Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 135 of 187
Found at i:40761291 original size:6 final size:6
Alignment explanation
Indices: 40761280--40761316 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
40761270 ATTCAGTCAA
*
40761280 CATTTT CATTTT CATTTT CATTTT -ATTCT -ATTTT CAT
1 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CAT
40761317 ATAACCAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 8 0.29
6 20 0.71
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (6 bp):
CATTTT
Found at i:40776740 original size:19 final size:18
Alignment explanation
Indices: 40776716--40776775 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
40776706 TCTTAATCCC
*
40776716 TTTATTTCCTTATATTTTA
1 TTTATTTACTT-TATTTTA
*
40776735 TTTATTTACTTTCTTTTA
1 TTTATTTACTTTATTTTA
* *
40776753 TTTTCTTTTCTTTGATTTTA
1 -TTTATTTACTTT-ATTTTA
40776773 TTT
1 TTT
40776776 TTTGTTTCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.18
19 23 0.68
20 5 0.15
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTATTTACTTTATTTTA
Found at i:40776764 original size:15 final size:15
Alignment explanation
Indices: 40776735--40776776 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
40776725 TTATATTTTA
*
40776735 TTTATTTAC-TTTCT
1 TTTATTTTCTTTTCT
40776749 TTTATTTTCTTTTCT
1 TTTATTTTCTTTTCT
* *
40776764 TTGATTTTATTTT
1 TTTATTTTCTTTT
40776777 TTGTTTCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTATTTTCTTTTCT
Found at i:40777682 original size:138 final size:138
Alignment explanation
Indices: 40777460--40777747 Score: 531
Period size: 138 Copynumber: 2.1 Consensus size: 138
40777450 CTTCGCGTCT
*
40777460 AAAGATTGAGTGGCATTCTAAGCTATTCATTTTCTCCACTAGTCTTAACAATTATGAGTAAAGCT
1 AAAGATTGAGTGGCATTCTAAGCTATTCACTTTCTCCACTAGTCTTAACAATTATGAGTAAAGCT
*
40777525 AGTAGCCATCTAGAGATGTGACTAATTGAGTAACCGGGGTGGGGTGTTTGGGTTTTCATTCTTCT
66 AGTAGCCATCTAGAGATGTGACTAATCGAGTAACCGGGGTGGGGTGTTTGGGTTTTCATTCTTCT
40777590 TTGCGTAA
131 TTGCGTAA
*
40777598 AAATATTGAGTGGCATTCTAAGCTATTCACTTTCTCCACTAGTCTTAACAATTATGAGTAAAGCT
1 AAAGATTGAGTGGCATTCTAAGCTATTCACTTTCTCCACTAGTCTTAACAATTATGAGTAAAGCT
*
40777663 AGTAGCCATCTAGAGATGTGACTGATCGAGTAACCGGGGTGGGGTGTTTGGGTTTTCATTCTTCT
66 AGTAGCCATCTAGAGATGTGACTAATCGAGTAACCGGGGTGGGGTGTTTGGGTTTTCATTCTTCT
40777728 TTGCGTAA
131 TTGCGTAA
*
40777736 AAAGATTTAGTG
1 AAAGATTGAGTG
40777748 ACAATCTAGA
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 144 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.35
Consensus pattern (138 bp):
AAAGATTGAGTGGCATTCTAAGCTATTCACTTTCTCCACTAGTCTTAACAATTATGAGTAAAGCT
AGTAGCCATCTAGAGATGTGACTAATCGAGTAACCGGGGTGGGGTGTTTGGGTTTTCATTCTTCT
TTGCGTAA
Found at i:40779966 original size:21 final size:19
Alignment explanation
Indices: 40779940--40779978 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
40779930 AGGGAAGGAA
40779940 AAGAAGGAAGAAGAAAAAAAT
1 AAGAA-GAA-AAGAAAAAAAT
40779961 AAGAAGAAAAGAAAAAAA
1 AAGAAGAAAAGAAAAAAA
40779979 ACTTAACAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (19 bp):
AAGAAGAAAAGAAAAAAAT
Found at i:40781470 original size:20 final size:20
Alignment explanation
Indices: 40781447--40781484 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40781437 AATTTTTTTT
*
40781447 AAAAAAT-ATATAAAATTTC
1 AAAAAATAAAATAAAATTTC
40781466 AAAAAATAAAATAAAATTT
1 AAAAAATAAAATAAAATTT
40781485 GAAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATAAAATAAAATTTC
Found at i:40782437 original size:17 final size:17
Alignment explanation
Indices: 40782415--40782462 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
40782405 ATGTTATATG
* *
40782415 TTAAAAAATTTATAATT
1 TTAAAAAATTAAAAATT
40782432 TTAAAAAGA-TAAAAATT
1 TTAAAAA-ATTAAAAATT
40782449 TTAAAAAA-TAAAAA
1 TTAAAAAATTAAAAA
40782463 AACGTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.25
17 20 0.71
18 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
TTAAAAAATTAAAAATT
Found at i:40782454 original size:16 final size:17
Alignment explanation
Indices: 40782428--40782462 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40782418 AAAAATTTAT
*
40782428 AATTTTAAAAAGATAAA
1 AATTTTAAAAAAATAAA
40782445 AATTTT-AAAAAATAAA
1 AATTTTAAAAAAATAAA
40782461 AA
1 AA
40782463 AACGTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AATTTTAAAAAAATAAA
Found at i:40782463 original size:17 final size:17
Alignment explanation
Indices: 40782428--40782462 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
40782418 AAAAATTTAT
40782428 AATTTTAAAAAGATAAA
1 AATTTTAAAAAGATAAA
40782445 AATTTTAAAAA-ATAAA
1 AATTTTAAAAAGATAAA
40782461 AA
1 AA
40782463 AACGTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AATTTTAAAAAGATAAA
Found at i:40784064 original size:16 final size:16
Alignment explanation
Indices: 40784043--40784074 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40784033 TAATTTTTTT
*
40784043 TATAAAATTGTAAAAA
1 TATAAAATTATAAAAA
40784059 TATAAAATTATAAAAA
1 TATAAAATTATAAAAA
40784075 AATTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
TATAAAATTATAAAAA
Found at i:40784078 original size:11 final size:11
Alignment explanation
Indices: 40784062--40784094 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
40784052 GTAAAAATAT
40784062 AAAATTATAAA
1 AAAATTATAAA
40784073 AAAATTAT-AA
1 AAAATTATAAA
40784083 AAAATTATAAA
1 AAAATTATAAA
40784094 A
1 A
40784095 TCAAATAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:40784084 original size:10 final size:10
Alignment explanation
Indices: 40784062--40784094 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
40784052 GTAAAAATAT
40784062 AAAATTATAAA
1 AAAATTAT-AA
40784073 AAAATTATAA
1 AAAATTATAA
40784083 AAAATTATAA
1 AAAATTATAA
40784093 AA
1 AA
40784095 TCAAATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATTATAA
Found at i:40784605 original size:39 final size:41
Alignment explanation
Indices: 40784548--40784633 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 41
40784538 ATTTCTTTAC
* *
40784548 ATTTTTTTTATAATTTTCT-TATGACTTTATAAAATTTTATT
1 ATTTTTTCTATAATTTTCTATAT-ACTTTATAAAATTTTATG
* **
40784589 ATTTTTTCTAT-A-TTTCTATATATTTTATAATTTTTTATG
1 ATTTTTTCTATAATTTTCTATATACTTTATAAAATTTTATG
40784628 ATTTTT
1 ATTTTT
40784634 ATAAAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
39 25 0.64
40 4 0.10
41 10 0.26
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (41 bp):
ATTTTTTCTATAATTTTCTATATACTTTATAAAATTTTATG
Found at i:40784623 original size:9 final size:10
Alignment explanation
Indices: 40784526--40784695 Score: 50
Period size: 10 Copynumber: 17.0 Consensus size: 10
40784516 ATGAGATACA
40784526 ATAA-TTTTT
1 ATAATTTTTT
40784535 ATAATTTCTTT
1 ATAATTT-TTT
* *
40784546 ACATTTTTTTT
1 ATA-ATTTTTT
40784557 ATAATTTTCTT
1 ATAATTTT-TT
* * *
40784568 ATGACTTTAT
1 ATAATTTTTT
*
40784578 AAAATTTTATT
1 ATAATTTT-TT
40784589 AT--TTTTTCT
1 ATAATTTTT-T
*
40784598 AT-A-TTTCT
1 ATAATTTTTT
*
40784606 AT-ATATTTT
1 ATAATTTTTT
40784615 ATAATTTTTT
1 ATAATTTTTT
*
40784625 ATGA-TTTTT
1 ATAATTTTTT
**
40784634 ATAAAAATTTT
1 AT-AATTTTTT
* *
40784645 CTAATTTTTA
1 ATAATTTTTT
*
40784655 ATAA-CTTTT
1 ATAATTTTTT
*
40784664 AAATATTTTTT
1 ATA-ATTTTTT
**
40784675 ATTAAAATTTT
1 A-TAATTTTTT
*
40784686 ATTATTTTTT
1 ATAATTTTTT
40784696 TTATCTTTTT
Statistics
Matches: 113, Mismatches: 34, Indels: 27
0.65 0.20 0.16
Matches are distributed among these distances:
8 5 0.04
9 31 0.27
10 37 0.33
11 36 0.32
12 4 0.04
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:40784633 original size:19 final size:18
Alignment explanation
Indices: 40784529--40784637 Score: 60
Period size: 19 Copynumber: 5.6 Consensus size: 18
40784519 AGATACAATA
40784529 ATTTTTATAATTTCTTTACATT
1 ATTTTTATAATTT-TTT--A-T
*
40784551 TTTTTTATAATTTTCTTAT
1 ATTTTTATAATTTT-TTAT
* *
40784570 GACTTTATAAAATTTTATTAT
1 -A-TTTTTATAATTTT-TTAT
* *
40784591 -TTTTTCT-ATATTTCTAT
1 ATTTTTATAAT-TTTTTAT
40784608 ATATTTTATAATTTTTTAT
1 AT-TTTTATAATTTTTTAT
40784627 GATTTTTATAA
1 -ATTTTTATAA
40784638 AAATTTTCTA
Statistics
Matches: 68, Mismatches: 11, Indels: 19
0.69 0.11 0.19
Matches are distributed among these distances:
17 5 0.07
18 8 0.12
19 20 0.29
20 5 0.07
21 16 0.24
22 14 0.21
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTTTATAATTTTTTAT
Found at i:40784644 original size:30 final size:30
Alignment explanation
Indices: 40784553--40784653 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 30
40784543 TTTACATTTT
*
40784553 TTTTATAATTTTCTTATGA-CTTTAT-AAAA
1 TTTTATAATTTT-TTATGATATTTATAAAAA
* * * * *
40784582 TTTTATTATTTTTTCT-ATATTTCTATATA
1 TTTTATAATTTTTTATGATATTTATAAAAA
*
40784611 TTTTATAATTTTTTATGATTTTTATAAAAA
1 TTTTATAATTTTTTATGATATTTATAAAAA
*
40784641 TTTTCTAATTTTT
1 TTTTATAATTTTT
40784654 AATAACTTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
27 1 0.02
28 7 0.12
29 27 0.48
30 21 0.38
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTTATAATTTTTTATGATATTTATAAAAA
Found at i:40784670 original size:58 final size:58
Alignment explanation
Indices: 40784553--40784672 Score: 138
Period size: 58 Copynumber: 2.1 Consensus size: 58
40784543 TTTACATTTT
* ** *
40784553 TTTTATAATTTTCTTATGACTTTATAAAATTTTATTATTTTTTCTATATTTCTATATA
1 TTTTATAATTTTCTTATGACTTTATAAAATTTTATAATTTTTAATATATTTCTAAATA
* *
40784611 TTTTATAATTTT-TTATGATTTTTATAAAAATTTTCTAATTTTTAATA-ACTTT-TAAATA
1 TTTTATAATTTTCTTATGA-CTTTAT-AAAATTTTATAATTTTTAATATA-TTTCTAAATA
40784669 TTTT
1 TTTT
40784673 TTATTAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
57 6 0.11
58 27 0.51
59 20 0.38
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (58 bp):
TTTTATAATTTTCTTATGACTTTATAAAATTTTATAATTTTTAATATATTTCTAAATA
Found at i:40785120 original size:2 final size:2
Alignment explanation
Indices: 40785113--40785194 Score: 62
Period size: 2 Copynumber: 42.0 Consensus size: 2
40785103 AATATTCTAT
* * * * *
40785113 TA TA TA TA TA TA TA TA TA TA TG TA T- TA TT TG TA TC TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
40785154 TA AA T- TA TT TA TA -A TC TA TCA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
40785195 AGCACGAATT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
1 3 0.05
2 56 0.92
3 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40786731 original size:34 final size:34
Alignment explanation
Indices: 40786685--40786767 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
40786675 AGAATTTAAT
* *
40786685 TATGCTTTTAACAGAACAATACAGTAAC-AATAAA
1 TATGCTTATAACAGAACAATACAATAACAAAT-AA
*** *
40786719 TATGCTTATAACATTTCAATACAATAGCAAATAA
1 TATGCTTATAACAGAACAATACAATAACAAATAA
*
40786753 TATGTTTATAACAGA
1 TATGCTTATAACAGA
40786768 TAAACTCAGT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
34 36 0.92
35 3 0.08
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.31
Consensus pattern (34 bp):
TATGCTTATAACAGAACAATACAATAACAAATAA
Found at i:40788435 original size:25 final size:25
Alignment explanation
Indices: 40788405--40788470 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 25
40788395 TTAGCTCTTA
40788405 TGAGCTTCCTGATATAGGCTCTTCG
1 TGAGCTTCCTGATATAGGCTCTTCG
* *
40788430 TGAGCTTCCT-ATTAAATTGGCTCTTTG
1 TGAGCTTCCTGA-T--ATAGGCTCTTCG
*
40788457 TGAGCTTCATGATA
1 TGAGCTTCCTGATA
40788471 GTGCTCGCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 1 0.03
25 12 0.35
27 20 0.59
28 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (25 bp):
TGAGCTTCCTGATATAGGCTCTTCG
Found at i:40788681 original size:25 final size:26
Alignment explanation
Indices: 40788631--40788691 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
40788621 CCGAGATAAG
*
40788631 CTTCCTGTTACATGGCTCACATGAGT
1 CTTCCTGTTAAATGGCTCACATGAGT
*
40788657 -TTCCTGTTAAATGGCTCGAGA-GAGT
1 CTTCCTGTTAAATGGCTC-ACATGAGT
40788682 GCTTCCTGTT
1 -CTTCCTGTT
40788692 TAAGTGTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 20 0.67
26 2 0.07
27 8 0.27
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
CTTCCTGTTAAATGGCTCACATGAGT
Found at i:40790922 original size:28 final size:28
Alignment explanation
Indices: 40790890--40790952 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
40790880 TATCTTAGGA
40790890 TGTTACATTTTAATTATCACTTAATTAG
1 TGTTACATTTTAATTATCACTTAATTAG
40790918 TGTTACATTTTAATTATCACTTAATTAG
1 TGTTACATTTTAATTATCACTTAATTAG
*
40790946 TATTACA
1 TGTTACA
40790953 GTTATATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.49
Consensus pattern (28 bp):
TGTTACATTTTAATTATCACTTAATTAG
Found at i:40791160 original size:3 final size:3
Alignment explanation
Indices: 40791152--40791205 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
40791142 TCTTTTTACC
40791152 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40791200 TTA TTA
1 TTA TTA
40791206 AAAAAAGATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40791775 original size:13 final size:13
Alignment explanation
Indices: 40791757--40791782 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40791747 AAATCAATTT
40791757 TTTTAATTAAATA
1 TTTTAATTAAATA
40791770 TTTTAATTAAATA
1 TTTTAATTAAATA
40791783 AATATAATTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTAATTAAATA
Found at i:40791822 original size:17 final size:19
Alignment explanation
Indices: 40791769--40791815 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
40791759 TTAATTAAAT
*
40791769 ATTTTAATTAAATAAATATA
1 ATTTT-ATTATATAAATATA
* *
40791789 ATTTTTTTATATAAATATG
1 ATTTTATTATATAAATATA
40791808 ATTTTATT
1 ATTTTATT
40791816 TTAAATACGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTTTATTATATAAATATA
Found at i:40792001 original size:20 final size:21
Alignment explanation
Indices: 40791978--40792031 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
40791968 AACTGGAATT
* *
40791978 TTTTTATAATAAATTATATA-
1 TTTTTATAATAAATTAAAAAC
40791998 -TTTTATAATTAAATTAAAAAC
1 TTTTTATAA-TAAATTAAAAAC
40792019 TTTTTAT-ATAAAT
1 TTTTTATAATAAAT
40792032 ACTAATTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 8 0.28
20 14 0.48
21 1 0.03
22 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTATAATAAATTAAAAAC
Found at i:40792610 original size:23 final size:23
Alignment explanation
Indices: 40792561--40792615 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
40792551 ATGATTTTCG
*
40792561 TTATTATTTGATATGTTTAGTTA
1 TTATTATTTGATATGTATAGTTA
40792584 TTATTATTTGATAT-TCGATAGTT-
1 TTATTATTTGATATGT--ATAGTTA
40792607 TTATTATTT
1 TTATTATTT
40792616 TTTATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 1 0.03
23 23 0.79
24 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.11, T:0.62
Consensus pattern (23 bp):
TTATTATTTGATATGTATAGTTA
Found at i:40797269 original size:21 final size:21
Alignment explanation
Indices: 40797237--40797287 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
40797227 AAGCCAAAGC
40797237 AGTAAG-AACTAACTTAAATA
1 AGTAAGAAACTAACTTAAATA
40797257 AGTAAGAAACTAACTTAAATA
1 AGTAAGAAACTAACTTAAATA
40797278 AGCT-AGAAAC
1 AG-TAAGAAAC
40797288 AATAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.21
21 22 0.76
22 1 0.03
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (21 bp):
AGTAAGAAACTAACTTAAATA
Found at i:40801114 original size:23 final size:22
Alignment explanation
Indices: 40801088--40801151 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
40801078 TATGTTCTGT
40801088 ATTAATATTTATATATTTTTATA
1 ATTAA-ATTTATATATTTTTATA
* * *
40801111 ATTAAATTTAAATAAATTATATA
1 ATTAAATTTATAT-ATTTTTATA
* *
40801134 TTTAAATTTATTTATTTT
1 ATTAAATTTATATATTTT
40801152 AAATGTAGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAAATTTATATATTTTTATA
Found at i:40801389 original size:12 final size:11
Alignment explanation
Indices: 40801361--40801394 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
40801351 ATCTTTAATT
40801361 TTTATTAAAAA
1 TTTATTAAAAA
40801372 TTTATTAAAAA
1 TTTATTAAAAA
40801383 TTGTATTTAAAA
1 TT-TA-TTAAAA
40801395 CGCATGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.62
12 2 0.10
13 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TTTATTAAAAA
Found at i:40802142 original size:22 final size:24
Alignment explanation
Indices: 40802117--40802160 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
40802107 TGTGTATTTC
40802117 ATAAAA-TTAAAAAAT-AATAATA
1 ATAAAATTTAAAAAATCAATAATA
*
40802139 ATAAAATTTTAAAAATCAATAA
1 ATAAAATTTAAAAAATCAATAA
40802161 ATTTGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 8 0.42
24 5 0.26
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
ATAAAATTTAAAAAATCAATAATA
Found at i:40802519 original size:59 final size:58
Alignment explanation
Indices: 40802409--40802519 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
40802399 CTTAATATTA
**
40802409 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGGTACTAATTTTTTTTGGGCCC
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGGTACTAATGCTTTTTGGGCCC
* *
40802467 AATTTGGTATCTGAACTTG-CATTTTTCTTCTTAATTTGGTACCTAA-GCTTTTT
1 AATTTGATACCTGAACTTGACA-TTTT-TTCTTAATTTGGTA-CTAATGCTTTTT
40802520 CTTAGATTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 2 0.04
58 21 0.46
59 19 0.41
60 4 0.09
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.50
Consensus pattern (58 bp):
AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGGTACTAATGCTTTTTGGGCCC
Found at i:40803043 original size:60 final size:59
Alignment explanation
Indices: 40802909--40803054 Score: 154
Period size: 59 Copynumber: 2.5 Consensus size: 59
40802899 AAACATTTGA
* ** *
40802909 CAAGTTCAAGTACCAAATTGAACAAAAAAAAAAGTTCAGGTACCAAATTAGGAAAGAGT
1 CAAGTTCAAGTACCAAATTGAACAAAAAAAAAAGATCAAATACCAAATTAGAAAAGAGT
* *** *
40802968 CAAGTTCAGGTACCAAATTGAAC-TCCAAAAAAGATCAAATACCAAATTAAGAAAAAGTGT
1 CAAGTTCAAGTACCAAATTGAACAAAAAAAAAAGATCAAATACCAAATT-AG-AAAAGAGT
*
40803028 CAAGCTT-AAGTACCAAATT-AAGAAAAA
1 CAAG-TTCAAGTACCAAATTGAACAAAAA
40803055 GTGTCAAGTT
Statistics
Matches: 69, Mismatches: 14, Indels: 7
0.77 0.16 0.08
Matches are distributed among these distances:
58 19 0.28
59 26 0.38
60 22 0.32
61 2 0.03
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.19
Consensus pattern (59 bp):
CAAGTTCAAGTACCAAATTGAACAAAAAAAAAAGATCAAATACCAAATTAGAAAAGAGT
Found at i:40803045 original size:31 final size:31
Alignment explanation
Indices: 40803007--40803076 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
40802997 AAAGATCAAA
40803007 TACCAAATTAAGAAAAAGTGTCAAGCTTAAG
1 TACCAAATTAAGAAAAAGTGTCAAGCTTAAG
*
40803038 TACCAAATTAAGAAAAAGTGTCAAGTTTAAG
1 TACCAAATTAAGAAAAAGTGTCAAGCTTAAG
40803069 TACCAAAT
1 TACCAAAT
40803077 ATTATATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (31 bp):
TACCAAATTAAGAAAAAGTGTCAAGCTTAAG
Found at i:40805175 original size:2 final size:2
Alignment explanation
Indices: 40805168--40805192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40805158 GAAAATAGTA
40805168 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
40805193 GCAGAAAATG
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:40808965 original size:5 final size:5
Alignment explanation
Indices: 40808957--40809017 Score: 50
Period size: 5 Copynumber: 12.2 Consensus size: 5
40808947 TAACATATTG
* * * * * * *
40808957 TATCA TATCA TATCA TTTCG TAACA TAGCG TAACA TATCA TAACA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
*
40809007 TAACA TATCA T
1 TATCA TATCA T
40809018 GTCCTATCCC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (5 bp):
TATCA
Found at i:40808970 original size:10 final size:10
Alignment explanation
Indices: 40808945--40809017 Score: 74
Period size: 10 Copynumber: 7.3 Consensus size: 10
40808935 CTTATTAAAA
40808945 CATAACATAT
1 CATAACATAT
** *
40808955 TGTATCATAT
1 CATAACATAT
* *
40808965 CATATCATTT
1 CATAACATAT
* *
40808975 CGTAACATAG
1 CATAACATAT
*
40808985 CGTAACATAT
1 CATAACATAT
40808995 CATAACATAT
1 CATAACATAT
40809005 CATAACATAT
1 CATAACATAT
40809015 CAT
1 CAT
40809018 GTCCTATCCC
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 51 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (10 bp):
CATAACATAT
Found at i:40808981 original size:30 final size:30
Alignment explanation
Indices: 40808945--40809015 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
40808935 CTTATTAAAA
* * * *
40808945 CATAACATATTGTATCATATCATATCATTT
1 CATAACATATCGTAACATATCATAACATAT
* *
40808975 CGTAACATAGCGTAACATATCATAACATAT
1 CATAACATATCGTAACATATCATAACATAT
40809005 CATAACATATC
1 CATAACATATC
40809016 ATGTCCTATC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.34
Consensus pattern (30 bp):
CATAACATATCGTAACATATCATAACATAT
Found at i:40812606 original size:28 final size:28
Alignment explanation
Indices: 40812566--40812622 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
40812556 TTTAATCAAT
*
40812566 TAACACATTTAAACTAATTGCGATTGAC
1 TAACACATTTAAACTAATAGCGATTGAC
40812594 TAACACATTTAAACTAATAGCGATTGAC
1 TAACACATTTAAACTAATAGCGATTGAC
40812622 T
1 T
40812623 TATCAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (28 bp):
TAACACATTTAAACTAATAGCGATTGAC
Found at i:40813174 original size:18 final size:17
Alignment explanation
Indices: 40813148--40813194 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
40813138 GTCGAAAATC
*
40813148 AAATTGATAAAAT-AAA
1 AAATAGATAAAATGAAA
40813164 TAAATAAGATAAAAATGAAA
1 -AAAT-AGAT-AAAATGAAA
40813184 AAATAGATAAA
1 AAATAGATAAA
40813195 TATTAAGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 7 0.27
18 7 0.27
19 9 0.35
20 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
AAATAGATAAAATGAAA
Found at i:40814243 original size:21 final size:21
Alignment explanation
Indices: 40814217--40814266 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
40814207 TGCTTTCTTA
*
40814217 TTTTCTTCTTTTATTACTTCT
1 TTTTCTCCTTTTATTACTTCT
*
40814238 TTTTCTCCTTTTATTATTTCT
1 TTTTCTCCTTTTATTACTTCT
40814259 TTTTCTCC
1 TTTTCTCC
40814267 ATAGAAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCCTTTTATTACTTCT
Found at i:40822057 original size:8 final size:8
Alignment explanation
Indices: 40822046--40822129 Score: 84
Period size: 8 Copynumber: 10.5 Consensus size: 8
40822036 AAGTAATTTT
40822046 AAAATTAAA
1 AAAATT-AA
40822055 AAAATTAA
1 AAAATTAA
40822063 AAAATTAAA
1 AAAATT-AA
40822072 AAAATTAA
1 AAAATTAA
*
40822080 AAAA--AG
1 AAAATTAA
* *
40822086 TAATTTAA
1 AAAATTAA
40822094 AAAATTAAA
1 AAAATT-AA
*
40822103 AAAATT-T
1 AAAATTAA
40822110 AAAATTAA
1 AAAATTAA
40822118 AAAATTAA
1 AAAATTAA
40822126 AAAA
1 AAAA
40822130 AGTAATTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
6 3 0.05
7 6 0.10
8 31 0.50
9 22 0.35
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (8 bp):
AAAATTAA
Found at i:40822060 original size:9 final size:9
Alignment explanation
Indices: 40822046--40822130 Score: 88
Period size: 9 Copynumber: 9.4 Consensus size: 9
40822036 AAGTAATTTT
40822046 AAAATTAAA
1 AAAATTAAA
40822055 AAAATT-AA
1 AAAATTAAA
40822063 AAAATTAAA
1 AAAATTAAA
40822072 AAAATTAAAAA
1 AAAATT--AAA
*
40822083 AAGTAATTTAA
1 AA--AATTAAA
40822094 AAAATTAAA
1 AAAATTAAA
*
40822103 AAAATT--T
1 AAAATTAAA
40822110 AAAATT-AA
1 AAAATTAAA
40822118 AAAATTAAA
1 AAAATTAAA
40822127 AAAA
1 AAAA
40822131 GTAATTTAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
7 6 0.09
8 14 0.22
9 32 0.49
11 9 0.14
13 4 0.06
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (9 bp):
AAAATTAAA
Found at i:40822081 original size:47 final size:46
Alignment explanation
Indices: 40822012--40822140 Score: 194
Period size: 47 Copynumber: 2.8 Consensus size: 46
40822002 AATTTATTTT
*
40822012 AAAAATT-AAAA-T-AAAAATTAAAAAAAGTAATTT-TAAAATTAA
1 AAAAATTAAAAATTAAAAAATTAAAAAAAGTAATTTAAAAAATTAA
40822054 AAAAATTAAAAAATTAAAAAAATTAAAAAAAGTAATTTAAAAAATTAA
1 AAAAATT-AAAAATT-AAAAAATTAAAAAAAGTAATTTAAAAAATTAA
*
40822102 AAAAATTTAAAATTAAAAAATTAAAAAAAGTAATTTAAA
1 AAAAATTAAAAATTAAAAAATTAAAAAAAGTAATTTAAA
40822141 GTATTTAAAG
Statistics
Matches: 79, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
42 7 0.09
44 4 0.05
45 1 0.01
46 25 0.32
47 27 0.34
48 15 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (46 bp):
AAAAATTAAAAATTAAAAAATTAAAAAAAGTAATTTAAAAAATTAA
Found at i:40822146 original size:9 final size:9
Alignment explanation
Indices: 40822128--40822158 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
40822118 AAAATTAAAA
40822128 AAAGTAATTT
1 AAAGT-ATTT
40822138 AAAGTATTT
1 AAAGTATTT
40822147 AAAGTATTT
1 AAAGTATTT
40822156 AAA
1 AAA
40822159 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (9 bp):
AAAGTATTT
Found at i:40822156 original size:46 final size:44
Alignment explanation
Indices: 40822012--40822171 Score: 186
Period size: 46 Copynumber: 3.6 Consensus size: 44
40822002 AATTTATTTT
40822012 AAAAA-TTAAAA-T-AAAAATTAAAAAAAGTAATTTTAAAATTAA
1 AAAAATTTAAAATTAAAAAATTAAAAAAAGTAA-TTTAAAATTAA
*
40822054 AAAAATTAAAAAATTAAAAAAATTAAAAAAAGTAATTTAAAAAATTAA
1 AAAAATT-TAAAATT-AAAAAATTAAAAAAAGTAATTT--AAAATTAA
*
40822102 AAAAATTTAAAATTAAAAAATTAAAAAAAGTAATTTAAAGTATTTA
1 AAAAATTTAAAATTAAAAAATTAAAAAAAGTAATTTAAA--ATTAA
**
40822148 AAGTATTT-AAATTAAAAAA-TAAAA
1 AAAAATTTAAAATTAAAAAATTAAAA
40822172 TATTATTATT
Statistics
Matches: 104, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
42 5 0.05
43 1 0.01
44 12 0.12
45 12 0.12
46 35 0.34
47 24 0.23
48 15 0.14
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (44 bp):
AAAAATTTAAAATTAAAAAATTAAAAAAAGTAATTTAAAATTAA
Found at i:40824185 original size:20 final size:20
Alignment explanation
Indices: 40824153--40824190 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40824143 CTGTTGTTTG
*
40824153 TAAATTTTCATAT-TTTCCC
1 TAAAATTTCATATGTTTCCC
40824172 TAAAATTTCTATATGTTTC
1 TAAAATTTC-ATATGTTTC
40824191 TGATTTCGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 4 0.25
21 4 0.25
ACGTcount: A:0.29, C:0.16, G:0.03, T:0.53
Consensus pattern (20 bp):
TAAAATTTCATATGTTTCCC
Found at i:40828424 original size:27 final size:27
Alignment explanation
Indices: 40828340--40828432 Score: 116
Period size: 27 Copynumber: 3.5 Consensus size: 27
40828330 TGGCTAAATT
*
40828340 TGAAAGAATAGTACATATGAAAAACTC
1 TGAAAGAATAGTACATATGGAAAACTC
* * *
40828367 TAAAAGAATAGTACGTATGGAAAACAC
1 TGAAAGAATAGTACATATGGAAAACTC
** *
40828394 TGAAAGAATAGTACATATGGCGAACTT
1 TGAAAGAATAGTACATATGGAAAACTC
40828421 TG-AAGAATAGTA
1 TGAAAGAATAGTA
40828433 TGTATAATGA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
26 10 0.18
27 46 0.82
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (27 bp):
TGAAAGAATAGTACATATGGAAAACTC
Found at i:40831535 original size:27 final size:27
Alignment explanation
Indices: 40831504--40831584 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
40831494 ATACACTGGA
* *
40831504 AAAATGAAAGCCTTTGTGGCAGTCTAT
1 AAAATGGAAGCCTTTGTGGCAATCTAT
* **
40831531 AAAATGGAAGACTACGTGGCAATCTAT
1 AAAATGGAAGCCTTTGTGGCAATCTAT
* * *
40831558 GAAATGGAAGCCTTTGTAGCGATCTAT
1 AAAATGGAAGCCTTTGTGGCAATCTAT
40831585 GGAAAGAAAC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (27 bp):
AAAATGGAAGCCTTTGTGGCAATCTAT
Found at i:40831745 original size:27 final size:27
Alignment explanation
Indices: 40831715--40831840 Score: 117
Period size: 27 Copynumber: 4.7 Consensus size: 27
40831705 ATGATATGTG
* *
40831715 TGGATAACTTTGAAGGAATAGTACGTA
1 TGGAGAACTTTGAAAGAATAGTACGTA
* * *
40831742 TGGAAAATTTTGAAAGAATAGTGCGTA
1 TGGAGAACTTTGAAAGAATAGTACGTA
* * *
40831769 TGGAGAACATTGAAAAAATAGTACATA
1 TGGAGAACTTTGAAAGAATAGTACGTA
* * * *
40831796 TGGCGAACTCTGAAGGAATGGTACGTA
1 TGGAGAACTTTGAAAGAATAGTACGTA
* * *
40831823 TGGTGAACATTGAGAGAA
1 TGGAGAACTTTGAAAGAA
40831841 ACAATTTGGT
Statistics
Matches: 77, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.40, C:0.08, G:0.27, T:0.25
Consensus pattern (27 bp):
TGGAGAACTTTGAAAGAATAGTACGTA
Found at i:40831789 original size:54 final size:54
Alignment explanation
Indices: 40831731--40831835 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 54
40831721 ACTTTGAAGG
* * * *
40831731 AATAGTACGTATGGAAAATTTTGAAAGAATAGTGCGTATGGAGAACATTGAAAA
1 AATAGTACATATGGAAAACTCTGAAAGAATAGTACGTATGGAGAACATTGAAAA
** * * *
40831785 AATAGTACATATGGCGAACTCTGAAGGAATGGTACGTATGGTGAACATTGA
1 AATAGTACATATGGAAAACTCTGAAAGAATAGTACGTATGGAGAACATTGA
40831836 GAGAAACAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (54 bp):
AATAGTACATATGGAAAACTCTGAAAGAATAGTACGTATGGAGAACATTGAAAA
Found at i:40836987 original size:7 final size:7
Alignment explanation
Indices: 40836976--40837009 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
40836966 AAAAAAACAA
40836976 AAAAAATG
1 AAAAAA-G
*
40836984 AAAAATG
1 AAAAAAG
40836991 AAAAAAG
1 AAAAAAG
40836998 AAAAAAG
1 AAAAAAG
40837005 AAAAA
1 AAAAA
40837010 GGAGAGGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:40837447 original size:98 final size:99
Alignment explanation
Indices: 40837338--40837630 Score: 330
Period size: 98 Copynumber: 2.9 Consensus size: 99
40837328 TCTCATTTCA
*
40837338 TATCTTAGCAAAATTTTCTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTT
1 TATCTTAGCAAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCTTTGTTCTCAATAAAATTT
*
40837403 TCATCTTATCCATTGTGATAATCTTTTTCA-TCT
66 TCATCTTATCCATTGTGATAATCTTTTTCAGTCG
* * *
40837436 TATTTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCCTTGTTCTCAATAAAATCT
1 TATCTTAGCAAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCTTTGTTCTCAATAAAAT-T
* * *
40837501 TATCCATTGTGATAATCC-TT-TG--CATCTTATTCAGTTCG
65 T-T-CA-TCT--T-ATCCATTGTGATAATCTTTTTCAG-TCG
* * * *
40837539 TATCTTAGCAAAAGTTGTC-ATCTTGATTAATTTATTCATTGCGAGCTTCGTTCTCTATAAAA-T
1 TATCTTAGCAAAA-TTTTCTATCTTGATTAATTTATTCATTTCGAGCTTTGTTCTCAATAAAATT
* *
40837602 TTCATCTTGTCCATTGTAATAATCTTTTT
65 TTCATCTTATCCATTGTGATAATCTTTTT
40837631 AAAGCAATTT
Statistics
Matches: 161, Mismatches: 20, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
95 3 0.02
96 3 0.02
97 1 0.01
98 61 0.38
99 11 0.07
100 2 0.01
101 13 0.08
102 2 0.01
103 55 0.34
104 6 0.04
105 4 0.02
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (99 bp):
TATCTTAGCAAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCTTTGTTCTCAATAAAATTT
TCATCTTATCCATTGTGATAATCTTTTTCAGTCG
Found at i:40837498 original size:49 final size:49
Alignment explanation
Indices: 40837347--40837498 Score: 125
Period size: 49 Copynumber: 3.1 Consensus size: 49
40837337 ATATCTTAGC
* *
40837347 AAAATTTTCTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAAT
1 AAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCCTTGTTCTCAAT
** * * * * **
40837396 AAAATTTTC-ATCTT-ATCCATTGTGATAATCTTTTTC-A-TCTTATT-TTAGC
1 AAAATTTTCTATCTTGATTAATT-T-AT--TC-ATTTCGAGCCTTGTTCTCAAT
*
40837445 AAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCCTTGTTCTCAAT
1 AAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCCTTGTTCTCAAT
40837494 AAAAT
1 AAAAT
40837499 CTTATCCATT
Statistics
Matches: 74, Mismatches: 19, Indels: 20
0.65 0.17 0.18
Matches are distributed among these distances:
46 4 0.05
47 8 0.11
48 11 0.15
49 30 0.41
50 10 0.14
51 8 0.11
52 3 0.04
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.49
Consensus pattern (49 bp):
AAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCCTTGTTCTCAAT
Found at i:40838577 original size:46 final size:46
Alignment explanation
Indices: 40838525--40838663 Score: 215
Period size: 46 Copynumber: 3.0 Consensus size: 46
40838515 AATAGACTAA
*
40838525 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGAGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
40838571 AAGATAGTAGATCTTGTCTTCCTGTATTTGGCAACAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
40838617 AAGATAGCAGATCTTATCTTCATGTATTTGGCAGCAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
40838663 A
1 A
40838664 CAGCGGAGTA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (46 bp):
AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
Found at i:40838672 original size:16 final size:16
Alignment explanation
Indices: 40838648--40838679 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40838638 ATGTATTTGG
40838648 CAGCAGAGTAGATCGA
1 CAGCAGAGTAGATCGA
*
40838664 CAGCGGAGTAGATCGA
1 CAGCAGAGTAGATCGA
40838680 AGATAGCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.34, T:0.12
Consensus pattern (16 bp):
CAGCAGAGTAGATCGA
Found at i:40838720 original size:62 final size:62
Alignment explanation
Indices: 40838607--40838723 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
40838597 TTTGGCAACA
*
40838607 GAGTAGATCGAAGATAGCAGATCTTATCTTCATGTATTTGGCAGCAGAGTAGATCGACAGCG
1 GAGTAGATCGAAGATAGCAGATCTTATCTTCATGTATTTGGCAGAAGAGTAGATCGACAGCG
* *
40838669 GAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCA-AAGAAGTAGATC
1 GAGTAGATCGAAGATAGCAGATCTTATCTTCATGTATTTGGCAGAAG-AGTAGATC
40838724 AAAGATAGCA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
61 2 0.04
62 49 0.96
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (62 bp):
GAGTAGATCGAAGATAGCAGATCTTATCTTCATGTATTTGGCAGAAGAGTAGATCGACAGCG
Found at i:40838723 original size:46 final size:46
Alignment explanation
Indices: 40838664--40840070 Score: 2112
Period size: 46 Copynumber: 30.6 Consensus size: 46
40838654 AGTAGATCGA
40838664 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
** * * *
40838710 CAAAGAAGTAGATCAAAGATAGCAGATCTTGTCTTCTTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* *
40838756 CAGAGGAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * * * *
40838802 TAGCGAAGTAGATCAAAGATAGCAGATCTTATCTTCCTATATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
*
40838848 CAGCGGAGTAGATCCAAGATAGCAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
*
40838894 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * * *
40838940 CAGCAGAATAGATTGAAAATAGCAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * * *
40838986 CAGCAGAGAAGATCGAAGATAGCAGATCTTGTTTTCATGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* *
40839032 CAGCGGAGTAGATCGAAAATAGTAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* *
40839078 TAGCGGAGTAGATCAAAGATAGCAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
*
40839124 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTAG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* *
40839170 CAGAGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGA
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * *
40839216 CAGCGGAGTAGATTGAAGATAGCAGATATTATCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
*
40839262 CAGAGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* *
40839308 CAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * * *
40839354 CAGCAGAGAAGATCGAAGATAGCAGATCTTGTTTTCATGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* *
40839400 CAGCGGAGTAGATCGAAAATAGTAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* *
40839446 TAGCGGAGTAGATCAAAGATAGCAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
*
40839492 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTAG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* *
40839538 CAGAGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGA
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * *
40839584 CAGCGGAGTAGATTGAAGATAGCAGATATTATCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
*
40839630 CAGAGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * *
40839676 CAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGCATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
** * *
40839722 CAAAGGAGTAGATCGAAGATAGCAGATATTGTCTTCCTGTATTTAG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* *
40839768 CAGAGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGA
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * *
40839814 CAGCGGAGTAGATTGAAGATAGCAGATATTATCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
*
40839860 CAGAGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * *
40839906 CAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGCATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
** *
40839952 CAAAGGAGTAGATCGAAGATAGCAGATATTGTCTTCCTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * * **
40839998 CAGTGGAGTAGATCGAAGACAGTAGATCTTGTCTTTTTGTATTTGG
1 CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
* * * *
40840044 CAGCGAAGTCGATTGAAGATTGCAGAT
1 CAGCGGAGTAGATCGAAGATAGCAGAT
40840071 TCTATCACCC
Statistics
Matches: 1220, Mismatches: 141, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 1220 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (46 bp):
CAGCGGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
Found at i:40838751 original size:108 final size:108
Alignment explanation
Indices: 40838560--40838771 Score: 356
Period size: 108 Copynumber: 2.0 Consensus size: 108
40838550 ATTTGGCAGA
* *
40838560 GGAGTAGATCGAAGATAGTAGATCTTGTCTTCCTGTATTTGGCAACAGAGTAGATCGAAGATAGC
1 GGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAACAGAGTAGATCAAAGATAGC
40838625 AGATCTTATCTTCATGTATTTGGCAGCA-GAGTAGATCGACAGC
66 AGATCTTATCTTCATGTATTTGGCAG-AGGAGTAGATCGACAGC
40838668 GGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAA-AGAAGTAGATCAAAGATAG
1 GGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAACAG-AGTAGATCAAAGATAG
* *
40838732 CAGATCTTGTCTTCTTGTATTTGGCAGAGGAGTAGATCGA
65 CAGATCTTATCTTCATGTATTTGGCAGAGGAGTAGATCGA
40838772 AGATAGCAGA
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
107 3 0.03
108 95 0.97
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (108 bp):
GGAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAACAGAGTAGATCAAAGATAGC
AGATCTTATCTTCATGTATTTGGCAGAGGAGTAGATCGACAGC
Found at i:40842273 original size:2 final size:2
Alignment explanation
Indices: 40842266--40842295 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
40842256 TAAATTTATC
*
40842266 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40842296 TTATCTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40844065 original size:51 final size:51
Alignment explanation
Indices: 40843986--40844179 Score: 246
Period size: 51 Copynumber: 3.8 Consensus size: 51
40843976 AGTTACTAGA
40843986 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
* * * * * *** *
40844037 TAATGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT-GG
*
40844088 TCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
* * * *
40844139 TCACATGTGTAGTACTATGTGTAGGCTACTATGTGAATCGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG
40844180 GTACCATTTA
Statistics
Matches: 117, Mismatches: 24, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
50 2 0.02
51 113 0.97
52 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
Found at i:40844165 original size:102 final size:102
Alignment explanation
Indices: 40843984--40844171 Score: 331
Period size: 102 Copynumber: 1.8 Consensus size: 102
40843974 GAAGTTACTA
* **
40843984 GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTAATGTGTGTAG
1 GATCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTAACATGTGTAG
40844049 TACTATGTGCAGGCTACTATGCGTACCGGATAGCTTC
66 TACTATGTGCAGGCTACTATGCGTACCGGATAGCTTC
*
40844086 GATCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACATGTGTAG
1 GATCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTAACATGTGTAG
*
40844151 TACTATGTGTAGGCTACTATG
66 TACTATGTGCAGGCTACTATG
40844172 TGAATCGGGT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 81 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (102 bp):
GATCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTAACATGTGTAG
TACTATGTGCAGGCTACTATGCGTACCGGATAGCTTC
Found at i:40847235 original size:19 final size:18
Alignment explanation
Indices: 40847213--40847252 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40847203 CGTAACCCTT
*
40847213 AAAACCATAAGCTCTAATA
1 AAAACCATAA-CCCTAATA
*
40847232 AAAATCATAACCCTAATA
1 AAAACCATAACCCTAATA
40847250 AAA
1 AAA
40847253 TAAAACCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (18 bp):
AAAACCATAACCCTAATA
Found at i:40847991 original size:25 final size:25
Alignment explanation
Indices: 40847958--40848020 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
40847948 CCCCAACGTT
*
40847958 TGCTGCATCGCCGTCGACAGTCCTC
1 TGCTGCATCGCCGTCAACAGTCCTC
40847983 TGCTGCATCGCCGTCAACAGTCCTC
1 TGCTGCATCGCCGTCAACAGTCCTC
* *
40848008 CGCTG-ATCACCGT
1 TGCTGCATCGCCGT
40848021 GTAAGTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 7 0.20
25 28 0.80
ACGTcount: A:0.14, C:0.40, G:0.22, T:0.24
Consensus pattern (25 bp):
TGCTGCATCGCCGTCAACAGTCCTC
Found at i:40851649 original size:36 final size:36
Alignment explanation
Indices: 40851584--40851653 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
40851574 TTAATTAATT
*
40851584 TTTATATTTTTAATAACTTTTAAATTTTAAAAATATA
1 TTTATATTTTT-ATAACTTTTAAAATTTAAAAATATA
*
40851621 TTTATATTTTT-TGAATTTTTAAAATTTAAAAAT
1 TTTATATTTTTAT-AACTTTTAAAATTTAAAAAT
40851654 TAATTAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 1 0.03
36 18 0.60
37 11 0.37
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (36 bp):
TTTATATTTTTATAACTTTTAAAATTTAAAAATATA
Found at i:40851790 original size:22 final size:21
Alignment explanation
Indices: 40851753--40851812 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
40851743 AAGGTAATTT
40851753 AATAAATAAAAT-AAATT-TAA
1 AATAAA-AAAATAAAATTATAA
40851773 AAGCTAAAAAAATAAAATTAATAA
1 AA--TAAAAAAATAAAATT-ATAA
*
40851797 AATAAAAAACTAAAAT
1 AATAAAAAAATAAAAT
40851813 ATTTTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 2 0.06
21 5 0.15
22 22 0.65
24 5 0.15
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (21 bp):
AATAAAAAAATAAAATTATAA
Found at i:40852703 original size:114 final size:113
Alignment explanation
Indices: 40852547--40852901 Score: 478
Period size: 114 Copynumber: 3.1 Consensus size: 113
40852537 GTTTTTATTA
* * * * * *
40852547 TAAAA-GCCGTAAAATGAAGCAATAGCGGTGTTTGGACAAAAAATGCCGCAAATATGTATTAAAA
1 TAAAACGCCGCAAAAGGAAGCAATAGCGGCGTTTGGACCAAAAACGCCGCGAATATGTATTAAAA
40852611 TTTTGCAAAACGGCACCATTTTTAGCAGCTCTTTTAGTGGCGTTTGGGC
66 TTTTGCAAAACGGCACCATTTTTAGCAGCT-TTTTAGTGGCGTTTGGGC
*
40852660 TAAAACGCCGCAAAAGGAAGCAATAGCGGCGTTTAGACCAAAAACGCCGCGAATATGTATTAAAA
1 TAAAACGCCGCAAAAGGAAGCAATAGCGGCGTTTGGACCAAAAACGCCGCGAATATGTATTAAAA
**** * * *
40852725 TTTTGCAAAACAATGCCATTTTTAGCAGCTTTTTTAGTAGCATTTAGGC
66 TTTTGCAAAACGGCACCATTTTTAGCAGC-TTTTTAGTGGCGTTTGGGC
* * *
40852774 TAAAACACCGCAAAAGGAAGCAATTGCGGCGTTTGGACCAAAAACGCCGTGAATATGTATTAAAA
1 TAAAACGCCGCAAAAGGAAGCAATAGCGGCGTTTGGACCAAAAACGCCGCGAATATGTATTAAAA
** *
40852839 TTTTGCAAAACGGCACTGTTTTTAGTAGCATTTTTAGTGGCGTTTGGGC
66 TTTTGCAAAACGGCACCATTTTTAGCAGC-TTTTTAGTGGCGTTTGGGC
* *
40852888 TAAAATGCTGCAAA
1 TAAAACGCCGCAAA
40852902 GGTTATACAT
Statistics
Matches: 208, Mismatches: 32, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
113 5 0.02
114 202 0.97
115 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (113 bp):
TAAAACGCCGCAAAAGGAAGCAATAGCGGCGTTTGGACCAAAAACGCCGCGAATATGTATTAAAA
TTTTGCAAAACGGCACCATTTTTAGCAGCTTTTTAGTGGCGTTTGGGC
Found at i:40859113 original size:21 final size:21
Alignment explanation
Indices: 40859088--40859131 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40859078 ATCTTCGAGG
40859088 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
40859109 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
40859130 AT
1 AT
40859132 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:40859137 original size:19 final size:19
Alignment explanation
Indices: 40859087--40859142 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
40859077 AATCTTCGAG
40859087 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40859106 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
40859127 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
40859143 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40859149 original size:22 final size:23
Alignment explanation
Indices: 40859121--40859165 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40859111 ATGCAATCTT
*
40859121 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATATTAGA
*
40859143 AGATATGATTTTGTAATATTAGA
1 AGATATGATTATGTAATATTAGA
40859166 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATATTAGA
Found at i:40859175 original size:22 final size:23
Alignment explanation
Indices: 40859131--40859175 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40859121 AGATATGATA
* *
40859131 TGTAATCTTAGAAGATATGATTT
1 TGTAATATTAGAAGATATAATTT
*
40859154 TGTAATATTAG-AGATTTAATTT
1 TGTAATATTAGAAGATATAATTT
40859176 GTAGATACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATATTAGAAGATATAATTT
Found at i:40859362 original size:19 final size:21
Alignment explanation
Indices: 40859338--40859376 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40859328 GCTTACTGTT
*
40859338 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
40859357 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
40859377 TTAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:40859606 original size:15 final size:15
Alignment explanation
Indices: 40859582--40859637 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
40859572 GTTTTTAGTC
40859582 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
40859596 TGTTATTATTATTTT
1 TATTATTATTAATTT
*
40859611 TATTATTCTATTATATAT
1 TATTA-T-TATTA-ATTT
40859629 TATTATTAT
1 TATTATTAT
40859638 ACCTACATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.09
15 13 0.39
16 4 0.12
17 6 0.18
18 7 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:40859613 original size:24 final size:24
Alignment explanation
Indices: 40859584--40859637 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
40859574 TTTTAGTCTA
* *
40859584 TTTTATTAATTTTGTTAT-TATTAT
1 TTTTATT-ATTCTATTATATATTAT
40859608 TTTTATTATTCTATTATATATTAT
1 TTTTATTATTCTATTATATATTAT
*
40859632 TATTAT
1 TTTTAT
40859638 ACCTACATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTATTATTCTATTATATATTAT
Found at i:40866062 original size:16 final size:16
Alignment explanation
Indices: 40866040--40866072 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
40866030 AATCATTCTC
40866040 AAAAAAATAAAATAAAT
1 AAAAAAAT-AAATAAAT
40866057 AAAAAAATAAATAAAT
1 AAAAAAATAAATAAAT
40866073 TATGCATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAAAATAAATAAAT
Found at i:40866520 original size:44 final size:44
Alignment explanation
Indices: 40866296--40866615 Score: 112
Period size: 44 Copynumber: 7.3 Consensus size: 44
40866286 AATAACAGAT
* * *
40866296 CTTGCCTTCCTGCACCGACAGCGAAACAGATCAAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
**** * * * * * * * *
40866340 CTTGCCTCCCTG-GGTTACAGTGTAGCAG-GCTAAAAATAGCAGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATC-GAAGACACCAG-C
* * * *
40866384 CTTGCCTTCCTGCACCGACAACAAAGCAGATCGAAGTCACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
**** * * * * * * * *
40866428 CTTGCCTCCCTGGGTTG-CAGTGGAGCATGCT-AAAAATAGCAGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCA-GATCGAAGACACCAG-C
* *
40866472 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACATCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
**** * * * * * * * *
40866516 CTTGCCTCCCTGGGTTG-TAGTGAAGTAG-GCTGAAAATAGCAGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATC-GAAGACACCAG-C
** *
40866560 CTTGCCTTTCTGCACCGACAGCGAAGCAGATCAAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
40866604 CTTGCCTCCCTG
1 CTTGCCTCCCTG
40866616 GGTTGCAGCG
Statistics
Matches: 176, Mismatches: 88, Indels: 24
0.61 0.31 0.08
Matches are distributed among these distances:
42 2 0.01
43 45 0.26
44 83 0.47
45 44 0.25
46 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (44 bp):
CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:40866677 original size:264 final size:264
Alignment explanation
Indices: 40866203--40866678 Score: 765
Period size: 264 Copynumber: 1.8 Consensus size: 264
40866193 GTGAAGATAA
* * * *
40866203 CAGATCTTGCCTTCCTATACTGGCAGCGAAGCAGATCGAAGTCAGCAACCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACAGCAACCTTGCCTCCCTGGGTT
40866268 GCAGCAGAGTAGGCTAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCAAAGA
66 GCAGCAGAGTAGGCTAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCAAAGA
* *
40866333 CACCAGCCTTGCCTCCCTGGGTTACAGTGTAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCA
131 CACCAGCCTTGCCTCCCTGGGTTACAGCGTAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTACA
40866398 CCGACAACAAAGCAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTTGCAGTGGAGCATGCTAAAA
196 CCGACAACAAAGCAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTTGCAGTGGAGCATGCTAAAA
40866463 ATAG
261 ATAG
* * *
40866467 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACATCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACAGCAACCTTGCCTCCCTGGGTT
* * * * * *
40866532 GTAG-TGAAGTAGGCTGAAAATAGCAGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCAAAG
66 GCAGCAG-AGTAGGCTAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCAAAG
* *
40866596 ACACCAGCCTTGCCTCCCTGGGTTGCAGCGTAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTAC
130 ACACCAGCCTTGCCTCCCTGGGTTACAGCGTAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTAC
* *
40866661 ACCGACAGCGAAGCAGAT
195 ACCGACAACAAAGCAGAT
40866679 TGATGACCCT
Statistics
Matches: 192, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
263 1 0.01
264 191 0.99
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (264 bp):
CAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACAGCAACCTTGCCTCCCTGGGTT
GCAGCAGAGTAGGCTAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCAAAGA
CACCAGCCTTGCCTCCCTGGGTTACAGCGTAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTACA
CCGACAACAAAGCAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTTGCAGTGGAGCATGCTAAAA
ATAG
Found at i:40866704 original size:88 final size:88
Alignment explanation
Indices: 40866203--40866678 Score: 684
Period size: 88 Copynumber: 5.4 Consensus size: 88
40866193 GTGAAGATAA
** * * * * *
40866203 CAGATCTTGCCTTCCTATACTGGCAGCGAAGCAGATCGAAGTCAGCAACCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * *
40866268 GCAGCAG-AGTAGGCTAAAAATAA
66 GCAG-TGTAGCAGGCTAAAAATAG
* *
40866291 CAGATCTTGCCTTCCTGCACCGACAGCGAAACAGATCAAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
40866356 ACAGTGTAGCAGGCTAAAAATAG
66 GCAGTGTAGCAGGCTAAAAATAG
* * *
40866379 CAGATCTTGCCTTCCTGCACCGACAACAAAGCAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
40866444 GCAGTGGAGCATGCTAAAAATAG
66 GCAGTGTAGCAGGCTAAAAATAG
*
40866467 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACATCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * * *
40866532 GTAGTGAAGTAGGCTGAAAATAG
66 GCAGTGTAGCAGGCTAAAAATAG
* *
40866555 CAGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
40866620 GCAGCGTAGCAGGTTAAAAATAG
66 GCAGTGTAGCAGGCTAAAAATAG
*
40866643 CAGATCTTGCCTTCCTACACCGACAGCGAAGCAGAT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGAT
40866679 TGATGACCCT
Statistics
Matches: 346, Mismatches: 41, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
87 1 0.00
88 345 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGTGTAGCAGGCTAAAAATAG
Found at i:40866741 original size:44 final size:44
Alignment explanation
Indices: 40866692--40867067 Score: 446
Period size: 44 Copynumber: 8.7 Consensus size: 44
40866682 TGACCCTAGC
*
40866692 CCTATCTTCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * *
40866736 CCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATTTTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
40866780 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * *
40866824 TCTATCTCCCTGGGCAGCAGTGGAATAGATT-AA-A----GAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
40866862 CCTATCTCCTTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
40866906 CCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAA-ATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTT-AAAGATTGTGAAT
* * * * * *
40866950 TCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGA-AT
* * * *
40866994 CTTATCTCCCTGGTCAGCAGTGTAATAGGTTAAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
40867038 CCTATCTCCCTGAG-CAGCAGTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
40867068 GGAAAATAGC
Statistics
Matches: 282, Mismatches: 39, Indels: 22
0.82 0.11 0.06
Matches are distributed among these distances:
38 31 0.11
39 2 0.01
40 1 0.00
42 1 0.00
43 5 0.02
44 237 0.84
45 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:40866899 original size:126 final size:129
Alignment explanation
Indices: 40866693--40867074 Score: 511
Period size: 126 Copynumber: 2.9 Consensus size: 129
40866683 GACCCTAGCC
* * * * *
40866693 CTATCTTCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGTAGTG
1 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA---TGAATCCTATCTCCCTGGACAGCAGTG
* *
40866758 GAATAGGTTAAAGATTTTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAA
63 GAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGAGAA
40866823 TT
128 TT
*
40866825 CTATCTCCCTGGGCAGCAGTGGAATAGATT-AA-A-GAATCCTATCTCCTTGGACAGCAGTGGAA
1 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATGAATCCTATCTCCCTGGACAGCAGTGGAA
*
40866887 TAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAAATTGAGAATT
66 TAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGAGAATT
* * * *
40866951 CTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTGTAGGTCTTATCTCCCTGGTCAGCAGTG
1 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA-TG-A-ATCCTATCTCCCTGGACAGCAGTG
* * * * *
40867016 TAATAGGTTAAAGATCGTGAACCCTATCTCCCTGAG-CAGCAGTGGAGTAGGTGGAAAAT
63 GAATAGGTTAAAGATTGTGAATCCTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAAAAT
40867075 AGCAGATCTT
Statistics
Matches: 224, Mismatches: 19, Indels: 14
0.87 0.07 0.05
Matches are distributed among these distances:
126 117 0.52
127 2 0.01
128 1 0.00
130 2 0.01
131 3 0.01
132 98 0.44
133 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (129 bp):
CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATGAATCCTATCTCCCTGGACAGCAGTGGAA
TAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGAGAATT
Found at i:40866974 original size:170 final size:170
Alignment explanation
Indices: 40866692--40867029 Score: 504
Period size: 170 Copynumber: 2.0 Consensus size: 170
40866682 TGACCCTAGC
*
40866692 CCTATCTTCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGTAGT
1 CCTATCTTCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGTAGT
** * *
40866757 GGAATAGGTTAAAGATTTTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTG-AG
66 GGAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAG
*
40866821 AAT-TCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAAT
131 -GTCT-TATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAAT
*
40866862 CCTATC-TCCTTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGTAG
1 CCTATCTTCC-TGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGTAG
* *
40866926 TGGAATAGGTTGAAA-ATTGAGAATTCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTGT
65 TGGAATAGGTT-AAAGATTGAGAATCCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGT
* * *
40866990 AGGTCTTATCTCCCTGGTCAGCAGTGTAATAGGTTAAAGA
129 AGGTCTTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGA
40867030 TCGTGAACCC
Statistics
Matches: 152, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
169 3 0.02
170 143 0.94
171 6 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (170 bp):
CCTATCTTCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGTAGT
GGAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAG
GTCTTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAAT
Found at i:40867933 original size:19 final size:19
Alignment explanation
Indices: 40867909--40867983 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
40867899 AATCTTCGAG
40867909 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40867928 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40867947 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
40867968 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
40867984 AGAAATGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 34 0.64
21 19 0.36
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40867955 original size:21 final size:21
Alignment explanation
Indices: 40867910--40867972 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
40867900 ATCTTCGAGG
40867910 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
40867929 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
40867950 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
40867971 AT
1 AT
40867973 GTAATCTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.45
21 23 0.55
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:40868204 original size:19 final size:21
Alignment explanation
Indices: 40868180--40868218 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40868170 ACTGTTTTCT
*
40868180 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
40868199 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
40868219 TTAAAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:40868448 original size:3 final size:3
Alignment explanation
Indices: 40868440--40868479 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
40868430 ATTAATTTTG
*
40868440 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
40868480 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40868448 original size:15 final size:15
Alignment explanation
Indices: 40868424--40868478 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
40868414 GTTTTTAGTC
40868424 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
40868438 TGTTATTATTATTTT
1 TATTATTATTAATTT
40868453 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
40868467 ATATTATTATTA
1 -TATTATTATTA
40868479 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:40868455 original size:12 final size:12
Alignment explanation
Indices: 40868426--40868477 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
40868416 TTTTAGTCTA
40868426 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
40868438 TGTTATTATTAT
1 TTTTATTATTAT
40868450 TTTTATTATTAT
1 TTTTATTATTAT
40868462 ATTATATATTATTAT
1 -TT-T-TATTATTAT
40868477 T
1 T
40868478 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:40877099 original size:15 final size:15
Alignment explanation
Indices: 40877076--40877106 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40877066 GCAGAAAAAA
*
40877076 TATTGTTGTTATTAT
1 TATTATTGTTATTAT
40877091 TATTATTGTTATTAT
1 TATTATTGTTATTAT
40877106 T
1 T
40877107 TTTTTTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (15 bp):
TATTATTGTTATTAT
Found at i:40877356 original size:22 final size:22
Alignment explanation
Indices: 40877328--40877396 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
40877318 TATTTAGTGT
40877328 ATGGCTAACGTACTAAGCTCTC
1 ATGGCTAACGTACTAAGCTCTC
40877350 ATGGCTAACGTACTAAGCTCTC
1 ATGGCTAACGTACTAAGCTCTC
** *
40877372 ATGTTTCACGTACTAAGCTCTC
1 ATGGCTAACGTACTAAGCTCTC
40877394 ATG
1 ATG
40877397 TTTGAACAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
ATGGCTAACGTACTAAGCTCTC
Found at i:40877729 original size:15 final size:15
Alignment explanation
Indices: 40877709--40877737 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40877699 TTATTTAATT
40877709 ATTAAATTTTTTGAA
1 ATTAAATTTTTTGAA
40877724 ATTAAATTTTTTGA
1 ATTAAATTTTTTGA
40877738 TATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
ATTAAATTTTTTGAA
Found at i:40879312 original size:30 final size:28
Alignment explanation
Indices: 40879276--40879347 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 28
40879266 AATATAAATT
* *
40879276 TAATCTAAAATATTAATATTTTCTTTTATC
1 TAATCTAAAATATTAATAATAT-TTTTA-C
* *
40879306 TAATCTAAAATTTTTGATAATATTTTTAC
1 TAATCTAAAA-TATTAATAATATTTTTAC
40879335 TAATCTAAAATAT
1 TAATCTAAAATAT
40879348 ATTTTGATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.06
29 11 0.31
30 15 0.42
31 8 0.22
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.50
Consensus pattern (28 bp):
TAATCTAAAATATTAATAATATTTTTAC
Found at i:40882030 original size:37 final size:37
Alignment explanation
Indices: 40881984--40882169 Score: 300
Period size: 37 Copynumber: 5.0 Consensus size: 37
40881974 GGTAGTTTTA
* *
40881984 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
40882021 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
40882058 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
40882095 GTTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
40882132 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
40882169 G
1 G
40882170 TAGCTTCAGC
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 141 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:40882241 original size:45 final size:46
Alignment explanation
Indices: 40882132--40882255 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
40882122 GTGATAAGTG
* *
40882132 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
40882178 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
40882223 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
40882256 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:40884421 original size:17 final size:17
Alignment explanation
Indices: 40884399--40884446 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
40884389 TTGATTACCC
40884399 AATTAAATTAATTCTAT
1 AATTAAATTAATTCTAT
*
40884416 AATTAAATTAATTCTGT
1 AATTAAATTAATTCTAT
*
40884433 AATTAATTTAATTC
1 AATTAAATTAATTC
40884447 ATGCGACAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTAAATTAATTCTAT
Found at i:40888963 original size:20 final size:20
Alignment explanation
Indices: 40888919--40888961 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
40888909 AAAATAAAAG
40888919 TTTTAAAATATCTTTTTAGA
1 TTTTAAAATATCTTTTTAGA
* *
40888939 ATTTAAAATATTTTTTTA-A
1 TTTTAAAATATCTTTTTAGA
40888958 TTTT
1 TTTT
40888962 TAGAATTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTAAAATATCTTTTTAGA
Found at i:40889560 original size:20 final size:19
Alignment explanation
Indices: 40889528--40889585 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
40889518 TTTGAATGTG
40889528 AAATAATATTTATATTTTCTT
1 AAATAA-ATTTATATTTT-TT
**
40889549 TTATAAATTTATATATTTTT
1 AAATAAATTTATAT-TTTTT
*
40889569 AAATAATTTTATATTTT
1 AAATAAATTTATATTTT
40889586 ATATATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 3 0.10
20 21 0.68
21 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATAAATTTATATTTTTT
Found at i:40902581 original size:132 final size:132
Alignment explanation
Indices: 40901956--40902567 Score: 811
Period size: 132 Copynumber: 4.6 Consensus size: 132
40901946 CCAGTATGAA
* **
40901956 AAGACAAGATCTGC-ATCTTCGATCTACTTCGTCACCAGTATGGGAAGACAAGATCTGCATCTTC
1 AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTC
* * *
40902020 GATCCACTTCCTACAAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACA
66 GATCCACTTCCTGCCAATATAGGAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACA
40902085 TG
131 TG
40902087 AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTC
1 AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTC
40902152 GATCCACTTCCTGCCAATATAGGAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACA
66 GATCCACTTCCTGCCAATATAGGAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACA
40902217 TG
131 TG
40902219 AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTC
1 AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTC
40902284 GATCCACTTCCTGCCAATATAGGAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACA
66 GATCCACTTCCTGCCAATATAGGAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACA
40902349 TG
131 TG
* * * * * *
40902351 AAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGCAGATAGGACCTTCTATCTT
1 AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC-ATCTT
* * * * * * ** * * * *
40902416 CGATCTACTTCAC-GCCAACACATGAAGACAAGATATACTTTCTTCGATCTACTTCGCCACCAGT
65 CGATCCACTTC-CTGCCAATATAGGAAGATAGGACCTACTATCTTCGATCTACTTC-ACGCCAAT
***
40902480 ATGGG
128 ACATG
* * * * * * * *
40902485 AAGACAAGATCTGC-ATCTTTGATCCACTTC-CTACCAATATAGGAAGACAGGACCTGCTATCTT
1 AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC-ATCTT
* *
40902548 TGATCTACTTCAC-GCCAATA
65 CGATCCACTTC-CTGCCAATA
40902568 CATGAAGACA
Statistics
Matches: 439, Mismatches: 38, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
131 14 0.03
132 341 0.78
133 62 0.14
134 22 0.05
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (132 bp):
AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTC
GATCCACTTCCTGCCAATATAGGAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACA
TG
Found at i:40902785 original size:44 final size:44
Alignment explanation
Indices: 40901956--40902803 Score: 709
Period size: 44 Copynumber: 19.3 Consensus size: 44
40901946 CCAGTATGAA
* * * *
40901956 AAGACAAGATCTGC-ATCTTCGATCTACTTCGTCACCAGTATGGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATATAGG
* * *
40902000 AAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACAAATATAGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAGG
* * * * *
40902043 AAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAGG
* * * *
40902087 AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCA-CGCCAATATAGG
*
40902132 AAGACAAGATCTGC-ATCTTCGATCCACTTC-CTGCCAATATAGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAGG
* * * * * *
40902175 AAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACATG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAGG
* * * *
40902219 AAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCA-CGCCAATATAGG
*
40902264 AAGACAAGATCTGC-ATCTTCGATCCACTTC-CTGCCAATATAGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAGG
* * * * * *
40902307 AAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACATG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAGG
* * * * *
40902351 AAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATATAGG
* * * * * * * *
40902396 CAGATAGGACCTTCTATCTTCGATCTACTTCACGCCAACACATG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAGG
* * * * * * *
40902440 AAGACAAGATATACTTTCTTCGATCTACTTCGCCACCAGTATGGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATATAGG
* * *
40902485 AAGACAAGATCTGC-ATCTTTGATCCACTTC-CTACCAATATAGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAGG
* * * * *
40902528 AAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAGG
* * *
40902572 AAGACAAGATCTGC-ATCTTCGATCCAC-TCCCTACCAATATAGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAGG
* * * * * *
40902615 AAGA-TAGAACCTGTTATCTTCGATCTACTTCACGCCAACACATG
1 AAGACAAG-ATCTGCTATCTTCGATCTACTTCACGCCAATATAGG
* * * * *
40902659 AAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATATAGG
* * *
40902704 AAGACAAGATCTGC-ATCTTTGATCCACTTC-CTACCAATATAGG
1 AAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAGG
* * * * *
40902747 AAGATAGGA-CATGCTATCTTCGATCTACTTCATGCCAATACATG
1 AAGACAAGATC-TGCTATCTTCGATCTACTTCACGCCAATATAGG
40902791 AAGACAAGATCTG
1 AAGACAAGATCTG
40902804 TTTTAATGAC
Statistics
Matches: 628, Mismatches: 149, Indels: 54
0.76 0.18 0.06
Matches are distributed among these distances:
42 11 0.02
43 122 0.19
44 373 0.59
45 122 0.19
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (44 bp):
AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAGG
Found at i:40914462 original size:107 final size:107
Alignment explanation
Indices: 40914225--40914631 Score: 665
Period size: 107 Copynumber: 3.8 Consensus size: 107
40914215 AAGTTAAGAA
* * * * * *
40914225 GATATTTGGCTATTTGGTCAAACGAGAAATTGAGACCCAGCACGTTAGGGCACATTCTCTCAAAT
1 GATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATT
* *
40914290 TTCCAAACGC-AAATATTGCCTTACTTTGAAAGTTT-AAAAG
66 TTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAG
* * * *
40914330 GATATTTGGCTATTTGGTCAAACGAGAAGTCGAAACCCAACACGTTAGGGTACGTTTGCTCGATT
1 GATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATT
40914395 TTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAG
66 TTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAG
*
40914437 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATT
1 GATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATT
40914502 TTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAG
66 TTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAG
*
40914544 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATT
1 GATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATT
*
40914609 TTCCAAACGCAAAATATTGCCTT
66 TTCCAAACGCGAAATATTGCCTT
40914632 GTTTAGAAAA
Statistics
Matches: 282, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
105 65 0.23
106 23 0.08
107 194 0.69
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (107 bp):
GATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATT
TTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAG
Found at i:40915421 original size:15 final size:15
Alignment explanation
Indices: 40915398--40915428 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40915388 ATTTTAACAT
40915398 AGATAATAATATATA
1 AGATAATAATATATA
*
40915413 AGATGATAATATATA
1 AGATAATAATATATA
40915428 A
1 A
40915429 ATTTAAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (15 bp):
AGATAATAATATATA
Found at i:40918381 original size:16 final size:16
Alignment explanation
Indices: 40918360--40918391 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40918350 ACATCATATA
40918360 CAAGCCAATTTTATTG
1 CAAGCCAATTTTATTG
40918376 CAAGCCAATTTTATTG
1 CAAGCCAATTTTATTG
40918392 TGAAGTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
CAAGCCAATTTTATTG
Found at i:40918924 original size:17 final size:17
Alignment explanation
Indices: 40918904--40918942 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40918894 TGATTTTATC
*
40918904 ATTTGTTTATTTTTCTT
1 ATTTATTTATTTTTCTT
* *
40918921 ATTTATTTGTTTTTGTT
1 ATTTATTTATTTTTCTT
40918938 ATTTA
1 ATTTA
40918943 AATTTTCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTTTCTT
Found at i:40921055 original size:56 final size:55
Alignment explanation
Indices: 40920970--40921076 Score: 169
Period size: 56 Copynumber: 1.9 Consensus size: 55
40920960 TTATAGATTG
* *
40920970 CAAATTAATTATTCATGAGCACTATTCAAATTAAAAGTGATGATTTATCATTTTA
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGACGATTTATCATTTTA
* *
40921025 CAAATTTAATTATTCATAAGGATTATTCAAATTAAAAGTGACGATTTATCAT
1 CAAA-TTAATTATTCATAAGCACTATTCAAATTAAAAGTGACGATTTATCAT
40921077 CCAATGGATA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 4 0.09
56 43 0.91
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.39
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGACGATTTATCATTTTA
Found at i:40923331 original size:56 final size:55
Alignment explanation
Indices: 40923246--40923354 Score: 184
Period size: 56 Copynumber: 2.0 Consensus size: 55
40923236 TTATAGATTG
*
40923246 CAAATTAATTATTCATGAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTA
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTA
40923301 CAAATTTAATTATTCATAAGCA-TCATTCAAATTAAAAGTGATGATTTATCATCT
1 CAAA-TTAATTATTCATAAGCACT-ATTCAAATTAAAAGTGATGATTTATCATCT
40923355 AATGGATAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
55 5 0.10
56 46 0.90
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTA
Found at i:40925132 original size:100 final size:100
Alignment explanation
Indices: 40924956--40925136 Score: 222
Period size: 100 Copynumber: 1.8 Consensus size: 100
40924946 TTAGTTACGG
** * *
40924956 AAGGATATTTTCGTAATTTCTCTAATCGAGTTGGTACTCGGTTGACTTAAGACACCAACTCTATT
1 AAGGATATTTTCGTAATTTCTCTAATCGAGTTGGTACTCAATTGACTCAAGACACCAACTCTATC
* **
40925021 AGGGGTTTAAATAATAGTATAAATACAAATTATGA
66 AAGGGCCTAAATAATAGTATAAATACAAATTATGA
* * ** *
40925056 AAGGATATTTTCGTAATTTTTCTAATTGAGTTGGTAC-CTAATTGACTCGTGATACCAACT-TAG
1 AAGGATATTTTCGTAATTTCTCTAATCGAGTTGGTACTC-AATTGACTCAAGACACCAACTCTA-
40925119 TCAAGGGCCTAAATAATA
64 TCAAGGGCCTAAATAATA
40925137 AAAACAATAA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
99 3 0.04
100 64 0.96
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (100 bp):
AAGGATATTTTCGTAATTTCTCTAATCGAGTTGGTACTCAATTGACTCAAGACACCAACTCTATC
AAGGGCCTAAATAATAGTATAAATACAAATTATGA
Found at i:40937572 original size:18 final size:17
Alignment explanation
Indices: 40937539--40937577 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
40937529 TTGTATAAAT
40937539 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
40937557 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
40937574 TGTG
1 TGTG
40937578 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:40937596 original size:17 final size:17
Alignment explanation
Indices: 40937576--40937609 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40937566 ATATTGAATG
40937576 TGGAAGGAAAATTGTTC
1 TGGAAGGAAAATTGTTC
40937593 TGGAAGGAAAATTGTTC
1 TGGAAGGAAAATTGTTC
40937610 ATGAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (17 bp):
TGGAAGGAAAATTGTTC
Found at i:40937712 original size:8 final size:8
Alignment explanation
Indices: 40937699--40937727 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
40937689 CACCAGAGAC
40937699 CAGTGTTA
1 CAGTGTTA
40937707 CAGTGTTA
1 CAGTGTTA
40937715 CAGTGTTA
1 CAGTGTTA
40937723 CAGTG
1 CAGTG
40937728 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:40937841 original size:23 final size:23
Alignment explanation
Indices: 40937814--40937866 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
40937804 AGTGTTATTG
40937814 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
40937837 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
40937860 ATCAGTG
1 ATCAGTG
40937867 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:40951525 original size:45 final size:45
Alignment explanation
Indices: 40951474--40951629 Score: 215
Period size: 45 Copynumber: 3.5 Consensus size: 45
40951464 CACGAGTAAA
*
40951474 ACCATAGTTGAAAGACGCTATGGCATCATGATGGAAATGAATAAG
1 ACCATAGTTGAAAGACACTATGGCATCATGATGGAAATGAATAAG
* * *
40951519 ACCATAGTTGAAAGACACTATGGCAACATGACGAAAATGAATAAG
1 ACCATAGTTGAAAGACACTATGGCATCATGATGGAAATGAATAAG
* *
40951564 ACCATAGTTGAAAGACACTATGGCATCATG-TCAGAAATAAATAAG
1 ACCATAGTTGAAAGACACTATGGCATCATGAT-GGAAATGAATAAG
** *
40951609 ACTGTAGTTGAAAGAAACTAT
1 ACCATAGTTGAAAGACACTAT
40951630 AACATCATTT
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
45 98 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.22
Consensus pattern (45 bp):
ACCATAGTTGAAAGACACTATGGCATCATGATGGAAATGAATAAG
Found at i:40961411 original size:27 final size:30
Alignment explanation
Indices: 40961356--40961422 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 30
40961346 TTAGTTGTTT
*
40961356 TTATTTTATTTGTGAGACTTCTTTGTTTTA
1 TTATTTTATTTGTGAGACTTCTTTATTTTA
*
40961386 TTTTTTTATTT-TGA-ACTT-TTTATTTTA
1 TTATTTTATTTGTGAGACTTCTTTATTTTA
40961413 TTATTTTATT
1 TTATTTTATT
40961423 GGTTGTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.50
28 4 0.12
29 3 0.09
30 10 0.29
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.70
Consensus pattern (30 bp):
TTATTTTATTTGTGAGACTTCTTTATTTTA
Found at i:40963812 original size:42 final size:42
Alignment explanation
Indices: 40963693--40963812 Score: 118
Period size: 44 Copynumber: 2.8 Consensus size: 42
40963683 TCCGATACAT
* * *
40963693 GATTTCGTGTAAGACCGCGTCTGGGACATTGGCAGTGATTTGA
1 GATTTCGTGTAAGACC-TGTCTGGGACATTGGCAGCGATATGA
* *
40963736 GATTTACGTGTAAGAACATGTCTGGAACATTGGCAGCGTATAT-A
1 GATTT-CGTGTAAG-ACCTGTCTGGGACATTGGCAGCG-ATATGA
* *
40963780 -ATTTCGTGTAAGATCCTGTTTGGGACAGTGGCA
1 GATTTCGTGTAAGA-CCTGTCTGGGACATTGGCA
40963813 TCGTTATTTG
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
41 1 0.02
42 23 0.36
43 9 0.14
44 26 0.41
45 5 0.08
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (42 bp):
GATTTCGTGTAAGACCTGTCTGGGACATTGGCAGCGATATGA
Found at i:40966408 original size:12 final size:12
Alignment explanation
Indices: 40966388--40966417 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40966378 TATTCAAGAA
*
40966388 AACAACTCGAAG
1 AACATCTCGAAG
40966400 AACATCTCGAAG
1 AACATCTCGAAG
40966412 AACATC
1 AACATC
40966418 ATTGAAGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.27, G:0.13, T:0.13
Consensus pattern (12 bp):
AACATCTCGAAG
Found at i:40982805 original size:20 final size:20
Alignment explanation
Indices: 40982767--40982806 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40982757 AGGCTGTTAA
* * *
40982767 TAATGTGTTTGTAATGTGTT
1 TAATGTGTATGAAAAGTGTT
40982787 TAATGTGTATGAAAAGTGTT
1 TAATGTGTATGAAAAGTGTT
40982807 GGACTCGTCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (20 bp):
TAATGTGTATGAAAAGTGTT
Found at i:40983842 original size:24 final size:24
Alignment explanation
Indices: 40983812--40983858 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
40983802 CAAATAATAG
40983812 AGGCAATGTGGGACTCATACATAT
1 AGGCAATGTGGGACTCATACATAT
*
40983836 AGGCAATGTGGTACTCATACATA
1 AGGCAATGTGGGACTCATACATA
40983859 GAGGGAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (24 bp):
AGGCAATGTGGGACTCATACATAT
Found at i:40989181 original size:6 final size:6
Alignment explanation
Indices: 40989170--40989216 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
40989160 ATACCTCTTT
* * *
40989170 TTTTTC TTTTTC CTTTTC TTTTTC TTTTTC TTTTTA TTTTTA TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
40989217 TTATCTCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:40992121 original size:3 final size:3
Alignment explanation
Indices: 40992113--40992166 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
40992103 AGTACTAATG
40992113 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
40992161 TCT TCT
1 TCT TCT
40992167 CNNNNNNNNN
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:40992276 original size:3 final size:3
Alignment explanation
Indices: 40992268--40992296 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40992258 NNNNNNNNNN
40992268 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
40992297 TAGATTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:40995567 original size:3 final size:3
Alignment explanation
Indices: 40995561--40995626 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
40995551 AAAAGTAATA
* *
40995561 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
40995609 TAT TGT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT
40995627 ATCTCCATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:40995684 original size:8 final size:9
Alignment explanation
Indices: 40995672--40995728 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
40995662 ATATGTGTCT
40995672 TATTATAT-
1 TATTATATA
40995680 TATTAT-TA
1 TATTATATA
*
40995688 TAATTATTTA
1 T-ATTATATA
40995698 TA-TATATA
1 TATTATATA
40995706 TATATATATA
1 TAT-TATATA
40995716 TATATATATA
1 TAT-TATATA
40995726 TAT
1 TAT
40995729 CTTTTCTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
7 1 0.02
8 14 0.33
9 6 0.14
10 22 0.51
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATATA
Done.