Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 142 of 172
Found at i:40982296 original size:31 final size:31
Alignment explanation
Indices: 40982236--40982302 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
40982226 TGAAAATTTA
* * * *
40982236 AAAAACTTGAAGGGTCTAATTAAATTTTTTT
1 AAAAACTTGAAGGGACTAATGAAACTTTTTC
* *
40982267 AAAAACTTTAAGGGAGTAATGAAACTTTTTC
1 AAAAACTTGAAGGGACTAATGAAACTTTTTC
40982298 AAAAA
1 AAAAA
40982303 TTTTGGGAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.34
Consensus pattern (31 bp):
AAAAACTTGAAGGGACTAATGAAACTTTTTC
Found at i:40984441 original size:50 final size:50
Alignment explanation
Indices: 40984317--40984563 Score: 266
Period size: 50 Copynumber: 4.8 Consensus size: 50
40984307 GATAATAACA
* * ** * *
40984317 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
40984368 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
40984418 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
40984467 TGCCCATGCCATGT-CCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
40984521 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
40984564 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
48 21 0.13
49 29 0.17
50 40 0.24
51 33 0.20
52 2 0.01
53 1 0.01
54 2 0.01
55 13 0.08
56 25 0.15
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:40984542 original size:104 final size:101
Alignment explanation
Indices: 40984316--40984563 Score: 351
Period size: 101 Copynumber: 2.4 Consensus size: 101
40984306 TGATAATAAC
*
40984316 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAT-CTCTCGTGATGGTGCCCATGCCATG
* *
40984381 TCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCATCTAGG
* *
40984418 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCGTGAT-GGTGCCCATGCCATG
40984480 T-CCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-AGG
*
40984521 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
40984564 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 6, Indels: 13
0.87 0.04 0.09
Matches are distributed among these distances:
98 28 0.21
99 22 0.17
101 39 0.30
102 1 0.01
103 2 0.02
104 36 0.27
105 4 0.03
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (101 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCATCTAGG
Found at i:40984679 original size:13 final size:13
Alignment explanation
Indices: 40984658--40984689 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40984648 GCTTGGATCA
*
40984658 TCATCAAATAAAT
1 TCATAAAATAAAT
40984671 TCATAAAATAAAT
1 TCATAAAATAAAT
40984684 TCATAA
1 TCATAA
40984690 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:40985356 original size:38 final size:38
Alignment explanation
Indices: 40985305--40985380 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
40985295 CATTACAGAA
40985305 TGAATATTATCCCAAAGAGATAAATGATATCTTATGAG
1 TGAATATTATCCCAAAGAGATAAATGATATCTTATGAG
40985343 TGAATATTATCCCAAAGAGATAAATGATATCTTATGAG
1 TGAATATTATCCCAAAGAGATAAATGATATCTTATGAG
40985381 GGTAACACAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (38 bp):
TGAATATTATCCCAAAGAGATAAATGATATCTTATGAG
Found at i:40985964 original size:25 final size:26
Alignment explanation
Indices: 40985898--40985967 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
40985888 TTTCTTGAAT
* *
40985898 TTTTATC-AGGGTAAAATCGTCAAAA
1 TTTTATCGAAGGTAAAATTGTCAAAA
40985923 TTTTATCGAAGGT-AAATTGTCAAAA
1 TTTTATCGAAGGTAAAATTGTCAAAA
*
40985948 TTTTATTG-AGGTAAAATTGT
1 TTTTATCGAAGGTAAAATTGT
40985968 GGTGAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
24 4 0.10
25 32 0.80
26 4 0.10
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (26 bp):
TTTTATCGAAGGTAAAATTGTCAAAA
Found at i:40997466 original size:59 final size:59
Alignment explanation
Indices: 40997401--40997517 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 59
40997391 AAGCATACAG
40997401 TGAGTTGACACAAGAAATGAACAAGCCATGAATCTGAAGGTCAGGCAAAGCTCACTAAA
1 TGAGTTGACACAAGAAATGAACAAGCCATGAATCTGAAGGTCAGGCAAAGCTCACTAAA
* *
40997460 TGAGTTGACACAAGAATTGAACAAGCCATGAATCTGACGGTCAGGCAAAGCTCACTAA
1 TGAGTTGACACAAGAAATGAACAAGCCATGAATCTGAAGGTCAGGCAAAGCTCACTAA
40997518 TGCCGTGTCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (59 bp):
TGAGTTGACACAAGAAATGAACAAGCCATGAATCTGAAGGTCAGGCAAAGCTCACTAAA
Found at i:41005718 original size:14 final size:13
Alignment explanation
Indices: 41005699--41005757 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
41005689 AATATTGAGT
41005699 ATTTAAAATTCGAA
1 ATTTAAAATT-GAA
*
41005713 ATTTAAAATTAAA
1 ATTTAAAATTGAA
*
41005726 ATTTGAAGATTGAAA
1 ATTT-AAAATTG-AA
*
41005741 ATATAAAATTGGAA
1 ATTTAAAATT-GAA
41005755 ATT
1 ATT
41005758 GGGGATTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
13 6 0.17
14 24 0.67
15 6 0.17
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.36
Consensus pattern (13 bp):
ATTTAAAATTGAA
Found at i:41013929 original size:17 final size:18
Alignment explanation
Indices: 41013895--41013931 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
41013885 ATTATAGTTT
41013895 AATTCTTAAAAATGATAA
1 AATTCTTAAAAATGATAA
41013913 AATTC-TAAAATAT-ATAA
1 AATTCTTAAAA-ATGATAA
41013930 AA
1 AA
41013932 ATATACTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (18 bp):
AATTCTTAAAAATGATAA
Found at i:41019342 original size:3 final size:3
Alignment explanation
Indices: 41019334--41019389 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
41019324 CAATAATGTA
41019334 ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41019380 ATT ATT ATT A
1 ATT ATT ATT A
41019390 CAATGATGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 47 0.92
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:41019358 original size:17 final size:17
Alignment explanation
Indices: 41019336--41019387 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
41019326 ATAATGTAAT
41019336 TATTATTATTATTATTA
1 TATTATTATTATTATTA
41019353 TATTATTATTATTATTA
1 TATTATTATTATTATTA
41019370 TATTATTATTATTATTA
1 TATTATTATTATTATTA
41019387 T
1 T
41019388 TACAATGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:41019504 original size:29 final size:30
Alignment explanation
Indices: 41019451--41019509 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
41019441 ATATAATAAA
*
41019451 ATAATTTATGATAATTCATTGTT-AATATT
1 ATAATTTATGATAATTAATTGTTAAATATT
41019480 ATAATTTATGA-AATATAAATT-TTAAATATT
1 ATAATTTATGATAAT-T-AATTGTTAAATATT
41019510 TTTAAGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 3 0.12
29 14 0.54
30 9 0.35
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (30 bp):
ATAATTTATGATAATTAATTGTTAAATATT
Found at i:41020394 original size:13 final size:13
Alignment explanation
Indices: 41020378--41020428 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
41020368 TTTAAACCAA
*
41020378 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
*
41020391 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
41020404 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
41020417 ACTTTTCAAAAG
1 ACTTTTCAAAAG
41020429 TAATAAAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.29
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:41033457 original size:76 final size:76
Alignment explanation
Indices: 41033373--41033592 Score: 209
Period size: 78 Copynumber: 2.9 Consensus size: 76
41033363 ACACATATGC
* * ** * *
41033373 ATATATATATATAGAA-AT-CATACTTTTAATTCCATTCAAAAACTTATACATGTATATACTTAT
1 ATATATATAAATAGAACATCCATACCTTTAATTAAATTCAAAAACTTATACATATATATA--TAC
*
41033436 ATATTCGAACCTT
64 ATATTCAAACCTT
* * *
41033449 ATATATATAAATATAACATCCATACCTTTAATTAAATTCAAGATCTTATACATATATATATACAT
1 ATATATATAAATAGAACATCCATACCTTTAATTAAATTCAAAAACTTATACATATATATATACAT
41033514 ATTCAAACC-T
66 ATTCAAACCTT
* * * * * *
41033524 -TATATATACAT--AACATTCTTACCTTTTAACTAAATTCAAGATCTTATACATATATATATATA
1 ATATATATAAATAGAACATCCATACC-TTTAATTAAATTCAAAAACTTATAC--ATATATATATA
41033586 CATATTC
63 CATATTC
41033593 GAACTTCATT
Statistics
Matches: 125, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
72 10 0.08
73 24 0.19
74 10 0.08
75 19 0.15
76 26 0.21
77 2 0.02
78 34 0.27
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.40
Consensus pattern (76 bp):
ATATATATAAATAGAACATCCATACCTTTAATTAAATTCAAAAACTTATACATATATATATACAT
ATTCAAACCTT
Found at i:41033574 original size:73 final size:75
Alignment explanation
Indices: 41033406--41033592 Score: 218
Period size: 73 Copynumber: 2.5 Consensus size: 75
41033396 TTTTAATTCC
* * * * * *
41033406 ATTCAAAAACTTATACATGTATATACTTATATATTCGAACCTTATATATATAAATATAACATCCA
1 ATTCAAGATCTTATACATATATATA--TACATATTCAAACCTTATATATAT-AACATAACATCCA
*
41033471 TACCTTTAATTAA
63 TACCTTTAACTAA
* *
41033484 ATTCAAGATCTTATACATATATATATACATATTCAAACC-T-TATATAT-ACATAACATTCTTAC
1 ATTCAAGATCTTATACATATATATATACATATTCAAACCTTATATATATAACATAACATCCATAC
41033546 CTTTTAACTAA
66 C-TTTAACTAA
41033557 ATTCAAGATCTTATACATATATATATATACATATTC
1 ATTCAAGATCTTATAC--ATATATATATACATATTC
41033593 GAACTTCATT
Statistics
Matches: 97, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
72 13 0.13
73 24 0.25
74 7 0.07
75 19 0.20
76 12 0.12
78 22 0.23
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (75 bp):
ATTCAAGATCTTATACATATATATATACATATTCAAACCTTATATATATAACATAACATCCATAC
CTTTAACTAA
Found at i:41041620 original size:39 final size:37
Alignment explanation
Indices: 41041553--41041645 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
41041543 ACCAGAATGG
* *
41041553 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
41041592 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
41041629 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
41041646 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:41042008 original size:3 final size:3
Alignment explanation
Indices: 41042000--41042047 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
41041990 ATTCCCACTC
* * * *
41042000 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41042048 CTTACCTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:41042048 original size:18 final size:18
Alignment explanation
Indices: 41042001--41042049 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
41041991 TTCCCACTCA
*
41042001 TAATAATAATAATAATAC
1 TAATAATAATACTAATAC
41042019 TAATAATAATACTAATAC
1 TAATAATAATACTAATAC
*
41042037 TAATATTAATACT
1 TAATAATAATACT
41042050 TACCTCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATAATACTAATAC
Found at i:41042049 original size:12 final size:12
Alignment explanation
Indices: 41042000--41042047 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
41041990 ATTCCCACTC
*
41042000 ATAATAATAATA
1 ATAATACTAATA
41042012 ATAATACTAATA
1 ATAATACTAATA
41042024 ATAATACTAATA
1 ATAATACTAATA
* *
41042036 CTAATATTAATA
1 ATAATACTAATA
41042048 CTTACCTCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:41042788 original size:20 final size:20
Alignment explanation
Indices: 41042754--41042793 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41042744 TTCTATTCTG
*
41042754 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
41042774 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
41042794 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:41042960 original size:31 final size:28
Alignment explanation
Indices: 41042924--41042991 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
41042914 TTGTCTTTAT
**
41042924 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
41042954 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
41042983 TTAATTTAT
1 TTAATTTAT
41042992 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:41043008 original size:21 final size:20
Alignment explanation
Indices: 41042970--41043008 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
41042960 TAATTTAATA
*
41042970 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
41042990 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
41043009 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:41044483 original size:29 final size:30
Alignment explanation
Indices: 41044446--41044502 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41044436 TCCGAGCCTT
*
41044446 GGGGAAAAA-TGTAATTATGTAAAAGTTTA
1 GGGGAAAAATTGTAATTATGAAAAAGTTTA
* *
41044475 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTGTAATTATGAAAAAGTT
41044503 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTGTAATTATGAAAAAGTTTA
Found at i:41044732 original size:13 final size:13
Alignment explanation
Indices: 41044714--41044745 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41044704 TTTCCAGCAA
41044714 TTATGAATTTATT
1 TTATGAATTTATT
41044727 TTATGAATTTATT
1 TTATGAATTTATT
*
41044740 TGATGA
1 TTATGA
41044746 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:41044953 original size:50 final size:50
Alignment explanation
Indices: 41044840--41045181 Score: 393
Period size: 50 Copynumber: 6.7 Consensus size: 50
41044830 ATTTGGGTAA
* * *
41044840 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
41044896 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41044946 AGAGGTCCCATGTAAGACCATGTC-GGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41044995 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
** * * *
41045045 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41045096 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
41045146 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
41045182 TTTGGCATGT
Statistics
Matches: 246, Mismatches: 34, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
49 46 0.19
50 85 0.35
51 69 0.28
52 2 0.01
53 3 0.01
55 2 0.01
56 39 0.16
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:41045108 original size:101 final size:101
Alignment explanation
Indices: 41044844--41045188 Score: 543
Period size: 101 Copynumber: 3.4 Consensus size: 101
41044834 GGGTAAAGAG
* * *
41044844 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCCTGT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC----GA-GATGAGAGGTCCCCTAT
* *
41044909 AAGACCATGTCTGGGACATGGCATGGGCACCGA-GACGAG-AG
60 AAGACCATGTCTGGGACATGGCATGGGCACC-ATCACGAGAAC
*
41044950 GTCCCATGTAAGACCATGTC-GGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
41045014 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
66 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
41045050 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
41045115 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
66 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
*
41045151 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
41045189 TGTTATTATC
Statistics
Matches: 228, Mismatches: 8, Indels: 11
0.92 0.03 0.04
Matches are distributed among these distances:
98 1 0.00
99 51 0.22
100 22 0.10
101 117 0.51
104 2 0.01
105 16 0.07
106 19 0.08
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20
Consensus pattern (101 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
Found at i:41053143 original size:26 final size:26
Alignment explanation
Indices: 41053112--41053164 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
41053102 ATAAAAGGTA
41053112 AAAGGAAAGAAAATGGACAAGCTACC
1 AAAGGAAAGAAAATGGACAAGCTACC
41053138 AAAGGAAAGAAAATGGACAAGCTACC
1 AAAGGAAAGAAAATGGACAAGCTACC
41053164 A
1 A
41053165 TCACTTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.23, T:0.08
Consensus pattern (26 bp):
AAAGGAAAGAAAATGGACAAGCTACC
Found at i:41058398 original size:20 final size:20
Alignment explanation
Indices: 41058375--41058443 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 20
41058365 AAGCTTGCAT
*
41058375 TTTTTTTTAA-TTTTTAATA
1 TTTTTTATAACTTTTTAATA
41058394 TTTTTTATAACTTTTTAATAA
1 TTTTTTATAACTTTTTAAT-A
* * *
41058415 TTTATTATAAAATTTTAAATAA
1 TTTTTTAT-AACTTTTTAAT-A
41058437 TTTTTTA
1 TTTTTTA
41058444 GAGATTTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.21
20 8 0.19
21 8 0.19
22 17 0.40
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTATAACTTTTTAATA
Found at i:41058408 original size:11 final size:10
Alignment explanation
Indices: 41058375--41058443 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
41058365 AAGCTTGCAT
*
41058375 TTTTTTTTAA
1 TTTTTTATAA
*
41058385 TTTTTAAT-A
1 TTTTTTATAA
41058394 TTTTTTATAA
1 TTTTTTATAA
*
41058404 CTTTTTAATAA
1 -TTTTTTATAA
*
41058415 TTTATTATAAAA
1 TTT-TT-TATAA
**
41058427 TTTTAAATAA
1 TTTTTTATAA
41058437 TTTTTTA
1 TTTTTTA
41058444 GAGATTTGTT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
9 8 0.18
10 18 0.41
11 12 0.27
12 6 0.14
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:41058409 original size:21 final size:21
Alignment explanation
Indices: 41058373--41058443 Score: 81
Period size: 20 Copynumber: 3.4 Consensus size: 21
41058363 CGAAGCTTGC
* *
41058373 ATTTTTTTTTAATTTTTAAT-
1 ATTTTTTATAAATTTTTAATA
*
41058393 ATTTTTTATAACTTTTTAATA
1 ATTTTTTATAAATTTTTAATA
* *
41058414 ATTTATTATAAAATTTTAAATA
1 ATTTTTTAT-AAATTTTTAATA
41058436 ATTTTTTA
1 ATTTTTTA
41058444 GAGATTTGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.40
21 8 0.19
22 17 0.40
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTTTATAAATTTTTAATA
Found at i:41058435 original size:22 final size:21
Alignment explanation
Indices: 41058383--41058439 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
41058373 ATTTTTTTTT
*
41058383 AATTTTTAAT-ATTTTTTATA
1 AATTTTTAATAATTTATTATA
*
41058403 ACTTTTTAATAATTTATTATAA
1 AATTTTTAATAATTTATTAT-A
*
41058425 AATTTTAAATAATTT
1 AATTTTTAATAATTT
41058440 TTTAGAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.29
21 8 0.26
22 14 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTTTAATAATTTATTATA
Found at i:41065821 original size:19 final size:18
Alignment explanation
Indices: 41065797--41065839 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
41065787 TTTCATGTAA
* *
41065797 AATTTTGGGATGACTCTTG
1 AATTTTAGGATGACAC-TG
*
41065816 AATTTTAGGATTACACTG
1 AATTTTAGGATGACACTG
41065834 AATTTT
1 AATTTT
41065840 CATTTTATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (18 bp):
AATTTTAGGATGACACTG
Found at i:41066921 original size:17 final size:17
Alignment explanation
Indices: 41066899--41066932 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41066889 ACAATTAAGA
*
41066899 TAATATTTTTACATTAT
1 TAATATTATTACATTAT
*
41066916 TAATATTATTATATTAT
1 TAATATTATTACATTAT
41066933 ATTTTGGTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATATTATTACATTAT
Found at i:41075644 original size:17 final size:17
Alignment explanation
Indices: 41075622--41075655 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41075612 ATCCACTAAT
*
41075622 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
41075639 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
41075656 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:41080281 original size:17 final size:17
Alignment explanation
Indices: 41080259--41080292 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41080249 ATCCACTAAT
*
41080259 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
41080276 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
41080293 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:41081915 original size:19 final size:20
Alignment explanation
Indices: 41081876--41081915 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
41081866 TCTTTAACAA
* *
41081876 TATATATTTTTATTTTTATT
1 TATATATTTTTATTATGATT
41081896 TATA-ATTTTTATTATGATT
1 TATATATTTTTATTATGATT
41081915 T
1 T
41081916 GAAACTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TATATATTTTTATTATGATT
Found at i:41082497 original size:13 final size:13
Alignment explanation
Indices: 41082479--41082503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41082469 CTTGAGAACT
41082479 CAAACAACAAAAC
1 CAAACAACAAAAC
41082492 CAAACAACAAAA
1 CAAACAACAAAA
41082504 AGTTTCTCTC
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:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAACAACAAAAC
Found at i:41083462 original size:20 final size:20
Alignment explanation
Indices: 41083434--41083473 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41083424 TTTTAGATTG
41083434 TAAAAAATTATTATAATTTT
1 TAAAAAATTATTATAATTTT
*
41083454 TAAATAATTATTATAATTTT
1 TAAAAAATTATTATAATTTT
41083474 ATTCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAAAATTATTATAATTTT
Found at i:41099294 original size:7 final size:7
Alignment explanation
Indices: 41099284--41099308 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41099274 TGCACATTGC
41099284 TCAGCAT
1 TCAGCAT
41099291 TCAGCAT
1 TCAGCAT
41099298 TCAGCAT
1 TCAGCAT
41099305 TCAG
1 TCAG
41099309 GATCCAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (7 bp):
TCAGCAT
Found at i:41100708 original size:27 final size:27
Alignment explanation
Indices: 41100678--41100752 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
41100668 ATACAAGAGT
41100678 GTGATGCCTATTTGATAGGCGGCACTA
1 GTGATGCCTATTTGATAGGCGGCACTA
* * *
41100705 GTGA-CCCTTATCTGATAGGCGGCACTG
1 GTGATGCC-TATTTGATAGGCGGCACTA
* *
41100732 GTGGTGCCTATTTAATAGGCG
1 GTGATGCCTATTTGATAGGCG
41100753 ACACAGCTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.05
27 35 0.90
28 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (27 bp):
GTGATGCCTATTTGATAGGCGGCACTA
Found at i:41101978 original size:22 final size:24
Alignment explanation
Indices: 41101947--41102019 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 24
41101937 CGGCCCGAAT
41101947 TATATATTAAAAATATATATTTT-
1 TATATATTAAAAATATATATTTTA
*
41101970 TAT-TTTTAATCAAATATATATTTTA
1 TATATATTAA--AAATATATATTTTA
*
41101995 TATATATT--AAATATATATTTAA
1 TATATATTAAAAATATATATTTTA
41102017 TAT
1 TAT
41102020 GGGTCGGGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
22 21 0.49
23 3 0.07
24 13 0.30
25 3 0.07
26 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATATTAAAAATATATATTTTA
Found at i:41101999 original size:11 final size:11
Alignment explanation
Indices: 41101982--41102019 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
41101972 TTTTTAATCA
41101982 AATATATATTT
1 AATATATATTT
* *
41101993 TATATATATTA
1 AATATATATTT
41102004 AATATATATTT
1 AATATATATTT
41102015 AATAT
1 AATAT
41102020 GGGTCGGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:41102666 original size:25 final size:24
Alignment explanation
Indices: 41102612--41102669 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
41102602 TTCACTAAGA
*
41102612 TAATGAAATTTATTATATAATATAT
1 TAAT-AAATTTATTACATAATATAT
*
41102637 AAATAAATTTATTTACATAATA-ATT
1 TAATAAATTTA-TTACATAATATA-T
41102662 TAATAAAT
1 TAATAAAT
41102670 ATGTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
TAATAAATTTATTACATAATATAT
Found at i:41106463 original size:5 final size:5
Alignment explanation
Indices: 41106453--41106481 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
41106443 AAGTGAGAAA
41106453 GAAGG GAAGG GAAGG GAAGG GAAGG GAAG
1 GAAGG GAAGG GAAGG GAAGG GAAGG GAAG
41106482 TCGGAACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (5 bp):
GAAGG
Found at i:41107251 original size:22 final size:24
Alignment explanation
Indices: 41107209--41107252 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
41107199 TTAATATAAA
41107209 TTTAATATGTTATGATAAAACTAT
1 TTTAATATGTTATGATAAAACTAT
*
41107233 TTTAAT-TTTTAT-ATAAAACT
1 TTTAATATGTTATGATAAAACT
41107253 TAAAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (24 bp):
TTTAATATGTTATGATAAAACTAT
Found at i:41109690 original size:28 final size:27
Alignment explanation
Indices: 41109658--41109718 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
41109648 TTAAAATTTT
*
41109658 AATTAAGCT-TTAATAAAAAATTGTAATA
1 AATTAAGCTATTAATAAAAAAGT-TAA-A
* *
41109686 AATTAAGTTATTAATCAAAAAGTTAAA
1 AATTAAGCTATTAATAAAAAAGTTAAA
41109713 AATTAA
1 AATTAA
41109719 TTAAGTCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 11 0.38
29 11 0.38
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (27 bp):
AATTAAGCTATTAATAAAAAAGTTAAA
Found at i:41112771 original size:14 final size:15
Alignment explanation
Indices: 41112752--41112783 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
41112742 TTATTAACAC
41112752 TGTTAAATTT-TTTT
1 TGTTAAATTTATTTT
41112766 TGTTAAATTTATTTT
1 TGTTAAATTTATTTT
41112781 TGT
1 TGT
41112784 GACATTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (15 bp):
TGTTAAATTTATTTT
Found at i:41118296 original size:4 final size:4
Alignment explanation
Indices: 41118280--41118358 Score: 52
Period size: 4 Copynumber: 18.5 Consensus size: 4
41118270 ATACAAGAAG
* * * *
41118280 AATA AAGA AATA AATA AATGC AA-A AATA AATA AATA AATG AATAA AACA
1 AATA AATA AATA AATA AAT-A AATA AATA AATA AATA AATA AAT-A AATA
*
41118329 GAATAA CAATG AATA AATA AACTA AATA AA
1 -AAT-A -AATA AATA AATA AA-TA AATA AA
41118359 CTTGACATTA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
3 2 0.03
4 42 0.72
5 10 0.17
6 4 0.07
ACGTcount: A:0.70, C:0.05, G:0.06, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:41130960 original size:21 final size:21
Alignment explanation
Indices: 41130934--41130974 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41130924 AGACGAGCAA
* *
41130934 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
41130955 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
41130975 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:41139439 original size:14 final size:14
Alignment explanation
Indices: 41139396--41139431 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
41139386 AATTTAAATT
41139396 TAATTATAAAATATA
1 TAATTA-AAAATATA
*
41139411 CAATTAAAAATATA
1 TAATTAAAAATATA
41139425 TAATTAA
1 TAATTAA
41139432 TATTATATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATTAAAAATATA
Found at i:41142204 original size:79 final size:81
Alignment explanation
Indices: 41142069--41142252 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
41142059 TGAATGATGT
* *
41142069 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
*
41142133 GTGCGAGATACTAATTA
66 GTGCGAGATACT-ATAA
* * * **
41142150 -CGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAAT
*
41142211 TGTGCGAGTTACTATAA
65 TGTGCGAGATACTATAA
*
41142228 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
41142253 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
78 4 0.04
79 55 0.62
80 30 0.34
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATAA
Found at i:41142266 original size:40 final size:40
Alignment explanation
Indices: 41142069--41142252 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
41142059 TGAATGATGT
* * * *
41142069 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
41142109 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT-ATAA
41142150 -CGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
41142187 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41142228 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
41142253 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 15, Indels: 16
0.80 0.10 0.11
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 31 0.26
40 76 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41142274 original size:79 final size:79
Alignment explanation
Indices: 41142121--41142285 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
41142111 GGACTAAGAT
* * **
41142121 CCGAAGGCATTTGTGCGAGATACTAATTACGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
41142186 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
41142200 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAATAA-CGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
41142263 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
41142279 CCGAAGG
1 CCGAAGG
41142286 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:41154038 original size:21 final size:22
Alignment explanation
Indices: 41154005--41154045 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41153995 ACAAATGAGT
41154005 TTTTATATTTATAATTTATTTA
1 TTTTATATTTATAATTTATTTA
*
41154027 TTTTAT-TTTATATTTTATT
1 TTTTATATTTATAATTTATT
41154046 ATTGTTCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATATTTATAATTTATTTA
Found at i:41156465 original size:39 final size:40
Alignment explanation
Indices: 41156403--41156491 Score: 126
Period size: 39 Copynumber: 2.2 Consensus size: 40
41156393 TAAAAAGTAT
* * * * *
41156403 TTATATTAAAAAATATACCATAAATATAATAGATGTTTTA
1 TTATATTAAAAAACACACAATAAATATAATAAATATTTTA
41156443 TTATATTAAAAAACACA-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACACAATAAATATAATAAATATTTTA
41156482 TTATATTAAA
1 TTATATTAAA
41156492 TATAATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.66
40 15 0.34
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAAACACACAATAAATATAATAAATATTTTA
Found at i:41158677 original size:26 final size:25
Alignment explanation
Indices: 41158646--41158696 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
41158636 TTCATTTTAT
41158646 ATTTAAAAAATTCAT-TATATTTATAA
1 ATTTAAAAAA--CATATATATTTATAA
41158672 ATTTAAAAAACATATATATTTATAA
1 ATTTAAAAAACATATATATTTATAA
41158697 TATTATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 3 0.12
25 11 0.46
26 10 0.42
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTTAAAAAACATATATATTTATAA
Found at i:41159390 original size:16 final size:16
Alignment explanation
Indices: 41159356--41159390 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41159346 TTTGAAATTT
*
41159356 AAACAAATAATTATCC
1 AAACAAATAATCATCC
*
41159372 AAACAAATAATCATTC
1 AAACAAATAATCATCC
41159388 AAA
1 AAA
41159391 TAAAAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (16 bp):
AAACAAATAATCATCC
Found at i:41160059 original size:96 final size:96
Alignment explanation
Indices: 41159891--41160188 Score: 537
Period size: 96 Copynumber: 3.1 Consensus size: 96
41159881 AATTACTTTA
*
41159891 GAAAAAAAAAGTCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATC
1 GAAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATC
41159956 TATATCTCCACGGTCATTTGTTTACTTTGTG
66 TATATCTCCACGGTCATTTGTTTACTTTGTG
41159987 GAAAAAAAAACATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACT-TAAAAATGGCCATTTTAT
1 GAAAAAAAAA-ATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTAT
41160051 CTATATCTCCACGGTCATTTGTTTACTTTGTG
65 CTATATCTCCACGGTCATTTGTTTACTTTGTG
** *
41160083 G-GGAAAAAAATCGTCTTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATC
1 GAAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATC
41160147 TATATCTCCACGGTCATTTGTTTACTTTGTG
66 TATATCTCCACGGTCATTTGTTTACTTTGTG
41160178 GAAAAAAAAAA
1 GAAAAAAAAAA
41160189 CCTTAGTATA
Statistics
Matches: 193, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
94 34 0.18
95 57 0.30
96 68 0.35
97 34 0.18
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (96 bp):
GAAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATC
TATATCTCCACGGTCATTTGTTTACTTTGTG
Found at i:41160157 original size:95 final size:95
Alignment explanation
Indices: 41159891--41160187 Score: 533
Period size: 95 Copynumber: 3.1 Consensus size: 95
41159881 AATTACTTTA
41159891 GAAAAAAAAAGTCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATC
1 GAAAAAAAAA-TCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATC
41159956 TATATCTCCACGGTCATTTGTTTACTTTGTG
65 TATATCTCCACGGTCATTTGTTTACTTTGTG
41159987 GAAAAAAAAACATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACT-TAAAAATGGCCATTTTAT
1 G-AAAAAAAA-ATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTAT
41160051 CTATATCTCCACGGTCATTTGTTTACTTTGTG
64 CTATATCTCCACGGTCATTTGTTTACTTTGTG
** *
41160083 GGGAAAAAAATCGTCTTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
1 GAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
41160148 ATATCTCCACGGTCATTTGTTTACTTTGTG
66 ATATCTCCACGGTCATTTGTTTACTTTGTG
41160178 GAAAAAAAAA
1 GAAAAAAAAA
41160188 ACCTTAGTAT
Statistics
Matches: 193, Mismatches: 5, Indels: 7
0.94 0.02 0.03
Matches are distributed among these distances:
94 34 0.18
95 64 0.33
96 52 0.27
97 42 0.22
98 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (95 bp):
GAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
ATATCTCCACGGTCATTTGTTTACTTTGTG
Found at i:41164497 original size:29 final size:28
Alignment explanation
Indices: 41164452--41164506 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
41164442 TCATCTAATT
* *
41164452 ATAAAAAATTTTCATTTTAGAACTCAAA
1 ATAAAAAATTTGCATTTAAGAACTCAAA
* *
41164480 ATAAAAAGTTTGCAATTTAAGCACTCA
1 ATAAAAAATTTGC-ATTTAAGAACTCA
41164507 CGTTACATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 11 0.50
29 11 0.50
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (28 bp):
ATAAAAAATTTGCATTTAAGAACTCAAA
Found at i:41164738 original size:22 final size:22
Alignment explanation
Indices: 41164700--41164752 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
41164690 TCTGAAAAAT
* **
41164700 AAAAAAATACATAAATATTTTC
1 AAAAAAATAAATAAATAGATTC
41164722 AAAAAAATATAAT-AATAGATTC
1 AAAAAAATA-AATAAATAGATTC
*
41164744 TAAAAAATA
1 AAAAAAATA
41164753 CATGGAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAAAATAAATAAATAGATTC
Found at i:41164829 original size:59 final size:53
Alignment explanation
Indices: 41164687--41164859 Score: 154
Period size: 59 Copynumber: 3.2 Consensus size: 53
41164677 TTTTGATCCT
* *
41164687 AATTCTGAAAAATAA-AAAAATACATAAATATTTTCAAAAAAATATAATAATA
1 AATTCTAAAAAATAATAAAAATAGATAAATATTTTCAAAAAAATATAATAATA
* ** * * * *
41164739 GATTCTAAAAAATACATGGAAATGGAAAAATATTGTTGACAAGAAATATTAATATATAA
1 AATTCTAAAAAATA-ATAAAAATAGATAAATATT-TTCA-AAAAAATA-TAATA-AT-A
* * *
41164798 AATTTTAAAAAATATATAAAAATAGATAAATATTTT-TAAAAAGTATAATAATA
1 AATTCTAAAAAATA-ATAAAAATAGATAAATATTTTCAAAAAAATATAATAATA
41164851 AATT-TAAAA
1 AATTCTAAAA
41164860 TTTATATTAA
Statistics
Matches: 95, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
52 17 0.18
53 6 0.06
54 14 0.15
55 8 0.08
56 13 0.14
57 5 0.05
58 4 0.04
59 28 0.29
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (53 bp):
AATTCTAAAAAATAATAAAAATAGATAAATATTTTCAAAAAAATATAATAATA
Found at i:41164850 original size:21 final size:21
Alignment explanation
Indices: 41164826--41164873 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
41164816 AAAATAGATA
41164826 AATATTTTTAAAAAGTATAAT
1 AATATTTTTAAAAAGTATAAT
** ** *
41164847 AATAAATTTAAAATTTATATT
1 AATATTTTTAAAAAGTATAAT
41164868 AATATT
1 AATATT
41164874 AATATTAAAT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AATATTTTTAAAAAGTATAAT
Found at i:41166232 original size:6 final size:6
Alignment explanation
Indices: 41166224--41166253 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
41166214 TAGATTCATG
*
41166224 AATATG AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA
41166254 TAAATTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:41168178 original size:21 final size:21
Alignment explanation
Indices: 41168152--41168193 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
41168142 AATATATATA
41168152 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTGAATTT
41168173 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTGAATTT
41168194 GATTTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (21 bp):
TATGTTCTATAAGCTGAATTT
Found at i:41168536 original size:13 final size:13
Alignment explanation
Indices: 41168520--41168544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41168510 TGATATGAAA
41168520 TATATATATATAT
1 TATATATATATAT
41168533 TATATATATATA
1 TATATATATATA
41168545 AAAGAGGTTA
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:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATATATAT
Found at i:41168865 original size:41 final size:41
Alignment explanation
Indices: 41168820--41168911 Score: 132
Period size: 41 Copynumber: 2.2 Consensus size: 41
41168810 GGCTATGTGC
*
41168820 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACCT-TATGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGA-CTATAGGT
* * *
41168861 CTAGCAGGCTTAATGCCGGTGATATATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTATAGGT
41168902 CTAGCAGGCT
1 CTAGCAGGCT
41168912 AAGAGCTGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 2 0.04
41 44 0.96
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTATAGGT
Found at i:41172003 original size:29 final size:29
Alignment explanation
Indices: 41171965--41172030 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
41171955 TATTTAGAGT
* *
41171965 TTTTAATTTAATATATTTATATATTTA-AA
1 TTTTATTTTAATATATTTACA-ATTTACAA
* *
41171994 TTTTATTTTATTTTATTTACAATTTACAA
1 TTTTATTTTAATATATTTACAATTTACAA
41172023 -TTTATTTT
1 TTTTATTTT
41172031 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTATTTTAATATATTTACAATTTACAA
Found at i:41172031 original size:29 final size:29
Alignment explanation
Indices: 41171978--41172036 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
41171968 TAATTTAATA
*
41171978 TATTTATATATTTAAATTTTATTTTATTT
1 TATTTACATATTTAAATTTTATTTTATTT
41172007 TATTTACA-ATTTACAA-TTTATTTTTATTT
1 TATTTACATATTTA-AATTTTA-TTTTATTT
41172036 T
1 T
41172037 TTATTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (29 bp):
TATTTACATATTTAAATTTTATTTTATTT
Found at i:41176412 original size:4 final size:4
Alignment explanation
Indices: 41176403--41176428 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41176393 GTATTATTTC
41176403 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
41176429 TTCTCTTCAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:41190515 original size:10 final size:9
Alignment explanation
Indices: 41190487--41190562 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 9
41190477 TAAAAATTGT
41190487 TAAAA-TTA
1 TAAAATTTA
41190495 TAAAA-TTA
1 TAAAATTTA
41190503 TAAAATTTTA
1 TAAAA-TTTA
41190513 TAAAAATCTTA
1 T-AAAAT-TTA
*
41190524 -AAAAATTA
1 TAAAATTTA
*
41190532 TAAAATATA
1 TAAAATTTA
41190541 TAGAAA--TA
1 TA-AAATTTA
41190549 TAAAATTTTA
1 TAAAA-TTTA
41190559 TAAA
1 TAAA
41190563 GTCGTAAGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
7 3 0.05
8 20 0.36
9 12 0.21
10 14 0.25
11 7 0.12
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (9 bp):
TAAAATTTA
Found at i:41190551 original size:36 final size:33
Alignment explanation
Indices: 41190453--41190553 Score: 87
Period size: 36 Copynumber: 2.8 Consensus size: 33
41190443 GAAAAAAATT
* * *
41190453 AAAATATAAAAAATTAGAAAAATATAAAAATTGTT
1 AAAAT-TATAAAATTA-TAAAATATAAAAATTGTA
41190488 AAAATTATAAAATTATAAAATTTTATAAAAATCT-TAA
1 AAAATTATAAAATTATAAAA---TATAAAAAT-TGT-A
41190525 AAAATTATAAAATATATAGAAATATAAAA
1 AAAATTATAAAAT-TATA-AAATATAAAA
41190554 TTTTATAAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
33 4 0.07
34 9 0.16
35 5 0.09
36 17 0.30
37 14 0.25
38 4 0.07
39 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (33 bp):
AAAATTATAAAATTATAAAATATAAAAATTGTA
Found at i:41190551 original size:46 final size:44
Alignment explanation
Indices: 41190478--41190600 Score: 131
Period size: 46 Copynumber: 2.6 Consensus size: 44
41190468 AGAAAAATAT
* *
41190478 AAAAATTGTTAAAATTATA-AAATTATAAAATTTTATAAAAATCTTA
1 AAAAATT-ATAAAATTATAGAAA-TATAAAATTTTAT-AAAATCGTA
*
41190524 AAAAATTATAAAATATATAGAAATATAAAATTTTATAAAGTCGTA
1 AAAAATTATAAAAT-TATAGAAATATAAAATTTTATAAAATCGTA
*
41190569 AGAAAATTATACAAAATGTAAAGAAATATAAA
1 A-AAAATTAT--AAAAT-TATAGAAATATAAA
41190601 TTTCGTAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
45 14 0.21
46 32 0.48
47 3 0.04
48 18 0.27
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (44 bp):
AAAAATTATAAAATTATAGAAATATAAAATTTTATAAAATCGTA
Found at i:41190823 original size:14 final size:15
Alignment explanation
Indices: 41190780--41190820 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
41190770 ATGATTTTTA
*
41190780 TAAAATTTTCTAATT
1 TAAAATTTTATAATT
*
41190795 T-AATTTTTATAATT
1 TAAAATTTTATAATT
41190809 TAAAATTTTATA
1 TAAAATTTTATA
41190821 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TAAAATTTTATAATT
Found at i:41192433 original size:132 final size:136
Alignment explanation
Indices: 41192244--41192487 Score: 460
Period size: 133 Copynumber: 1.8 Consensus size: 136
41192234 TTAAAGAATA
41192244 TTCACATGCGAATACTGTTCTTTTACGCAGAAAATTTCAGGCCCTGTTGCATGTACGCTTC-TCT
1 TTCACATGCGAATACTGTTCTTTTACGCAGAAAATTTCAGGCCCTGTTGCATGTACGCTTCTTCT
41192308 CTTCAAACTCTGTTTTACTGCACTCTTATTCTAATTTTTGGCAAAATAAATCCGTGGTCTATGTC
66 CTTCAAACTCTGTTTTACTGCACTCTTATTCTAATTTTTGGCAAAATAAATCCGTGGTCTATGTC
41192373 AGGTGT
131 AGGTGT
41192379 TTCA-ATGCGAATA-T-TTCTTTTACGCAGAAAATTTCAGGCCCTGTTGCATGTACGCTTCTTCT
1 TTCACATGCGAATACTGTTCTTTTACGCAGAAAATTTCAGGCCCTGTTGCATGTACGCTTCTTCT
41192441 CTTCAAACTCTGTTTTACTGCACTCTTATTCTAATTTTTGGCAAAAT
66 CTTCAAACTCTGTTTTACTGCACTCTTATTCTAATTTTTGGCAAAAT
41192488 TGAACGTGAT
Statistics
Matches: 108, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
132 44 0.41
133 51 0.47
134 9 0.08
135 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (136 bp):
TTCACATGCGAATACTGTTCTTTTACGCAGAAAATTTCAGGCCCTGTTGCATGTACGCTTCTTCT
CTTCAAACTCTGTTTTACTGCACTCTTATTCTAATTTTTGGCAAAATAAATCCGTGGTCTATGTC
AGGTGT
Found at i:41200571 original size:6 final size:6
Alignment explanation
Indices: 41200562--41200590 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
41200552 AAATAAAATT
41200562 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
41200591 GTCTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:41200683 original size:44 final size:45
Alignment explanation
Indices: 41200634--41200731 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 45
41200624 TGATTCAATT
**
41200634 CGGTTAATTCAGGTAATTTGGTTAATTCGGGTAATCCGG-TAATC
1 CGGTTAATTCAGGTAATCCGGTTAATTCGGGTAATCCGGTTAATC
* * *
41200678 CGGTTAATTCGGGTAATCCGGTTAATTCGGGTAATTCGGTTAATT
1 CGGTTAATTCAGGTAATCCGGTTAATTCGGGTAATCCGGTTAATC
*
41200723 CTGTTAATT
1 CGGTTAATT
41200732 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 35 0.74
45 12 0.26
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.39
Consensus pattern (45 bp):
CGGTTAATTCAGGTAATCCGGTTAATTCGGGTAATCCGGTTAATC
Found at i:41200728 original size:9 final size:9
Alignment explanation
Indices: 41200630--41200731 Score: 109
Period size: 9 Copynumber: 11.4 Consensus size: 9
41200620 GTAGTGATTC
41200630 AATTCGGTT
1 AATTCGGTT
41200639 AATTCAGG-T
1 AATTC-GGTT
*
41200648 AATTTGGTT
1 AATTCGGTT
*
41200657 AATTCGGGT
1 AATTCGGTT
*
41200666 AATCCGG-T
1 AATTCGGTT
*
41200674 AATCCGGTT
1 AATTCGGTT
*
41200683 AATTCGGGT
1 AATTCGGTT
*
41200692 AATCCGGTT
1 AATTCGGTT
*
41200701 AATTCGGGT
1 AATTCGGTT
41200710 AATTCGGTT
1 AATTCGGTT
*
41200719 AATTCTGTT
1 AATTCGGTT
41200728 AATT
1 AATT
41200732 TTTAACCAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
8 10 0.13
9 66 0.85
10 2 0.03
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:41205716 original size:7 final size:7
Alignment explanation
Indices: 41205704--41205736 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
41205694 AATAAATATA
41205704 TATTTTT
1 TATTTTT
41205711 TATTTTT
1 TATTTTT
41205718 TA-TTTT
1 TATTTTT
41205724 TA-TTTT
1 TATTTTT
41205730 TATTTTT
1 TATTTTT
41205737 AAAATACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:41205723 original size:6 final size:6
Alignment explanation
Indices: 41205707--41205737 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
41205697 AAATATATAT
41205707 TTTTTA TTTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA
41205738 AAATACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:41205787 original size:27 final size:28
Alignment explanation
Indices: 41205744--41205807 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 28
41205734 TTTAAAATAC
*
41205744 TTTTAAAATAAATTTTTTTAATTTTTTAT
1 TTTTAAAATAAATTTTTTTAA-TGTTTAT
41205773 TTTTAAAAT-AA-TTTTTTAATGTTTAT
1 TTTTAAAATAAATTTTTTTAATGTTTAT
*
41205799 TTTAAAAAT
1 TTTTAAAAT
41205808 GGGCCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 14 0.42
27 8 0.24
28 2 0.06
29 9 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTAAAATAAATTTTTTTAATGTTTAT
Found at i:41206959 original size:10 final size:10
Alignment explanation
Indices: 41206944--41206972 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41206934 TAGACAAAAA
41206944 TTTATATTTT
1 TTTATATTTT
41206954 TTTATATTTT
1 TTTATATTTT
41206964 TTTAT-TTTT
1 TTTATATTTT
41206973 AAAGATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTATATTTT
Found at i:41206971 original size:18 final size:17
Alignment explanation
Indices: 41206948--41206997 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
41206938 CAAAAATTTA
41206948 TATTTTTTTATATTTTTT
1 TATTTTTTTA-ATTTTTT
** *
41206966 TATTTTTAAAGATATTTT
1 TATTTTTTTA-ATTTTTT
41206984 TATTTTTTTAATTT
1 TATTTTTTTAATTT
41206998 ATGCTCGTTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TATTTTTTTAATTTTTT
Found at i:41206980 original size:20 final size:20
Alignment explanation
Indices: 41206957--41206994 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41206947 ATATTTTTTT
41206957 ATATTTTT-TTATTTTTAAAG
1 ATATTTTTATT-TTTTTAAAG
41206977 ATATTTTTATTTTTTTAA
1 ATATTTTTATTTTTTTAA
41206995 TTTATGCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
ATATTTTTATTTTTTTAAAG
Found at i:41210654 original size:6 final size:6
Alignment explanation
Indices: 41210643--41210668 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41210633 TATTTTATAA
41210643 TTAAAT TTAAAT TTAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT
41210669 TTATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:41219451 original size:6 final size:6
Alignment explanation
Indices: 41219402--41219472 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
41219392 TTATAGTAAT
* *
41219402 AAAAGA AAAA-A AAAAGA CAAAAGCA AAACGA AACAGAA AGAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA -AAAAG-A AAAAGA AAAAG-A A-AAAGA AAAAGA
* *
41219453 AAAATA GAAAGA AAGAAGA A
1 AAAAGA AAAAGA AA-AAGA A
41219473 CCCGCGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
5 5 0.10
6 24 0.47
7 18 0.35
8 4 0.08
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:41219899 original size:19 final size:20
Alignment explanation
Indices: 41219875--41219915 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
41219865 GAATTTAGGC
41219875 AAATATTGAATA-AAAATTG
1 AAATATTGAATATAAAATTG
* *
41219894 AAATATTTAATATGAAATTG
1 AAATATTGAATATAAAATTG
41219914 AA
1 AA
41219916 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (20 bp):
AAATATTGAATATAAAATTG
Found at i:41222949 original size:13 final size:13
Alignment explanation
Indices: 41222931--41222970 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
41222921 CCAATTTCCC
41222931 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
41222944 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
* *
41222957 C-ATTCTTTCCTT
1 CTTTTCTTTCTTT
41222969 CT
1 CT
41222971 CTATTTCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.70
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:41223052 original size:13 final size:13
Alignment explanation
Indices: 41223034--41223060 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41223024 TTAATTAAAG
41223034 TAATATAATAATA
1 TAATATAATAATA
41223047 TAATATAATAATA
1 TAATATAATAATA
41223060 T
1 T
41223061 TTTAATCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATATAATAATA
Found at i:41226418 original size:11 final size:11
Alignment explanation
Indices: 41226402--41226427 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41226392 TAGAAGAGAC
41226402 GAAACAGGGGA
1 GAAACAGGGGA
41226413 GAAACAGGGGA
1 GAAACAGGGGA
41226424 GAAA
1 GAAA
41226428 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:41227115 original size:3 final size:3
Alignment explanation
Indices: 41227089--41227136 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
41227079 GTGAGGTAAG
* * *
41227089 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41227137 GAGTGGGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:41227331 original size:24 final size:24
Alignment explanation
Indices: 41227277--41227348 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
41227267 TGTGTGAAGT
*
41227277 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
41227300 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
41227325 TGTGAAAAATTGTAATTGAATTGA
1 TGTGAAAAA-TG--ATTGAATTGA
41227349 GAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.22
24 14 0.35
25 7 0.17
27 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:41227551 original size:37 final size:39
Alignment explanation
Indices: 41227492--41227587 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
41227482 CGGATAGATT
* * * *
41227492 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
41227529 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
41227568 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
41227588 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:41229644 original size:39 final size:38
Alignment explanation
Indices: 41229574--41229710 Score: 109
Period size: 39 Copynumber: 3.5 Consensus size: 38
41229564 CACTCCAGCA
*
41229574 TGACACCCAGTGCCTCATCGG-ATAGTTCGAAGCAATAGT
1 TGACACCCAGTGCCTCATCGGTATAG-CCGAAG-AATAGT
* *
41229613 TGACACCCAGTGTCTCATCGGTAAAGCCGAAGAA-AGT
1 TGACACCCAGTGCCTCATCGGTATAGCCGAAGAATAGT
** * * * *
41229650 TGGTACCCAGTACCTCATCGAATCTATCCGAAGAAATA-T
1 TGACACCCAGTGCCTCATCG-GTATAGCCGAAG-AATAGT
*
41229689 AGTGACACCCAGTGTCTCATCG
1 --TGACACCCAGTGCCTCATCG
41229711 ACTCGAGGTT
Statistics
Matches: 77, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
37 19 0.25
38 10 0.13
39 28 0.36
40 4 0.05
41 16 0.21
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (38 bp):
TGACACCCAGTGCCTCATCGGTATAGCCGAAGAATAGT
Found at i:41231150 original size:13 final size:15
Alignment explanation
Indices: 41231118--41231149 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41231108 GGTTAATAAT
41231118 TATAATATTTATATA
1 TATAATATTTATATA
*
41231133 TATAATATTTATGTA
1 TATAATATTTATATA
41231148 TA
1 TA
41231150 ACGTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TATAATATTTATATA
Found at i:41234210 original size:11 final size:11
Alignment explanation
Indices: 41234173--41234228 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
41234163 ATATTCAAAC
*
41234173 AATAATAACAA
1 AATAATAGCAA
**
41234184 AATTGTAGCAA
1 AATAATAGCAA
* *
41234195 TATAATAGCGA
1 AATAATAGCAA
41234206 AATAATAGCAA
1 AATAATAGCAA
*
41234217 AACAATAG-AA
1 AATAATAGCAA
41234227 AA
1 AA
41234229 ACAATGACAA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
10 4 0.11
11 31 0.89
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.20
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:41234229 original size:11 final size:11
Alignment explanation
Indices: 41234209--41234254 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
41234199 ATAGCGAAAT
*
41234209 AATAGCAAAAC
1 AATAGAAAAAC
41234220 AATAGAAAAAC
1 AATAGAAAAAC
41234231 AAT-GACAAAAC
1 AATAGA-AAAAC
41234242 AATA-AAAAA-
1 AATAGAAAAAC
41234251 AATA
1 AATA
41234255 ACAACAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 4 0.12
10 6 0.19
11 22 0.69
ACGTcount: A:0.72, C:0.11, G:0.07, T:0.11
Consensus pattern (11 bp):
AATAGAAAAAC
Found at i:41234239 original size:22 final size:20
Alignment explanation
Indices: 41234209--41234258 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
41234199 ATAGCGAAAT
*
41234209 AATAGCAAAACAATAGAAAAA
1 AATAACAAAACAATA-AAAAA
*
41234230 CAATGACAAAACAATAAAAAA
1 -AATAACAAAACAATAAAAAA
41234251 AATAACAA
1 AATAACAA
41234259 CAAATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 5 0.20
22 13 0.52
ACGTcount: A:0.72, C:0.12, G:0.06, T:0.10
Consensus pattern (20 bp):
AATAACAAAACAATAAAAAA
Found at i:41235242 original size:14 final size:14
Alignment explanation
Indices: 41235225--41235275 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
41235215 TAGATTATAC
*
41235225 CCTAAATATTAAAT
1 CCTAAATTTTAAAT
41235239 CCTAAATTTTAAAAT
1 CCTAAATTTT-AAAT
*
41235254 TCTAAATTTTAAAT
1 CCTAAATTTTAAAT
*
41235268 CTTAAATT
1 CCTAAATT
41235276 CTTTAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (14 bp):
CCTAAATTTTAAAT
Found at i:41235701 original size:10 final size:10
Alignment explanation
Indices: 41235686--41235773 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 10
41235676 TTAGCAACTT
41235686 AAAATTATAA
1 AAAATTATAA
*
41235696 AAAATTGTAA
1 AAAATTATAA
***
41235706 AGTTTTATTAA
1 AAAATTA-TAA
*
41235717 AAACATTA-AC
1 AAA-ATTATAA
41235727 AAAATTATAAA
1 AAAATTAT-AA
*
41235738 AAAATTGTTAA
1 AAAATT-ATAA
* *
41235749 AAACTAATAA
1 AAAATTATAA
41235759 AAAATTATATA
1 AAAATTATA-A
41235770 AAAA
1 AAAA
41235774 AGCATTTATA
Statistics
Matches: 56, Mismatches: 16, Indels: 11
0.67 0.19 0.13
Matches are distributed among these distances:
9 4 0.07
10 26 0.46
11 22 0.39
12 4 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:41235750 original size:32 final size:33
Alignment explanation
Indices: 41235713--41235774 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
41235703 TAAAGTTTTA
*
41235713 TTAAAAAC-ATTAACAAAATTATA-AAAAAATTG
1 TTAAAAACTAATAA-AAAATTATATAAAAAATTG
41235745 TTAAAAACTAATAAAAAATTATATAAAAAA
1 TTAAAAACTAATAAAAAATTATATAAAAAA
41235775 GCATTTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (33 bp):
TTAAAAACTAATAAAAAATTATATAAAAAATTG
Found at i:41235770 original size:12 final size:12
Alignment explanation
Indices: 41235727--41235774 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
41235717 AAACATTAAC
41235727 AAAATTATA-AA
1 AAAATTATATAA
*
41235738 AAAATTGT-T-A
1 AAAATTATATAA
*
41235748 AAAACTA-ATAA
1 AAAATTATATAA
41235759 AAAATTATATAA
1 AAAATTATATAA
41235771 AAAA
1 AAAA
41235775 GCATTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
10 7 0.24
11 14 0.48
12 8 0.28
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAATTATATAA
Found at i:41236621 original size:17 final size:17
Alignment explanation
Indices: 41236599--41236631 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41236589 AATTTCGATT
41236599 CTTTTCTCACTCAATTC
1 CTTTTCTCACTCAATTC
*
41236616 CTTTTCTCACTGAATT
1 CTTTTCTCACTCAATT
41236632 TCGACCGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.30, G:0.03, T:0.48
Consensus pattern (17 bp):
CTTTTCTCACTCAATTC
Found at i:41236976 original size:6 final size:6
Alignment explanation
Indices: 41236965--41236989 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41236955 AAATACCTTT
41236965 GGCAGG GGCAGG GGCAGG GGCAGG G
1 GGCAGG GGCAGG GGCAGG GGCAGG G
41236990 TCGGTAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.68, T:0.00
Consensus pattern (6 bp):
GGCAGG
Found at i:41249490 original size:15 final size:17
Alignment explanation
Indices: 41249472--41249508 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
41249462 AATAAAAATC
41249472 ATATAAAATT-AT-TAA
1 ATATAAAATTAATATAA
*
41249487 ATATTAAATTAATATAA
1 ATATAAAATTAATATAA
41249504 ATATA
1 ATATA
41249509 TTTTTAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.50
16 2 0.11
17 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAAAATTAATATAA
Found at i:41272887 original size:22 final size:25
Alignment explanation
Indices: 41272862--41272907 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
41272852 TGACGAATTT
41272862 TGCACGTA-TTA-CT-TTTTACCTC
1 TGCACGTATTTACCTCTTTTACCTC
*
41272884 TGCAGGTATTTACCTCTTTTACCT
1 TGCACGTATTTACCTCTTTTACCT
41272908 TTTGTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 2 0.10
25 8 0.40
ACGTcount: A:0.17, C:0.26, G:0.11, T:0.46
Consensus pattern (25 bp):
TGCACGTATTTACCTCTTTTACCTC
Found at i:41275289 original size:16 final size:16
Alignment explanation
Indices: 41275268--41275300 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41275258 ACAATATATA
41275268 AAACTTGTGTCTAAAT
1 AAACTTGTGTCTAAAT
41275284 AAACTTGTGTCTAAAT
1 AAACTTGTGTCTAAAT
41275300 A
1 A
41275301 GCTTTACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
AAACTTGTGTCTAAAT
Found at i:41291973 original size:3 final size:3
Alignment explanation
Indices: 41291965--41292026 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
41291955 ACAAGAGCAA
41291965 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
41292013 GAT GAT GAT AAT GA
1 GAT GAT GAT GAT GA
41292027 GCATGAATCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:41310887 original size:25 final size:24
Alignment explanation
Indices: 41310792--41310892 Score: 87
Period size: 25 Copynumber: 4.1 Consensus size: 24
41310782 TAACGGGTAA
* *
41310792 CTCCGAAGAGCCATTAATCAGGAAG
1 CTCCGGAGAGCCA-TAATCAAGAAG
* * *
41310817 CTTCGGATAGCCATATATCTAGAAG
1 CTCCGGAGAGCCATA-ATCAAGAAG
* ** *
41310842 TTCAAGCGAGCCAT-ATCAAGAAG
1 CTCCGGAGAGCCATAATCAAGAAG
41310865 CTCCGGAGAGCCATTAATCAAGAAG
1 CTCCGGAGAGCCA-TAATCAAGAAG
41310890 CTC
1 CTC
41310893 ACAAAGAGCC
Statistics
Matches: 57, Mismatches: 16, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
23 17 0.30
24 3 0.05
25 37 0.65
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (24 bp):
CTCCGGAGAGCCATAATCAAGAAG
Found at i:41310907 original size:26 final size:25
Alignment explanation
Indices: 41310792--41310935 Score: 80
Period size: 25 Copynumber: 5.7 Consensus size: 25
41310782 TAACGGGTAA
* *
41310792 CTCCGAAGAGCCATTAATCAGGAAG
1 CTCCAAAGAGCCATTAATCAAGAAG
* ** * *
41310817 CTTCGGATAGCCA-TATATCTAGAAG
1 CTCCAAAGAGCCATTA-ATCAAGAAG
* *
41310842 -TTCAAGCGAGCCA-T-ATCAAGAAG
1 CTCCAA-AGAGCCATTAATCAAGAAG
**
41310865 CTCCGGAGAGCCATTAATCAAGAAG
1 CTCCAAAGAGCCATTAATCAAGAAG
* **
41310890 CTCACAAAGAGCCTTTAATCGGGAAG
1 CTC-CAAAGAGCCATTAATCAAGAAG
*
41310916 CTCGAGAAGAGCCATATAAT
1 CTCCA-AAGAGCCAT-TAAT
41310936 GGGACGCTCA
Statistics
Matches: 90, Mismatches: 21, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
23 14 0.16
24 8 0.09
25 36 0.40
26 28 0.31
27 4 0.04
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (25 bp):
CTCCAAAGAGCCATTAATCAAGAAG
Found at i:41310939 original size:26 final size:25
Alignment explanation
Indices: 41310886--41310952 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
41310876 CATTAATCAA
* *
41310886 GAAGCTCACAAAGAGCCTTTAATCGG
1 GAAGCTCA-GAAGAGCCTATAATCGG
41310912 GAAGCTCGAGAAGAGCCATATAAT-GG
1 GAAGCTC-AGAAGAGCC-TATAATCGG
* *
41310938 GACGCTCATAAGAGC
1 GAAGCTCAGAAGAGC
41310953 TGCGGTGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.20
26 22 0.63
27 6 0.17
ACGTcount: A:0.36, C:0.21, G:0.27, T:0.16
Consensus pattern (25 bp):
GAAGCTCAGAAGAGCCTATAATCGG
Found at i:41324237 original size:18 final size:17
Alignment explanation
Indices: 41324210--41324245 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
41324200 TTCGTTTTTC
41324210 TTTTCTTTTTGTTTCTG
1 TTTTCTTTTTGTTTCTG
41324227 TTTTGCTTTTTGTTTCTG
1 TTTT-CTTTTTGTTTCTG
41324245 T
1 T
41324246 GTTTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.75
Consensus pattern (17 bp):
TTTTCTTTTTGTTTCTG
Found at i:41327412 original size:28 final size:28
Alignment explanation
Indices: 41327380--41327436 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41327370 TATACGATAA
41327380 CAAGTTTAATTGAAATGCACTAAGTGTG
1 CAAGTTTAATTGAAATGCACTAAGTGTG
41327408 CAAGTTTAATTGAAATGCACTAAGTGTG
1 CAAGTTTAATTGAAATGCACTAAGTGTG
41327436 C
1 C
41327437 GTACTTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (28 bp):
CAAGTTTAATTGAAATGCACTAAGTGTG
Found at i:41328372 original size:22 final size:22
Alignment explanation
Indices: 41328341--41328488 Score: 113
Period size: 22 Copynumber: 6.5 Consensus size: 22
41328331 GTGTTATAAA
*
41328341 TTTAATGTATAATGCTATCTAAT
1 TTTAA-GTATAATGCTATCCAAT
* * *
41328364 TTTGAGTATATTGATGCTGTTC-AT
1 TTTAAGTATA---ATGCTATCCAAT
41328388 TTTAATGTATAATGCTATCCAAT
1 TTTAA-GTATAATGCTATCCAAT
41328411 TTTAAGTAT-ATGCTATCCAAT
1 TTTAAGTATAATGCTATCCAAT
* * *
41328432 TTTGAGTATATTGATGATGTCC-AT
1 TTTAAGTATA---ATGCTATCCAAT
*
41328456 TTTAATGTATAATGCTGTCCAAT
1 TTTAA-GTATAATGCTATCCAAT
*
41328479 TTTGAGTATA
1 TTTAAGTATA
41328489 TTTAAGCTGT
Statistics
Matches: 101, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
21 20 0.20
22 29 0.29
23 17 0.17
24 12 0.12
25 23 0.23
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (22 bp):
TTTAAGTATAATGCTATCCAAT
Found at i:41328425 original size:21 final size:21
Alignment explanation
Indices: 41328386--41328489 Score: 93
Period size: 21 Copynumber: 4.6 Consensus size: 21
41328376 GATGCTGTTC
41328386 ATTTTAATGTATAATGCTATCCA
1 ATTTTAA-GTAT-ATGCTATCCA
41328409 ATTTTAAGTATATGCTATCCA
1 ATTTTAAGTATATGCTATCCA
* *
41328430 ATTTTGAGTATATTGATGATGTCC-
1 ATTTTAAGTATA-TGCT-A--TCCA
*
41328454 ATTTTAATGTATAATGCTGTCCA
1 ATTTTAA-GTAT-ATGCTATCCA
*
41328477 ATTTTGAGTATAT
1 ATTTTAAGTATAT
41328490 TTAAGCTGTC
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
21 23 0.34
22 14 0.21
23 14 0.21
24 6 0.09
25 10 0.15
26 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (21 bp):
ATTTTAAGTATATGCTATCCA
Found at i:41328457 original size:68 final size:68
Alignment explanation
Indices: 41328341--41328489 Score: 235
Period size: 68 Copynumber: 2.2 Consensus size: 68
41328331 GTGTTATAAA
* * *
41328341 TTTAATGTATAATGCTATCTAATTTTGAGTATATTGATGCTGTTCATTTTAATGTATAATGCTAT
1 TTTAA-GTAT-ATGCTATCCAATTTTGAGTATATTGATGATGTCCATTTTAATGTATAATGCTAT
41328406 CCAAT
64 CCAAT
*
41328411 TTTAAGTATATGCTATCCAATTTTGAGTATATTGATGATGTCCATTTTAATGTATAATGCTGTCC
1 TTTAAGTATATGCTATCCAATTTTGAGTATATTGATGATGTCCATTTTAATGTATAATGCTATCC
41328476 AAT
66 AAT
*
41328479 TTTGAGTATAT
1 TTTAAGTATAT
41328490 TTAAGCTGTC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
68 65 0.88
69 4 0.05
70 5 0.07
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (68 bp):
TTTAAGTATATGCTATCCAATTTTGAGTATATTGATGATGTCCATTTTAATGTATAATGCTATCC
AAT
Found at i:41328477 original size:47 final size:46
Alignment explanation
Indices: 41328399--41328571 Score: 172
Period size: 47 Copynumber: 3.7 Consensus size: 46
41328389 TTAATGTATA
* *
41328399 ATGCTATCCAATTTTAA-GTAT-ATGCTATCCAATTTTGAGTATATT
1 ATGCTGTCCAA-TTTAATGTATAATGCTGTCCAATTTTGAGTATATT
* *
41328444 GATGATGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTT
1 -ATGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTGAGTATA-TT
* * * * * *
41328492 AAGCTGTCTAATTTGATGTATAATGTTGTCC-ATTTAGAGCATATT
1 ATGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTGAGTATATT
* *
41328537 ATTGCTGTCCAATTTGATGAATAATTGCTGTCCAA
1 A-TGCTGTCCAATTTAATGTATAA-TGCTGTCCAA
41328572 AACAGGGTTG
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
45 8 0.08
46 41 0.39
47 53 0.50
48 3 0.03
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (46 bp):
ATGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTGAGTATATT
Found at i:41328565 original size:23 final size:23
Alignment explanation
Indices: 41328339--41328571 Score: 101
Period size: 22 Copynumber: 10.1 Consensus size: 23
41328329 TTGTGTTATA
* * *
41328339 AATTTAATGTATAA-TGCTATCT
1 AATTTGATGTATAATTGCTGTCC
* *
41328361 AATTTTGA-GTATATTGATGCTGTTC
1 AA-TTTGATGTATAAT--TGCTGTCC
* * *
41328386 ATTTTAATGTATAA-TGCTATCC
1 AATTTGATGTATAATTGCTGTCC
* * *
41328408 AATTTTAAGTAT-A-TGCTATCC
1 AATTTGATGTATAATTGCTGTCC
* *
41328429 AATTTTGA-GTATATTGATGATGTCC
1 AA-TTTGATGTATAAT--TGCTGTCC
* *
41328454 ATTTTAATGTATAA-TGCTGTCC
1 AATTTGATGTATAATTGCTGTCC
* *
41328476 AATTTTGA-GTATATTTAAGCTGTCT
1 AA-TTTGATGTATAATT--GCTGTCC
*
41328501 AATTTGATGTATAA-TGTTGTCC
1 AATTTGATGTATAATTGCTGTCC
*
41328523 -ATTTAGA-GCATATTATTGCTGTCC
1 AATTT-GATG--TATAATTGCTGTCC
*
41328547 AATTTGATGAATAATTGCTGTCC
1 AATTTGATGTATAATTGCTGTCC
41328570 AA
1 AA
41328572 AACAGGGTTG
Statistics
Matches: 157, Mismatches: 32, Indels: 43
0.68 0.14 0.19
Matches are distributed among these distances:
21 20 0.13
22 46 0.29
23 27 0.17
24 23 0.15
25 41 0.26
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (23 bp):
AATTTGATGTATAATTGCTGTCC
Found at i:41333283 original size:30 final size:30
Alignment explanation
Indices: 41333223--41333285 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
41333213 ATTCAAAAAT
*
41333223 AAATTATAAAAATTATTTTTAAAAAGTTAA
1 AAATTATAAAAATTATTTTTAAAAACTTAA
* *
41333253 AAATTATAAAAATTATTTTTTATAACTTAA
1 AAATTATAAAAATTATTTTTAAAAACTTAA
41333283 AAA
1 AAA
41333286 ATAATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
AAATTATAAAAATTATTTTTAAAAACTTAA
Found at i:41335907 original size:11 final size:10
Alignment explanation
Indices: 41335888--41335921 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
41335878 TATTTTAAGC
41335888 TTTTT-TTAA
1 TTTTTATTAA
41335897 TTTTTAATTAA
1 TTTTT-ATTAA
41335908 TTTTTATTAA
1 TTTTTATTAA
41335918 TTTT
1 TTTT
41335922 ATCCTTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.22
10 9 0.39
11 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTATTAA
Done.