Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 90 of 240
Found at i:28262580 original size:25 final size:25
Alignment explanation
Indices: 28262534--28262581 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28262524 ATTTAATCAT
* * *
28262534 TTTTTATTTTATTTTAATATTCTTG
1 TTTTAATTTAATTTTAACATTCTTG
*
28262559 TTTTAATTTAATTTTTACATTCT
1 TTTTAATTTAATTTTAACATTCT
28262582 AATTTTTTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTAATTTAATTTTAACATTCTTG
Found at i:28270316 original size:8 final size:8
Alignment explanation
Indices: 28270299--28270339 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
28270289 AAATAGTGAT
28270299 AAAAAATA
1 AAAAAATA
*
28270307 AAATAATA
1 AAAAAATA
28270315 AAAAAATA
1 AAAAAATA
28270323 AAAAAAGTA
1 AAAAAA-TA
28270332 AAAAAATA
1 AAAAAATA
28270340 GTAGGTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (8 bp):
AAAAAATA
Found at i:28270317 original size:15 final size:15
Alignment explanation
Indices: 28270299--28270339 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 15
28270289 AAATAGTGAT
28270299 AAAAAATAAAATAATA
1 AAAAAATAAAA-AATA
28270315 AAAAAATAAAAAAAGTA
1 AAAAAAT-AAAAAA-TA
28270332 AAAAAATA
1 AAAAAATA
28270340 GTAGGTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Found at i:28272002 original size:15 final size:16
Alignment explanation
Indices: 28271973--28272004 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
28271963 ATATTGAAAG
28271973 TTTATCTGCAAAAAAT
1 TTTATCTGCAAAAAAT
28271989 TTTATCTG-AAAAAAT
1 TTTATCTGCAAAAAAT
28272004 T
1 T
28272005 GGTTGTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (16 bp):
TTTATCTGCAAAAAAT
Found at i:28274630 original size:13 final size:14
Alignment explanation
Indices: 28274599--28274630 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28274589 GATTAAATGT
28274599 TAAAATAAGTAAAA
1 TAAAATAAGTAAAA
28274613 T-AAATAA-TAAAA
1 TAAAATAAGTAAAA
28274625 TAAAAT
1 TAAAAT
28274631 GTTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 10 0.59
14 1 0.06
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
TAAAATAAGTAAAA
Found at i:28274925 original size:18 final size:18
Alignment explanation
Indices: 28274888--28274925 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
28274878 TAAATGATGA
28274888 ATTTAAAATATTAATTGTT
1 ATTTAAAATATT-ATTGTT
28274907 ATTTAAAAATATT-TTGTT
1 ATTT-AAAATATTATTGTT
28274925 A
1 A
28274926 AGCGATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
ATTTAAAATATTATTGTT
Found at i:28275565 original size:20 final size:20
Alignment explanation
Indices: 28275542--28275770 Score: 127
Period size: 20 Copynumber: 11.4 Consensus size: 20
28275532 GAAGTGTCAT
*
28275542 TGTTTGCACATCAGTGCCCC
1 TGTTTGTACATCAGTGCCCC
* * *
28275562 TGTTTGTACTTCAATACCCC
1 TGTTTGTACATCAGTGCCCC
* *
28275582 TATTTGTACATCAGTGCCCT
1 TGTTTGTACATCAGTGCCCC
* * * *
28275602 TGATTGTACTTC-GATACCAC
1 TGTTTGTACATCAG-TGCCCC
* *
28275622 TATTTGCACATCAGTGCCCC
1 TGTTTGTACATCAGTGCCCC
* * ** *
28275642 TGATTGTACTTTGGTACCCC
1 TGTTTGTACATCAGTGCCCC
* * * *
28275662 TATTTGCACATAAATGCCCC
1 TGTTTGTACATCAGTGCCCC
** * ** *
28275682 TAATTGTACTTTGGTACCCC
1 TGTTTGTACATCAGTGCCCC
*
28275702 TGTTTGCACATCAGTGCCCC
1 TGTTTGTACATCAGTGCCCC
* * *
28275722 TGTTTGTACTTCGGTACCCC
1 TGTTTGTACATCAGTGCCCC
* * *
28275742 TATTTGCACATCAGTGCTCC
1 TGTTTGTACATCAGTGCCCC
*
28275762 TGATTGTAC
1 TGTTTGTAC
28275771 TTCGATTCCC
Statistics
Matches: 144, Mismatches: 63, Indels: 4
0.68 0.30 0.02
Matches are distributed among these distances:
19 1 0.01
20 142 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (20 bp):
TGTTTGTACATCAGTGCCCC
Found at i:28275609 original size:40 final size:40
Alignment explanation
Indices: 28275544--28275802 Score: 338
Period size: 40 Copynumber: 6.5 Consensus size: 40
28275534 AGTGTCATTG
* *
28275544 TTTGCACATCAGTGCCCCTGTTTGTACTTCAATACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* * *
28275584 TTTGTACATCAGTGCCCTTGATTGTACTTCGATACCACTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* *
28275624 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* * * * * *
28275664 TTTGCACATAAATGCCCCTAATTGTACTTTGGTACCCCTG
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* *
28275704 TTTGCACATCAGTGCCCCTGTTTGTACTTCGGTACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* *
28275744 TTTGCACATCAGTGCTCCTGATTGTACTTCGATTCCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
** *
28275784 AATGCACATCTGTGCCCCT
1 TTTGCACATCAGTGCCCCT
28275803 ATTTGCACTT
Statistics
Matches: 191, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 191 1.00
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.35
Consensus pattern (40 bp):
TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
Found at i:28275809 original size:20 final size:20
Alignment explanation
Indices: 28275544--28275810 Score: 121
Period size: 20 Copynumber: 13.3 Consensus size: 20
28275534 AGTGTCATTG
*
28275544 TTTGCACATCAGTGCCCCTG
1 TTTGCACATCAGTGCCCCTA
* * * *
28275564 TTTGTACTTCAATACCCCTA
1 TTTGCACATCAGTGCCCCTA
* *
28275584 TTTGTACATCAGTGCCCTTGA
1 TTTGCACATCAGTGCCCCT-A
* * * *
28275605 -TTGTACTTC-GATACCACTA
1 TTTGCACATCAG-TGCCCCTA
28275624 TTTGCACATCAGTGCCCCTGA
1 TTTGCACATCAGTGCCCCT-A
* * ** *
28275645 -TTGTACTTTGGTACCCCTA
1 TTTGCACATCAGTGCCCCTA
* *
28275664 TTTGCACATAAATGCCCCTA
1 TTTGCACATCAGTGCCCCTA
* * * ** * *
28275684 ATTGTACTTTGGTACCCCTG
1 TTTGCACATCAGTGCCCCTA
*
28275704 TTTGCACATCAGTGCCCCTG
1 TTTGCACATCAGTGCCCCTA
* * * *
28275724 TTTGTACTTCGGTACCCCTA
1 TTTGCACATCAGTGCCCCTA
*
28275744 TTTGCACATCAGTGCTCCTGA
1 TTTGCACATCAGTGCCCCT-A
* * *
28275765 -TTGTACTTC-GATTCCCCTA
1 TTTGCACATCAG-TGCCCCTA
** *
28275784 AATGCACATCTGTGCCCCTA
1 TTTGCACATCAGTGCCCCTA
28275804 TTTGCAC
1 TTTGCAC
28275811 TTTGGTGCCC
Statistics
Matches: 175, Mismatches: 62, Indels: 20
0.68 0.24 0.08
Matches are distributed among these distances:
19 5 0.03
20 165 0.94
21 5 0.03
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.35
Consensus pattern (20 bp):
TTTGCACATCAGTGCCCCTA
Found at i:28275818 original size:20 final size:20
Alignment explanation
Indices: 28275621--28275876 Score: 81
Period size: 20 Copynumber: 12.8 Consensus size: 20
28275611 TTCGATACCA
* **
28275621 CTATTTGCACATCAGTGCCC
1 CTATTTGCACTTTGGTGCCC
* *
28275641 CTGA-TTGTACTTTGGTACCC
1 CT-ATTTGCACTTTGGTGCCC
* ***
28275661 CTATTTGCACATAAATGCCC
1 CTATTTGCACTTTGGTGCCC
* * *
28275681 CTAATTGTACTTTGGTACCC
1 CTATTTGCACTTTGGTGCCC
* * **
28275701 CTGTTTGCACATCAGTGCCC
1 CTATTTGCACTTTGGTGCCC
* * * *
28275721 CTGTTTGTACTTCGGTACCC
1 CTATTTGCACTTTGGTGCCC
* ** *
28275741 CTATTTGCACATCAGTGCTC
1 CTATTTGCACTTTGGTGCCC
* * * *
28275761 CTGA-TTGTACTTCGATTCCC
1 CT-ATTTGCACTTTGGTGCCC
** *
28275781 CTAAATGCACATCT-GTGCCC
1 CTATTTGCAC-TTTGGTGCCC
28275801 CTATTTGCACTTTGGTGCCC
1 CTATTTGCACTTTGGTGCCC
** * * *
28275821 CTGA-TCACACATTCGTGCTC
1 CT-ATTTGCACTTTGGTGCCC
*
28275841 CTGA-TTGCACTTTGGTGCTC
1 CT-ATTTGCACTTTGGTGCCC
* *
28275861 CTAATTGCATTTTGGT
1 CTATTTGCACTTTGGT
28275877 TCCCTGTTAT
Statistics
Matches: 168, Mismatches: 60, Indels: 16
0.69 0.25 0.07
Matches are distributed among these distances:
19 5 0.03
20 159 0.95
21 4 0.02
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (20 bp):
CTATTTGCACTTTGGTGCCC
Found at i:28275822 original size:40 final size:40
Alignment explanation
Indices: 28275544--28275856 Score: 326
Period size: 40 Copynumber: 7.8 Consensus size: 40
28275534 AGTGTCATTG
* ***
28275544 TTTGCACATCAGTGCCCCTGTTTGTACTTCAATACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
* * * * *
28275584 TTTGTACATCAGTGCCCTTGATTGTACTTCGATACCACTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
28275624 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
* * * *
28275664 TTTGCACATAAATGCCCCTAATTGTACTTTGGTACCCCTG
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
* *
28275704 TTTGCACATCAGTGCCCCTGTTTGTACTTCGGTACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
* * * *
28275744 TTTGCACATCAGTGCTCCTGATTGTACTTCGATTCCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
** * * *
28275784 AATGCACATCTGTGCCCCT-ATTTGCACTTTGGTGCCCCTGA
1 TTTGCACATCAGTGCCCCTGA-TTGTACTTTGGTACCCCT-A
** * *
28275825 -TCACACATTC-GTGCTCCTGATTGCACTTTGGT
1 TTTGCACA-TCAGTGCCCCTGATTGTACTTTGGT
28275857 GCTCCTAATT
Statistics
Matches: 233, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.00
40 228 0.98
41 4 0.02
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (40 bp):
TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
Found at i:28281495 original size:18 final size:17
Alignment explanation
Indices: 28281475--28281525 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 17
28281465 TAAGATTAAT
28281475 AAAATAAAATAAACGAATA
1 AAAATAAAATAAA--AATA
28281494 AAAATAAAAATAAAAATA
1 AAAAT-AAAATAAAAATA
*
28281512 AAAACAAAATAAAA
1 AAAATAAAATAAAA
28281526 TTTAAAACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 9 0.30
18 8 0.27
19 5 0.17
20 8 0.27
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:28281501 original size:6 final size:6
Alignment explanation
Indices: 28281475--28281525 Score: 61
Period size: 6 Copynumber: 8.5 Consensus size: 6
28281465 TAAGATTAAT
*
28281475 AAAAT- AAAATA AACGAATA AAAATA AAAATA AAAATA AAAA-C AAAATA
1 AAAATA AAAATA AA--AATA AAAATA AAAATA AAAATA AAAATA AAAATA
28281523 AAA
1 AAA
28281526 TTTAAAACAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 9 0.22
6 25 0.62
8 6 0.15
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:28287893 original size:26 final size:25
Alignment explanation
Indices: 28287849--28287899 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
28287839 GTTTTTTCTC
28287849 TTCTTTTTATTATTATTTTTTCTTTT
1 TTCTTTTTATTA-TATTTTTTCTTTT
* * *
28287875 TTCTTTTTCTTCTTTTTTTTCTTTT
1 TTCTTTTTATTATATTTTTTCTTTT
28287900 ATAACATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (25 bp):
TTCTTTTTATTATATTTTTTCTTTT
Found at i:28296431 original size:18 final size:17
Alignment explanation
Indices: 28296385--28296438 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
28296375 TTTCCAATTC
28296385 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
* *
28296402 TCATTTCAAAATTTACTT
1 TCAATTC-AAATTCACTT
28296420 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
28296438 T
1 T
28296439 TTCATTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 23 0.74
19 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:28296521 original size:32 final size:32
Alignment explanation
Indices: 28296481--28296545 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
28296471 TAGAACACAT
28296481 ATATACATAATATCTATCACCAAATAAAATTC
1 ATATACATAATATCTATCACCAAATAAAATTC
28296513 ATATACATAATATCTATCACCAAATAAAATTC
1 ATATACATAATATCTATCACCAAATAAAATTC
28296545 A
1 A
28296546 CTTTAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (32 bp):
ATATACATAATATCTATCACCAAATAAAATTC
Found at i:28298353 original size:30 final size:30
Alignment explanation
Indices: 28298310--28298384 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
28298300 CTTATATACT
*
28298310 AAATATAATAAAATAATA-ATATCTCATTA
1 AAATATAATAAAATAATATATATCTAATTA
* *
28298339 AAATATTATTAAAATAATATTTATCTAATTA
1 AAATA-TAATAAAATAATATATATCTAATTA
* *
28298370 AAAAATCATAAAATA
1 AAATATAATAAAATA
28298385 TTATTAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 5 0.13
30 20 0.53
31 13 0.34
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATATAATAAAATAATATATATCTAATTA
Found at i:28299398 original size:17 final size:17
Alignment explanation
Indices: 28299368--28299405 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
28299358 ACATGAAATT
28299368 TAATCATTTTATTGAAA
1 TAATCATTTTATTGAAA
*
28299385 TAAT-ATTTTAATTGAGA
1 TAATCATTTT-ATTGAAA
28299402 TAAT
1 TAAT
28299406 TTTCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (17 bp):
TAATCATTTTATTGAAA
Found at i:28299738 original size:31 final size:29
Alignment explanation
Indices: 28299702--28299773 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
28299692 GATTAAATCA
*
28299702 AAATTAAAGTTTTA-TGTATACATTTGAACC
1 AAATTAAAGTTTCACTGTATA-A-TTGAACC
* *
28299732 ACAATTAGAGTTTCACGTGTATAATTGCACC
1 A-AATTAAAGTTTCAC-TGTATAATTGAACC
28299763 AAATTAAAGTT
1 AAATTAAAGTT
28299774 CTTCTATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.29
31 18 0.51
32 1 0.03
33 6 0.17
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (29 bp):
AAATTAAAGTTTCACTGTATAATTGAACC
Found at i:28299976 original size:16 final size:17
Alignment explanation
Indices: 28299939--28299982 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
28299929 TTTTAAAACC
28299939 TGGTTGTTATAGCGAAA
1 TGGTTGTTATAGCGAAA
**
28299956 T-GTTGTTATAGC-ATG
1 TGGTTGTTATAGCGAAA
28299971 TGGTTGTTATAG
1 TGGTTGTTATAG
28299983 AGAGGATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 21 0.88
17 1 0.04
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.43
Consensus pattern (17 bp):
TGGTTGTTATAGCGAAA
Found at i:28300204 original size:13 final size:13
Alignment explanation
Indices: 28300186--28300210 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28300176 TTAATATATA
28300186 CAATATTATAGAT
1 CAATATTATAGAT
28300199 CAATATTATAGA
1 CAATATTATAGA
28300211 GATATCAAAT
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
CAATATTATAGAT
Found at i:28303066 original size:20 final size:20
Alignment explanation
Indices: 28303041--28303083 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
28303031 AAATATCATT
28303041 AAACCGTTTACTGATAACGG
1 AAACCGTTTACTGATAACGG
*
28303061 AAACCGTTTACTGGTAACGG
1 AAACCGTTTACTGATAACGG
28303081 AAA
1 AAA
28303084 AATGATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (20 bp):
AAACCGTTTACTGATAACGG
Found at i:28304167 original size:24 final size:21
Alignment explanation
Indices: 28304143--28304186 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28304133 AAGAAGAAAG
*
28304143 GGAAAAGAGAGAAAATAAAATAA
1 GGAAAA-AAAGAAAA-AAAATAA
28304166 GGAAAAAAAGAAAAAAAATAA
1 GGAAAAAAAGAAAAAAAATAA
28304187 AAATTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (21 bp):
GGAAAAAAAGAAAAAAAATAA
Found at i:28310132 original size:3 final size:3
Alignment explanation
Indices: 28310124--28310153 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
28310114 ATTAAGGGGA
28310124 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28310154 TTGAGTTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28329293 original size:23 final size:24
Alignment explanation
Indices: 28329256--28329315 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
28329246 AGCTTCTCGT
* *
28329256 TAATGGCTCTCCGGAGCTTCCCGA
1 TAATGGCTCTTCGGAGCTACCCGA
* *
28329280 T-ATGGCTATTCGGAGCTACCCGT
1 TAATGGCTCTTCGGAGCTACCCGA
28329303 TAATGGCTCTTCG
1 TAATGGCTCTTCG
28329316 AAGTTGCCCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (24 bp):
TAATGGCTCTTCGGAGCTACCCGA
Found at i:28329315 original size:24 final size:24
Alignment explanation
Indices: 28329235--28329335 Score: 98
Period size: 24 Copynumber: 4.2 Consensus size: 24
28329225 CTTGATCATA
* *
28329235 GGCTCTTCTTGAGCTTCTCGTTAAT
1 GGCTCTTC-GGAGCTTCCCGTTAAT
* *
28329260 GGCTCTCCGGAGCTTCCCGAT-AT
1 GGCTCTTCGGAGCTTCCCGTTAAT
* *
28329283 GGCTATTCGGAGCTACCCGTTAAT
1 GGCTCTTCGGAGCTTCCCGTTAAT
* *
28329307 GGCTCTTCGAAG-TTGCCCGTTATT
1 GGCTCTTCGGAGCTT-CCCGTTAAT
28329331 GGCTC
1 GGCTC
28329336 GCATGAGCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
23 20 0.32
24 35 0.56
25 7 0.11
ACGTcount: A:0.14, C:0.28, G:0.25, T:0.34
Consensus pattern (24 bp):
GGCTCTTCGGAGCTTCCCGTTAAT
Found at i:28331432 original size:10 final size:10
Alignment explanation
Indices: 28331417--28331471 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
28331407 CATTCAAATA
28331417 TTTTTATAAT
1 TTTTTATAAT
* *
28331427 TTTTTAAAAC
1 TTTTTATAAT
*
28331437 TTTATATAAT
1 TTTTTATAAT
*
28331447 TTTTT-TTAT
1 TTTTTATAAT
28331456 ATTTTTA-AAT
1 -TTTTTATAAT
28331466 TTTTTA
1 TTTTTA
28331472 AGTGATTATG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
9 9 0.26
10 26 0.74
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:28332887 original size:36 final size:36
Alignment explanation
Indices: 28332842--28332918 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
28332832 TACACATCAA
*
28332842 CAAG-CCATGACAATGCATTCAACACAGGCTAAAAT
1 CAAGTCCATGACAATGCATTCAACACAAGCTAAAAT
28332877 CAAGTCCATGACAATGCATTCAACACAAGCTAAAAT
1 CAAGTCCATGACAATGCATTCAACACAAGCTAAAAT
28332913 CAAGTC
1 CAAGTC
28332919 TTAAACATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 4 0.10
36 36 0.90
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.18
Consensus pattern (36 bp):
CAAGTCCATGACAATGCATTCAACACAAGCTAAAAT
Found at i:28333065 original size:4 final size:4
Alignment explanation
Indices: 28333056--28333081 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28333046 TATATTTCAA
28333056 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
28333082 CACTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:28335591 original size:37 final size:37
Alignment explanation
Indices: 28335541--28335626 Score: 172
Period size: 37 Copynumber: 2.3 Consensus size: 37
28335531 GGATTTTTTG
28335541 TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
1 TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
28335578 TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
1 TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
28335615 TATTGGGTTATC
1 TATTGGGTTATC
28335627 AAGTTAGTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (37 bp):
TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
Found at i:28335990 original size:28 final size:28
Alignment explanation
Indices: 28335950--28336008 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
28335940 GATTTATGAC
28335950 TCTTCCTATTATATTGTCAAATAGTAAG
1 TCTTCCTATTATATTGTCAAATAGTAAG
28335978 TCTTCCTATTATATTGTCAAATAGTAAG
1 TCTTCCTATTATATTGTCAAATAGTAAG
28336006 TCT
1 TCT
28336009 GTTGGATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (28 bp):
TCTTCCTATTATATTGTCAAATAGTAAG
Found at i:28338919 original size:18 final size:17
Alignment explanation
Indices: 28338892--28338926 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28338882 GCAACTATAT
28338892 GAATGAATGTTATAGATA
1 GAATGAATGTTAT-GATA
*
28338910 GAATGCATGTTATGATA
1 GAATGAATGTTATGATA
28338927 TGGAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (17 bp):
GAATGAATGTTATGATA
Found at i:28339307 original size:26 final size:26
Alignment explanation
Indices: 28339278--28339338 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
28339268 TTAGGAAGGA
* *
28339278 AAAGCCTTTGTGGCATAATATGAAAG
1 AAAGCCTTTATGGCACAATATGAAAG
* *
28339304 AAAGCCTTTATGGCGCAATATGAAAT
1 AAAGCCTTTATGGCACAATATGAAAG
28339330 AAATGCCTT
1 AAA-GCCTT
28339339 CAGGCCGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (26 bp):
AAAGCCTTTATGGCACAATATGAAAG
Found at i:28345641 original size:2 final size:2
Alignment explanation
Indices: 28345634--28345659 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28345624 TCAATGGATA
28345634 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
28345660 ACACTACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:28359341 original size:16 final size:17
Alignment explanation
Indices: 28359311--28359343 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28359301 TTGTTTATTA
*
28359311 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
28359328 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
28359344 AATTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:28359497 original size:11 final size:11
Alignment explanation
Indices: 28359470--28359513 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
28359460 TTTCACAATA
28359470 TAATAAT-ATT
1 TAATAATAATT
28359480 T-ATAATAATT
1 TAATAATAATT
28359490 TAATAATAATT
1 TAATAATAATT
28359501 TAATAATATATT
1 TAATAATA-ATT
28359513 T
1 T
28359514 TACACATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.16
10 5 0.16
11 17 0.55
12 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATAATAATT
Found at i:28365129 original size:193 final size:193
Alignment explanation
Indices: 28364795--28365174 Score: 670
Period size: 193 Copynumber: 2.0 Consensus size: 193
28364785 TCTCCACTCC
*
28364795 ATTCCACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
1 ATTCAACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
*
28364860 CACATGTATATTCAAAGCTGTCTATCCAAGTCAGAGTCACTAAATTATTTTTATCCGAAGCTATA
66 CACATGTATATTCAAAGCTGTCTATCCAAGTCAGAGTCACTAAATTATTTTTATCCGAAGCTACA
* *
28364925 GTTGTCCAAATTAAGATATGTTAATTTTCCCTGAAACTAGATTCACATATATTCTTAATGTAT
131 GTTGTCCAAATTAAGATACGTTAATTTTCCCTAAAACTAGATTCACATATATTCTTAATGTAT
28364988 ATTCAACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
1 ATTCAACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
* * *
28365053 CACATGTATATTCAAAGCTGTCTATCCGAGTCAGAGTCACTAAGTTATTTTTATCCGGAGCTACA
66 CACATGTATATTCAAAGCTGTCTATCCAAGTCAGAGTCACTAAATTATTTTTATCCGAAGCTACA
* * *
28365118 GTTGTCCAAATTAAGATCCGTTAATTTTTCCTAAAACTAGATTTACATATATTCTTA
131 GTTGTCCAAATTAAGATACGTTAATTTTCCCTAAAACTAGATTCACATATATTCTTA
28365175 CCATAAAATT
Statistics
Matches: 177, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
193 177 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.39
Consensus pattern (193 bp):
ATTCAACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
CACATGTATATTCAAAGCTGTCTATCCAAGTCAGAGTCACTAAATTATTTTTATCCGAAGCTACA
GTTGTCCAAATTAAGATACGTTAATTTTCCCTAAAACTAGATTCACATATATTCTTAATGTAT
Found at i:28365837 original size:23 final size:23
Alignment explanation
Indices: 28365811--28365909 Score: 137
Period size: 23 Copynumber: 4.3 Consensus size: 23
28365801 ATAAGTGCAA
28365811 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28365834 CACTGATACGTAGCCCTAA-CTAC
1 CACTGATATGTAG-CCGAAGCTAC
* *
28365857 CACTGAAATGCAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28365880 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
28365903 CACTGAT
1 CACTGAT
28365910 CAATAACATT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
22 4 0.06
23 57 0.88
24 4 0.06
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:28365878 original size:46 final size:46
Alignment explanation
Indices: 28365811--28365908 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
28365801 ATAAGTGCAA
* *
28365811 CACTGATATGTAGCCGAAGCTACCACTGATACGTAGCCCTAACTAC
1 CACTGAAATGCAGCCGAAGCTACCACTGATACGTAGCCCTAACTAC
* * *
28365857 CACTGAAATGCAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGCAGCCGAAGCTACCACTGATACGTAGCCCTAACTAC
28365903 CACTGA
1 CACTGA
28365909 TCAATAACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CACTGAAATGCAGCCGAAGCTACCACTGATACGTAGCCCTAACTAC
Found at i:28366161 original size:18 final size:17
Alignment explanation
Indices: 28366135--28366173 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28366125 ATTTTCCTTC
28366135 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
28366152 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
28366170 CACA
1 CACA
28366174 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:28370289 original size:16 final size:17
Alignment explanation
Indices: 28370259--28370291 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28370249 TTGTTTATTA
*
28370259 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
28370276 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
28370292 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:28377311 original size:34 final size:35
Alignment explanation
Indices: 28377251--28377317 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
28377241 CAAACACCAG
*
28377251 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* * *
28377286 AAAACATTTTCCCG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28377318 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28394279 original size:49 final size:49
Alignment explanation
Indices: 28394190--28394284 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 49
28394180 CTATTTATAG
* * * *
28394190 GTTGAAAAACCTTATTCTAATCATTGTCAAATAGATGAAGTGTAGTAAA
1 GTTGAAAAACCTTATTCTAATCAATGTCAAATAAAAGAAGTATAGTAAA
28394239 GTTGAAAAA-CTTGATTCTAATCAATGT-AAAGTAAAAGAAGTATAGT
1 GTTGAAAAACCTT-ATTCTAATCAATGTCAAA-TAAAAGAAGTATAGT
28394285 TCTATATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
48 6 0.15
49 34 0.85
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (49 bp):
GTTGAAAAACCTTATTCTAATCAATGTCAAATAAAAGAAGTATAGTAAA
Found at i:28400511 original size:28 final size:27
Alignment explanation
Indices: 28400470--28400572 Score: 88
Period size: 28 Copynumber: 3.9 Consensus size: 27
28400460 TTTTATTTTC
*
28400470 TTAAAAATACTTTTTAACATCAATAGTT
1 TTAAAAACACTTTTTAACATCAATA-TT
*** *
28400498 TTAAAAACA-TTTTTTTTATC--T-TC
1 TTAAAAACACTTTTTAACATCAATATT
*
28400521 TTAAAAATACTTTTTAACATCAATAATT
1 TTAAAAACACTTTTTAACATCAAT-ATT
* *
28400549 TTAAAAACATTTTTTAACCTCAAT
1 TTAAAAACACTTTTTAACATCAAT
28400573 GGTGTAATAG
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
23 9 0.16
24 8 0.14
25 1 0.02
26 1 0.02
27 8 0.14
28 30 0.53
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.46
Consensus pattern (27 bp):
TTAAAAACACTTTTTAACATCAATATT
Found at i:28400522 original size:51 final size:51
Alignment explanation
Indices: 28400460--28400563 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
28400450 AAAATAGAAA
* *
28400460 TTTTATTTTCTTAAAAATACTTTTTAACATCAATAGTTTTAAAAACATTTT
1 TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
28400511 TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
1 TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
28400562 TT
1 TT
28400564 AACCTCAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.51
Consensus pattern (51 bp):
TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
Found at i:28400818 original size:3 final size:3
Alignment explanation
Indices: 28400810--28400860 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
28400800 AGTAGGTCTT
28400810 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
28400858 TTA
1 TTA
28400861 ATTAAGTGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28411601 original size:27 final size:27
Alignment explanation
Indices: 28411530--28411601 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
28411520 ATATTGGGTG
* * * *
28411530 TGCCGCCTATCAAATAGACACCACCAG
1 TGCCGCCTATCAGATAGGCACAACCAA
28411557 TGCCGCCTATCAGATAGGCACAACCAA
1 TGCCGCCTATCAGATAGGCACAACCAA
28411584 TGCCGCCTATCAGATAGG
1 TGCCGCCTATCAGATAGG
28411602 GGTCGCTGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (27 bp):
TGCCGCCTATCAGATAGGCACAACCAA
Found at i:28421324 original size:16 final size:17
Alignment explanation
Indices: 28421285--28421326 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
28421275 TTTCAGTTTC
28421285 TGTTC-TTAGTAAATTT
1 TGTTCTTTAGTAAATTT
*
28421301 T-ATCTTTA-TAAATTT
1 TGTTCTTTAGTAAATTT
28421316 TGTTCTTTAGT
1 TGTTCTTTAGT
28421327 TTTAGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.48
16 10 0.48
17 1 0.05
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.60
Consensus pattern (17 bp):
TGTTCTTTAGTAAATTT
Found at i:28422977 original size:15 final size:15
Alignment explanation
Indices: 28422959--28423008 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
28422949 ATAGATACAA
28422959 ATTTTATTTTTAGTT
1 ATTTTATTTTTAGTT
* *
28422974 ATTTTCTTTTTACTT
1 ATTTTATTTTTAGTT
28422989 AATTTTATTTTTCAGTT
1 -ATTTTATTTTT-AGTT
28423006 ATT
1 ATT
28423009 AATTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 13 0.45
16 13 0.45
17 3 0.10
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (15 bp):
ATTTTATTTTTAGTT
Found at i:28431906 original size:21 final size:22
Alignment explanation
Indices: 28431871--28431911 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28431861 GCATCTACTC
* *
28431871 AGGGAAATTATAATCCACAATA
1 AGGGAAATTACAATCAACAATA
28431893 AGGG-AATTACAATCAACAA
1 AGGGAAATTACAATCAACAA
28431912 CAAAACTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20
Consensus pattern (22 bp):
AGGGAAATTACAATCAACAATA
Found at i:28441362 original size:18 final size:19
Alignment explanation
Indices: 28441324--28441362 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28441314 GGTTTATTGA
*
28441324 TTTCTTTCATTTGTTTATT
1 TTTCTTTCATTTATTTATT
*
28441343 TTTCTTT-ATTTATTTCTT
1 TTTCTTTCATTTATTTATT
28441361 TT
1 TT
28441363 AGTTATTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTCTTTCATTTATTTATT
Found at i:28462340 original size:30 final size:31
Alignment explanation
Indices: 28462266--28462355 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 31
28462256 TCCAAACACA
* *
28462266 TAGATAGCCATAAAGGCATCCACATAATAGT
1 TAGATAGCCATAAAGGCATCCATATAACAGT
* *
28462297 T--ATAACCAAAAAGGC-TCTCATATAACA-T
1 TAGATAGCCATAAAGGCATC-CATATAACAGT
*
28462325 TAGATAGCCATAAAGGCGTCCACATATAACA
1 TAGATAGCCATAAAGGCAT-C-CATATAACA
28462356 AACTTCACCA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 4 0.09
29 19 0.40
30 12 0.26
31 2 0.04
32 10 0.21
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.22
Consensus pattern (31 bp):
TAGATAGCCATAAAGGCATCCATATAACAGT
Found at i:28474211 original size:140 final size:141
Alignment explanation
Indices: 28473958--28474242 Score: 482
Period size: 140 Copynumber: 2.0 Consensus size: 141
28473948 CTAATTCCGT
* *
28473958 TAAAATCATAACGATTTTACCGTAAAAGAATCTATGAGAAATTATATTTAATATTTCTACATTAT
1 TAAAATCATAACGATTTTACCGTAAAAGAACCTATGAGAAAATATATTTAATATTTCTACATTAT
* *
28474023 AATATCTCGCCTAACGAAGCCCTAGTATTTGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
66 AAAATCTCGCCTAACGAAGCCCTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
28474088 CCCTAGATAAG
131 CCCTAGATAAG
*
28474099 TAAAATCATAACGATTTTACCGTAAAATAACCTATG-GAAAATATATTTAATATTTCTACATTAT
1 TAAAATCATAACGATTTTACCGTAAAAGAACCTATGAGAAAATATATTTAATATTTCTACATTAT
* *
28474163 AAAATCTCGCCTAGCGAAGCCTTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
66 AAAATCTCGCCTAACGAAGCCCTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
* *
28474228 CCTTGGATAAG
131 CCCTAGATAAG
28474239 TAAA
1 TAAA
28474243 GTGATGGATT
Statistics
Matches: 135, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
140 101 0.75
141 34 0.25
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (141 bp):
TAAAATCATAACGATTTTACCGTAAAAGAACCTATGAGAAAATATATTTAATATTTCTACATTAT
AAAATCTCGCCTAACGAAGCCCTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
CCCTAGATAAG
Found at i:28479211 original size:42 final size:41
Alignment explanation
Indices: 28479165--28479286 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 41
28479155 GATATGTGAT
*
28479165 TTACGTGTAAGACCATGTCTGGGACATTGGCAACGTATATGA
1 TTACGTGTAAGACCATGTCTGGGA-ATTGGCATCGTATATGA
* * * *
28479207 TTACGTGTAAGACCCTGTCTGGCATAGTGGCATCGTTATTTGA
1 TTACGTGTAAGACCATGTCTGGGA-ATTGGCATCG-TATATGA
* *
28479250 TTACATGTAAGACCACGTCTGGGAAGTTGGCATCGTA
1 TTACGTGTAAGACCATGTCTGGGAA-TTGGCATCGTA
28479287 CGAGCTTTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 33 0.49
43 34 0.51
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (41 bp):
TTACGTGTAAGACCATGTCTGGGAATTGGCATCGTATATGA
Found at i:28481191 original size:59 final size:57
Alignment explanation
Indices: 28481088--28481247 Score: 189
Period size: 59 Copynumber: 2.8 Consensus size: 57
28481078 ACTATCTCTA
* * * *
28481088 AAATG-AAGCCTTTGTGACTATCTCTGTTAAAGAAAGCCTTTGTGGTGATCTTTGTT
1 AAATGAAAGCTTTTGTGACAATCTCTATTAAAGAAAGCCTTTGTGGCGATCTTTGTT
* *
28481144 AAATGAAAGCTTTTGTGACAAATCTCTATTATAAGGAAGTCTTTGTGGCGATCTTTGTT
1 AAATGAAAGCTTTTGTGAC-AATCTCTATTA-AAGAAAGCCTTTGTGGCGATCTTTGTT
* * *
28481203 AAATGAAAG-TCTTTGTGGCGATCTCTATTAAATGAATGCCTTTGT
1 AAATGAAAGCT-TTTGTGACAATCTCTATTAAA-GAAAGCCTTTGT
28481248 TGTTGTTTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
56 5 0.06
57 14 0.16
58 29 0.33
59 40 0.45
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.39
Consensus pattern (57 bp):
AAATGAAAGCTTTTGTGACAATCTCTATTAAAGAAAGCCTTTGTGGCGATCTTTGTT
Found at i:28481212 original size:29 final size:29
Alignment explanation
Indices: 28481088--28481320 Score: 170
Period size: 29 Copynumber: 8.1 Consensus size: 29
28481078 ACTATCTCTA
* * *
28481088 AAATG-AAGCCTTTGTGACTATCTCTGTT
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
*
28481116 AAA-GAAAGCCTTTGTGGTGATCTTTGTT
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
* * * * *
28481144 AAATGAAAGCTTTTGTGACAAATCTCTATT
1 AAATGAAAGCCTTTGTGGC-GATCTTTGTT
* *
28481174 ATAA-GGAAGTCTTTGTGGCGATCTTTGTT
1 A-AATGAAAGCCTTTGTGGCGATCTTTGTT
* * *
28481203 AAATGAAAGTCTTTGTGGCGATCTCTATT
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
* ** * *
28481232 AAATGAATGCCTTTGTTGTTG-TTTTTGTC
1 AAATGAAAGCCTTTG-TGGCGATCTTTGTT
* * *
28481261 AAA-GGAAGCCTTTGTGGCTATCTTTGTC
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
* * * *
28481289 AAAAGGATGCCTTTGTGGCTATCTTTGTT
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
28481318 AAA
1 AAA
28481321 GGAATGTCTT
Statistics
Matches: 161, Mismatches: 36, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
27 3 0.02
28 46 0.29
29 88 0.55
30 22 0.14
31 2 0.01
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (29 bp):
AAATGAAAGCCTTTGTGGCGATCTTTGTT
Found at i:28481316 original size:57 final size:57
Alignment explanation
Indices: 28481092--28481358 Score: 166
Period size: 57 Copynumber: 4.6 Consensus size: 57
28481082 TCTCTAAAAT
* * * * *
28481092 GAAGCCTTTGTGACTATCTCTGT-TAAAGAAAGCCTTTGTGG-TGATCTTTGTTAAATG
1 GAAGCCTTTGTGGCGATCTCTATCAAAAGAATGCCTTTGTGGCT-ATCTTTGTTAAA-G
* * * * * * * *
28481149 AAAGCTTTTGTGACAAATCTCTATTATAAGGAA-GTCTTTGTGGCGATCTTTGTTAAATG
1 GAAGCCTTTGTGGC-GATCTCTATCA-AAAGAATGCCTTTGTGGCTATCTTTGTTAAA-G
* * * * * * * * *
28481208 AAAGTCTTTGTGGCGATCTCTATTAAATGAATGCCTTTGTTGTTGTTTTTGTCAAAG
1 GAAGCCTTTGTGGCGATCTCTATCAAAAGAATGCCTTTGTGGCTATCTTTGTTAAAG
* * * *
28481265 GAAGCCTTTGTGGCTATCTTTGTCAAAAGGATGCCTTTGTGGCTATCTTTGTTAAAG
1 GAAGCCTTTGTGGCGATCTCTATCAAAAGAATGCCTTTGTGGCTATCTTTGTTAAAG
* * * *
28481322 GAATGTC-TTGTGGCAAAT-TCTATTAAAAGGATGCCTT
1 GAA-GCCTTTGTGGC-GATCTCTATCAAAAGAATGCCTT
28481359 GAAGACAACT
Statistics
Matches: 165, Mismatches: 38, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
57 88 0.53
58 38 0.23
59 34 0.21
60 5 0.03
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.39
Consensus pattern (57 bp):
GAAGCCTTTGTGGCGATCTCTATCAAAAGAATGCCTTTGTGGCTATCTTTGTTAAAG
Found at i:28486185 original size:60 final size:60
Alignment explanation
Indices: 28486036--28486194 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
28486026 CTTTTTTTTT
* * * * * *
28486036 AATTTTTAAAATTAAAACTAAATTGATAAATTTTGTAGATGTTATAGACTAAATTTATTA
1 AATTTTTAGAATTAGAATTAAATTGATAAATTCTGTAAATATTATAGACTAAATTTATTA
* * * * *
28486096 AATTTTTAGAATTCGAATTAAAATAATAAATTCTGTAAATATTAT-GGCTAAATTTATTG
1 AATTTTTAGAATTAGAATTAAATTGATAAATTCTGTAAATATTATAGACTAAATTTATTA
* * * *
28486155 AATTTATTAGATTTAGGATTAAATTGATAAAATGTGTAAA
1 AATTT-TTAGAATTAGAATTAAATTGATAAATTCTGTAAA
28486195 CATTGAAATG
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 17 0.21
60 63 0.79
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (60 bp):
AATTTTTAGAATTAGAATTAAATTGATAAATTCTGTAAATATTATAGACTAAATTTATTA
Found at i:28490164 original size:23 final size:24
Alignment explanation
Indices: 28490138--28490201 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 24
28490128 TAATTTTTAA
*
28490138 ATTTTA-AATTATTTAGTGATAAT
1 ATTTTAGAATTATTTAGTAATAAT
28490161 A-TTTAGAATTATTTAGTAATAAT
1 ATTTTAGAATTATTTAGTAATAAT
* **
28490184 ATTTAAGAAAAATTTAGT
1 ATTTTAGAATTATTTAGT
28490202 TAAATTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.11
23 18 0.51
24 13 0.37
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTTTAGAATTATTTAGTAATAAT
Found at i:28491070 original size:22 final size:23
Alignment explanation
Indices: 28491045--28491102 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
28491035 TTATTTATCC
*
28491045 ATTTATTTTATTTTCTTAA-AT-T
1 ATTTATTTTATTTT-TGAATATAT
*
28491067 ATTTTTTTTATTTTTGAATATAT
1 ATTTATTTTATTTTTGAATATAT
*
28491090 TTTTATTTTATTT
1 ATTTATTTTATTT
28491103 ACTTTTCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 15 0.50
23 12 0.40
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
ATTTATTTTATTTTTGAATATAT
Found at i:28491754 original size:17 final size:17
Alignment explanation
Indices: 28491732--28491765 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28491722 CTGAAAGAGT
28491732 TCCACATGGTTTGTCTA
1 TCCACATGGTTTGTCTA
28491749 TCCACATGGTTTGTCTA
1 TCCACATGGTTTGTCTA
28491766 AGCATGAAAC
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:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (17 bp):
TCCACATGGTTTGTCTA
Found at i:28498273 original size:23 final size:23
Alignment explanation
Indices: 28498247--28498298 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
28498237 TGATTTTTAA
*
28498247 ATTTTGAATCATTTAGTGATAAT
1 ATTTAGAATCATTTAGTGATAAT
*
28498270 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATCATTTAGTGATAAT
28498293 ATTTAG
1 ATTTAG
28498299 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (23 bp):
ATTTAGAATCATTTAGTGATAAT
Found at i:28498275 original size:13 final size:13
Alignment explanation
Indices: 28498257--28498298 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
28498247 ATTTTGAATC
28498257 ATTTAGTGATAAT
1 ATTTAGTGATAAT
*
28498270 ATTTA--GA-ATT
1 ATTTAGTGATAAT
28498280 ATTTAGTGATAAT
1 ATTTAGTGATAAT
28498293 ATTTAG
1 ATTTAG
28498299 GAAAAATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
ATTTAGTGATAAT
Found at i:28500117 original size:16 final size:16
Alignment explanation
Indices: 28500096--28500131 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
28500086 TTTGGTTCGT
28500096 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28500112 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28500128 TGTA
1 TGTA
28500132 ATAGTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28500456 original size:24 final size:24
Alignment explanation
Indices: 28500416--28500494 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 24
28500406 TAATTAGCAG
*
28500416 AAAT-TTGTT-TTGGTAAATTATT
1 AAATATTGTTATTGTTAAATTATT
28500438 AAATATTGTTATTGTTAAA-TATT
1 AAATATTGTTATTGTTAAATTATT
** *
28500461 -GTTATTGTTA-T-TTAATATATAAT
1 AAATATTGTTATTGTTAA-AT-TATT
28500484 AAATATTGTTA
1 AAATATTGTTA
28500495 ATAATTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 4 0.09
21 2 0.04
22 12 0.27
23 12 0.27
24 15 0.33
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (24 bp):
AAATATTGTTATTGTTAAATTATT
Found at i:28500457 original size:16 final size:16
Alignment explanation
Indices: 28500436--28500470 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
28500426 TGGTAAATTA
28500436 TTAAATATTGTTATTG
1 TTAAATATTGTTATTG
28500452 TTAAATATTGTTATTG
1 TTAAATATTGTTATTG
28500468 TTA
1 TTA
28500471 TTTAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (16 bp):
TTAAATATTGTTATTG
Found at i:28500642 original size:16 final size:16
Alignment explanation
Indices: 28500605--28500646 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28500595 TTAATCATAT
*
28500605 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28500621 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28500636 TTAAAATATAT
1 TTAAAATATAT
28500647 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28500653 original size:14 final size:15
Alignment explanation
Indices: 28500614--28500655 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28500604 TTTAAACATA
*
28500614 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28500629 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28500643 A-TATAATTTAATA
1 ATTATAATTAAATA
28500656 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28500740 original size:120 final size:121
Alignment explanation
Indices: 28500603--28500900 Score: 496
Period size: 120 Copynumber: 2.5 Consensus size: 121
28500593 TTTTAATCAT
*
28500603 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
28500668 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
*
28500725 A-TT-AACATAATTATTATTAAATATATTATAGTTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
28500788 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * *
28500844 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
28500901 TAAAATAATT
Statistics
Matches: 167, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
119 7 0.04
120 155 0.93
121 4 0.02
122 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:28500748 original size:259 final size:259
Alignment explanation
Indices: 28500281--28500748 Score: 608
Period size: 259 Copynumber: 1.8 Consensus size: 259
28500271 GATAAATGAT
*
28500281 TATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATAT
1 TATTGTTATTGTTATTTAAATTTGAATAAGATTATTATTATCAATAATAAATATTTTAATCATAT
*
28500346 TTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAATTATTAATAATT
66 TTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAATTATTAATAATT
* * * * ** * * * * * * * **
28500411 AGCAGAAATTTGTTTTGGTAAATTATTAAATATTGTTATTGTTAAATATTGTTATTGTTATTTAA
131 AACACAAATATGATTTACTAAATCATTAAATATTGATACTGTTAAATATTATAAATGTAACATAA
28500476 TATATAATAAATATTGTTAATAATTAATATATAAGTATTGTTATTAGCAGAAATTTATATTAAA
196 TATATAATAAATATTGTTAATAATTAATATATAAGTATTGTTATTAGCAGAAATTTATATTAAA
**
28500540 TATTGTTATTGTTATTTAAATTTGCTTAAGATTATTATTATCAATAATAAATATTTTAATCATAT
1 TATTGTTATTGTTATTTAAATTTGAATAAGATTATTATTATCAATAATAAATATTTTAATCATAT
*
28500605 TTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
66 TTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAAT-AAATTATTAATAAT
* **
28500670 TAATATTCTTATATGAATTTACTCAAATCA-T-AATATATGATACTG-TAAA-A-TATAAAT-TA
130 TAACA--CAAATATG-ATTTACT-AAATCATTAAATAT-TGATACTGTTAAATATTATAAATGTA
*
28500729 ACATAAT-TATTATTAAATAT
190 ACATAATATA-TAATAAATAT
28500749 ATTATAGTTA
Statistics
Matches: 178, Mismatches: 24, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
258 2 0.01
259 126 0.71
260 20 0.11
261 1 0.01
262 13 0.07
263 11 0.06
264 5 0.03
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (259 bp):
TATTGTTATTGTTATTTAAATTTGAATAAGATTATTATTATCAATAATAAATATTTTAATCATAT
TTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAATTATTAATAATT
AACACAAATATGATTTACTAAATCATTAAATATTGATACTGTTAAATATTATAAATGTAACATAA
TATATAATAAATATTGTTAATAATTAATATATAAGTATTGTTATTAGCAGAAATTTATATTAAA
Found at i:28500825 original size:61 final size:61
Alignment explanation
Indices: 28500640--28500827 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
28500630 TTATAATTAA
28500640 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
28500701 AATATATGATACT-GTAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAGTTA
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTCA-AATCA
*
28500759 A
61 T
28500760 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
28500821 AATATAT
1 AATATAT
28500828 GATACTATAA
Statistics
Matches: 93, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
57 4 0.04
58 5 0.05
59 26 0.28
60 16 0.17
61 33 0.35
62 5 0.05
63 4 0.04
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:28500986 original size:24 final size:25
Alignment explanation
Indices: 28500940--28500987 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
28500930 TTATGAATTT
28500940 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
28500966 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
28500988 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:28504534 original size:21 final size:22
Alignment explanation
Indices: 28504484--28504534 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
28504474 CTTTTATAAC
*
28504484 ATTTTAA-ATTTAAATTTCTTT
1 ATTTTAATATTTAAATTTCTTG
**
28504505 ATTAAAATA-TTAAATTTCTTG
1 ATTTTAATATTTAAATTTCTTG
28504526 ATTTTAATA
1 ATTTTAATA
28504535 AAATATTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTAATATTTAAATTTCTTG
Found at i:28504567 original size:25 final size:25
Alignment explanation
Indices: 28504539--28504661 Score: 150
Period size: 25 Copynumber: 5.1 Consensus size: 25
28504529 TTAATAAAAT
28504539 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
* *
28504564 ATT--AGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAAT-TATTG
28504587 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
* *
28504612 ATT--AGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAAT-TATTG
28504635 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
28504660 AT
1 AT
28504662 GTAATTTTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
23 36 0.44
24 8 0.10
25 38 0.46
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (25 bp):
ATTAAAGTCCTTATTTTAATTATTG
Found at i:28504574 original size:23 final size:24
Alignment explanation
Indices: 28504543--28504661 Score: 138
Period size: 23 Copynumber: 5.0 Consensus size: 24
28504533 TAAAATATTA
28504543 AAGTCCTTATTTTAATTATTGATT
1 AAGTCCTTATTTTAATTATTGATT
* *
28504567 -AGTCCTTATTTTAATAAAAT-ATT
1 AAGTCCTTATTTTAAT-TATTGATT
28504590 AAAGTCCTTATTTTAATTATTGATT
1 -AAGTCCTTATTTTAATTATTGATT
* *
28504615 -AGTCCTTATTTTAATAAAAT-ATT
1 AAGTCCTTATTTTAAT-TATTGATT
28504638 AAAGTCCTTATTTTAATTATTGAT
1 -AAGTCCTTATTTTAATTATTGAT
28504662 GTAATTTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
23 36 0.46
24 8 0.10
25 35 0.44
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.50
Consensus pattern (24 bp):
AAGTCCTTATTTTAATTATTGATT
Found at i:28504578 original size:48 final size:48
Alignment explanation
Indices: 28504526--28504661 Score: 272
Period size: 48 Copynumber: 2.8 Consensus size: 48
28504516 AAATTTCTTG
28504526 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
1 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
28504574 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
1 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
28504622 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGAT
1 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGAT
28504662 GTAATTTTTA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.50
Consensus pattern (48 bp):
ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
Found at i:28509167 original size:13 final size:13
Alignment explanation
Indices: 28509149--28509199 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
28509139 TTTGACAATA
28509149 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
28509162 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
*
28509175 -TTGTGGAAAAGTG
1 CTT-TTGAAAAGTG
28509188 CTTTTGAAAAGT
1 CTTTTGAAAAGT
28509200 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:28510892 original size:32 final size:32
Alignment explanation
Indices: 28510856--28510924 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
28510846 TGATATTGCG
*
28510856 ATGTCTTTGATATGTGAGGATGGGTGATTGTA
1 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
28510888 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
1 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
28510920 ATGTC
1 ATGTC
28510925 AGTTTGGTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (32 bp):
ATGTCTTTGATATGTGAGGATAGGTGATTGTA
Found at i:28518351 original size:18 final size:18
Alignment explanation
Indices: 28518328--28518377 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
28518318 CTAAGCAAAG
*
28518328 GAAACAATCAATTTTTAT
1 GAAACAATCAATTTTCAT
28518346 GAAACAATCAATTTTCAT
1 GAAACAATCAATTTTCAT
28518364 GAAACAATCTAATT
1 GAAACAATC-AATT
28518378 ACAATATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (18 bp):
GAAACAATCAATTTTCAT
Found at i:28521664 original size:17 final size:17
Alignment explanation
Indices: 28521620--28521676 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
28521610 TGAGATAACA
28521620 TAAA-TAAACAATTAAA-
1 TAAATTAAA-AATTAAAT
*
28521636 TAAATCAAAAATTAAAT
1 TAAATTAAAAATTAAAT
*
28521653 TAAATTAGAAATTAAAT
1 TAAATTAAAAATTAAAT
28521670 TCAAATT
1 T-AAATT
28521677 TTATAAACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.31
17 19 0.54
18 5 0.14
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAATTAAAAATTAAAT
Found at i:28523671 original size:12 final size:13
Alignment explanation
Indices: 28523646--28523676 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
28523636 TGCAAATGAA
28523646 TCATTTCTCATTT
1 TCATTTCTCATTT
28523659 TCATTTC-CATTT
1 TCATTTCTCATTT
28523671 TCATTT
1 TCATTT
28523677 TGAGAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:28531391 original size:18 final size:19
Alignment explanation
Indices: 28531360--28531395 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28531350 ACCCATTAGG
28531360 TTAATTTAGGTTAATTAAT
1 TTAATTTAGGTTAATTAAT
*
28531379 TTAA-TTAGTTTAATTAA
1 TTAATTTAGGTTAATTAA
28531396 AATATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TTAATTTAGGTTAATTAAT
Found at i:28536330 original size:6 final size:6
Alignment explanation
Indices: 28536312--28536349 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
28536302 TATATCCCAA
28536312 TTTTAT CTTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
28536350 CGCATTTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:28541836 original size:21 final size:22
Alignment explanation
Indices: 28541791--28541836 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
28541781 TAGATTTTTT
*
28541791 AATTTTAAATAGTTTTATTATA
1 AATTTTAAATAGTTTTATTAGA
* *
28541813 AATTTT-AATATTTTTATTGGA
1 AATTTTAAATAGTTTTATTAGA
28541834 AAT
1 AAT
28541837 AGAATAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (22 bp):
AATTTTAAATAGTTTTATTAGA
Found at i:28551984 original size:34 final size:34
Alignment explanation
Indices: 28551946--28552015 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
28551936 AAACATGAAA
28551946 TATTTGTT-AATCATTGGATAACCTAAGGAAGTGG
1 TATTT-TTCAATCATTGGATAACCTAAGGAAGTGG
* *
28551980 TATTTTTCTATCATTGGATAACCTAAGGTAGTGG
1 TATTTTTCAATCATTGGATAACCTAAGGAAGTGG
28552014 TA
1 TA
28552016 GTACCTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 2 0.06
34 31 0.94
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (34 bp):
TATTTTTCAATCATTGGATAACCTAAGGAAGTGG
Found at i:28554766 original size:29 final size:29
Alignment explanation
Indices: 28554733--28554788 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
28554723 AAGGCCGGTT
28554733 TTTTTTCAA-AATTTACCGAAATGGGCCGG
1 TTTTTT-AATAATTTACCGAAATGGGCCGG
* *
28554762 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGAAATGGGCC
28554789 ATTTTCCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCGG
Found at i:28579164 original size:25 final size:24
Alignment explanation
Indices: 28579135--28579200 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
28579125 TCCTATACAT
28579135 GTATGCTCATACGAGCTATGAATCG
1 GTATGCTCATACGAGCTAT-AATCG
* *
28579160 GTATGCTCTTACGAGCTGTAATCG
1 GTATGCTCATACGAGCTATAATCG
*
28579184 GTAAGCTCATACGAGCT
1 GTATGCTCATACGAGCT
28579201 GAGTAACAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 20 0.54
25 17 0.46
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (24 bp):
GTATGCTCATACGAGCTATAATCG
Found at i:28579191 original size:24 final size:24
Alignment explanation
Indices: 28579139--28579227 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 24
28579129 ATACATGTAT
* *
28579139 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTGT-AATCGGTAA
*
28579164 GCTCTTACGAGCTGTAATCGGTAA
1 GCTCATACGAGCTGTAATCGGTAA
*
28579188 GCTCATACGAGCTGAGTAA-CAGTAA
1 GCTCATACGAGCT--GTAATCGGTAA
*
28579213 GCTCATTCGAGCTGT
1 GCTCATACGAGCTGT
28579228 GTTGTGTCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.04
24 20 0.36
25 30 0.54
26 4 0.07
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (24 bp):
GCTCATACGAGCTGTAATCGGTAA
Found at i:28583263 original size:19 final size:20
Alignment explanation
Indices: 28583239--28583276 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28583229 TAATTTTTGA
28583239 AGTTTATT-CAATTTAGTCT
1 AGTTTATTGCAATTTAGTCT
28583258 AGTTTATTGCAATTTAGTC
1 AGTTTATTGCAATTTAGTC
28583277 GCTGACCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (20 bp):
AGTTTATTGCAATTTAGTCT
Found at i:28583729 original size:20 final size:21
Alignment explanation
Indices: 28583704--28583742 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28583694 ATGAAAGAAA
28583704 AACCT-AAACTAAAGCTTTCT
1 AACCTAAAACTAAAGCTTTCT
*
28583724 AACCTAAAACTACAGCTTT
1 AACCTAAAACTAAAGCTTT
28583743 TTTTTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (21 bp):
AACCTAAAACTAAAGCTTTCT
Found at i:28585705 original size:19 final size:19
Alignment explanation
Indices: 28585681--28585719 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28585671 TTTTTTAACT
28585681 ATTTTAAAATTTCATTAGA
1 ATTTTAAAATTTCATTAGA
* *
28585700 ATTTTATAATTTTATTAGA
1 ATTTTAAAATTTCATTAGA
28585719 A
1 A
28585720 GAGGCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTTTAAAATTTCATTAGA
Found at i:28586716 original size:17 final size:18
Alignment explanation
Indices: 28586689--28586723 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28586679 AATTCAGTTT
*
28586689 GAAATTAAATAATTAATA
1 GAAATTAAATAATAAATA
28586707 GAAA-TAAATAATAAATA
1 GAAATTAAATAATAAATA
28586724 TTATATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
GAAATTAAATAATAAATA
Found at i:28589892 original size:42 final size:42
Alignment explanation
Indices: 28589833--28589917 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
28589823 CTTGATTAAT
28589833 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
1 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
28589875 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
1 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
28589917 T
1 T
28589918 CAGTTATTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.16, C:0.12, G:0.33, T:0.39
Consensus pattern (42 bp):
TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
Found at i:28597665 original size:42 final size:40
Alignment explanation
Indices: 28597618--28597700 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
28597608 TTTCGAGATG
* * *
28597618 TGATTTCACGTAAGACCATGTTTGGGACATTGGCATCGTATA
1 TGATTTCACGTAAGACC-TGTCTGAGACAGTGGCATCG-ATA
**
28597660 TGATTTCGTGTAAGACCTGTCTGAGACAGTGGCATCGATA
1 TGATTTCACGTAAGACCTGTCTGAGACAGTGGCATCGATA
28597700 T
1 T
28597701 CTTATAACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 4 0.11
41 17 0.47
42 15 0.42
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TGATTTCACGTAAGACCTGTCTGAGACAGTGGCATCGATA
Found at i:28598332 original size:25 final size:25
Alignment explanation
Indices: 28598296--28598382 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
28598286 AAATTGGGGC
28598296 TTAATTGCTGTCCATTTTTTAGCATA
1 TTAA-TGCTGTCCATTTTTTAGCATA
* **
28598322 TTAATGCTGTCCAAATTAGT-GC-T-
1 TTAATGCTGTCC-ATTTTTTAGCATA
* *
28598345 TAAATGCTTTCCATTTTTTAGCATA
1 TTAATGCTGTCCATTTTTTAGCATA
*
28598370 TTAGTGCTGTCCA
1 TTAATGCTGTCCA
28598383 AATTAGTGCT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
22 4 0.09
23 12 0.26
24 2 0.04
25 20 0.43
26 8 0.17
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (25 bp):
TTAATGCTGTCCATTTTTTAGCATA
Found at i:28598350 original size:23 final size:23
Alignment explanation
Indices: 28598324--28598405 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
28598314 TTAGCATATT
28598324 AATGCTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
* * ** *
28598347 AATGCTTTCC-ATTTTTTAGCATATT
1 AATGCTGTCCAAATTAGT-GC-T-TA
*
28598372 AGTGCTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
28598395 AATGCTGTCCA
1 AATGCTGTCCA
28598406 TTTTTTTTGA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
22 4 0.09
23 22 0.51
24 2 0.05
25 11 0.26
26 4 0.09
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (23 bp):
AATGCTGTCCAAATTAGTGCTTA
Found at i:28598358 original size:48 final size:49
Alignment explanation
Indices: 28598277--28598505 Score: 300
Period size: 48 Copynumber: 4.7 Consensus size: 49
28598267 TGATGATAAG
* * *
28598277 ATGCTGTCCAAATTGGGGCTTAATTGCTGTCCATTTTTT-AGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
*
28598325 ATGCTGTCCAAATTAGTGCTTAAATGCTTTCCATTTTTT-AGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
* *
28598373 GTGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTTGAGCACATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCA--TTTTTTGAGCATATTA
* * * * *
28598424 ATGCTATCCAAATTAATGCTTAATTGCTATCCATTTTTTGAGTATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
* * *
28598473 ATGCTGTCCAAATTGGTACTTAAATGTTGTCCA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCA
28598506 AATATTTGTG
Statistics
Matches: 157, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
48 75 0.48
49 40 0.25
50 6 0.04
51 36 0.23
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (49 bp):
ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
Found at i:28598457 original size:99 final size:97
Alignment explanation
Indices: 28598277--28598505 Score: 316
Period size: 99 Copynumber: 2.3 Consensus size: 97
28598267 TGATGATAAG
* * * * *
28598277 ATGCTGTCCAAATTGGGGCTTAATTGCTGTCCATTTTTTAGCATATTAATGCTGTCCAAATTAGT
1 ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCACATTAATGCTATCCAAATTAAT
*
28598342 GCTTAAATGCTTTCCATTTTTT-AGCATATTA
66 GCTTAAATGCTATCCATTTTTTGAGCATATTA
* *
28598373 GTGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTTGAGCACATTAATGCTATCCAAATT
1 ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCA--TTTTTT-AGCACATTAATGCTATCCAAATT
* *
28598438 AATGCTTAATTGCTATCCATTTTTTGAGTATATTA
63 AATGCTTAAATGCTATCCATTTTTTGAGCATATTA
* *
28598473 ATGCTGTCCAAATTGGTACTTAAATGTTGTCCA
1 ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCA
28598506 AATATTTGTG
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
96 29 0.25
98 6 0.05
99 43 0.37
100 37 0.32
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (97 bp):
ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCACATTAATGCTATCCAAATTAAT
GCTTAAATGCTATCCATTTTTTGAGCATATTA
Found at i:28605589 original size:42 final size:42
Alignment explanation
Indices: 28605479--28605590 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
28605469 TGTGATCTAG
* ** *
28605479 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTCG
1 TGTAAGACCATGTCTGGGACAGTGGCATCGTATATGATAACA
* * * *
28605521 TGGAAGACCCTGTCTGAGACAGTGGCATCGATATATTATAACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCG-TATATGATAACA
* *
28605564 TGTAAGACCATATCTGGGATA-TGGCAT
1 TGTAAGACCATGTCTGGGACAGTGGCAT
28605591 TGTACGAGCT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 32 0.57
43 24 0.43
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGTATATGATAACA
Found at i:28606186 original size:25 final size:25
Alignment explanation
Indices: 28606151--28606237 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
28606141 AAATTGGTGC
28606151 TTAATTGCTGTCCATTTTTTAGCATA
1 TTAA-TGCTGTCCATTTTTTAGCATA
* **
28606177 TTAATGCTGTCCAAATTAGT-GC-T-
1 TTAATGCTGTCC-ATTTTTTAGCATA
* *
28606200 TAAATGCTTTCCATTTTTTAGCATA
1 TTAATGCTGTCCATTTTTTAGCATA
*
28606225 TTAGTGCTGTCCA
1 TTAATGCTGTCCA
28606238 AATTAGTGCT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
22 4 0.09
23 12 0.26
24 2 0.04
25 20 0.43
26 8 0.17
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (25 bp):
TTAATGCTGTCCATTTTTTAGCATA
Found at i:28606205 original size:23 final size:23
Alignment explanation
Indices: 28606179--28606260 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
28606169 TTAGCATATT
28606179 AATGCTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
* * ** *
28606202 AATGCTTTCC-ATTTTTTAGCATATT
1 AATGCTGTCCAAATTAGT-GC-T-TA
*
28606227 AGTGCTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
*
28606250 AATGTTGTCCA
1 AATGCTGTCCA
28606261 TTTTTTTTGA
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
22 4 0.10
23 21 0.50
24 2 0.05
25 11 0.26
26 4 0.10
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (23 bp):
AATGCTGTCCAAATTAGTGCTTA
Found at i:28606213 original size:48 final size:48
Alignment explanation
Indices: 28606136--28606359 Score: 288
Period size: 48 Copynumber: 4.6 Consensus size: 48
28606126 GATAAGATGT
* *
28606136 TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTAATGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
* *
28606184 TGTCCAAATTAGTGCTTAAATGCTTTCCATTTTTTAGCATATTAGTGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
*
28606232 TGTCCAAATTAGTGCTTAAATGTTGTCCATTTTTTTTGAGCATATTAATGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCA--TTTTTT-AGCATATTAATGC
* * * *
28606283 TATCCAAATT-GATGCTTAATTGCTGTCCATTTTTGAGTATATTAATGC
1 TGTCCAAATTAG-TGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
* * * *
28606331 TGTCCAAATTGGTACGTAAATGTTGTCCA
1 TGTCCAAATTAGTGCTTAAATGCTGTCCA
28606360 AATATTTGTG
Statistics
Matches: 154, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
48 105 0.68
49 6 0.04
50 7 0.05
51 36 0.23
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (48 bp):
TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
Found at i:28606312 original size:99 final size:96
Alignment explanation
Indices: 28606136--28606359 Score: 306
Period size: 99 Copynumber: 2.3 Consensus size: 96
28606126 GATAAGATGT
* * *
28606136 TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTAATGCTGTCCAAATTAGTGCTT
1 TGTCCAAATTGGTGCTTAAATGTTGTCCATTTTTTAGCATATTAATGCTATCCAAATTAGTGCTT
* * *
28606201 AAATGCTTTCCATTTTTTAGCATATTAGTGC
66 AAATGCTGTCCATTTTTGAGCATATTAATGC
*
28606232 TGTCCAAATTAGTGCTTAAATGTTGTCCATTTTTTTTGAGCATATTAATGCTATCCAAATT-GAT
1 TGTCCAAATTGGTGCTTAAATGTTGTCCA--TTTTTT-AGCATATTAATGCTATCCAAATTAG-T
* *
28606296 GCTTAATTGCTGTCCATTTTTGAGTATATTAATGC
62 GCTTAAATGCTGTCCATTTTTGAGCATATTAATGC
* *
28606331 TGTCCAAATTGGTACGTAAATGTTGTCCA
1 TGTCCAAATTGGTGCTTAAATGTTGTCCA
28606360 AATATTTGTG
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
96 26 0.23
98 7 0.06
99 79 0.71
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (96 bp):
TGTCCAAATTGGTGCTTAAATGTTGTCCATTTTTTAGCATATTAATGCTATCCAAATTAGTGCTT
AAATGCTGTCCATTTTTGAGCATATTAATGC
Found at i:28607480 original size:27 final size:27
Alignment explanation
Indices: 28607419--28607481 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
28607409 CTGAAAAATG
* *
28607419 AATCAA-TCCAAAAATAATAGAGACTC
1 AATCAATTCCAAAAAGAATAGAAACTC
* *
28607445 AATTC-ATTCGAAAAAGAATAGAAACTT
1 AA-TCAATTCCAAAAAGAATAGAAACTC
28607472 AATCAATTCC
1 AATCAATTCC
28607482 CAATGATTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (27 bp):
AATCAATTCCAAAAAGAATAGAAACTC
Found at i:28621224 original size:25 final size:24
Alignment explanation
Indices: 28621196--28621253 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
28621186 TATTATCAAT
* *
28621196 AATTTTATGAAATTATATATTATTA
1 AATTATATGAAATAATA-ATTATTA
*
28621221 AATTATATGTAATAATAATTATTTTA
1 AATTATATGAAATAATAATTA--TTA
28621247 AATTATA
1 AATTATA
28621254 CAAATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 14 0.50
26 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTATATGAAATAATAATTATTA
Found at i:28621320 original size:47 final size:49
Alignment explanation
Indices: 28621196--28621321 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 49
28621186 TATTATCAAT
* *
28621196 AATTTTATGAAATTATATATTATTAAATTATATGTAATAATAATTATTTTA
1 AATTTTATCAAATCATATATT-TT-AATTATATGTAATAATAATTATTTTA
* *** * *
28621247 AATTATA-CAAATTCATATAAGATAATT-TAT-TAGTTATAATTATTTTA
1 AATTTTATCAAA-TCATATATTTTAATTATATGTAATAATAATTATTTTA
*
28621294 AATTTTATTAAATCATATATTTTAATTA
1 AATTTTATCAAATCATATATTTTAATTA
28621322 AAATATATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
47 33 0.56
48 6 0.10
49 4 0.07
50 4 0.07
51 12 0.20
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (49 bp):
AATTTTATCAAATCATATATTTTAATTATATGTAATAATAATTATTTTA
Found at i:28621460 original size:25 final size:26
Alignment explanation
Indices: 28621428--28621482 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
28621418 TTATTAAATT
*
28621428 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
28621453 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
28621478 A-ATAT
1 ATATAT
28621483 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:28621650 original size:39 final size:41
Alignment explanation
Indices: 28621607--28621706 Score: 105
Period size: 44 Copynumber: 2.4 Consensus size: 41
28621597 TCTATTATGT
28621607 TATTACACCTCTATTC-CATTCAACCAAACACAAGA-TTAC
1 TATTACACCTCTATTCACATTCAACCAAACACAAGATTTAC
* *** *
28621646 TATTACGCCTCTATTTCATTACATTCAACCAAACAGTTGATTTGC
1 TATTACACCTCTA-TTC---ACATTCAACCAAACACAAGATTTAC
28621691 TATTACACCTCTATTC
1 TATTACACCTCTATTC
28621707 TATTACACCT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
39 12 0.24
40 3 0.06
44 19 0.39
45 15 0.31
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (41 bp):
TATTACACCTCTATTCACATTCAACCAAACACAAGATTTAC
Found at i:28621704 original size:45 final size:44
Alignment explanation
Indices: 28621616--28621713 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 44
28621606 TTATTACACC
* *
28621616 TCTATTCCATTCAACCAAACACAAGATTACTATTACGCCTCTAT
1 TCTATTACATTCAACCAAACACAAGATTACTATTACACCTCTAT
*** *
28621660 T-TCATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTAT
1 TCT-ATTACATTCAACCAAACACAAGA-TTACTATTACACCTCTAT
28621705 TCTATTACA
1 TCTATTACA
28621714 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 1 0.02
44 20 0.44
45 23 0.51
46 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.36
Consensus pattern (44 bp):
TCTATTACATTCAACCAAACACAAGATTACTATTACACCTCTAT
Found at i:28621739 original size:16 final size:16
Alignment explanation
Indices: 28621694--28621745 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
28621684 GATTTGCTAT
* * *
28621694 TACACCTCTATTCTAT
1 TACACCTCTAATCCAA
28621710 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28621726 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28621742 TACA
1 TACA
28621746 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28626593 original size:18 final size:19
Alignment explanation
Indices: 28626570--28626611 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
28626560 AAAAACTCAA
28626570 TTAAAACATT-TTTGA-AAT
1 TTAAAA-ATTATTTGAGAAT
28626588 TTAAAAATTATTTGAGAAT
1 TTAAAAATTATTTGAGAAT
28626607 TTAAA
1 TTAAA
28626612 TCATAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
19 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (19 bp):
TTAAAAATTATTTGAGAAT
Found at i:28626622 original size:20 final size:18
Alignment explanation
Indices: 28626580--28626622 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
28626570 TTAAAACATT
*
28626580 TTTGAAATTTAAAAATTA
1 TTTGAAATTTAAAAATAA
*
28626598 TTTGAGAATTTAAATCATAA
1 TTTGA-AATTTAAA-AATAA
28626618 TTTGA
1 TTTGA
28626623 TGATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (18 bp):
TTTGAAATTTAAAAATAA
Found at i:28647019 original size:9 final size:9
Alignment explanation
Indices: 28647002--28647038 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28646992 TGAGTTTTAG
28647002 AATTCGAAT
1 AATTCGAAT
*
28647011 AACTCGAAT
1 AATTCGAAT
28647020 AATTCGAAT
1 AATTCGAAT
28647029 AATTCGAAT
1 AATTCGAAT
28647038 A
1 A
28647039 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28654745 original size:27 final size:27
Alignment explanation
Indices: 28654715--28654773 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
28654705 TATCAAAGAA
*
28654715 ACCAAATCTCAAACATTAATAAACCAC
1 ACCAAACCTCAAACATTAATAAACCAC
28654742 ACCAAACCTCAAACATTAATAAACCAC
1 ACCAAACCTCAAACATTAATAAACCAC
28654769 ACCAA
1 ACCAA
28654774 CTTTATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (27 bp):
ACCAAACCTCAAACATTAATAAACCAC
Found at i:28663007 original size:617 final size:617
Alignment explanation
Indices: 28661834--28663070 Score: 2339
Period size: 617 Copynumber: 2.0 Consensus size: 617
28661824 TGTATTTCTA
* *
28661834 AACATTTTACACACTAGGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAACCCGTTAGGGTT
1 AACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAAACCGTTAGGGTT
*
28661899 AAACGAAAACTCATATGAGTTAACAAAAGCTCGTGAGAGCTAAACGGAAAGTAAATACGAAAGTT
66 AAACGAAAACTCATATGAGTTAACAAAAGCTCGTGAGAGCTAAACGGAAAGTAAATACAAAAGTT
*
28661964 CGCAACAAATGCCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
131 CGCAACAAATACCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
*
28662029 GACTGTACTCAATCCCGCGTTCCGTTTACTTCGAACGTTCAATTCAATTTCATAGCTTTAACAAT
196 GACTGTACTCAATCCCGCGTTCCGTTTACTTCGAACGTTCAATTCAATTTCATAGCTGTAACAAT
28662094 AATTTTATTTTCAACAAACGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
261 AATTTTATTTTCAACAAACGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
*
28662159 TTAAATTTCAACTATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
326 TTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
* * *
28662224 TCTGTTAATTTCCCTTTTTTATGATTATCTACGGGATCTTGATTTAAAATGTTTATGACTTGATT
391 TCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGATT
28662289 TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
456 TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
28662354 CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
521 CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
*
28662419 CACAAGCTCACTTGTCAGATTTGGTGGTCTCG
586 CACAAGCTCACTTGTCAAATTTGGTGGTCTCG
28662451 AACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAAACCGTTAGGGTT
1 AACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAAACCGTTAGGGTT
**
28662516 AAACGAAAACTCATATGAGTTAACGGAAGCTCGTGAGAGCTAAACGGAAAGTAAATACAAAAGTT
66 AAACGAAAACTCATATGAGTTAACAAAAGCTCGTGAGAGCTAAACGGAAAGTAAATACAAAAGTT
*
28662581 CGCAACAAATACCGAACCTTGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
131 CGCAACAAATACCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
*
28662646 GACTGTACTCAATCCCGCGTTCCGTTTGCTTCGAACGTTCAATTCAATTTCATAGCTGTAACAAT
196 GACTGTACTCAATCCCGCGTTCCGTTTACTTCGAACGTTCAATTCAATTTCATAGCTGTAACAAT
*
28662711 AATTTTATTTTCAACAAATGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
261 AATTTTATTTTCAACAAACGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
28662776 TTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
326 TTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
28662841 TCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGATT
391 TCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGATT
28662906 TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
456 TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
28662971 CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
521 CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
28663036 CACAAGCTCACTTGTCAAATTTGGTGGTCTCG
586 CACAAGCTCACTTGTCAAATTTGGTGGTCTCG
28663068 AAC
1 AAC
28663071 CACTATTTCT
Statistics
Matches: 605, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
617 605 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (617 bp):
AACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAAACCGTTAGGGTT
AAACGAAAACTCATATGAGTTAACAAAAGCTCGTGAGAGCTAAACGGAAAGTAAATACAAAAGTT
CGCAACAAATACCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
GACTGTACTCAATCCCGCGTTCCGTTTACTTCGAACGTTCAATTCAATTTCATAGCTGTAACAAT
AATTTTATTTTCAACAAACGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
TTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
TCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGATT
TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
CACAAGCTCACTTGTCAAATTTGGTGGTCTCG
Found at i:28676089 original size:73 final size:73
Alignment explanation
Indices: 28675970--28676138 Score: 254
Period size: 73 Copynumber: 2.3 Consensus size: 73
28675960 TTCACAAGCC
* *
28675970 AAAATAGTCGTAGAAAATAACAAAACTAAGCATAAGGAACAATTAAAGAGAAGAATAGAAGAAGA
1 AAAATAGTCGTAGAAAACAACAAAACTAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAG-
28676035 T-AACAACT
65 TGAACAACT
*
28676043 AAAATAGTCATAGAAAACAACTAAAA-TAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAG
1 AAAATAGTCGTAGAAAACAAC-AAAACTAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAG
28676107 TGAACAACT
65 TGAACAACT
*
28676116 AAAACAGTCGTAGAAGAA-AACAA
1 AAAATAGTCGTAGAA-AACAACAA
28676139 GCTCACCAGT
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
72 3 0.03
73 79 0.90
74 6 0.07
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.14
Consensus pattern (73 bp):
AAAATAGTCGTAGAAAACAACAAAACTAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAGT
GAACAACT
Found at i:28678830 original size:27 final size:27
Alignment explanation
Indices: 28678786--28678843 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
28678776 AGTTTGCCAG
28678786 AAAGACATTCCTTTCATATTCTACCAC
1 AAAGACATTCCTTTCATATTCTACCAC
* * *
28678813 AAAGGCATT-CTTTCCATATTGTGCCAC
1 AAAGACATTCCTTT-CATATTCTACCAC
28678840 AAAG
1 AAAG
28678844 CTGTTCCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAGACATTCCTTTCATATTCTACCAC
Found at i:28683452 original size:28 final size:28
Alignment explanation
Indices: 28683388--28683453 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
28683378 TGGTTTATTG
* *
28683388 ATTTATTTTGTTTTTTTTATTTTTCCTT
1 ATTTATTTTATTTTTTTTATTTTTCCTA
28683416 ATTTA-TTTATTTATTTTTATTTCTT-C-A
1 ATTTATTTTATTT-TTTTTATTT-TTCCTA
28683443 ATTTATTTTAT
1 ATTTATTTTAT
28683454 GGTTTTTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 11 0.33
28 20 0.61
29 2 0.06
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (28 bp):
ATTTATTTTATTTTTTTTATTTTTCCTA
Found at i:28687457 original size:20 final size:19
Alignment explanation
Indices: 28687432--28687486 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
28687422 ACCAAGCAGG
*
28687432 GGTATCGATAATTTTTGAAA
1 GGTATCGATACTTTTT-AAA
*
28687452 GGTATCGATACTTTGTTAAG
1 GGTATCGATACTTT-TTAAA
28687472 GGTATCGATACTTTT
1 GGTATCGATACTTTT
28687487 ATTTTTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (19 bp):
GGTATCGATACTTTTTAAA
Found at i:28687629 original size:93 final size:92
Alignment explanation
Indices: 28687452--28687630 Score: 231
Period size: 93 Copynumber: 1.9 Consensus size: 92
28687442 ATTTTTGAAA
*
28687452 GGTATCGATACTTTGTTAAGGGTATCGATACTTTTATTTTTGTTTAATTTTCCAAAATATCGAAG
1 GGTATCGATACTTTGTTAAGGATATCGATACTTTTATTTTTGTTTAATTTTCCAAAATATCGAAG
*
28687517 CTCAAATTGGTATTGATACCAGGTCAT
66 CTCAAATTGGTATCGATACCAGGTCAT
*
28687544 GGTATCGATACTTT-TATAAGGATATCGATACTTTTGATTTTT-TCTATAGTTTT-CAAAACT-T
1 GGTATCGATACTTTGT-TAAGGATATCGATACTTTT-ATTTTTGT-T-TAATTTTCCAAAA-TAT
* **
28687605 TGAAGCTCATTTTGGTATCGATACCA
61 CGAAGCTCAAATTGGTATCGATACCA
28687631 ATCATAGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
91 1 0.01
92 33 0.43
93 35 0.46
94 7 0.09
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (92 bp):
GGTATCGATACTTTGTTAAGGATATCGATACTTTTATTTTTGTTTAATTTTCCAAAATATCGAAG
CTCAAATTGGTATCGATACCAGGTCAT
Done.