Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 16 of 335
Found at i:5828753 original size:53 final size:53
Alignment explanation
Indices: 5828612--5828762 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
5828602 ATAAGTGCGC
* * **
5828612 CCGTTTAAGACCATAGCTGGGTTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTATAATGTGATAATGTGACT
* *
5828665 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTATAATGTGATAATGTGACT
*
5828718 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGATATGGCATCGGTAT-A-ATGTGA
5828763 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGATATGGCATCGGTATAATGTGATAATGTGACT
Found at i:5832377 original size:46 final size:44
Alignment explanation
Indices: 5832273--5832380 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
5832263 TGTCTTTGAC
** * * *
5832273 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
5832317 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5832363 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5832381 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:5838437 original size:23 final size:24
Alignment explanation
Indices: 5838377--5838437 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
5838367 ATATATAAAC
5838377 ATTTATTTTA-ATATTTTTAACAT
1 ATTTATTTTATATATTTTTAACAT
* *
5838400 ATTTAATTTATTATATTTTTTA-A-
1 ATTTATTTTA-TATATTTTTAACAT
5838423 ATTTATTTTTATATA
1 ATTTA-TTTTATATA
5838438 ATAGACTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 18 0.56
24 5 0.16
25 9 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
ATTTATTTTATATATTTTTAACAT
Found at i:5852793 original size:28 final size:28
Alignment explanation
Indices: 5852732--5852793 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
5852722 AAATATCTCA
*
5852732 ATTTTTAATAAAAAAGATAATTTATTTT
1 ATTTTTAATAAAAAAGATAATTCATTTT
* *
5852760 AATTTTAATAAAATA-A-AATTCATTTAAT
1 ATTTTTAATAAAAAAGATAATTCATTT--T
5852788 ATTTTT
1 ATTTTT
5852794 TACATAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 8 0.29
27 1 0.04
28 19 0.68
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
ATTTTTAATAAAAAAGATAATTCATTTT
Found at i:5864023 original size:17 final size:16
Alignment explanation
Indices: 5864007--5864058 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5863997 CATTTTATAT
5864007 TATATAAAATTAAATA
1 TATATAAAATTAAATA
*
5864023 TATATAACA-T-AATA
1 TATATAAAATTAAATA
*
5864037 CTATATAGAAATTAAAAA
1 -TATATA-AAATTAAATA
5864055 TATA
1 TATA
5864059 GTTTTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 4 0.14
15 7 0.24
16 10 0.34
17 5 0.17
18 3 0.10
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
TATATAAAATTAAATA
Found at i:5865287 original size:21 final size:21
Alignment explanation
Indices: 5865261--5865313 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5865251 CGCTGTTTCT
*
5865261 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
5865282 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
5865303 AATCTCACCGC
1 AATCTCACCGC
5865314 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:5867959 original size:8 final size:8
Alignment explanation
Indices: 5867946--5867974 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
5867936 CAAATTGAAA
5867946 AAAAAAAG
1 AAAAAAAG
5867954 AAAAAAAG
1 AAAAAAAG
5867962 AAAAAAAG
1 AAAAAAAG
5867970 AAAAA
1 AAAAA
5867975 GGAAAGCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5874938 original size:88 final size:88
Alignment explanation
Indices: 5874774--5874942 Score: 209
Period size: 88 Copynumber: 1.9 Consensus size: 88
5874764 AATACTACTG
* * * *
5874774 TATATATACATCATGTTATACATCACATGATAATAGCATGGATTTACTCCTAACACTATACGCAC
1 TATATATACATCATATTAAACATCACATGATAATAGCATGGAATTACTCCTAACACTATACACAC
*
5874839 TTATATAAAGACTGTAATATATA
66 TTATACAAAGACTGTAATATATA
* * *
5874862 TATATATATATCATATTAAAGATCACATG--AATAAGCATGGAATTACTCCTAACACTATATACA
1 TATATATACATCATATTAAACATCACATGATAAT-AGCATGGAATTACTCCTAACACTATACACA
*
5874925 CATT-TACCCAAGACTGTA
65 C-TTATA-CAAAGACTGTA
5874943 TCCAGATCAT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
86 3 0.04
87 30 0.43
88 36 0.52
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.33
Consensus pattern (88 bp):
TATATATACATCATATTAAACATCACATGATAATAGCATGGAATTACTCCTAACACTATACACAC
TTATACAAAGACTGTAATATATA
Found at i:5884215 original size:17 final size:18
Alignment explanation
Indices: 5884193--5884226 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5884183 TAAAATAAAT
5884193 TCTTCTATATC-CATTTA
1 TCTTCTATATCTCATTTA
*
5884210 TCTTCTCTATCTCATTT
1 TCTTCTATATCTCATTT
5884227 TAAGTTCAAT
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:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTTCTATATCTCATTTA
Found at i:5884746 original size:21 final size:21
Alignment explanation
Indices: 5884720--5884761 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5884710 TGGCATCTCA
5884720 TATCTCTCGTATAAAAGCTCT
1 TATCTCTCGTATAAAAGCTCT
5884741 TATCTCTCGTATAAAAGCTCT
1 TATCTCTCGTATAAAAGCTCT
5884762 CTAGTTCAAT
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:0.24, G:0.10, T:0.38
Consensus pattern (21 bp):
TATCTCTCGTATAAAAGCTCT
Found at i:5884763 original size:23 final size:22
Alignment explanation
Indices: 5884715--5884763 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
5884705 TACAATGGCA
*
5884715 TCTCATATCTCTCGTATAAAAG
1 TCTCTTATCTCTCGTATAAAAG
5884737 -CTCTTATCTCTCGTATAAAAG
1 TCTCTTATCTCTCGTATAAAAG
5884758 CTCTCT
1 -TCTCT
5884764 AGTTCAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 20 0.83
23 4 0.17
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.39
Consensus pattern (22 bp):
TCTCTTATCTCTCGTATAAAAG
Found at i:5886074 original size:23 final size:23
Alignment explanation
Indices: 5886047--5886104 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
5886037 ATTAATTTTT
5886047 ATATTTTAATTTTAAAAAATTT-A
1 ATATTTTAATTTT-AAAAATTTCA
* *
5886070 ATATTTTTATTTTTAAAATTTCA
1 ATATTTTAATTTTAAAAATTTCA
* *
5886093 AAATTTAAATTT
1 ATATTTTAATTT
5886105 AACTGTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 7 0.24
23 22 0.76
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTTTAATTTTAAAAATTTCA
Found at i:5901419 original size:41 final size:41
Alignment explanation
Indices: 5901374--5901452 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
5901364 TTGTTGAGTC
5901374 AACTTGTCCAATGATTTTGTTTGAACTGATACCCTAGATAG
1 AACTTGTCCAATGATTTTGTTTGAACTGATACCCTAGATAG
*
5901415 AACTTGTCCAATGATTTTGTTTGAACTGGTACCCTAGA
1 AACTTGTCCAATGATTTTGTTTGAACTGATACCCTAGA
5901453 CAAAATTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (41 bp):
AACTTGTCCAATGATTTTGTTTGAACTGATACCCTAGATAG
Found at i:5902756 original size:17 final size:18
Alignment explanation
Indices: 5902719--5902756 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5902709 ATTTATTCTA
*
5902719 TAATTAAATTGTAACATT
1 TAATTAAATTGTAACAGT
*
5902737 TAATTTAATT-TAACAGT
1 TAATTAAATTGTAACAGT
5902754 TAA
1 TAA
5902757 ATTTTTTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
TAATTAAATTGTAACAGT
Found at i:5902813 original size:15 final size:15
Alignment explanation
Indices: 5902795--5902833 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
5902785 AGAATTAAAT
5902795 AAAATGATTATTATA
1 AAAATGATTATTATA
* *
5902810 AAAATGAATATTCTA
1 AAAATGATTATTATA
5902825 AAAAT-ATTA
1 AAAATGATTA
5902834 GTTTTGAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (15 bp):
AAAATGATTATTATA
Found at i:5912179 original size:17 final size:17
Alignment explanation
Indices: 5912157--5912190 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5912147 AAAAAGAAAT
5912157 AAAATAA-AATATTTAAA
1 AAAATAATAAT-TTTAAA
5912174 AAAATAATAATTTTAAA
1 AAAATAATAATTTTAAA
5912191 CTAAGATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAATAATTTTAAA
Found at i:5916278 original size:6 final size:6
Alignment explanation
Indices: 5916267--5916298 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5916257 ATTGCTTGGG
5916267 TGTGGC TGTGGC TGTGGC TGTGGC TGTGGC TG
1 TGTGGC TGTGGC TGTGGC TGTGGC TGTGGC TG
5916299 CCTTCCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
TGTGGC
Found at i:5926517 original size:5 final size:5
Alignment explanation
Indices: 5926507--5926539 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
5926497 AGAACCATCC
5926507 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCC
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCC
5926540 GGTCCTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (5 bp):
CCCTT
Found at i:5932889 original size:142 final size:142
Alignment explanation
Indices: 5932633--5932919 Score: 556
Period size: 142 Copynumber: 2.0 Consensus size: 142
5932623 AAATTAGGTC
*
5932633 TCTTTGCTTTTATTTATAGAAATTTAGTTTCTTTATCTGTTTGATTTGAAAATGCATTCCCAATT
1 TCTTTGCTTTTATTTATAGAAATTTAGTTTCTTTATCTGTTTGATTTAAAAATGCATTCCCAATT
*
5932698 GGTGACATTGTTAATAGGTTTCCATCAAATACAAATGTGTCATTTTATTATTTAAGAGTCTAATT
66 GGTAACATTGTTAATAGGTTTCCATCAAATACAAATGTGTCATTTTATTATTTAAGAGTCTAATT
5932763 TGAAAATTAAAG
131 TGAAAATTAAAG
5932775 TCTTTGCTTTTATTTATAGAAATTTAGTTTCTTTATCTGTTTGATTTAAAAATGCATTCCCAATT
1 TCTTTGCTTTTATTTATAGAAATTTAGTTTCTTTATCTGTTTGATTTAAAAATGCATTCCCAATT
5932840 GGTAACATTGTTAATAGGTTTCCATCAAATACAAATGTGTCATTTTATTATTTAAGAGTCTAATT
66 GGTAACATTGTTAATAGGTTTCCATCAAATACAAATGTGTCATTTTATTATTTAAGAGTCTAATT
5932905 TGAAAATTAAAG
131 TGAAAATTAAAG
5932917 TCT
1 TCT
5932920 AATTGATAGC
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 143 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (142 bp):
TCTTTGCTTTTATTTATAGAAATTTAGTTTCTTTATCTGTTTGATTTAAAAATGCATTCCCAATT
GGTAACATTGTTAATAGGTTTCCATCAAATACAAATGTGTCATTTTATTATTTAAGAGTCTAATT
TGAAAATTAAAG
Found at i:5940737 original size:411 final size:411
Alignment explanation
Indices: 5939970--5940799 Score: 1437
Period size: 411 Copynumber: 2.0 Consensus size: 411
5939960 TGACTCTAAT
*
5939970 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTTGCCAAAAAGTTATGATGATTAGAAG
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCAAAAAGTTATGATGATTAGAAG
* * *
5940035 TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGTGTAACTGATTGAAGGTCTGCCTCA
66 TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACCGATTGAAGATCTGCCTCA
* *
5940100 AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
131 AGATCAGCTACTCTCTTTTCTGACCCCTCCAAATCAGCAGCTACTGACCCATAATAATTTTCAAG
*
5940165 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAATCGCCCTCCCTAACC
196 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCTAACC
*
5940230 ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGT
261 ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGC
*
5940295 TCCTCCCATTTTTGCACCAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAATTCATTTCGTTC
326 TCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAATTCATTTCGTTC
* *
5940360 TACCAAACTATAAATCTTGCC
391 TACCAAACTATAAAACTTACC
* * *
5940381 CTGAAGGTTTTTATTCTCAACTTCAAATTGAGCTGCCTTCGCC-GAAAGATTATGATGATTAGAA
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCAAAAAG-TTATGATGATTAGAA
5940445 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACCGATTGAAGATCTGCCTC
65 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACCGATTGAAGATCTGCCTC
* *
5940510 AAGATCAGCTACTCTCTTTTCTGACCCCTCCAACTCAGCAGCTACTGACCTATAATAATTTTCAA
130 AAGATCAGCTACTCTCTTTTCTGACCCCTCCAAATCAGCAGCTACTGACCCATAATAATTTTCAA
*
5940575 GATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTTCCTAAC
195 GATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCTAAC
*
5940640 CATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAGGGCATGTCGATTCCATCCAAAAG
260 CATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAG
* * *
5940705 CTCCTCCCATTTTTGCAACAAGTGGTTCCTTTCCATTAAGGATTGTTCCAGCATTTCATTTCGTT
325 CTCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAATTCATTTCGTT
* *
5940770 CTGCCAACCTATAAAACTTACC
390 CTACCAAACTATAAAACTTACC
5940792 CTGAAGGT
1 CTGAAGGT
5940800 CCTCATATTT
Statistics
Matches: 395, Mismatches: 23, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
410 4 0.01
411 391 0.99
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.34
Consensus pattern (411 bp):
CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCAAAAAGTTATGATGATTAGAAG
TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACCGATTGAAGATCTGCCTCA
AGATCAGCTACTCTCTTTTCTGACCCCTCCAAATCAGCAGCTACTGACCCATAATAATTTTCAAG
ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCTAACC
ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGC
TCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAATTCATTTCGTTC
TACCAAACTATAAAACTTACC
Found at i:5947609 original size:15 final size:15
Alignment explanation
Indices: 5947574--5947603 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5947564 TTTAATCATT
5947574 TATAAATTATAAAAA
1 TATAAATTATAAAAA
5947589 TATAAATTATAAAAA
1 TATAAATTATAAAAA
5947604 ATTAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TATAAATTATAAAAA
Found at i:5952563 original size:17 final size:17
Alignment explanation
Indices: 5952544--5952610 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
5952534 TCTGACATCT
*
5952544 TTTTGTTTTC-TTTTTC
1 TTTTGTTTTCATATTTC
*
5952560 TTTTATTTTCATATTTC
1 TTTTGTTTTCATATTTC
*
5952577 TTTTG-TTT--T-TTTA
1 TTTTGTTTTCATATTTC
*
5952590 TTTTATTTTCATATTTC
1 TTTTGTTTTCATATTTC
5952607 TTTT
1 TTTT
5952611 TTTCTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 7 0.17
14 4 0.10
16 13 0.32
17 16 0.40
ACGTcount: A:0.10, C:0.09, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTGTTTTCATATTTC
Found at i:5952588 original size:8 final size:8
Alignment explanation
Indices: 5952560--5952634 Score: 53
Period size: 8 Copynumber: 9.1 Consensus size: 8
5952550 TTTCTTTTTC
5952560 TTTTATTT
1 TTTTATTT
**
5952568 TCATATTT
1 TTTTATTT
*
5952576 CTTTTGTTT
1 -TTTTATTT
5952585 TTTTATTT
1 TTTTATTT
*
5952593 TATTT-TCAT
1 T-TTTAT-TT
* *
5952602 ATTTCTTT
1 TTTTATTT
*
5952610 TTTTCTTT
1 TTTTATTT
5952618 TTTTATTT
1 TTTTATTT
5952626 TTTTATTT
1 TTTTATTT
5952634 T
1 T
5952635 GTTCCTTAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
8 42 0.81
9 10 0.19
ACGTcount: A:0.12, C:0.07, G:0.01, T:0.80
Consensus pattern (8 bp):
TTTTATTT
Found at i:5952594 original size:30 final size:28
Alignment explanation
Indices: 5952549--5952626 Score: 111
Period size: 30 Copynumber: 2.7 Consensus size: 28
5952539 CATCTTTTTG
* *
5952549 TTTTCTTTTTCTTTTATTTTCATATTTC
1 TTTTTTTTTTTTTTTATTTTCATATTTC
5952577 TTTTGTTTTTTTATTTTATTTTCATATTTC
1 TTTT-TTTTTTT-TTTTATTTTCATATTTC
*
5952607 TTTTTTTCTTTTTTTATTTT
1 TTTTTTTTTTTTTTTATTTT
5952627 TTTATTTTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 13 0.29
29 11 0.24
30 21 0.47
ACGTcount: A:0.10, C:0.09, G:0.01, T:0.79
Consensus pattern (28 bp):
TTTTTTTTTTTTTTTATTTTCATATTTC
Found at i:5952708 original size:5 final size:5
Alignment explanation
Indices: 5952656--5952718 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
5952646 AATTTTGTCT
* * * *
5952656 TTTTA TTTT- TTTTA CTTT- TTTGA TTTTTT TTCTTA TTTCA TTTT- TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TT-TTA TTTTA TTTTA TTTTA
5952705 TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTT
5952719 TTATTATTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
4 10 0.22
5 28 0.62
6 7 0.16
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:5952710 original size:19 final size:19
Alignment explanation
Indices: 5952660--5952726 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
5952650 TTGTCTTTTT
* *
5952660 ATTTTTTTTACTTT-TTTG
1 ATTTTTTTTATTTTATTTC
*
5952678 A-TTTTTTT-TCTTATTTC
1 ATTTTTTTTATTTTATTTC
*
5952695 ATTTTTTTTATTTTATTTT
1 ATTTTTTTTATTTTATTTC
5952714 ATTTTTTATTATT
1 ATTTTTT-TTATT
5952727 AACTTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 2 0.05
17 11 0.28
18 8 0.20
19 14 0.35
20 5 0.12
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (19 bp):
ATTTTTTTTATTTTATTTC
Found at i:5952719 original size:34 final size:34
Alignment explanation
Indices: 5952647--5952726 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
5952637 TCCTTAATAA
*
5952647 ATTTTGTCTT-TTTATTTTTTTTACTTTTTTGATT
1 ATTTTTTCTTATTTATTTTTTTTACTTTTTT-ATT
5952681 -TTTTTTCTTATTTCATTTTTTTTA-TTTTATT-TT
1 ATTTTTTCTTATTT-ATTTTTTTTACTTTT-TTATT
*
5952714 ATTTTTTATTATT
1 ATTTTTTCTTATT
5952727 AACTTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
33 10 0.25
34 18 0.45
35 12 0.30
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.79
Consensus pattern (34 bp):
ATTTTTTCTTATTTATTTTTTTTACTTTTTTATT
Found at i:5952721 original size:17 final size:17
Alignment explanation
Indices: 5952663--5952723 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
5952653 TCTTTTTATT
* *
5952663 TTTTTTACTTT-TTTGA
1 TTTTTTATTTTATTTTA
*
5952679 TTTTTT-TTCTTATTTCATT
1 TTTTTTATT-TTATTT--TA
5952698 TTTTTTATTTTATTTTA
1 TTTTTTATTTTATTTTA
5952715 TTTTTTATT
1 TTTTTTATT
5952724 ATTAACTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
15 1 0.03
16 8 0.22
17 13 0.36
19 12 0.33
20 2 0.06
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTTTATTTTATTTTA
Found at i:5952725 original size:10 final size:9
Alignment explanation
Indices: 5952655--5952726 Score: 74
Period size: 9 Copynumber: 7.9 Consensus size: 9
5952645 AAATTTTGTC
5952655 TTTTTATTT
1 TTTTTATTT
*
5952664 TTTTTACTT
1 TTTTTATTT
*
5952673 TTTTGATTT
1 TTTTTATTT
*
5952682 TTTTT-CTT
1 TTTTTATTT
* *
5952690 ATTTCATTT
1 TTTTTATTT
5952699 TTTTTATTT
1 TTTTTATTT
5952708 TATTTTATTT
1 T-TTTTATTT
5952718 TTTATTATT
1 TTT-TTATT
5952727 AACTTTAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
8 5 0.10
9 31 0.62
10 14 0.28
ACGTcount: A:0.14, C:0.04, G:0.01, T:0.81
Consensus pattern (9 bp):
TTTTTATTT
Found at i:5952905 original size:14 final size:14
Alignment explanation
Indices: 5952888--5952914 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5952878 TTTTTTAAAA
5952888 TTTTAAATATTAAT
1 TTTTAAATATTAAT
5952902 TTTTAAATATTAA
1 TTTTAAATATTAA
5952915 CCATATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAATATTAAT
Found at i:5952914 original size:37 final size:35
Alignment explanation
Indices: 5952772--5952914 Score: 119
Period size: 37 Copynumber: 4.0 Consensus size: 35
5952762 TTTATAATAC
* * *
5952772 TTTTTTAAAATTTTAATTATCATTTTTAAAAAT-A
1 TTTTTTAAAATTTTAAATATAATTTTTAAAATTAA
* * * * *
5952806 TTTTTT-TAACTTTAGATATATATTTGTGAAATTAA
1 TTTTTTAAAATTTTAAATATA-ATTTTTAAAATTAA
* * * *
5952841 TTTTTTATATATTTTAAAAATGTATTTTTCAAATTAA
1 TTTTTTA-AAATTTTAAATAT-AATTTTTAAAATTAA
5952878 TTTTTTAAAATTTTAAATATTAATTTTTAAATATTAA
1 TTTTTTAAAATTTTAAATA-TAATTTTTAAA-ATTAA
5952915 CCATATTTTT
Statistics
Matches: 82, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
33 9 0.11
34 15 0.18
35 7 0.09
36 18 0.22
37 33 0.40
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (35 bp):
TTTTTTAAAATTTTAAATATAATTTTTAAAATTAA
Found at i:5952921 original size:23 final size:23
Alignment explanation
Indices: 5952873--5952914 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
5952863 TATTTTTCAA
*
5952873 ATTAATTTTTTAAAATTTTAAAT
1 ATTAATTTTTTAAAATATTAAAT
5952896 ATTAA-TTTTT-AAATATTAA
1 ATTAATTTTTTAAAATATTAA
5952915 CCATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 5 0.28
23 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTAATTTTTTAAAATATTAAAT
Found at i:5953004 original size:12 final size:11
Alignment explanation
Indices: 5952972--5953014 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
5952962 ATACAATTTC
*
5952972 TTTAATTTCTT
1 TTTAATTTTTT
*
5952983 TTTAA-ATTTT
1 TTTAATTTTTT
5952993 TTTAACTTTTTT
1 TTTAA-TTTTTT
5953005 TTTAATTTTT
1 TTTAATTTTT
5953015 GAAAAGTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.30
11 10 0.37
12 9 0.33
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTAATTTTTT
Found at i:5953011 original size:21 final size:21
Alignment explanation
Indices: 5952966--5953014 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
5952956 TTGTAAATAC
*
5952966 AATTTCTTTAATTTCTTTTTA
1 AATTTTTTTAATTTCTTTTTA
*
5952987 AATTTTTTTAACTTT-TTTTTT
1 AATTTTTTTAA-TTTCTTTTTA
5953008 AATTTTT
1 AATTTTT
5953015 GAAAAGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (21 bp):
AATTTTTTTAATTTCTTTTTA
Found at i:5953130 original size:17 final size:17
Alignment explanation
Indices: 5953110--5953157 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
5953100 TTTTTTACTT
5953110 TTTTATTAAATTTTGTC
1 TTTTATTAAATTTTGTC
* *
5953127 TTTTACTTAATTTTTTTC
1 TTTTA-TTAAATTTTGTC
*
5953145 TTTT-TTAAGTTTT
1 TTTTATTAAATTTT
5953158 ATATTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 14 0.52
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTATTAAATTTTGTC
Found at i:5953345 original size:36 final size:35
Alignment explanation
Indices: 5953243--5953351 Score: 123
Period size: 34 Copynumber: 3.1 Consensus size: 35
5953233 ATTTTTACAA
* *
5953243 TTTTTTTAAATTTTAATTAT-TATTTTTAAAATTA
1 TTTTTTTAAATTTTAAATATATATTTTTAAAATTG
* * * *
5953277 TTTTTTT-AACTTTAGATATATATTTGTGAAATTG
1 TTTTTTTAAATTTTAAATATATATTTTTAAAATTG
*
5953311 TTTTTTATAAATTTTAAATATATATTTTTCAAATTAG
1 TTTTTT-TAAATTTTAAATATATATTTTTAAAATT-G
5953348 TTTT
1 TTTT
5953352 GAAATTAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 9 0.15
34 24 0.39
35 1 0.02
36 22 0.36
37 5 0.08
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (35 bp):
TTTTTTTAAATTTTAAATATATATTTTTAAAATTG
Found at i:5953357 original size:34 final size:34
Alignment explanation
Indices: 5953233--5953357 Score: 105
Period size: 36 Copynumber: 3.7 Consensus size: 34
5953223 TATATTATTA
* *
5953233 ATTTTTACAATT--TTTTTAAATTTTAATTAT-T
1 ATTTTTAAAATTAGTTTTTAAATTTTAAATATAT
* * * *
5953264 ATTTTTAAAATTATTTTTTTAACTTTAGATATAT
1 ATTTTTAAAATTAGTTTTTAAATTTTAAATATAT
* *
5953298 ATTTGTGAAATT-GTTTTTTATAAATTTTAAATATAT
1 ATTTTTAAAATTAG--TTTT-TAAATTTTAAATATAT
* *
5953334 ATTTTTCAAATTAGTTTTGAAATT
1 ATTTTTAAAATTAGTTTTTAAATT
5953358 AATAGTTTTA
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
31 11 0.15
33 14 0.19
34 16 0.22
35 8 0.11
36 23 0.32
37 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.58
Consensus pattern (34 bp):
ATTTTTAAAATTAGTTTTTAAATTTTAAATATAT
Found at i:5953570 original size:7 final size:7
Alignment explanation
Indices: 5953542--5953602 Score: 58
Period size: 7 Copynumber: 9.1 Consensus size: 7
5953532 TGACTATTAA
5953542 TAAAT-T
1 TAAATAT
5953548 TAAATAT
1 TAAATAT
5953555 T-AATA-
1 TAAATAT
5953560 TAAATAT
1 TAAATAT
*
5953567 TAAAAAAT
1 T-AAATAT
5953575 TAAATAT
1 TAAATAT
* *
5953582 T-ATTTT
1 TAAATAT
5953588 TAAATAT
1 TAAATAT
5953595 TAAATAT
1 TAAATAT
5953602 T
1 T
5953603 TTTTTTCTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
5 1 0.02
6 17 0.39
7 20 0.45
8 6 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TAAATAT
Found at i:5953591 original size:28 final size:27
Alignment explanation
Indices: 5953536--5953598 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
5953526 GTGATGTGAC
*
5953536 TATTAATAAATTTAAATATTAATATAAA
1 TATTAA-AAAATTAAATATTAATATAAA
* *
5953564 TATTAAAAAATTAAATATTATTTTTAAA
1 TATTAAAAAATTAAATATTA-ATATAAA
5953592 TATTAAA
1 TATTAAA
5953599 TATTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TATTAAAAAATTAAATATTAATATAAA
Found at i:5953596 original size:20 final size:20
Alignment explanation
Indices: 5953546--5953607 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
5953536 TATTAATAAA
* *
5953546 TTTAAATATT-AATATAAATA
1 TTTAAATATTAAATAT-TATT
* *
5953566 TTAAAAAATTAAATATTATT
1 TTTAAATATTAAATATTATT
5953586 TTTAAATATTAAATATT-TT
1 TTTAAATATTAAATATTATT
5953605 TTT
1 TTT
5953608 TCTTTTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
19 5 0.14
20 25 0.71
21 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAAATATTAAATATTATT
Found at i:5953884 original size:21 final size:21
Alignment explanation
Indices: 5953840--5953885 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
5953830 TATTATTAAT
*
5953840 TTTAAAATTTTTGTAATGTATA
1 TTTAAAATTTTTATAA-GTATA
5953862 TTTAAAATGTTTTATAA-TATA
1 TTTAAAAT-TTTTATAAGTATA
5953883 TTT
1 TTT
5953886 TTTACAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAAAATTTTTATAAGTATA
Found at i:5953910 original size:21 final size:21
Alignment explanation
Indices: 5953871--5953914 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5953861 ATTTAAAATG
5953871 TTTTATAATATATTTTTTACAA
1 TTTTATAATATATTTTTTA-AA
5953893 TTTTA-AATAT-TATTTTTAAA
1 TTTTATAATATAT-TTTTTAAA
5953913 TT
1 TT
5953915 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATAATATATTTTTTAAA
Found at i:5955618 original size:20 final size:20
Alignment explanation
Indices: 5955590--5955636 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
5955580 CAAACTTTTC
5955590 AAAAA-TTAAAAA-AAAGTTA
1 AAAAATTTAAAAAGAAA-TTA
5955609 AAAAATTTAAAAAGAAATTA
1 AAAAATTTAAAAAGAAATTA
5955629 AAGAAATT
1 AA-AAATT
5955637 GTATTTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 8 0.32
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (20 bp):
AAAAATTTAAAAAGAAATTA
Found at i:5955964 original size:8 final size:8
Alignment explanation
Indices: 5955951--5955978 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5955941 ATTAAGGAAC
5955951 AAAATAAA
1 AAAATAAA
5955959 AAAATAAA
1 AAAATAAA
5955967 AAAATAAA
1 AAAATAAA
5955975 AAAA
1 AAAA
5955979 AGAAATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:5955975 original size:21 final size:20
Alignment explanation
Indices: 5955951--5956002 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
5955941 ATTAAGGAAC
5955951 AAAATAAAAAAATAAAAAAAT
1 AAAA-AAAAAAATAAAAAAAT
**
5955972 AAAAAAAAGAAATATGAAAAT
1 AAAAAAAA-AAATAAAAAAAT
5955993 AAAAGAAAAA
1 AAAA-AAAAA
5956003 GAAAACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAAATAAAAAAAT
Found at i:5956013 original size:17 final size:17
Alignment explanation
Indices: 5955972--5956014 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
5955962 ATAAAAAAAT
*
5955972 AAAAAAAAGAAATATGA
1 AAAAAAAAGAAATAAGA
*
5955989 AAATAAAAGAAA-AAGA
1 AAAAAAAAGAAATAAGA
5956005 AAACAAAAAG
1 AAA-AAAAAG
5956015 GTGTCAGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (17 bp):
AAAAAAAAGAAATAAGA
Found at i:5959698 original size:17 final size:17
Alignment explanation
Indices: 5959664--5959716 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
5959654 AGATGTGATA
*
5959664 AAAAAATTTAAAAATTT
1 AAAAAATTTAATAATTT
**
5959681 AAAAAATTTAATTTTTT
1 AAAAAATTTAATAATTT
*
5959698 AAATATATTTAATAATTT
1 AAA-AAATTTAATAATTT
5959716 A
1 A
5959717 TAAATAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAAAATTTAATAATTT
Found at i:5962964 original size:3 final size:3
Alignment explanation
Indices: 5962956--5962993 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5962946 GAAGAAACCC
5962956 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
5962994 AATGACAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:5963709 original size:29 final size:29
Alignment explanation
Indices: 5963667--5963732 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
5963657 GATGTGAGAA
5963667 ATTAATAAGAGTAGCTGCAGGTTGAATTC
1 ATTAATAAGAGTAGCTGCAGGTTGAATTC
*
5963696 ATTAATAAGAGTAGCTGCAGGTTGAATTT
1 ATTAATAAGAGTAGCTGCAGGTTGAATTC
*
5963725 ATGAATAA
1 ATTAATAA
5963733 ATTTGAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (29 bp):
ATTAATAAGAGTAGCTGCAGGTTGAATTC
Found at i:5964405 original size:26 final size:26
Alignment explanation
Indices: 5964376--5964428 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
5964366 TGGTACAAAT
*
5964376 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
5964402 TGATAATAGTTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5964428 T
1 T
5964429 TATGGGCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5968228 original size:47 final size:47
Alignment explanation
Indices: 5968119--5968230 Score: 147
Period size: 47 Copynumber: 2.4 Consensus size: 47
5968109 CCGGGATAAG
* *
5968119 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGAAACAAATCCGGAACTTTAACAGTATAGTA
* * *
5968166 CACAAAGTACTTCATCGAAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGAAACAAATCCGGAACTTTAACAGTA-TAGTA
5968213 CACATAGTG-TCTCATCGA
1 CACATAGTGCT-TCATCGA
5968231 CTCAATGTCG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGAAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:5970399 original size:22 final size:22
Alignment explanation
Indices: 5970371--5970414 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5970361 ATGGTGAATG
5970371 AACCAAGATGATTTTCTTTCTT
1 AACCAAGATGATTTTCTTTCTT
5970393 AACCAAGATGATTTTCTTTCTT
1 AACCAAGATGATTTTCTTTCTT
5970415 TTCTTTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (22 bp):
AACCAAGATGATTTTCTTTCTT
Found at i:5970953 original size:27 final size:27
Alignment explanation
Indices: 5970900--5970954 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5970890 ATACATACAT
* *
5970900 GTTGTGCCTACCTGACAGGCTCAACTA
1 GTTGAGCCTACCTGACAGGCACAACTA
* *
5970927 GTTGAGCCTATCTGACAGGCACGACTA
1 GTTGAGCCTACCTGACAGGCACAACTA
5970954 G
1 G
5970955 GTGCATGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (27 bp):
GTTGAGCCTACCTGACAGGCACAACTA
Found at i:5971860 original size:22 final size:22
Alignment explanation
Indices: 5971826--5971889 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
5971816 TCAACATTTT
*
5971826 AATAAATCA-ATAAAAATTATCA
1 AATAAAT-ATATAAAAATTATAA
*
5971848 AATAAATATATAATAA-TATAA
1 AATAAATATATAAAAATTATAA
*
5971869 AATTACATTATATAAAAATTA
1 AA-TA-AATATATAAAAATTA
5971890 CATTAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 15 0.44
23 10 0.29
24 2 0.06
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATATATAAAAATTATAA
Found at i:5971883 original size:15 final size:16
Alignment explanation
Indices: 5971863--5971894 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5971853 ATATATAATA
5971863 ATAT-AAAATTACATT
1 ATATAAAAATTACATT
5971878 ATATAAAAATTACATT
1 ATATAAAAATTACATT
5971894 A
1 A
5971895 AAAAATCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:5972189 original size:115 final size:114
Alignment explanation
Indices: 5972048--5972376 Score: 540
Period size: 112 Copynumber: 2.9 Consensus size: 114
5972038 AACCTAATCT
*
5972048 TAAATTAGCTATAAAATATTTTTTTAAAATATATTACTAAAAAAATTCACAATACACTAATACAC
1 TAAAATAGCTATAAAATATTTTTTTAAAATATATTACTAAAAAAATTCACAATACACTAATACAC
*
5972113 TAAACTACTAAACACTAATAATTTATATAACCTAATCTTAAATTACTAA
66 TAAACTACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAA
*
5972162 TAAAATAGCTATATAAATATTTTTTTAAAATATATTACTAAAAAAATT-ACAATACGCTAAT--A
1 TAAAATAGCTATA-AAATATTTTTTTAAAATATATTACTAAAAAAATTCACAATACACTAATACA
* *
5972224 CTAAACCACTAAACACTAACAATTTATATAACCTAATATTAAATTACTAA
65 CTAAACTACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAA
5972274 TAAAATAGCTATAAAATTATTTTTTTAAAAATATATTACTAAAAAAA-TCACAATACACTAATAC
1 TAAAATAGCTATAAAA-TATTTTTTT-AAAATATATTACTAAAAAAATTCACAATACACTAATAC
* *
5972338 ACTAAATTACTAAACACTAACAATTTATATAACCAAATC
64 ACTAAACTACTAAACACTAACAATTTATATAACCTAATC
5972377 AACTATAAAT
Statistics
Matches: 199, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
111 3 0.02
112 71 0.36
113 32 0.16
114 24 0.12
115 69 0.35
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.34
Consensus pattern (114 bp):
TAAAATAGCTATAAAATATTTTTTTAAAATATATTACTAAAAAAATTCACAATACACTAATACAC
TAAACTACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAA
Found at i:5973864 original size:2 final size:2
Alignment explanation
Indices: 5973857--5973886 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5973847 TACTTCAAAC
*
5973857 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5973887 TTCTTTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5981177 original size:15 final size:14
Alignment explanation
Indices: 5981153--5981197 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
5981143 AAGTATAAAA
*
5981153 TATTTATTAATTTT
1 TATTTTTTAATTTT
*
5981167 GTATTTTTTAAATTT
1 -TATTTTTTAATTTT
5981182 TATTTTTGTAATTTT
1 TATTTTT-TAATTTT
5981197 T
1 T
5981198 TTTAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:5981199 original size:24 final size:22
Alignment explanation
Indices: 5981157--5981208 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
5981147 ATAAAATATT
*
5981157 TATTAATTTTGTATTTTTTAAA
1 TATTATTTTTGTATTTTTTAAA
* *
5981179 TTTTATTTTTGTAATTTTTTTTAA
1 TATTATTTTTGT-A-TTTTTTAAA
5981203 TATTAT
1 TATTAT
5981209 ACAATATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.42
23 1 0.04
24 13 0.54
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TATTATTTTTGTATTTTTTAAA
Found at i:5997890 original size:12 final size:12
Alignment explanation
Indices: 5997875--5998034 Score: 76
Period size: 12 Copynumber: 13.3 Consensus size: 12
5997865 CCGCCTTTTG
*
5997875 CTTTGCCTCTGC
1 CTTTGTCTCTGC
* *
5997887 CTTTGGCTCTGT
1 CTTTGTCTCTGC
*
5997899 CTTTTTCTCTGC
1 CTTTGTCTCTGC
* *
5997911 CTCTGTCTCTGT
1 CTTTGTCTCTGC
5997923 CTTT-TGCTCTGC
1 CTTTGT-CTCTGC
* *
5997935 CTCTGTATCTGTC
1 CTTTGTCTCTG-C
* *
5997948 TTTTGT-TCTAC
1 CTTTGTCTCTGC
* *
5997959 CTGTGTCTCTGT
1 CTTTGTCTCTGC
*
5997971 CTTT-TGCTGTGC
1 CTTTGT-CTCTGC
**
5997983 CTCCGTCTCTGC
1 CTTTGTCTCTGC
*
5997995 CTTT-TGGTCTGC
1 CTTTGT-CTCTGC
* *
5998007 CTCTGGCTCTGC
1 CTTTGTCTCTGC
* *
5998019 CTCTATCTCTGC
1 CTTTGTCTCTGC
5998031 CTTT
1 CTTT
5998035 TGCTCTTTCT
Statistics
Matches: 106, Mismatches: 34, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
11 8 0.08
12 91 0.86
13 7 0.07
ACGTcount: A:0.02, C:0.33, G:0.17, T:0.48
Consensus pattern (12 bp):
CTTTGTCTCTGC
Found at i:5998020 original size:24 final size:24
Alignment explanation
Indices: 5997876--5998017 Score: 167
Period size: 24 Copynumber: 5.9 Consensus size: 24
5997866 CGCCTTTTGC
* *
5997876 TTTGCCTCTGCCTTTGGCTCTGTCT
1 TTTG-CTCTGCCTCTGTCTCTGTCT
*
5997901 TTTTCTCTGCCTCTGTCTCTGTCT
1 TTTGCTCTGCCTCTGTCTCTGTCT
*
5997925 TTTGCTCTGCCTCTGTATCTGTCT
1 TTTGCTCTGCCTCTGTCTCTGTCT
* * *
5997949 TTTGTTCTACCTGTGTCTCTGTCT
1 TTTGCTCTGCCTCTGTCTCTGTCT
* * *
5997973 TTTGCTGTGCCTCCGTCTCTGCCT
1 TTTGCTCTGCCTCTGTCTCTGTCT
* *
5997997 TTTGGTCTGCCTCTGGCTCTG
1 TTTGCTCTGCCTCTGTCTCTG
5998018 CCTCTATCTC
Statistics
Matches: 98, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
24 95 0.97
25 3 0.03
ACGTcount: A:0.01, C:0.31, G:0.19, T:0.49
Consensus pattern (24 bp):
TTTGCTCTGCCTCTGTCTCTGTCT
Found at i:5998047 original size:36 final size:36
Alignment explanation
Indices: 5997988--5998059 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
5997978 TGTGCCTCCG
*
5997988 TCTCTGCCTTTTGGTCTGCCTCTGGCTCTGCCTCTA
1 TCTCTGCCTTTTGCTCTGCCTCTGGCTCTGCCTCTA
** *
5998024 TCTCTGCCTTTTGCTCTTTCTCTGGCTCTGCGTCTA
1 TCTCTGCCTTTTGCTCTGCCTCTGGCTCTGCCTCTA
5998060 ATTCTTTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.03, C:0.35, G:0.18, T:0.44
Consensus pattern (36 bp):
TCTCTGCCTTTTGCTCTGCCTCTGGCTCTGCCTCTA
Found at i:5998433 original size:18 final size:18
Alignment explanation
Indices: 5998412--5998448 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5998402 ACGGACTCTG
5998412 AGGCTCGGGCTCAGTCTC
1 AGGCTCGGGCTCAGTCTC
* *
5998430 AGGCTCTGTCTCAGTCTC
1 AGGCTCGGGCTCAGTCTC
5998448 A
1 A
5998449 TTATGTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (18 bp):
AGGCTCGGGCTCAGTCTC
Found at i:6000848 original size:17 final size:17
Alignment explanation
Indices: 6000800--6000850 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
6000790 ATTACATTTA
6000800 TTTTAATATTTTTAGTATT
1 TTTTAAT-TTTTTA-TATT
* *
6000819 TTTT-ATGTATTATATT
1 TTTTAATTTTTTATATT
6000835 TTTTAATTTTTTATAT
1 TTTTAATTTTTTATAT
6000851 AAAAAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 8 0.30
17 13 0.48
18 2 0.07
19 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTTTATATT
Found at i:6002277 original size:27 final size:27
Alignment explanation
Indices: 6002223--6002277 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
6002213 TGAGCCCCAC
* **
6002223 CACAACCATTTGCACCTCTGAGGTAGG
1 CACAACCATTTGCACCTCAGAGAAAGG
* *
6002250 CACAATCATTTGCGCCTCAGAGAAAGG
1 CACAACCATTTGCACCTCAGAGAAAGG
6002277 C
1 C
6002278 TCGATTAATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (27 bp):
CACAACCATTTGCACCTCAGAGAAAGG
Found at i:6005798 original size:42 final size:42
Alignment explanation
Indices: 6005751--6005833 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
6005741 TCTACAGGGA
6005751 GAGGCATATTGAAATATTAGTAGTCTATTTGTAGTATCATTG
1 GAGGCATATTGAAATATTAGTAGTCTATTTGTAGTATCATTG
* *
6005793 GAGGCATATTGAAATCTTAGTAGTCTGTTTGTAGTATCATT
1 GAGGCATATTGAAATATTAGTAGTCTATTTGTAGTATCATT
6005834 ATATTATTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (42 bp):
GAGGCATATTGAAATATTAGTAGTCTATTTGTAGTATCATTG
Found at i:6006755 original size:82 final size:82
Alignment explanation
Indices: 6006616--6006779 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 82
6006606 CTGGTGCCCT
*
6006616 ATTTGCAAAGCATCAGCAGAACCCACCCAGTCGTGTTCGCCTACTTCATATTTGAGTTGAATTTG
1 ATTTGCAAAGCATCAGCAGAACCCACCCAGTCGTGTTCGCCTACTTCATATTCGAGTTGAATTTG
6006681 ACAAAAAGGAAGCAAGA
66 ACAAAAAGGAAGCAAGA
* *
6006698 ATTTGCAAAGCATCAGCAGAACCCACCCAGTCTTGTTTGCCTACTTCATATTCGAGTTGAATTTG
1 ATTTGCAAAGCATCAGCAGAACCCACCCAGTCGTGTTCGCCTACTTCATATTCGAGTTGAATTTG
6006763 ACAAAAAGGAAGCAAGA
66 ACAAAAAGGAAGCAAGA
6006780 GACCGAGTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (82 bp):
ATTTGCAAAGCATCAGCAGAACCCACCCAGTCGTGTTCGCCTACTTCATATTCGAGTTGAATTTG
ACAAAAAGGAAGCAAGA
Found at i:6007316 original size:8 final size:8
Alignment explanation
Indices: 6007303--6007327 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6007293 AACTTATTAT
6007303 GTTTTGAG
1 GTTTTGAG
6007311 GTTTTGAG
1 GTTTTGAG
6007319 GTTTTGAG
1 GTTTTGAG
6007327 G
1 G
6007328 ATGCAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (8 bp):
GTTTTGAG
Found at i:6016932 original size:1 final size:1
Alignment explanation
Indices: 6016926--6016950 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
6016916 TTGGAATTGC
6016926 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
6016951 GAAAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6042626 original size:12 final size:12
Alignment explanation
Indices: 6042609--6042644 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
6042599 ATAGTCGTAG
6042609 TCATCATAATCA
1 TCATCATAATCA
*
6042621 TCATCATAACCA
1 TCATCATAATCA
6042633 TCATCATAATCA
1 TCATCATAATCA
6042645 ATTCCATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.31
Consensus pattern (12 bp):
TCATCATAATCA
Found at i:6044192 original size:21 final size:23
Alignment explanation
Indices: 6044150--6044192 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
6044140 GTTATTTGTT
* *
6044150 TATTATAATTATTTTTTTAATGA
1 TATTATAATTATTATTTGAATGA
6044173 TATTAT-A-TATTATTTGAATG
1 TATTATAATTATTATTTGAATG
6044193 TTAAATACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (23 bp):
TATTATAATTATTATTTGAATGA
Found at i:6044595 original size:22 final size:23
Alignment explanation
Indices: 6044548--6044596 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6044538 TTTAATTAAA
*
6044548 AATTCTATTTTTTTCATATTTTT
1 AATTCAATTTTTTTCATATTTTT
6044571 AATTCAATTATTTTT-ATA-TTTT
1 AATTCAATT-TTTTTCATATTTTT
6044593 AATT
1 AATT
6044597 TCCTATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 8 0.33
23 11 0.46
24 5 0.21
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (23 bp):
AATTCAATTTTTTTCATATTTTT
Found at i:6045638 original size:30 final size:30
Alignment explanation
Indices: 6045604--6045664 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
6045594 TTAATATCAC
6045604 AAGTTAACTCGATACCAACTAAATAAACTA
1 AAGTTAACTCGATACCAACTAAATAAACTA
6045634 AAGTTAACTCGATACCAACTAAATAAACTA
1 AAGTTAACTCGATACCAACTAAATAAACTA
6045664 A
1 A
6045665 GTATTGACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.51, C:0.20, G:0.07, T:0.23
Consensus pattern (30 bp):
AAGTTAACTCGATACCAACTAAATAAACTA
Found at i:6054851 original size:20 final size:21
Alignment explanation
Indices: 6054813--6054852 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
6054803 CTATTAATTT
6054813 TTTATATTTTTCAAATTTAGAC
1 TTTATATTTTT-AAATTTAGAC
6054835 TTTATATTTTT-AATTTAG
1 TTTATATTTTTAAATTTAG
6054853 TTAATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTATATTTTTAAATTTAGAC
Found at i:6057623 original size:18 final size:18
Alignment explanation
Indices: 6057602--6057636 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6057592 TAATATTAAA
6057602 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
6057620 AAATAAAATAATTATTT
1 AAATAAAATAATTATTT
6057637 TTATATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:6057843 original size:19 final size:20
Alignment explanation
Indices: 6057801--6057843 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
6057791 TATTGCACAT
*
6057801 ATAAA-AATTATATTTACTA
1 ATAAATAATAATATTTACTA
6057820 A-AAATAATAATATTTA-TA
1 ATAAATAATAATATTTACTA
6057838 ATAAAT
1 ATAAAT
6057844 TATTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAATAATAATATTTACTA
Found at i:6061864 original size:5 final size:6
Alignment explanation
Indices: 6061849--6061889 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
6061839 AATTATATGT
*
6061849 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
6061890 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:6067962 original size:18 final size:18
Alignment explanation
Indices: 6067916--6067964 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
6067906 TAACTTATCC
*
6067916 ATTTTTTTTAAAAAGAAT
1 ATTTTATTTAAAAAGAAT
* *
6067934 ATCTCTA-TTAAAAATAAT
1 AT-TTTATTTAAAAAGAAT
6067952 ATTTTATTTAAAA
1 ATTTTATTTAAAA
6067965 GGAACTACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 20 0.80
19 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTTATTTAAAAAGAAT
Found at i:6069866 original size:10 final size:10
Alignment explanation
Indices: 6069853--6069887 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
6069843 TTTCCAGTTT
6069853 TTTTTTTCAA
1 TTTTTTTCAA
6069863 TTTTTTTCAA
1 TTTTTTTCAA
6069873 TTTTTCTT-AA
1 TTTTT-TTCAA
6069883 TTTTT
1 TTTTT
6069888 CTTATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 22 0.92
11 2 0.08
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:6083129 original size:4 final size:4
Alignment explanation
Indices: 6083120--6083206 Score: 86
Period size: 4 Copynumber: 21.2 Consensus size: 4
6083110 AGCAAACGTG
* * * * **
6083120 AGAA AGAA AGAA AGAA AGAA AGAT AGAA AGACT A-AC AGAG AGCAA ACGTG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA-A AGAA AGAA AG-AA A-GAA
6083170 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
6083207 TAAAAAAGGG
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
3 1 0.01
4 63 0.91
5 4 0.06
6 1 0.01
ACGTcount: A:0.67, C:0.05, G:0.25, T:0.03
Consensus pattern (4 bp):
AGAA
Found at i:6083158 original size:50 final size:50
Alignment explanation
Indices: 6083104--6083200 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
6083094 TAGAAAAGTT
*
6083104 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGATAGAAAGACTA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGACTA
6083154 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA
6083201 AAGAAATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.62, C:0.07, G:0.27, T:0.04
Consensus pattern (50 bp):
ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGACTA
Found at i:6092875 original size:5 final size:5
Alignment explanation
Indices: 6092867--6092893 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6092857 AGATTGAATT
6092867 GATCA GATCA GATCA GATCA GATCA GA
1 GATCA GATCA GATCA GATCA GATCA GA
6092894 GTAAGTGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (5 bp):
GATCA
Found at i:6099529 original size:13 final size:13
Alignment explanation
Indices: 6099506--6099555 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
6099496 AATTGATTAT
* *
6099506 GAAAAATAAAATT
1 GAAAAAGAAAATA
* *
6099519 TAAAAAGAAAAAA
1 GAAAAAGAAAATA
6099532 GAAAAAGAAAA-A
1 GAAAAAGAAAATA
6099544 GAAAAAGAAAAT
1 GAAAAAGAAAAT
6099556 TCTTTTGCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 12 0.39
13 19 0.61
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (13 bp):
GAAAAAGAAAATA
Found at i:6099530 original size:7 final size:6
Alignment explanation
Indices: 6099520--6099554 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
6099510 AATAAAATTT
6099520 AAAAAG AAAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAA
6099555 TTCTTTTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:6105497 original size:16 final size:16
Alignment explanation
Indices: 6105476--6105507 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6105466 TCAAGCCATG
*
6105476 CAAATATATTGTCAGA
1 CAAATATATTGACAGA
6105492 CAAATATATTGACAGA
1 CAAATATATTGACAGA
6105508 TTTTGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
CAAATATATTGACAGA
Found at i:6110099 original size:64 final size:64
Alignment explanation
Indices: 6110027--6110150 Score: 203
Period size: 64 Copynumber: 1.9 Consensus size: 64
6110017 TATCTGTTTC
* ** *
6110027 GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTTGGGATGAGTGGAGCTATGTTGCTCCTGG
1 GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGTTGCTCCTGG
*
6110091 GAATGATGAAAAGGTTTAAATGTTTCAATATTGTTGGGGATGAGAAGAACTATGTTGCTC
1 GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGTTGCTC
6110151 TGACTCTTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (64 bp):
GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGTTGCTCCTGG
Found at i:6112235 original size:24 final size:23
Alignment explanation
Indices: 6112208--6112255 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
6112198 GACAAAAAAA
* *
6112208 TTTGTCTAAGTTACTTCGTTTTTT
1 TTTGTCCAACTTACTTC-TTTTTT
6112232 TTTGTCCAACTTACTTCTTTTTT
1 TTTGTCCAACTTACTTCTTTTTT
6112255 T
1 T
6112256 CTTTTTGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.12, C:0.17, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTGTCCAACTTACTTCTTTTTT
Found at i:6116597 original size:30 final size:30
Alignment explanation
Indices: 6116561--6116621 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
6116551 TAGGTTGTCA
6116561 ACAGTAAAAACTAGGTGATGTACAACTTTG
1 ACAGTAAAAACTAGGTGATGTACAACTTTG
6116591 ACAGTAAAAACTAGGTGATGTACAACTTTG
1 ACAGTAAAAACTAGGTGATGTACAACTTTG
6116621 A
1 A
6116622 GAAACTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (30 bp):
ACAGTAAAAACTAGGTGATGTACAACTTTG
Found at i:6118184 original size:18 final size:19
Alignment explanation
Indices: 6118161--6118205 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
6118151 AATGCCTGGA
*
6118161 TTTTCTTTTCTTTTCT-CT
1 TTTTCTTTCCTTTTCTACT
*
6118179 TTTTCTATCCTTTTCTACT
1 TTTTCTTTCCTTTTCTACT
6118198 TTCTTCTT
1 TT-TTCTT
6118206 CTGTTTGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 14 0.64
19 4 0.18
20 4 0.18
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCTTTCCTTTTCTACT
Found at i:6119007 original size:10 final size:10
Alignment explanation
Indices: 6118992--6119017 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6118982 AATATACAAA
6118992 ATATATACAT
1 ATATATACAT
6119002 ATATATACAT
1 ATATATACAT
6119012 ATATAT
1 ATATAT
6119018 TTTGCGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATACAT
Found at i:6126415 original size:17 final size:17
Alignment explanation
Indices: 6126393--6126426 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6126383 ATTGAAATGC
6126393 CCTTTTGCTCAAGTTTG
1 CCTTTTGCTCAAGTTTG
6126410 CCTTTTGCTCAAGTTTG
1 CCTTTTGCTCAAGTTTG
6126427 ACTTCGCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (17 bp):
CCTTTTGCTCAAGTTTG
Found at i:6146718 original size:9 final size:9
Alignment explanation
Indices: 6146704--6146729 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6146694 AAATAGTTTG
6146704 AGTTATTCA
1 AGTTATTCA
6146713 AGTTATTCA
1 AGTTATTCA
6146722 AGTTATTC
1 AGTTATTC
6146730 GAATCAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (9 bp):
AGTTATTCA
Found at i:6150511 original size:35 final size:35
Alignment explanation
Indices: 6150462--6150533 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
6150452 ATATTTTATC
*
6150462 TCACTATTACCATTACATTTGAAT-TCAAATACATA
1 TCACTATTACCATTACATTTAAATCT-AAATACATA
*
6150497 TCACTATTATCATTACATTTAAATCTAAATACATA
1 TCACTATTACCATTACATTTAAATCTAAATACATA
6150532 TC
1 TC
6150534 TCACTGTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 33 0.97
36 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.01, T:0.39
Consensus pattern (35 bp):
TCACTATTACCATTACATTTAAATCTAAATACATA
Found at i:6153950 original size:16 final size:16
Alignment explanation
Indices: 6153926--6153959 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6153916 TATAAAATTT
*
6153926 TATTGTTTTCATTTTA
1 TATTATTTTCATTTTA
*
6153942 TATTATTTTTATTTTA
1 TATTATTTTCATTTTA
6153958 TA
1 TA
6153960 GTGACTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (16 bp):
TATTATTTTCATTTTA
Found at i:6158337 original size:39 final size:39
Alignment explanation
Indices: 6158290--6158377 Score: 140
Period size: 39 Copynumber: 2.3 Consensus size: 39
6158280 AGCCCGAAGT
* *
6158290 CTAACTGAAGCATATAAGTGCTAAACGGAATACCGAAAG
1 CTAACTGAAGCACATAAGTGCTAAACGGAAGACCGAAAG
* *
6158329 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGG
1 CTAACTGAAGCACATAAGTGCTAAACGGAAGACCGAAAG
6158368 CTAACTGAAG
1 CTAACTGAAG
6158378 TTCATCAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (39 bp):
CTAACTGAAGCACATAAGTGCTAAACGGAAGACCGAAAG
Found at i:6158360 original size:21 final size:21
Alignment explanation
Indices: 6158296--6158360 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
6158286 AAGTCTAACT
*
6158296 GAAGCATATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
* ** * *
6158317 GAA-TACCGAA-AGCT-AACT
1 GAAGCACATAAGTGCTAAACG
6158335 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
6158356 GAAGC
1 GAAGC
6158361 CCGAAGGCTA
Statistics
Matches: 30, Mismatches: 11, Indels: 6
0.64 0.23 0.13
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 6 0.20
21 11 0.37
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.15
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:6159502 original size:18 final size:18
Alignment explanation
Indices: 6159479--6159516 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
6159469 TTCATACAAT
6159479 TCGGTCCTTGCTCAACTA
1 TCGGTCCTTGCTCAACTA
6159497 TCGGTCCTTGCTCAACTA
1 TCGGTCCTTGCTCAACTA
6159515 TC
1 TC
6159517 CCCTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.34, G:0.16, T:0.34
Consensus pattern (18 bp):
TCGGTCCTTGCTCAACTA
Found at i:6162140 original size:5 final size:5
Alignment explanation
Indices: 6162119--6162171 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
6162109 TGTTAAAATA
* *
6162119 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
6162167 TATAT
1 TATAT
6162172 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:6162150 original size:10 final size:9
Alignment explanation
Indices: 6162116--6162172 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
6162106 ATGTGTTAAA
6162116 ATATATATT
1 ATATATATT
*
6162125 AAAT-TATT
1 ATATATATT
6162133 AT-TATATT
1 ATATATATT
6162141 ATAGTATATT
1 ATA-TATATT
6162151 ATAT-TA-T
1 ATATATATT
6162158 ATATTATATT
1 ATA-TATATT
6162168 ATATA
1 ATATA
6162173 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:6162162 original size:12 final size:12
Alignment explanation
Indices: 6162117--6162172 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
6162107 TGTGTTAAAA
*
6162117 TATATATTAAAT
1 TATATATTATAT
6162129 TAT-TATTATATT
1 TATATATTATA-T
6162141 ATAGTATATTATAT
1 -TA-TATATTATAT
6162155 TATATATTATAT
1 TATATATTATAT
6162167 TATATA
1 TATATA
6162173 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:6163459 original size:11 final size:11
Alignment explanation
Indices: 6163443--6163469 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6163433 TGTGATGAAT
6163443 TATTGAATTTA
1 TATTGAATTTA
6163454 TATTGAATTTA
1 TATTGAATTTA
6163465 TATTG
1 TATTG
6163470 GTTGAATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (11 bp):
TATTGAATTTA
Found at i:6163518 original size:18 final size:19
Alignment explanation
Indices: 6163495--6163533 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
6163485 ATATATAGAT
6163495 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
6163513 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
6163532 AT
1 AT
6163534 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:6169817 original size:35 final size:35
Alignment explanation
Indices: 6169773--6169900 Score: 130
Period size: 35 Copynumber: 3.7 Consensus size: 35
6169763 TTCCTCATTG
* *
6169773 AAATATCATACCTACATTTCACAACTCCGTATGAA
1 AAATATCATACCTACGTTTCACAACTCAGTATGAA
* * ** *
6169808 AAATGTCATATCTACGTTTCTTAACTCAGTATGGA
1 AAATATCATACCTACGTTTCACAACTCAGTATGAA
* * **
6169843 TAATATCATACTTACGTTTCACAACTCAGTATGGT
1 AAATATCATACCTACGTTTCACAACTCAGTATGAA
* * *
6169878 TAATACCATACCTATGTTTCACA
1 AAATATCATACCTACGTTTCACA
6169901 CTTTGCCATG
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 76 1.00
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (35 bp):
AAATATCATACCTACGTTTCACAACTCAGTATGAA
Found at i:6172549 original size:2 final size:2
Alignment explanation
Indices: 6172544--6172579 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6172534 TTTCCAGTTT
*
6172544 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
6172580 AAAAAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6174411 original size:44 final size:44
Alignment explanation
Indices: 6174348--6174435 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
6174338 TCTTGACAGA
6174348 TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
1 TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
6174392 TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
1 TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
6174436 CTCACCAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.36
Consensus pattern (44 bp):
TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
Found at i:6178779 original size:12 final size:12
Alignment explanation
Indices: 6178762--6178788 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6178752 TCTTAAGATT
6178762 AAAAAAAAAACA
1 AAAAAAAAAACA
6178774 AAAAAAAAAACA
1 AAAAAAAAAACA
6178786 AAA
1 AAA
6178789 GAGGAATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:6178890 original size:19 final size:18
Alignment explanation
Indices: 6178848--6178904 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
6178838 GTGTACTTCG
6178848 ATAAAAATTTTAAAATAT
1 ATAAAAATTTTAAAATAT
6178866 ATAAAAATTTTAAAATAT
1 ATAAAAATTTTAAAATAT
* **
6178884 TTGAAAAACGTTAAAATAT
1 AT-AAAAATTTTAAAATAT
6178903 AT
1 AT
6178905 TTTTATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (18 bp):
ATAAAAATTTTAAAATAT
Found at i:6187992 original size:31 final size:30
Alignment explanation
Indices: 6187968--6188033 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 30
6187958 GCAGTTACTT
6187968 GACAAGTTAAATAATGTGGCAGCAGGCTTAA
1 GACAAGTTAAATAATGTGGCAGCA-GCTTAA
6187999 GACAAGTTAAATAATGTGGCAGCAGGCTTAA
1 GACAAGTTAAATAATGTGGCAGCA-GCTTAA
6188030 GACA
1 GACA
6188034 GAAGCTATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (30 bp):
GACAAGTTAAATAATGTGGCAGCAGCTTAA
Found at i:6192808 original size:22 final size:22
Alignment explanation
Indices: 6192758--6192829 Score: 63
Period size: 27 Copynumber: 2.9 Consensus size: 22
6192748 AAGATTAATT
*
6192758 TTATTTTATTTTATACTTGTTTATA
1 TTATTTTATTTTA-A--TATTTATA
6192783 TTATTTTTTATTTTTTAAATATTTATA
1 TTA--TTTTA--TTTT-AATATTTATA
6192810 TTATTTTATTTTAATATTTA
1 TTATTTTATTTTAATATTTA
6192830 ATAATTTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
22 8 0.20
23 4 0.10
25 8 0.20
27 15 0.37
29 5 0.12
30 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (22 bp):
TTATTTTATTTTAATATTTATA
Found at i:6192830 original size:30 final size:27
Alignment explanation
Indices: 6192777--6192852 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 27
6192767 TTTATACTTG
6192777 TTTATATTATTTT-TTATTTTTTAA-ATA
1 TTTATATTATTTTATT-TTTTTTAATA-A
6192804 TTTATATTATTTTATTTTAATATTTAATAA
1 TTTATATTATTTTATTTT--T-TTTAATAA
*
6192834 TTTCATATATTTTTTATTT
1 TTT-ATAT-TATTTTATTT
6192853 ATTGAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
27 15 0.37
28 2 0.05
29 1 0.02
30 9 0.22
31 5 0.12
32 9 0.22
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTATATTATTTTATTTTTTTTAATAA
Found at i:6192974 original size:15 final size:16
Alignment explanation
Indices: 6192941--6192994 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
6192931 TAATGTCTTC
6192941 TAAAAT-ATATAATATA
1 TAAAATAATATAA-ATA
6192957 TAAAATAATAT-AATA
1 TAAAATAATATAAATA
* *
6192972 TAAAATATTATAAATT
1 TAAAATAATATAAATA
6192988 TAAAATA
1 TAAAATA
6192995 GGTCAAGTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 13 0.38
16 17 0.50
17 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATAATATAAATA
Found at i:6193828 original size:25 final size:24
Alignment explanation
Indices: 6193800--6193903 Score: 59
Period size: 25 Copynumber: 4.1 Consensus size: 24
6193790 ATATATGTCA
6193800 AATTATATTTTTTAATTAAAAAATT
1 AATTA-ATTTTTTAATTAAAAAATT
* ** *
6193825 AATT-TTTATATATTAAATTAAGGAATA
1 AATTAATT-T-T-TT-AATTAAAAAATT
* *
6193852 AATTAATTATTTTGATTAAAAATTT
1 AATTAATT-TTTTAATTAAAAAATT
* *
6193877 TATTAATTTATATAATT-AAAAATT
1 AATTAATTT-TTTAATTAAAAAATT
6193901 AAT
1 AAT
6193904 ATGACTGATG
Statistics
Matches: 58, Mismatches: 15, Indels: 13
0.67 0.17 0.15
Matches are distributed among these distances:
23 2 0.03
24 10 0.17
25 24 0.41
26 4 0.07
27 14 0.24
28 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (24 bp):
AATTAATTTTTTAATTAAAAAATT
Found at i:6193831 original size:20 final size:23
Alignment explanation
Indices: 6193799--6193841 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
6193789 AATATATGTC
6193799 AAATTATATTTTT-TA-ATTAAA
1 AAATTATATTTTTATATATTAAA
6193820 AAATTA-ATTTTTATATATTAAA
1 AAATTATATTTTTATATATTAAA
6193842 TTAAGGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 8 0.40
22 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTATATTTTTATATATTAAA
Found at i:6193987 original size:35 final size:35
Alignment explanation
Indices: 6193944--6194010 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
6193934 ATTACTGTCA
* *
6193944 TATGTAATTCTTGTTAATTTGTGAAAATTAAAATG
1 TATGTAATTCTTATTAATTTGTGAAAAATAAAATG
6193979 TATGTAATTCTTATTAATTTGTGAAAAATAAA
1 TATGTAATTCTTATTAATTTGTGAAAAATAAA
6194011 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (35 bp):
TATGTAATTCTTATTAATTTGTGAAAAATAAAATG
Found at i:6194258 original size:21 final size:21
Alignment explanation
Indices: 6194232--6194272 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6194222 TAACAGAATT
6194232 GCTGATGTGGCAAGTTAACTA
1 GCTGATGTGGCAAGTTAACTA
*
6194253 GCTGATGTGGCCAGTTAACT
1 GCTGATGTGGCAAGTTAACT
6194273 TGCCACGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (21 bp):
GCTGATGTGGCAAGTTAACTA
Found at i:6195933 original size:46 final size:45
Alignment explanation
Indices: 6195883--6196056 Score: 199
Period size: 46 Copynumber: 3.8 Consensus size: 45
6195873 TTTGAGCATT
6195883 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTC
*** * *
6195929 CGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TC
1 CGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTC
* *
6195976 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTC
* *
6196022 CGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
6196057 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.61
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTC
Found at i:6196046 original size:93 final size:93
Alignment explanation
Indices: 6195878--6196049 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
6195868 GGATGTTTGA
* * *
6195878 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
6195943 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
6195971 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
6196036 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
6196050 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:6196883 original size:46 final size:45
Alignment explanation
Indices: 6196823--6197075 Score: 322
Period size: 46 Copynumber: 5.7 Consensus size: 45
6196813 TTTGACATGA
* * * * * *
6196823 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
*** *
6196869 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
6196915 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
6196961 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
6197007 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
6197045 TGCCATGGTATCTTTCAACCATGGTCTTACA
1 TGCCATGGTATCTTTCAACCATGGTCTTACA
6197076 TTTCATATCA
Statistics
Matches: 190, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
38 34 0.18
40 1 0.01
44 3 0.02
45 4 0.02
46 145 0.76
47 3 0.02
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:6197052 original size:38 final size:38
Alignment explanation
Indices: 6197001--6197075 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
6196991 ACATTTTATA
6197001 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
6197039 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
6197076 TTTCATATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:6199238 original size:11 final size:11
Alignment explanation
Indices: 6199222--6199273 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
6199212 TATACTAAAT
6199222 AAATAATAATA
1 AAATAATAATA
*
6199233 AAATAAT-ATT
1 AAATAATAATA
6199243 AAAT-ATCACATA
1 AAATAAT-A-ATA
*
6199255 AAATATTAATA
1 AAATAATAATA
6199266 AAATAATA
1 AAATAATA
6199274 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 2 0.06
10 6 0.18
11 17 0.52
12 7 0.21
13 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATAATAATA
Done.