Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 125 of 150
Found at i:37886369 original size:27 final size:26
Alignment explanation
Indices: 37886337--37886556 Score: 188
Period size: 22 Copynumber: 8.9 Consensus size: 26
37886327 ATTTCCTCAC
*
37886337 ATTACAATATTCATGCAAAATTACAAA
1 ATTACAATATTCATACAAAATTA-AAA
37886364 ATTACAATATTCATAC--AA--AAAA
1 ATTACAATATTCATACAAAATTAAAA
*
37886386 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAA
*
37886413 ATTACAACATTCATA-AAAA--AAAA
1 ATTACAATATTCATACAAAATTAAAA
37886436 A-T--AATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTA-AAA
37886460 ATTACAATATTCATAC--AA--AAAA
1 ATTACAATATTCATACAAAATTAAAA
* *
37886482 ATTGCAATATTCATACAAAACTATAATATT
1 ATTACAATATTCATACAAAA-T-TAA-A-A
37886512 ATTACAATATTCATAC--AA--AAAA
1 ATTACAATATTCATACAAAATTAAAA
* *
37886534 TTTATAATATTCATACAAAATTA
1 ATTACAATATTCATACAAAATTA
37886557 CAATATTCAT
Statistics
Matches: 158, Mismatches: 11, Indels: 49
0.72 0.05 0.22
Matches are distributed among these distances:
20 9 0.06
21 4 0.03
22 52 0.33
23 7 0.04
24 13 0.08
25 5 0.03
26 6 0.04
27 42 0.27
28 4 0.03
29 1 0.01
30 15 0.09
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAA
Found at i:37886392 original size:96 final size:96
Alignment explanation
Indices: 37886289--37886559 Score: 307
Period size: 96 Copynumber: 2.8 Consensus size: 96
37886279 TTTATAAACT
* * * * ** *
37886289 AATTACAATATTCATACAAAAAATTGA-AATATTACAATATTTCCT-CACATTACAATATTCATG
1 AATTACAATATTCATACAAAAAATT-ATAATATTACAACA-TTCATAAAAAAAACAATATTCATA
37886352 CAAAATTACAAAATTACAATATTCATACAAAAA
64 CAAAATTACAAAATTACAATATTCATACAAAAA
*
37886385 AATTACAATATTCATAC--AAAATTATAATATTACAACATTCATAAAAAAAAAATAATATTCATA
1 AATTACAATATTCATACAAAAAATTATAATATTACAACATTCAT--AAAAAAAACAATATTCATA
37886448 CAAAATTACAAAATTACAATATTCATACAAAAA
64 CAAAATTACAAAATTACAATATTCATACAAAAA
* * * * * *
37886481 AATTGCAATATTCATACAAAACTATAATATTATTACAATATTCATACAAAAAATTTATAATATTC
1 AATTACAATATTCATACAAAA-AATTATAATATTACAACATTCATA-AAAAAA---ACAATATTC
37886546 ATACAAAATTACAA
61 ATACAAAATTACAA
37886560 TATTCATACA
Statistics
Matches: 151, Mismatches: 13, Indels: 17
0.83 0.07 0.09
Matches are distributed among these distances:
93 5 0.03
94 17 0.11
96 78 0.52
97 1 0.01
98 8 0.05
99 19 0.13
101 23 0.15
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (96 bp):
AATTACAATATTCATACAAAAAATTATAATATTACAACATTCATAAAAAAAACAATATTCATACA
AAATTACAAAATTACAATATTCATACAAAAA
Found at i:37886405 original size:49 final size:49
Alignment explanation
Indices: 37886337--37886559 Score: 306
Period size: 49 Copynumber: 4.5 Consensus size: 49
37886327 ATTTCCTCAC
*
37886337 ATTACAATATTCATGCAAAATTACAAAATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAA
* * *
37886386 ATTACAATATTCATACAAAATTATAATATTACAACATTCATA-AAAAAA
1 ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAA
* *
37886434 A-AATAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAA
* * *
37886482 ATTGCAATATTCATACAAAACTATAATATTATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAATTACAA-A--ATTACAATATTCATACAAAAAA
* *
37886534 TTTATAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAATTACAA
37886560 TATTCATACA
Statistics
Matches: 150, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
47 35 0.23
48 14 0.09
49 57 0.38
50 1 0.01
52 43 0.29
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (49 bp):
ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAA
Found at i:37886414 original size:41 final size:41
Alignment explanation
Indices: 37886358--37886572 Score: 123
Period size: 47 Copynumber: 5.2 Consensus size: 41
37886348 CATGCAAAAT
*
37886358 TACAAAATTACAATATTCATACAAAAAAATTACAATATTCA
1 TACAAAATTATAATATTCATACAAAAAAATTACAATATTCA
* ** *
37886399 TACAAAATTATAATATTACAACATTCATAAAAAAAAAATAATATTCA
1 TACAAAATTATAATATT----CA-T-ACAAAAAAATTACAATATTCA
*
37886446 TACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCA
1 TACAAAATT-----A-T--AATATTCATACAAAAAAATTACAATATTCA
* *
37886495 TACAAAACTATAATATT-ATTAC---AATATT-C-ATA--CA
1 TACAAAATTATAATATTCA-TACAAAAAAATTACAATATTCA
37886529 -A-AAAATTTATAATATTCATAC---AAAATTACAATATTCA
1 TACAAAA-TTATAATATTCATACAAAAAAATTACAATATTCA
37886566 TACAAAA
1 TACAAAA
37886573 AATTACTAAT
Statistics
Matches: 137, Mismatches: 14, Indels: 48
0.69 0.07 0.24
Matches are distributed among these distances:
32 4 0.03
33 18 0.13
34 4 0.03
35 3 0.02
36 3 0.02
37 3 0.02
38 6 0.04
39 4 0.03
40 1 0.01
41 25 0.18
43 1 0.01
44 1 0.01
45 2 0.01
46 1 0.01
47 26 0.19
49 24 0.18
50 1 0.01
51 2 0.01
52 1 0.01
53 1 0.01
55 6 0.04
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (41 bp):
TACAAAATTATAATATTCATACAAAAAAATTACAATATTCA
Found at i:37886542 original size:22 final size:22
Alignment explanation
Indices: 37886513--37886576 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
37886503 TATAATATTA
37886513 TTACAATATTCATACAAAAAAT
1 TTACAATATTCATACAAAAAAT
*
37886535 TTATAATATTCATAC--AAAA-
1 TTACAATATTCATACAAAAAAT
37886554 TTACAATATTCATACAAAAAAT
1 TTACAATATTCATACAAAAAAT
37886576 T
1 T
37886577 ACTAATCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 14 0.38
20 4 0.11
21 4 0.11
22 15 0.41
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (22 bp):
TTACAATATTCATACAAAAAAT
Found at i:37886573 original size:41 final size:40
Alignment explanation
Indices: 37886512--37886677 Score: 162
Period size: 41 Copynumber: 4.1 Consensus size: 40
37886502 CTATAATATT
37886512 ATTACAATATTCATACAAAAAATTTATAATATTCATACAAA
1 ATTACAATATTCATACAAAAAA-TTATAATATTCATACAAA
* *
37886553 ATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAA
1 ATTACAATATTCATACAAAAAATTA-TAATATTC-ATAC-A-AA
* * ** *
37886595 A-TAC-ATATTTAATTATAAAATAATTGCAATATTCATACAAC
1 ATTACAATA-TTCA-TACAAAA-AATTATAATATTCATACAAA
37886636 ATTACAATATTCATA-AAAAAATTATAATATTCATACAAA
1 ATTACAATATTCATACAAAAAATTATAATATTCATACAAA
37886675 ATT
1 ATT
37886678 CTAATCTAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
39 23 0.23
40 14 0.14
41 34 0.34
42 16 0.16
43 11 0.11
44 3 0.03
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.34
Consensus pattern (40 bp):
ATTACAATATTCATACAAAAAATTATAATATTCATACAAA
Found at i:37886854 original size:3 final size:3
Alignment explanation
Indices: 37886846--37886884 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
37886836 TTTATAAACT
*
37886846 TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TCC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
37886885 CCTCTTCTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:37886869 original size:14 final size:14
Alignment explanation
Indices: 37886850--37886893 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
37886840 TAAACTTTCT
37886850 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
37886864 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
*
37886878 TCCTTC-TCCTCTTC
1 T-CTTCTTCTTCTTC
37886892 TC
1 TC
37886894 CTTTCTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 1 0.04
14 23 0.82
15 4 0.14
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TCTTCTTCTTCTTC
Found at i:37886871 original size:20 final size:20
Alignment explanation
Indices: 37886846--37886892 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
37886836 TTTATAAACT
*
37886846 TTCTTCTTCTTCTTCTTCTC
1 TTCTTCTTCTTCTCCTTCTC
37886866 TTCTTCTTCTTCTCCTTCTC
1 TTCTTCTTCTTCTCCTTCTC
*
37886886 CTCTTCT
1 TTCTTCT
37886893 CCTTTCTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
TTCTTCTTCTTCTCCTTCTC
Found at i:37886894 original size:14 final size:13
Alignment explanation
Indices: 37886847--37886904 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 13
37886837 TTATAAACTT
*
37886847 TCTTCTTCTTCT-
1 TCTTCTCCTTCTC
37886859 TCTTCT-CTTCTTC
1 TCTTCTCCTTC-TC
37886872 TTCTTCTCCTTCTCC
1 -TCTTCTCCTTCT-C
37886887 TCTTCTCCTTTCTC
1 TCTTCTCC-TTCTC
37886901 TCTT
1 TCTT
37886905 TTTTTTTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.10
12 7 0.17
14 20 0.50
15 9 0.22
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
TCTTCTCCTTCTC
Found at i:37893775 original size:50 final size:50
Alignment explanation
Indices: 37893660--37893850 Score: 283
Period size: 50 Copynumber: 3.8 Consensus size: 50
37893650 GATAATAACA
* ** *
37893660 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * **
37893711 TACCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
37893761 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
37893811 TGCCAACGCCATGTCCCAGACATGATCTTACATGGGACCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCT
37893851 ATTTACCCAA
Statistics
Matches: 126, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 94 0.75
51 32 0.25
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:37900934 original size:51 final size:49
Alignment explanation
Indices: 37900743--37901318 Score: 314
Period size: 44 Copynumber: 12.5 Consensus size: 49
37900733 CATCATGGTG
*
37900743 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCATTAG----
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA-TAGAACA
*
37900789 --TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCATTAG----
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA-TAGAACA
* *
37900833 --TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAG--ATAG-A-A
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGAACA
* *
37900876 AATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTGAAGCTAAAGACCACA
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGA--ACA
*
37900927 AATCTTATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGATTACA
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGA--ACA
* *
37900978 AATGTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T----C-AT--ATCA
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGAACA
* *
37901019 AATATTATCTCTCTGAAGTTGCAGTAGAGCATATT--A--TAT----CA
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGAACA
* * * * **
37901060 AACCTTATAT-TCCTGAAGTTGCAGTGGAGCAGGTT-AA-AAATA-AATCA
1 AATCTTATCTCT-CTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGAA-CA
* * * * ** *
37901107 AATATTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--ACGGGTTACA
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA-TAG-AACA
* * * * *
37901156 AATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTAAAGC-----CACA
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGAACA
* * *
37901200 AACCTTATCTCTCTGAAGTTGCAATAGAGCAGGTTGAAG---T--AACA
1 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGAACA
* * * * * ** * *
37901244 AACCTTATCCCCCTGAAGTTGCAATAG-GTCAGATTAAATATACCACAACA
1 AATCTTATCTCTCTGAAGTTGCAGTAGAG-CAGATTGAAGCTA-TAGAACA
* *
37901294 AGTCTTATCTCCCTGAAGTTGCAGT
1 AATCTTATCTCTCTGAAGTTGCAGT
37901319 GGAACAGACT
Statistics
Matches: 441, Mismatches: 54, Indels: 66
0.79 0.10 0.12
Matches are distributed among these distances:
40 1 0.00
41 65 0.15
42 3 0.01
43 6 0.01
44 149 0.34
45 36 0.08
46 1 0.00
47 35 0.08
48 2 0.00
49 37 0.08
50 28 0.06
51 78 0.18
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (49 bp):
AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTATAGAACA
Found at i:37901033 original size:41 final size:41
Alignment explanation
Indices: 37900976--37901140 Score: 161
Period size: 41 Copynumber: 3.9 Consensus size: 41
37900966 CTATAGATTA
* *
37900976 CAAATGTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAT
1 CAAATATTATCTCTCTGAAGTTGCAGTAGAGCAGATAATAT
* *
37901017 CAAATATTATCTCTCTGAAGTTGCAGTAGAGCATATTATAT
1 CAAATATTATCTCTCTGAAGTTGCAGTAGAGCAGATAATAT
** * * *
37901058 CAAACCTTATAT-TCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAAT
1 CAAATATTATCTCT-CTGAAGTTGCAGTAGAGCA-G---ATAAT--AT
* *
37901105 CAAATATTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1 CAAATATTATCTCTCTGAAGTTGCAGTAGAGCAGAT
37901141 TAAAGACGGG
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
40 1 0.01
41 65 0.64
43 1 0.01
45 3 0.03
46 1 0.01
47 30 0.30
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (41 bp):
CAAATATTATCTCTCTGAAGTTGCAGTAGAGCAGATAATAT
Found at i:37901477 original size:17 final size:18
Alignment explanation
Indices: 37901445--37901478 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
37901435 GGACTGAAAT
*
37901445 GAAGCTACTTGAAGAAGA
1 GAAGCTACTAGAAGAAGA
37901463 GAAGC-ACTAGAAGAAG
1 GAAGCTACTAGAAGAAG
37901479 TAAAGAATTG
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:0.47, C:0.12, G:0.29, T:0.12
Consensus pattern (18 bp):
GAAGCTACTAGAAGAAGA
Found at i:37902867 original size:3 final size:3
Alignment explanation
Indices: 37902859--37902908 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
37902849 AAATTAGATT
37902859 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
37902907 TT
1 TT
37902909 GGTTGCTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:37908033 original size:46 final size:46
Alignment explanation
Indices: 37907931--37908301 Score: 466
Period size: 46 Copynumber: 8.6 Consensus size: 46
37907921 TACGTATGAT
* *
37907931 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
* *
37907974 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
37908020 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-A-G----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
* * *
37908056 CACTTATCACTTTTTCACTTGATCAGATAAGTGCAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
37908102 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A-G----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
37908138 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
37908184 CACTTAT-ACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
37908229 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
37908275 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
37908302 AGTACTCAAA
Statistics
Matches: 293, Mismatches: 11, Indels: 45
0.84 0.03 0.13
Matches are distributed among these distances:
36 57 0.19
38 4 0.01
39 1 0.00
40 4 0.01
41 4 0.01
42 4 0.01
43 11 0.04
44 9 0.03
45 64 0.22
46 135 0.46
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
Found at i:37908061 original size:36 final size:36
Alignment explanation
Indices: 37908020--37908174 Score: 175
Period size: 36 Copynumber: 4.0 Consensus size: 36
37908010 CTAAGGCTAA
37908020 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
37908056 CACTTATCACTTTTTCACTTGATCAGATAAGTGCAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGT--A--T--AG
* *
37908098 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
37908138 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
37908174 C
1 C
37908175 TAATGCTACC
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 66 0.64
38 1 0.01
40 3 0.03
42 3 0.03
46 30 0.29
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:37908081 original size:82 final size:82
Alignment explanation
Indices: 37907974--37908301 Score: 469
Period size: 82 Copynumber: 3.9 Consensus size: 82
37907964 GCTAGGCTAC
* * *
37907974 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACT
37908039 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
* * *
37908056 CACTTATCACTTTTTCACTTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACT
*
37908121 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAG
*
37908138 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTAT-ACTTTCTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACT
37908202 TGATCAGATAAGTGTAGCTAATG
66 TGATCAGATAA--GTA--T-A-G
* *
37908225 CTACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTAT
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGT
37908290 CACTTGATCAGA
62 CACTTGATCAGA
37908302 AGTACTCAAA
Statistics
Matches: 222, Mismatches: 13, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
81 20 0.09
82 127 0.57
83 2 0.01
85 1 0.00
86 1 0.00
87 1 0.00
91 52 0.23
92 18 0.08
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACT
TGATCAGATAAGTATAG
Found at i:37921990 original size:47 final size:48
Alignment explanation
Indices: 37921933--37922027 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 48
37921923 AAAATGACGT
*
37921933 CAATTCATTTTCATTTGCAGTTTAACTTTAAAT-AAAATAATTATAAA
1 CAATTCATTTTCATTTGCAATTTAACTTTAAATAAAAATAATTATAAA
*
37921980 CAATTTATTTTCATTTGCAATTTAACTTTAAATAAAAATAATTATAAA
1 CAATTCATTTTCATTTGCAATTTAACTTTAAATAAAAATAATTATAAA
37922028 AACTTTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 31 0.69
48 14 0.31
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (48 bp):
CAATTCATTTTCATTTGCAATTTAACTTTAAATAAAAATAATTATAAA
Found at i:37922067 original size:23 final size:21
Alignment explanation
Indices: 37922036--37922079 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
37922026 AAAACTTTAA
*
37922036 AAATATTAACTTTGTTATAAAAT
1 AAATATTAA-TTT-TGATAAAAT
*
37922059 AAATGTTAATTTTGATAAAAT
1 AAATATTAATTTTGATAAAAT
37922080 TTAACCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (21 bp):
AAATATTAATTTTGATAAAAT
Found at i:37922571 original size:31 final size:30
Alignment explanation
Indices: 37922535--37922603 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
37922525 GATTAAATAA
*
37922535 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAAGTTTCAAGTATATAATTGAACC
* * *
37922565 ACAATTAGAGTTTCACGTATATAATTGCACC
1 A-AATTAAAGTTTCAAGTATATAATTGAACC
37922596 AAATTAAA
1 AAATTAAA
37922604 ATTCATGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATATAATTGAACC
Found at i:37922608 original size:29 final size:29
Alignment explanation
Indices: 37922535--37922619 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
37922525 GATTAAATAA
*
37922535 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAA-TTTCAAGTATATAATTGAACC
* * *
37922565 ACAATTAGAGTTTCACGTATATAATTGCACC
1 A-AATTA-AATTTCAAGTATATAATTGAACC
* * *
37922596 AAATTAAAATTCATGTATACAATT
1 AAATTAAATTTCAAGTATATAATT
37922620 ATACATTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
29 14 0.31
30 6 0.13
31 24 0.53
32 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (29 bp):
AAATTAAATTTCAAGTATATAATTGAACC
Found at i:37925226 original size:30 final size:30
Alignment explanation
Indices: 37925190--37925250 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
37925180 TTTTAATACA
37925190 AAATTTAGAAGTTCATTTTGAATGTGATGT
1 AAATTTAGAAGTTCATTTTGAATGTGATGT
37925220 AAATTTAGAAGTTCATTTTGAATGTGATGT
1 AAATTTAGAAGTTCATTTTGAATGTGATGT
37925250 A
1 A
37925251 GCTAGCTAAG
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:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (30 bp):
AAATTTAGAAGTTCATTTTGAATGTGATGT
Found at i:37927789 original size:17 final size:18
Alignment explanation
Indices: 37927758--37927791 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
37927748 GTTGATTATT
37927758 TTTTATTTATTTAAAAAA
1 TTTTATTTATTTAAAAAA
37927776 TTTTATTT-TTTAAAAA
1 TTTTATTTATTTAAAAA
37927792 TATTCATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATTTATTTAAAAAA
Found at i:37928259 original size:22 final size:22
Alignment explanation
Indices: 37928234--37928275 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37928224 AATTATAAAA
37928234 TTAAAATAATATAAATATACTT
1 TTAAAATAATATAAATATACTT
** *
37928256 TTAATTTAATATATATATAC
1 TTAAAATAATATAAATATAC
37928276 ATGCGGACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAATAATATAAATATACTT
Found at i:37928547 original size:33 final size:33
Alignment explanation
Indices: 37928504--37928570 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
37928494 AATTAGAAAG
* *
37928504 GTTCATATAGACCTTTGACTGAATCCAGTTGCA
1 GTTCAAATAGACCTTTGACAGAATCCAGTTGCA
* *
37928537 GTTCAAATAGAGCTTTGACAGAATTCAGTTGCA
1 GTTCAAATAGACCTTTGACAGAATCCAGTTGCA
37928570 G
1 G
37928571 GTCGTTGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (33 bp):
GTTCAAATAGACCTTTGACAGAATCCAGTTGCA
Found at i:37929353 original size:30 final size:30
Alignment explanation
Indices: 37929317--37929398 Score: 146
Period size: 30 Copynumber: 2.7 Consensus size: 30
37929307 ATGGTCATGA
*
37929317 TGTTCGTGGTGGTGGTGGTGGTCATGCAGG
1 TGTTCGTGGTGGTGGTGGTGGTCATGCAAG
37929347 TGTTCGTGGTGGTGGTGGTGGTCATGCAAG
1 TGTTCGTGGTGGTGGTGGTGGTCATGCAAG
*
37929377 TGTACGTGGTGGTGGTGGTGGT
1 TGTTCGTGGTGGTGGTGGTGGT
37929399 GGTGGTGGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.07, C:0.09, G:0.50, T:0.34
Consensus pattern (30 bp):
TGTTCGTGGTGGTGGTGGTGGTCATGCAAG
Found at i:37929390 original size:3 final size:3
Alignment explanation
Indices: 37929382--37929411 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
37929372 GCAAGTGTAC
37929382 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
37929412 ATTGTTTCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:37932545 original size:29 final size:29
Alignment explanation
Indices: 37932495--37932573 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
37932485 TAATAAATTT
*
37932495 AGGTACCAAATT-GAACCTAAAA-AAAGCTT-
1 AGGTACCAAATTAGAA--AAAAACAAAG-TTC
*
37932524 AGGTACCAAATTAGGAAAAAAACCAAGTTC
1 AGGTACCAAATTA-GAAAAAAACAAAGTTC
37932554 AGGTACCAAATTAGAAAAAA
1 AGGTACCAAATTAGAAAAAA
37932574 GTGTCAAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 25 0.57
30 16 0.36
31 3 0.07
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (29 bp):
AGGTACCAAATTAGAAAAAAACAAAGTTC
Found at i:37932585 original size:31 final size:29
Alignment explanation
Indices: 37932524--37932652 Score: 104
Period size: 31 Copynumber: 4.4 Consensus size: 29
37932514 AAAAAAGCTT
**
37932524 AGGTACCAAATTAGGAAAAAAACCAAGTTC
1 AGGTACCAAATTA-GAAAAAAGTCAAGTTC
37932554 AGGTACCAAATTAGAAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGAAAAAA--GTCAAGTTC
* * **
37932585 AGGTACCAATTTGGGCAAAA---AAGTT-
1 AGGTACCAAATTAGAAAAAAGTCAAGTTC
*
37932610 ATGTACCAAATTAGAAAACAAATGTCAAGTTC
1 AGGTACCAAATTAG-AAA-AAA-GTCAAGTTC
*
37932642 AAGTACCAAAT
1 AGGTACCAAAT
37932653 GTTATATTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
25 11 0.14
26 6 0.08
27 3 0.04
29 7 0.09
30 13 0.17
31 28 0.36
32 10 0.13
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.22
Consensus pattern (29 bp):
AGGTACCAAATTAGAAAAAAGTCAAGTTC
Found at i:37937356 original size:25 final size:25
Alignment explanation
Indices: 37937205--37937359 Score: 125
Period size: 25 Copynumber: 6.2 Consensus size: 25
37937195 AGCCATGTAA
* * * *
37937205 CGGGAAGCTCATGTGAGCTATATAA
1 CGGGAAGCTCATGCGAGCCAAATAT
***
37937230 CGGGAAGCTCAAT-CGAGCTGTATAT
1 CGGGAAGCTC-ATGCGAGCCAAATAT
* * *
37937255 CAGAAAGCTCATGCGAGCCAATTAT
1 CGGGAAGCTCATGCGAGCCAAATAT
* * *
37937280 CAGAAAGCTCATGCGAGCCAATTAT
1 CGGGAAGCTCATGCGAGCCAAATAT
* * *
37937305 CGGGAAGCTCAAGAGAG-CAATTAAT
1 CGGGAAGCTCATGCGAGCCAAAT-AT
*
37937330 CGGGAAGCTCATGAGAGCCAAATAT
1 CGGGAAGCTCATGCGAGCCAAATAT
37937355 CGGGA
1 CGGGA
37937360 TGCCCATAAG
Statistics
Matches: 111, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
24 7 0.06
25 98 0.88
26 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCATGCGAGCCAAATAT
Found at i:37937371 original size:25 final size:25
Alignment explanation
Indices: 37937259--37937372 Score: 106
Period size: 25 Copynumber: 4.6 Consensus size: 25
37937249 GTATATCAGA
** * *
37937259 AAGCTCATGCGAGCCAATTATCAGA
1 AAGCTCATAAGAGCCAATTATCGGG
**
37937284 AAGCTCATGCGAGCCAATTATCGGG
1 AAGCTCATAAGAGCCAATTATCGGG
37937309 AAGCTCA-AGAGAG-CAATTAATCGGG
1 AAGCTCATA-AGAGCCAATT-ATCGGG
* *
37937334 AAGCTCATGAGAGCCAAATATCGGG
1 AAGCTCATAAGAGCCAATTATCGGG
* *
37937359 ATGCCCATAAGAGC
1 AAGCTCATAAGAGC
37937373 TGTGATGTGT
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
24 5 0.07
25 67 0.88
26 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (25 bp):
AAGCTCATAAGAGCCAATTATCGGG
Found at i:37945078 original size:2 final size:2
Alignment explanation
Indices: 37945066--37945096 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
37945056 CAAAAACAAG
*
37945066 TA TA TA CA 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 T
37945097 GATAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:37946032 original size:53 final size:56
Alignment explanation
Indices: 37945933--37946046 Score: 198
Period size: 53 Copynumber: 2.1 Consensus size: 56
37945923 CGTTTTGTTA
37945933 AAAAAGTAGAAAACAAACAACAAAATAAAATAAAATAAACAAAAATGCAAGAACAG
1 AAAAAGTAGAAAACAAACAACAAAATAAAATAAAATAAACAAAAATGCAAGAACAG
*
37945989 AAAAGGTAGAAAACAAAC-ACAAAAT-AAAT-AAATAAACAAAAATGCAAGAACAG
1 AAAAAGTAGAAAACAAACAACAAAATAAAATAAAATAAACAAAAATGCAAGAACAG
37946042 AAAAA
1 AAAAA
37946047 AAATTGGAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
53 28 0.50
54 4 0.07
55 7 0.12
56 17 0.30
ACGTcount: A:0.71, C:0.11, G:0.10, T:0.09
Consensus pattern (56 bp):
AAAAAGTAGAAAACAAACAACAAAATAAAATAAAATAAACAAAAATGCAAGAACAG
Found at i:37948655 original size:19 final size:19
Alignment explanation
Indices: 37948615--37948661 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
37948605 TTTAAAAGAT
37948615 AAAAGGAAAATAATTTAGA
1 AAAAGGAAAATAATTTAGA
* *
37948634 AAAATGAAATTAATTCT--A
1 AAAAGGAAAATAATT-TAGA
37948652 AAAAGGAAAA
1 AAAAGGAAAA
37948662 AATAAAGGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 9 0.39
19 13 0.57
20 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.13, T:0.21
Consensus pattern (19 bp):
AAAAGGAAAATAATTTAGA
Found at i:37961211 original size:25 final size:26
Alignment explanation
Indices: 37961150--37961213 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
37961140 TTCCAATATG
*
37961150 CAAGCTGCAAGCTCAACAAAAATGTG
1 CAAGCTGCAAGCTCAACAAAAATGTC
* *
37961176 CAAGCTGCAAGCTCAGC-AAGATG-C
1 CAAGCTGCAAGCTCAACAAAAATGTC
37961200 CAAAGCTGCAAGCT
1 C-AAGCTGCAAGCT
37961214 TAGCGAGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.03
25 17 0.50
26 16 0.47
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (26 bp):
CAAGCTGCAAGCTCAACAAAAATGTC
Found at i:37961398 original size:16 final size:16
Alignment explanation
Indices: 37961377--37961409 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
37961367 AGACAGTAAG
37961377 CAAAGTGCGAGCCTGT
1 CAAAGTGCGAGCCTGT
*
37961393 CAAAGTGTGAGCCTGT
1 CAAAGTGCGAGCCTGT
37961409 C
1 C
37961410 GAATTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.21
Consensus pattern (16 bp):
CAAAGTGCGAGCCTGT
Found at i:37976961 original size:31 final size:31
Alignment explanation
Indices: 37976926--37976987 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
37976916 CCCCTCTGCA
37976926 CATAGATAAATCAATCAAGCTAGCGTAATGG
1 CATAGATAAATCAATCAAGCTAGCGTAATGG
37976957 CATAGATAAATCAATCAAGCTAGCGTAATGG
1 CATAGATAAATCAATCAAGCTAGCGTAATGG
37976988 TAAATGCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (31 bp):
CATAGATAAATCAATCAAGCTAGCGTAATGG
Found at i:37979026 original size:25 final size:24
Alignment explanation
Indices: 37978993--37979050 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
37978983 CAATTTTTGA
*
37978993 ATATTATTTAATATT-TTTTTCATTT
1 ATATAATTTAA-ATTATTTTT-ATTT
37979018 ATATAATTTAAATTAATTTTTATTT
1 ATATAATTTAAATT-ATTTTTATTT
37979043 -TATAATTT
1 ATATAATTT
37979051 TTTATAACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 11 0.37
25 14 0.47
26 5 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
ATATAATTTAAATTATTTTTATTT
Found at i:37982326 original size:126 final size:124
Alignment explanation
Indices: 37982060--37982327 Score: 353
Period size: 125 Copynumber: 2.1 Consensus size: 124
37982050 GGCCAAGCAG
* * ** * *
37982060 GAACTACTATAGAAAAATAGCATCCATGTGGGAGCTTTTTTCAGTAATTTTTCTGACAGTGCATC
1 GAACTACTATAGAAAAAGAGCACCCACATGGGAGCTTTTGTCAATAATTTTTCTGACAGTGCATC
* *
37982125 CTGCTTGAAGCATTTTTTACACTATTTTTCAGAACTGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAA-CATTTTTTACACTATTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCAA
37982185 GAACTACTATAGAAAAAGAGCACCCACATGGGAGCTTTTGTCAATAATTTTGT-TGACAGTGCAT
1 GAACTACTATAGAAAAAGAGCACCCACATGGGAGCTTTTGTCAATAATTTT-TCTGACAGTGCAT
* * *
37982249 CCTGCTTGAA-ATGTTTTTAACATTATCTTTTCAGAACCGTCTTCTTAAAATTAATTTTTC-T
65 CCTGCTTGAACAT-TTTTT-ACACTAT-TTTTCAGAACCGTCTTCTCAAAATTAATTTTTCAA
*
37982310 GAAACTACTGTAGAAAAA
1 G-AACTACTATAGAAAAA
37982328 AAAAACAAAG
Statistics
Matches: 126, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
123 2 0.02
124 5 0.04
125 73 0.58
126 46 0.37
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (124 bp):
GAACTACTATAGAAAAAGAGCACCCACATGGGAGCTTTTGTCAATAATTTTTCTGACAGTGCATC
CTGCTTGAACATTTTTTACACTATTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCAA
Found at i:37982450 original size:9 final size:9
Alignment explanation
Indices: 37982438--37982467 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
37982428 AACTAAACCC
37982438 TAATTTAAT
1 TAATTTAAT
37982447 TAATTTAAT
1 TAATTTAAT
37982456 TAATTTAAT
1 TAATTTAAT
37982465 TAA
1 TAA
37982468 AACCCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TAATTTAAT
Found at i:37986036 original size:13 final size:13
Alignment explanation
Indices: 37986018--37986043 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37986008 AAGAATTTGA
37986018 CAACAATCAAGAT
1 CAACAATCAAGAT
37986031 CAACAATCAAGAT
1 CAACAATCAAGAT
37986044 AGAAATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (13 bp):
CAACAATCAAGAT
Found at i:37990823 original size:27 final size:27
Alignment explanation
Indices: 37990791--37991017 Score: 292
Period size: 27 Copynumber: 8.4 Consensus size: 27
37990781 CCCTAAAATA
* *
37990791 GGTAAAATGACCAAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
37990818 AGTAAAATGACCGAAATACCCCCATAT
1 GGTAAAATGACCGAAATACCCCCATAG
* * * *
37990845 GGTAAAATAATCAAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
** *
37990872 GGTAAAATGATTGAAATACCCCAATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
37990899 GGTAAAATAACTGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
37990926 GGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
***
37990953 GGTAAAATGACCGAAATACCTTTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
37990980 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
37991007 GGTAAAATGAC
1 GGTAAAATGAC
37991018 TGTTATACCC
Statistics
Matches: 173, Mismatches: 27, Indels: 0
0.87 0.14 0.00
Matches are distributed among these distances:
27 173 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAG
Found at i:37994061 original size:23 final size:23
Alignment explanation
Indices: 37993972--37994061 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
37993962 ACCTAATCAG
*
37993972 TATACGGCACAT-AAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
** *
37993994 -A-ACGACACACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* *
37994015 AATAGGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
37994038 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
37994061 T
1 T
37994062 CGGCAAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.12
21 10 0.18
22 1 0.02
23 38 0.68
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:37996427 original size:50 final size:50
Alignment explanation
Indices: 37996312--37996554 Score: 342
Period size: 50 Copynumber: 4.8 Consensus size: 50
37996302 GATAATAACA
* * * ** *
37996312 TGCCAAAGCCATGTCCCAGACATGGCCTTACATGGAATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * **
37996363 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
**
37996413 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTAACATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
37996463 TGCCAATGCCATGTTCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
37996513 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
37996555 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 23, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
50 138 0.82
51 31 0.18
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:37997837 original size:18 final size:19
Alignment explanation
Indices: 37997816--37997851 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
37997806 ATTATTTATC
37997816 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
37997834 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
37997852 TATACAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:37997962 original size:16 final size:16
Alignment explanation
Indices: 37997943--37997973 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37997933 TAATATCATG
37997943 ATAATAATAATAATAA
1 ATAATAATAATAATAA
*
37997959 ATAATATTAATAATA
1 ATAATAATAATAATA
37997974 TTAATTAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAATAATAATAA
Found at i:37998147 original size:17 final size:15
Alignment explanation
Indices: 37998111--37998150 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
37998101 ATTTATTTCA
37998111 TAATATAATAATAAT
1 TAATATAATAATAAT
*
37998126 TAATATAATTTATAATT
1 TAATATAA-TAATAA-T
37998143 TAATATAA
1 TAATATAA
37998151 AACCTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATAATAATAAT
Found at i:38000157 original size:51 final size:50
Alignment explanation
Indices: 38000036--38000221 Score: 178
Period size: 51 Copynumber: 3.7 Consensus size: 50
38000026 GAAAGTGATG
* * * * * * *
38000036 GTCACACGTGTAGTACTATGTGTAGGCTACTACGTGTACTGGAATAATA-G
1 GTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGG-ATAGTATT
*
38000086 GTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-TT
1 GTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATT
* * * * * *
38000135 CGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGTATGGTAATT
1 -G-TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATT
* *
38000188 GTCACATATGTAGTATTATGTGCAGGCTACTATG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTATG
38000222 TGAACTGAAC
Statistics
Matches: 112, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
49 4 0.04
50 37 0.33
51 68 0.61
52 1 0.01
53 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (50 bp):
GTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATT
Found at i:38005215 original size:23 final size:21
Alignment explanation
Indices: 38005163--38005227 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 21
38005153 CCTGATCAGT
*
38005163 ATACGGCACATAAGTGCCTGA
1 ATACGACACATAAGTGCCTGA
*
38005184 A-ACGACACATGAAGTGCTTGAA
1 ATACGACACAT-AAGTGCCTG-A
38005206 ATACGACACATAAAGTGCCTGA
1 ATACGACACAT-AAGTGCCTGA
38005228 TCGACAAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 8 0.22
21 9 0.24
22 3 0.08
23 17 0.46
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (21 bp):
ATACGACACATAAGTGCCTGA
Found at i:38008316 original size:4 final size:4
Alignment explanation
Indices: 38008307--38008331 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
38008297 TTTTTGACTT
38008307 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
38008332 ATTATTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:38013589 original size:17 final size:17
Alignment explanation
Indices: 38013556--38013589 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38013546 TTTATAATAC
* *
38013556 TTTATATTGTGTTATTT
1 TTTATATTATGTAATTT
38013573 TTTATATTATGTAATTT
1 TTTATATTATGTAATTT
38013590 ATAACACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (17 bp):
TTTATATTATGTAATTT
Found at i:38017641 original size:9 final size:9
Alignment explanation
Indices: 38017629--38017665 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
38017619 TTTTATTACA
38017629 ACAATTAAT
1 ACAATTAAT
38017638 ACAATTAAT
1 ACAATTAAT
38017647 ACAATTAAT
1 ACAATTAAT
38017656 ACAATTAAT
1 ACAATTAAT
38017665 A
1 A
38017666 ATTTGATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:38017651 original size:77 final size:75
Alignment explanation
Indices: 38017569--38017731 Score: 308
Period size: 77 Copynumber: 2.1 Consensus size: 75
38017559 ATTTTGTTAC
38017569 AACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAAT
1 AACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAAT
38017634 TAATACAATT
66 TAATACAATT
38017644 AATACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACA
1 -A-ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACA
38017709 ATTAATACAATT
64 ATTAATACAATT
38017721 AACAATTAATA
1 AACAATTAATA
38017732 ATTTGATAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
75 10 0.12
76 2 0.02
77 74 0.86
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (75 bp):
AACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAAT
TAATACAATT
Found at i:38017766 original size:16 final size:16
Alignment explanation
Indices: 38017747--38017779 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38017737 ATAATTATAC
38017747 TAACAATTAATTTTAA
1 TAACAATTAATTTTAA
*
38017763 TAACAATTAGTTTTAA
1 TAACAATTAATTTTAA
38017779 T
1 T
38017780 TTTATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
TAACAATTAATTTTAA
Found at i:38024081 original size:5 final size:5
Alignment explanation
Indices: 38024071--38024103 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
38024061 GTTCATCGTT
38024071 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
38024104 GAATCACAAT
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:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:38024604 original size:27 final size:25
Alignment explanation
Indices: 38024574--38024635 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
38024564 ATCTGGACTA
38024574 ATTTTTTT-GAATTTTTATGAACTTTTT
1 ATTTTTTTAG-ATTTTTAT--ACTTTTT
* *
38024601 ATTTCTTTAGATTTTTATATTTTTT
1 ATTTTTTTAGATTTTTATACTTTTT
38024626 ATTATTTTTA
1 ATT-TTTTTA
38024636 TAAATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 9 0.30
26 5 0.17
27 15 0.50
28 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (25 bp):
ATTTTTTTAGATTTTTATACTTTTT
Found at i:38024933 original size:14 final size:14
Alignment explanation
Indices: 38024914--38024944 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38024904 GGAATTGTTT
*
38024914 TAATCTAAATTTAC
1 TAATCTAAATTAAC
38024928 TAATCTAAATTAAC
1 TAATCTAAATTAAC
38024942 TAA
1 TAA
38024945 GAACGCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:38029681 original size:22 final size:22
Alignment explanation
Indices: 38029648--38029705 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
38029638 TGTACTAATG
*
38029648 AACATAGAGCACTAAAGTGCTA
1 AACAAAGAGCACTAAAGTGCTA
* ** *
38029670 TACAAAGAGCACGGATGTGCTA
1 AACAAAGAGCACTAAAGTGCTA
*
38029692 AACAGAGAGCACTA
1 AACAAAGAGCACTA
38029706 GCATGCTAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (22 bp):
AACAAAGAGCACTAAAGTGCTA
Found at i:38030914 original size:5 final size:5
Alignment explanation
Indices: 38030904--38030964 Score: 122
Period size: 5 Copynumber: 12.2 Consensus size: 5
38030894 TAATTAAGTA
38030904 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
38030954 AATAT AATAT A
1 AATAT AATAT A
38030965 TATTTTAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:38033977 original size:14 final size:15
Alignment explanation
Indices: 38033953--38033981 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38033943 ATTTTTTGTG
38033953 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
38033968 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
38033982 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:38034219 original size:28 final size:28
Alignment explanation
Indices: 38034173--38034228 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
38034163 TATAGTTTTT
38034173 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
38034201 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
38034229 TAAAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:38034227 original size:31 final size:28
Alignment explanation
Indices: 38034173--38034232 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 28
38034163 TATAGTTTTT
*
38034173 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGATTATAATAATAA
38034201 ATAATATATTATAAAGTTATTATAATAATAA
1 ATAATA-ATTATAAAG--ATTATAATAATAA
38034232 A
1 A
38034233 AGAAAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.21
29 9 0.32
31 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (28 bp):
ATAATAATTATAAAGATTATAATAATAA
Found at i:38035216 original size:44 final size:41
Alignment explanation
Indices: 38035135--38035283 Score: 124
Period size: 41 Copynumber: 3.6 Consensus size: 41
38035125 ATATGTGTTA
* * * *
38035135 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATT
1 TCGTATAAGACCATGTCTGGGACATCGGCATCGATTT--GATT
* *
38035178 TATGTATAAGACCATGTC-GGGACATCGGCATCATATTTGATT
1 T-CGTATAAGACCATGTCTGGGACATCGGCATC-GATTTGATT
*
38035220 TCGTATAAGACCCTGTCTGGGACA--GTGCATCGATATTGATT
1 TCGTATAAGACCATGTCTGGGACATCG-GCATCGAT-TTGATT
* * * *
38035261 ACATGTAAGACCACGTCTGGGAC
1 TCGTATAAGACCATGTCTGGGAC
38035284 GTTGGCATTG
Statistics
Matches: 87, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
40 3 0.03
41 43 0.49
42 11 0.13
43 13 0.15
44 17 0.20
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (41 bp):
TCGTATAAGACCATGTCTGGGACATCGGCATCGATTTGATT
Found at i:38035634 original size:17 final size:18
Alignment explanation
Indices: 38035590--38035634 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
38035580 TATGAAATTT
38035590 TGATATGAAATGTGAGTA
1 TGATATGAAATGTGAGTA
*
38035608 TGAT-TAAAATGATGA-TA
1 TGATATGAAATG-TGAGTA
38035625 T-ATATGAAAT
1 TGATATGAAAT
38035635 AAATATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (18 bp):
TGATATGAAATGTGAGTA
Found at i:38058040 original size:34 final size:35
Alignment explanation
Indices: 38057985--38058051 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
38057975 CAAACACCAG
*
38057985 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
38058020 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
38058052 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:38058312 original size:31 final size:32
Alignment explanation
Indices: 38058264--38058324 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
38058254 TTTTTTTACA
* *
38058264 TATACATTTTGTATTTTTAGAAATATTTTATT
1 TATACATTTTGTATTTTTAAAAATAATTTATT
38058296 TATA-ATTTT-TATTTTTTAAAAATAATTTA
1 TATACATTTTGTA-TTTTTAAAAATAATTTA
38058325 ATCTTTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.08
31 20 0.77
32 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (32 bp):
TATACATTTTGTATTTTTAAAAATAATTTATT
Found at i:38058600 original size:12 final size:13
Alignment explanation
Indices: 38058581--38058618 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
38058571 CAATTTTATA
38058581 TATTTATATATTC
1 TATTTATATATTC
*
38058594 T-TTTATAAATTTC
1 TATTTATATA-TTC
38058607 TATTTATATATT
1 TATTTATATATT
38058619 TTTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 7 0.33
13 7 0.33
14 7 0.33
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTATATATTC
Found at i:38058614 original size:14 final size:14
Alignment explanation
Indices: 38058581--38058619 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
38058571 CAATTTTATA
38058581 TATTTATATA-TTC
1 TATTTATATATTTC
*
38058594 T-TTTATAAATTTC
1 TATTTATATATTTC
38058607 TATTTATATATTT
1 TATTTATATATTT
38058620 TTAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 5 0.23
14 10 0.45
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTTATATATTTC
Found at i:38058634 original size:30 final size:34
Alignment explanation
Indices: 38058575--38058635 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
38058565 GTTTCTCAAT
*
38058575 TTTATATATTTATATATTCTTTTATAAATTTCTA
1 TTTATATATTTATATAATCTTTTATAAATTTCTA
38058609 TTTATATATTT-T-TAAT-TTTTA-AAATTT
1 TTTATATATTTATATAATCTTTTATAAATTT
38058636 TTAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 3 0.12
33 1 0.04
34 11 0.42
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (34 bp):
TTTATATATTTATATAATCTTTTATAAATTTCTA
Found at i:38063380 original size:41 final size:44
Alignment explanation
Indices: 38063274--38063393 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 44
38063264 TGTGTTTTCA
38063274 TGTAAGACCAC-GTCTGGGACGATGGCATCGATATCTGTGATTACG
1 TGTAAGACC-CTGTCTGGGAC-ATGGCATCGATATCTGTGATTACG
* *
38063319 TGTAAGACCATGTCTAGGACATTGGCATCG-TAT-T-TGATT-CG
1 TGTAAGACCCTGTCTGGGACA-TGGCATCGATATCTGTGATTACG
*
38063360 TGTAAGACCCTGTCCGGGACAGTGGCATCGATAT
1 TGTAAGACCCTGTCTGGGACA-TGGCATCGATAT
38063394 GAGATAGCAT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
41 28 0.42
42 8 0.12
43 1 0.02
44 4 0.06
45 25 0.38
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (44 bp):
TGTAAGACCCTGTCTGGGACATGGCATCGATATCTGTGATTACG
Found at i:38065256 original size:2 final size:2
Alignment explanation
Indices: 38065249--38065275 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38065239 GCATGACCGG
38065249 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38065276 ATAAATTGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38066151 original size:14 final size:14
Alignment explanation
Indices: 38066124--38066157 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
38066114 GTTATAATTA
38066124 TATGAACATATGAGT
1 TATG-ACATATGAGT
*
38066139 TATGACATTTGAGT
1 TATGACATATGAGT
38066153 TATGA
1 TATGA
38066158 TGCTATATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (14 bp):
TATGACATATGAGT
Found at i:38070055 original size:41 final size:43
Alignment explanation
Indices: 38069936--38070068 Score: 139
Period size: 45 Copynumber: 3.0 Consensus size: 43
38069926 ACGATTTTCG
*
38069936 ATATGTGTTTTCGTGTAAGACCAC-GTCTGGGACGATGGCATCGAT
1 ATATGTG-ATTCGTGTAAGACC-CTGTCTGGGAC-ATGGCATCGAT
* *
38069981 ATATGTGATTACGTGTAAGACCATGTCTAGGACATTGGCATCG-T
1 ATATGTGATT-CGTGTAAGACCCTGTCTGGGACA-TGGCATCGAT
* *
38070025 AT-T-TGATTCGTGTAAGACCCTGTCCGGGACAGTGTCATCGAT
1 ATATGTGATTCGTGTAAGACCCTGTCTGGGACA-TGGCATCGAT
38070067 AT
1 AT
38070069 GAGATAGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
41 27 0.36
42 8 0.11
43 1 0.01
44 6 0.08
45 34 0.45
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
ATATGTGATTCGTGTAAGACCCTGTCTGGGACATGGCATCGAT
Found at i:38071134 original size:2 final size:2
Alignment explanation
Indices: 38071127--38071156 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38071117 AGACGTAATG
*
38071127 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
38071157 GGTTTATAAT
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:38071938 original size:2 final size:2
Alignment explanation
Indices: 38071931--38071979 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
38071921 GCATGACCGG
38071931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38071973 AT AT AT A
1 AT AT AT A
38071980 ATAAATTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38076831 original size:21 final size:22
Alignment explanation
Indices: 38076751--38076831 Score: 69
Period size: 21 Copynumber: 3.7 Consensus size: 22
38076741 TGTATATATG
* *
38076751 TATAT-ATTATGTTAAATT-TG
1 TATATCATTATTTTAAATTCTT
* *
38076771 TATATGATTATTTTAACTTGCTT
1 TATATCATTATTTTAAATT-CTT
38076794 TATAGATCATTATTTTAAATTCTT
1 TAT--ATCATTATTTTAAATTCTT
*
38076818 TATAT-ATCATTTTA
1 TATATCATTATTTTA
38076832 TTTTAAGTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 5 0.10
21 19 0.38
22 2 0.04
23 4 0.08
24 6 0.12
25 14 0.28
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (22 bp):
TATATCATTATTTTAAATTCTT
Found at i:38076832 original size:26 final size:25
Alignment explanation
Indices: 38076777--38076837 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
38076767 TTTGTATATG
*
38076777 ATTATTTTAACTTGCTTTATAGATC
1 ATTATTTTAAATTGCTTTATAGATC
*
38076802 ATTATTTTAAATT-CTTTATATATC
1 ATTATTTTAAATTGCTTTATAGATC
38076826 ATTTTATTTTAA
1 A--TTATTTTAA
38076838 GTTATTTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 11 0.34
25 12 0.38
26 9 0.28
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.57
Consensus pattern (25 bp):
ATTATTTTAAATTGCTTTATAGATC
Found at i:38078664 original size:30 final size:30
Alignment explanation
Indices: 38078601--38078664 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
38078591 AAACATTAAA
* ***
38078601 AAAATTATTTTAAAAATAAAAAATAATTTT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAT
*
38078631 AAAAGTATTTTAAAATTAAAAAATAAAAAT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAT
38078661 AAAA
1 AAAA
38078665 AATATATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAAT
Found at i:38080915 original size:31 final size:31
Alignment explanation
Indices: 38080880--38080950 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
38080870 ACTTAACAAC
*
38080880 TTAGTGACTTAAATGAAAATTTTTGAATAGT
1 TTAGTGACTTAAATGAAAACTTTTGAATAGT
38080911 TTAGTGACTTAAATGAAAACTTTTGAATAGT
1 TTAGTGACTTAAATGAAAACTTTTGAATAGT
38080942 TTAGTGACT
1 TTAGTGACT
38080951 AATTTATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (31 bp):
TTAGTGACTTAAATGAAAACTTTTGAATAGT
Found at i:38090109 original size:11 final size:11
Alignment explanation
Indices: 38090073--38090122 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
38090063 TTTGATTTAA
*
38090073 AAAAAAATCTT
1 AAAAAAATTTT
* *
38090084 AACAATAATTCT
1 AA-AAAAATTTT
38090096 AAAAAAATTTT
1 AAAAAAATTTT
38090107 AAAAAAATCTTT
1 AAAAAAAT-TTT
38090119 AAAA
1 AAAA
38090123 TAAAAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 17 0.53
12 15 0.47
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAAAATTTT
Found at i:38090806 original size:24 final size:24
Alignment explanation
Indices: 38090779--38090830 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
38090769 TTTCTAGAAG
38090779 ATTTAGTATCTATTAATATAATAT
1 ATTTAGTATCTATTAATATAATAT
** * * *
38090803 ATTTTTTATTTATTAGTATAATTT
1 ATTTAGTATCTATTAATATAATAT
38090827 ATTT
1 ATTT
38090831 GACCTACGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (24 bp):
ATTTAGTATCTATTAATATAATAT
Found at i:38092661 original size:43 final size:43
Alignment explanation
Indices: 38092608--38092734 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 43
38092598 ATAGGACCTC
* * *
38092608 CGATATGTGTTTTCGTGTAAGACCACGTTTGGGACGTTGGCAT
1 CGATTTGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
*
38092651 CGATTTGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCTT
1 CGATTTGTGTTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* *
38092694 CGATATT-TGATTACATGTAAGACCACGTCTGGGACGTTGGC
1 CGAT-TTGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGC
38092735 TTGTACGAGC
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
42 2 0.03
43 67 0.92
44 4 0.05
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (43 bp):
CGATTTGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:38106765 original size:15 final size:16
Alignment explanation
Indices: 38106734--38106769 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
38106724 AAAATAGATA
38106734 TTTTCTTTTGTCCTTT
1 TTTTCTTTTGTCCTTT
*
38106750 TTTTCTTTT-TCTTTT
1 TTTTCTTTTGTCCTTT
38106765 TTTTC
1 TTTTC
38106770 CGAAGTGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTCTTTTGTCCTTT
Found at i:38119198 original size:33 final size:33
Alignment explanation
Indices: 38119156--38119224 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
38119146 TGAAATGAAG
38119156 TAAGGCCACAAATTTGTCAGAGACACATGGATA
1 TAAGGCCACAAATTTGTCAGAGACACATGGATA
38119189 TAAGGCCACAAATTTGTCAGAGACACATGGATA
1 TAAGGCCACAAATTTGTCAGAGACACATGGATA
38119222 TAA
1 TAA
38119225 CTGTGCAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (33 bp):
TAAGGCCACAAATTTGTCAGAGACACATGGATA
Found at i:38123403 original size:21 final size:20
Alignment explanation
Indices: 38123374--38123418 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
38123364 AAACTGAATA
*
38123374 TATTAAAAATTATTTAATTAT
1 TATTAAAAATT-TTCAATTAT
*
38123395 TATTGAAAATTTTCAATTA-
1 TATTAAAAATTTTCAATTAT
38123414 TATTA
1 TATTA
38123419 TTTGAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 10 0.48
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TATTAAAAATTTTCAATTAT
Found at i:38123786 original size:17 final size:18
Alignment explanation
Indices: 38123754--38123787 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38123744 TGAAATCATG
38123754 ATAATTACACATTTAAAA
1 ATAATTACACATTTAAAA
*
38123772 ATAATTAGA-ATTTAAA
1 ATAATTACACATTTAAA
38123788 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAATTACACATTTAAAA
Found at i:38125594 original size:20 final size:22
Alignment explanation
Indices: 38125559--38125598 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
38125549 AATAATATCA
38125559 TTTTCGTTATGTTTTAGTTAAG
1 TTTTCGTTATGTTTTAGTTAAG
38125581 TTTTC-TTA-GTTTTAGTTA
1 TTTTCGTTATGTTTTAGTTA
38125599 TATTCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.62
Consensus pattern (22 bp):
TTTTCGTTATGTTTTAGTTAAG
Found at i:38130760 original size:14 final size:14
Alignment explanation
Indices: 38130741--38130781 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
38130731 TGATTAAAGA
* *
38130741 TTAATTAATTTAGT
1 TTAATTAATTAAGC
38130755 TTAATTAACTTAAGC
1 TTAATTAA-TTAAGC
38130770 TTAATTAATTAA
1 TTAATTAATTAA
38130782 CCATTAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (14 bp):
TTAATTAATTAAGC
Found at i:38131126 original size:13 final size:13
Alignment explanation
Indices: 38131108--38131132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38131098 ATTATTAATA
38131108 TTATTTTGTGTGT
1 TTATTTTGTGTGT
38131121 TTATTTTGTGTG
1 TTATTTTGTGTG
38131133 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:38131893 original size:17 final size:17
Alignment explanation
Indices: 38131860--38131893 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38131850 TTGTGTTTTG
*
38131860 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
38131877 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
38131894 GTTAAGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:38132875 original size:41 final size:41
Alignment explanation
Indices: 38132779--38132893 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
38132769 GAATGTAATA
* *
38132779 CGGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAATT
1 CGGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATT
* * * *
38132820 CAGACTTTATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CGGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATT
* * * * *
38132861 CGGACTATAGGTCTAGTAGGCTAAAAGCCGGTG
1 CGGACTTTACGTCTAGCAGGCTTAATGCCGGTG
38132894 TACTGAATCA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (41 bp):
CGGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATT
Found at i:38144970 original size:2 final size:2
Alignment explanation
Indices: 38144958--38145008 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
38144948 TCAATTTATC
*
38144958 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38145000 AT AT A- AT AT
1 AT AT AT AT AT
38145009 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38145129 original size:2 final size:2
Alignment explanation
Indices: 38145122--38145176 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
38145112 TAGTTAGTAG
38145122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38145164 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
38145177 TAAATGATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38153200 original size:30 final size:31
Alignment explanation
Indices: 38153146--38153246 Score: 102
Period size: 30 Copynumber: 3.3 Consensus size: 31
38153136 ACTAAAATGA
*
38153146 TAAATTTTGTAAAGATTAAGGGATAAATTTAT
1 TAAATTTT-TAAACATTAAGGGATAAATTTAT
* *
38153178 TAAATTTTTAGA-A-TAGAGGGATAAATGTA-
1 TAAATTTTTAAACATTA-AGGGATAAATTTAT
*
38153207 -AAATTTTATAAACATTAAGGGCTAAATTTAT
1 TAAATTTT-TAAACATTAAGGGATAAATTTAT
*
38153238 TAATTTTTT
1 TAAATTTTT
38153247 TACATGTGGG
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
28 7 0.12
29 5 0.09
30 25 0.44
31 6 0.11
32 14 0.25
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.42
Consensus pattern (31 bp):
TAAATTTTTAAACATTAAGGGATAAATTTAT
Found at i:38154541 original size:16 final size:16
Alignment explanation
Indices: 38154520--38154571 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
38154510 TTTGGTTCGC
38154520 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
38154536 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
38154552 TGTAATGTAATAGAGG
1 TGTATTGGATTAGAGG
38154568 TGTA
1 TGTA
38154572 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:38154618 original size:45 final size:44
Alignment explanation
Indices: 38154552--38154642 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
38154542 GGATTAGAGG
* *
38154552 TGTAATGTAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
38154597 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
38154641 TG
1 TG
38154643 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:38154828 original size:18 final size:17
Alignment explanation
Indices: 38154807--38154841 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38154797 TTATTATTAA
*
38154807 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38154825 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38154842 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:38155004 original size:16 final size:16
Alignment explanation
Indices: 38154967--38155008 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38154957 NNNNNNNTAT
*
38154967 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
38154983 TT-AAATATATTATAA
1 TTAAAATATATTATAA
38154998 TTAAAATATAT
1 TTAAAATATAT
38155009 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:38155015 original size:14 final size:15
Alignment explanation
Indices: 38154976--38155017 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38154966 TTTAAACATA
*
38154976 ATTATTATTAAATAT
1 ATTATAATTAAATAT
38154991 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
38155005 A-TATAATTTAATA
1 ATTATAATTAAATA
38155018 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:38155107 original size:15 final size:16
Alignment explanation
Indices: 38155086--38155128 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
38155076 GTAAAATATA
38155086 AATTAAAATA-ATTAT
1 AATTAAAATATATTAT
*
38155101 TATT-AAATATATTAT
1 AATTAAAATATATTAT
38155116 AATTAAAATATAT
1 AATTAAAATATAT
38155129 AATTTAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 11 0.46
16 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:38155186 original size:120 final size:120
Alignment explanation
Indices: 38154965--38155262 Score: 508
Period size: 120 Copynumber: 2.5 Consensus size: 120
38154955 NNNNNNNNNT
38154965 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAA-ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
38155030 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
*
38155087 A-TTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAAGAAAATTCTTAATAA
1 ATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
38155151 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* * * *
38155206 ATTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
38155263 TAAAATAATT
Statistics
Matches: 167, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
119 3 0.02
120 158 0.95
121 5 0.03
122 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (120 bp):
ATTTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:38155187 original size:61 final size:60
Alignment explanation
Indices: 38155002--38155189 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 60
38154992 TTATAATTAA
38155002 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAA-AAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * ** * * *
38155063 AATATATGATACTGTAAAATATAAATTAA-AA-TAATTATTATTAAAT--ATATTA-T--AATTA
1 AATATAT-A-A-TTTAAAAAAT-TCTTAATAATTAA-TATTCTTATATGAAT-TTACTCAAATCA
*
38155121 A
60 T
38155122 AATATATAATTTAAGAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAA-AAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
38155183 AATATAT
1 AATATAT
38155190 GATACTATAA
Statistics
Matches: 97, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
56 8 0.08
57 16 0.16
58 7 0.07
59 14 0.14
61 21 0.22
62 7 0.07
63 16 0.16
64 8 0.08
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (60 bp):
AATATATAATTTAAAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:38155188 original size:59 final size:58
Alignment explanation
Indices: 38155005--38155188 Score: 164
Period size: 57 Copynumber: 3.1 Consensus size: 58
38154995 TAATTAAAAT
38155005 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAA-AAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
* ** * * * *
38155064 ATATATGATACTGTAAAATATAAATTAA-AA-TAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATA--AT--T-TAAAAAAT-TCTTAATAATTAA-TATTCTTATATGA-ATT-TACTCAAATCA
38155124 T-
57 TA
38155125 ATATAATTTAAGAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAA-AAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
38155184 ATATA
1 ATATA
38155189 TGATACTATA
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
56 13 0.14
57 19 0.20
58 6 0.06
59 12 0.13
61 7 0.07
62 6 0.06
63 19 0.20
64 13 0.14
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (58 bp):
ATATAATTTAAAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
Found at i:38155800 original size:30 final size:31
Alignment explanation
Indices: 38155749--38155810 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
38155739 CGGGCCAGCA
38155749 GAATTATGAGCCGAGGGGAGTCGAGCAAAAT
1 GAATTATGAGCCGAGGGGAGTCGAGCAAAAT
*
38155780 GAATTATGAGCTGA-GGGAGTCGAGCAAAAT
1 GAATTATGAGCCGAGGGGAGTCGAGCAAAAT
38155810 G
1 G
38155811 GAAAACAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.35, C:0.11, G:0.35, T:0.18
Consensus pattern (31 bp):
GAATTATGAGCCGAGGGGAGTCGAGCAAAAT
Found at i:38155994 original size:16 final size:16
Alignment explanation
Indices: 38155973--38156008 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
38155963 NAAGAAATCA
38155973 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
38155989 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
38156005 CAGC
1 CAGC
38156009 TCCTGAGTTA
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:0.19, C:0.39, G:0.19, T:0.22
Consensus pattern (16 bp):
CAGCCATGTACTCCTG
Found at i:38162952 original size:17 final size:16
Alignment explanation
Indices: 38162930--38162972 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
38162920 TATATTTGTG
38162930 TATATATAATGTACGA-A
1 TATATATAATGTA--ATA
38162947 TATATATATATGTAATA
1 TATATATA-ATGTAATA
38162964 TATATATAA
1 TATATATAA
38162973 ATTCTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 17 0.71
18 5 0.21
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (16 bp):
TATATATAATGTAATA
Found at i:38163231 original size:76 final size:76
Alignment explanation
Indices: 38163151--38163350 Score: 176
Period size: 78 Copynumber: 2.6 Consensus size: 76
38163141 GAAATTAGGG
* *
38163151 ATGTATATATTAGATTCGAATATGTATGAGTATACAAGTATAAGTTCATGTTTTGATTATAAG-T
1 ATGTATATATTAGATTCGAATATGTATGAGTATACAAGTATAAGTTCATGTATTGA-AATAAGAT
38163215 ATGTAA-TTATAT
65 ATG-AATTTATAT
* * * * * * *
38163227 ATGTATATGA-TAGACTCGAATATATATATAAATATACATA-TATAAATTCTTGTATTGAAATTA
1 ATGTATAT-ATTAGATTCG-A-ATATGTATGAGTATACA-AGTATAAGTTCATGTATTGAAATAA
38163290 GATATGAATTTATAT
62 GATATGAATTTATAT
* * * * *
38163305 ATGTATATGTGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATATTAGATTCGAATATGTATGAG-TATACAAGTATAAGTT
38163351 TTATATTGAA
Statistics
Matches: 96, Mismatches: 19, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
76 34 0.35
77 9 0.09
78 52 0.54
79 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (76 bp):
ATGTATATATTAGATTCGAATATGTATGAGTATACAAGTATAAGTTCATGTATTGAAATAAGATA
TGAATTTATAT
Found at i:38163978 original size:41 final size:41
Alignment explanation
Indices: 38163749--38163971 Score: 392
Period size: 41 Copynumber: 5.4 Consensus size: 41
38163739 CAGGCTTAGC
* *
38163749 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAA
*
38163790 GCTTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAA
38163831 GCCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAA
38163872 GCCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAA
* * *
38163913 GCCTAGCAGGCTAAGTGCTAGTGAACTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAA
38163954 GCCTAGCAGGCTAAGTGC
1 GCCTAGCAGGCTAAGTGC
38163972 CAGTGAATCT
Statistics
Matches: 175, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 175 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAA
Found at i:38164018 original size:2 final size:2
Alignment explanation
Indices: 38164011--38164043 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38164001 ATGCATTGGG
38164011 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 T
38164044 GATTTTGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38164242 original size:34 final size:35
Alignment explanation
Indices: 38164173--38164246 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 35
38164163 TTGTTGGATA
*
38164173 TATATATGTATGCATTCGACATATGTGGATTATAAG
1 TATATATG-ATGCATTCGACATATGTAGATTATAAG
38164209 TATATATG-TGCATTCGACACT-TGTAG-TTGATAAG
1 TATATATGATGCATTCGACA-TATGTAGATT-ATAAG
38164243 TATA
1 TATA
38164247 AATATATGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
33 2 0.06
34 24 0.69
35 1 0.03
36 8 0.23
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.39
Consensus pattern (35 bp):
TATATATGATGCATTCGACATATGTAGATTATAAG
Found at i:38167853 original size:2 final size:2
Alignment explanation
Indices: 38167842--38167870 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38167832 CTTTAAAGAA
38167842 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38167871 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:38168825 original size:29 final size:30
Alignment explanation
Indices: 38168793--38168857 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
38168783 TTTTGACAAT
* *
38168793 TTTTAATAAATTTTAAGGTTTTT-TTATAA
1 TTTTAACAAATTTTAAGGTTTTTGTTAAAA
* * *
38168822 TTTTAACCATTTTTAATGTTTTTGTTAAAA
1 TTTTAACAAATTTTAAGGTTTTTGTTAAAA
38168852 TTTTAA
1 TTTTAA
38168858 AATAATTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (30 bp):
TTTTAACAAATTTTAAGGTTTTTGTTAAAA
Found at i:38172325 original size:14 final size:14
Alignment explanation
Indices: 38172306--38172335 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38172296 AATATTCTCT
38172306 CATAGATTCTTTTA
1 CATAGATTCTTTTA
38172320 CATAGATTCTTTTA
1 CATAGATTCTTTTA
38172334 CA
1 CA
38172336 ATATAGTCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.47
Consensus pattern (14 bp):
CATAGATTCTTTTA
Found at i:38172787 original size:58 final size:57
Alignment explanation
Indices: 38172696--38172866 Score: 155
Period size: 61 Copynumber: 2.9 Consensus size: 57
38172686 TTTTTATAAT
* * * ***
38172696 ATTATATATTATGATTATTTAATTCATATTTTAATGATAACTATATTAAGAATGTTATTAA
1 ATTATATATTAT-TTTATTAAATT-ATA-TTTAATAATAACTATATTAA-AATAAGATTAA
* * *
38172757 ATTATATATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATAAGATTAA
1 ATTATATATTATTTTATTAAATTATATTTAATAATAACTATATTAAAATAAGATTAA
* *
38172814 ATTATTTATTTTTATTTTTATTAAAATATATTTAATAATAATCT-TATTAAAAT
1 ATTA--TA-TATTA-TTTTATTAAATTATATTTAATAATAA-CTATATTAAAAT
38172867 TTAATAACAA
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
57 12 0.13
58 17 0.19
59 4 0.04
60 13 0.14
61 44 0.48
62 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (57 bp):
ATTATATATTATTTTATTAAATTATATTTAATAATAACTATATTAAAATAAGATTAA
Found at i:38173079 original size:16 final size:16
Alignment explanation
Indices: 38173043--38173085 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
38173033 AATTATAGCT
* *
38173043 CTATTTTATTACAACT
1 CTATTTCATTACAACC
*
38173059 GTATTTCATTACAACC
1 CTATTTCATTACAACC
*
38173075 CTATTCCATTA
1 CTATTTCATTA
38173086 TAGTGAAGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.44
Consensus pattern (16 bp):
CTATTTCATTACAACC
Found at i:38187639 original size:85 final size:86
Alignment explanation
Indices: 38187485--38187654 Score: 218
Period size: 85 Copynumber: 2.0 Consensus size: 86
38187475 GCTAAAGTTA
* * * ** *
38187485 AGTTAAATATTTCCGTAGGATGTATTTTAGTTAGAGTCATTGTTTTGATTGAGGACAAGCAAAAT
1 AGTTAAATATTTCCGTAAGATGCATTTTAGTTAGAGTCATTGTTTTGATTGAGGAAAAAAAAAAG
*
38187550 TTTAAGTGTTGGAGTATGATG
66 TTTAAGTGTGGGAGTATGATG
* * *
38187571 AGTTAAAT-TTTTCGTAAGATGCATTTTAGTTAGAGTCATTGTGTTT-CTTGGGGAAAAAAAAAA
1 AGTTAAATATTTCCGTAAGATGCATTTTAGTTAGAGTCATTGT-TTTGATTGAGGAAAAAAAAAA
*
38187634 GTTTAAGTGTGGGGGTATGAT
65 GTTTAAGTGTGGGAGTATGAT
38187655 TAATCCTCAT
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
85 61 0.85
86 11 0.15
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.39
Consensus pattern (86 bp):
AGTTAAATATTTCCGTAAGATGCATTTTAGTTAGAGTCATTGTTTTGATTGAGGAAAAAAAAAAG
TTTAAGTGTGGGAGTATGATG
Found at i:38190502 original size:24 final size:24
Alignment explanation
Indices: 38190455--38190502 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
38190445 TCGTTTTGTG
* *
38190455 GCAAATGATGAATTGATGATAAAT
1 GCAAAGGATGAATTGAGGATAAAT
38190479 GCAAAGGATGAATTGACGGA-AAAT
1 GCAAAGGATGAATTGA-GGATAAAT
38190503 TACCCAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.23
Consensus pattern (24 bp):
GCAAAGGATGAATTGAGGATAAAT
Found at i:38190680 original size:42 final size:42
Alignment explanation
Indices: 38190602--38190689 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 42
38190592 GTTTCTGTTT
* * * *
38190602 AACCTTTATGGGTTTCCGTTCAGCTCCTATGAGCTTCCGTTC
1 AACCCTTACGGGTTTCCGTTCAGCACCTATGAGCTTCCGTGC
* * * * *
38190644 AACCCTTACGGGTTTCTGTTTAGCACTTATGTGCTTCTGTGC
1 AACCCTTACGGGTTTCCGTTCAGCACCTATGAGCTTCCGTGC
38190686 AACC
1 AACC
38190690 TCCGGGCTTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (42 bp):
AACCCTTACGGGTTTCCGTTCAGCACCTATGAGCTTCCGTGC
Found at i:38193315 original size:12 final size:13
Alignment explanation
Indices: 38193288--38193321 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
38193278 CGACATTGAT
*
38193288 TTTTATTTTTAGG
1 TTTTCTTTTTAGG
38193301 TTTTCTTTTTA-G
1 TTTTCTTTTTAGG
38193313 TTTTCTTTT
1 TTTTCTTTT
38193322 GAAGTAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (13 bp):
TTTTCTTTTTAGG
Done.