Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 159 of 202
Found at i:49707856 original size:27 final size:27
Alignment explanation
Indices: 49707818--49708362 Score: 545
Period size: 27 Copynumber: 20.2 Consensus size: 27
49707808 ATTTGTGGGA
* *
49707818 AAAATTACCGAAATACTCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
*
49707845 AAAATTATCGAAATACCCTTGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
49707872 AAAATTATCGAAATACCTTCGATGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
49707899 AAAATTATCGAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
49707926 AAAATTA-CTGAAACACCCTAGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
* **
49707953 AAAATTA-CTAAAATACCCTTAAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
*
49707980 AAAATTATCGAAACA-CCTCTGAAGGGT
1 AAAATTATCGAAATACCCTC-GAAGGGT
*
49708007 AAAATTATCAAAATACCC-CTGAAGGGT
1 AAAATTATCGAAATACCCTC-GAAGGGT
* *
49708034 AAAATTATCAAAATACCCTC-AATAGGT
1 AAAATTATCGAAATACCCTCGAA-GGGT
* ** *
49708061 AAAATTA-CTAAAATACCCTTAAAAGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
* * *
49708088 AAAATTATCGAAATAACCTCAAATGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
*
49708115 AAAATTA-CTGAAATACCCCCGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
**
49708142 AAAATTATCGAAATACCCTTAAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
** *
49708169 AAAATTA-CTGAAGCACCC-CTAAAGGGT
1 AAAATTATC-GAAATACCCTC-GAAGGGT
* *
49708196 AAAATTA-CTAAAATTCCCTCGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
* * *
49708223 AAAATTATCGAAACACCCCCAAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* * *
49708250 AAAAATTATCGACATACCCTTGAAGGGA
1 -AAAATTATCGAAATACCCTCGAAGGGT
*
49708278 AAAATTA-CCAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
49708304 AAAATTATTGAAATGCCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* * *
49708331 AAAATTATTGAAATACCCCCGAGGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
49708358 AAAAT
1 AAAAT
49708363 GACCGTTTAC
Statistics
Matches: 439, Mismatches: 62, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
26 31 0.07
27 377 0.86
28 31 0.07
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (27 bp):
AAAATTATCGAAATACCCTCGAAGGGT
Found at i:49708618 original size:52 final size:52
Alignment explanation
Indices: 49708556--49708662 Score: 180
Period size: 52 Copynumber: 2.1 Consensus size: 52
49708546 TTTGCCACAA
49708556 ATACTGTTACTGGCAGCTTTGCTGC-TATACTGATACTGGCAGCTCTACTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCGT-TACTGATACTGGCAGCTCTACTGCG
* *
49708608 ATACTGTTACTGGCAGCTTTGCTGCGTTACTGATACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCGTTACTGATACTGGCAGCTCTACTGCG
49708660 ATA
1 ATA
49708663 TTGGTGTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 51 0.98
53 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (52 bp):
ATACTGTTACTGGCAGCTTTGCTGCGTTACTGATACTGGCAGCTCTACTGCG
Found at i:49708659 original size:26 final size:26
Alignment explanation
Indices: 49708557--49708659 Score: 145
Period size: 26 Copynumber: 4.0 Consensus size: 26
49708547 TTGCCACAAA
*
49708557 TACTGTTACTGGCAGCTTTGCTGC-T
1 TACTGATACTGGCAGCTTTGCTGCGT
* * *
49708582 ATACTGATACTGGCAGCTCTACTGCGA
1 -TACTGATACTGGCAGCTTTGCTGCGT
*
49708609 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGATACTGGCAGCTTTGCTGCGT
49708635 TACTGATACTGGCAGCTTTGCTGCG
1 TACTGATACTGGCAGCTTTGCTGCG
49708660 ATATTGGTGT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (26 bp):
TACTGATACTGGCAGCTTTGCTGCGT
Found at i:49708810 original size:28 final size:29
Alignment explanation
Indices: 49708765--49708841 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
49708755 ACTGCATTTG
* * *
49708765 TACTGATTACTATTTTGGGCTAAGGCCCA
1 TACTGATTACTGTATTGGGCTAAAGCCCA
49708794 TACT-ATTACTGTATTGGGCTAAAGCCCA
1 TACTGATTACTGTATTGGGCTAAAGCCCA
49708822 TATTCTGA-TACTGTATTGGG
1 TA--CTGATTACTGTATTGGG
49708842 TTATGACCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 23 0.55
29 4 0.10
30 14 0.33
31 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (29 bp):
TACTGATTACTGTATTGGGCTAAAGCCCA
Found at i:49716537 original size:81 final size:80
Alignment explanation
Indices: 49716355--49716739 Score: 483
Period size: 81 Copynumber: 4.8 Consensus size: 80
49716345 GTATAACAGC
* *
49716355 CATTTTACCTTATTGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCG-TCATTCTACCTT
1 CATTTTACCCTA-TGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTT
* *
49716419 GT-GGGGTATTTCGGT
65 ATGGGGGTATTTCGAT
*
49716434 CATTTTACCCTATGAGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTT
1 CATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTT
*
49716499 ATGGGGGTATTTCTAT
65 ATGGGGGTATTTCGAT
* ** *
49716515 CATTTTACCTTATAGGGGTATTTTTGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCTT
1 CATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTT
49716580 ATGGGGGTATTTCGAT
65 ATGGGGGTATTTCGAT
* * *
49716596 CATTTTACCCTATGGTGTATTTCGGTCATTCTACCCTATAGGGGTATTTC-AGTCATTTTACCTT
1 CATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCTT
* *
49716660 ATGAGGGTATTT-TAGT
65 ATGGGGGTATTTCGA-T
* * * * * *
49716676 CATTTTATCCTATGGGGGTATTTCGGTCATTCTACCTTATGAGGGTACTTC-ATTCATTCTACCT
1 CATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCT
49716740 ATTTTTGGGT
Statistics
Matches: 272, Mismatches: 27, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
78 2 0.01
79 49 0.18
80 79 0.29
81 141 0.52
82 1 0.00
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (80 bp):
CATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTA
TGGGGGTATTTCGAT
Found at i:49716732 original size:27 final size:27
Alignment explanation
Indices: 49716355--49716739 Score: 369
Period size: 27 Copynumber: 14.4 Consensus size: 27
49716345 GTATAACAGC
*
49716355 CATTTTACCTTATTG-GGGTATTTCGGT
1 CATTTTACCTTA-TGAGGGTATTTCAGT
* *
49716382 CATTTTACCCTATGGGGGTATTTC-GT
1 CATTTTACCTTATGAGGGTATTTCAGT
* * *
49716408 CATTCTACCTTGTG-GGGTATTTCGGT
1 CATTTTACCTTATGAGGGTATTTCAGT
* **
49716434 CATTTTACCCTATGAGGGTATTTTGGT
1 CATTTTACCTTATGAGGGTATTTCAGT
* *
49716461 CATTTTACCCTATGGGGGTATTTC-GAT
1 CATTTTACCTTATGAGGGTATTTCAG-T
*
49716488 CATTTTACCTTATGGGGGTATTTCTA-T
1 CATTTTACCTTATGAGGGTATTTC-AGT
**
49716515 CATTTTACCTTAT-AGGGGTATTTTTGT
1 CATTTTACCTTATGA-GGGTATTTCAGT
*
49716542 CATTTTACCCTATGAGGGTATTTC-GAT
1 CATTTTACCTTATGAGGGTATTTCAG-T
*
49716569 CATTTTACCTTATGGGGGTATTTC-GAT
1 CATTTTACCTTATGAGGGTATTTCAG-T
* * *
49716596 CATTTTACCCTATG-GTGTATTTCGGT
1 CATTTTACCTTATGAGGGTATTTCAGT
* *
49716622 CATTCTACCCTAT-AGGGGTATTTCAGT
1 CATTTTACCTTATGA-GGGTATTTCAGT
*
49716649 CATTTTACCTTATGAGGGTATTTTAGT
1 CATTTTACCTTATGAGGGTATTTCAGT
* *
49716676 CATTTTATCC-TATGGGGGTATTTCGGT
1 CATTTTA-CCTTATGAGGGTATTTCAGT
* * *
49716703 CATTCTACCTTATGAGGGTACTTCATT
1 CATTTTACCTTATGAGGGTATTTCAGT
*
49716730 CATTCTACCT
1 CATTTTACCT
49716740 ATTTTTGGGT
Statistics
Matches: 308, Mismatches: 34, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.03
26 53 0.17
27 242 0.79
28 4 0.01
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (27 bp):
CATTTTACCTTATGAGGGTATTTCAGT
Found at i:49716733 original size:54 final size:53
Alignment explanation
Indices: 49716355--49716741 Score: 442
Period size: 54 Copynumber: 7.2 Consensus size: 53
49716345 GTATAACAGC
* *
49716355 CATTTTACCTTATTGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC-GT
1 CATTTTACC-TATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
* **
49716408 CATTCTACCT-TGTGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTTGGT
1 CATTTTACCTATG-GGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
* * *
49716461 CATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTATGGGGGTATTTCTA-T
1 CATTTTA-CCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTC-AGT
* **
49716515 CATTTTACCTTATAGGGGTATTTTTGTCATTTTACCCTATGAGGGTATTTC-GAT
1 CATTTTACC-TATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAG-T
* * *
49716569 CATTTTACCTTATGGGGGTATTTCGATCATTTTACCCTATG-GTGTATTTCGGT
1 CATTTTACC-TATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
* * * * *
49716622 CATTCTACCCTATAGGGGTATTTCAGTCATTTTACCTTATGAGGGTATTTTAGT
1 CATTTTA-CCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
* * * *
49716676 CATTTTATCCTATGGGGGTATTTCGGTCATTCTACCTTATGAGGGTACTTCATT
1 CATTTTA-CCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
*
49716730 CATTCTACCTAT
1 CATTTTACCTAT
49716742 TTTTGGGTCT
Statistics
Matches: 285, Mismatches: 38, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
51 1 0.00
52 36 0.13
53 65 0.23
54 181 0.64
55 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (53 bp):
CATTTTACCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
Found at i:49724325 original size:16 final size:15
Alignment explanation
Indices: 49724301--49724331 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
49724291 TTCTATAGAC
49724301 AAAAAAAAAAGAGGA
1 AAAAAAAAAAGAGGA
49724316 AAAAAGAAAAAGAGGA
1 AAAAA-AAAAAGAGGA
49724332 TTTCAGGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAGGA
Found at i:49731177 original size:18 final size:19
Alignment explanation
Indices: 49731154--49731198 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
49731144 TAGTTTTATA
49731154 ATTTATTTTCATTAT-TGAT
1 ATTTATTTTC-TTATCTGAT
*
49731173 A-TTATTGTCTTATCTGAT
1 ATTTATTTTCTTATCTGAT
49731191 ATTTATTT
1 ATTTATTT
49731199 ATTTATGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (19 bp):
ATTTATTTTCTTATCTGAT
Found at i:49765806 original size:13 final size:13
Alignment explanation
Indices: 49765788--49765815 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49765778 AACAAGGCTC
49765788 CTTTGTTCCTTTG
1 CTTTGTTCCTTTG
49765801 CTTTGTTCCTTTG
1 CTTTGTTCCTTTG
49765814 CT
1 CT
49765816 GATGGCTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.25, G:0.14, T:0.61
Consensus pattern (13 bp):
CTTTGTTCCTTTG
Found at i:49772411 original size:19 final size:17
Alignment explanation
Indices: 49772375--49772413 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
49772365 TTTTTCTATC
*
49772375 TTTATTTTATTGTTTCT
1 TTTATTTTATTCTTTCT
49772392 TTTATTTTCATTTCTTTCT
1 TTTATTTT-A-TTCTTTCT
49772411 TTT
1 TTT
49772414 GTTTAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTATTTTATTCTTTCT
Found at i:49777593 original size:23 final size:23
Alignment explanation
Indices: 49777567--49777610 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49777557 AAATATGTAT
49777567 ATATATTAATTACAAATGTATAC
1 ATATATTAATTACAAATGTATAC
* * *
49777590 ATATATTTATTATACATGTAT
1 ATATATTAATTACAAATGTAT
49777611 TTATAATTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (23 bp):
ATATATTAATTACAAATGTATAC
Found at i:49777605 original size:15 final size:15
Alignment explanation
Indices: 49777585--49777614 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49777575 ATTACAAATG
49777585 TATACATATATTTAT
1 TATACATATATTTAT
*
49777600 TATACATGTATTTAT
1 TATACATATATTTAT
49777615 AATTACCACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (15 bp):
TATACATATATTTAT
Found at i:49790313 original size:14 final size:15
Alignment explanation
Indices: 49790292--49790336 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
49790282 CTAATTTTTT
49790292 TCTC-CTTTTTCTTC
1 TCTCTCTTTTTCTTC
*
49790306 T-TTTCTTTTTCTT-
1 TCTCTCTTTTTCTTC
49790319 TCTCTCTTTTTCTTC
1 TCTCTCTTTTTCTTC
49790334 TCT
1 TCT
49790337 GTTTCGTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.08
14 21 0.81
15 3 0.12
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTCTCTTTTTCTTC
Found at i:49790331 original size:25 final size:27
Alignment explanation
Indices: 49790286--49790346 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 27
49790276 AAAATCCTAA
* *
49790286 TTTT-TTTCTCCTTTTTCTTCTTTTCT
1 TTTTCTTTCTCCTCTTTCTTCTTCTCT
49790312 TTTTCTTTCT-CTCTTT-TTCTTCTCT
1 TTTTCTTTCTCCTCTTTCTTCTTCTCT
* *
49790337 GTTTCGTTCT
1 TTTTCTTTCT
49790347 ACTTTGTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 16 0.53
26 9 0.30
27 5 0.17
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (27 bp):
TTTTCTTTCTCCTCTTTCTTCTTCTCT
Found at i:49799319 original size:83 final size:83
Alignment explanation
Indices: 49799216--49799375 Score: 284
Period size: 83 Copynumber: 1.9 Consensus size: 83
49799206 TTAACGGATA
49799216 TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
1 TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
*
49799281 TAAAATTGTATACAATTG
66 TAAAACTGTATACAATTG
* * *
49799299 TATGTTTAACGTATTAACCACTAAAAACCAATAGTATTAGTAAATCATAATATTACTGTATATTA
1 TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
49799364 TAAAACTGTATA
66 TAAAACTGTATA
49799376 TTATAATATT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (83 bp):
TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
TAAAACTGTATACAATTG
Found at i:49799373 original size:15 final size:15
Alignment explanation
Indices: 49799353--49799381 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49799343 TCATAATATT
49799353 ACTGTATATTATAAA
1 ACTGTATATTATAAA
49799368 ACTGTATATTATAA
1 ACTGTATATTATAA
49799382 TATTATGAAT
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:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
ACTGTATATTATAAA
Found at i:49802726 original size:45 final size:45
Alignment explanation
Indices: 49802657--49802856 Score: 138
Period size: 45 Copynumber: 4.5 Consensus size: 45
49802647 TACACGGTGG
* * * *
49802657 ATCAGCACACAAC-ACCACCCTTATAGTCAATAGTA-CTCGGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATC-CGGTGAA
* *
49802701 ATCAGCACATAGCAACCACCTTTATACTCAATGGTA-CCAGGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCC-GGTGAA
* * * * * *
49802746 TTCAGGACATAGCAATCA-CTTATATAACCATTGGTATCCGGTGAA
1 ATCAGCACATAGCAACCACCTT-TATAATCAATAGTATCCGGTGAA
* * * * ** * * *
49802791 ATCAACATATAGCGATCACCTTTATTTTCATTAATATCCGGTGGA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCCGGTGAA
* *
49802836 ATCTGCACATAGCATCCACCT
1 ATCAGCACATAGCAACCACCT
49802857 ATATTTCCAA
Statistics
Matches: 123, Mismatches: 28, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
44 15 0.12
45 103 0.84
46 5 0.04
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (45 bp):
ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCCGGTGAA
Found at i:49802873 original size:45 final size:45
Alignment explanation
Indices: 49802780--49802875 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 45
49802770 TAACCATTGG
* * * *
49802780 TATCCGGTGAAATCAACATATAGCGATCACCTTTATTTTCATTAA
1 TATCCGGTGAAATCAACACATAGCGATCACCTATATTTCCAATAA
* ** *
49802825 TATCCGGTGGAATCTGCACATAGC-ATCCACCTATATTTCCAATGA
1 TATCCGGTGAAATCAACACATAGCGAT-CACCTATATTTCCAATAA
49802870 TATCCG
1 TATCCG
49802876 ATCCATTCCG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 2 0.05
45 40 0.95
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (45 bp):
TATCCGGTGAAATCAACACATAGCGATCACCTATATTTCCAATAA
Found at i:49808826 original size:17 final size:17
Alignment explanation
Indices: 49808804--49808848 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
49808794 TTAAGTATAT
49808804 AAAAAAGAAACAAGAAC
1 AAAAAAGAAACAAGAAC
* *
49808821 AAAAAAGATAGAAGAAC
1 AAAAAAGAAACAAGAAC
49808838 AGAAAAA-AAAC
1 A-AAAAAGAAAC
49808849 TTTGAAGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAACAAGAAC
Found at i:49809827 original size:44 final size:44
Alignment explanation
Indices: 49809768--49810296 Score: 275
Period size: 44 Copynumber: 11.3 Consensus size: 44
49809758 CCTTTATTTT
* * *
49809768 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
** * *
49809812 AATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * * *
49809856 AATCTGATACGATCTACTCTACTATAACTTCAGAGAGATAAGATCCT-TTA-TTTT
1 AATCTG---C--TCCACTGTA--AT--C-TCAGGGAGATAAGAT--TACTAGCTTC
* *
49809910 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
49809954 AATCTGCACCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * *
49809998 AATCTGATGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAAATCCT-TTA-TTTT
1 AATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* *
49810052 AATCTACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
** * *
49810096 AATCTGC-CTTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTC-CACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
49810140 AATCTGATGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTT
1 AATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* * * *
49810194 AATCCGCTCCACTGTAATCTTAGAGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
49810238 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
49810282 AATCTGCTCCACTGT
1 AATCTGCTCCACTGT
49810297 TGCTTAGGAA
Statistics
Matches: 368, Mismatches: 70, Indels: 94
0.69 0.13 0.18
Matches are distributed among these distances:
42 3 0.01
43 7 0.02
44 234 0.64
45 5 0.01
46 2 0.01
47 9 0.02
49 17 0.05
51 6 0.02
52 1 0.00
53 6 0.02
54 72 0.20
55 3 0.01
56 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:49809979 original size:142 final size:142
Alignment explanation
Indices: 49809718--49810287 Score: 1025
Period size: 142 Copynumber: 4.0 Consensus size: 142
49809708 AGATAAGACT
49809718 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
* *
49809783 AATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
49809848 CTGGCTTCAATC
131 CTGGCTTCAATC
* *
49809860 TGATACGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
*
49809925 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCACCGCTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
49809990 CTGGCTTCAATC
131 CTGGCTTCAATC
* **
49810002 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTATTTTAATCTACTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
*
49810067 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC-CTTGCTGTAATCTCAGGGAGATAAGATT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTC-CGCTGTAATCTCAGGGAGATAAGATT
49810131 TCTGGCTTCAATC
130 TCTGGCTTCAATC
49810144 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
* *
49810209 AATCTTAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
49810274 CTGGCTTCAATC
131 CTGGCTTCAATC
49810286 TG
1 TG
49810288 CTCCACTGTT
Statistics
Matches: 409, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
141 1 0.00
142 407 1.00
143 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
CTGGCTTCAATC
Found at i:49828677 original size:25 final size:28
Alignment explanation
Indices: 49828643--49828715 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
49828633 TTTCAAAGGT
*
49828643 TTTAGCAGAAA-G-AAT-CACAAATTAG
1 TTTAGAAGAAACGAAATGCACAAATTAG
49828668 TTTAGAAGAAAACGAAATGCACAAATTAG
1 TTTAGAAG-AAACGAAATGCACAAATTAG
49828697 TTTAGAAGAAAACGAAATG
1 TTTAGAAG-AAACGAAATG
49828716 ACATTAATCC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 7 0.16
26 3 0.07
27 1 0.02
28 3 0.07
29 29 0.67
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.22
Consensus pattern (28 bp):
TTTAGAAGAAACGAAATGCACAAATTAG
Found at i:49828691 original size:29 final size:29
Alignment explanation
Indices: 49828658--49828715 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
49828648 CAGAAAGAAT
49828658 CACAAATTAGTTTAGAAGAAAACGAAATG
1 CACAAATTAGTTTAGAAGAAAACGAAATG
49828687 CACAAATTAGTTTAGAAGAAAACGAAATG
1 CACAAATTAGTTTAGAAGAAAACGAAATG
49828716 ACATTAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21
Consensus pattern (29 bp):
CACAAATTAGTTTAGAAGAAAACGAAATG
Found at i:49843123 original size:16 final size:16
Alignment explanation
Indices: 49843102--49843132 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
49843092 TTTCTAGTAT
49843102 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTG
49843118 TTTATTTACTAGCGT
1 TTTATTTACTAGCGT
49843133 ATTTGCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (16 bp):
TTTATTTACTAGCGTG
Found at i:49848768 original size:15 final size:15
Alignment explanation
Indices: 49848744--49848783 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
49848734 TGAATTTTAT
*
49848744 ATTGAATTGAATTGA
1 ATTGATTTGAATTGA
*
49848759 ATTGATTTGATTTGA
1 ATTGATTTGAATTGA
*
49848774 TTTGATTTGA
1 ATTGATTTGA
49848784 GAAAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (15 bp):
ATTGATTTGAATTGA
Found at i:49852450 original size:17 final size:17
Alignment explanation
Indices: 49852408--49852451 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
49852398 AAAGACTGTT
*
49852408 GAACAAAACAAGTTAGC
1 GAACAAAATAAGTTAGC
*
49852425 GAACAAAATACGTTAGC
1 GAACAAAATAAGTTAGC
49852442 GAACAAAATA
1 GAACAAAATA
49852452 TATAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.14
Consensus pattern (17 bp):
GAACAAAATAAGTTAGC
Found at i:49852473 original size:23 final size:22
Alignment explanation
Indices: 49852446--49852492 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
49852436 GTTAGCGAAC
49852446 AAAATATATAAATATATAAATAA
1 AAAATATATAAATATA-AAATAA
* *
49852469 AAAATATTTATATATAAAATAA
1 AAAATATATAAATATAAAATAA
49852491 AA
1 AA
49852493 TATAAATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATATATAAATATAAAATAA
Found at i:49852475 original size:21 final size:20
Alignment explanation
Indices: 49852446--49852499 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
49852436 GTTAGCGAAC
*
49852446 AAAATATATAAATATATAAA
1 AAAAAATATAAATATATAAA
**
49852466 TAAAAAATATTTATATATAAA
1 -AAAAAATATAAATATATAAA
*
49852487 ATAAAATATAAAT
1 AAAAAATATAAAT
49852500 TGAATAGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATATAAATATATAAA
Found at i:49852964 original size:20 final size:20
Alignment explanation
Indices: 49852939--49853007 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
49852929 AGTGGCTATT
* * *
49852939 AAATCAATTTGATAAAAATC
1 AAATCAAATTGATTAGAATC
49852959 AAATCAAATTGATTAGAATC
1 AAATCAAATTGATTAGAATC
*
49852979 AAATAAAATTGATTAGAATC
1 AAATCAAATTGATTAGAATC
*
49852999 AAATAAAAT
1 AAATCAAAT
49853008 AAGGATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATCAAATTGATTAGAATC
Found at i:49856887 original size:24 final size:23
Alignment explanation
Indices: 49856858--49856903 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
49856848 TTAGTGAACA
49856858 AAATATATAAATATATAAATAAAC
1 AAATATATAAATATA-AAATAAAC
* *
49856882 AAATATTTATATATAAAATAAA
1 AAATATATAAATATAAAATAAA
49856904 ATATAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAC
Found at i:49857381 original size:20 final size:20
Alignment explanation
Indices: 49857358--49857398 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
49857348 TTAAATCAAT
*
49857358 TTGATTAAAATCAAATTAAA
1 TTGATTAAAATCAAATAAAA
*
49857378 TTGATTAGAATCAAATAAAA
1 TTGATTAAAATCAAATAAAA
49857398 T
1 T
49857399 CAGGATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (20 bp):
TTGATTAAAATCAAATAAAA
Found at i:49858666 original size:12 final size:14
Alignment explanation
Indices: 49858636--49858667 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
49858626 AATCAAATAA
49858636 AAAAATTAGAATGT
1 AAAAATTAGAATGT
49858650 AAAAATTA-AAT-T
1 AAAAATTAGAATGT
49858662 AAAAAT
1 AAAAAT
49858668 AAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATGT
Found at i:49858694 original size:12 final size:12
Alignment explanation
Indices: 49858677--49858717 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
49858667 TAAAAAATAT
*
49858677 TAAAACGAAAAC
1 TAAAACTAAAAC
49858689 TAAAACTAAAAC
1 TAAAACTAAAAC
*
49858701 TAAAACTAAAAA
1 TAAAACTAAAAC
49858713 TAAAA
1 TAAAA
49858718 ATGGCTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.15
Consensus pattern (12 bp):
TAAAACTAAAAC
Found at i:49858699 original size:34 final size:34
Alignment explanation
Indices: 49858630--49858705 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
49858620 TGTAAGAATC
* * * *
49858630 AAATAAAAAAATTAGAATGTAAAAATTAAATTAA
1 AAATAAAAAAATTAAAACGTAAAAATAAAACTAA
*
49858664 AAATAAAAAATATTAAAACG-AAAACTAAAACTAA
1 AAATAAAAAA-ATTAAAACGTAAAAATAAAACTAA
*
49858698 AACTAAAA
1 AAATAAAA
49858706 CTAAAAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 28 0.80
35 7 0.20
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (34 bp):
AAATAAAAAAATTAAAACGTAAAAATAAAACTAA
Found at i:49858700 original size:18 final size:18
Alignment explanation
Indices: 49858677--49858717 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
49858667 TAAAAAATAT
*
49858677 TAAAACGAAAACTAAAAC
1 TAAAACGAAAACTAAAAA
*
49858695 TAAAACTAAAACTAAAAA
1 TAAAACGAAAACTAAAAA
49858713 TAAAA
1 TAAAA
49858718 ATGGCTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.15
Consensus pattern (18 bp):
TAAAACGAAAACTAAAAA
Found at i:49860706 original size:66 final size:66
Alignment explanation
Indices: 49860617--49860771 Score: 274
Period size: 66 Copynumber: 2.3 Consensus size: 66
49860607 TATTTAACTC
*
49860617 TAAATTTAATTATCAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGAT
1 TAAATTTAATCA--AAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGAT
49860682 AAA
64 AAA
49860685 TAAATTTAATCAAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGATAA
1 TAAATTTAATCAAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGATAA
49860750 A
66 A
*
49860751 TAAATTTAATCAAACTCAAAA
1 TAAATTTAATCAAAGTCAAAA
49860772 GTAAAATATC
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
66 74 0.87
68 11 0.13
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.32
Consensus pattern (66 bp):
TAAATTTAATCAAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGATAA
A
Found at i:49868664 original size:24 final size:23
Alignment explanation
Indices: 49868637--49868699 Score: 54
Period size: 25 Copynumber: 2.6 Consensus size: 23
49868627 TAGCTCAAAA
*
49868637 GAGTGTCCCGTTATTAGCTCTCAT
1 GAGT-TCCCGTTATTAGCTCTCAC
* * *
49868661 GAGTATCCTGATATTTGGCTCTCAC
1 GAGT-TCCCGTTA-TTAGCTCTCAC
49868686 GAGCTTCCCGTTAT
1 GAG-TTCCCGTTAT
49868700 ATGGTTCTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
24 11 0.37
25 18 0.60
26 1 0.03
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (23 bp):
GAGTTCCCGTTATTAGCTCTCAC
Found at i:49868858 original size:25 final size:24
Alignment explanation
Indices: 49868789--49868858 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
49868779 CACAACTCTT
* * **
49868789 ATGAGCGTCCTGATATTTGGCTCTT
1 ATGAGC-TCCTGTTATATGGCTCAA
* *
49868814 ATGAGCTCCCGTTACATGGCTCAA
1 ATGAGCTCCTGTTATATGGCTCAA
49868838 ATGAGCTTCCTGTTATATGGC
1 ATGAGC-TCCTGTTATATGGC
49868859 ACGAGAGAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (24 bp):
ATGAGCTCCTGTTATATGGCTCAA
Found at i:49876100 original size:24 final size:24
Alignment explanation
Indices: 49876072--49876152 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
49876062 CATGTAATGA
*
49876072 GAAGCTCTAGAGAGCCATTAACGG
1 GAAGCTCTAGAGAGCAATTAACGG
* * *
49876096 GAAGCT-TATACGAGCAAATATCGG
1 GAAGCTCTAGA-GAGCAATTAACGG
*
49876120 GAAGCTCTAGAGAGGCAATTAATCGA
1 GAAGCTCTAGAGA-GCAATTAA-CGG
49876146 GAAGCTC
1 GAAGCTC
49876153 CGAAGAGCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
23 3 0.07
24 24 0.53
25 9 0.20
26 9 0.20
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.19
Consensus pattern (24 bp):
GAAGCTCTAGAGAGCAATTAACGG
Found at i:49876263 original size:24 final size:25
Alignment explanation
Indices: 49876236--49876284 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
49876226 GGATGCTTTG
* *
49876236 AAGAACTAT-TAATGGGAAGCTCGT
1 AAGAACCATATAACGGGAAGCTCGT
49876260 AAGAACCATATAACGGGAAGCTCGT
1 AAGAACCATATAACGGGAAGCTCGT
49876285 GAGAGCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (25 bp):
AAGAACCATATAACGGGAAGCTCGT
Found at i:49915064 original size:27 final size:27
Alignment explanation
Indices: 49915033--49915112 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
49915023 ATATGTGCAA
* *
49915033 AGGGTAAAATGACTGAAATACCCTCG-
1 AGGGTAAAATGACTAAAATACCCCCGC
* *
49915059 ATGGGTAAAATGGCTAAAATGCCCCCGC
1 A-GGGTAAAATGACTAAAATACCCCCGC
*
49915087 AGGGTAAAATGACCAAAATACCCCCG
1 AGGGTAAAATGACTAAAATACCCCCG
49915113 GAGGATAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.02
27 43 0.96
28 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.16
Consensus pattern (27 bp):
AGGGTAAAATGACTAAAATACCCCCGC
Found at i:49915174 original size:27 final size:27
Alignment explanation
Indices: 49915139--49915403 Score: 268
Period size: 27 Copynumber: 9.9 Consensus size: 27
49915129 AATACCTCCA
* * **
49915139 TAGGATAAAATAATCGTAATAACCCTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
* *
49915166 TGGGGTAAAATGA-CTGTAATGCCCCTA
1 TAGGGTAAAATGATC-GTAATGCCCCTG
* * *
49915193 TAGGGTAAAATAATCGTAATACCCTTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
* * *
49915220 TAGGATAAAATGACCGTAATGCCCTTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
*
49915247 TAGGGTAAAATGATCGTAATACCCCTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
* *
49915274 TAGGGTAAATTGACCGTAATGCCCCT-
1 TAGGGTAAAATGATCGTAATGCCCCTG
49915300 TAGGGTAAAATGAAT-GTAATGCCCCTG
1 TAGGGTAAAATG-ATCGTAATGCCCCTG
* *
49915327 TAGGGTAAAATGATCGTAATGTCCTTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
* * * * *
49915354 TAAGGTAAAATGACCATAATACCTCTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
*
49915381 TAAGGTAAAATGA-CGGTAATGCC
1 TAGGGTAAAATGATC-GTAATGCC
49915404 TTAGTGGGTA
Statistics
Matches: 197, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
26 26 0.13
27 170 0.86
28 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (27 bp):
TAGGGTAAAATGATCGTAATGCCCCTG
Found at i:49915229 original size:54 final size:54
Alignment explanation
Indices: 49915138--49915403 Score: 311
Period size: 54 Copynumber: 4.9 Consensus size: 54
49915128 AAATACCTCC
* * * *
49915138 ATAGGATAAAATAATCGTAATAACCCTGTGGGGTAAAATGACTGTAATGCCCCT
1 ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
* * *
49915192 ATAGGGTAAAATAATCGTAATACCCTTGTAGGATAAAATGACCGTAATGCCCTT
1 ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
* * *
49915246 GTAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAATTGACCGTAATGCCCCT
1 ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
* * * *
49915300 -TAGGGTAAAATGAAT-GTAATGCCCCTGTAGGGTAAAATGATCGTAATGTCCTT
1 ATAGGGTAAAAT-AATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
* * * * * * * *
49915353 GTAAGGTAAAATGACCATAATACCTCTGTAAGGTAAAATGACGGTAATGCC
1 ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCC
49915404 TTAGTGGGTA
Statistics
Matches: 180, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
53 45 0.25
54 135 0.75
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (54 bp):
ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
Found at i:49915353 original size:107 final size:108
Alignment explanation
Indices: 49915139--49915403 Score: 354
Period size: 107 Copynumber: 2.5 Consensus size: 108
49915129 AATACCTCCA
* * * * *
49915139 TAGGATAAAATAATCGTAATAACCCTGTGGGGTAAAATGACTGTAATGCCCCTATAGGGTAAAAT
1 TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAAT
*
49915204 AATCGTAATACCCTTGTAGGATAAAATGACCGTAATGCCCTTG
66 AATCGTAATACCCCTGTAGGATAAAATGACCGTAATGCCCTTG
*
49915247 TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAATTGACCGTAATGCCCCT-TAGGGTAAAAT
1 TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAAT
* * * *
49915311 GAAT-GTAATGCCCCTGTAGGGTAAAATGATCGTAATGTCCTTG
66 -AATCGTAATACCCCTGTAGGATAAAATGACCGTAATGCCCTTG
* * * * * *
49915354 TAAGGTAAAATGACCATAATACCTCTGTAAGGTAAAATGACGGTAATGCC
1 TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCC
49915404 TTAGTGGGTA
Statistics
Matches: 138, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
107 88 0.64
108 50 0.36
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (108 bp):
TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAAT
AATCGTAATACCCCTGTAGGATAAAATGACCGTAATGCCCTTG
Found at i:49915519 original size:24 final size:24
Alignment explanation
Indices: 49915441--49915522 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
49915431 CTCGAGGTCA
* * * *
49915441 AATGATTGTTTTGTCTGT-AATTA
1 AATGACTGATTTGTCTGTGATTTG
*
49915464 AATGACTGATTTGTTTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
* *
49915488 TATAACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
49915512 AATGACTGATT
1 AATGACTGATT
49915523 CTGAGCATGG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
23 17 0.37
24 26 0.57
25 3 0.07
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.49
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:49915676 original size:26 final size:26
Alignment explanation
Indices: 49915621--49915676 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
49915611 ATACTATTAC
* ** *
49915621 TGGCAGCTTTGCTGCGATATTGTTGC
1 TGGCAGCTTTGCTGCGATACTACTGA
49915647 TGGCAGCTTTGCTGCGATACTACTGA
1 TGGCAGCTTTGCTGCGATACTACTGA
49915673 TGGC
1 TGGC
49915677 TTTGTGCCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.34
Consensus pattern (26 bp):
TGGCAGCTTTGCTGCGATACTACTGA
Found at i:49915708 original size:32 final size:32
Alignment explanation
Indices: 49915667--49915887 Score: 185
Period size: 32 Copynumber: 6.9 Consensus size: 32
49915657 GCTGCGATAC
*
49915667 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* *
49915699 TACTGATGGCTTTGTGCTGATCATAGTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* * ****
49915731 TACTGATGGCTTTGTGCTGATCATGTTATTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* * *
49915763 TACCGATGGCTGTGTGCCGATCAT-TTCACTAT
1 TACTGATGGCTTTGTGCCGATCATATT-ACCAT
* * * *
49915795 CACTGATGTCTGTGTGCCGATCATGTTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* * * * ***
49915827 TACTAATGGCTGTGT-CCCAGTCATATCACTGC
1 TACTGATGGCTTTGTGCCGA-TCATATTACCAT
* *
49915859 TACTGATGGCTTTGTGCCAATCACATTAC
1 TACTGATGGCTTTGTGCCGATCATATTAC
49915888 TGTGCTTATG
Statistics
Matches: 152, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
31 5 0.03
32 142 0.93
33 5 0.03
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCAT
Found at i:49915860 original size:96 final size:96
Alignment explanation
Indices: 49915666--49915887 Score: 243
Period size: 96 Copynumber: 2.3 Consensus size: 96
49915656 TGCTGCGATA
* * * *
49915666 CTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGCTGATCATAGTACCAT
1 CTACTGATGGCTTTGTGCCGATCATATTACCATCACTGATGGCTGTGTGCCGATCATAGTACCAT
* * * * * * *
49915731 TACTGATGGCTTTGTGCTGATCATGTTATTG
66 TACTAATGGCTGTGTCCAGATCATATCACTG
* * * *
49915762 CTACCGATGGCTGTGTGCCGATCAT-TTCACTATCACTGATGTCTGTGTGCCGATCAT-GTTACC
1 CTACTGATGGCTTTGTGCCGATCATATT-ACCATCACTGATGGCTGTGTGCCGATCATAG-TACC
49915825 ATTACTAATGGCTGTGTCCCAG-TCATATCACTG
64 ATTACTAATGGCTGTGT-CCAGATCATATCACTG
* *
49915858 CTACTGATGGCTTTGTGCCAATCACATTAC
1 CTACTGATGGCTTTGTGCCGATCATATTAC
49915888 TGTGCTTATG
Statistics
Matches: 103, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
95 3 0.03
96 96 0.93
97 4 0.04
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (96 bp):
CTACTGATGGCTTTGTGCCGATCATATTACCATCACTGATGGCTGTGTGCCGATCATAGTACCAT
TACTAATGGCTGTGTCCAGATCATATCACTG
Found at i:49915936 original size:26 final size:26
Alignment explanation
Indices: 49915907--49915959 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
49915897 GGCTTATAGC
* *
49915907 CATTCTAACTACTGGCAGCTCTGCTG
1 CATTATAACTACTGGCAGCTATGCTG
*
49915933 CATTATTACTACTGGCAGCTATGCTG
1 CATTATAACTACTGGCAGCTATGCTG
49915959 C
1 C
49915960 GATTTTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (26 bp):
CATTATAACTACTGGCAGCTATGCTG
Found at i:49917179 original size:34 final size:34
Alignment explanation
Indices: 49917136--49917260 Score: 171
Period size: 34 Copynumber: 3.7 Consensus size: 34
49917126 AGGTGGATGG
*
49917136 ATTTGGTGTGCTGGATGGATTAACTCATACGAGC
1 ATTTGGTGTGCTAGATGGATTAACTCATACGAGC
* *
49917170 ATTTGGTGTGCTAGATGGATTAGCTCATATGAGC
1 ATTTGGTGTGCTAGATGGATTAACTCATACGAGC
* * * *
49917204 ATTTGATGTGCTGGATGGATTAGCTCTTACGAGC
1 ATTTGGTGTGCTAGATGGATTAACTCATACGAGC
*
49917238 ATCTGGTGTGCTAGATGG-TTAAC
1 ATTTGGTGTGCTAGATGGATTAAC
49917261 CGTGTACTCG
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 4 0.05
34 76 0.95
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (34 bp):
ATTTGGTGTGCTAGATGGATTAACTCATACGAGC
Found at i:49919156 original size:23 final size:23
Alignment explanation
Indices: 49919130--49919265 Score: 132
Period size: 23 Copynumber: 5.9 Consensus size: 23
49919120 TGCCACAGAA
*
49919130 TATGCCACAAAGGCTTCAAAGAT
1 TATGCCACAAAGGCTTCATAGAT
* * * *
49919153 TATGCCACAAAGGCTCCACAAAG
1 TATGCCACAAAGGCTTCATAGAT
* *
49919176 TGTGCTACAAAGGCTTCATAGAT
1 TATGCCACAAAGGCTTCATAGAT
*
49919199 TATACCACAAAGGCTTCATTA-AT
1 TATGCCACAAAGGCTTCA-TAGAT
** *
49919222 TCCGCCACAAAGGCTTTATAGAAT
1 TATGCCACAAAGGCTTCATAG-AT
*
49919246 GA-GCCACAAAGGCTTCATAG
1 TATGCCACAAAGGCTTCATAG
49919266 GTAACTTTCC
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
22 2 0.02
23 84 0.93
24 4 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (23 bp):
TATGCCACAAAGGCTTCATAGAT
Found at i:49926778 original size:39 final size:40
Alignment explanation
Indices: 49926719--49926847 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
49926709 TACAACACCA
* * * *
49926719 GCACAATGCATGCTAGGCACAAAACCTC-ATAAACACACCG
1 GCACAAAGCCTGCTAGGCACAAAACC-CGATAAATACACTG
* *
49926759 GCACAAA-CCTGCTAGGCACAAACCCCGATAAATACACTA
1 GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
* * *
49926798 GCATAAAGCCTACTAGGCACAAAGCCCGATAAATACACTG
1 GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
49926838 GCACAAAGCC
1 GCACAAAGCC
49926848 ACTAACTCGT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 1 0.01
39 31 0.41
40 44 0.58
ACGTcount: A:0.40, C:0.32, G:0.16, T:0.12
Consensus pattern (40 bp):
GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
Found at i:49931314 original size:4 final size:4
Alignment explanation
Indices: 49931305--49931366 Score: 106
Period size: 4 Copynumber: 15.0 Consensus size: 4
49931295 CTAGTTTCTC
49931305 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT
49931354 CTTT CCTTT CTTT
1 CTTT -CTTT CTTT
49931367 TTCTCCCTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 48 0.86
5 8 0.14
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:49931433 original size:22 final size:23
Alignment explanation
Indices: 49931396--49931463 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 23
49931386 ACTTTTGTTC
49931396 TTTA-TTTATT-TCATTTACTTA-
1 TTTATTTTATTAT-ATTTACTTAT
49931417 TTTATTTTATTATATTTACCTTAT
1 TTTATTTTATTATATTTA-CTTAT
* *
49931441 TATTATATTATTATATATACTTA
1 T-TTATTTTATTATATTTACTTA
49931464 CTTAAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.10
22 11 0.28
23 5 0.12
24 5 0.12
25 15 0.38
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTATTTTATTATATTTACTTAT
Found at i:49939263 original size:17 final size:17
Alignment explanation
Indices: 49939243--49939303 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
49939233 TAGAATTGAG
49939243 TTGAAAAAATAATTTAA
1 TTGAAAAAATAATTTAA
* * *
49939260 TTGAGAAATTAATCTAA
1 TTGAAAAAATAATTTAA
* *
49939277 TT---AATATAAATTAA
1 TTGAAAAAATAATTTAA
49939291 TTGAAAAAATAAT
1 TTGAAAAAATAAT
49939304 ATTTTAGGAA
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
14 10 0.31
17 22 0.69
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (17 bp):
TTGAAAAAATAATTTAA
Found at i:49950522 original size:19 final size:18
Alignment explanation
Indices: 49950485--49950524 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
49950475 CGTAAAAATG
*
49950485 AATTTGAAAATGTATTTT
1 AATTTGAAAATGTAATTT
*
49950503 AATTTGATAAATTTAATTT
1 AATTTGA-AAATGTAATTT
49950522 AAT
1 AAT
49950525 CATTATATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
AATTTGAAAATGTAATTT
Found at i:49961974 original size:40 final size:40
Alignment explanation
Indices: 49961923--49962006 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
49961913 TTAAGTTAAA
*
49961923 TTTT-CTCCTACCCTAGCCATTCTCCTCCCTTCTCTTATT
1 TTTTACTCCTACCCTAGCCATTCTCCTCCCCTCTCTTATT
49961962 TTTTACTCCTACCCTAGCCATTCTCCTCCCCTCTCTTATT
1 TTTTACTCCTACCCTAGCCATTCTCCTCCCCTCTCTTATT
49962002 TTTTA
1 TTTTA
49962007 TCTCAAAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.12, C:0.39, G:0.02, T:0.46
Consensus pattern (40 bp):
TTTTACTCCTACCCTAGCCATTCTCCTCCCCTCTCTTATT
Found at i:49963835 original size:11 final size:12
Alignment explanation
Indices: 49963819--49963847 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
49963809 TTATTAACGG
49963819 TGAATG-ATATT
1 TGAATGAATATT
49963830 TGAATGAATATT
1 TGAATGAATATT
49963842 TGAATG
1 TGAATG
49963848 TTCTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (12 bp):
TGAATGAATATT
Found at i:49971182 original size:44 final size:42
Alignment explanation
Indices: 49971084--49971184 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 42
49971074 ACCAACATCT
* * *
49971084 CAGACGTGGTCTTACATGTAACCACATATTGATGCCACTATC
1 CAGACGTGGTCTTACACGTAACCACAAATCGATGCCACTATC
*
49971126 CTAGACAG-GGTCTTACACGTAAGTCACAAATCGATGCCAACGT-TC
1 C-AGAC-GTGGTCTTACACGTAA-CCACAAATCGATGCC-AC-TATC
49971171 CAGACGTGGTCTTA
1 CAGACGTGGTCTTA
49971185 GATGATAACA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
42 1 0.02
43 18 0.37
44 24 0.49
45 5 0.10
46 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (42 bp):
CAGACGTGGTCTTACACGTAACCACAAATCGATGCCACTATC
Found at i:49978484 original size:44 final size:43
Alignment explanation
Indices: 49978377--49978486 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 43
49978367 TCGTACAACA
* * *
49978377 CCAACATCCCAGGCGTGGTCTTACATGTAACCACATATCGATG
1 CCAACATCCCAGACGTGGTCTTACACGTAACCACAAATCGATG
* ** *
49978420 CC-ACTATCCTAGACAAGGTCTTACACGTAAGTCACAAATCGATG
1 CCAAC-ATCCCAGACGTGGTCTTACACGTAA-CCACAAATCGATG
*
49978464 CCAACGTCCCAGACGTGGTCTTA
1 CCAACATCCCAGACGTGGTCTTA
49978487 GATGATAACA
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
42 2 0.04
43 22 0.42
44 27 0.51
45 2 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (43 bp):
CCAACATCCCAGACGTGGTCTTACACGTAACCACAAATCGATG
Found at i:49990754 original size:23 final size:22
Alignment explanation
Indices: 49990730--49990780 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
49990720 CAGAGTCTTA
49990730 AAAAT-AATATAAATAAATAAAT
1 AAAATCAATATAAAT-AATAAAT
*
49990752 AAAATCAATATACATAATAAA-
1 AAAATCAATATAAATAATAAAT
49990773 AATAATCA
1 AA-AATCA
49990781 CATACAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 16 0.62
23 8 0.31
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAATCAATATAAATAATAAAT
Found at i:49993131 original size:173 final size:172
Alignment explanation
Indices: 49992774--49993154 Score: 412
Period size: 173 Copynumber: 2.2 Consensus size: 172
49992764 AATTTGCTAT
* * * *
49992774 CTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCA
1 CTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAAACGCGATCTGCTATCTACAACTTCA
* * * * * *
49992839 GAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTACCATTTCAGGGAGGTAGGATTTGCCATCT
66 GAGAGATAAGATCCAAGGTTGTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTTGCCAGCT
* * * *
49992904 TTAGTCTGCCTCGCTGCAACTTTAGGAGGATAAGACTTGCTTA
131 TAAATCTGCCTCGC-GCAACTTTAGGAAGATAAGACTTGCGTA
* *
49992947 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAACGGGATCTGCTATCTACAACTTCA
1 CTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAAACGCGATCTGCTATCTACAACTTCA
* * ** ***
49993012 GAGAGATAAGTTCCAAGGTTGTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGATTTGGTGGCT
66 GAGAGATAAGATCCAAGGTTGTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTTGCCAGCT
* * *
49993077 TAAATCTGCTTC-C-C-ACTATCTTGGAAAGATAAGATTTGCCGT-
131 TAAATCTGCCTCGCGCAACT-T-TAGG-AAGATAAGACTTG-CGTA
* **
49993119 CTTCGATCTGCTCCACTACTGCTT-AGGGAGATAAGA
1 CTTAG-TCTGCTCCACTACAACTTCAGGGAGATAAGA
49993155 TCTACAATCT
Statistics
Matches: 173, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
169 3 0.02
170 2 0.01
171 3 0.02
172 28 0.16
173 137 0.79
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (172 bp):
CTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAAACGCGATCTGCTATCTACAACTTCA
GAGAGATAAGATCCAAGGTTGTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTTGCCAGCT
TAAATCTGCCTCGCGCAACTTTAGGAAGATAAGACTTGCGTA
Found at i:49993150 original size:132 final size:131
Alignment explanation
Indices: 49993039--49993593 Score: 748
Period size: 132 Copynumber: 4.2 Consensus size: 131
49993029 GTTGTAATCC
* * *
49993039 GCTCCGCTGTAACTTCAGGGAGA-TAGGATTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAA
1 GCTCCGCTGT-AC-TCAGGGAGACAAGG-CTTGGTAGCTTAAATCTGCTTCCCACTATCTTGGAA
49993103 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
63 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
49993168 ACCT
128 ACCT
* * * * * *
49993172 TCTCTGCTGCTACTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCGCTATTTTGGAAAG
1 GCTCCGCTG-TACTCAGGGAGACAAGGCTTGGTAGCTTAAATCTGCTTCCCACTATCTTGGAAAG
* * * * *
49993237 ATAAGATTTGCTGTCTTTGATCTGCTCCACTACTGCTTAGGGATATAGGATCTACAA-CATTC-T
65 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC-TTCAA
49993300 CC-
129 CCT
* *
49993302 GCT--GCTG--CTCAGGGAGACAAGGCTTTGTAGCTTAAATTTGCTTCCCACTATCTTGGAAAGA
1 GCTCCGCTGTACTCAGGGAGACAAGGCTTGGTAGCTTAAATCTGCTTCCCACTATCTTGGAAAGA
* *
49993363 TAAGACTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACC
66 TAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACC
49993428 T
131 T
* ** *
49993429 ACTCCGCTGTTGGTCAGGGAGACAAGGCTTGGTAGCTTAAATCTACTTCCCACTATCTTGGAAAG
1 GCTCCGCTG-TACTCAGGGAGACAAGGCTTGGTAGCTTAAATCTGCTTCCCACTATCTTGGAAAG
49993494 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
65 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
49993559 CT
130 CT
* * * * *
49993561 TCTCCGCTACTTCTCAGAGAGACAGGGCTTGGT
1 GCTCCGCT-GTACTCAGGGAGACAAGGCTTGGT
49993594 GTTTCACCGG
Statistics
Matches: 373, Mismatches: 37, Indels: 25
0.86 0.09 0.06
Matches are distributed among these distances:
125 103 0.28
126 3 0.01
127 2 0.01
128 4 0.01
129 4 0.01
130 2 0.01
131 3 0.01
132 239 0.64
133 12 0.03
134 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (131 bp):
GCTCCGCTGTACTCAGGGAGACAAGGCTTGGTAGCTTAAATCTGCTTCCCACTATCTTGGAAAGA
TAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACC
T
Found at i:49993518 original size:257 final size:257
Alignment explanation
Indices: 49993074--49993550 Score: 801
Period size: 257 Copynumber: 1.9 Consensus size: 257
49993064 GGATTTGGTG
*
49993074 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACT
1 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTCGATCTGCTCCACTACT
* *
49993139 GCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCTGCTGCTACTCAGAGAGACAAGGCTTGG
66 GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAGAGAGACAAGGCTTGG
* * * * * *
49993204 TGGCTTAAATCTGCTTCCCGCTATTTTGGAAAGATAAGATTTGCTGTCTTTGATCTGCTCCACTA
131 TAGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTA
* *
49993269 CTGCTTAGGGATATAGGATCTACAACATTCTCCGCTGCTGCTCAGGGAGACAAGGCTTTGTA
196 CTGCTTAGGGAGATAAGATCTACAACATTCTCCGCTGCTGCTCAGGGAGACAAGGCTTTGTA
* *
49993331 GCTTAAATTTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCCACTACT
1 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTCGATCTGCTCCACTACT
* ** *
49993396 GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGTTGGTCAGGGAGACAAGGCTTGG
66 GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAGAGAGACAAGGCTTGG
49993461 TAGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTA
131 TAGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTA
49993526 CTGCTTAGGGAGATAAGATCTACAA
196 CTGCTTAGGGAGATAAGATCTACAA
49993551 TCTTCAACCT
Statistics
Matches: 203, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
257 203 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (257 bp):
GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTCGATCTGCTCCACTACT
GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAGAGAGACAAGGCTTGG
TAGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTA
CTGCTTAGGGAGATAAGATCTACAACATTCTCCGCTGCTGCTCAGGGAGACAAGGCTTTGTA
Found at i:49998074 original size:36 final size:36
Alignment explanation
Indices: 49998027--49998099 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
49998017 TTTGTGAGGT
49998027 AGGATTTGCTTTTCCTCTTGTTCTACCATCCTCAGC
1 AGGATTTGCTTTTCCTCTTGTTCTACCATCCTCAGC
49998063 AGGATTTGCTTTTCCTCTTGTTCTACCATCCTCAGC
1 AGGATTTGCTTTTCCTCTTGTTCTACCATCCTCAGC
49998099 A
1 A
49998100 AGTCCAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.15, C:0.30, G:0.14, T:0.41
Consensus pattern (36 bp):
AGGATTTGCTTTTCCTCTTGTTCTACCATCCTCAGC
Found at i:49999740 original size:12 final size:12
Alignment explanation
Indices: 49999725--49999753 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
49999715 CTTTTTTACT
49999725 CCCCTATTATGA
1 CCCCTATTATGA
49999737 CCCCTATTATGA
1 CCCCTATTATGA
49999749 CCCCT
1 CCCCT
49999754 TTCATAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.41, G:0.07, T:0.31
Consensus pattern (12 bp):
CCCCTATTATGA
Found at i:50001705 original size:24 final size:24
Alignment explanation
Indices: 50001677--50001722 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
50001667 ATCATTTTTT
*
50001677 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTGCTTTTGAA
* *
50001701 GCTGCTCCTGCATTTTCTTTTG
1 GCTGCTCATGCATTTGCTTTTG
50001723 GGACTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (24 bp):
GCTGCTCATGCATTTGCTTTTGAA
Found at i:50005877 original size:26 final size:27
Alignment explanation
Indices: 50005848--50005901 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
50005838 ATATGTATAC
* **
50005848 ATACATATATATACTAAAATTA-ATAT
1 ATACATATAGATAAAAAAATTACATAT
50005874 ATACATATAGATAAAAAAATTACATAT
1 ATACATATAGATAAAAAAATTACATAT
50005901 A
1 A
50005902 AATAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (27 bp):
ATACATATAGATAAAAAAATTACATAT
Found at i:50009198 original size:3 final size:3
Alignment explanation
Indices: 50009183--50009240 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
50009173 ATAAATAGCT
*
50009183 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
50009231 ATA ATA ATA A
1 ATA ATA ATA A
50009241 GACTAGATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:50010602 original size:10 final size:10
Alignment explanation
Indices: 50010589--50010639 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
50010579 AAAATGTTTC
50010589 AAAAATATAA
1 AAAAATATAA
* *
50010599 AAAAATCTTA
1 AAAAATATAA
50010609 AAAAATA-AA
1 AAAAATATAA
50010618 TAAAAATATAA
1 -AAAAATATAA
*
50010629 AATAAT-TAA
1 AAAAATATAA
50010638 AA
1 AA
50010640 TTAATAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 6 0.18
10 26 0.76
11 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATATAA
Found at i:50010646 original size:30 final size:29
Alignment explanation
Indices: 50010589--50010649 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 29
50010579 AAAATGTTTC
50010589 AAAAATATAAAAAAATCTTAAAAAATAAAT
1 AAAAATATAAAAAAA-CTTAAAAAATAAAT
*
50010619 AAAAATATAAAATAA-TTAAAATTAATAAAT
1 AAAAATATAAAAAAACTTAAAA--AATAAAT
50010649 A
1 A
50010650 TTATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.21
30 22 0.79
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (29 bp):
AAAAATATAAAAAAACTTAAAAAATAAAT
Found at i:50011933 original size:25 final size:23
Alignment explanation
Indices: 50011912--50011955 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
50011902 ATATTTTAGG
*
50011912 TCTGCTACTCTAGCACGTTTTTA
1 TCTGCTACCCTAGCACGTTTTTA
* *
50011935 TCTGTTGCCCTAGCACGTTTT
1 TCTGCTACCCTAGCACGTTTT
50011956 GGCTTTTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (23 bp):
TCTGCTACCCTAGCACGTTTTTA
Found at i:50016757 original size:6 final size:6
Alignment explanation
Indices: 50016743--50016776 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
50016733 TTGTGGAGGA
* *
50016743 ATGTAT ATGTGT ATGTAT ATGTAT ATGAAT ATGT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGT
50016777 GTTTCCTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (6 bp):
ATGTAT
Found at i:50021824 original size:38 final size:38
Alignment explanation
Indices: 50021773--50021845 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
50021763 AAGTCAACCT
*
50021773 AACTCGTGCAAAGTGAAAATTCTCTATAGAAATTCTCA
1 AACTCGTGCAAAGTAAAAATTCTCTATAGAAATTCTCA
50021811 AACTCGTGCAAAGTAAAAATTCTCTATAGAAATTC
1 AACTCGTGCAAAGTAAAAATTCTCTATAGAAATTC
50021846 CCATAAGGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (38 bp):
AACTCGTGCAAAGTAAAAATTCTCTATAGAAATTCTCA
Found at i:50022917 original size:34 final size:34
Alignment explanation
Indices: 50022877--50022956 Score: 142
Period size: 34 Copynumber: 2.4 Consensus size: 34
50022867 ATATGTTCAT
*
50022877 ACAACCAATATGCCCAAAGGGCATCTCAATCACA
1 ACAACCAACATGCCCAAAGGGCATCTCAATCACA
50022911 ACAACCAACATGCCCAAAGGGCATCTCAATCACA
1 ACAACCAACATGCCCAAAGGGCATCTCAATCACA
*
50022945 AAAACCAACATG
1 ACAACCAACATG
50022957 TACAACCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.44, C:0.33, G:0.11, T:0.12
Consensus pattern (34 bp):
ACAACCAACATGCCCAAAGGGCATCTCAATCACA
Found at i:50023616 original size:15 final size:16
Alignment explanation
Indices: 50023587--50023616 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50023577 CAAACATGCT
50023587 TTAACACATTATCAAA
1 TTAACACATTATCAAA
50023603 TTAACACA-TATCAA
1 TTAACACATTATCAA
50023617 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:50040821 original size:12 final size:12
Alignment explanation
Indices: 50040804--50040828 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50040794 TGATTCACCA
50040804 ACTAGAACGTGG
1 ACTAGAACGTGG
50040816 ACTAGAACGTGG
1 ACTAGAACGTGG
50040828 A
1 A
50040829 AAGTTGAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (12 bp):
ACTAGAACGTGG
Found at i:50042674 original size:91 final size:92
Alignment explanation
Indices: 50042503--50042725 Score: 281
Period size: 91 Copynumber: 2.4 Consensus size: 92
50042493 ATTGGTGTAA
* * * * * *
50042503 AAAAAAACCCTCAAGCTTTTTCAAAAAAAGCAATGAAGCCTTTCCTTTTTTTTTTTTACTCTCAA
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCTCC-TTTATTTTTTTACACTCAA
*
50042568 TTGAGCACTTGAACTTTCAAAATGCACC
65 TTGAGCACTTGAACTTTCAAAATGAACC
* * *
50042596 AAAAAGGCCCTCAAACTTCTTCAGAAAAAAGCAATTAAGCCTCTGC-TTATTTTTTT-CACTCAA
1 AAAAAGACCCTCAAACTTTTTCA-AAAAAAGCAATTAAGCCTCTCCTTTATTTTTTTACACTCAA
* * *
50042659 TTGGGTACTTGAACTTTCAAAATGAATC
65 TTGAGCACTTGAACTTTCAAAATGAACC
*
50042687 AAAAAGACCCTCAAAATTTTTC-AAAAAAGCAATTAAGCC
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCC
50042726 CCTGGTCTTA
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
89 17 0.15
91 49 0.43
92 9 0.08
93 19 0.17
94 19 0.17
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.31
Consensus pattern (92 bp):
AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCTCCTTTATTTTTTTACACTCAAT
TGAGCACTTGAACTTTCAAAATGAACC
Found at i:50042762 original size:9 final size:9
Alignment explanation
Indices: 50042749--50042862 Score: 83
Period size: 10 Copynumber: 12.4 Consensus size: 9
50042739 AAAATTAGAA
50042749 AAAAAGTTAT
1 AAAAA-TTAT
50042759 AAAAATTATT
1 AAAAATTA-T
**
50042769 AAATTTTAAT
1 AAAAATT-AT
*
50042779 AAAAATATAA
1 AAAAAT-TAT
50042789 AAAAATTAT
1 AAAAATTAT
50042798 --AAATTAT
1 AAAAATTAT
50042805 AAAAATTAT
1 AAAAATTAT
50042814 AAAAA-TA-
1 AAAAATTAT
* *
50042821 AAAAACTGT
1 AAAAATTAT
*
50042830 AAAATTTTAT
1 AAAA-ATTAT
*
50042840 AAAAATCAT
1 AAAAATTAT
50042849 AAAAAATTAT
1 -AAAAATTAT
50042859 AAAA
1 AAAA
50042863 TGTATCAAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
7 12 0.15
8 3 0.04
9 28 0.34
10 37 0.45
11 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:50042782 original size:29 final size:25
Alignment explanation
Indices: 50042749--50042851 Score: 80
Period size: 26 Copynumber: 3.8 Consensus size: 25
50042739 AAAATTAGAA
50042749 AAAAAGTTATAAAAATTATTAAATTTTAAT
1 AAAAA-TTATAAAAATTA-TAAA--TT-AT
*
50042779 AAAAATATAAAAAAATTATAAATTAT
1 AAAAAT-TATAAAAATTATAAATTAT
* * * *
50042805 AAAAATTATAAAAATAAAAAACTGT
1 AAAAATTATAAAAATTATAAATTAT
* *
50042830 AAAATTTTATAAAAATCATAAA
1 AAAA-ATTATAAAAATTATAAA
50042852 AAATTATAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
25 18 0.29
26 22 0.35
27 2 0.03
29 5 0.08
30 15 0.24
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAAATTATAAAAATTATAAATTAT
Found at i:50042805 original size:18 final size:17
Alignment explanation
Indices: 50042781--50042825 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
50042771 ATTTTAATAA
50042781 AAATATAAAAAAATTAT
1 AAATATAAAAAAATTAT
*
50042798 AAAT-TATAAAAATTAT
1 AAATATAAAAAAATTAT
*
50042814 AAAAATAAAAAA
1 AAATATAAAAAA
50042826 CTGTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATATAAAAAAATTAT
Found at i:50042809 original size:27 final size:30
Alignment explanation
Indices: 50042759--50042818 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 30
50042749 AAAAAGTTAT
*
50042759 AAAAATTATTAAATTTTAATAAAAATATAA
1 AAAAATTATTAAATTATAATAAAAATATAA
*
50042789 AAAAATTA-TAAATTAT-A-AAAATTATAA
1 AAAAATTATTAAATTATAATAAAAATATAA
50042816 AAA
1 AAA
50042819 TAAAAAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.43
28 1 0.04
29 7 0.25
30 8 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAAATTATTAAATTATAATAAAAATATAA
Found at i:50042872 original size:29 final size:29
Alignment explanation
Indices: 50042818--50042873 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
50042808 AATTATAAAA
* *
50042818 ATAAAAAACTGTAAAATTTTATAAAAATC
1 ATAAAAAACTATAAAATTGTATAAAAATC
*
50042847 ATAAAAAATTATAAAA-TGTATCAAAAA
1 ATAAAAAACTATAAAATTGTAT-AAAAA
50042874 GTCCCTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (29 bp):
ATAAAAAACTATAAAATTGTATAAAAATC
Found at i:50042968 original size:29 final size:28
Alignment explanation
Indices: 50042928--50042987 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
50042918 GAATCCTAGC
* *
50042928 TTTTTTATATTTCTATATTTTTATAGTT
1 TTTTTTAGATTTCTATATTTTTATAATT
* *
50042956 TTTTTTACGATTTTTATATTTTTCTAATT
1 TTTTTTA-GATTTCTATATTTTTATAATT
50042985 TTT
1 TTT
50042988 AATAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (28 bp):
TTTTTTAGATTTCTATATTTTTATAATT
Found at i:50043194 original size:89 final size:89
Alignment explanation
Indices: 50043093--50043287 Score: 234
Period size: 89 Copynumber: 2.2 Consensus size: 89
50043083 TAATAAAATC
* * * * *
50043093 AGGGACTTAATTACTTTTTTTGGAAAA-TTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAG
1 AGGGACTTAATTACTTTTTTT-GAAAAGATTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAA
* * * *
50043157 TATCCAATTGAGTGTAAAAAAAAGT
65 TACCCAAATGAATGCAAAAAAAAGT
* * *
50043182 AGGGGCTTAATTACTTTTTTTGAAAAGATTTGAGGGCCTTTTTGATATATTTTAAAAGTTTAAAT
1 AGGGACTTAATTACTTTTTTTGAAAAGATTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAAT
50043247 ACCCAAATGAATGCAAAAAAAA--
66 ACCCAAATGAATGCAAAAAAAAGT
**
50043269 AAAGACTTAATTACTTTTT
1 AGGGACTTAATTACTTTTT
50043288 CTTTTTTGAA
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
87 16 0.18
88 5 0.06
89 69 0.77
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (89 bp):
AGGGACTTAATTACTTTTTTTGAAAAGATTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAAT
ACCCAAATGAATGCAAAAAAAAGT
Found at i:50045001 original size:15 final size:15
Alignment explanation
Indices: 50044977--50045113 Score: 54
Period size: 15 Copynumber: 9.1 Consensus size: 15
50044967 TTTAAACATA
*
50044977 ATTATTATTAAATAT
1 ATTATAATTAAATAT
50044992 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
50045006 A-TATAATTTAATAAT
1 ATTATAATTAAAT-AT
* * * *
50045021 ATTCTTATATGAATTT
1 ATTATAAT-TAAATAT
* *
50045037 ACTCA-AATCATAATAT
1 A-TTATAATTA-AATAT
* *
50045053 ATGATACTATAAA-AT
1 ATTATAAT-TAAATAT
50045068 A-TA-AATTAACATA-
1 ATTATAATTAA-ATAT
*
50045081 ATTATTATTAAATAT
1 ATTATAATTAAATAT
*
50045096 ATTTTAATTAAAATAT
1 ATTATAATT-AAATAT
50045112 AT
1 AT
50045114 GATTTAATAA
Statistics
Matches: 88, Mismatches: 20, Indels: 27
0.65 0.15 0.20
Matches are distributed among these distances:
12 3 0.03
13 13 0.15
14 10 0.11
15 31 0.35
16 25 0.28
17 6 0.07
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:50045005 original size:16 final size:16
Alignment explanation
Indices: 50044968--50045009 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
50044958 TTAATCATAT
*
50044968 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
50044984 TT-AAATATATTATAA
1 TTAAAATATATTATAA
50044999 TTAAAATATAT
1 TTAAAATATAT
50045010 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:50045113 original size:18 final size:17
Alignment explanation
Indices: 50045090--50045126 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
50045080 AATTATTATT
50045090 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
50045106 AAATATATGATTTAATA
1 AAATATATGATTTAATA
50045123 AAAT
1 AAAT
50045127 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:50045175 original size:47 final size:46
Alignment explanation
Indices: 50045109--50045276 Score: 143
Period size: 47 Copynumber: 3.7 Consensus size: 46
50045099 TTAATTAAAA
*
50045109 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * **
50045156 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATTA-TAATA-ATA-AATTTTCT
* * *
50045204 TA-AT-AA--TATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
50045247 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
50045277 ATATTAAATA
Statistics
Matches: 94, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
42 2 0.02
43 8 0.09
44 18 0.19
45 5 0.05
46 5 0.05
47 40 0.43
48 14 0.15
49 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:50045198 original size:26 final size:28
Alignment explanation
Indices: 50045168--50045228 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
50045158 TATGAATTTG
*
50045168 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
50045194 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
50045222 TAAAATT
1 TATAATT
50045229 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:50045203 original size:101 final size:93
Alignment explanation
Indices: 50045066--50045350 Score: 328
Period size: 91 Copynumber: 3.0 Consensus size: 93
50045056 ATACTATAAA
* * * * *
50045066 ATATAAATTAACATAATTATTATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTA
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT-
*
50045130 AAATAATTATAACTAATAAATTTTCTTATATGAATTT
64 ---T--CT-TAA-TAATAAATTTTCTTATATGAATTT
* *
50045167 GTATAATTTAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCATAAAA--TTC
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTC
*
50045230 TTGATAATAAATTTTCTTATATGAATTT
66 TTAATAATAAATTTTCTTATATGAATTT
* * *
50045258 ATACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTC
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTC
*
50045321 TTAATAATAAAATGTTCTTATATGAATTT
66 TTAATAAT-AAATTTTCTTATATGAATTT
50045350 A
1 A
50045351 CTAAAATCAA
Statistics
Matches: 166, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
91 89 0.54
92 22 0.13
93 1 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 49 0.30
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (93 bp):
ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTC
TTAATAATAAATTTTCTTATATGAATTT
Found at i:50045238 original size:91 final size:91
Alignment explanation
Indices: 50045143--50045350 Score: 344
Period size: 91 Copynumber: 2.3 Consensus size: 91
50045133 TAATTATAAC
* * * *
50045143 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
50045208 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
50045234 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
50045299 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
50045325 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
50045351 CTAAAATCAA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 89 0.82
92 20 0.18
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:50045310 original size:44 final size:43
Alignment explanation
Indices: 50045168--50045310 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
50045158 TATGAATTTG
* *
50045168 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
50045212 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
50045259 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
50045303 TATAATTT
1 TATAATTT
50045311 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:50045325 original size:47 final size:47
Alignment explanation
Indices: 50045193--50045331 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
50045183 TTATTATTAC
* *
50045193 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
50045240 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
50045284 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
50045331 A
1 A
50045332 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:50048455 original size:15 final size:15
Alignment explanation
Indices: 50048435--50048470 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
50048425 GGTATATGTA
50048435 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
50048450 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
50048465 TAATTG
1 TAATTG
50048471 TTGTTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (15 bp):
TAATTGACCTAAAAT
Found at i:50048692 original size:6 final size:6
Alignment explanation
Indices: 50048681--50048716 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
50048671 TAGTTTGAAC
50048681 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
50048717 TTTCGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:50049173 original size:13 final size:13
Alignment explanation
Indices: 50049155--50049179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50049145 ATCAAATTTG
50049155 TATGTACTCTTTA
1 TATGTACTCTTTA
50049168 TATGTACTCTTT
1 TATGTACTCTTT
50049180 CACTAATAAA
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:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:50049701 original size:29 final size:29
Alignment explanation
Indices: 50049668--50049735 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
50049658 AACAAATGCA
50049668 ACAATTTCCAGTTTCATTGAAAACAGCAG
1 ACAATTTCCAGTTTCATTGAAAACAGCAG
*
50049697 ACAATTTCCAGTTTCATTGAAAACTGCAG
1 ACAATTTCCAGTTTCATTGAAAACAGCAG
50049726 ACAATTTCCA
1 ACAATTTCCA
50049736 TTGCAACAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (29 bp):
ACAATTTCCAGTTTCATTGAAAACAGCAG
Found at i:50050842 original size:15 final size:15
Alignment explanation
Indices: 50050822--50050850 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
50050812 GCAATACAAA
50050822 CATACAAAACAGAAC
1 CATACAAAACAGAAC
50050837 CATACAAAACAGAA
1 CATACAAAACAGAA
50050851 ACCACAAAAG
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:0.62, C:0.24, G:0.07, T:0.07
Consensus pattern (15 bp):
CATACAAAACAGAAC
Found at i:50053156 original size:52 final size:52
Alignment explanation
Indices: 50053098--50053202 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
50053088 GAACTAAACC
* *
50053098 CCCTCGAGTGCTAAATTTCTTTCTCAATTAACCAAAAGCAACATTACTTAAA
1 CCCTCGAGTGCTAAATTTCTTTCTCAAATAACCAAAAGCAACATCACTTAAA
* *
50053150 CCCTCGAGTGCTAAATTTCTTTCTCAAATAACCAATAGCAACATCATTTAAA
1 CCCTCGAGTGCTAAATTTCTTTCTCAAATAACCAAAAGCAACATCACTTAAA
50053202 C
1 C
50053203 TTGCATTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (52 bp):
CCCTCGAGTGCTAAATTTCTTTCTCAAATAACCAAAAGCAACATCACTTAAA
Found at i:50053838 original size:16 final size:16
Alignment explanation
Indices: 50053817--50053853 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
50053807 TTCACAATAT
50053817 TTACATTTAGCCTTGC
1 TTACATTTAGCCTTGC
50053833 TTACATTTAGCCTTGC
1 TTACATTTAGCCTTGC
50053849 TTACA
1 TTACA
50053854 CCCTCACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
TTACATTTAGCCTTGC
Found at i:50055220 original size:21 final size:21
Alignment explanation
Indices: 50055195--50055235 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
50055185 GGACTTGAGA
50055195 AATTTTAGATTAGGGATTTTC
1 AATTTTAGATTAGGGATTTTC
* *
50055216 AATTTTGGGTTAGGGATTTT
1 AATTTTAGATTAGGGATTTT
50055236 TGAGTCTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (21 bp):
AATTTTAGATTAGGGATTTTC
Found at i:50066647 original size:2 final size:2
Alignment explanation
Indices: 50066640--50066670 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
50066630 TGAAAATTGA
50066640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50066671 ACCTAGTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50067326 original size:18 final size:18
Alignment explanation
Indices: 50067291--50067330 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50067281 TGGTGGACGG
* **
50067291 TTTAATTTTTTATTTTAT
1 TTTAATTTTATAAGTTAT
50067309 TTTAATTTTATAAGTTAT
1 TTTAATTTTATAAGTTAT
50067327 TTTA
1 TTTA
50067331 TTATTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTAATTTTATAAGTTAT
Found at i:50067369 original size:3 final size:3
Alignment explanation
Indices: 50067361--50067404 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
50067351 GGTTAAAAAT
*
50067361 ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
50067405 TAAAGTTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:50071510 original size:3 final size:3
Alignment explanation
Indices: 50071502--50071536 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
50071492 TGCTTTCAAA
*
50071502 AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
50071537 AGTGTGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:50073999 original size:11 final size:11
Alignment explanation
Indices: 50073978--50074008 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
50073968 TTATAAATTT
50073978 ATTAATATTTAA
1 ATTAAT-TTTAA
50073990 ATTAATTTTAA
1 ATTAATTTTAA
50074001 ATTAATTT
1 ATTAATTT
50074009 AATGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTAATTTTAA
Found at i:50088037 original size:13 final size:13
Alignment explanation
Indices: 50088000--50088040 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
50087990 TTTTGCTTTA
50088000 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
50088013 CT--TTGTGCCTCTG
1 CTGCTT-TG-CTCTG
50088026 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
50088039 CT
1 CT
50088041 TTGCTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 16 0.67
14 2 0.08
15 2 0.08
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (13 bp):
CTGCTTTGCTCTG
Found at i:50091065 original size:18 final size:18
Alignment explanation
Indices: 50091042--50091081 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
50091032 GGAAATGATA
*
50091042 TTCACATTTTAAAGGATG
1 TTCACATTTCAAAGGATG
*
50091060 TTCACATTTCAAATGATG
1 TTCACATTTCAAAGGATG
50091078 TTCA
1 TTCA
50091082 AATTGATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (18 bp):
TTCACATTTCAAAGGATG
Found at i:50091679 original size:72 final size:72
Alignment explanation
Indices: 50091510--50091746 Score: 313
Period size: 72 Copynumber: 3.3 Consensus size: 72
50091500 CAATGCTAAA
* *
50091510 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTAGATATTGAATTTATGTTCTACTTA--TAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGCTTTTTAGATATTGAATTTATGTTCTACTTATTTAT
50091573 GTGTAAT
66 GTGTAAT
* *
50091580 CTAGTTTTATCAATGGCTGTTTATGTTTGCTTTTTAGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGCTTTTTAGATATTGAATTTATGTTCTACTTATTTAT
50091645 GTGTAAT
66 GTGTAAT
* * * * *
50091652 CTAGTTTTATTAGTAGTTGTTTATGTTT-CGTCTTTGGATATTAAATTTATGTTCTACTTATTTA
1 CTAGTTTTATCAATAGTTGTTTATGTTTGC-TTTTTAGATATTGAATTTATGTTCTACTTATTTA
* *
50091716 TACT-AAAT
65 T-GTGTAAT
*
50091724 -TAATTTTATCAATAGTTGTTTAT
1 CTAGTTTTATCAATAGTTGTTTAT
50091747 TTATGATTTT
Statistics
Matches: 147, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
70 56 0.38
71 21 0.14
72 69 0.47
73 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGCTTTTTAGATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:50091762 original size:142 final size:142
Alignment explanation
Indices: 50091510--50091771 Score: 323
Period size: 142 Copynumber: 1.8 Consensus size: 142
50091500 CAATGCTAAA
* * * *
50091510 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTAGATATTGAATTTATGTTCTACTTATATGT
1 CTAGTTTTATCAATAGTTATTTATGTTTCGTCTTTAGATATTAAATTTATGTTCTACTTATATAT
* * * * **
50091575 GTAATCTAGTTTTATCAATGGCTGTTTATGTTTGCTTTTTAGATATTGAATTTATGTTCTACTTA
66 CTAATCTAATTTTATCAATAGCTGTTTATGTTTGCATTTTAGATATAAAATTTATGTTCTACTTA
50091640 TTTATGTGTAAT
131 TTTATGTGTAAT
* * * * *
50091652 CTAGTTTTATTAGTAGTTGTTTATGTTTCGTCTTTGGATATTAAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTATTTATGTTTCGTCTTTAGATATTAAATTTATGTTCTACTTATATAT
* *
50091717 ACTAAAT-TAATTTTATCAATAGTTGTTTAT-TTATG-ATTTTGGATATAAAATTTAT
66 -CT-AATCTAATTTTATCAATAGCTGTTTATGTT-TGCATTTTAGATATAAAATTTAT
50091772 TCATAGGTGA
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
142 74 0.74
143 23 0.23
144 3 0.03
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.54
Consensus pattern (142 bp):
CTAGTTTTATCAATAGTTATTTATGTTTCGTCTTTAGATATTAAATTTATGTTCTACTTATATAT
CTAATCTAATTTTATCAATAGCTGTTTATGTTTGCATTTTAGATATAAAATTTATGTTCTACTTA
TTTATGTGTAAT
Found at i:50098203 original size:22 final size:23
Alignment explanation
Indices: 50098173--50098219 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
50098163 AAGTTGGTTA
50098173 TTTACATGTTTAGGG-CTTAGGG
1 TTTACATGTTTAGGGTCTTAGGG
* *
50098195 TTTAGATGTTTAGGGTTTTAGGG
1 TTTACATGTTTAGGGTCTTAGGG
50098218 TT
1 TT
50098220 GGGATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.17, C:0.04, G:0.32, T:0.47
Consensus pattern (23 bp):
TTTACATGTTTAGGGTCTTAGGG
Found at i:50098308 original size:28 final size:29
Alignment explanation
Indices: 50098277--50098344 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 29
50098267 GATTTTGGAG
*
50098277 AAAATAAATTGGGTTTTAGGA-ATTTTAA
1 AAAATAAATTAGGTTTTAGGATATTTTAA
* * *
50098305 AAAATAAATTAGGTTTTATGATTTTTTTA
1 AAAATAAATTAGGTTTTAGGATATTTTAA
50098334 AAAATAAATTA
1 AAAATAAATTA
50098345 AATTAGGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
28 19 0.54
29 16 0.46
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.43
Consensus pattern (29 bp):
AAAATAAATTAGGTTTTAGGATATTTTAA
Found at i:50098413 original size:28 final size:27
Alignment explanation
Indices: 50098366--50098420 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
50098356 ATTGTTTATA
50098366 AAAAATAAATTAGAGCTTAGGGATTTTT
1 AAAAATAAATTAGAGCTTAGGG-TTTTT
* * *
50098394 AAAAATAAATTTGTGTTTAGGGTTTTT
1 AAAAATAAATTAGAGCTTAGGGTTTTT
50098421 GTAATAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (27 bp):
AAAAATAAATTAGAGCTTAGGGTTTTT
Found at i:50098718 original size:124 final size:127
Alignment explanation
Indices: 50098492--50098760 Score: 363
Period size: 125 Copynumber: 2.2 Consensus size: 127
50098482 TTTTGTTCAG
**
50098492 TCAGCAAAAGTACT-AAAAAAGCTCCCAGCTGGATGCTATTTTTCTAAAGTAGTTTCTAAAAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTATTTTTCTAAAGTAGTTTCTAAAAAAA
* * * *
50098556 TAATTTTGAGAAGATGATTCTGAAAAATAGGGTCAAAAA-TGCTTTAAGCATGATGCACT-T
66 TAATTTTGAGAAGATGATTCTAAAAAATAGGGTCAAAAAGCGCTTCAAGCAGGATGCACTGT
* * *
50098616 TCAGCAAAAATACTGAAAAAAGCTCCCA-CATGGACATTATTTTTCTACAGTAGTTTCT-AAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCAGC-TGGACACTATTTTTCTAAAGTAGTTTCTAAAAAA
* * *
50098679 ATAATTTTGAGAAGATGGTTCTAAAAAATTAGTGT-AAAAAGCGCTTCAAGCAGGATGTACTGT
65 ATAATTTTGAGAAGATGATTCTAAAAAA-TAGGGTCAAAAAGCGCTTCAAGCAGGATGCACTGT
50098742 T-AGCAAAAGTACTGAAAAA
1 TCAGCAAAAGTACTGAAAAA
50098761 TGGAAGAGTG
Statistics
Matches: 127, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
124 50 0.39
125 75 0.59
126 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (127 bp):
TCAGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTATTTTTCTAAAGTAGTTTCTAAAAAAA
TAATTTTGAGAAGATGATTCTAAAAAATAGGGTCAAAAAGCGCTTCAAGCAGGATGCACTGT
Found at i:50099793 original size:59 final size:59
Alignment explanation
Indices: 50099674--50099805 Score: 171
Period size: 59 Copynumber: 2.2 Consensus size: 59
50099664 TCTATTACCT
* *
50099674 TATTTAAAAGAACTTATATTTTATTAAATAGGACAAAATATAAAAACAATTTGTATAAATA
1 TATTTAAAA-AAATTATATTTTATTAAATA-GACAAAATATAAAAACAATTTGTACAAATA
* *
50099735 TATTTAAAACAAATTCTATTTTATTAAAT-GA-AATAATATAAAAACAGTTTGTACAAATA
1 TATTTAAAA-AAATTATATTTTATTAAATAGACAA-AATATAAAAACAATTTGTACAAATA
50099794 TA-TTAAAAAAAT
1 TATTTAAAAAAAT
50099806 AAATACATGT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
57 4 0.06
58 8 0.12
59 27 0.42
61 26 0.40
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (59 bp):
TATTTAAAAAAATTATATTTTATTAAATAGACAAAATATAAAAACAATTTGTACAAATA
Found at i:50101945 original size:12 final size:11
Alignment explanation
Indices: 50101930--50101968 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
50101920 AGTTTTTTTG
50101930 AGAAATTTAGAA
1 AGAAATTTAG-A
50101942 AGAAATTTAGA
1 AGAAATTTAGA
50101953 AGAAA-TTA-A
1 AGAAATTTAGA
50101962 AGAAATT
1 AGAAATT
50101969 GTATGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.23
10 4 0.15
11 6 0.23
12 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (11 bp):
AGAAATTTAGA
Found at i:50102286 original size:29 final size:30
Alignment explanation
Indices: 50102228--50102288 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
50102218 TTTTGGCCCA
** *
50102228 TTCCGATAAATAAAGTTTAAAGTGGCCCAT
1 TTCCGATAAATAAAGTGGAAAGTGGACCAT
50102258 TTCCG-TAAATAAAGTAGGAAA-TGGACCAT
1 TTCCGATAAATAAAGT-GGAAAGTGGACCAT
50102287 TT
1 TT
50102289 TTAGTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (30 bp):
TTCCGATAAATAAAGTGGAAAGTGGACCAT
Found at i:50107136 original size:1 final size:1
Alignment explanation
Indices: 50107130--50107155 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
50107120 GGAACTTTCC
50107130 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
50107156 GCAGAGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.