Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 89 of 131
Found at i:29774849 original size:9 final size:9
Alignment explanation
Indices: 29774753--29774888 Score: 53
Period size: 9 Copynumber: 14.6 Consensus size: 9
29774743 TTTTTATAAA
*
29774753 AAAAATCAT
1 AAAAATTAT
29774762 AAAAATTAT
1 AAAAATTAT
*
29774771 AAAATAATTTT
1 -AAA-AATTAT
29774782 AAAAATTAT
1 AAAAATTAT
*
29774791 AAAAA-AAT
1 AAAAATTAT
*
29774799 -TAAA-TATT
1 AAAAATTA-T
*
29774807 AGAAATTAT
1 AAAAATTAT
* *
29774816 TAAAATTTT
1 AAAAATTAT
*
29774825 ATAAACTTATT
1 A-AAAATTA-T
29774836 AAAAAATTAT
1 -AAAAATTAT
* *
29774846 AAAACTAAT
1 AAAAATTAT
*
29774855 AAAACTTATT
1 AAAAATTA-T
* *
29774865 TAAAATTAA
1 AAAAATTAT
*
29774874 AAACAATTTT
1 AAA-AATTAT
29774884 AAAAA
1 AAAAA
29774889 ACTTGAACTG
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
7 4 0.04
8 3 0.03
9 46 0.49
10 28 0.30
11 12 0.13
12 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29774857 original size:19 final size:18
Alignment explanation
Indices: 29774762--29774858 Score: 59
Period size: 18 Copynumber: 5.2 Consensus size: 18
29774752 AAAAAATCAT
*
29774762 AAAAATTATAAAATAATTTT
1 AAAAATTATAAAATAA--TA
* *
29774782 AAAAATTATAAAAAAATT
1 AAAAATTATAAAATAATA
* * * *
29774800 AAATATTAGAAATTATTA
1 AAAAATTATAAAATAATA
** * *
29774818 AAATTTTATAAACTTATTA
1 AAAAATTATAAA-ATAATA
29774837 AAAAATTATAAAACTAATA
1 AAAAATTATAAAA-TAATA
29774856 AAA
1 AAA
29774859 CTTATTTAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
18 24 0.39
19 23 0.37
20 15 0.24
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (18 bp):
AAAAATTATAAAATAATA
Found at i:29774886 original size:29 final size:32
Alignment explanation
Indices: 29774819--29774887 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 32
29774809 AAATTATTAA
29774819 AATTTTATAAACTTATTAAAAAATTATAAAACT
1 AATTTTA-AAACTTATTAAAAAATTATAAAACT
*
29774852 AA---TAAAACTTATT-TAAAATTA-AAAAC-
1 AATTTTAAAACTTATTAAAAAATTATAAAACT
29774878 AATTTTAAAA
1 AATTTTAAAA
29774888 AACTTGAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
26 2 0.06
27 5 0.16
28 7 0.22
29 14 0.44
30 2 0.06
33 2 0.06
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (32 bp):
AATTTTAAAACTTATTAAAAAATTATAAAACT
Found at i:29775527 original size:19 final size:19
Alignment explanation
Indices: 29775499--29775541 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
29775489 CTTTAAATTA
29775499 TTTT-TAATATTTAATAAT
1 TTTTATAATATTTAATAAT
*
29775517 TTTTATAATATTTAATCAT
1 TTTTATAATATTTAATAAT
29775536 TTTTAT
1 TTTTAT
29775542 GGAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATAATATTTAATAAT
Found at i:29776512 original size:19 final size:19
Alignment explanation
Indices: 29776484--29776526 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
29776474 CATTAAATTA
29776484 TTTT-TAATATTTAATAAT
1 TTTTATAATATTTAATAAT
*
29776502 TTTTATAATATTTAATCAT
1 TTTTATAATATTTAATAAT
29776521 TTTTAT
1 TTTTAT
29776527 GGAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATAATATTTAATAAT
Found at i:29777401 original size:985 final size:985
Alignment explanation
Indices: 29775491--29777462 Score: 3944
Period size: 985 Copynumber: 2.0 Consensus size: 985
29775481 TTTTCATACT
29775491 TTAAATTATTTTTAATATTTAATAATTTTTATAATATTTAATCATTTTTATGGAAAAATATTAGA
1 TTAAATTATTTTTAATATTTAATAATTTTTATAATATTTAATCATTTTTATGGAAAAATATTAGA
29775556 TTAAATAATAATGTGCCATTTGTCACCATCTAATTAGCCCGTCAATTTATTTTAACAGTTATGTG
66 TTAAATAATAATGTGCCATTTGTCACCATCTAATTAGCCCGTCAATTTATTTTAACAGTTATGTG
29775621 GTCAATCATGAAAATCATTAATGGAAGGGTTTAATTGATTATTTTAATTAACAACAATGACTTAA
131 GTCAATCATGAAAATCATTAATGGAAGGGTTTAATTGATTATTTTAATTAACAACAATGACTTAA
29775686 TTAGATGTGAATTTGATATAAAGGCTTAAACTGATTTTTTTACAATTTCTTAAGGTTTTCTTTTA
196 TTAGATGTGAATTTGATATAAAGGCTTAAACTGATTTTTTTACAATTTCTTAAGGTTTTCTTTTA
29775751 CATATAAACCTATATTTTATATAAAATCAATAAAAAAACTATACACCAACTTAAGATGTCATGAT
261 CATATAAACCTATATTTTATATAAAATCAATAAAAAAACTATACACCAACTTAAGATGTCATGAT
29775816 TTTCAAATATTTTAGTTTTCAATTTCAATTAAAACATCATCTTATTTTATATAAATGGTGTGAAA
326 TTTCAAATATTTTAGTTTTCAATTTCAATTAAAACATCATCTTATTTTATATAAATGGTGTGAAA
29775881 AGTGTACAAATTTGAATTTATTAAATTTACAAAGATTATAAGAATTTCAATTTTGATATAAAAAA
391 AGTGTACAAATTTGAATTTATTAAATTTACAAAGATTATAAGAATTTCAATTTTGATATAAAAAA
29775946 TAAATATAGAAATGAGAAATAATCATAAATTACATTTGTATGGCACAATGTACACTATTTTGAAA
456 TAAATATAGAAATGAGAAATAATCATAAATTACATTTGTATGGCACAATGTACACTATTTTGAAA
29776011 CCAACGTTATAATTTGAATTTAATCATAAATTGCATTTGTATGTGTTTTATGGCACCATTTGTAC
521 CCAACGTTATAATTTGAATTTAATCATAAATTGCATTTGTATGTGTTTTATGGCACCATTTGTAC
29776076 TATTTTGAAATCAAATTTACAATTTGAATTTCAAGTTCTCAAATGCTATTTTAAGAATTTTTTTA
586 TATTTTGAAATCAAATTTACAATTTGAATTTCAAGTTCTCAAATGCTATTTTAAGAATTTTTTTA
29776141 TAAAAAAGAATTATTCCAAAATTTGTGTTTTAAAAAAAAAATATTTTATGGCATTTTAAAGAAGT
651 TAAAAAAGAATTATTCCAAAATTTGTGTTTTAAAAAAAAAATATTTTATGGCATTTTAAAGAAGT
29776206 TTAATAAATTATCATATATTTTTAATTATTTTCATTTTAAATACTTTGGAAATATTTGTTCAAAT
716 TTAATAAATTATCATATATTTTTAATTATTTTCATTTTAAATACTTTGGAAATATTTGTTCAAAT
29776271 ACATAAATAAGTTGCGGATATAGTTGAAGTAATAAATGCTCAAATTTCTTTTGGTTTGTAAGTCC
781 ACATAAATAAGTTGCGGATATAGTTGAAGTAATAAATGCTCAAATTTCTTTTGGTTTGTAAGTCC
29776336 AATATAATCAGATACTTTATTAAGTCATATAACTCTCAAAATAATGCTTCTGATTGAAAAGATAA
846 AATATAATCAGATACTTTATTAAGTCATATAACTCTCAAAATAATGCTTCTGATTGAAAAGATAA
29776401 ACTCAAGGTTAATAATCCAATTGTTGAGTGACAAATAATTTTTTAGAAGAAAGAAAATAAGTTAT
911 ACTCAAGGTTAATAATCCAATTGTTGAGTGACAAATAATTTTTTAGAAGAAAGAAAATAAGTTAT
29776466 TAGTAAAACA
976 TAGTAAAACA
29776476 TTAAATTATTTTTAATATTTAATAATTTTTATAATATTTAATCATTTTTATGGAAAAATATTAGA
1 TTAAATTATTTTTAATATTTAATAATTTTTATAATATTTAATCATTTTTATGGAAAAATATTAGA
29776541 TTAAATAATAATGTGCCATTTGTCACCATCTAATTAGCCCGTCAATTTATTTTAACAGTTATGTG
66 TTAAATAATAATGTGCCATTTGTCACCATCTAATTAGCCCGTCAATTTATTTTAACAGTTATGTG
29776606 GTCAATCATGAAAATCATTAATGGAAGGGTTTAATTGATTATTTTAATTAACAACAATGACTTAA
131 GTCAATCATGAAAATCATTAATGGAAGGGTTTAATTGATTATTTTAATTAACAACAATGACTTAA
29776671 TTAGATGTGAATTTGATATAAAGGCTTAAACTGATTTTTTTACAATTTCTTAAGGTTTTCTTTTA
196 TTAGATGTGAATTTGATATAAAGGCTTAAACTGATTTTTTTACAATTTCTTAAGGTTTTCTTTTA
29776736 CATATAAACCTATATTTTATATAAAATCAATAAAAAAACTATACACCAACTTAAGATGTCATGAT
261 CATATAAACCTATATTTTATATAAAATCAATAAAAAAACTATACACCAACTTAAGATGTCATGAT
29776801 TTTCAAATATTTTAGTTTTCAATTTCAATTAAAACATCATCTTATTTTATATAAATGGTGTGAAA
326 TTTCAAATATTTTAGTTTTCAATTTCAATTAAAACATCATCTTATTTTATATAAATGGTGTGAAA
29776866 AGTGTACAAATTTGAATTTATTAAATTTACAAAGATTATAAGAATTTCAATTTTGATATAAAAAA
391 AGTGTACAAATTTGAATTTATTAAATTTACAAAGATTATAAGAATTTCAATTTTGATATAAAAAA
29776931 TAAATATAGAAATGAGAAATAATCATAAATTACATTTGTATGGCACAATGTACACTATTTTGAAA
456 TAAATATAGAAATGAGAAATAATCATAAATTACATTTGTATGGCACAATGTACACTATTTTGAAA
29776996 CCAACGTTATAATTTGAATTTAATCATAAATTGCATTTGTATGTGTTTTATGGCACCATTTGTAC
521 CCAACGTTATAATTTGAATTTAATCATAAATTGCATTTGTATGTGTTTTATGGCACCATTTGTAC
29777061 TATTTTGAAATCAAATTTACAATTTGAATTTCAAGTTCTCAAATGCTATTTTAAGAATTTTTTTA
586 TATTTTGAAATCAAATTTACAATTTGAATTTCAAGTTCTCAAATGCTATTTTAAGAATTTTTTTA
29777126 TAAAAAAGAATTATTCCAAAATTTGTGTTTTAAAAAAAAAATATTTTATGGCATTTTAAAGAAGT
651 TAAAAAAGAATTATTCCAAAATTTGTGTTTTAAAAAAAAAATATTTTATGGCATTTTAAAGAAGT
29777191 TTAATAAATTATCATATATTTTTAATTATTTTCATTTTAAATACTTTGGAAATATTTGTTCAAAT
716 TTAATAAATTATCATATATTTTTAATTATTTTCATTTTAAATACTTTGGAAATATTTGTTCAAAT
29777256 ACATAAATAAGTTGCGGATATAGTTGAAGTAATAAATGCTCAAATTTCTTTTGGTTTGTAAGTCC
781 ACATAAATAAGTTGCGGATATAGTTGAAGTAATAAATGCTCAAATTTCTTTTGGTTTGTAAGTCC
29777321 AATATAATCAGATACTTTATTAAGTCATATAACTCTCAAAATAATGCTTCTGATTGAAAAGATAA
846 AATATAATCAGATACTTTATTAAGTCATATAACTCTCAAAATAATGCTTCTGATTGAAAAGATAA
29777386 ACTCAAGGTTAATAATCCAATTGTTGAGTGACAAATAATTTTTTAGAAGAAAGAAAATAAGTTAT
911 ACTCAAGGTTAATAATCCAATTGTTGAGTGACAAATAATTTTTTAGAAGAAAGAAAATAAGTTAT
29777451 TAGTAAAACA
976 TAGTAAAACA
29777461 TT
1 TT
29777463 GCTTCTTTCA
Statistics
Matches: 987, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
985 987 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (985 bp):
TTAAATTATTTTTAATATTTAATAATTTTTATAATATTTAATCATTTTTATGGAAAAATATTAGA
TTAAATAATAATGTGCCATTTGTCACCATCTAATTAGCCCGTCAATTTATTTTAACAGTTATGTG
GTCAATCATGAAAATCATTAATGGAAGGGTTTAATTGATTATTTTAATTAACAACAATGACTTAA
TTAGATGTGAATTTGATATAAAGGCTTAAACTGATTTTTTTACAATTTCTTAAGGTTTTCTTTTA
CATATAAACCTATATTTTATATAAAATCAATAAAAAAACTATACACCAACTTAAGATGTCATGAT
TTTCAAATATTTTAGTTTTCAATTTCAATTAAAACATCATCTTATTTTATATAAATGGTGTGAAA
AGTGTACAAATTTGAATTTATTAAATTTACAAAGATTATAAGAATTTCAATTTTGATATAAAAAA
TAAATATAGAAATGAGAAATAATCATAAATTACATTTGTATGGCACAATGTACACTATTTTGAAA
CCAACGTTATAATTTGAATTTAATCATAAATTGCATTTGTATGTGTTTTATGGCACCATTTGTAC
TATTTTGAAATCAAATTTACAATTTGAATTTCAAGTTCTCAAATGCTATTTTAAGAATTTTTTTA
TAAAAAAGAATTATTCCAAAATTTGTGTTTTAAAAAAAAAATATTTTATGGCATTTTAAAGAAGT
TTAATAAATTATCATATATTTTTAATTATTTTCATTTTAAATACTTTGGAAATATTTGTTCAAAT
ACATAAATAAGTTGCGGATATAGTTGAAGTAATAAATGCTCAAATTTCTTTTGGTTTGTAAGTCC
AATATAATCAGATACTTTATTAAGTCATATAACTCTCAAAATAATGCTTCTGATTGAAAAGATAA
ACTCAAGGTTAATAATCCAATTGTTGAGTGACAAATAATTTTTTAGAAGAAAGAAAATAAGTTAT
TAGTAAAACA
Found at i:29777932 original size:5 final size:5
Alignment explanation
Indices: 29777924--29777949 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29777914 AATTTTTGTA
29777924 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
29777950 GATAGTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:29778756 original size:7 final size:7
Alignment explanation
Indices: 29778731--29778802 Score: 72
Period size: 7 Copynumber: 10.3 Consensus size: 7
29778721 TCCATCCTAT
29778731 ATTTTCA
1 ATTTTCA
* *
29778738 ATCTTAA
1 ATTTTCA
29778745 ATTTTCA
1 ATTTTCA
29778752 ATTTTCA
1 ATTTTCA
29778759 ATTTTCA
1 ATTTTCA
*
29778766 AATTTCA
1 ATTTTCA
*
29778773 AATTTCA
1 ATTTTCA
**
29778780 ATCCTCA
1 ATTTTCA
**
29778787 ATCCTCA
1 ATTTTCA
29778794 ATTTTCA
1 ATTTTCA
29778801 AT
1 AT
29778803 CCTCAATCCT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (7 bp):
ATTTTCA
Found at i:29778804 original size:21 final size:21
Alignment explanation
Indices: 29778770--29778817 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
29778760 TTTTCAAATT
*
29778770 TCAAATTTCAATCCTCAATCC
1 TCAATTTTCAATCCTCAATCC
29778791 TCAATTTTCAATCCTCAATCC
1 TCAATTTTCAATCCTCAATCC
*
29778812 TTAATT
1 TCAATT
29778818 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (21 bp):
TCAATTTTCAATCCTCAATCC
Found at i:29778808 original size:7 final size:7
Alignment explanation
Indices: 29778777--29778812 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
29778767 ATTTCAAATT
29778777 TCAATCC
1 TCAATCC
29778784 TCAATCC
1 TCAATCC
**
29778791 TCAATTT
1 TCAATCC
29778798 TCAATCC
1 TCAATCC
29778805 TCAATCC
1 TCAATCC
29778812 T
1 T
29778813 TAATTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (7 bp):
TCAATCC
Found at i:29784047 original size:3 final size:3
Alignment explanation
Indices: 29784039--29784064 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29784029 AGAGCGCGAA
29784039 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
29784065 AAGCCTGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29784377 original size:19 final size:19
Alignment explanation
Indices: 29784324--29784381 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
29784314 CCATTTGTTC
*
29784324 ATCTCCGTTTCAATTTTTT
1 ATCTCCATTTCAATTTTTT
*
29784343 -CCTTCCGGATTT-AATTTTTT
1 ATC-TCC--ATTTCAATTTTTT
29784363 ATCTCCATTTCAATTTTTT
1 ATCTCCATTTCAATTTTTT
29784382 CTATACCGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 11 0.35
21 4 0.13
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
ATCTCCATTTCAATTTTTT
Found at i:29786860 original size:84 final size:86
Alignment explanation
Indices: 29786713--29786882 Score: 211
Period size: 84 Copynumber: 2.0 Consensus size: 86
29786703 CTCTCAAGTG
* * * *
29786713 TTTGAGCTTAGTTCTAAAACATTAATGTAAAGGTTTTACTTGAGCAGATCAAACAAAATTATTCT
1 TTTGAGCTTAGTTCTAAAACATCAATGGAAAGGTCTTACTTGAGCAGACCAAACAAAATTATTCT
*
29786778 CAGACAGT-AAAACAAAAGCA
66 AAGACAGTAAAAACAAAAGCA
* * * *
29786798 TTTGA-CTTAGTTCTATAACATCAATGGACAGGTCTTATTTTG-GCGGACCAAACAAAATTATTC
1 TTTGAGCTTAGTTCTAAAACATCAATGGAAAGGTCTTA-CTTGAGCAGACCAAACAAAATTATTC
* *
29786861 TAAGACGGTAAAAACAGAAGCA
65 TAAGACAGTAAAAACAAAAGCA
29786883 GATAAGGTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
84 53 0.74
85 19 0.26
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (86 bp):
TTTGAGCTTAGTTCTAAAACATCAATGGAAAGGTCTTACTTGAGCAGACCAAACAAAATTATTCT
AAGACAGTAAAAACAAAAGCA
Found at i:29787247 original size:9 final size:9
Alignment explanation
Indices: 29787235--29787268 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
29787225 GAGGAAGAAC
29787235 AAGAAGATG
1 AAGAAGATG
* *
29787244 AAGAACAAG
1 AAGAAGATG
29787253 AAGAAGATG
1 AAGAAGATG
29787262 AAGAAGA
1 AAGAAGA
29787269 GGCAGGAGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.62, C:0.03, G:0.29, T:0.06
Consensus pattern (9 bp):
AAGAAGATG
Found at i:29787248 original size:15 final size:15
Alignment explanation
Indices: 29787228--29787256 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29787218 AAAGGGAGAG
29787228 GAAGAACAAGAAGAT
1 GAAGAACAAGAAGAT
29787243 GAAGAACAAGAAGA
1 GAAGAACAAGAAGA
29787257 AGATGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.28, T:0.03
Consensus pattern (15 bp):
GAAGAACAAGAAGAT
Found at i:29788273 original size:18 final size:18
Alignment explanation
Indices: 29788229--29788274 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
29788219 ATTTAATTGG
*
29788229 GACCAAATTAAAATTTAA
1 GACCAAATTAAAATTGAA
29788247 GTACCAAATTAAACATTGAA
1 G-ACCAAATTAAA-ATTGAA
29788267 G-CCAAATT
1 GACCAAATT
29788275 TAAGTGCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (18 bp):
GACCAAATTAAAATTGAA
Found at i:29788339 original size:22 final size:23
Alignment explanation
Indices: 29788294--29788340 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
29788284 AATTGGAACA
*
29788294 AAAAATACTCAAGTATCAAATTG
1 AAAAATACTCAAGTACCAAATTG
* *
29788317 AAAAA-ACTCAAGTCCCAATTTG
1 AAAAATACTCAAGTACCAAATTG
29788339 AA
1 AA
29788341 TATTGAAGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (23 bp):
AAAAATACTCAAGTACCAAATTG
Found at i:29808277 original size:67 final size:68
Alignment explanation
Indices: 29808161--29808295 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 68
29808151 GAGAAGATAA
* *
29808161 AGTTAAAATGGAATATTCAGAACATATAGAGACAATAAGCCCAAGAAACATTTAGGA-TTTATCC
1 AGTTAAAATGGAATATTCAAAACATATAAAGACAATAAGCCCAAGAAACATTTAGGATTTTATCC
29808225 TAT
66 TAT
* **
29808228 AGTTAAAATGGAATATTCAAAACATATAAAGACAATAAGCCTATTAAACATTTAGGATTTTATCC
1 AGTTAAAATGGAATATTCAAAACATATAAAGACAATAAGCCCAAGAAACATTTAGGATTTTATCC
29808293 TAT
66 TAT
29808296 GTCTCTTGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
67 52 0.84
68 10 0.16
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (68 bp):
AGTTAAAATGGAATATTCAAAACATATAAAGACAATAAGCCCAAGAAACATTTAGGATTTTATCC
TAT
Found at i:29811042 original size:3 final size:3
Alignment explanation
Indices: 29811034--29811087 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
29811024 CAAACGAAAC
29811034 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29811082 ATA ATA
1 ATA ATA
29811088 TGCTGAGAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29814899 original size:16 final size:16
Alignment explanation
Indices: 29814878--29814909 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29814868 GTTTTGTTGC
*
29814878 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
29814894 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
29814910 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:29815194 original size:51 final size:50
Alignment explanation
Indices: 29815136--29815307 Score: 195
Period size: 51 Copynumber: 3.4 Consensus size: 50
29815126 CACATAATAA
*
29815136 CCTGCACATAGTACTACACATGTGACAATCACTATCCGATACACGTAGTAG
1 CCTGCACATAGTACTACACATGTGACAAT-ACTATCCGGTACACGTAGTAG
* * * *
29815187 CCTGCACATAGTACTACACACGTGATCGAA-GCTATCCGGTACGCATAGTAG
1 CCTGCACATAGTACTACACATGTGA-C-AATACTATCCGGTACACGTAGTAG
* * * * **
29815238 CCTGCACATAGTATTACACATGCGAC-CTACCATTTTGGTACACGTAGTAG
1 CCTGCACATAGTACTACACATGTGACAATACTA-TCCGGTACACGTAGTAG
29815288 CCTGCACATAGTACTACACA
1 CCTGCACATAGTACTACACA
29815308 CATGACCATC
Statistics
Matches: 101, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.02
50 33 0.33
51 63 0.62
52 1 0.01
53 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CCTGCACATAGTACTACACATGTGACAATACTATCCGGTACACGTAGTAG
Found at i:29816087 original size:196 final size:195
Alignment explanation
Indices: 29815753--29816136 Score: 750
Period size: 196 Copynumber: 2.0 Consensus size: 195
29815743 CTTGTTTTCA
29815753 CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
1 CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
29815818 AAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
66 AAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
29815883 AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAACATTGGAATCACTTACCCGGAC
131 AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAACATT-GAATCACTTACCCGGAC
29815948 T
195 T
29815949 CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
1 CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
29816014 AAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
66 AAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
*
29816079 AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAATATTGAATCACTTAC
131 AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAACATTGAATCACTTAC
29816137 TATGGAGCTT
Statistics
Matches: 187, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
195 11 0.06
196 176 0.94
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.30
Consensus pattern (195 bp):
CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
AAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAACATTGAATCACTTACCCGGACT
Found at i:29819898 original size:90 final size:90
Alignment explanation
Indices: 29819745--29819922 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
29819735 AATTTGATAT
* * * *
29819745 TTTATTATGTTTTTTGGATTATTGGGGTAAAAAGGTCAAGAAATGATGAATGGTACAATATTTTT
1 TTTATTATATTTTTTGGATTATTGGGGTAAAAAGGTCAAAAAACGATGAATGGTACAACATTTTT
29819810 ACCTAAATAATATAAAAAATAATGC
66 ACCTAAATAATATAAAAAATAATGC
*
29819835 TTTATTATATTTTTTGGATTATTGGGGTAAAAAGGTCAAAAAACGATGTATGGTACAACATTTTT
1 TTTATTATATTTTTTGGATTATTGGGGTAAAAAGGTCAAAAAACGATGAATGGTACAACATTTTT
*
29819900 ACCTAAATAATATAAAAATTAAT
66 ACCTAAATAATATAAAAAATAAT
29819923 TAAATACAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (90 bp):
TTTATTATATTTTTTGGATTATTGGGGTAAAAAGGTCAAAAAACGATGAATGGTACAACATTTTT
ACCTAAATAATATAAAAAATAATGC
Found at i:29822197 original size:30 final size:31
Alignment explanation
Indices: 29822158--29822217 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
29822148 TTAATTTAGA
*
29822158 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
29822189 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
29822218 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:29822542 original size:9 final size:9
Alignment explanation
Indices: 29822525--29822555 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29822515 TCGAGTTGAT
29822525 TCGAATAAC
1 TCGAATAAC
*
29822534 TCGATTAAC
1 TCGAATAAC
29822543 TCGAATAAC
1 TCGAATAAC
29822552 TCGA
1 TCGA
29822556 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:29835763 original size:26 final size:26
Alignment explanation
Indices: 29835734--29835787 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
29835724 TAATTAGTAT
*
29835734 AAAATATT-AATAATTCAAT-AAATTG
1 AAAA-ATTAAATAATTAAATAAAATTG
*
29835759 AAAAATTAAATACTTAAATAAAATTG
1 AAAAATTAAATAATTAAATAAAATTG
29835785 AAA
1 AAA
29835788 TTTAGGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAAAATTG
Found at i:29836481 original size:19 final size:19
Alignment explanation
Indices: 29836457--29836517 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
29836447 CTATTAATTT
29836457 ATTAAAATAAAAACTATTA
1 ATTAAAATAAAAACTATTA
* *
29836476 ATTAAAAT----A-TGTTT
1 ATTAAAATAAAAACTATTA
*
29836490 ATTAAAATAAAAACGATTA
1 ATTAAAATAAAAACTATTA
29836509 ATTAAAATA
1 ATTAAAATA
29836518 TGATCAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 11 0.34
15 1 0.03
18 1 0.03
19 19 0.59
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (19 bp):
ATTAAAATAAAAACTATTA
Found at i:29836491 original size:33 final size:33
Alignment explanation
Indices: 29836454--29836519 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
29836444 TTGCTATTAA
*
29836454 TTTATTAAAATAAAAACTATTAATTAAAATATG
1 TTTATTAAAATAAAAACGATTAATTAAAATATG
29836487 TTTATTAAAATAAAAACGATTAATTAAAATATG
1 TTTATTAAAATAAAAACGATTAATTAAAATATG
29836520 ATCAAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (33 bp):
TTTATTAAAATAAAAACGATTAATTAAAATATG
Found at i:29836585 original size:16 final size:15
Alignment explanation
Indices: 29836560--29836593 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
29836550 AAACTTGATA
*
29836560 ATAATTAATATATATT
1 ATAATAAATATA-ATT
29836576 ATAATAAATATAATT
1 ATAATAAATATAATT
29836591 ATA
1 ATA
29836594 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:29857518 original size:11 final size:11
Alignment explanation
Indices: 29857502--29857531 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29857492 ATTAGATCTC
*
29857502 TACTTCTTTTA
1 TACTTCTTCTA
29857513 TACTTCTTCTA
1 TACTTCTTCTA
29857524 TACTTCTT
1 TACTTCTT
29857532 ATGCCTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (11 bp):
TACTTCTTCTA
Found at i:29858491 original size:18 final size:18
Alignment explanation
Indices: 29858452--29858504 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
29858442 TCTAAAAATT
* *
29858452 AAATTTAAAATTATTA-AT
1 AAATTTAAAAATA-TACAA
29858470 AAATTTAAAAATATACAA
1 AAATTTAAAAATATACAA
29858488 AAATTATAAAAATATAC
1 AAATT-TAAAAATATAC
29858505 TCCCCCTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 2 0.06
18 18 0.58
19 11 0.35
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTTAAAAATATACAA
Found at i:29870025 original size:55 final size:55
Alignment explanation
Indices: 29869941--29870050 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
29869931 AAATAGGCTC
*
29869941 TGTCAACACATGTTATAGATACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
1 TGTCAACACATGTTATAGACACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
29869996 TGTCAACACATGTTATAGACACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
1 TGTCAACACATGTTATAGACACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
29870051 AGGCTTTAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.46
Consensus pattern (55 bp):
TGTCAACACATGTTATAGACACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
Found at i:29882369 original size:13 final size:13
Alignment explanation
Indices: 29882351--29882375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29882341 AGTTTGGTAC
29882351 GTTATTGTTGCTT
1 GTTATTGTTGCTT
29882364 GTTATTGTTGCT
1 GTTATTGTTGCT
29882376 GGTTTATTGA
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:0.08, G:0.24, T:0.60
Consensus pattern (13 bp):
GTTATTGTTGCTT
Found at i:29892728 original size:69 final size:69
Alignment explanation
Indices: 29892617--29892745 Score: 204
Period size: 69 Copynumber: 1.9 Consensus size: 69
29892607 TGTAGTAAAA
* * ** * *
29892617 TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGGAAACTAATACCAAAGTTTAAGTGTG
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGCAGGAAACTAAAAACAAAGTTTAAGTGTG
29892682 AAAC
66 AAAC
29892686 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGCAGGAAACTAAAAACAAAGTTTAA
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGCAGGAAACTAAAAACAAAGTTTAA
29892746 CTGGGAGAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (69 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAGCAGGAAACTAAAAACAAAGTTTAAGTGTG
AAAC
Found at i:29895516 original size:8 final size:8
Alignment explanation
Indices: 29895503--29895530 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
29895493 CTTCCTTCAC
29895503 AAAAAAGA
1 AAAAAAGA
29895511 AAAAAAGA
1 AAAAAAGA
29895519 AAAAAAGA
1 AAAAAAGA
29895527 AAAA
1 AAAA
29895531 CTTATACAGC
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:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:29898587 original size:14 final size:14
Alignment explanation
Indices: 29898565--29898595 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29898555 TTTTTAGTAA
29898565 AATAAGTAAAATAT
1 AATAAGTAAAATAT
*
29898579 AATAGGTAAAATAT
1 AATAAGTAAAATAT
29898593 AAT
1 AAT
29898596 TTAATTCTTA
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:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (14 bp):
AATAAGTAAAATAT
Found at i:29903789 original size:675 final size:675
Alignment explanation
Indices: 29902879--29904231 Score: 2706
Period size: 675 Copynumber: 2.0 Consensus size: 675
29902869 CTTATACGAG
29902879 TTTTGTGATATCCATGTAAAATAGAATCTTTATTTAATTACAACAAAAGAAGAATCCTAAGTTTT
1 TTTTGTGATATCCATGTAAAATAGAATCTTTATTTAATTACAACAAAAGAAGAATCCTAAGTTTT
29902944 TTTTTTCTAGTCTTAACTGCATTTGCGTGCACCTTCACTTTTACTATCGATTCTTTTTTATTTTT
66 TTTTTTCTAGTCTTAACTGCATTTGCGTGCACCTTCACTTTTACTATCGATTCTTTTTTATTTTT
29903009 TTCGTTTACGAAATTTAACTATTATACACTTATAATAATATTTAGATATTATACTTATTTTTTCA
131 TTCGTTTACGAAATTTAACTATTATACACTTATAATAATATTTAGATATTATACTTATTTTTTCA
29903074 GCTTAAAGAAAATAAAAGTATATTTAATTTAAAATTTTTAATTATATTTATATTTCATTAATAAA
196 GCTTAAAGAAAATAAAAGTATATTTAATTTAAAATTTTTAATTATATTTATATTTCATTAATAAA
29903139 TTGAATAAAACTATTAAAACAACAACATAAAAATTTAAAAATTATTTAAACAAGTTTGGTAGATT
261 TTGAATAAAACTATTAAAACAACAACATAAAAATTTAAAAATTATTTAAACAAGTTTGGTAGATT
29903204 ACATTATCTTGATGCCAATATAATGCTTACATTCGCAAAGAATTAATTAATAATGTGTTACAAAG
326 ACATTATCTTGATGCCAATATAATGCTTACATTCGCAAAGAATTAATTAATAATGTGTTACAAAG
29903269 TTAAGTAATTGGTTTATAAATTTGTGATGCTTCATATTCATAGTAGAATATTTAATTAGAAAATT
391 TTAAGTAATTGGTTTATAAATTTGTGATGCTTCATATTCATAGTAGAATATTTAATTAGAAAATT
29903334 TAATAATTAATTGAATTGATATCTTTAATTCTATTTATTAAATATTATTTTTATTTAAAAATATG
456 TAATAATTAATTGAATTGATATCTTTAATTCTATTTATTAAATATTATTTTTATTTAAAAATATG
29903399 ATTAATATTTTTTATGTGAAATTTGAATATTTTATCAAAATAACATCTTAACTAAGATATTTTTA
521 ATTAATATTTTTTATGTGAAATTTGAATATTTTATCAAAATAACATCTTAACTAAGATATTTTTA
29903464 TTTAACAAAATATAGTTAATAAATTTACTTATATGAAATTGCTATAATTTTATTTAAAATACGAG
586 TTTAACAAAATATAGTTAATAAATTTACTTATATGAAATTGCTATAATTTTATTTAAAATACGAG
29903529 ACAACAAAATGTTATAGAAAATTAA
651 ACAACAAAATGTTATAGAAAATTAA
29903554 TTTTGTGATATCCATGTAAAATAGAATCTTTATTTAATTACAACAAAAGAAGAATCCTAAGTTTT
1 TTTTGTGATATCCATGTAAAATAGAATCTTTATTTAATTACAACAAAAGAAGAATCCTAAGTTTT
29903619 TTTTTTCTAGTCTTAACTGCATTTGCGTGCACCTTCACTTTTACTATCGATTCTTTTTTATTTTT
66 TTTTTTCTAGTCTTAACTGCATTTGCGTGCACCTTCACTTTTACTATCGATTCTTTTTTATTTTT
29903684 TTCGTTTACGAAATTTAACTATTATACACTTATAATAATATTTAGATATTATACTTATTTTTTCA
131 TTCGTTTACGAAATTTAACTATTATACACTTATAATAATATTTAGATATTATACTTATTTTTTCA
29903749 GCTTAAAGAAAATAAAAGTATATTTAATTTAAAATTTTTAATTATATTTATATTTCATTAATAAA
196 GCTTAAAGAAAATAAAAGTATATTTAATTTAAAATTTTTAATTATATTTATATTTCATTAATAAA
29903814 TTGAATAAAACTATTAAAACAACAACATAAAAATTTAAAAATTATTTAAACAAGTTTGGTAGATT
261 TTGAATAAAACTATTAAAACAACAACATAAAAATTTAAAAATTATTTAAACAAGTTTGGTAGATT
29903879 ACATTATCTTGATGCCAATATAATGCTTACATTCGCAAAGAATTAATTAATAATGTGTTACAAAG
326 ACATTATCTTGATGCCAATATAATGCTTACATTCGCAAAGAATTAATTAATAATGTGTTACAAAG
29903944 TTAAGTAATTGGTTTATAAATTTGTGATGCTTCATATTCATAGTAGAATATTTAATTAGAAAATT
391 TTAAGTAATTGGTTTATAAATTTGTGATGCTTCATATTCATAGTAGAATATTTAATTAGAAAATT
29904009 TAATAATTAATTGAATTGATATCTTTAATTCTATTTATTAAATATTATTTTTATTTAAAAATATG
456 TAATAATTAATTGAATTGATATCTTTAATTCTATTTATTAAATATTATTTTTATTTAAAAATATG
29904074 ATTAATATTTTTTATGTGAAATTTGAATATTTTATCAAAATAACATCTTAACTAAGATATTTTTA
521 ATTAATATTTTTTATGTGAAATTTGAATATTTTATCAAAATAACATCTTAACTAAGATATTTTTA
29904139 TTTAACAAAATATAGTTAATAAATTTACTTATATGAAATTGCTATAATTTTATTTAAAATACGAG
586 TTTAACAAAATATAGTTAATAAATTTACTTATATGAAATTGCTATAATTTTATTTAAAATACGAG
29904204 ACAACAAAATGTTATAGAAAATTAA
651 ACAACAAAATGTTATAGAAAATTAA
29904229 TTT
1 TTT
29904232 AATAAAAATG
Statistics
Matches: 678, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
675 678 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (675 bp):
TTTTGTGATATCCATGTAAAATAGAATCTTTATTTAATTACAACAAAAGAAGAATCCTAAGTTTT
TTTTTTCTAGTCTTAACTGCATTTGCGTGCACCTTCACTTTTACTATCGATTCTTTTTTATTTTT
TTCGTTTACGAAATTTAACTATTATACACTTATAATAATATTTAGATATTATACTTATTTTTTCA
GCTTAAAGAAAATAAAAGTATATTTAATTTAAAATTTTTAATTATATTTATATTTCATTAATAAA
TTGAATAAAACTATTAAAACAACAACATAAAAATTTAAAAATTATTTAAACAAGTTTGGTAGATT
ACATTATCTTGATGCCAATATAATGCTTACATTCGCAAAGAATTAATTAATAATGTGTTACAAAG
TTAAGTAATTGGTTTATAAATTTGTGATGCTTCATATTCATAGTAGAATATTTAATTAGAAAATT
TAATAATTAATTGAATTGATATCTTTAATTCTATTTATTAAATATTATTTTTATTTAAAAATATG
ATTAATATTTTTTATGTGAAATTTGAATATTTTATCAAAATAACATCTTAACTAAGATATTTTTA
TTTAACAAAATATAGTTAATAAATTTACTTATATGAAATTGCTATAATTTTATTTAAAATACGAG
ACAACAAAATGTTATAGAAAATTAA
Found at i:29909005 original size:50 final size:49
Alignment explanation
Indices: 29908928--29909089 Score: 171
Period size: 50 Copynumber: 3.2 Consensus size: 49
29908918 TGTGATGTCA
* * *
29908928 GGGAAGCAAGATTCGCCGCTGTGGCTTTAATCTGTTCCACCGCACTATCT
1 GGGAAGTAAGATTCGCCGATGTGGCTTTAATCTGTTCCACTGCA-TATCT
* * * * ** *
29908978 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATATCA
1 GGGAAGTAAGATTCGCCGATGTGGCTTTAATCTGTTCCACTGC-ATATCT
* * * *
29909028 GGGAAATAAGATTCACCGATGTGGTTTTAATCTGTTCCACTGCATCACCT
1 GGGAAGTAAGATTCGCCGATGTGGCTTTAATCTGTTCCACTGCAT-ATCT
29909078 GGGAAGTAAGAT
1 GGGAAGTAAGAT
29909090 CTAAAATTCT
Statistics
Matches: 89, Mismatches: 21, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 86 0.97
51 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (49 bp):
GGGAAGTAAGATTCGCCGATGTGGCTTTAATCTGTTCCACTGCATATCT
Found at i:29909371 original size:44 final size:43
Alignment explanation
Indices: 29909280--29909401 Score: 127
Period size: 44 Copynumber: 2.8 Consensus size: 43
29909270 NNCTGATGCG
* ** * * *
29909280 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTACTCCACTACAACTTCAGGGAGATAAGAT-TATTAATTCA
* *
29909324 ATCTGCTCCACTACAACTTCAGGGAGATAGGATTATTGAATTCA
1 ATCTACTCCACTACAACTTCAGGGAGATAAGATTATT-AATTCA
* * *
29909368 ATCTACTCCACTGCAACCTCAGGGATATAAGATT
1 ATCTACTCCACTACAACTTCAGGGAGATAAGATT
29909402 TGCTTCTTCA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 4 0.06
44 60 0.94
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (43 bp):
ATCTACTCCACTACAACTTCAGGGAGATAAGATTATTAATTCA
Found at i:29909683 original size:84 final size:84
Alignment explanation
Indices: 29909427--29909743 Score: 248
Period size: 84 Copynumber: 3.7 Consensus size: 84
29909417 CCCCACTGTG
* * ** * *
29909427 ACTTTAGGGGGATAAGACTTGT-TGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGA
1 ACTTCAGGGAGATAAGACCCGTATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTG-
*
29909491 TTTTAATCCACTCCACTGCA
65 TTTTAATCCGCTCCACTGCA
* * * *** * * *
29909511 ATTTTAGGGAGATAGGATTGGTTTTTTTTTCG-TCTGCTTCACTACTGCTTAGGGAGATAAGA-C
1 ACTTCAGGGAGATAAGACCCG-----TATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC
* * * *
29909574 TTGTTTTCTTAGTCTGCTCCGCTGCA
61 TT-TGTT-TTAATCCGCTCCACTGCA
29909600 ACTTCAGGGAGATAAGACCCG-ATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTG
1 ACTTCAGGGAGATAAGACCCGTATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-TTG
*
29909664 TTTTAATCCGCTTCACTGCA
65 TTTTAATCCGCTCCACTGCA
* ** * * *
29909684 ACTTCAGGGAGATAAAATTTACTTCTTCTG-TCTGCTCCACTACTGCTTAGGGAGATAAGA
1 ACTTCAGGGAGATAAGA--CCCGTATGC-GATCTGCTCCACTACTGCTTAGGGAGATAAGA
29909744 CTTGATGCGA
Statistics
Matches: 184, Mismatches: 34, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
83 3 0.02
84 75 0.41
85 5 0.03
86 2 0.01
87 32 0.17
88 5 0.03
89 59 0.32
90 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (84 bp):
ACTTCAGGGAGATAAGACCCGTATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTGT
TTTAATCCGCTCCACTGCA
Found at i:29909741 original size:43 final size:43
Alignment explanation
Indices: 29909626--29909781 Score: 122
Period size: 40 Copynumber: 3.7 Consensus size: 43
29909616 ACCCGATGCG
* * *
29909626 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAAATCTATTCTTCTA
* * * ** *
29909669 ATCCGCTTCACTGCAACTTCAGGGAGATAAAATTTACTTCTTCT-
1 ATCTGCTCCACTACTGCTT-AGGGAGATAAAATCTA-TTCTTCTA
* * ** * *
29909713 GTCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGC-G
1 ATCTGCTCCACTACTGCTTAGGGAGATAAAATCTATTCTTCTA
*
29909753 ATCTGCTCTACTACTGCTTAGGGAGATAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAA
29909782 GATTTGTTGT
Statistics
Matches: 88, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
40 30 0.34
42 1 0.01
43 25 0.28
44 27 0.31
45 5 0.06
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (43 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAAATCTATTCTTCTA
Found at i:29909872 original size:127 final size:127
Alignment explanation
Indices: 29909605--29909874 Score: 416
Period size: 127 Copynumber: 2.1 Consensus size: 127
29909595 CTGCAACTTC
**
29909605 AGGGAGATAAGACCCGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAA
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAA
*
29909670 TCCGCTTCACTGCAACTTCAGGGAGATAAAATTTACTTCTTCTGTCTGCTCCACTACTGCTT
66 TCCGCTTCACTGCAACTTCAGGGAGATAAAATTGACTTCTTCTGTCTGCTCCACTACTGCTT
* * *
29909732 AGGGAGATAAGACTTGATGCGATCTGCTCTACTACTGCTTAGGGAGATAAGATTTGTTGTTTTAA
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAA
* * *** *
29909797 TCCGC-TCTATTGCAACTTTAGGGAGATTGGATTGATTTCTTCTGTCTGCTCCACTACTGCTT
66 TCCGCTTC-ACTGCAACTTCAGGGAGATAAAATTGACTTCTTCTGTCTGCTCCACTACTGCTT
29909859 AGGGAGATAAGACTTG
1 AGGGAGATAAGACTTG
29909875 TAATTTCCAA
Statistics
Matches: 130, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
126 2 0.02
127 128 0.98
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (127 bp):
AGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAA
TCCGCTTCACTGCAACTTCAGGGAGATAAAATTGACTTCTTCTGTCTGCTCCACTACTGCTT
Found at i:29911302 original size:21 final size:21
Alignment explanation
Indices: 29911278--29911318 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29911268 TTAGCCTCTC
29911278 CATTTTAC-TCTTTCATTTTTT
1 CATTTTACAT-TTTCATTTTTT
*
29911299 CATTTTTCATTTTCATTTTT
1 CATTTTACATTTTCATTTTT
29911319 CATCTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (21 bp):
CATTTTACATTTTCATTTTTT
Found at i:29911306 original size:7 final size:7
Alignment explanation
Indices: 29911288--29911321 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
29911278 CATTTTACTC
29911288 TTTCATTT
1 TTTCA-TT
29911296 TTTCATT
1 TTTCATT
29911303 TTTCA-T
1 TTTCATT
29911309 TTTCATT
1 TTTCATT
29911316 TTTCAT
1 TTTCAT
29911322 CTATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 14 0.56
8 5 0.20
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTCATT
Found at i:29911311 original size:13 final size:13
Alignment explanation
Indices: 29911295--29911321 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29911285 CTCTTTCATT
29911295 TTTTCATTTTTCA
1 TTTTCATTTTTCA
29911308 TTTTCATTTTTCA
1 TTTTCATTTTTCA
29911321 T
1 T
29911322 CTATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:29911766 original size:26 final size:25
Alignment explanation
Indices: 29911703--29911779 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 25
29911693 TCTTTTCATA
**
29911703 TTTGTTTTGACTTTGATTGATTTCTTTT
1 TTTGTTTTGACTTTGATT--TTT-TCCT
29911731 TTTGCTTTTGACTTTGATTTTTTCCT
1 TTTG-TTTTGACTTTGATTTTTTCCT
*
29911757 TTTGATTTTGATTTTGATTTTTT
1 TTTG-TTTTGACTTTGATTTTTT
29911780 TTTTGAATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 23 0.52
27 3 0.07
28 4 0.09
29 14 0.32
ACGTcount: A:0.10, C:0.08, G:0.13, T:0.69
Consensus pattern (25 bp):
TTTGTTTTGACTTTGATTTTTTCCT
Found at i:29911779 original size:20 final size:20
Alignment explanation
Indices: 29911728--29911771 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29911718 ATTGATTTCT
*
29911728 TTTTTTGCTTTTGACTTTGA
1 TTTTTTCCTTTTGACTTTGA
*
29911748 TTTTTTCCTTTTGATTTTGA
1 TTTTTTCCTTTTGACTTTGA
29911768 TTTT
1 TTTT
29911772 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.09, G:0.11, T:0.70
Consensus pattern (20 bp):
TTTTTTCCTTTTGACTTTGA
Found at i:29915692 original size:17 final size:18
Alignment explanation
Indices: 29915670--29915711 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
29915660 CTAATGAACA
29915670 CAAATAATCAAT-CAATG
1 CAAATAATCAATACAATG
*
29915687 CAAATAATTAATACAATG
1 CAAATAATCAATACAATG
*
29915705 CACATAA
1 CAAATAA
29915712 GAGCAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.24
Consensus pattern (18 bp):
CAAATAATCAATACAATG
Found at i:29915978 original size:143 final size:143
Alignment explanation
Indices: 29915678--29915963 Score: 509
Period size: 143 Copynumber: 2.0 Consensus size: 143
29915668 CACAAATAAT
*
29915678 CAATCAATGCAAATAATTAATACAATGCACATAAGAGCAATAATCTCACATCATATATTATGTTG
1 CAATCAATACAAATAATTAATACAATGCACATAAGAGCAATAATCTCACATCATATATTATGTTG
* *
29915743 ACATTCCAAGGCTAGTGAATTAAAGGTCAATCATAGCACCAAACAAATTAACACATATGAAATTG
66 ACATTCAAAGGCTAATGAATTAAAGGTCAATCATAGCACCAAACAAATTAACACATATGAAATTG
29915808 TATGAACCTTAAA
131 TATGAACCTTAAA
*
29915821 CAATCAATACAAATAATTAATACAATGCACATAAGAGCAATAATCTGACATCATATATTATGTTG
1 CAATCAATACAAATAATTAATACAATGCACATAAGAGCAATAATCTCACATCATATATTATGTTG
* *
29915886 ACATTCAAAGGCTAATGAGTTAAAGGTCAATCATAGCACCAAACAAATTAACACTTATGAAATTG
66 ACATTCAAAGGCTAATGAATTAAAGGTCAATCATAGCACCAAACAAATTAACACATATGAAATTG
*
29915951 TATGAATCTTAAA
131 TATGAACCTTAAA
29915964 ATAACTTAAG
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
143 136 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (143 bp):
CAATCAATACAAATAATTAATACAATGCACATAAGAGCAATAATCTCACATCATATATTATGTTG
ACATTCAAAGGCTAATGAATTAAAGGTCAATCATAGCACCAAACAAATTAACACATATGAAATTG
TATGAACCTTAAA
Found at i:29916426 original size:2 final size:2
Alignment explanation
Indices: 29916380--29916408 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29916370 AACGTATACG
29916380 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 T
29916409 TAGAATCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29917962 original size:82 final size:82
Alignment explanation
Indices: 29917825--29917978 Score: 299
Period size: 82 Copynumber: 1.9 Consensus size: 82
29917815 AGGAAAAATC
*
29917825 AAATTGAAGTGGAGTGAGAGGGGTGATGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
1 AAATTGAAGTGGAGTGAGAGGGGTGAGGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
29917890 TCAAGATTATAAAATTT
66 TCAAGATTATAAAATTT
29917907 AAATTGAAGTGGAGTGAGAGGGGTGAGGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
1 AAATTGAAGTGGAGTGAGAGGGGTGAGGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
29917972 TCAAGAT
66 TCAAGAT
29917979 GATACATTCA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.29, C:0.06, G:0.34, T:0.30
Consensus pattern (82 bp):
AAATTGAAGTGGAGTGAGAGGGGTGAGGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
TCAAGATTATAAAATTT
Found at i:29919623 original size:22 final size:22
Alignment explanation
Indices: 29919597--29919640 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29919587 AGAATGCCTG
*
29919597 ATATTGATGTAGCCCTGAACAT
1 ATATTGATGCAGCCCTGAACAT
*
29919619 ATATTGATGCAGTCCTGAACAT
1 ATATTGATGCAGCCCTGAACAT
29919641 TGTACAGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (22 bp):
ATATTGATGCAGCCCTGAACAT
Found at i:29925372 original size:42 final size:43
Alignment explanation
Indices: 29925280--29925424 Score: 136
Period size: 42 Copynumber: 3.4 Consensus size: 43
29925270 AGTCTTGTAT
* * * * * **
29925280 ATCACATA-CAATGCC-ATATCCCGAATATGGTCTTACATGTT
1 ATCACATATCGATGCCAATAGCCCAAACATGGTCTTACACGAA
* **
29925321 ATCACATATCGATGCCAATAGCCC-AGCAATTTTCTTACACG-A
1 ATCACATATCGATGCCAATAGCCCAAAC-ATGGTCTTACACGAA
* *
29925363 ATCATATATCGATGCCAATATCCCAAACATGGTCTTACACGAA
1 ATCACATATCGATGCCAATAGCCCAAACATGGTCTTACACGAA
*
29925406 ATCACATAACGATGCCAAT
1 ATCACATATCGATGCCAAT
29925425 GTCCCAGACA
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
41 8 0.10
42 40 0.48
43 36 0.43
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (43 bp):
ATCACATATCGATGCCAATAGCCCAAACATGGTCTTACACGAA
Found at i:29925423 original size:43 final size:42
Alignment explanation
Indices: 29925280--29925435 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 42
29925270 AGTCTTGTAT
* * * * *
29925280 ATCACAT-ACAATGCC-ATATCCCGAATATGGTCTTACATGTT
1 ATCACATAACGATGCCAATATCCCAAACATGGTCTTACACG-A
* * * **
29925321 ATCACATATCGATGCCAATAGCCC-AGCAATTTTCTTACACGA
1 ATCACATAACGATGCCAATATCCCAAAC-ATGGTCTTACACGA
* *
29925363 ATCATATATCGATGCCAATATCCCAAACATGGTCTTACACGAA
1 ATCACATAACGATGCCAATATCCCAAACATGGTCTTACACG-A
* *
29925406 ATCACATAACGATGCCAATGTCCCAGACAT
1 ATCACATAACGATGCCAATATCCCAAACAT
29925436 ATATCCCAGA
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 7 0.08
42 40 0.43
43 45 0.49
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (42 bp):
ATCACATAACGATGCCAATATCCCAAACATGGTCTTACACGA
Found at i:29930374 original size:6 final size:6
Alignment explanation
Indices: 29930363--29930414 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
29930353 ACGAAGGAAT
* * *
29930363 AAGATG AAGATG AAGATG AAGGTG AAGGTG AATG-TG GAGATG AAGATG
1 AAGATG AAGATG AAGATG AAGATG AAGATG AA-GATG AAGATG AAGATG
29930411 AAGA
1 AAGA
29930415 AGATGGGGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
5 1 0.02
6 39 0.95
7 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.17
Consensus pattern (6 bp):
AAGATG
Found at i:29931962 original size:12 final size:12
Alignment explanation
Indices: 29931947--29931990 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
29931937 CCCCCAGCTC
*
29931947 CTCCCGCTGGTT
1 CTCCCGCTGGCT
29931959 CTCCCGCTGGCT
1 CTCCCGCTGGCT
*
29931971 CTCCCTCTGGCT
1 CTCCCGCTGGCT
*
29931983 CCCCCGCT
1 CTCCCGCT
29931991 AGCGCTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.00, C:0.52, G:0.20, T:0.27
Consensus pattern (12 bp):
CTCCCGCTGGCT
Found at i:29942487 original size:25 final size:25
Alignment explanation
Indices: 29942459--29942506 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29942449 CTGTCTTTGA
*
29942459 TAGTATATCCTGAAACTACTATATG
1 TAGTATATACTGAAACTACTATATG
* *
29942484 TAGTATATATTGAGACTACTATA
1 TAGTATATACTGAAACTACTATA
29942507 GATAGATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATATG
Found at i:29946955 original size:22 final size:22
Alignment explanation
Indices: 29946930--29946983 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
29946920 AAAGAGTCAT
* *
29946930 TTTTCACTCCATCTTTCTAATG
1 TTTTCTCTCCATCTTTCTAACG
* *
29946952 TTTTCTCTCTATCTTTCTGACG
1 TTTTCTCTCCATCTTTCTAACG
29946974 TTTTCTCTCC
1 TTTTCTCTCC
29946984 CCCATCTCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.11, C:0.30, G:0.06, T:0.54
Consensus pattern (22 bp):
TTTTCTCTCCATCTTTCTAACG
Found at i:29954462 original size:75 final size:75
Alignment explanation
Indices: 29954339--29954488 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
29954329 AAAAAATGAG
29954339 AAAAAGTGAGAAATTTCCCGATTGAACATTCAGAATAAAAAGGGATACGAATGAAGTGACAGAAA
1 AAAAAGTGAGAAATTTCCCGATTGAACATTCAGAATAAAAAGGGATACGAATGAAGTGACAGAAA
29954404 TGATCACATA
66 TGATCACATA
*
29954414 AAAAAGTGAGAAATTTCCCGATTGAACATTCAGAATAAAAAGGGATACGAATGAAGTGATAGAAA
1 AAAAAGTGAGAAATTTCCCGATTGAACATTCAGAATAAAAAGGGATACGAATGAAGTGACAGAAA
29954479 TGATCACATA
66 TGATCACATA
29954489 TGTGGCATGG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.21
Consensus pattern (75 bp):
AAAAAGTGAGAAATTTCCCGATTGAACATTCAGAATAAAAAGGGATACGAATGAAGTGACAGAAA
TGATCACATA
Found at i:29954655 original size:101 final size:102
Alignment explanation
Indices: 29954537--29954721 Score: 286
Period size: 101 Copynumber: 1.8 Consensus size: 102
29954527 AAAGTGATGG
* *
29954537 TCACGTGTGTAGAACTATGTGTAGGCTACTACGTGT-TCCAGA-A-TGATAGGTCGCATGTGTAG
1 TCACGTGTGTAGAACTATGTGCAGGCTACTACGTGTAT-CAGATAGTGAT-GGTCACATGTGTAG
29954599 TACTATGTGCAGGCTACTATGCGTATCGGATATCTTCGA
64 TACTATGTGCAGGCTACTATGCGTATCGGATATCTTCGA
* *
29954638 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGAACTATGTGCAGGCTACTACGTGTATCAGATAGTGATGGTCACATGTGTAGTA
*
29954703 CTATGTGCATGCTACTATG
66 CTATGTGCAGGCTACTATG
29954722 TGAATCCGCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
101 37 0.49
102 35 0.46
103 4 0.05
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGAACTATGTGCAGGCTACTACGTGTATCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTATCGGATATCTTCGA
Found at i:29954657 original size:51 final size:51
Alignment explanation
Indices: 29954590--29954721 Score: 185
Period size: 51 Copynumber: 2.6 Consensus size: 51
29954580 TGATAGGTCG
*
29954590 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATA-TCTTCGATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTCAT-GATCA
* * * * *
29954641 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTCATGATCA
*
29954692 CATGTGTAGTACTATGTGCATGCTACTATG
1 CATGTGTAGTACTATGTGCAGGCTACTATG
29954722 TGAATCCGCA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 69 0.97
52 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (51 bp):
CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTCATGATCA
Found at i:29954723 original size:26 final size:26
Alignment explanation
Indices: 29954643--29954723 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
29954633 TTCGATCACG
*
29954643 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
29954669 CGTGTA-T-CGGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCATGCT-ACTA
29954694 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
29954720 TGTG
1 TGTG
29954724 AATCCGCATC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:29954846 original size:41 final size:42
Alignment explanation
Indices: 29954732--29954859 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 42
29954722 TGAATCCGCA
* * * *
29954732 TCATTGAATATAAAGGTGGTTGCTAAGTGCTGACTCCACCATA
1 TCATTGATTAT-AAGGTGGTTGCTAAGTGCTGATTCCACCGTG
* *
29954775 TCCTTGACTGTGA-AAGG-GGTTGCTATGTGCTGATTCC-CCGTG
1 TCATTGA-T-T-ATAAGGTGGTTGCTAAGTGCTGATTCCACCGTG
29954817 TCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTG
1 TCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTG
29954859 T
1 T
29954860 AACGGTTAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
39 1 0.01
40 5 0.07
41 20 0.28
42 15 0.21
43 24 0.34
44 4 0.06
45 1 0.01
46 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (42 bp):
TCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTG
Found at i:29958534 original size:18 final size:18
Alignment explanation
Indices: 29958500--29958535 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
29958490 GTAAATTGAC
29958500 ATTTAGAAACTTAAAAAG
1 ATTTAGAAACTTAAAAAG
29958518 ATTTAAGAAACTTAAAAA
1 ATTT-AGAAACTTAAAAA
29958536 TTCAACATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (18 bp):
ATTTAGAAACTTAAAAAG
Found at i:29961536 original size:18 final size:18
Alignment explanation
Indices: 29961513--29961547 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29961503 AGGAATCTTC
29961513 TTTTC-TTTCTTTCTTTCT
1 TTTTCTTTTCTTT-TTTCT
29961531 TTTTCTTTTCTTTTTTC
1 TTTTCTTTTCTTTTTTC
29961548 CCTCACTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTTCT
Found at i:29965212 original size:37 final size:37
Alignment explanation
Indices: 29965170--29965244 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
29965160 TTAACCTCGT
* *
29965170 TAATAAATGGTCGAATTACCATCTAAGTCTACTAACA
1 TAATAAATGGTCCAATTACCATCTAAGTCCACTAACA
*
29965207 TAATAAATGGTCCAATTACCATCTAAGTCCACTCACA
1 TAATAAATGGTCCAATTACCATCTAAGTCCACTAACA
29965244 T
1 T
29965245 TGTAACACCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (37 bp):
TAATAAATGGTCCAATTACCATCTAAGTCCACTAACA
Found at i:29966875 original size:27 final size:27
Alignment explanation
Indices: 29966844--29966997 Score: 181
Period size: 27 Copynumber: 5.7 Consensus size: 27
29966834 CTGCATCAAG
29966844 ACCCCCATAGGGTAAAATGATCGAAAT
1 ACCCCCATAGGGTAAAATGATCGAAAT
* *
29966871 ACCCCTATAGGATAAAATGA-CAGAAAT
1 ACCCCCATAGGGTAAAATGATC-GAAAT
* *
29966898 ACCCTCATAGGGTAAAAT-AACTGAAAT
1 ACCCCCATAGGGTAAAATGATC-GAAAT
29966925 ACCCCCATAGGGTAAAATGAAT-GAAAT
1 ACCCCCATAGGGTAAAATG-ATCGAAAT
* * *
29966952 ACCCCCATAGGGGAAAATTACCGAAAT
1 ACCCCCATAGGGTAAAATGATCGAAAT
*
29966979 ACCCCTA-AGGGTAAAATGA
1 ACCCCCATAGGGTAAAATGA
29966998 CTATTATACC
Statistics
Matches: 108, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
26 13 0.12
27 94 0.87
29 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATGATCGAAAT
Found at i:29966913 original size:54 final size:54
Alignment explanation
Indices: 29966844--29966998 Score: 208
Period size: 54 Copynumber: 2.9 Consensus size: 54
29966834 CTGCATCAAG
* *
29966844 ACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGGATAAAATGACA-GAAAT
1 ACCCCCATAGGGTAAAAT-AACGAAATACCCCTATAGGGTAAAATGACATGAAAT
* *
29966898 ACCCTCATAGGGTAAAATAACTGAAATACCCCCATAGGGTAAAATGA-ATGAAAT
1 ACCCCCATAGGGTAAAATAAC-GAAATACCCCTATAGGGTAAAATGACATGAAAT
* *
29966952 ACCCCCATAGGGGAAAATTACCGAAATACCCCTA-AGGGTAAAATGAC
1 ACCCCCATAGGGTAAAA-TAACGAAATACCCCTATAGGGTAAAATGAC
29966999 TATTATACCC
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
53 15 0.17
54 71 0.80
55 3 0.03
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18
Consensus pattern (54 bp):
ACCCCCATAGGGTAAAATAACGAAATACCCCTATAGGGTAAAATGACATGAAAT
Found at i:29966979 original size:81 final size:80
Alignment explanation
Indices: 29966844--29966995 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 80
29966834 CTGCATCAAG
* *
29966844 ACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGGATAAAATGACAGAAATA-CCCTCATAG
1 ACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGAGAAAATGACAGAAATACCCCT-A-AG
29966908 GGTAAAATAACTGAAAT
64 GGTAAAATAACTGAAAT
* * *
29966925 ACCCCCATAGGGTAAAATGAAT-GAAATACCCCCATAGGGGAAAATTACCGAAATACCCCTAAGG
1 ACCCCCATAGGGTAAAATG-ATCGAAATACCCCCATAGGAGAAAATGACAGAAATACCCCTAAGG
29966989 GTAAAAT
65 GTAAAAT
29966996 GACTATTATA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
80 10 0.16
81 48 0.75
82 6 0.09
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18
Consensus pattern (80 bp):
ACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGAGAAAATGACAGAAATACCCCTAAGGG
TAAAATAACTGAAAT
Found at i:29975891 original size:84 final size:86
Alignment explanation
Indices: 29975735--29975967 Score: 283
Period size: 84 Copynumber: 2.7 Consensus size: 86
29975725 GATTTCCACA
* * * *
29975735 TATAACATAAAACAGCCACAAATGCTTCAACTTATCAGAGAACAACCATAGAGGCTTCCACATAT
1 TATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTCCACATAT
*
29975800 AACATATTTTTCCATTAA-GG-
66 AACATATTTCTCCA-TAAGGGC
* * * * **
29975820 T-TCATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGTACAACTACAGAGGCTTCGGCATAT
1 TATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTCCACATAT
*
29975884 AATATATTTCTCCATAAGGGCTCAC
66 AACATATTTCTCCATAAGGG----C
29975909 ATATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTC
1 -TATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTC
29975968 TATATTTGAG
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
83 3 0.02
84 67 0.54
85 1 0.01
90 1 0.01
91 52 0.42
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (86 bp):
TATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTCCACATAT
AACATATTTCTCCATAAGGGC
Found at i:29979340 original size:11 final size:11
Alignment explanation
Indices: 29979326--29979358 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29979316 AAATTATACC
29979326 AAACCCAATTA
1 AAACCCAATTA
29979337 AAACCCAAATT-
1 AAACCC-AATTA
29979348 AAACCCAATTA
1 AAACCCAATTA
29979359 CACCGGGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.20
11 12 0.60
12 4 0.20
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (11 bp):
AAACCCAATTA
Found at i:29987194 original size:131 final size:131
Alignment explanation
Indices: 29986952--29987896 Score: 1260
Period size: 131 Copynumber: 7.3 Consensus size: 131
29986942 TCGGTGAAAT
* * * **
29986952 CACAAGTCCTATGTCCCTGACCAGCAATGGAATGGGTTGGAAATTGTAGATCTTGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
29987017 CAATAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
29987082 C
131 C
*
29987083 CACACGTCCTATGTCCCTGACCATCAGTGGAATAGGTTGGAAATTGA-AGATCTTGTCTCCCTAA
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATT-ACAGATCTTGTCTCCCTAA
* * * *
29987147 GCAGTAGCGAAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGAGTAGGGAAATAGATTTAA
65 GCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAA
29987212 GC
130 GC
* * * *
29987214 CACACGTCCTATGTCCCTGACCAACAATGGAATAGGTTGGAAATCACAGATCTTTTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * *
29987279 CAGTAGCGGAGTAGATCAAAGACGGTGAATCTTATCTTTCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
29987344 C
131 C
* * *
29987345 CGCACGTCCTATGTCCCTGACCAGCAATGGAATAGGTTTGAAATTACAGATCTTGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
29987410 CAGTAGCGGAGCATATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAAGGAAACATAATTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
29987475 C
131 C
29987476 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * * * * *
29987541 CAATAGCAGAGCAAATCAAAGACGGTGAATCTTATCTTCCCCAGGAGTAAGGAAACATAATTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
29987606 C
131 C
*
29987607 CACACGTCCTATGTCCCTGACTAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
29987672 CAGTAGCGGAGTAGATCAAAGATGACGAATCTTATTTTCCCC------A--G-----GATTTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
29987724 C
131 C
* * * *
29987725 CACACGTCCTCTGTCCCTGACCAGCAGTGGAATTGGTTGGAAATTGCAGATCTCGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * * * * * *
29987790 TAGTAACGGAGCAGATCGAAGACGACGAATCTTATCTT---CAAGTGTA-AGAAAGCAAATTTAA
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAA-CAGATTTAA
29987851 GC
130 GC
* *
29987853 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAAT
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAAT
29987897 CAGATTGAAG
Statistics
Matches: 731, Mismatches: 68, Indels: 33
0.88 0.08 0.04
Matches are distributed among these distances:
115 1 0.00
118 99 0.14
121 1 0.00
122 1 0.00
123 1 0.00
125 1 0.00
128 48 0.07
130 1 0.00
131 578 0.79
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (131 bp):
CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
C
Found at i:29987817 original size:118 final size:118
Alignment explanation
Indices: 29987601--29987896 Score: 358
Period size: 118 Copynumber: 2.4 Consensus size: 118
29987591 GGAAACATAA
* *
29987601 TTAAGCCACACGTCCTATGTCCCTGACTAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTC
1 TTAAGCCACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTCGTCTC
* * *
29987666 CCTAAGCAGTAGCGGAGTAGATCAAAGATGACGAATCTTATTTTCCCCAGGAT
66 CCTAAGCAGTAACGGAGCAGATCAAAGACGACGAATCTTATTTTCCCCAGGAT
* * *
29987719 TTAAGCCACACGTCCTCTGTCCCTGACCAGCAGTGGAATTGGTTGGAAATTGCAGATCTCGTCTC
1 TTAAGCCACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTCGTCTC
* * * ***
29987784 CCTAAGTAGTAACGGAGCAGATCGAAGACGACGAATCTTATCTTCAAGTGTAAGAAAGCAAAT
66 CCTAAGCAGTAACGGAGCAGATCAAAGACGACGAATCTTATTTTC----CCCAG---G---AT
* *
29987847 TTAAGCCACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAAT
1 TTAAGCCACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAAT
29987897 CAGATTGAAG
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
118 99 0.66
122 2 0.01
125 1 0.01
128 48 0.32
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (118 bp):
TTAAGCCACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTCGTCTC
CCTAAGCAGTAACGGAGCAGATCAAAGACGACGAATCTTATTTTCCCCAGGAT
Found at i:29987965 original size:44 final size:44
Alignment explanation
Indices: 29987897--29988132 Score: 172
Period size: 44 Copynumber: 5.1 Consensus size: 44
29987887 GGTTGGAAAT
* *
29987897 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
* *
29987941 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
* ** * *
29987985 CGGATT-AAAATAAAGT-ATCTTATCTCTCTGA-AGTTACAGTAGAGCAGATCGCAT
1 CAGATTGAAGCT--AGTAATCTTATCTCCCTGAGA-TTAC-----AGC-G---G-AG
* *
29988039 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
* * * * * *
29988083 CAGATGGAAGTTAATAACCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
*
29988127 CTGATT
1 CAGATT
29988133 AAAATAAAGG
Statistics
Matches: 148, Mismatches: 28, Indels: 32
0.71 0.13 0.15
Matches are distributed among these distances:
43 4 0.03
44 103 0.70
45 4 0.03
48 1 0.01
49 5 0.03
50 1 0.01
53 3 0.02
54 24 0.16
55 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (44 bp):
CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
Found at i:29988120 original size:98 final size:98
Alignment explanation
Indices: 29987941--29988127 Score: 225
Period size: 98 Copynumber: 1.9 Consensus size: 98
29987931 TACAGCGGAG
* * * * * * *
29987941 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGTATCTT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATGAAAATAAAGTACCCT
*
29988006 ATCTCTCTGAAGTTACAGTAGAGCAGATCGCAT
66 ATCTCCCTGAAGTTACAGTAGAGCAGATCGCAT
* * * *
29988039 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGTTAA-TAACCC
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATGAAAATAAAGT-ACCC
*
29988103 TATCTCCCTG-AGATTACAGTGGAGC
65 TATCTCCCTGAAG-TTACAGTAGAGC
29988128 TGATTAAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
97 3 0.04
98 71 0.96
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (98 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATGAAAATAAAGTACCCT
ATCTCCCTGAAGTTACAGTAGAGCAGATCGCAT
Found at i:29988156 original size:142 final size:142
Alignment explanation
Indices: 29987895--29988183 Score: 497
Period size: 142 Copynumber: 2.0 Consensus size: 142
29987885 TAGGTTGGAA
* * *
29987895 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
1 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGCTAATAACC
* * *
29987960 CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGTATCTTATCTCTCTGAAGTTACAGT
66 CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCACTCTGAAGTTACAAT
29988025 AGAGCAGATCGC
131 AGAGCAGATCGC
*
29988037 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGTTAATAACC
1 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGCTAATAACC
*
29988102 CTATCTCCCTGAGATTACAGTGGAGCTGATTAAAATAAAGGATCTTATCACTCTGAAGTTACAAT
66 CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCACTCTGAAGTTACAAT
*
29988167 AGAGTAGATCGC
131 AGAGCAGATCGC
29988179 ATCAG
1 ATCAG
29988184 GTCTTATCTC
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 138 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (142 bp):
ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGCTAATAACC
CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCACTCTGAAGTTACAAT
AGAGCAGATCGC
Found at i:29996363 original size:17 final size:18
Alignment explanation
Indices: 29996343--29996379 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
29996333 GGATTCACCA
29996343 TTTGGCAAACTCT-AGGT
1 TTTGGCAAACTCTAAGGT
29996360 TTTGGCAAACTCTAAGGT
1 TTTGGCAAACTCTAAGGT
29996378 TT
1 TT
29996380 GACAGACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (18 bp):
TTTGGCAAACTCTAAGGT
Found at i:30002171 original size:50 final size:50
Alignment explanation
Indices: 30002109--30002210 Score: 152
Period size: 50 Copynumber: 2.0 Consensus size: 50
30002099 TTTATCTAGA
* *
30002109 TGAAAAAGTAATTTC-CTCGCCTATCATCAATGAAATCATTTTCATTTGTT
1 TGAAAAAGTAATTTCTC-CACCCATCATCAATGAAATCATTTTCATTTGTT
* *
30002159 TGAAAAAGTAATTTCTCCACCCATTATCAATGGAATCATTTTCATTTGTT
1 TGAAAAAGTAATTTCTCCACCCATCATCAATGAAATCATTTTCATTTGTT
30002209 TG
1 TG
30002211 TGGCAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
50 46 0.98
51 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (50 bp):
TGAAAAAGTAATTTCTCCACCCATCATCAATGAAATCATTTTCATTTGTT
Found at i:30002980 original size:25 final size:25
Alignment explanation
Indices: 30002951--30002999 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
30002941 TGATGCATGT
* * *
30002951 ATATAACCTATTATTATATTATATG
1 ATATAACATATCATTATATAATATG
*
30002976 ATATAATATATCATTATATAATAT
1 ATATAACATATCATTATATAATAT
30003000 AGTGGGAGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (25 bp):
ATATAACATATCATTATATAATATG
Found at i:30003671 original size:16 final size:16
Alignment explanation
Indices: 30003638--30003675 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
30003628 CTCTAATTAT
30003638 TTTATATAAAAATAAA
1 TTTATATAAAAATAAA
*
30003654 TTTAT-TAAATATATAA
1 TTTATATAAAAATA-AA
30003670 TTTATA
1 TTTATA
30003676 CTTTTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTATATAAAAATAAA
Found at i:30004227 original size:15 final size:15
Alignment explanation
Indices: 30004207--30004263 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
30004197 TTTGACAAAC
30004207 TGAAAAATTAAGTGT
1 TGAAAAATTAAGTGT
*
30004222 TGAAAAAATAAGTGT
1 TGAAAAATTAAGTGT
*
30004237 TG-AAAATTAAGTAT
1 TGAAAAATTAAGTGT
*
30004251 TGAAAATTTAAGT
1 TGAAAAATTAAGT
30004264 ACTAAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 12 0.32
15 25 0.68
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (15 bp):
TGAAAAATTAAGTGT
Found at i:30004242 original size:14 final size:14
Alignment explanation
Indices: 30004207--30004256 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
30004197 TTTGACAAAC
30004207 TGAAAAATTAAGTGT
1 TGAAAAA-TAAGTGT
30004222 TGAAAAAATAAGTGT
1 TG-AAAAATAAGTGT
* *
30004237 TGAAAATTAAGTAT
1 TGAAAAATAAGTGT
30004251 TGAAAA
1 TGAAAA
30004257 TTTAAGTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 16 0.50
15 11 0.34
16 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (14 bp):
TGAAAAATAAGTGT
Found at i:30007262 original size:3 final size:3
Alignment explanation
Indices: 30007254--30007290 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
30007244 TTTCGAAAAC
30007254 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
30007291 GTTTTGCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:30013654 original size:626 final size:626
Alignment explanation
Indices: 30012463--30013720 Score: 2176
Period size: 626 Copynumber: 2.0 Consensus size: 626
30012453 CCTTTTAAAT
*
30012463 TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTTATATGTTTAATTTAATTAA
1 TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTAATATGTTTAATTTAATTAA
** ** **
30012528 TATGGCTTAAATGTAATTTGTGTTAGGTTGATTGCATTTTGTCTACTTGAGTTATTAAAATTGTG
66 TATGGCTTAAATGTAATTCCTGTTAGGTCAATTGCATTTCATCTACTTGAGTTATTAAAATTGTG
*
30012593 TTTGTGTTGTTATAGGCCTCGGCAAGATGTTTGATTAAGTAAAACCATGACTAATTTATTCTTGC
131 TTTGTGTTGTTATAGGCCTCGGCAAGATGTTTGATTAAGTAAAACCATGACTAAGTTATTCTTGC
30012658 ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGCTTGAAATTATAATTAATTGACA
196 ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGCTTGAAATTATAATTAATTGACA
* * *
30012723 TGAGATTTAATCAGTGCATGTTTAATCATCTAAGGTAGCTGAGGGTTAAATTAGCAACGGTATCT
261 AGAGATTTAATCAGTCCAAGTTTAATCATCTAAGGTAGCTGAGGGTTAAATTAGCAACGGTATCT
*
30012788 AACGATACATTAGCCTTGTATAACTTGCAAGAGTATTGTGATTAAACTGTTTCAAGGTAGAAATA
326 AACGATACATTAGCCTTGCATAACTTGCAAGAGTATTGTGATTAAACTGTTTCAAGGTAGAAATA
* * *
30012853 CATTGTTACCTTAAGTAATCTTTTATGTGCTTCTGAGATTGAATTAATTGTTTGAATTGGCATAG
391 CATTGTTACCTCAAGTAATCTTTTATGTGCTTATGAGATTGAATTAATTGTTTGAATTGGAATAG
*
30012918 AGACATGTACAAGAGATTATTTTAATTTCATAAGTATGTATGTGCATTAACACATTTATTTATTA
456 AGACATGTACAAGAGATTATTTTAATTTCATAAGTATGTATGTGCATTAACACATTTACTTATTA
*
30012983 AAATTTGTTTAATCTATTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGGT
521 AAATTTGTTTAATCGATTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGGT
*
30013048 AAGTATGTTCATAAGTTAGCAAATTACCGAGTTGCCATGAA
586 AAGTATGTTCATAAGTTAGCAAATTACCGAATTGCCATGAA
30013089 TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTAATATGTTTAATTTAATTAA
1 TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTAATATGTTTAATTTAATTAA
* *
30013154 TATGGCTTAAATTTAATTCCTGTTTGGTCAATTGCATTTCATCTACTTGAGTTATTAAAATTGTG
66 TATGGCTTAAATGTAATTCCTGTTAGGTCAATTGCATTTCATCTACTTGAGTTATTAAAATTGTG
*
30013219 TTTGTGTTGTTATAGGCCTCGGTAAGATGTTTGATTAAGTAAAACCATGACTAAGTTATTCTTGC
131 TTTGTGTTGTTATAGGCCTCGGCAAGATGTTTGATTAAGTAAAACCATGACTAAGTTATTCTTGC
* *
30013284 ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGGTTGAAATTGTAATTAATTGACA
196 ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGCTTGAAATTATAATTAATTGACA
* * ** *
30013349 AGATATTTAATCAGTCCAAGTTTAATCATCTAAGGTAGGTGAGTTTTAAATTAGCAATGGTATCT
261 AGAGATTTAATCAGTCCAAGTTTAATCATCTAAGGTAGCTGAGGGTTAAATTAGCAACGGTATCT
* *
30013414 AACGTTACATTAGCCTTGCATAACTTGCAAGATTATTGTGATTAAACTGTTTCAAGGTAGAAATA
326 AACGATACATTAGCCTTGCATAACTTGCAAGAGTATTGTGATTAAACTGTTTCAAGGTAGAAATA
*
30013479 CATTGTTACCTCACGTAATCTTTTATGTGCTTATGAGATTGAATTAATTGTTTGAATTGGAATAG
391 CATTGTTACCTCAAGTAATCTTTTATGTGCTTATGAGATTGAATTAATTGTTTGAATTGGAATAG
* * * *
30013544 AGATATGTTCAAGAGATTATTTTAATTTC-TTAGTTTTGTATGTGCATTAACACATTTACTTATT
456 AGACATGTACAAGAGATTATTTTAATTTCATAAG-TATGTATGTGCATTAACACATTTACTTATT
*
30013608 AAAATTTGTTTAATCGGTTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGG
520 AAAATTTGTTTAATCGATTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGG
30013673 TAAGTATGTTCATAAGTTAGCAAATTACCGAATTGCCATGAA
585 TAAGTATGTTCATAAGTTAGCAAATTACCGAATTGCCATGAA
30013715 TTTATT
1 TTTATT
30013721 CGTAACAACA
Statistics
Matches: 595, Mismatches: 36, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
625 3 0.01
626 592 0.99
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (626 bp):
TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTAATATGTTTAATTTAATTAA
TATGGCTTAAATGTAATTCCTGTTAGGTCAATTGCATTTCATCTACTTGAGTTATTAAAATTGTG
TTTGTGTTGTTATAGGCCTCGGCAAGATGTTTGATTAAGTAAAACCATGACTAAGTTATTCTTGC
ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGCTTGAAATTATAATTAATTGACA
AGAGATTTAATCAGTCCAAGTTTAATCATCTAAGGTAGCTGAGGGTTAAATTAGCAACGGTATCT
AACGATACATTAGCCTTGCATAACTTGCAAGAGTATTGTGATTAAACTGTTTCAAGGTAGAAATA
CATTGTTACCTCAAGTAATCTTTTATGTGCTTATGAGATTGAATTAATTGTTTGAATTGGAATAG
AGACATGTACAAGAGATTATTTTAATTTCATAAGTATGTATGTGCATTAACACATTTACTTATTA
AAATTTGTTTAATCGATTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGGT
AAGTATGTTCATAAGTTAGCAAATTACCGAATTGCCATGAA
Found at i:30021007 original size:66 final size:66
Alignment explanation
Indices: 30020894--30021024 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
30020884 GGTTCTTATC
* **
30020894 CAGACAGCTGTCAGGTGCGGTGACAATTCTGAACACAATCTGTAATTAACCCATGCAGCGACATT
1 CAGACAGCTGTCAGATGCGACGACAATTCTGAACACAATCTGTAATTAACCCATGCAGCGACATT
30020959 G
66 G
* * * *
30020960 CAGACATCTGTCAGATGCGACGACAATTCTGGACACCATCTAG-AATTAACTCATGCAGCGACAT
1 CAGACAGCTGTCAGATGCGACGACAATTCTGAACACAATCT-GTAATTAACCCATGCAGCGACAT
30021024 T
65 T
30021025 AATGTAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 56 0.98
67 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (66 bp):
CAGACAGCTGTCAGATGCGACGACAATTCTGAACACAATCTGTAATTAACCCATGCAGCGACATT
G
Found at i:30021966 original size:21 final size:21
Alignment explanation
Indices: 30021940--30022008 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
30021930 TCATTTTTAG
30021940 CAACTTCCTCTTCTTCAGCAA
1 CAACTTCCTCTTCTTCAGCAA
30021961 CAACTTCCTCTT-TT--GCAA
1 CAACTTCCTCTTCTTCAGCAA
* * *
30021979 CAACTT-TTGCTTCTGCAGCAT
1 CAACTTCCT-CTTCTTCAGCAA
30022000 CAACTTCCT
1 CAACTTCCT
30022009 TCTAAACAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.03
18 13 0.33
19 1 0.03
20 2 0.05
21 21 0.54
22 1 0.03
ACGTcount: A:0.22, C:0.35, G:0.07, T:0.36
Consensus pattern (21 bp):
CAACTTCCTCTTCTTCAGCAA
Found at i:30040770 original size:6 final size:6
Alignment explanation
Indices: 30040759--30040788 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30040749 TGAATCTTGG
*
30040759 TGTGTA TGTGTA TGTGTA TGTGTG TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
30040789 ACATGACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (6 bp):
TGTGTA
Found at i:30041936 original size:28 final size:26
Alignment explanation
Indices: 30041890--30042011 Score: 145
Period size: 26 Copynumber: 4.6 Consensus size: 26
30041880 AACAGATAAG
30041890 GAAAACCTTTGTGGCGTAATATGAAAA
1 GAAAACCTTTGTGGCGTAATATG-AAA
*
30041917 GAATAACCTTTGTGGAGTAATATGAAA
1 GAA-AACCTTTGTGGCGTAATATGAAA
* * **
30041944 GAAAGCCTTTGTGTCGCCATATGAAA
1 GAAAACCTTTGTGGCGTAATATGAAA
* *
30041970 GAAAACCTTTGTGGCGTAAAATGAATT
1 GAAAACCTTTGTGGCGTAATATGAA-A
*
30041997 GAAAGCCTTTGTGGC
1 GAAAACCTTTGTGGC
30042012 AAACCATGAA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 38 0.47
27 23 0.29
28 19 0.24
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (26 bp):
GAAAACCTTTGTGGCGTAATATGAAA
Found at i:30042021 original size:53 final size:52
Alignment explanation
Indices: 30041890--30042027 Score: 136
Period size: 54 Copynumber: 2.6 Consensus size: 52
30041880 AACAGATAAG
* * * *
30041890 GAAAACCTTTGTGGCGTAATATGAAAAGAATAACCTTTGTGGAGTAATATGAAA
1 GAAAGCCTTTGT-GCGCAACATGAAAAGAA-AACCTTTGTGGAGTAAAATGAAA
* * * *
30041944 GAAAGCCTTTGTGTCGCCATATG-AAAGAAAACCTTTGTGGCGTAAAATGAATT
1 GAAAGCCTTTGTG-CGCAACATGAAAAGAAAACCTTTGTGGAGTAAAATGAA-A
30041997 GAAAGCCTTTGTG-GCAAACCATGAAAAGAAA
1 GAAAGCCTTTGTGCGC-AA-CATGAAAAGAAA
30042028 GCCTCTATGA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
51 2 0.03
52 21 0.30
53 23 0.32
54 25 0.35
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.25
Consensus pattern (52 bp):
GAAAGCCTTTGTGCGCAACATGAAAAGAAAACCTTTGTGGAGTAAAATGAAA
Found at i:30042347 original size:13 final size:13
Alignment explanation
Indices: 30042313--30042345 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
30042303 AAAGGCATAG
30042313 TTGTATTTACTCA
1 TTGTATTTACTCA
*
30042326 TTGTATTTACTTA
1 TTGTATTTACTCA
30042339 -TGTATTT
1 TTGTATTT
30042346 TAGTTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (13 bp):
TTGTATTTACTCA
Found at i:30042690 original size:32 final size:32
Alignment explanation
Indices: 30042653--30042714 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
30042643 TTGCAATTTC
30042653 CATTCATAAATATAGAGAATTTGAGTAGTTCA
1 CATTCATAAATATAGAGAATTTGAGTAGTTCA
* * *
30042685 CATTCATGAATCTAGAGAGTTTGAGTAGTT
1 CATTCATAAATATAGAGAATTTGAGTAGTT
30042715 GGTTTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (32 bp):
CATTCATAAATATAGAGAATTTGAGTAGTTCA
Found at i:30048141 original size:13 final size:13
Alignment explanation
Indices: 30048123--30048147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30048113 CTGTCGAGGG
30048123 AGCCTTACATTAC
1 AGCCTTACATTAC
30048136 AGCCTTACATTA
1 AGCCTTACATTA
30048148 TTGCACTGTC
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:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (13 bp):
AGCCTTACATTAC
Found at i:30048549 original size:41 final size:41
Alignment explanation
Indices: 30048492--30048573 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
30048482 TTGTGCATTT
30048492 ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
1 ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
30048533 ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
1 ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
30048574 TTCAACTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (41 bp):
ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
Found at i:30050011 original size:21 final size:21
Alignment explanation
Indices: 30049969--30050012 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
30049959 TAATAAAGAA
*
30049969 TATTATATATTATTTTTATAG
1 TATTATATATTATATTTATAG
*
30049990 TATTATATTTTATGATTT-TAG
1 TATTATATATTAT-ATTTATAG
30050011 TA
1 TA
30050013 AATTCATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
TATTATATATTATATTTATAG
Found at i:30050039 original size:12 final size:12
Alignment explanation
Indices: 30050019--30050065 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
30050009 AGTAAATTCA
*
30050019 TATAATAATAAT
1 TATATTAATAAT
30050031 TATATTAATAAT
1 TATATTAATAAT
*
30050043 TTTATT-A-AAT
1 TATATTAATAAT
30050053 TATATTTAATAAT
1 TATA-TTAATAAT
30050066 AATTATGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 6 0.21
11 3 0.10
12 17 0.59
13 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATTAATAAT
Found at i:30050063 original size:38 final size:37
Alignment explanation
Indices: 30050004--30050076 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
30049994 ATATTTTATG
30050004 ATTTTAGTAAATTCATATAATAATAATTATATTAATA
1 ATTTTAGTAAATTCATATAATAATAATTATATTAATA
* *
30050041 ATTTTATTAAATT-ATATTTAATAATAATTATGTTAA
1 ATTTTAGTAAATTCATA--TAATAATAATTATATTAA
30050077 AATATGGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 3 0.09
37 12 0.38
38 17 0.53
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
ATTTTAGTAAATTCATATAATAATAATTATATTAATA
Found at i:30050290 original size:44 final size:46
Alignment explanation
Indices: 30050227--30050321 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 46
30050217 TATTAAAACA
*
30050227 TCATTCCATTCAACCAAACAAAAGAA-TGCT-ATTACAGCTCTATT
1 TCATTCCATTCAACCAAACAAAAGAATTACTGATTACAGCTCTATT
**
30050271 TCATTCCATTCAACCAAACAATTGAATTACTGATTACAGCTCTATT
1 TCATTCCATTCAACCAAACAAAAGAATTACTGATTACAGCTCTATT
*
30050317 CCATT
1 TCATT
30050322 ACAGCTCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 24 0.53
45 3 0.07
46 18 0.40
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (46 bp):
TCATTCCATTCAACCAAACAAAAGAATTACTGATTACAGCTCTATT
Found at i:30050324 original size:16 final size:16
Alignment explanation
Indices: 30050303--30050373 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
30050293 TGAATTACTG
*
30050303 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCC
*
30050319 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCC
* *
30050335 CTTACAGCCCTATTCA
1 ATTACAGCCCTATTCC
* *
30050351 ATTACAACCCTATTCG
1 ATTACAGCCCTATTCC
30050367 ATTACAG
1 ATTACAG
30050374 TGAACCAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:30055363 original size:3 final size:3
Alignment explanation
Indices: 30055350--30055388 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
30055340 CATCATTGTT
*
30055350 ATC AAC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
30055389 GCCTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:30075372 original size:47 final size:47
Alignment explanation
Indices: 30075321--30075429 Score: 173
Period size: 47 Copynumber: 2.3 Consensus size: 47
30075311 AGTAACGTAG
** *
30075321 ATAAACTGCCAATAATCAATATTGTGGACAAGCCACCAAAATCGCAA
1 ATAAACTGCCAATAATCAATATCATGGACAAGCCACCAAAATCACAA
* *
30075368 ATAAACTGCCAATAATCAATATCATGGACAAGCCACCAAAATCATAG
1 ATAAACTGCCAATAATCAATATCATGGACAAGCCACCAAAATCACAA
30075415 ATAAACTGCCAATAA
1 ATAAACTGCCAATAA
30075430 ATTCCACCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (47 bp):
ATAAACTGCCAATAATCAATATCATGGACAAGCCACCAAAATCACAA
Found at i:30084600 original size:29 final size:28
Alignment explanation
Indices: 30084566--30084777 Score: 186
Period size: 29 Copynumber: 7.4 Consensus size: 28
30084556 AAGAAGTTGA
30084566 CCACAAAGGCTTACCTTTCTAGAGCTTTT
1 CCACAAAGGCTTACCTTTCTAGAG-TTTT
* * *
30084595 CCAC-AAGGGTTATCCTTTAATAG-GTTTG
1 CCACAAAGGCTTA-CCTTT-CTAGAGTTTT
30084623 CCACAAAGGCTTACCTTT-TAAGAGTTTTT
1 CCACAAAGGCTTACCTTTCT-AGAG-TTTT
* * **
30084652 CCACAAAGG-TTGTCCTTTAATAG-GTTCA
1 CCACAAAGGCTT-ACCTTT-CTAGAGTTTT
*
30084680 CCACAAAGGCTTACCTTTCCAGAGTTTT
1 CCACAAAGGCTTACCTTTCTAGAGTTTT
**
30084708 ACCACAAAGGCTTACCTTTAAC-AG-GTTCG
1 -CCACAAAGGCTTACCTTT--CTAGAGTTTT
30084737 CCACAAAGGCTTACCTTTCTAGAGTTTT
1 CCACAAAGGCTTACCTTTCTAGAGTTTT
30084765 GCCACAAAGGCTT
1 -CCACAAAGGCTT
30084778 TTTTTCTCCT
Statistics
Matches: 149, Mismatches: 17, Indels: 34
0.75 0.09 0.17
Matches are distributed among these distances:
26 2 0.01
27 6 0.04
28 62 0.42
29 70 0.47
30 7 0.05
31 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (28 bp):
CCACAAAGGCTTACCTTTCTAGAGTTTT
Found at i:30084657 original size:114 final size:115
Alignment explanation
Indices: 30084523--30084772 Score: 334
Period size: 114 Copynumber: 2.2 Consensus size: 115
30084513 GAAGGAATTT
* *
30084523 CCTTTC-AGAGATTTTT-CACAAAAGG-TGTTCTTTAAGAAGTTGACCACAAAGGCTTACCTTTC
1 CCTTTCTAGAG-TTTTTCCACAAAAGGTTGTCCTTTAAGAAGTTCACCACAAAGGCTTACCTTTC
* * * *
30084585 TAGAGCTTTT-CCAC-AAGGGTTATCCTTTAATAGGTTTGCCACAAAGGCTTA
65 CAGAG-TTTTACCACAAAGGCTTA-CCTTTAACAGGTTCGCCACAAAGGCTTA
* *
30084636 CCTTT-TAAGAGTTTTTCCAC-AAAGGTTGTCCTTTAATAGGTTCACCACAAAGGCTTACCTTTC
1 CCTTTCT-AGAGTTTTTCCACAAAAGGTTGTCCTTTAAGAAGTTCACCACAAAGGCTTACCTTTC
30084699 CAGAGTTTTACCACAAAGGCTTACCTTTAACAGGTTCGCCACAAAGGCTTA
65 CAGAGTTTTACCACAAAGGCTTACCTTTAACAGGTTCGCCACAAAGGCTTA
*
30084750 CCTTTCTAGAGTTTTGCCACAAA
1 CCTTTCTAGAGTTTTTCCACAAA
30084773 GGCTTTTTTT
Statistics
Matches: 120, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
113 19 0.16
114 91 0.76
115 10 0.08
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (115 bp):
CCTTTCTAGAGTTTTTCCACAAAAGGTTGTCCTTTAAGAAGTTCACCACAAAGGCTTACCTTTCC
AGAGTTTTACCACAAAGGCTTACCTTTAACAGGTTCGCCACAAAGGCTTA
Found at i:30084772 original size:57 final size:56
Alignment explanation
Indices: 30084566--30084777 Score: 286
Period size: 57 Copynumber: 3.7 Consensus size: 56
30084556 AAGAAGTTGA
* *
30084566 CCACAAAGGCTTACCTTTCTAGAGCTTTTCCAC-AAGGGTTATCCTTTAATAGGTTTG
1 CCACAAAGGCTTACCTTTCTAGAG-TTTTCCACAAAGGCTTA-CCTTTAATAGGTTCG
* *
30084623 CCACAAAGGCTTACCTTT-TAAGAGTTTTTCCACAAAGG-TTGTCCTTTAATAGGTTCA
1 CCACAAAGGCTTACCTTTCT-AGAG-TTTTCCACAAAGGCTT-ACCTTTAATAGGTTCG
* *
30084680 CCACAAAGGCTTACCTTTCCAGAGTTTTACCACAAAGGCTTACCTTTAACAGGTTCG
1 CCACAAAGGCTTACCTTTCTAGAGTTTT-CCACAAAGGCTTACCTTTAATAGGTTCG
30084737 CCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTT
1 CCACAAAGGCTTACCTTTCTAGAGTTTT-CCACAAAGGCTT
30084778 TTTTTCTCCT
Statistics
Matches: 139, Mismatches: 10, Indels: 12
0.86 0.06 0.07
Matches are distributed among these distances:
56 5 0.04
57 128 0.92
58 6 0.04
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (56 bp):
CCACAAAGGCTTACCTTTCTAGAGTTTTCCACAAAGGCTTACCTTTAATAGGTTCG
Found at i:30110890 original size:65 final size:65
Alignment explanation
Indices: 30110786--30110921 Score: 245
Period size: 65 Copynumber: 2.1 Consensus size: 65
30110776 TTAATCTAGT
30110786 TTGAAAATGACTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTCGTTGATGAA
1 TTGAAAATGACTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTCGTTGATGAA
* * *
30110851 TTGAAAATGATTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTGGTTGATTAA
1 TTGAAAATGACTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTCGTTGATGAA
30110916 TTGAAA
1 TTGAAA
30110922 TGTTCATTGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (65 bp):
TTGAAAATGACTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTCGTTGATGAA
Found at i:30124777 original size:368 final size:368
Alignment explanation
Indices: 30124100--30124835 Score: 1472
Period size: 368 Copynumber: 2.0 Consensus size: 368
30124090 ACCTTTTGAA
30124100 AGCTGTAGAGGACACACAACCGTGTCACTTGGTCATGTGTCACACACAGTTGAGACACACGACCA
1 AGCTGTAGAGGACACACAACCGTGTCACTTGGTCATGTGTCACACACAGTTGAGACACACGACCA
30124165 TCTCGATGAAAAATAGGCTATTTCCAAGTCATTTTTTCACCCATTCAATACATATACCTACAATC
66 TCTCGATGAAAAATAGGCTATTTCCAAGTCATTTTTTCACCCATTCAATACATATACCTACAATC
30124230 ATTTTTCTACATATAAACAAGCCTTCAAATTACACCAAAACCATGCATAATCAAGCTATTCAAAT
131 ATTTTTCTACATATAAACAAGCCTTCAAATTACACCAAAACCATGCATAATCAAGCTATTCAAAT
30124295 AAGTTCAATACACATACAACCAATATGCTCCAAGGCACCCCAATAACAACATATAAACATATATA
196 AAGTTCAATACACATACAACCAATATGCTCCAAGGCACCCCAATAACAACATATAAACATATATA
30124360 TAACCATATGCATCATTTAAACAAAAACCATCACTTTGTTCACATAACAAATTCACATCCTCAAA
261 TAACCATATGCATCATTTAAACAAAAACCATCACTTTGTTCACATAACAAATTCACATCCTCAAA
30124425 TACCAAATTTACCATTTAGCAATTAGCATCATAACTCATATAT
326 TACCAAATTTACCATTTAGCAATTAGCATCATAACTCATATAT
30124468 AGCTGTAGAGGACACACAACCGTGTCACTTGGTCATGTGTCACACACAGTTGAGACACACGACCA
1 AGCTGTAGAGGACACACAACCGTGTCACTTGGTCATGTGTCACACACAGTTGAGACACACGACCA
30124533 TCTCGATGAAAAATAGGCTATTTCCAAGTCATTTTTTCACCCATTCAATACATATACCTACAATC
66 TCTCGATGAAAAATAGGCTATTTCCAAGTCATTTTTTCACCCATTCAATACATATACCTACAATC
30124598 ATTTTTCTACATATAAACAAGCCTTCAAATTACACCAAAACCATGCATAATCAAGCTATTCAAAT
131 ATTTTTCTACATATAAACAAGCCTTCAAATTACACCAAAACCATGCATAATCAAGCTATTCAAAT
30124663 AAGTTCAATACACATACAACCAATATGCTCCAAGGCACCCCAATAACAACATATAAACATATATA
196 AAGTTCAATACACATACAACCAATATGCTCCAAGGCACCCCAATAACAACATATAAACATATATA
30124728 TAACCATATGCATCATTTAAACAAAAACCATCACTTTGTTCACATAACAAATTCACATCCTCAAA
261 TAACCATATGCATCATTTAAACAAAAACCATCACTTTGTTCACATAACAAATTCACATCCTCAAA
30124793 TACCAAATTTACCATTTAGCAATTAGCATCATAACTCATATAT
326 TACCAAATTTACCATTTAGCAATTAGCATCATAACTCATATAT
30124836 GCCAACTACA
Statistics
Matches: 368, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
368 368 1.00
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (368 bp):
AGCTGTAGAGGACACACAACCGTGTCACTTGGTCATGTGTCACACACAGTTGAGACACACGACCA
TCTCGATGAAAAATAGGCTATTTCCAAGTCATTTTTTCACCCATTCAATACATATACCTACAATC
ATTTTTCTACATATAAACAAGCCTTCAAATTACACCAAAACCATGCATAATCAAGCTATTCAAAT
AAGTTCAATACACATACAACCAATATGCTCCAAGGCACCCCAATAACAACATATAAACATATATA
TAACCATATGCATCATTTAAACAAAAACCATCACTTTGTTCACATAACAAATTCACATCCTCAAA
TACCAAATTTACCATTTAGCAATTAGCATCATAACTCATATAT
Found at i:30128323 original size:22 final size:22
Alignment explanation
Indices: 30128297--30128341 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
30128287 ATTATGTGTA
30128297 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
30128319 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
30128341 T
1 T
30128342 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:30134058 original size:14 final size:12
Alignment explanation
Indices: 30134037--30134079 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
30134027 AATGCTAGTG
30134037 AAAAAAAGAACA
1 AAAAAAAGAACA
30134049 AAAAGCAAAGAA-A
1 AAAA--AAAGAACA
*
30134062 AGAAAAAGAACA
1 AAAAAAAGAACA
30134074 AAAAAA
1 AAAAAA
30134080 GAGAGCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.23
12 10 0.38
13 4 0.15
14 6 0.23
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAACA
Found at i:30134064 original size:19 final size:17
Alignment explanation
Indices: 30134037--30134081 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
30134027 AATGCTAGTG
30134037 AAAAAAAGAACAAA-AAGC
1 AAAAAAAGAA-AAAGAA-C
30134055 AAAGAAAAGAAAAAGAAC
1 AAA-AAAAGAAAAAGAAC
30134073 AAAAAAAGA
1 AAAAAAAGA
30134082 GAGCATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAGAAC
Found at i:30136684 original size:17 final size:14
Alignment explanation
Indices: 30136638--30136688 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
30136628 AATATTTATT
30136638 TCTAAAAAAACAAG
1 TCTAAAAAAACAAG
30136652 TCTAAAAAACACAAG
1 TCTAAAAAA-ACAAG
30136667 TCTAAATTGAAAACAAG
1 TCTAAA---AAAACAAG
30136684 TCTAA
1 TCTAA
30136689 GAAAGTCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.27
15 11 0.33
17 10 0.30
18 3 0.09
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.20
Consensus pattern (14 bp):
TCTAAAAAAACAAG
Found at i:30137260 original size:15 final size:15
Alignment explanation
Indices: 30137236--30137265 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30137226 GAAACTAGAC
*
30137236 TCATATATTTTTTTA
1 TCATAAATTTTTTTA
30137251 TCATAAATTTTTTTA
1 TCATAAATTTTTTTA
30137266 GAATTTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TCATAAATTTTTTTA
Found at i:30148334 original size:27 final size:27
Alignment explanation
Indices: 30148294--30148744 Score: 441
Period size: 27 Copynumber: 16.7 Consensus size: 27
30148284 GTAATGGGCC
*
30148294 TAAAATGATTGAAATACCCTCAAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* * * *
30148321 TAAAACGACCGAAATATCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* * * * * *
30148348 TAAAATGATTAAAATTCCTTCGAAGGA
1 TAAAATGACTGAAATACCCTCAAAGGG
* * *
30148375 TAAAATGACCGAAATACCCTCGAAGGT
1 TAAAATGACTGAAATACCCTCAAAGGG
30148402 TAAAATGACTGAAATACCCTCAAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
** *
30148429 TAAAATGACCAAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* *
30148456 TAAAATAACTGAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* *
30148483 TAAAATGATTGAAATACCCTTGAAA-GG
1 TAAAATGACTGAAATACCC-TCAAAGGG
* *
30148510 TAAAATGACCGAAATACCCCTGACAA--G
1 TAAAATGACTGAAATA-CCCTCA-AAGGG
* * *
30148537 TAAAATAATTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* ** *
30148564 TAAAATAACTGAAATATGCTCAAAAGG
1 TAAAATGACTGAAATACCCTCAAAGGG
30148591 TAAAATGACTGAAATAGCCC-CAAAGGG
1 TAAAATGACTGAAATA-CCCTCAAAGGG
* * *
30148618 TAAAATAACCGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
*
30148645 TAAAATGACTGAAATACCC-CTAAAGGT
1 TAAAATGACTGAAATACCCTC-AAAGGG
*
30148672 TAAAATGACTGACATAACCC-C-AAGGG
1 TAAAATGACTGAAAT-ACCCTCAAAGGG
*
30148698 TAAAATGACTGAAATA-CCTCTGAAGGG
1 TAAAATGACTGAAATACCCTC-AAAGGG
**
30148725 TAAAATGACTGTTATACCCT
1 TAAAATGACTGAAATACCCT
30148745 TAGGAGTTGA
Statistics
Matches: 349, Mismatches: 62, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
24 2 0.01
25 4 0.01
26 26 0.07
27 300 0.86
28 17 0.05
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCAAAGGG
Found at i:30148925 original size:27 final size:26
Alignment explanation
Indices: 30148895--30148951 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
30148885 TGTATTGGTG
30148895 GCTTTGCCACATATACCGTTACTAGCA
1 GCTTTGCCACAT-TACCGTTACTAGCA
** * *
30148922 GCTTTGCTGCATTACTGTTACTGGCA
1 GCTTTGCCACATTACCGTTACTAGCA
30148948 GCTT
1 GCTT
30148952 CGCTGCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.35
Consensus pattern (26 bp):
GCTTTGCCACATTACCGTTACTAGCA
Found at i:30156493 original size:51 final size:50
Alignment explanation
Indices: 30156438--30156622 Score: 196
Period size: 51 Copynumber: 3.7 Consensus size: 50
30156428 CCGGTTCACA
* *
30156438 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCATCCGATACACG
* * * *
30156489 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCC-AGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATATC-ATCCGA-TACACG
* * * * **
30156540 TAGTAGCCTACACATAGTACTACACATGTGGCC-TATCATTCTGGCACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATATCA-TCCGATACACG
30156590 TAGTAGCCTGCACATAGTACTACACACGTGACC
1 TAGTAGCCTGCACATAGTACTACACACGTGACC
30156623 TAGCAACTTC
Statistics
Matches: 109, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
49 1 0.01
50 40 0.37
51 66 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATATCATCCGATACACG
Found at i:30156620 original size:101 final size:101
Alignment explanation
Indices: 30156436--30156620 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
30156426 ATCCGGTTCA
* * *
30156436 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGTGACCA-TATCATCCGACACACGTAGTAGCCTGCA
30156501 CATAGTACTACACACGTGATCGAAGCTATCCAGTACG
65 CATAGTACTACACACGTGATCGAAGCTATCCAGTACG
* * *
30156538 CATAGTAGCCTACACATAGTACTACACATGTGGCC-TATCATTCTGGCACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGTGACCATATCA-TCCGACACACGTAGTAGCCTGCA
30156602 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
30156621 CCTAGCAACT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 33 0.43
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGTGACCATATCATCCGACACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTATCCAGTACG
Found at i:30160319 original size:41 final size:40
Alignment explanation
Indices: 30160250--30160348 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 40
30160240 CTCGGTGGAC
*
30160250 TCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAA
1 TCAGCACATAGCAACC-CCTTATAATCAATGATACGGGGAA
* * **
30160291 TCAGCACATAGCAACCCCTTTTTGATCAATGATTTGGGGAA
1 TCAGCACATAGCAACCCC-TTATAATCAATGATACGGGGAA
* *
30160332 TCTGCACCTAGCAACCC
1 TCAGCACATAGCAACCC
30160349 TTTACAGTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 2 0.04
41 48 0.96
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (40 bp):
TCAGCACATAGCAACCCCTTATAATCAATGATACGGGGAA
Found at i:30164270 original size:18 final size:18
Alignment explanation
Indices: 30164229--30164263 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30164219 GAAGCATACC
*
30164229 AAAAGAAAATGAAAATTA
1 AAAAAAAAATGAAAATTA
*
30164247 AAAAAAAAATTAAAATT
1 AAAAAAAAATGAAAATT
30164264 TTAAAAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAAAAAAATGAAAATTA
Found at i:30175125 original size:3 final size:3
Alignment explanation
Indices: 30175117--30175150 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
30175107 TTTACTTCAA
30175117 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
30175151 CTTGTGTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:30178572 original size:228 final size:226
Alignment explanation
Indices: 30178177--30178623 Score: 718
Period size: 228 Copynumber: 2.0 Consensus size: 226
30178167 ATCGGGTCGA
30178177 TATGGGTGTTACAAAACAACACAATAAAATCAAGTTACAAGAAAGTGAAAATAGATTGCAACGAA
1 TATGGGTGTTACAAAACAACACAATAAAATCAAGTTACAAGAAAGTGAAAATAGATTGCAACGAA
* * ***
30178242 GAAACTCCCCCTTATCTCTAGTAGTTCCCCTTATTTTCATAGGTTGTGGTGTTATAGTATGCCTC
66 GAAACTCCCCCTTAGCTCTAGTAGTTCCCCTTATTTTCATAGGGTGCAATGTTATAGTATGCCTC
* * * *
30178307 ATAATGCCCTAAATTTGGGCTTCGAAGAAATAGGCCTTAAGCGTAGGAACACATAAAAGTTTATG
131 ATAACGCCCCAAATTTGGGCTTAGAAGAAATAGGCCTTAAGCGTAAGAACACATAAAAGTTTATG
30178372 TGTGCAAGGAAATAACACAATTGATTGTTGG
196 TGTGCAAGGAAATAACACAATTGATTGTTGG
*
30178403 TATGGGTGTTACAAAACAACACAATAAAATC-AGATTACAAGAGAGTGAAAATAGATTGCAACGA
1 TATGGGTGTTACAAAACAACACAATAAAATCAAG-TTACAAGAAAGTGAAAATAGATTGCAACGA
*
30178467 AGAAACTCCTCCCCTTAGCTCTAGTAGTTCCCCTTATTTTCATGGGGTGCAATGTTATAGTATGC
65 AGAAACT-C-CCCCTTAGCTCTAGTAGTTCCCCTTATTTTCATAGGGTGCAATGTTATAGTATGC
* * *
30178532 C-CTATAACGCCCCGAATTTGGGCTTAGAAGAAATAGGCCTTGAGCGTAAGAAGACATAAAAGTT
128 CTC-ATAACGCCCCAAATTTGGGCTTAGAAGAAATAGGCCTTAAGCGTAAGAACACATAAAAGTT
30178596 TATGTGTGCAAGGAAATAACACAATTGA
192 TATGTGTGCAAGGAAATAACACAATTGA
30178624 CTGTCTGCTT
Statistics
Matches: 203, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
225 2 0.01
226 67 0.33
227 2 0.01
228 132 0.65
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (226 bp):
TATGGGTGTTACAAAACAACACAATAAAATCAAGTTACAAGAAAGTGAAAATAGATTGCAACGAA
GAAACTCCCCCTTAGCTCTAGTAGTTCCCCTTATTTTCATAGGGTGCAATGTTATAGTATGCCTC
ATAACGCCCCAAATTTGGGCTTAGAAGAAATAGGCCTTAAGCGTAAGAACACATAAAAGTTTATG
TGTGCAAGGAAATAACACAATTGATTGTTGG
Found at i:30181636 original size:50 final size:50
Alignment explanation
Indices: 30181561--30181666 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
30181551 GGGGAGTGAG
*
30181561 TTTTGGAGATTTTCAAGAAATTTGAAGCGTGAGGGGAGTTGTAGTCGAAT
1 TTTTGGAGATTTCCAAGAAATTTGAAGCGTGAGGGGAGTTGTAGTCGAAT
*
30181611 TTTTGGAGATTTCCAAGAAATTTGAAGTGTGAGGGGAGTTGTAGTCGAAT
1 TTTTGGAGATTTCCAAGAAATTTGAAGCGTGAGGGGAGTTGTAGTCGAAT
30181661 TTTTGG
1 TTTTGG
30181667 TTGTTCCTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.36
Consensus pattern (50 bp):
TTTTGGAGATTTCCAAGAAATTTGAAGCGTGAGGGGAGTTGTAGTCGAAT
Found at i:30182202 original size:326 final size:316
Alignment explanation
Indices: 30181609--30182305 Score: 1232
Period size: 326 Copynumber: 2.2 Consensus size: 316
30181599 TTGTAGTCGA
* *
30181609 ATTTTTGGAGATTTCCAAGAAATTTGAAGTGTGAGGGGAGTTGTAGTCGAATTTTTGGTTGTTCC
1 ATTTTTGGAGATTTTCAAGAAATTTGAAGTGTGAGGGGAGTTGTAGTCGAATTTGTGGTTGTTCC
30181674 TTAAATAAACCTGGATATTGGCGTGAAGGCTTCATAAAATATTGAGGATAAGGTATGACATAAAG
66 TTAAATAAACCTGGATATTGGCGTGAAGGCTTCATAAAATATTGAGGATAAGGTATGACATAAAG
*
30181739 AGCCTATTGGCTTGATGGTAAGTGTTGTGATAAAGCATCAAAGGGGATGGTGTTCGAGTCATGCT
131 AGCCTATTGGCTTGATGGTAAGTGGTGTGATAAAGCATCAAAGGGGATGGTGTTCGAGTCATGCT
* *
30181804 TGGAGCAAAGAAATTTTTAATTTGCTAACATGGTACGGCAAGTGTTGGAAGTAGATTCGAACTCT
196 TGGAGCAAAGAAATTTTTAATTTGCTAACATGGTACGACAACTGTTGGAAGTAGATTCGAACTCT
30181869 ATTGAGTGAAAGTTTGAACTGGTCATGGAGTTGTTATGGAGGATATCAAGGATCGAAAGGGGAGT
261 ATTGAGTGAAAGTTTGAACTGGTCATGGAGTTGTTAT---GG------AGGATCGAAAGGGGAGT
30181934 GATTTTTGGAGATTTTCAAGAAATTTGAAGTGTGAGGGGAGTTGTAGTCGAATTTGTGGTTGTTC
1 -ATTTTTGGAGATTTTCAAGAAATTTGAAGTGTGAGGGGAGTTGTAGTCGAATTTGTGGTTGTTC
30181999 CTTAAATAAACCTGGATATTGGCGTGAAGGCTTCATAAAATATTGAGGATAAGGTATGACATAAA
65 CTTAAATAAACCTGGATATTGGCGTGAAGGCTTCATAAAATATTGAGGATAAGGTATGACATAAA
30182064 GAGCCTATTGGCTTGATGGTAAGTGGTGTGATAAAGCATCAAAGGGGATGGTGTTCGAGTCATGC
130 GAGCCTATTGGCTTGATGGTAAGTGGTGTGATAAAGCATCAAAGGGGATGGTGTTCGAGTCATGC
*
30182129 TTGTAGCAAAGAAATTTTTAATTTGCTAACATGGTACGACAACTGTTGGAAGTAGATTCGAACTC
195 TTGGAGCAAAGAAATTTTTAATTTGCTAACATGGTACGACAACTGTTGGAAGTAGATTCGAACTC
30182194 TATTGAGTGAAAGTTTGAACTGGTCATGGAGTTGTTATGGAGGATCGAAAGGGGAGT
260 TATTGAGTGAAAGTTTGAACTGGTCATGGAGTTGTTATGGAGGATCGAAAGGGGAGT
* *
30182251 ATTTTTCGAGATTTTCAAGAAATTTGAAGTGTGAGGGGACTTGTAGTCGAATTTG
1 ATTTTTGGAGATTTTCAAGAAATTTGAAGTGTGAGGGGAGTTGTAGTCGAATTTG
30182306 GTATCTTGAG
Statistics
Matches: 363, Mismatches: 8, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
316 53 0.15
317 17 0.05
323 2 0.01
326 291 0.80
ACGTcount: A:0.30, C:0.09, G:0.29, T:0.32
Consensus pattern (316 bp):
ATTTTTGGAGATTTTCAAGAAATTTGAAGTGTGAGGGGAGTTGTAGTCGAATTTGTGGTTGTTCC
TTAAATAAACCTGGATATTGGCGTGAAGGCTTCATAAAATATTGAGGATAAGGTATGACATAAAG
AGCCTATTGGCTTGATGGTAAGTGGTGTGATAAAGCATCAAAGGGGATGGTGTTCGAGTCATGCT
TGGAGCAAAGAAATTTTTAATTTGCTAACATGGTACGACAACTGTTGGAAGTAGATTCGAACTCT
ATTGAGTGAAAGTTTGAACTGGTCATGGAGTTGTTATGGAGGATCGAAAGGGGAGT
Done.