Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 189 of 204
Found at i:55779231 original size:37 final size:36
Alignment explanation
Indices: 55779181--55779286 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 36
55779171 AGGAATATAG
*
55779181 CTTTCTTGTTTGTATTCTCATTCTATTTTGAACATAC
1 CTTTCTTG-TTGTATTCTCATTCTATTATGAACATAC
* *
55779218 CTTTCTTGCTTGTATTATCATTCTATTATGAATATAC
1 CTTTCTTG-TTGTATTCTCATTCTATTATGAACATAC
* *
55779255 CTTTCTTGTTCGTATCCTCGTTCTATTGATGA
1 CTTTCTTGTT-GTATTCTCATTCTATT-ATGA
55779287 TTAATGTTGC
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 2 0.03
37 54 0.90
38 4 0.07
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (36 bp):
CTTTCTTGTTGTATTCTCATTCTATTATGAACATAC
Found at i:55780980 original size:18 final size:16
Alignment explanation
Indices: 55780957--55780991 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
55780947 AATTTAAATT
55780957 TAATTAAATTATTTAAAA
1 TAATT-AATT-TTTAAAA
55780975 TAATTAATTTTTAAAA
1 TAATTAATTTTTAAAA
55780991 T
1 T
55780992 TATAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTAATTTTTAAAA
Found at i:55781202 original size:13 final size:13
Alignment explanation
Indices: 55781181--55781212 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
55781171 CCTTAAACTC
55781181 GAACTCTAAACCTT
1 GAAC-CTAAACCTT
55781195 GAACCTAAACCTT
1 GAACCTAAACCTT
55781208 GAACC
1 GAACC
55781213 CCAAATCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.22
Consensus pattern (13 bp):
GAACCTAAACCTT
Found at i:55783206 original size:10 final size:10
Alignment explanation
Indices: 55783191--55783225 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
55783181 GGACTTTATC
55783191 TCTTTTTTTT
1 TCTTTTTTTT
*
55783201 TCTTTTCTTT
1 TCTTTTTTTT
55783211 TCTTTTTTTT
1 TCTTTTTTTT
55783221 T-TTTT
1 TCTTTT
55783226 GGTGAAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.17
10 19 0.83
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:55784616 original size:21 final size:19
Alignment explanation
Indices: 55784592--55784630 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
55784582 ATTTGCCTCC
55784592 CTATCTAAGACCATGTTTCCT
1 CTATCTAAG-CCAT-TTTCCT
55784613 CTATCTAAGCCATTTTCC
1 CTATCTAAGCCATTTTCC
55784631 GGAGGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
CTATCTAAGCCATTTTCCT
Found at i:55797482 original size:15 final size:15
Alignment explanation
Indices: 55797448--55797480 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
55797438 TTTTTAAATT
*
55797448 TAAATTTTTAATTGA
1 TAAATTTTTAATTCA
55797463 TAAATTTTT-ATTCA
1 TAAATTTTTAATTCA
55797477 TAAA
1 TAAA
55797481 ATCAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (15 bp):
TAAATTTTTAATTCA
Found at i:55801426 original size:22 final size:22
Alignment explanation
Indices: 55801380--55801426 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
55801370 TTTTTTTTCC
*
55801380 AATTTTTTTACAAATTAATTAT
1 AATTTTTTTACAAATCAATTAT
55801402 AATTATTTTTA-AATATCAATT-T
1 AATT-TTTTTACAA-ATCAATTAT
55801424 AAT
1 AAT
55801427 AATATGATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTTTTTACAAATCAATTAT
Found at i:55801921 original size:224 final size:224
Alignment explanation
Indices: 55801527--55801940 Score: 738
Period size: 224 Copynumber: 1.8 Consensus size: 224
55801517 TTATGGTGGC
*
55801527 AAAAAAAATGTTTACAGGGTATATGTAAAGGCCATATACAATGGATAATCAAAGTATAAAGATTA
1 AAAAAAAATGTTTACAGGGTACATGTAAAGGCCATATACAATGGATAATCAAAGTATAAAGATTA
* *
55801592 GTGTTAGATAAAATGGAAGTGAGTTGATTAAGTCCTCCACTCATTTACCTACTCTTCCTTTTTTC
66 GTATTAGATAAAATGGAAGTGAGATGATTAAGTCCTCCACTCATTTACCTACTCTTCCTTTTTTC
*
55801657 TAATTAAATAACACTGACTATATACTTTTAAATCAAATACTTTCCTAGTCTTCCTTTTTTCCAAT
131 TAATTAAATAACACTGACTATATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTTTTCCAAT
55801722 TTTATAGTCAGCAGATCAAGATTATAACA
196 TTTATAGTCAGCAGATCAAGATTATAACA
* * *
55801751 AAAAAAAATGTTTATAGGGTACATGTAAGGGCCATATACAATGGATCATCAAAGTATAAAGATTA
1 AAAAAAAATGTTTACAGGGTACATGTAAAGGCCATATACAATGGATAATCAAAGTATAAAGATTA
*
55801816 GTATTAGATAAAGTGGAAGTGAGATGATTAAGTCCTCCACTCATTTACCTACTCTTCCTTTTTTC
66 GTATTAGATAAAATGGAAGTGAGATGATTAAGTCCTCCACTCATTTACCTACTCTTCCTTTTTTC
* *
55801881 TAATTAAATAAGACTGACTCTATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTTTT
131 TAATTAAATAACACTGACTATATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTTTT
55801941 TTTTTTCCAC
Statistics
Matches: 180, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
224 180 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (224 bp):
AAAAAAAATGTTTACAGGGTACATGTAAAGGCCATATACAATGGATAATCAAAGTATAAAGATTA
GTATTAGATAAAATGGAAGTGAGATGATTAAGTCCTCCACTCATTTACCTACTCTTCCTTTTTTC
TAATTAAATAACACTGACTATATACTTTTAAATAAAATACTTTCCTAGTCTTCCTTTTTTCCAAT
TTTATAGTCAGCAGATCAAGATTATAACA
Found at i:55803844 original size:3 final size:3
Alignment explanation
Indices: 55803836--55803880 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
55803826 CAACAATAGA
55803836 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55803881 AGCATAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55805433 original size:44 final size:44
Alignment explanation
Indices: 55805376--55805787 Score: 411
Period size: 44 Copynumber: 9.3 Consensus size: 44
55805366 ACCAGTATGG
*
55805376 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACAT
* *
55805420 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACAT
* * * * * ***
55805464 GAAGATAAAATCTGCTCTCTTCGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCA-CGCCAGTACAT
* *
55805509 GGAGACAAGATCTG-TTTCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACAT
* ***
55805552 GAAGACAAGATCTGCTTTCTTCGATCTACTTTTC-CACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTAC--TTCACGCCAGTACAT
* *
55805597 GGAGACAAGATCTG-TTTCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACAT
* ***
55805640 GAAGACAAGATCTGCTTTCTTCGATCTACTTTGC-CACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTAC-TT-CACGCCAGTACAT
* * * * * *
55805685 GGAGACAAGATCTGGTATCTTTGATCTAATTCACGCTAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACAT
* * * ***
55805729 GAAGACAAGATCTGCTTT-TTCCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTT-CGATCTACTTC-ACGCCAGTACAT
55805774 GAAGACAAGATCTG
1 GAAGACAAGATCTG
55805788 TTATTTCCAC
Statistics
Matches: 295, Mismatches: 62, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
42 3 0.01
43 43 0.15
44 154 0.52
45 91 0.31
46 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACAT
Found at i:55805529 original size:88 final size:88
Alignment explanation
Indices: 55805376--55805789 Score: 598
Period size: 88 Copynumber: 4.7 Consensus size: 88
55805366 ACCAGTATGG
* * * *** * *
55805376 GAAGACAAGATCTGCTTTCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGGAGACAAGATCTG-TTTCT
55805440 TTGATCTACTTCACGCCAGTACAT
65 TTGATCTACTTCACGCCAGTACAT
* * * * *
55805464 GAAGATAAAATCTGCTCTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGGAGACAAGATCTGTTTCTT
55805529 TGATCTACTTCACGCCAGTACAT
66 TGATCTACTTCACGCCAGTACAT
**
55805552 GAAGACAAGATCTGCTTTCTTCGATCTACTTTTCCACCAGTATGGGGAGACAAGATCTGTTTCTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGGAGACAAGATCTGTTTCTT
55805617 TGATCTACTTCACGCCAGTACAT
66 TGATCTACTTCACGCCAGTACAT
* *
55805640 GAAGACAAGATCTGCTTTCTTCGATCTACTTTGCCACCAGTATGGGGAGACAAGATCTGGTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGGAGACAAGATCT-GTTTCT
* *
55805705 TTGATCTAATTCACGCTAGTACAT
65 TTGATCTACTTCACGCCAGTACAT
* *
55805729 GAAGACAAGATCTGCTTT-TTCCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTT
1 GAAGACAAGATCTGCTTTCTT-CGATCTACTTCGCCACCAGTATGGGGAGACAAGATCTGTT
55805790 ATTTCCACCT
Statistics
Matches: 297, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
88 199 0.67
89 98 0.33
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (88 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGGAGACAAGATCTGTTTCTT
TGATCTACTTCACGCCAGTACAT
Found at i:55816493 original size:30 final size:29
Alignment explanation
Indices: 55816398--55816494 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 29
55816388 ACAAAAAATA
*** *
55816398 TAAATTACATTTTGGCCCCTGAACTTTTC
1 TAAATTACATTTCAACCCCTAAACTTTTC
55816427 TAAATTACATTTCAACCCCTAAACTTTTC
1 TAAATTACATTTCAACCCCTAAACTTTTC
55816456 TAAATTACATTTCAACCCCTAAACTTTCTC
1 TAAATTACATTTCAACCCCTAAACTTT-TC
*
55816486 AAAATTACA
1 TAAATTACA
55816495 CTTTGAGCCC
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
29 52 0.84
30 10 0.16
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
TAAATTACATTTCAACCCCTAAACTTTTC
Found at i:55816513 original size:58 final size:59
Alignment explanation
Indices: 55816398--55816527 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 59
55816388 ACAAAAAATA
*** * *
55816398 TAAATTACATTTTGGCCCCTGAACTTTTCTAAATTACATTTCAACCCCTAAACTTTT-C
1 TAAATTACATTTCAACCCCTAAACTTTTCAAAATTACATTTCAACCCCTAAACTTTTCC
* * *
55816456 TAAATTACATTTCAACCCCTAAACTTTCTCAAAATTACACTTT-GAGCCCTATA-TTTTCC
1 TAAATTACATTTCAACCCCTAAACTTT-TCAAAATTACA-TTTCAACCCCTAAACTTTTCC
55816515 TAAAATTACATTT
1 T-AAATTACATTT
55816528 TTACCCCAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
58 27 0.45
59 19 0.32
60 14 0.23
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (59 bp):
TAAATTACATTTCAACCCCTAAACTTTTCAAAATTACATTTCAACCCCTAAACTTTTCC
Found at i:55817054 original size:29 final size:30
Alignment explanation
Indices: 55817011--55817068 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
55817001 GGGCTTTCGA
* *
55817011 AAGAGAAAGAAAAAG-AAAAGGGGGAAGAG
1 AAGAAAAAGAAAAAGCAAAAGGGAGAAGAG
* *
55817040 AAGAAAAAGAGAAAGCCAAAGGGAGAAGA
1 AAGAAAAAGAAAAAGCAAAAGGGAGAAGA
55817069 TATGAGAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.62, C:0.03, G:0.34, T:0.00
Consensus pattern (30 bp):
AAGAAAAAGAAAAAGCAAAAGGGAGAAGAG
Found at i:55817253 original size:20 final size:19
Alignment explanation
Indices: 55817224--55817274 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
55817214 AAGTAAAGGG
* *
55817224 AAGAAGAAGAAGAAAGGAGA
1 AAGAAAAAGAAGAAA-AAGA
55817244 AAGAAAAAGAGAGAAAAAGA
1 AAGAAAAAGA-AGAAAAAGA
*
55817264 AATAAAAAGAA
1 AAGAAAAAGAA
55817275 AGATAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 21 0.78
21 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (19 bp):
AAGAAAAAGAAGAAAAAGA
Found at i:55817258 original size:10 final size:10
Alignment explanation
Indices: 55817241--55817282 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
55817231 AGAAGAAAGG
55817241 AGAAAGAAAA
1 AGAAAGAAAA
*
55817251 AGAGAGAAAA
1 AGAAAGAAAA
*
55817261 AGAAATAAAA
1 AGAAAGAAAA
55817271 AGAAAGATAAA
1 AGAAAGA-AAA
55817282 A
1 A
55817283 AAATAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 23 0.85
11 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:55817286 original size:20 final size:20
Alignment explanation
Indices: 55817241--55817289 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
55817231 AGAAGAAAGG
* *
55817241 AGAAAGAAAAAGAGAGAAAA
1 AGAAATAAAAAGAAAGAAAA
55817261 AGAAATAAAAAGAAAGATAAA
1 AGAAATAAAAAGAAAGA-AAA
55817282 A-AAATAAA
1 AGAAATAAA
55817290 TAAAGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (20 bp):
AGAAATAAAAAGAAAGAAAA
Found at i:55817931 original size:17 final size:18
Alignment explanation
Indices: 55817903--55817950 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
55817893 TTAAGAAAAA
55817903 TCATGT-TTCAAAATTT-
1 TCATGTCTTCAAAATTTC
55817919 TCATGTCTTCAAAATTTC
1 TCATGTCTTCAAAATTTC
*
55817937 TCGTG-CTTCAAAAT
1 TCATGTCTTCAAAAT
55817951 AATAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.21
17 19 0.66
18 4 0.14
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (18 bp):
TCATGTCTTCAAAATTTC
Found at i:55818014 original size:17 final size:17
Alignment explanation
Indices: 55817960--55818016 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
55817950 TAATAATAAT
55817960 AAAATTTTCCGTGTTTCA
1 AAAATTTT-CGTGTTTCA
* * ****
55817978 AAAATTCTCGGGAAAAA
1 AAAATTTTCGTGTTTCA
55817995 AAAATTTTCGTGTTTCA
1 AAAATTTTCGTGTTTCA
55818012 AAAAT
1 AAAAT
55818017 ATTCTCGCAT
Statistics
Matches: 27, Mismatches: 12, Indels: 1
0.68 0.30 0.03
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AAAATTTTCGTGTTTCA
Found at i:55818164 original size:17 final size:16
Alignment explanation
Indices: 55818142--55818203 Score: 70
Period size: 17 Copynumber: 3.8 Consensus size: 16
55818132 AAAATGTCTT
*
55818142 AATTTTCGTGTTTCTAA
1 AATTCTCGTGTTT-TAA
* *
55818159 AATTTTCGTGTTTAAA
1 AATTCTCGTGTTTTAA
*
55818175 AATTCTAGTGTTTTCAA
1 AATTCTCGTGTTTT-AA
55818192 AATTCTCGTGTT
1 AATTCTCGTGTT
55818204 AAAAAAAACT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.33
17 26 0.67
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (16 bp):
AATTCTCGTGTTTTAA
Found at i:55824408 original size:12 final size:11
Alignment explanation
Indices: 55824391--55824479 Score: 55
Period size: 10 Copynumber: 8.5 Consensus size: 11
55824381 ATTATGCCTA
*
55824391 AAAAAAAGAGAC
1 AAAAAAACA-AC
55824403 AAAAAAACAAC
1 AAAAAAACAAC
55824414 -AAAAAA-AAC
1 AAAAAAACAAC
* *** *
55824423 AAAGAGGTAAA
1 AAAAAAACAAC
55824434 AAAACAAACAA-
1 AAAA-AAACAAC
*
55824445 AAAAAAGCAAC
1 AAAAAAACAAC
55824456 AAAAAAAC-A-
1 AAAAAAACAAC
55824465 AAAAAAACAA-
1 AAAAAAACAAC
55824475 AAAAA
1 AAAAA
55824480 GAAAAAAGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
9 11 0.18
10 21 0.34
11 18 0.30
12 11 0.18
ACGTcount: A:0.81, C:0.11, G:0.07, T:0.01
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:55824427 original size:28 final size:28
Alignment explanation
Indices: 55824390--55824481 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 28
55824380 TATTATGCCT
55824390 AAAAAAAAGAGACAAAAAAAC-AACAAA
1 AAAAAAAAGAGACAAAAAAACAAACAAA
**
55824417 AAAAACAAAGAGGTAAAAAAACAAAC---
1 AAAAA-AAAGAGACAAAAAAACAAACAAA
*
55824443 AAAAAAAAGCA-ACAAAAAAACAAAAAAA
1 AAAAAAAAG-AGACAAAAAAACAAACAAA
55824471 ACAAAAAAAGA
1 A-AAAAAAAGA
55824482 AAAAAGAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
25 15 0.28
26 6 0.11
27 5 0.09
28 16 0.30
29 11 0.21
ACGTcount: A:0.80, C:0.11, G:0.08, T:0.01
Consensus pattern (28 bp):
AAAAAAAAGAGACAAAAAAACAAACAAA
Found at i:55824434 original size:25 final size:25
Alignment explanation
Indices: 55824405--55824475 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
55824395 AAAGAGACAA
**
55824405 AAAAACAACAAAAAAAACAAAG-AGGT
1 AAAAA-AACAAAAAAAACAAAGCA-AC
55824431 AAAAAAACAAACAAAAA-AAAGCAAC
1 AAAAAAACAAA-AAAAACAAAGCAAC
55824456 AAAAAAACAAAAAAAACAAA
1 AAAAAAACAAAAAAAACAAA
55824476 AAAAGAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.12
25 24 0.60
26 11 0.28
ACGTcount: A:0.80, C:0.13, G:0.06, T:0.01
Consensus pattern (25 bp):
AAAAAAACAAAAAAAACAAAGCAAC
Found at i:55824456 original size:17 final size:15
Alignment explanation
Indices: 55824403--55824492 Score: 62
Period size: 16 Copynumber: 5.9 Consensus size: 15
55824393 AAAAAGAGAC
55824403 AAAA-AAACAACAAAA
1 AAAACAAACAA-AAAA
* **
55824418 AAAACAAAGAGGTAAA
1 AAAACAAACA-AAAAA
55824434 AAAACAAACAAAAAA
1 AAAACAAACAAAAAA
*
55824449 AAGCAACAAA-AAAACA
1 AA--AACAAACAAAAAA
55824465 AAAA-AAACAAAAAA
1 AAAACAAACAAAAAA
*
55824479 AGAAA-AAAGAAAAA
1 A-AAACAAACAAAAA
55824493 TCAAAATCAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
13 3 0.05
14 8 0.13
15 20 0.33
16 23 0.38
17 6 0.10
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.01
Consensus pattern (15 bp):
AAAACAAACAAAAAA
Found at i:55824466 original size:8 final size:8
Alignment explanation
Indices: 55824431--55824486 Score: 60
Period size: 8 Copynumber: 6.8 Consensus size: 8
55824421 ACAAAGAGGT
55824431 AAAAAAAC
1 AAAAAAAC
55824439 AAACAAAA-
1 AAA-AAAAC
*
55824447 AAAAGCAAC
1 AAAA-AAAC
55824456 AAAAAAAC
1 AAAAAAAC
55824464 AAAAAAAAC
1 -AAAAAAAC
*
55824473 AAAAAAAG
1 AAAAAAAC
55824481 AAAAAA
1 AAAAAA
55824487 GAAAAATCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
7 1 0.02
8 24 0.59
9 16 0.39
ACGTcount: A:0.86, C:0.11, G:0.04, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:55824484 original size:25 final size:25
Alignment explanation
Indices: 55824405--55824486 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
55824395 AAAGAGACAA
* *
55824405 AAAAACAACAAAAAAAAC-AAAGAGG
1 AAAAA-AACAAAAAAAACAAAAAAAG
** *
55824430 TAAAAAAACAAACAAAAA-AAAGCAAC
1 -AAAAAAACAAA-AAAAACAAAAAAAG
55824456 AAAAAAACAAAAAAAACAAAAAAAG
1 AAAAAAACAAAAAAAACAAAAAAAG
55824481 AAAAAA
1 AAAAAA
55824487 GAAAAATCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
24 5 0.11
25 28 0.61
26 13 0.28
ACGTcount: A:0.82, C:0.11, G:0.06, T:0.01
Consensus pattern (25 bp):
AAAAAAACAAAAAAAACAAAAAAAG
Found at i:55825560 original size:75 final size:75
Alignment explanation
Indices: 55825381--55825728 Score: 439
Period size: 75 Copynumber: 4.6 Consensus size: 75
55825371 ATCTCTGTTT
55825381 TTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCC-GAGGTATTTCT
1 TTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCAT-CCTGAGGTA--TCT
55825444 TTTAAATTTCT-A
63 TTTAAATTTCTGA
55825456 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC-GGTCATGCC-GAGGTATTTC
1 -TTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCAT-CCTGAGGTA--TC
*
55825518 TTTTAAATTTC-CA
62 TTTTAAATTTCTGA
* *
55825531 TTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCATCCTAAGGTA--TTTT
1 TTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCATCCTGAGGTATCTTTT
* *
55825594 CAATTTCTGT
66 AAATTTCTGA
*
55825604 TTTTCAAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGAGTCATCCTGAGG--TCTT
1 TTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCATCCTGAGGTATCTT
*
55825667 TTAAATTTCTGT
64 TTAAATTTCTGA
* *
55825679 TTTTCAAAAAAGTCAACTCATAATTCGAGAGGTGAGTTGAGCCCCGGGTC
1 TTTTC-AAAAA-TCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
55825729 GCACGCCGAG
Statistics
Matches: 250, Mismatches: 12, Indels: 21
0.88 0.04 0.07
Matches are distributed among these distances:
72 10 0.04
73 5 0.02
74 29 0.12
75 153 0.61
76 53 0.21
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (75 bp):
TTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCATCCTGAGGTATCTTTT
AAATTTCTGA
Found at i:55826144 original size:30 final size:29
Alignment explanation
Indices: 55826049--55826145 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 29
55826039 ACAAAAAATA
*** *
55826049 TAAATTACATTTTGGCCCCTGAACTTTTC
1 TAAATTACATTTCAACCCCTAAACTTTTC
55826078 TAAATTACATTTCAACCCCTAAACTTTTC
1 TAAATTACATTTCAACCCCTAAACTTTTC
55826107 TAAATTACATTTCAACCCCTAAACTTTCTC
1 TAAATTACATTTCAACCCCTAAACTTT-TC
*
55826137 AAAATTACA
1 TAAATTACA
55826146 CTTTGAGCCC
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
29 52 0.84
30 10 0.16
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
TAAATTACATTTCAACCCCTAAACTTTTC
Found at i:55826164 original size:58 final size:59
Alignment explanation
Indices: 55826049--55826178 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 59
55826039 ACAAAAAATA
*** * *
55826049 TAAATTACATTTTGGCCCCTGAACTTTTCTAAATTACATTTCAACCCCTAAACTTTT-C
1 TAAATTACATTTCAACCCCTAAACTTTTCAAAATTACATTTCAACCCCTAAACTTTTCC
* * *
55826107 TAAATTACATTTCAACCCCTAAACTTTCTCAAAATTACACTTT-GAGCCCTATA-TTTTCC
1 TAAATTACATTTCAACCCCTAAACTTT-TCAAAATTACA-TTTCAACCCCTAAACTTTTCC
55826166 TAAAATTACATTT
1 T-AAATTACATTT
55826179 TTGCCCCAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
58 27 0.45
59 19 0.32
60 14 0.23
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (59 bp):
TAAATTACATTTCAACCCCTAAACTTTTCAAAATTACATTTCAACCCCTAAACTTTTCC
Found at i:55826904 original size:20 final size:19
Alignment explanation
Indices: 55826875--55826925 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
55826865 AAGCAAAGGG
* *
55826875 AAGAAGAAGAAGAAAGGAGA
1 AAGAAAAAGAAGAAA-AAGA
55826895 AAGAAAAAGAGAGAAAAAGA
1 AAGAAAAAGA-AGAAAAAGA
55826915 AAGAAAAAGAA
1 AAGAAAAAGAA
55826926 AGATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 22 0.79
21 5 0.18
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (19 bp):
AAGAAAAAGAAGAAAAAGA
Found at i:55826908 original size:14 final size:15
Alignment explanation
Indices: 55826881--55826918 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
55826871 AGGGAAGAAG
55826881 AAGAAGAAAG-GAGA
1 AAGAAGAAAGAGAGA
55826895 AAGAA-AAAGAGAGA
1 AAGAAGAAAGAGAGA
55826909 AA-AAGAAAGA
1 AAGAAGAAAGA
55826919 AAAAGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AAGAAGAAAGAGAGA
Found at i:55826909 original size:10 final size:10
Alignment explanation
Indices: 55826892--55826933 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
55826882 AGAAGAAAGG
55826892 AGAAAGAAAA
1 AGAAAGAAAA
*
55826902 AGAGAGAAAA
1 AGAAAGAAAA
55826912 AGAAAGAAAA
1 AGAAAGAAAA
55826922 AGAAAGATAAA
1 AGAAAGA-AAA
55826933 A
1 A
55826934 AAATAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 25 0.86
11 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:55827582 original size:17 final size:18
Alignment explanation
Indices: 55827556--55827603 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
55827546 TTAAAAAAAA
55827556 TCATGT-TTCAAAATTT-
1 TCATGTCTTCAAAATTTC
55827572 TCATGTCTTCAAAATTTC
1 TCATGTCTTCAAAATTTC
*
55827590 TCGTG-CTTCAAAAT
1 TCATGTCTTCAAAAT
55827604 AATAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.21
17 19 0.66
18 4 0.14
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (18 bp):
TCATGTCTTCAAAATTTC
Found at i:55827642 original size:17 final size:17
Alignment explanation
Indices: 55827622--55827669 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
55827612 TAAAATTTTC
55827622 CGTGTTTCAAAAATTCT
1 CGTGTTTCAAAAATTCT
**** *
55827639 CGTGAAAAAAAAATTTT
1 CGTGTTTCAAAAATTCT
55827656 CGTGTTTCAAAAAT
1 CGTGTTTCAAAAAT
55827670 ATTCTCGCAT
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
CGTGTTTCAAAAATTCT
Found at i:55827837 original size:33 final size:34
Alignment explanation
Indices: 55827795--55827863 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
55827785 AAAATGTCTT
* * * *
55827795 AATTTTCGTG-TTTCTAAAATTTTCGTGTTTAAA
1 AATTCTCGTGTTTTCAAAAATTCTCGTGTTAAAA
55827828 AATTCTCGTGTTTTCAAAAATTCTCGTGTTAAAA
1 AATTCTCGTGTTTTCAAAAATTCTCGTGTTAAAA
55827862 AA
1 AA
55827864 AACTTTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 9 0.29
34 22 0.71
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (34 bp):
AATTCTCGTGTTTTCAAAAATTCTCGTGTTAAAA
Found at i:55827848 original size:18 final size:17
Alignment explanation
Indices: 55827795--55827857 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
55827785 AAAATGTCTT
* *
55827795 AATTTTCGTGTTTCTAA
1 AATTCTCGTGTTTCAAA
*
55827812 AATTTTCGTGTTT-AAA
1 AATTCTCGTGTTTCAAA
55827828 AATTCTCGTGTTTTCAAA
1 AATTCTCGTG-TTTCAAA
55827846 AATTCTCGTGTT
1 AATTCTCGTGTT
55827858 AAAAAAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.26
17 18 0.43
18 13 0.31
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTCTCGTGTTTCAAA
Found at i:55827864 original size:18 final size:18
Alignment explanation
Indices: 55827825--55827883 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
55827815 TTTCGTGTTT
***
55827825 AAAAATTCTCGTGTTTTC
1 AAAAATTCTCGTGTTAAA
55827843 AAAAATTCTCGTGTTAAA
1 AAAAATTCTCGTGTTAAA
* *
55827861 AAAAACTT-TTGTTTTAAA
1 AAAAA-TTCTCGTGTTAAA
55827879 AAAAA
1 AAAAA
55827884 AAGAAATTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 33 0.94
19 2 0.06
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.37
Consensus pattern (18 bp):
AAAAATTCTCGTGTTAAA
Found at i:55829898 original size:3 final size:3
Alignment explanation
Indices: 55829890--55829934 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
55829880 CAACAATAGA
55829890 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55829935 AGCATAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55833274 original size:17 final size:18
Alignment explanation
Indices: 55833243--55833276 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55833233 AATTTAACTT
55833243 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
55833261 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
55833277 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:55844248 original size:22 final size:22
Alignment explanation
Indices: 55844220--55844269 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
55844210 CAAGAACAAG
55844220 CCATATATATGTGTGCATATAC
1 CCATATATATGTGTGCATATAC
55844242 CCATATATATGTGTGCATATAC
1 CCATATATATGTGTGCATATAC
55844264 CCATAT
1 CCATAT
55844270 TAAGGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (22 bp):
CCATATATATGTGTGCATATAC
Found at i:55848970 original size:22 final size:22
Alignment explanation
Indices: 55848945--55848988 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
55848935 TTTAAATTAA
*
55848945 TAAATATATT-ATTTTTATTTTT
1 TAAA-ATATTAATTTATATTTTT
*
55848967 TAAAATTTTAATTTATATTTTT
1 TAAAATATTAATTTATATTTTT
55848989 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TAAAATATTAATTTATATTTTT
Found at i:55849597 original size:34 final size:33
Alignment explanation
Indices: 55849559--55849622 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 33
55849549 GTATAACTCT
* *
55849559 TATTTTATTGTTAATTTTGTTAC-TATTTTAGAGG
1 TATTTGATTGTTAA-GTTG-TACTTATTTTAGAGG
*
55849593 TATTTGCTTGTTAAGTTGTACTTATTTTAG
1 TATTTGATTGTTAAGTTGTACTTATTTTAG
55849623 TATTATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 3 0.12
33 11 0.42
34 12 0.46
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.58
Consensus pattern (33 bp):
TATTTGATTGTTAAGTTGTACTTATTTTAGAGG
Found at i:55856203 original size:33 final size:34
Alignment explanation
Indices: 55856161--55856247 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 34
55856151 CGACTACTGT
55856161 TACTGTTACTGATT-C-GGCACTTTGTGTGTCGGA
1 TACTGTTACTG-TTACAGGCACTTTGTGTGTCGGA
55856194 TACTGTTACTGTTACCGACTAGGCACTTTGTGTGTCGGA
1 TACTGTTACTGTT----AC-AGGCACTTTGTGTGTCGGA
55856233 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
55856248 TGTTACCGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
32 2 0.04
33 11 0.23
35 2 0.04
37 1 0.02
39 31 0.66
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (34 bp):
TACTGTTACTGTTACAGGCACTTTGTGTGTCGGA
Found at i:55856243 original size:45 final size:45
Alignment explanation
Indices: 55856155--55856393 Score: 310
Period size: 45 Copynumber: 5.4 Consensus size: 45
55856145 ATGTGCCGAC
* *
55856155 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCG------GA
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
55856194 TACTGTTACTGTTACCGACTAGGCACTTTGTGTGTCGGATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
55856239 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
55856284 TACTGTTACTGTTATCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * * *
55856329 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
55856374 TACTGCTACCGTTACTGATT
1 TACTGTTACTGTTACCGATT
55856394 ACTGTATACT
Statistics
Matches: 177, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.19
45 143 0.81
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:55860197 original size:33 final size:33
Alignment explanation
Indices: 55860155--55860445 Score: 528
Period size: 33 Copynumber: 8.8 Consensus size: 33
55860145 TTCAAATGTC
*
55860155 GAGGATAGGAAGAAAAGAGACGAAGAATTAGCA
1 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
55860188 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
1 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
*
55860221 GAGGGTAGGAAGAAAAGAGATGAAGAATTAGCA
1 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
*
55860254 GAGGGTAGGAAGAAAAGAGATGAAGAATTAGCA
1 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
55860287 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
1 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
*
55860320 GAGGGTAGGAAGAAAAGAGATGAAGAATTAGCA
1 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
*
55860353 GAGGCTAGGAAGAAAAGAGATGAAGAATTAGCA
1 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
55860386 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
1 GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
*
55860419 GAGGGTAGGAAGAAAAGAGATGAAGAA
1 GAGGATAGGAAGAAAAGAGATGAAGAA
55860446 GATCAAGACT
Statistics
Matches: 251, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 251 1.00
ACGTcount: A:0.50, C:0.03, G:0.35, T:0.11
Consensus pattern (33 bp):
GAGGATAGGAAGAAAAGAGATGAAGAATTAGCA
Found at i:55861400 original size:20 final size:21
Alignment explanation
Indices: 55861361--55861402 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
55861351 ATTATTTTAT
*
55861361 CCTGAACCCAAAATCCCGAAC
1 CCTGAACCCAAAACCCCGAAC
*
55861382 CCTGAACTC-AAACCCCGAAC
1 CCTGAACCCAAAACCCCGAAC
55861402 C
1 C
55861403 TAAACCTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.36, C:0.45, G:0.10, T:0.10
Consensus pattern (21 bp):
CCTGAACCCAAAACCCCGAAC
Found at i:55867297 original size:22 final size:24
Alignment explanation
Indices: 55867254--55867297 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
55867244 GCATACAACA
*
55867254 TCTGGATTGAACCAGCATTTTTCT
1 TCTGGATTGAACCAGCACTTTTCT
*
55867278 TCTGGA-TG-ACCAGCCCTTTT
1 TCTGGATTGAACCAGCACTTTT
55867298 GCAGTGCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 2 0.11
24 6 0.33
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (24 bp):
TCTGGATTGAACCAGCACTTTTCT
Found at i:55870514 original size:21 final size:19
Alignment explanation
Indices: 55870490--55870528 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
55870480 ATTTGCCTCC
55870490 CTATCTAAGACCATGTTTCCT
1 CTATCTAAG-CCAT-TTTCCT
55870511 CTATCTAAGCCATTTTCC
1 CTATCTAAGCCATTTTCC
55870529 GGAGGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
CTATCTAAGCCATTTTCCT
Found at i:55873883 original size:2 final size:2
Alignment explanation
Indices: 55873876--55873912 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
55873866 CTACCAAATC
55873876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55873913 TAAGAGAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55875192 original size:25 final size:25
Alignment explanation
Indices: 55875094--55875202 Score: 82
Period size: 25 Copynumber: 4.4 Consensus size: 25
55875084 AATATTGAGT
*
55875094 TATAAATAAATAACAAATGAAATTA
1 TATATATAAATAACAAATGAAATTA
* * * ** *
55875119 TATATATAATTTATATATACAAAATTC
1 TATATATAA-ATA-ACAAATGAAATTA
* *
55875146 T-T-T-TAATTAA-AGATGAAATTA
1 TATATATAAATAACAAATGAAATTA
55875167 TATATATAAATAACAAATGAAATTA
1 TATATATAAATAACAAATGAAATTA
*
55875192 TATATACAAAT
1 TATATATAAAT
55875203 TTATAAGTGA
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
21 8 0.12
22 2 0.03
23 4 0.06
24 9 0.14
25 29 0.45
26 3 0.05
27 9 0.14
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.37
Consensus pattern (25 bp):
TATATATAAATAACAAATGAAATTA
Found at i:55877110 original size:31 final size:29
Alignment explanation
Indices: 55877040--55877113 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
55877030 GGCTCAGGTT
*
55877040 ACATTTTAGTCACTTATGTTTGAAATATT
1 ACATTTTAGTCACTTATGTTTGAAATATG
* * * *
55877069 ACGTTTTAGTCACTTATGTTATCGCATTGTG
1 ACATTTTAGTCACTTATGTT-T-GAAATATG
55877100 ACATTTTAGTCACT
1 ACATTTTAGTCACT
55877114 GAGCCGTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 1 0.03
31 17 0.46
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATATG
Found at i:55877792 original size:17 final size:18
Alignment explanation
Indices: 55877767--55877804 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
55877757 ACTTTAATTA
55877767 AATTATTTAAA-ATAAAT
1 AATTATTTAAATATAAAT
*
55877784 AATTTTTTAAATTATAAAT
1 AATTATTTAAA-TATAAAT
55877803 AA
1 AA
55877805 ACATCTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
19 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTATTTAAATATAAAT
Found at i:55881367 original size:21 final size:19
Alignment explanation
Indices: 55881343--55881381 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
55881333 ATTTGCCTCC
55881343 CTATCTAAGACCATGTTTCCT
1 CTATCTAAG-CCAT-TTTCCT
55881364 CTATCTAAGCCATTTTCC
1 CTATCTAAGCCATTTTCC
55881382 GGAGGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
CTATCTAAGCCATTTTCCT
Found at i:55898278 original size:24 final size:24
Alignment explanation
Indices: 55898251--55898299 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
55898241 TTGAGCTTTT
*
55898251 AACTTTAGCTACTGATTTGTAGCA
1 AACTTTAACTACTGATTTGTAGCA
55898275 AACTTTAACTACTGATTTGTAGCA
1 AACTTTAACTACTGATTTGTAGCA
55898299 A
1 A
55898300 CCAGTAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (24 bp):
AACTTTAACTACTGATTTGTAGCA
Found at i:55898469 original size:40 final size:39
Alignment explanation
Indices: 55898394--55898471 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 39
55898384 CACATGAAAC
*
55898394 GTGAGTCTAAATAAGTTTTGTATAATAAAGTAGTATCTTT
1 GTGAGTCTAAATAAGTCTTGTATAATAAAG-AGTATCTTT
55898434 GTGAGTCTAAATAAGTCTTGTATGATATAAA-AGTATCT
1 GTGAGTCTAAATAAGTCTTGTAT-A-ATAAAGAGTATCT
55898472 CATGAATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
40 29 0.83
41 1 0.03
42 5 0.14
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (39 bp):
GTGAGTCTAAATAAGTCTTGTATAATAAAGAGTATCTTT
Found at i:55906073 original size:6 final size:6
Alignment explanation
Indices: 55906060--55906101 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
55906050 TGATGGTTTT
* *
55906060 GCTTTG GTTTTG GTTTTG GCTTTG GCTTTG GCTTTG GCTTTG
1 GCTTTG GCTTTG GCTTTG GCTTTG GCTTTG GCTTTG GCTTTG
55906102 CATTTTGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.12, G:0.33, T:0.55
Consensus pattern (6 bp):
GCTTTG
Found at i:55906083 original size:18 final size:18
Alignment explanation
Indices: 55906053--55906101 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
55906043 GGGATTGTGA
*
55906053 TGGTTTT-GCTTTGGTTT
1 TGGTTTTGGCTTTGGCTT
55906070 TGGTTTTGGCTTTGGCTT
1 TGGTTTTGGCTTTGGCTT
*
55906088 TGGCTTTGGCTTTG
1 TGGTTTTGGCTTTG
55906102 CATTTTGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.00, C:0.10, G:0.33, T:0.57
Consensus pattern (18 bp):
TGGTTTTGGCTTTGGCTT
Found at i:55911276 original size:23 final size:23
Alignment explanation
Indices: 55911243--55911287 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
55911233 AACTTTTATA
*
55911243 TTTTTATAATTTCAAAAATATTT
1 TTTTTAAAATTTCAAAAATATTT
* *
55911266 TTTTTAAAATTTTAAAATTATT
1 TTTTTAAAATTTCAAAAATATT
55911288 GTTAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTTAAAATTTCAAAAATATTT
Found at i:55917603 original size:30 final size:30
Alignment explanation
Indices: 55917569--55917628 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
55917559 TTGGTAATTT
* *
55917569 AACTATT-AGAAAGTTTCATTTAAGTCACTG
1 AACTATTAAAAAAATTT-ATTTAAGTCACTG
55917599 AACTATTCAAAAAAATTTATTTAAGTCACT
1 AACTATT-AAAAAAATTTATTTAAGTCACT
55917629 AGGTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 12 0.46
32 7 0.27
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTATTAAAAAAATTTATTTAAGTCACTG
Found at i:55919531 original size:8 final size:8
Alignment explanation
Indices: 55919518--55919546 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
55919508 AAAATATATT
55919518 TTTTAAAA
1 TTTTAAAA
55919526 TTTTAAAA
1 TTTTAAAA
55919534 -TTTAAAA
1 TTTTAAAA
55919541 TTTTAA
1 TTTTAA
55919547 TTAATTACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:55921579 original size:14 final size:14
Alignment explanation
Indices: 55921560--55921608 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
55921550 TAATTATCTT
55921560 AATTAAAATAACTA
1 AATTAAAATAACTA
*
55921574 AATTAAGA-AA--A
1 AATTAAAATAACTA
55921585 AA-TAAAATAACTA
1 AATTAAAATAACTA
*
55921598 AAATAAAATAA
1 AATTAAAATAA
55921609 ACTCTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 4 0.14
11 5 0.17
13 5 0.17
14 15 0.52
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (14 bp):
AATTAAAATAACTA
Found at i:55930672 original size:11 final size:11
Alignment explanation
Indices: 55930656--55930699 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
55930646 TTCTTTTAAC
55930656 TTTCCTTCTCT
1 TTTCCTTCTCT
* *
55930667 TTTCCTTTTTT
1 TTTCCTTCTCT
55930678 TTTCCATTCTCT
1 TTTCC-TTCTCT
*
55930690 TTTACTTCTC
1 TTTCCTTCTC
55930700 CGGTTCTCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 19 0.70
12 8 0.30
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTCCTTCTCT
Found at i:55930674 original size:23 final size:23
Alignment explanation
Indices: 55930648--55930692 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
55930638 CTTTTATATT
55930648 CTTTTAACTTTCC-TTCTCTTTTC
1 CTTTT-ACTTTCCATTCTCTTTTC
**
55930671 CTTTTTTTTTCCATTCTCTTTT
1 CTTTTACTTTCCATTCTCTTTT
55930693 ACTTCTCCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (23 bp):
CTTTTACTTTCCATTCTCTTTTC
Found at i:55934793 original size:19 final size:19
Alignment explanation
Indices: 55934766--55934804 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
55934756 CCCTGTTTTA
55934766 CCCTCTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
*
55934785 CCCTTTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
55934804 C
1 C
55934805 TTCCTTCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.46, G:0.10, T:0.44
Consensus pattern (19 bp):
CCCTCTGCCTCTTCTGTTC
Found at i:55934871 original size:5 final size:5
Alignment explanation
Indices: 55934861--55934885 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55934851 GCTCCCTCTG
55934861 TTTCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT
55934886 GTCGATTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:55934918 original size:33 final size:33
Alignment explanation
Indices: 55934881--55934948 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
55934871 TTTCTTTTCT
* *
55934881 TTTCTGTCGATTTGCTCCCTTTGTTTCTCACAG
1 TTTCTGCCGATTTGCTCCCTCTGTTTCTCACAG
*
55934914 TTTCTGCCGATTTGCTCCCTCTGTTTCTCATAG
1 TTTCTGCCGATTTGCTCCCTCTGTTTCTCACAG
55934947 TT
1 TT
55934949 CTCCACACGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.09, C:0.28, G:0.15, T:0.49
Consensus pattern (33 bp):
TTTCTGCCGATTTGCTCCCTCTGTTTCTCACAG
Found at i:55938116 original size:59 final size:59
Alignment explanation
Indices: 55938053--55938236 Score: 153
Period size: 59 Copynumber: 3.1 Consensus size: 59
55938043 TATAGTATCA
*
55938053 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAACTTTATTAAATT
1 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAA-T
* * ** * * * * * * * *
55938113 ATATATTTTAATTAAAATATATTTA-ATAACAAT-TATG-TTAAATT-ATATTTTCTAGTATCA-
1 -TATATTATGATTTTAGTAAATTCATATAAGAATAT-TGATT--ATTAAGAATTT-TATTA-AAT
55938173 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
55938232 TATAT
1 TATAT
55938237 ATTTTAATTA
Statistics
Matches: 88, Mismatches: 25, Indels: 22
0.65 0.19 0.16
Matches are distributed among these distances:
58 1 0.01
59 32 0.36
60 27 0.31
61 27 0.31
62 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (59 bp):
TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
Found at i:55938117 original size:61 final size:60
Alignment explanation
Indices: 55938052--55938239 Score: 172
Period size: 61 Copynumber: 3.1 Consensus size: 60
55938042 TTATAGTATC
55938052 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAACTTTATTAAATT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAA-TTTATTAAATT
* * ** * * * * * * *
55938113 ATATATTTTAATTAAAATATATTTA-ATAACAAT-TATG-TTAAATT-A-TATTT-TCTAGTATC
1 ATATATTATGATTTTAGTAAATTCATATAAGAATAT-TGATT--ATTAAGAATTTAT-TA-AATT
55938172 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAA-TTTATTAAATT
55938233 ATATATT
1 ATATATT
55938240 TTAATTAAAA
Statistics
Matches: 93, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
57 1 0.01
58 5 0.05
59 27 0.29
60 20 0.22
61 34 0.37
62 5 0.05
63 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (60 bp):
ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTATTAAATT
Found at i:55938206 original size:120 final size:120
Alignment explanation
Indices: 55937993--55938274 Score: 521
Period size: 120 Copynumber: 2.4 Consensus size: 120
55937983 NNNNNNNNNN
55937993 ATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATA
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTATCATATA
55938057 TTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAACTTTATTAAATT
65 TTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAACTTTATTAAATT
* *
55938113 ATATATTTTAATTAAAATATATTTAATAACAATTATGTTAAATTATATTTTCTAGTATCATATAT
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATAT
*
55938178 TATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
66 TATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAACTTTATTAAATT
55938233 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
55938275 ATATGATTAA
Statistics
Matches: 157, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
120 155 0.99
121 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATAT
TATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAACTTTATTAAATT
Found at i:55938248 original size:18 final size:17
Alignment explanation
Indices: 55938220--55938254 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55938210 ATTATTAAGA
*
55938220 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
55938237 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
55938255 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:55938474 original size:44 final size:45
Alignment explanation
Indices: 55938411--55938507 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 45
55938401 CTATTACACC
* * * *
55938411 TCCATTCCATTTAACCAAACACA-AGAA-TACTATTACGCTTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTATAT
*
55938455 TCCATTACATTCAACCAAACAATTGAATTACTATTACGCCTATAT
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTATAT
*
55938500 TCAATTAC
1 TCCATTAC
55938508 CCCTCTATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.49
45 22 0.49
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTATAT
Found at i:55938534 original size:16 final size:16
Alignment explanation
Indices: 55938487--55938535 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
55938477 TTGAATTACT
* *
55938487 ATTACGCCTATATTCA
1 ATTACGCCTCTATTCC
*
55938503 ATTACCCCTCTATTCC
1 ATTACGCCTCTATTCC
55938519 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
55938535 A
1 A
55938536 ATACAGCGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.24, C:0.35, G:0.04, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:55939782 original size:16 final size:16
Alignment explanation
Indices: 55939761--55939796 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
55939751 AAATGGAAAG
55939761 TATATAGATATACATA
1 TATATAGATATACATA
55939777 TATATAGATATACATA
1 TATATAGATATACATA
55939793 TATA
1 TATA
55939797 AAAAAGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATAGATATACATA
Found at i:55939974 original size:3 final size:3
Alignment explanation
Indices: 55939952--55940021 Score: 113
Period size: 3 Copynumber: 23.0 Consensus size: 3
55939942 ATATAATGAG
* *
55939952 AAT AAC AAT GAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55939998 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
55940022 TTATTAAGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 59 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55942786 original size:44 final size:42
Alignment explanation
Indices: 55942730--55943009 Score: 222
Period size: 44 Copynumber: 6.5 Consensus size: 42
55942720 AAATCTACTT
* *
55942730 CACTACTGCTTAGGAAGATAATATTCGCCGTCTTCGATCTGCTC
1 CACTACTGCTTAGGGAGATAAGA-T-GCCGTCTTCGATCTGCTC
* * * * *
55942774 CGCTACTGCTTAGGGAGATAAGATCTACCATCTTTGACCTGCTC
1 CACTACTGCTTAGGGAGATAAGA--TGCCGTCTTCGATCTGCTC
* * *
55942818 CACTACTGCTTAGGGAGATAGGAT-CCATCTTCGACCTGCTC
1 CACTACTGCTTAGGGAGATAAGATGCCGTCTTCGATCTGCTC
* ** * ** * *
55942859 CACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTT
1 CACTACTGCTTAGGGAGATAAGA-TGCCGTCTTCGATCTGCTC
* *
55942902 CACTACTGCTTAGGAAGATAAGATTTGCCGTCTTTGATCTGCTC
1 CACTACTGCTTAGGGAGATAAGA--TGCCGTCTTCGATCTGCTC
* * * * *
55942946 CACTAATGCTTAGGGAGATAAGATCTACCATCTT-TAACTTGCTC
1 CACTACTGCTTAGGGAGATAAGA--TGCCGTCTTCGATC-TGCTC
*
55942990 CACTACTGCTTAGGCAGATA
1 CACTACTGCTTAGGGAGATA
55943010 GGACTACCAT
Statistics
Matches: 192, Mismatches: 39, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
41 39 0.20
42 2 0.01
43 31 0.16
44 119 0.62
45 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (42 bp):
CACTACTGCTTAGGGAGATAAGATGCCGTCTTCGATCTGCTC
Found at i:55942923 original size:128 final size:130
Alignment explanation
Indices: 55942776--55943014 Score: 356
Period size: 128 Copynumber: 1.8 Consensus size: 130
55942766 ATCTGCTCCG
* * *
55942776 CTACTGCTTAGGGAGATAAGATCTACCATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGA
1 CTACTGCTTAGGAAGATAAGATCTACCATCTTTGACCTGCTCCACTAATGCTTAGGGAGATAAGA
* *
55942841 -T-CCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCA
66 CTACCATCTTCAACCTGCTCCACTACTGCTTAGGCAGATAGGACTGGTGGCTTAAATCTACTTCA
* * * *
55942904 CTACTGCTTAGGAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTAATGCTTAGGGAGATAAGA
1 CTACTGCTTAGGAAGATAAGATCTACCATCTTTGACCTGCTCCACTAATGCTTAGGGAGATAAGA
* *
55942969 TCTACCATCTTTAACTTGCTCCACTACTGCTTAGGCAGATAGGACT
66 -CTACCATCTTCAACCTGCTCCACTACTGCTTAGGCAGATAGGACT
55943015 ACCATCTTCG
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
128 58 0.60
130 1 0.01
131 38 0.39
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (130 bp):
CTACTGCTTAGGAAGATAAGATCTACCATCTTTGACCTGCTCCACTAATGCTTAGGGAGATAAGA
CTACCATCTTCAACCTGCTCCACTACTGCTTAGGCAGATAGGACTGGTGGCTTAAATCTACTTCA
Found at i:55942978 original size:172 final size:174
Alignment explanation
Indices: 55942692--55943028 Score: 588
Period size: 172 Copynumber: 1.9 Consensus size: 174
55942682 NNNNNNNNNN
*
55942692 CTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATAATATTCG
1 CTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATAAGATTCG
* * *
55942757 CCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTACCATCTTTGACCTGCTCCACT
66 CCGTCTTCGATCTGCTCCACTAATGCTTAGGGAGATAAGATCTACCATCTTTAACCTGCTCCACT
*
55942822 ACTGCTTAGGGAGATAGGA-T-CCATCTTCGACCTGCTCCACTA
131 ACTGCTTAGGCAGATAGGACTACCATCTTCGACCTGCTCCACTA
*
55942864 CTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATAAGATTTG
1 CTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATAAGATTCG
* *
55942929 CCGTCTTTGATCTGCTCCACTAATGCTTAGGGAGATAAGATCTACCATCTTTAACTTGCTCCACT
66 CCGTCTTCGATCTGCTCCACTAATGCTTAGGGAGATAAGATCTACCATCTTTAACCTGCTCCACT
55942994 ACTGCTTAGGCAGATAGGACTACCATCTTCGACCT
131 ACTGCTTAGGCAGATAGGACTACCATCTTCGACCT
55943029 ATTTTCTGGG
Statistics
Matches: 155, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
172 141 0.91
173 1 0.01
174 13 0.08
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (174 bp):
CTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATAAGATTCG
CCGTCTTCGATCTGCTCCACTAATGCTTAGGGAGATAAGATCTACCATCTTTAACCTGCTCCACT
ACTGCTTAGGCAGATAGGACTACCATCTTCGACCTGCTCCACTA
Found at i:55944227 original size:7 final size:7
Alignment explanation
Indices: 55944217--55944256 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
55944207 CCACTTTTAC
55944217 TTTTTCA
1 TTTTTCA
55944224 TTTTTCA
1 TTTTTCA
55944231 TTTTTCA
1 TTTTTCA
55944238 -TTTTCA
1 TTTTTCA
55944244 TTTTTCA
1 TTTTTCA
55944251 TATTTT
1 T-TTTT
55944257 TTTCTGACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.19
7 21 0.68
8 4 0.13
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTCA
Found at i:55944234 original size:13 final size:13
Alignment explanation
Indices: 55944217--55944251 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
55944207 CCACTTTTAC
55944217 TTTTTCATTTTTCA
1 TTTTTCA-TTTTCA
55944231 TTTTTCATTTTCA
1 TTTTTCATTTTCA
55944244 TTTTTCAT
1 TTTTTCAT
55944252 ATTTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:55944241 original size:20 final size:21
Alignment explanation
Indices: 55944218--55944256 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
55944208 CACTTTTACT
55944218 TTTTCATTTTTCAT-TTTTCA
1 TTTTCATTTTTCATATTTTCA
55944238 TTTTCATTTTTCATATTTT
1 TTTTCATTTTTCATATTTT
55944257 TTTCTGACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCATTTTTCATATTTTCA
Found at i:55945180 original size:9 final size:8
Alignment explanation
Indices: 55945163--55945201 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
55945153 TTTTTTATTT
55945163 TTCTTTTC
1 TTCTTTTC
55945171 TTCTTCTTC
1 TTCTT-TTC
55945180 TTCTTTTTC
1 TTC-TTTTC
*
55945189 TTCTTTTT
1 TTCTTTTC
55945197 TTCTT
1 TTCTT
55945202 ATTTTTGACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 14 0.50
9 12 0.43
10 2 0.07
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:55945206 original size:9 final size:8
Alignment explanation
Indices: 55945160--55945207 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
55945150 GATTTTTTTA
55945160 TTTTTCTT
1 TTTTTCTT
*
55945168 TTCTTCTT
1 TTTTTCTT
*
55945176 CTTCTTCTT
1 -TTTTTCTT
55945185 TTTCTTCTT
1 TTT-TTCTT
55945194 TTTTTCTT
1 TTTTTCTT
55945202 ATTTTT
1 -TTTTT
55945208 GACTTTGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 14 0.40
9 21 0.60
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTCTT
Found at i:55945983 original size:25 final size:25
Alignment explanation
Indices: 55945934--55945991 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
55945924 AAGAAAATCC
*
55945934 AAAA-AATAAAAGAATAATTATTCA
1 AAAAGAATAAAAGAATAATTACTCA
*
55945958 AAAAGAATAAAAGAAT-ATTGGCTCA
1 AAAAGAATAAAAGAATAATT-ACTCA
55945983 AAAATGAAT
1 AAAA-GAAT
55945992 GCAAAGATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.24
25 18 0.62
26 4 0.14
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.22
Consensus pattern (25 bp):
AAAAGAATAAAAGAATAATTACTCA
Found at i:55949336 original size:16 final size:16
Alignment explanation
Indices: 55949315--55949350 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
55949305 AAATGGAAAG
55949315 TATATAGATATACATA
1 TATATAGATATACATA
55949331 TATATAGATATACATA
1 TATATAGATATACATA
55949347 TATA
1 TATA
55949351 AAAAAGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATAGATATACATA
Found at i:55949528 original size:3 final size:3
Alignment explanation
Indices: 55949506--55949575 Score: 113
Period size: 3 Copynumber: 23.0 Consensus size: 3
55949496 ATATAATGAG
* *
55949506 AAT AAC AAT GAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55949552 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
55949576 TTATTAAGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 59 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55953908 original size:20 final size:21
Alignment explanation
Indices: 55953880--55953919 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55953870 GTACATTTTT
55953880 TAAAGTTTATAT-ATATAAAC
1 TAAAGTTTATATGATATAAAC
* *
55953900 TAAATTTTATGTGATATAAA
1 TAAAGTTTATATGATATAAA
55953920 TTTTTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (21 bp):
TAAAGTTTATATGATATAAAC
Found at i:55962331 original size:60 final size:60
Alignment explanation
Indices: 55962258--55962378 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
55962248 ATTTCCGGAC
55962258 ATAATTGTTCTCCGGGCACTTTCGCTGCTAATTTAGGTGATTTAGAGATTTTGGGTCCTA
1 ATAATTGTTCTCCGGGCACTTTCGCTGCTAATTTAGGTGATTTAGAGATTTTGGGTCCTA
55962318 ATAATTGTTCTCCGGGCACTTTCGCTGCTAATTTAGGTGATTTAGAGATTTTGGGTCCTA
1 ATAATTGTTCTCCGGGCACTTTCGCTGCTAATTTAGGTGATTTAGAGATTTTGGGTCCTA
55962378 A
1 A
55962379 GGAATGCACC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (60 bp):
ATAATTGTTCTCCGGGCACTTTCGCTGCTAATTTAGGTGATTTAGAGATTTTGGGTCCTA
Found at i:55966644 original size:21 final size:21
Alignment explanation
Indices: 55966618--55966658 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55966608 CCAACTATAA
55966618 TAATTAAAATTT-CATAAATTT
1 TAATTAAAATTTACA-AAATTT
55966639 TAATTAAAATTTACAAAATT
1 TAATTAAAATTTACAAAATT
55966659 AATTATAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTAAAATTTACAAAATTT
Found at i:55967335 original size:2 final size:2
Alignment explanation
Indices: 55967328--55967354 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55967318 TTTGTACCTC
55967328 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55967355 GGGTAATGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55972475 original size:16 final size:16
Alignment explanation
Indices: 55972451--55972484 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
55972441 TTATTTTCTC
55972451 TTTCTATTTTTTTAAAT
1 TTTCTA-TTTTTTAAAT
55972468 TTTC-ATTTTTTAAAT
1 TTTCTATTTTTTAAAT
55972483 TT
1 TT
55972485 AAATGTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 1 0.06
17 4 0.24
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTATTTTTTAAAT
Found at i:55974565 original size:15 final size:17
Alignment explanation
Indices: 55974533--55974565 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
55974523 TATGTGATTA
55974533 AAAATATTACATAATTT
1 AAAATATTACATAATTT
55974550 AAAATA-TACA-AATTT
1 AAAATATTACATAATTT
55974565 A
1 A
55974566 TTTAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATATTACATAATTT
Found at i:55974570 original size:19 final size:19
Alignment explanation
Indices: 55974546--55974583 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
55974536 ATATTACATA
55974546 ATTTAAAATATACAA-ATTT
1 ATTT-AAATATACAATATTT
*
55974565 ATTTAATTATACAATATTT
1 ATTTAAATATACAATATTT
55974584 TAAATACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATATACAATATTT
Found at i:55975829 original size:18 final size:19
Alignment explanation
Indices: 55975789--55975830 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
55975779 CACATTATTA
* *
55975789 AAAATTTAATAGCATTAAT
1 AAAATTAAATAGCACTAAT
55975808 -AAATTAAATA-CACTAAT
1 AAAATTAAATAGCACTAAT
55975825 AAAATT
1 AAAATT
55975831 CATTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTAAATAGCACTAAT
Found at i:55976482 original size:23 final size:24
Alignment explanation
Indices: 55976456--55976501 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
55976446 ATGCACAATA
55976456 AACAAAATATCAAA-A-TACATTTG
1 AACAAAAT-TCAAATATTACATTTG
*
55976479 AACATAATTCAAATATTACATTT
1 AACAAAATTCAAATATTACATTT
55976502 ACACACTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 8 0.40
24 7 0.35
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (24 bp):
AACAAAATTCAAATATTACATTTG
Found at i:55979652 original size:19 final size:18
Alignment explanation
Indices: 55979630--55979672 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
55979620 TCTATAAAAG
*
55979630 TTTTAACTTTTTTATATAT
1 TTTTAACTTTTTTAAAT-T
*
55979649 TTTTAATTTTTTTAAATT
1 TTTTAACTTTTTTAAATT
55979667 TTTTAA
1 TTTTAA
55979673 AAATATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTAACTTTTTTAAATT
Found at i:55979673 original size:9 final size:9
Alignment explanation
Indices: 55979630--55979673 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
55979620 TCTATAAAAG
*
55979630 TTTTAACTT
1 TTTTAAATT
*
55979639 TTTTATATAT
1 TTTTAAAT-T
*
55979649 TTTTAATTT
1 TTTTAAATT
55979658 TTTTAAATT
1 TTTTAAATT
55979667 TTTTAAA
1 TTTTAAA
55979674 AATATATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAAATT
Found at i:55981558 original size:9 final size:9
Alignment explanation
Indices: 55981541--55981577 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55981531 TGAGTTTTTG
55981541 AATTCGAAT
1 AATTCGAAT
*
55981550 AACTCGAAT
1 AATTCGAAT
55981559 AATTCGAAT
1 AATTCGAAT
55981568 AATTCGAAT
1 AATTCGAAT
55981577 A
1 A
55981578 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55981827 original size:30 final size:31
Alignment explanation
Indices: 55981791--55981850 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
55981781 AAACCTTTTA
*
55981791 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
55981821 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
55981851 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:55982611 original size:5 final size:5
Alignment explanation
Indices: 55982601--55982631 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
55982591 CTCGAAAATT
55982601 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
55982632 CAAATGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:55994508 original size:13 final size:13
Alignment explanation
Indices: 55994451--55994511 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
55994441 ACACTCAAAT
*
55994451 TTTTCAAAAGCAA
1 TTTTCAAAAGCAC
* *
55994464 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
**
55994477 TTTTCTACTA-CAC
1 TTTTC-AAAAGCAC
*
55994490 TGTTCAAAAGCAC
1 TTTTCAAAAGCAC
55994503 TTTTCAAAA
1 TTTTCAAAA
55994512 TCAATGAAGA
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
12 2 0.06
13 31 0.89
14 2 0.06
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:55995964 original size:24 final size:24
Alignment explanation
Indices: 55995914--55995967 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
55995904 TTATTATTTG
** **
55995914 TTAATTTTATTTAATTTTTTGACA
1 TTAATTTTATTTAATTAATCAACA
*
55995938 TTAATTTTATTTAATTAATCAATA
1 TTAATTTTATTTAATTAATCAACA
55995962 TTAATT
1 TTAATT
55995968 AGATTAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (24 bp):
TTAATTTTATTTAATTAATCAACA
Found at i:56004196 original size:118 final size:118
Alignment explanation
Indices: 56003988--56004220 Score: 407
Period size: 118 Copynumber: 2.0 Consensus size: 118
56003978 GAGAGTATCG
56003988 CATGAGAATATGGCGGCACCTAATTAAACTTTTAGCCAATTTCCATGTTAAGTCTGTCCCATTTT
1 CATGAGAATATGGCGGCACCTAATTAAACTTTTAGCCAATTTCCATGTTAAGTCTGTCCCATTTT
56004053 GAAATTAAATTTAAATAGCCGTT-AAAGTATATAAGAATAACAAAAATAAATCA
66 GAAATTAAATTTAAATAGCCGTTAAAAG-ATATAAGAATAACAAAAATAAATCA
* * *
56004106 CATGAGAATATGGCGGCACCTAATTAAACTTTTAGTCGATTTCCATGTT-AGATCTGTTCCATTT
1 CATGAGAATATGGCGGCACCTAATTAAACTTTTAGCCAATTTCCATGTTAAG-TCTGTCCCATTT
56004170 TGAAATTAAATTTAAATAGCCGTTAAAAGATATAAGAATAACAAAAATAAA
65 TGAAATTAAATTTAAATAGCCGTTAAAAGATATAAGAATAACAAAAATAAA
56004221 CCTTTCAAAT
Statistics
Matches: 110, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
117 2 0.02
118 104 0.95
119 4 0.04
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (118 bp):
CATGAGAATATGGCGGCACCTAATTAAACTTTTAGCCAATTTCCATGTTAAGTCTGTCCCATTTT
GAAATTAAATTTAAATAGCCGTTAAAAGATATAAGAATAACAAAAATAAATCA
Found at i:56009026 original size:30 final size:30
Alignment explanation
Indices: 56008960--56009026 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
56008950 GGTTTGATTT
* * **
56008960 TAAAATAAATAAGTTATTGTGGTTCAATTT
1 TAAAATAAATAAATTATTGTGGCTCAATAA
* * *
56008990 TGAAATAAATAAATTTTTGTGGCTCGATAA
1 TAAAATAAATAAATTATTGTGGCTCAATAA
56009020 TAAAATA
1 TAAAATA
56009027 TGTTTTGGAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (30 bp):
TAAAATAAATAAATTATTGTGGCTCAATAA
Found at i:56010181 original size:3 final size:3
Alignment explanation
Indices: 56010173--56010210 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
56010163 ATGAATTAAA
56010173 TAT TAT TA- TAT TAT TAT TAT GTAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
56010211 ACTAATACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:56010202 original size:16 final size:14
Alignment explanation
Indices: 56010173--56010210 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 14
56010163 ATGAATTAAA
56010173 TATTATTATATTAT
1 TATTATTATATTAT
56010187 TATTATGTATTATTAT
1 TATTAT-TA-TATTAT
56010203 TATTATTA
1 TATTATTA
56010211 ACTAATACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 4 0.18
16 12 0.55
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TATTATTATATTAT
Found at i:56010481 original size:12 final size:11
Alignment explanation
Indices: 56010454--56010479 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56010444 AATTTTTTAA
56010454 TTTTAAAATAT
1 TTTTAAAATAT
56010465 TTTTAAAATAT
1 TTTTAAAATAT
56010476 TTTT
1 TTTT
56010480 TATTTTTATT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:56011769 original size:21 final size:21
Alignment explanation
Indices: 56011688--56011782 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
56011678 AGGTACTTTA
56011688 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
56011711 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
56011732 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* * **
56011753 TGTGTCGTTTCAAGCA-CTTA
1 TGTGTCGTATCAGGCACCTCG
56011773 TGTGTCGTAT
1 TGTGTCGTAT
56011783 ACTGATTAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.16
21 47 0.70
23 9 0.13
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:56022293 original size:19 final size:19
Alignment explanation
Indices: 56022248--56022303 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 19
56022238 TTCTCATATT
*
56022248 TTTTAAATAATTT-T-TAA
1 TTTTAAATAATTTATAAAA
56022265 TTTTAAAAATAATTTATAAAA
1 TTTT--AAATAATTTATAAAA
56022286 TTTTAAAT--TTTATAAAA
1 TTTTAAATAATTTATAAAA
56022303 T
1 T
56022304 CAATTAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 14 0.41
19 13 0.38
20 1 0.03
21 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTAAATAATTTATAAAA
Found at i:56023939 original size:72 final size:72
Alignment explanation
Indices: 56023807--56024123 Score: 465
Period size: 72 Copynumber: 4.4 Consensus size: 72
56023797 GTTACTCACC
* *
56023807 TTGATCTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTGTCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
*
56023872 GAGGAGT
66 AAGGAGT
* * *
56023879 TTGAAGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTCTG
1 TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
**
56023944 AAGTTGT
66 AAGGAGT
* * * *
56023951 TTGATGTTTCA-AGAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTT
1 TTGATGTTTCAGA-AAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTT
*
56024015 GGAGGAGT
65 GAAGGAGT
* *
56024023 TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCGTTGTCTATAGGGGAGTTATCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
**
56024088 AAGTTGT
66 AAGGAGT
56024095 TTGATGTTTCAGAAAATCAATTAAATGGT
1 TTGATGTTTCAGAAAATCAATTAAATGGT
56024124 ACTTTTCCTC
Statistics
Matches: 217, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
71 1 0.00
72 215 0.99
73 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (72 bp):
TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
AAGGAGT
Found at i:56024067 original size:144 final size:144
Alignment explanation
Indices: 56023807--56024119 Score: 547
Period size: 144 Copynumber: 2.2 Consensus size: 144
56023797 GTTACTCACC
* * *
56023807 TTGATCTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTGTCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAACGGCCAAATTCCATTGTCTATAGGGCAGTTGTCATCTTTG
56023872 GAGGAGTTTGAAGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATC
66 GAGGAGTTTGAAGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATC
56023937 ATCTCTGAAGTTGT
131 ATCTCTGAAGTTGT
*
56023951 TTGATGTTTCA-AGAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTT
1 TTGATGTTTCAGA-AAATCAATTAAACGGCCAAATTCCATTGTCTATAGGGCAGTTGTCATCTTT
* *
56024015 GGAGGAGTTTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCGTTGTCTATAGGGGAGTTAT
65 GGAGGAGTTTGAAGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTAT
*
56024080 CATCTTTGAAGTTGT
130 CATCTCTGAAGTTGT
56024095 TTGATGTTTCAGAAAATCAATTAAA
1 TTGATGTTTCAGAAAATCAATTAAA
56024120 TGGTACTTTT
Statistics
Matches: 160, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
143 1 0.01
144 158 0.99
145 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (144 bp):
TTGATGTTTCAGAAAATCAATTAAACGGCCAAATTCCATTGTCTATAGGGCAGTTGTCATCTTTG
GAGGAGTTTGAAGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATC
ATCTCTGAAGTTGT
Found at i:56030677 original size:23 final size:23
Alignment explanation
Indices: 56030651--56030700 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
56030641 GTTATTGATT
*
56030651 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCAGCTACATATC
*
56030674 AGTGGTAGCTTTAGCTACATATC
1 AGTGGTAGCTTCAGCTACATATC
56030697 AGTG
1 AGTG
56030701 TGGCACTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (23 bp):
AGTGGTAGCTTCAGCTACATATC
Found at i:56034133 original size:72 final size:72
Alignment explanation
Indices: 56034028--56034343 Score: 393
Period size: 72 Copynumber: 4.4 Consensus size: 72
56034018 CTTACTCAGC
* * * * * * *
56034028 TTGATCTTTCAGGAAATCAATTAAATGGTCAAATTCTATTGTCTATAGGGGAGTTATCGTCTCTG
1 TTGATGTTTCAAGAAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
*
56034093 AAGTTGT
66 AAGGTGT
* *
56034100 TTGATGTTTCAAGAAATCAATTAAATGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
1 TTGATGTTTCAAGAAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
* *
56034165 GAGGAGT
66 AAGGTGT
* * *
56034172 TTCATGTTTC-AGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTTT
1 TTGATGTTTCAAG-AAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTT
*
56034236 GAAGTTGT
65 GAAGGTGT
* * * *
56034244 TTGATGTTTCAACAAATCAGTTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTTG
1 TTGATGTTTCAAGAAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
* *
56034309 GAGGTAT
66 AAGGTGT
*
56034316 TTGCTGTTTC-AGAAAATCAATTAAATGG
1 TTGATGTTTCAAG-AAATCAATTAAATGG
56034344 TACTTTTCCT
Statistics
Matches: 207, Mismatches: 34, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
71 3 0.01
72 203 0.98
73 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (72 bp):
TTGATGTTTCAAGAAATCAATTAAATGGCCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
AAGGTGT
Found at i:56034294 original size:144 final size:144
Alignment explanation
Indices: 56034034--56034344 Score: 518
Period size: 144 Copynumber: 2.2 Consensus size: 144
56034024 CAGCTTGATC
* * *
56034034 TTTCAGGAAATCAATTAAATGGTCAAATTCTATTGTCTATAGGGGAGTTATCGTCTCTGAAGTTG
1 TTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTCTGAAGTTG
* * *
56034099 TTTGATGTTTCAAGAAATCAATTAAATGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTT
66 TTTGATGTTTCAACAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTT
56034164 GGAGG-AGTTT-CATG
131 GGAGGTA-TTTGC-TG
*
56034178 TTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTTTGAAGTTG
1 TTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTCTGAAGTTG
*
56034243 TTTGATGTTTCAACAAATCAGTTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTT
66 TTTGATGTTTCAACAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTT
56034308 GGAGGTATTTGCTG
131 GGAGGTATTTGCTG
56034322 TTTCAGAAAATCAATTAAATGGT
1 TTTCAGAAAATCAATTAAATGGT
56034345 ACTTTTCCTC
Statistics
Matches: 157, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
144 155 0.99
145 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (144 bp):
TTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTCTGAAGTTG
TTTGATGTTTCAACAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTATCATCTTT
GGAGGTATTTGCTG
Found at i:56037005 original size:71 final size:71
Alignment explanation
Indices: 56036889--56037027 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
56036879 TTTTCTGCTG
*
56036889 ACATGTCAGGAAAAATGTGCCAAGCTGGACGCACTTTCATTGAAATTTTCAAAAAACGTTTTCAA
1 ACATGTCAGGAAAAATCTGCCAAGCTGGACGCACTTTCATTGAAATTTTCAAAAAACGTTTTCAA
56036954 CTTCTA
66 CTTCTA
56036960 ACATGTCAGGAAAAATCTGCCAAGCTGGACGCACTTTCATTGAAATTTTCAAAAAACGTTTTCAA
1 ACATGTCAGGAAAAATCTGCCAAGCTGGACGCACTTTCATTGAAATTTTCAAAAAACGTTTTCAA
56037025 CTT
66 CTT
56037028 AGCACACTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (71 bp):
ACATGTCAGGAAAAATCTGCCAAGCTGGACGCACTTTCATTGAAATTTTCAAAAAACGTTTTCAA
CTTCTA
Found at i:56043038 original size:46 final size:45
Alignment explanation
Indices: 56042969--56043060 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 45
56042959 CATGGCAAAA
56042969 TGTGAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
*
56043014 TGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
1 TGTG-AAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
56043060 T
1 T
56043061 ATAGCAATGT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 4 0.09
46 41 0.91
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (45 bp):
TGTGAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
Found at i:56044839 original size:4 final size:4
Alignment explanation
Indices: 56044830--56044855 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
56044820 ATTTTACACG
56044830 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
56044856 AGGATAACTA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:56047260 original size:72 final size:72
Alignment explanation
Indices: 56047143--56047459 Score: 454
Period size: 72 Copynumber: 4.4 Consensus size: 72
56047133 GTTACTCAGC
* * * * * *
56047143 TTGATCTTTCAGTAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
*
56047208 GAGGAGT
66 AAGGAGT
* *
56047215 TTGATGCTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
**
56047280 AAGTTGT
66 AAGGAGT
* * * *
56047287 TTGATGTTTCAGAAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
*
56047352 GAGGAGT
66 AAGGAGT
* *
56047359 TTAATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
**
56047424 AAGTTGT
66 AAGGAGT
56047431 TTGATGTTTCAGAAAATCAATTAAATGGT
1 TTGATGTTTCAGAAAATCAATTAAATGGT
56047460 ACATTTCCTC
Statistics
Matches: 215, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 215 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (72 bp):
TTGATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGCAGTTATCATCTTTG
AAGGAGT
Found at i:56047403 original size:144 final size:144
Alignment explanation
Indices: 56047143--56047455 Score: 590
Period size: 144 Copynumber: 2.2 Consensus size: 144
56047133 GTTACTCAGC
* *
56047143 TTGATCTTTCAGTAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
*
56047208 GAGGAGTTTGATGCTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATC
66 GAGGAGTTTAATGCTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATC
56047273 ATCTTTGAAGTTGT
131 ATCTTTGAAGTTGT
56047287 TTGATGTTTCAGAAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
1 TTGATGTTTCAGAAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
*
56047352 GAGGAGTTTAATGTTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATC
66 GAGGAGTTTAATGCTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATC
56047417 ATCTTTGAAGTTGT
131 ATCTTTGAAGTTGT
56047431 TTGATGTTTCAGAAAATCAATTAAA
1 TTGATGTTTCAGAAAATCAATTAAA
56047456 TGGTACATTT
Statistics
Matches: 165, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 165 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (144 bp):
TTGATGTTTCAGAAAATCAATTAAACGGCCAAATTCCCTTGTCTATAGGGCAGTTGTCATCTTTG
GAGGAGTTTAATGCTTCAGAAAATCAATTAAATGGTCAAATTCCATTGTCTATAGGGGAGTTATC
ATCTTTGAAGTTGT
Found at i:56050841 original size:29 final size:28
Alignment explanation
Indices: 56050789--56050847 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
56050779 GTCAAATGGG
*
56050789 TAAGAGAAGAATAGTTTAAGTACC-ACT
1 TAAGAGAAAAATAGTTTAAGTACCAACT
56050816 TAAGAGCAAAAATATGTTT-AGATACCAACT
1 TAAGAG-AAAAATA-GTTTAAG-TACCAACT
56050846 TA
1 TA
56050848 TAAGTTAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.22
28 8 0.30
29 8 0.30
30 5 0.19
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (28 bp):
TAAGAGAAAAATAGTTTAAGTACCAACT
Found at i:56051122 original size:27 final size:26
Alignment explanation
Indices: 56051092--56051142 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
56051082 TATAATATTG
*
56051092 AATTTAGTTTTCAATTTTTTTTTTGTC
1 AATTTAGTTTT-AATTCTTTTTTTGTC
*
56051119 AATTTAGTTTTTATTCTTTTTTTG
1 AATTTAGTTTTAATTCTTTTTTTG
56051143 AGCTCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.69
Consensus pattern (26 bp):
AATTTAGTTTTAATTCTTTTTTTGTC
Done.