAAATCTAGATG
1 TATCGATACATTGATAAATATATTGATACATTGGGTAGAAAACCCAGATG
123263 TATCGATACATT
1 TATCGATACATT
123275 TCCTTGGTAG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
50 22 0.43
51 28 0.55
52 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (50 bp):
TATCGATACATTGATAAATATATTGATACATTGGGTAGAAAACCCAGATG
Found at i:123329 original size:11 final size:13
Alignment explanation
Indices: 123302--123335 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
123292 GGCAGTTTTA
123302 TATCGATACATTG
1 TATCGATACATTG
123315 TATCGATA-A-TG
1 TATCGATACATTG
123326 TATCGATACA
1 TATCGATACA
123336 AAACTTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.50
12 2 0.10
13 8 0.40
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:137369 original size:40 final size:39
Alignment explanation
Indices: 137279--137369 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 39
137269 TTAAAATATT
137279 TTAAATTTAATTAATAAAATAAAAAATATTTTTATCTTA
1 TTAAATTTAATTAATAAAATAAAAAATATTTTTATCTTA
* *
137318 -TATATTATAATTAAATTTAAAT-AAAAATATTTTTAT-TTA
1 TTAAATT-TAATT-AA-TAAAATAAAAAATATTTTTATCTTA
137357 TTAAATATTAATT
1 TTAAAT-TTAATT
137370 TTGATAAGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
38 5 0.11
39 8 0.18
40 25 0.57
41 6 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (39 bp):
TTAAATTTAATTAATAAAATAAAAAATATTTTTATCTTA
Found at i:138094 original size:20 final size:20
Alignment explanation
Indices: 138069--138106 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
138059 TAGTTTATGC
138069 TTTGTATTTTATGTTGATAT
1 TTTGTATTTTATGTTGATAT
138089 TTTGTATTTTATGTTGAT
1 TTTGTATTTTATGTTGAT
138107 TATCAAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (20 bp):
TTTGTATTTTATGTTGATAT
Found at i:139605 original size:17 final size:17
Alignment explanation
Indices: 139561--139611 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
139551 AAATAAAATA
*
139561 AAAATAATTATGTATTTT
1 AAAA-AATTATATATTTT
**
139579 AAAATTTTATATATTTT
1 AAAAAATTATATATTTT
*
139596 AAAAAATTATTTATTT
1 AAAAAATTATATATTT
139612 ATTTCTAAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AAAAAATTATATATTTT
Found at i:139614 original size:21 final size:23
Alignment explanation
Indices: 139584--139625 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
139574 ATTTTAAAAT
139584 TTTATATATTT-TAAA-AAATTA
1 TTTATATATTTCTAAACAAATTA
*
139605 TTTATTTATTTCTAAACAAAT
1 TTTATATATTTCTAAACAAAT
139626 CCACCCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATATATTTCTAAACAAATTA
Found at i:139998 original size:50 final size:51
Alignment explanation
Indices: 139922--140018 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 51
139912 ACTCACAGTA
*
139922 AATCTTAATAAGAACACTCCTGAAATCAATGTATCATTTAAACTTTTACAT
1 AATCTTAATAAGAACACTCCTGAAATCAACGTATCATTTAAACTTTTACAT
* * * *
139973 AATC-TAATAATAACACTCTTTAAATCTACGTATCATTTAAACTTTT
1 AATCTTAATAAGAACACTCCTGAAATCAACGTATCATTTAAACTTTT
140019 CTATGATCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 37 0.90
51 4 0.10
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (51 bp):
AATCTTAATAAGAACACTCCTGAAATCAACGTATCATTTAAACTTTTACAT
Found at i:140121 original size:15 final size:15
Alignment explanation
Indices: 140103--140138 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
140093 AAAATTGGCC
140103 AAAAGAAAAAAGGAA
1 AAAAGAAAAAAGGAA
*
140118 AAAAAAAAAAAGGAA
1 AAAAGAAAAAAGGAA
*
140133 TAAAGA
1 AAAAGA
140139 CGTAACAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAAGGAA
Found at i:140580 original size:23 final size:21
Alignment explanation
Indices: 140526--140580 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
140516 ATTAGCATAA
*
140526 TTAATATA-TTATATTAATAT
1 TTAATATATTTATATTAAAAT
* *
140546 GTATTATATTTATATTTAAAATT
1 TTAATATATTTATA-TTAAAA-T
140569 TTAATATATTTA
1 TTAATATATTTA
140581 ATAATTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 6 0.22
21 5 0.19
22 5 0.19
23 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTAATATATTTATATTAAAAT
Found at i:140590 original size:14 final size:15
Alignment explanation
Indices: 140573--140601 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
140563 AAAATTTTAA
140573 TATATTTA-ATAATT
1 TATATTTATATAATT
140587 TATATTTATATAATT
1 TATATTTATATAATT
140602 GACGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTTATATAATT
Found at i:141192 original size:29 final size:29
Alignment explanation
Indices: 141155--141210 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
141145 TTTAGAAGAT
*
141155 AATTATTAAAGATGAATTTTTATTTTTAA
1 AATTATTAAAAATGAATTTTTATTTTTAA
* *
141184 AATTTTTAAAAATGATTTTTTATTTTT
1 AATTATTAAAAATGAATTTTTATTTTT
141211 CGAAGACCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (29 bp):
AATTATTAAAAATGAATTTTTATTTTTAA
Found at i:143398 original size:17 final size:17
Alignment explanation
Indices: 143360--143392 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
143350 TATCGTATTA
*
143360 ATATTATTTTTTATATC
1 ATATTATATTTTATATC
143377 ATATTATATTTTATAT
1 ATATTATATTTTATAT
143393 TTTATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATC
Found at i:143879 original size:30 final size:31
Alignment explanation
Indices: 143843--143908 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
143833 CAAATTACCT
143843 AAAATCAAAA-TTAAGTGATAAAATT-AAATA
1 AAAATCAAAATTTAA-TGATAAAATTCAAATA
* *
143873 AAAATCAAAATTTAATGATAAATTTCAATTA
1 AAAATCAAAATTTAATGATAAAATTCAAATA
143904 AAAAT
1 AAAAT
143909 ATAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (31 bp):
AAAATCAAAATTTAATGATAAAATTCAAATA
Found at i:145569 original size:21 final size:21
Alignment explanation
Indices: 145526--145569 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
145516 GATTTAATGG
**
145526 TTTGATGAAAAAAAATATTTT
1 TTTGATGAAAAAAAATAACTT
**
145547 TTTGATGAAAAAATGTAACTT
1 TTTGATGAAAAAAAATAACTT
145568 TT
1 TT
145570 AATAATTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (21 bp):
TTTGATGAAAAAAAATAACTT
Found at i:148892 original size:21 final size:21
Alignment explanation
Indices: 148853--148892 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
148843 TAATAATTGG
**
148853 ATGAAAAAATACATTTTTTGA
1 ATGAAAAAATACAACTTTTGA
148874 ATGAAAAAATACAACTTTT
1 ATGAAAAAATACAACTTTT
148893 AATAACCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (21 bp):
ATGAAAAAATACAACTTTTGA
Found at i:150496 original size:20 final size:19
Alignment explanation
Indices: 150471--150561 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 19
150461 TGTCAGTTTT
*
150471 ATGTATCGATACAATTATGC
1 ATGTATCGATACAATAAT-C
*
150491 ATGTATCGATACTATAATC
1 ATGTATCGATACAATAATC
* *
150510 ATGTATCAATACAA-AGCATT
1 ATGTATCGATACAATA--ATC
*
150530 ATGTATCGATACATCTAGAT-
1 ATGTATCGATACA-ATA-ATC
150550 ATGTATCGATAC
1 ATGTATCGATAC
150562 TTTCAAGGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
18 1 0.02
19 13 0.22
20 42 0.71
21 2 0.03
22 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACAATAATC
Found at i:155746 original size:13 final size:13
Alignment explanation
Indices: 155728--155752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155718 ATTACTCAAA
155728 TGTATCGATACAT
1 TGTATCGATACAT
155741 TGTATCGATACA
1 TGTATCGATACA
155753 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:155817 original size:52 final size:52
Alignment explanation
Indices: 155761--155885 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
155751 CACTGATCTT
*
155761 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
155813 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
155865 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
155886 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:156670 original size:9 final size:9
Alignment explanation
Indices: 156656--156680 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
156646 GATTATTGTG
156656 ATGATTTTA
1 ATGATTTTA
156665 ATGATTTTA
1 ATGATTTTA
156674 ATGATTT
1 ATGATTT
156681 AAGGTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (9 bp):
ATGATTTTA
Found at i:161306 original size:6 final size:6
Alignment explanation
Indices: 161295--161334 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
161285 AGTCAACTTC
*
161295 ATCATT ATCATT ATCATT ATCATT ATCTATC ATCATT ATC
1 ATCATT ATCATT ATCATT ATCATT ATC-ATT ATCATT ATC
161335 TTCATCATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (6 bp):
ATCATT
Found at i:161339 original size:12 final size:12
Alignment explanation
Indices: 161301--161342 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
161291 CTTCATCATT
161301 ATCATTATCATT-
1 ATCATTATC-TTC
161313 ATCATTATCTATC
1 ATCATTATCT-TC
161326 ATCATTATCTTC
1 ATCATTATCTTC
161338 ATCAT
1 ATCAT
161343 CTCTGATGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.04
12 17 0.61
13 10 0.36
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (12 bp):
ATCATTATCTTC
Found at i:161578 original size:27 final size:27
Alignment explanation
Indices: 161518--161571 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
161508 GTTTTAGAAG
161518 ACTGTTGAGAAACTTCTTCACCATCTC
1 ACTGTTGAGAAACTTCTTCACCATCTC
161545 ACTGTTGAGAAACTTCTTCACCATCTC
1 ACTGTTGAGAAACTTCTTCACCATCTC
161572 TTTGTTGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (27 bp):
ACTGTTGAGAAACTTCTTCACCATCTC
Found at i:163160 original size:20 final size:20
Alignment explanation
Indices: 163113--163161 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
163103 TACAAAGCAT
*
163113 TATGTATAGATACATTTAGA
1 TATGTATCGATACATTTAGA
*
163133 TATGTATCGATATATTTAGA
1 TATGTATCGATACATTTAGA
163153 TATGTATCG
1 TATGTATCG
163162 GTGCTTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (20 bp):
TATGTATCGATACATTTAGA
Found at i:167190 original size:13 final size:13
Alignment explanation
Indices: 167172--167197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
167162 AATAGCTTCT
167172 AACCTAGCTACGG
1 AACCTAGCTACGG
167185 AACCTAGCTACGG
1 AACCTAGCTACGG
167198 GTGCATAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (13 bp):
AACCTAGCTACGG
Found at i:169496 original size:15 final size:15
Alignment explanation
Indices: 169478--169512 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
169468 CAAGTCAACT
169478 TCATCATTAT-TGTCA
1 TCATCATTATCT-TCA
169493 TCATCATTATCTTCA
1 TCATCATTATCTTCA
169508 TCATC
1 TCATC
169513 TCTGATGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.46
Consensus pattern (15 bp):
TCATCATTATCTTCA
Found at i:171003 original size:33 final size:32
Alignment explanation
Indices: 170948--171012 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
170938 TTTGAGACAA
170948 TGTATTGATACAATTCTTCATGTATCAATACAT
1 TGTATTGATACAATTC-TCATGTATCAATACAT
*
170981 TGTATTGATACAATGTGC-CATGTATCGATACA
1 TGTATTGATACAAT-T-CTCATGTATCAATACA
171013 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (32 bp):
TGTATTGATACAATTCTCATGTATCAATACAT
Found at i:171074 original size:20 final size:20
Alignment explanation
Indices: 171041--171096 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
171031 ACTGCCAGTT
*
171041 TCATATATCGATACAATTG-
1 TCATGTATCGATACAATTGA
*
171060 TGCATGTATCAATACAA-TGA
1 T-CATGTATCGATACAATTGA
171080 TCATGTATCGATACAAT
1 TCATGTATCGATACAAT
171097 GTATAGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (20 bp):
TCATGTATCGATACAATTGA
Found at i:171277 original size:21 final size:21
Alignment explanation
Indices: 171253--171295 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
171243 TTCGATTTAA
*
171253 AACTCGAAAATATTTATAGAT
1 AACTCGAAAACATTTATAGAT
*
171274 AACTCTAAAACATTTATAGAT
1 AACTCGAAAACATTTATAGAT
171295 A
1 A
171296 TTGAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.33
Consensus pattern (21 bp):
AACTCGAAAACATTTATAGAT
Found at i:171542 original size:57 final size:57
Alignment explanation
Indices: 171454--171568 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
171444 AAAAGGATAC
171454 TTCACTAATATTTTTACACCAAAATAAAAAAGATTATAAGCATGTGAATACACCATT
1 TTCACTAATATTTTTACACCAAAATAAAAAAGATTATAAGCATGTGAATACACCATT
*
171511 TTCACTAATATTTTTACACTAAAATAAAAAAGATTATAAGCATGTGAATACACCATT
1 TTCACTAATATTTTTACACCAAAATAAAAAAGATTATAAGCATGTGAATACACCATT
171568 T
1 T
171569 AGCTAAAACC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (57 bp):
TTCACTAATATTTTTACACCAAAATAAAAAAGATTATAAGCATGTGAATACACCATT
Found at i:172061 original size:13 final size:13
Alignment explanation
Indices: 172029--172062 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
172019 AGTAGCTAGT
**
172029 AAAAAAAAGAGCA
1 AAAAAAAAGAAAA
172042 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
172055 AAAAAAAA
1 AAAAAAAA
172063 AGATTGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:172963 original size:30 final size:30
Alignment explanation
Indices: 172871--172963 Score: 77
Period size: 29 Copynumber: 3.1 Consensus size: 30
172861 CACTTCAAGG
* * *
172871 TCATTTAAGTTATTTGTC-ATAATCTAGGAA
1 TCATTTAAATT-TTTTTCTATAATCTAGGGA
* * *
172901 TCATTTAACA-ATTTTTGTGT-ATCTTA-GGA
1 TCATTTAA-ATTTTTTTCTATAATC-TAGGGA
172930 TCATTTAAATTTTTTTCTATAATCTAGGGA
1 TCATTTAAATTTTTTTCTATAATCTAGGGA
172960 TCAT
1 TCAT
172964 GTGATAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 1 0.02
29 26 0.54
30 21 0.44
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (30 bp):
TCATTTAAATTTTTTTCTATAATCTAGGGA
Found at i:174320 original size:30 final size:32
Alignment explanation
Indices: 174284--174342 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
174274 ATATATATAT
174284 ATTAATTAAAATTTT-AAA-TTTTAATTATGC
1 ATTAATTAAAATTTTAAAATTTTTAATTATGC
*
174314 ATTAATTGAAATTTTAAAATTTTTAATTA
1 ATTAATTAAAATTTTAAAATTTTTAATTA
174343 AATTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 14 0.54
31 3 0.12
32 9 0.35
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (32 bp):
ATTAATTAAAATTTTAAAATTTTTAATTATGC
Found at i:174347 original size:20 final size:20
Alignment explanation
Indices: 174315--174355 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
174305 TAATTATGCA
174315 TTAATTGAAATTTTAAAATTT
1 TTAATTGAAATTTT-AAATTT
174336 TTAATT-AAATTTTAAATTT
1 TTAATTGAAATTTTAAATTT
174355 T
1 T
174356 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 7 0.35
21 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATTGAAATTTTAAATTT
Found at i:175220 original size:14 final size:16
Alignment explanation
Indices: 175193--175242 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 16
175183 ATTTAAATTA
175193 TTTATATTTATATAAAT
1 TTTATA-TTATATAAAT
175210 TTTA-A-TATATAAAT
1 TTTATATTATATAAAT
175224 AATTTATATTATATAAAT
1 --TTTATATTATATAAAT
175242 T
1 T
175243 ATAAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 9 0.31
16 6 0.21
17 5 0.17
18 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTATATTATATAAAT
Found at i:175225 original size:18 final size:18
Alignment explanation
Indices: 175186--175241 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 18
175176 TAATCGTATT
* *
175186 TAAATTATTTAT-ATTTA
1 TAAATAATTTATAATATA
*
175203 TATA-AATTT-TAATATA
1 TAAATAATTTATAATATA
*
175219 TAAATAATTTATATTATA
1 TAAATAATTTATAATATA
175237 TAAAT
1 TAAAT
175242 TATAAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.03
16 11 0.35
17 8 0.26
18 11 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAATAATTTATAATATA
Found at i:175229 original size:42 final size:41
Alignment explanation
Indices: 175150--175245 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 41
175140 TGTGCATTCA
*
175150 ATTTATAATTATATAATTTTATATTATAATCGTATTTAAATT
1 ATTTATAATTATATAATTTTATATTATAATC-AATTTAAATT
* *
175192 ATTTATATTTATATAAATTTTA-ATATATAAAT-AATTTATATT
1 ATTTATAATTATAT-AATTTTATAT-TAT-AATCAATTTAAATT
*
175234 ATATA-AATTATA
1 ATTTATAATTATA
175246 AAAATATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
41 6 0.13
42 27 0.59
43 10 0.22
44 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (41 bp):
ATTTATAATTATATAATTTTATATTATAATCAATTTAAATT
Found at i:178818 original size:12 final size:13
Alignment explanation
Indices: 178799--178838 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
178789 GCCAAGAAAA
178799 TATATCGATACAT
1 TATATCGATACAT
178812 T-TATCGATACAT
1 TATATCGATACAT
178824 TGATATCGATACAT
1 T-ATATCGATACAT
178838 T
1 T
178839 GATCTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.48
13 1 0.04
14 12 0.48
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:178832 original size:14 final size:14
Alignment explanation
Indices: 178800--178841 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
178790 CCAAGAAAAT
178800 ATATCGATACATT-
1 ATATCGATACATTG
178813 -TATCGATACATTG
1 ATATCGATACATTG
178826 ATATCGATACATTG
1 ATATCGATACATTG
178840 AT
1 AT
178842 CTTTGTTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.44
14 15 0.56
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (14 bp):
ATATCGATACATTG
Found at i:181141 original size:25 final size:25
Alignment explanation
Indices: 181107--181171 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
181097 ATCATTATCA
181107 AGGACACTCCAACCCTATTCCTCCG
1 AGGACACTCCAACCCTATTCCTCCG
*
181132 AGGATACTCCAACCCTATTCCTCCG
1 AGGACACTCCAACCCTATTCCTCCG
*
181157 AGGACACTCTAACCC
1 AGGACACTCCAACCC
181172 CGTTTTTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.26, C:0.42, G:0.12, T:0.20
Consensus pattern (25 bp):
AGGACACTCCAACCCTATTCCTCCG
Found at i:187485 original size:13 final size:13
Alignment explanation
Indices: 187467--187491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187457 TTAACAATAT
187467 TTATAAAAAATGC
1 TTATAAAAAATGC
187480 TTATAAAAAATG
1 TTATAAAAAATG
187492 TTCATTAACA
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:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
TTATAAAAAATGC
Found at i:193020 original size:24 final size:25
Alignment explanation
Indices: 192979--193041 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
192969 ATTATATATT
* * * *
192979 TAATATTTTATGTAATTTCTATCTA
1 TAATATTTAATATAATTTATAGCTA
193004 TAATATTTAATAT-ATTTATAGCTA
1 TAATATTTAATATAATTTATAGCTA
*
193028 TAATATAT-ATATAA
1 TAATATTTAATATAA
193042 AAGTATAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 4 0.12
24 17 0.53
25 11 0.34
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (25 bp):
TAATATTTAATATAATTTATAGCTA
Found at i:194284 original size:49 final size:51
Alignment explanation
Indices: 194224--194323 Score: 152
Period size: 49 Copynumber: 2.0 Consensus size: 51
194214 GCATAATGAT
*
194224 AGTTATAAGCCTTTGCAAAAGGC-AAGATAATAATTTGAA-CCTTTGTTGAA
1 AGTTATAAGCCTTTGCAAAAGGCGAA-ATAATAATTTCAAGCCTTTGTTGAA
*
194274 AGTTA-AAGCCTTTGCAAAAGGCGTAATAATAATTTCAAGCCTTTGTTGAA
1 AGTTATAAGCCTTTGCAAAAGGCGAAATAATAATTTCAAGCCTTTGTTGAA
194324 GGTGAGATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
49 29 0.63
50 17 0.37
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (51 bp):
AGTTATAAGCCTTTGCAAAAGGCGAAATAATAATTTCAAGCCTTTGTTGAA
Found at i:194332 original size:80 final size:79
Alignment explanation
Indices: 194242--194479 Score: 253
Period size: 80 Copynumber: 3.0 Consensus size: 79
194232 GCCTTTGCAA
* * * *
194242 AAGGCAAGATAATAATTTGAACCTTTGTTGAAAGTTAAAGCCTTTGCAAAAGGCGTAATAATAAT
1 AAGGCGAGATAATAATTTGAACATTTG-TGAAAGTTAAAGCCTTTGCTAAAGGCGTAATAATAGT
*
194307 TTCAAGCCTTTGTTG
65 CTCAAGCCTTTGTTG
* * * ** **
194322 AAGGTGAGATAATAATCTGAACTTTTGCAAAAGGTTAAAG-CTTCTGCTAAAGATGTAATAATAG
1 AAGGCGAGATAATAATTTGAACATTTGTGAAA-GTTAAAGCCTT-TGCTAAAGGCGTAATAATAG
*
194386 TCTCAAGCCTTTGCTG
64 TCTCAAGCCTTTGTTG
* * * ** *
194402 AAGGCGAGTTAATAATTTGAACATTTGCTGAAGGTTAAAGCTTTTATTGAAGGCGTAATAATAGT
1 AAGGCGAGATAATAATTTGAACATTTG-TGAAAGTTAAAGCCTTTGCTAAAGGCGTAATAATAGT
*
194467 CTCAAGCCCTTGT
65 CTCAAGCCTTTGT
194480 GTCTGTGAGA
Statistics
Matches: 127, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
79 6 0.05
80 117 0.92
81 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.32
Consensus pattern (79 bp):
AAGGCGAGATAATAATTTGAACATTTGTGAAAGTTAAAGCCTTTGCTAAAGGCGTAATAATAGTC
TCAAGCCTTTGTTG
Done.