Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 87 of 279
Found at i:28783461 original size:90 final size:87
Alignment explanation
Indices: 28783308--28783577 Score: 314
Period size: 87 Copynumber: 3.1 Consensus size: 87
28783298 GTCAAATAGC
* * *
28783308 CTTTTTAATGCA-TTTTACAA-TTCAAGTACCTAATTGAGTGTTAAAAAAAATCAAGGGCTTAAT
1 CTTTTTAATGCATTTTTA-AAGTTCAAGTACCCAATTGAGTG-AAAAAAAAAACAAGGGCTTAAT
28783371 TGCTTTATTTGAAAAAGTTTGAGGG
64 TGCTTT-TTTGAAAAAGTTTGAGGG
* * * *
28783396 CCTTTTAATGTATTTTTTAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAGCAGGGGCCTAAT
1 CTTTTTAATGCA-TTTTTAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAA-CAAGGGCTTAAT
****
28783461 T--TTTTTTTTTTAAGTTTGAGGG
64 TGCTTTTTTGAAAAAGTTTGAGGG
* * *
28783483 CATTTTTTATGCATTTTGAAAGTTCAAATACCCAATTGAGTGAAAAAAAAAACAAGGGCTTAATT
1 C-TTTTTAATGCATTTTTAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAACAAGGGCTTAATT
*
28783548 GCTTTTTTTGAAAAAGCTTGAGGG
65 GC-TTTTTTGAAAAAGTTTGAGGG
28783572 CTTTTT
1 CTTTTT
28783578 TACACCCTTA
Statistics
Matches: 151, Mismatches: 23, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
86 11 0.07
87 52 0.34
88 26 0.17
89 27 0.18
90 35 0.23
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (87 bp):
CTTTTTAATGCATTTTTAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAACAAGGGCTTAATTG
CTTTTTTGAAAAAGTTTGAGGG
Found at i:28789637 original size:58 final size:58
Alignment explanation
Indices: 28789542--28789654 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 58
28789532 CTTGGCTTCA
** * * *
28789542 ATAGATACCTTGTTCCTTTCTGAAAGGTTAGCCTTGACAAGTGAAATGGTAAGGCTGG
1 ATAGATACCTTGTTCCTTTCCAAAAGGCTAGCATTGACAAATGAAATGGTAAGGCTGG
*
28789600 ATAGATCCCTTGTTCCTTTCCAAAAGGCTAGCATTGACAAATGAAATGGTAAGGC
1 ATAGATACCTTGTTCCTTTCCAAAAGGCTAGCATTGACAAATGAAATGGTAAGGC
28789655 AGAAATTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (58 bp):
ATAGATACCTTGTTCCTTTCCAAAAGGCTAGCATTGACAAATGAAATGGTAAGGCTGG
Found at i:28790954 original size:43 final size:42
Alignment explanation
Indices: 28790906--28790990 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 42
28790896 CTTAGTGTCC
28790906 CACCTCATTCCTGCTGTAATCTTCTTAACTTTAATTAGAACA
1 CACCTCATTCCTGCTGTAATCTTCTTAACTTTAATTAGAACA
* *
28790948 NCACCTCATTCCTGCTGTTATCTTCTTCACTTTAATTAGAACA
1 -CACCTCATTCCTGCTGTAATCTTCTTAACTTTAATTAGAACA
28790991 TCAACTTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.07, T:0.39
Consensus pattern (42 bp):
CACCTCATTCCTGCTGTAATCTTCTTAACTTTAATTAGAACA
Found at i:28797785 original size:16 final size:18
Alignment explanation
Indices: 28797764--28797800 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28797754 TCAATATCAG
28797764 TCAAT-ATTTT-TCAATA
1 TCAATAATTTTATCAATA
28797780 TCAATAATTTTATCAATA
1 TCAATAATTTTATCAATA
28797798 TCA
1 TCA
28797801 TTCAGTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (18 bp):
TCAATAATTTTATCAATA
Found at i:28797823 original size:18 final size:18
Alignment explanation
Indices: 28797800--28797878 Score: 113
Period size: 18 Copynumber: 4.4 Consensus size: 18
28797790 TATCAATATC
28797800 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAATT
* *
28797818 ATTCAGTAGCAATCAGTT
1 ATTCAGTAACAATCAATT
28797836 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAATT
* * *
28797854 ATTCAGTAACAGTCAGTC
1 ATTCAGTAACAATCAATT
28797872 ATTCAGT
1 ATTCAGT
28797879 GCCTTTATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (18 bp):
ATTCAGTAACAATCAATT
Found at i:28797841 original size:36 final size:36
Alignment explanation
Indices: 28797798--28797878 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
28797788 TTTATCAATA
*
28797798 TCATTCAGTAACAATCAATTATTCAGTAGCAATCAG
1 TCATTCAGTAACAATCAATTATTCAGTAACAATCAG
* *
28797834 TTATTCAGTAACAATCAATTATTCAGTAACAGTCAG
1 TCATTCAGTAACAATCAATTATTCAGTAACAATCAG
28797870 TCATTCAGT
1 TCATTCAGT
28797879 GCCTTTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (36 bp):
TCATTCAGTAACAATCAATTATTCAGTAACAATCAG
Found at i:28798122 original size:44 final size:44
Alignment explanation
Indices: 28798032--28798123 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
28798022 CCGAAGTAAC
* * *
28798032 AGTAACAGTACGACACACATGGTGCCTCATCGACTCGAAGTTGA
1 AGTAACAATACGACACACATAGTGCCTCATCGACTCGAAGTCGA
**
28798076 AGTAACAATACGACACTTATAGTGCCTCATCGACTC-AAGGTCGA
1 AGTAACAATACGACACACATAGTGCCTCATCGACTCGAA-GTCGA
28798120 AGTA
1 AGTA
28798124 TCCCTGAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (44 bp):
AGTAACAATACGACACACATAGTGCCTCATCGACTCGAAGTCGA
Found at i:28799161 original size:9 final size:9
Alignment explanation
Indices: 28799144--28799207 Score: 64
Period size: 9 Copynumber: 7.3 Consensus size: 9
28799134 TTAGTTTATT
28799144 TATAA-TAA
1 TATAATTAA
28799152 TATAATTAA
1 TATAATTAA
28799161 TATAATTAA
1 TATAATTAA
*
28799170 TATAATTCA
1 TATAATTAA
*
28799179 -A-AATATGA
1 TATAAT-TAA
28799187 TATAA-TAA
1 TATAATTAA
28799195 TATAATTTAA
1 TATAA-TTAA
28799205 TAT
1 TAT
28799208 TTAACCAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
7 3 0.06
8 15 0.32
9 21 0.45
10 8 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (9 bp):
TATAATTAA
Found at i:28802627 original size:19 final size:19
Alignment explanation
Indices: 28802595--28802649 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
28802585 ATGCGTCAAG
* * *
28802595 ATGCACTTTGTGTGCTAGT
1 ATGCACTATATGTGCCAGT
*
28802614 ATGCATTATATGTGCCAGT
1 ATGCACTATATGTGCCAGT
28802633 ATGCACTATATGTGCCA
1 ATGCACTATATGTGCCA
28802650 ATTTTCCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (19 bp):
ATGCACTATATGTGCCAGT
Found at i:28809095 original size:174 final size:172
Alignment explanation
Indices: 28808757--28809099 Score: 526
Period size: 174 Copynumber: 2.0 Consensus size: 172
28808747 CAAATGGGCT
* * * * *
28808757 ATTTGCCCATTAGCCCTCTAACTCTAACTTATTTTCTAATTTTACTAAAATTCCTTATTTATTAT
1 ATTTGCCCATTAGCCCTCAAACTCTAACTCATTTCCTAATTCTACTAAAATTCCCTATTTATTAT
*
28808822 TTTATCAAATTGAAACCCTAACTTTCTCTATTTATACCCTAGTTTTCTATCAAAATTCTCTATTT
66 TTTATCAAATTGAAACCCTAACTCTCTCTATTTATACCCTAGTTTTCTATCAAAATTCTCTATTT
28808887 CAAAACTCTTTTAATCCCTTAAGTTCTACTGAAAAATAACTC
131 CAAAACTCTTTTAATCCCTTAAGTTCTACTGAAAAATAACTC
* * * *
28808929 ATTTGGCCATTAGTCCTCAAATTCTCTAAGTCATTTCCTAATTCTACTAAAATTCCCTATTTGTT
1 ATTTGCCCATTAGCCCTCAAA--CTCTAACTCATTTCCTAATTCTACTAAAATTCCCTATTTATT
* *
28808994 ATTTTATCAAATTGAAACCCTAACTCTCTCTATTTATAACCC-AGTTTTCTCTTAAAATTCTCTA
64 ATTTTATCAAATTGAAACCCTAACTCTCTCTATTTAT-ACCCTAGTTTTCTATCAAAATTCTCTA
* *
28809058 TTTCAAAACTCTTTTAATCCCTTAAGTTTTGCTGAAAAATAA
128 TTTCAAAACTCTTTTAATCCCTTAAGTTCTACTGAAAAATAA
28809100 TCTTTAAAGT
Statistics
Matches: 154, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
172 18 0.12
174 132 0.86
175 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.43
Consensus pattern (172 bp):
ATTTGCCCATTAGCCCTCAAACTCTAACTCATTTCCTAATTCTACTAAAATTCCCTATTTATTAT
TTTATCAAATTGAAACCCTAACTCTCTCTATTTATACCCTAGTTTTCTATCAAAATTCTCTATTT
CAAAACTCTTTTAATCCCTTAAGTTCTACTGAAAAATAACTC
Found at i:28811227 original size:8 final size:8
Alignment explanation
Indices: 28811216--28811249 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
28811206 TATATAGATG
*
28811216 TACATATA
1 TACAAATA
28811224 TACAAATA
1 TACAAATA
28811232 TACAAATA
1 TACAAATA
*
28811240 TACAGATA
1 TACAAATA
28811248 TA
1 TA
28811250 ATATATGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (8 bp):
TACAAATA
Found at i:28811235 original size:16 final size:16
Alignment explanation
Indices: 28811216--28811255 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
28811206 TATATAGATG
28811216 TACATATATACAAATA
1 TACATATATACAAATA
* *
28811232 TACAAATATACAGATA
1 TACATATATACAAATA
28811248 TA-ATATAT
1 TACATATAT
28811256 GCTTATACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (16 bp):
TACATATATACAAATA
Found at i:28814847 original size:18 final size:19
Alignment explanation
Indices: 28814804--28814845 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
28814794 AATGGCTTCC
28814804 AAAAAA-TTATTTTT-TAA
1 AAAAAATTTATTTTTCTAA
28814821 AAAATAATTTATTTTTCTAGA
1 AAAA-AATTTATTTTTCTA-A
28814842 AAAA
1 AAAA
28814846 TTAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
18 2 0.10
19 8 0.38
20 2 0.10
21 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAAAATTTATTTTTCTAA
Found at i:28815415 original size:13 final size:14
Alignment explanation
Indices: 28815377--28815418 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
28815367 TATGTGAATA
28815377 ATATTATTTAAAATT
1 ATATTA-TTAAAATT
*
28815392 ATAATTTTTAAAATT
1 AT-ATTATTAAAATT
28815407 -TATTATTAAAAT
1 ATATTATTAAAAT
28815419 AAAATTGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATTAAAATT
Found at i:28815453 original size:16 final size:19
Alignment explanation
Indices: 28815434--28815483 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
28815424 TGAACTATTA
28815434 AATAATTTATTAA-A-AT-
1 AATAATTTATTAATATATC
28815450 AATAAATTATATTAATTATATC
1 AAT-AATT-TATTAA-TATATC
28815472 AATAATTTATTA
1 AATAATTTATTA
28815484 TATGAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 6 0.21
20 6 0.21
21 6 0.21
22 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATTTATTAATATATC
Found at i:28816479 original size:16 final size:18
Alignment explanation
Indices: 28816452--28816486 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28816442 TCCTCTTCAT
28816452 CCTCTATTTC-TTTTCTC
1 CCTCTATTTCTTTTTCTC
28816469 CCTCT-TTTCTTTTTCTC
1 CCTCTATTTCTTTTTCTC
28816486 C
1 C
28816487 TATTTTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (18 bp):
CCTCTATTTCTTTTTCTC
Found at i:28816492 original size:16 final size:17
Alignment explanation
Indices: 28816458--28816494 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28816448 TCATCCTCTA
*
28816458 TTTC-TTTTCTCCCTCT
1 TTTCTTTTTCTCCCTAT
28816474 TTTCTTTTTCT-CCTAT
1 TTTCTTTTTCTCCCTAT
28816490 TTTCT
1 TTTCT
28816495 CTCATAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCTTTTTCTCCCTAT
Found at i:28817541 original size:43 final size:43
Alignment explanation
Indices: 28817479--28817725 Score: 220
Period size: 43 Copynumber: 5.8 Consensus size: 43
28817469 GAAAAGTGAC
** *
28817479 ATTTTATCTGTAAATATGTTGTGCATCCACAGCCTAGTGGCAG
1 ATTTTATCTACAAATATGTTGTGCATCCACAGCCCAGTGGCAG
* * *
28817522 ATTTTATCTACAACA-ATGTTGTGCACCCACAGCCCACTGACAG
1 ATTTTATCTACAA-ATATGTTGTGCATCCACAGCCCAGTGGCAG
* * * * * ** *
28817565 TTTTTATCTTCAAATATGTTGTGTATCCACAACTCAACGACA-
1 ATTTTATCTACAAATATGTTGTGCATCCACAGCCCAGTGGCAG
* * *
28817607 ATTTTTATTTGCAAATATGTTGTGCATCCACAACCCAGTGGCA-
1 A-TTTTATCTACAAATATGTTGTGCATCCACAGCCCAGTGGCAG
*** *
28817650 A-TTTATCTACAAATATAACGTGCATCCACAACCCAGTGGTC-G
1 ATTTTATCTACAAATATGTTGTGCATCCACAGCCCAGTGG-CAG
*
28817692 --TTTATCTATAAATATGTTGTGCATCCACAGCCCA
1 ATTTTATCTACAAATATGTTGTGCATCCACAGCCCA
28817726 ATGGTGGTTT
Statistics
Matches: 167, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
41 62 0.37
42 2 0.01
43 102 0.61
44 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (43 bp):
ATTTTATCTACAAATATGTTGTGCATCCACAGCCCAGTGGCAG
Found at i:28817673 original size:41 final size:41
Alignment explanation
Indices: 28817628--28817730 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
28817618 CAAATATGTT
28817628 GTGCATCCACAACCCAGTGG-CAATTTATCTACAAATATAAC
1 GTGCATCCACAACCCAGTGGTC-ATTTATCTACAAATATAAC
* * ***
28817669 GTGCATCCACAACCCAGTGGTCGTTTATCTATAAATATGTT
1 GTGCATCCACAACCCAGTGGTCATTTATCTACAAATATAAC
* *
28817710 GTGCATCCACAGCCCAATGGT
1 GTGCATCCACAACCCAGTGGT
28817731 GGTTTTTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 53 0.98
42 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (41 bp):
GTGCATCCACAACCCAGTGGTCATTTATCTACAAATATAAC
Found at i:28820710 original size:65 final size:65
Alignment explanation
Indices: 28820605--28820735 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
28820595 TTCCCATATG
*
28820605 TATTCTCGATGAGCTACCAGGGTTACCTCCAAACCGTGAGGTTTAATTCAAAATTGAGTTGTTGC
1 TATTCTCGATGAGCTACCAGGGTTACCTCCAAACCATGAGGTTTAATTCAAAATTGAGTTGTTGC
*
28820670 TATTCTCGATGAGCTACCAGGGTTACCTCCAAACTATGAGGTTTAATTCAAAATTGAGTTGTTGC
1 TATTCTCGATGAGCTACCAGGGTTACCTCCAAACCATGAGGTTTAATTCAAAATTGAGTTGTTGC
28820735 T
1 T
28820736 GGAAACTACT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (65 bp):
TATTCTCGATGAGCTACCAGGGTTACCTCCAAACCATGAGGTTTAATTCAAAATTGAGTTGTTGC
Found at i:28825751 original size:17 final size:17
Alignment explanation
Indices: 28825729--28825776 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
28825719 ACTAAAATTC
28825729 CTTTTCATCCTCTATTT
1 CTTTTCATCCTCTATTT
* * *
28825746 CTTTTCTTCCTTTTTTTT
1 CTTTTCATCC-TCTATTT
*
28825764 CTTTTCCTCCTCT
1 CTTTTCATCCTCT
28825777 TTTATCACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTTTCATCCTCTATTT
Found at i:28825766 original size:18 final size:19
Alignment explanation
Indices: 28825743--28825779 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28825733 TCATCCTCTA
*
28825743 TTTCTTTTCTTCCT-TTTT
1 TTTCTTTTCCTCCTCTTTT
28825761 TTTCTTTTCCTCCTCTTTT
1 TTTCTTTTCCTCCTCTTTT
28825780 ATCACATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTCTTTTCCTCCTCTTTT
Found at i:28828574 original size:18 final size:18
Alignment explanation
Indices: 28828551--28828588 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28828541 TTCATACAAA
28828551 TTCCAGTTTAAACTAAAT
1 TTCCAGTTTAAACTAAAT
28828569 TTCCAGTTTAAACTAAAT
1 TTCCAGTTTAAACTAAAT
28828587 TT
1 TT
28828589 AACTCCCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (18 bp):
TTCCAGTTTAAACTAAAT
Found at i:28836168 original size:25 final size:23
Alignment explanation
Indices: 28836140--28836185 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
28836130 ACTTTAATTA
28836140 ATATAATATATAAAATAAATTTAAC
1 ATATAATATAT-AAAT-AATTTAAC
*
28836165 ATATAATTTATAAATAATTTA
1 ATATAATATATAAATAATTTA
28836186 CTAATGCCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAATATATAAATAATTTAAC
Found at i:28836925 original size:12 final size:13
Alignment explanation
Indices: 28836903--28836931 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28836893 GATATTATTA
28836903 TATAGAGAGATAT
1 TATAGAGAGATAT
28836916 TATA-AGAGATAT
1 TATAGAGAGATAT
28836928 TATA
1 TATA
28836932 CCAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (13 bp):
TATAGAGAGATAT
Found at i:28838147 original size:16 final size:16
Alignment explanation
Indices: 28838128--28838169 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
28838118 AATTTGATCG
28838128 AATTAATAATAAATTT
1 AATTAATAATAAATTT
*
28838144 AATTTAATTA-AAATTT
1 AA-TTAATAATAAATTT
28838160 AATTAATAAT
1 AATTAATAAT
28838170 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAATAATAAATTT
Found at i:28838158 original size:11 final size:11
Alignment explanation
Indices: 28838144--28838181 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28838134 TAATAAATTT
28838144 AATTTAATTAA
1 AATTTAATTAA
28838155 AATTTAATTAA
1 AATTTAATTAA
*
28838166 TAATTT-TTTAA
1 -AATTTAATTAA
28838177 AATTT
1 AATTT
28838182 CGATTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAATTAA
Found at i:28839254 original size:33 final size:31
Alignment explanation
Indices: 28839215--28839323 Score: 100
Period size: 33 Copynumber: 3.4 Consensus size: 31
28839205 AGAAAGTGGT
28839215 AAGAGAACAAGTTGATTGAGAGATATAGAAAG
1 AAGAGAACAAGTTGA-TGAGAGATATAGAAAG
* *
28839247 AGAGAGAACAAGTTTAGATGCG-GA-A-AG-GAG
1 A-AGAGAACAAG-TT-GATGAGAGATATAGAAAG
28839277 CAAGAGAACAAGTTGACTGAGAGATATAGAAAG
1 -AAGAGAACAAGTTGA-TGAGAGATATAGAAAG
*
28839310 AACGAGCACAAGTT
1 AA-GAGAACAAGTT
28839324 TGCTTAGAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
28 2 0.03
29 5 0.08
30 14 0.23
31 4 0.06
32 6 0.10
33 24 0.39
34 5 0.08
35 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.29, T:0.16
Consensus pattern (31 bp):
AAGAGAACAAGTTGATGAGAGATATAGAAAG
Found at i:28842050 original size:18 final size:17
Alignment explanation
Indices: 28842029--28842071 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28842019 TCATATACAT
28842029 TATAAAAA-AAGTATATAA
1 TATAAAAACAA-TA-ATAA
*
28842047 TATAAAAACAATACTAA
1 TATAAAAACAATAATAA
28842064 TATAAAAA
1 TATAAAAA
28842072 TGATATAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 11 0.48
18 10 0.43
19 2 0.09
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (17 bp):
TATAAAAACAATAATAA
Found at i:28843605 original size:28 final size:28
Alignment explanation
Indices: 28843574--28843685 Score: 70
Period size: 28 Copynumber: 3.9 Consensus size: 28
28843564 TAATATAATT
28843574 ATATTTATAAAAATATTTAAATAATTTA
1 ATATTTATAAAAATATTTAAATAATTTA
* * *
28843602 ATATAATGATAGATAAA-ATATGAATTAATTTA
1 ATAT--TTATA-A-AAATAT-TTAAATAATTTA
*
28843634 A-ATTTTTAAATACAT-TTTAAATAA-TTA
1 ATATTTATAAA-A-ATATTTAAATAATTTA
** *
28843661 ATATAAATAAAAATATTTTAATAAT
1 ATATTTATAAAAATATTTAAATAAT
28843686 CTATACTTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 22
0.65 0.12 0.23
Matches are distributed among these distances:
26 2 0.03
27 14 0.23
28 18 0.29
29 5 0.08
30 4 0.06
31 5 0.08
32 14 0.23
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
ATATTTATAAAAATATTTAAATAATTTA
Found at i:28845796 original size:30 final size:30
Alignment explanation
Indices: 28845745--28845801 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
28845735 AAATAGATAA
* *
28845745 ATATAAATAAATATTTATATATATAATGAC
1 ATATAAATAAAAAATTATATATATAATGAC
*
28845775 ATATAAATAGAAAAATT-TATATTTAAT
1 ATATAAATA-AAAAATTATATATATAAT
28845802 TTTCGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (30 bp):
ATATAAATAAAAAATTATATATATAATGAC
Found at i:28847722 original size:36 final size:36
Alignment explanation
Indices: 28847668--28847739 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
28847658 GTGTAGGAGT
*
28847668 TTGAGAAGACTCGATATCTCATTCAAGATCTTGGGA
1 TTGAGAAGACTCGATATCTCATTCAAGAGCTTGGGA
* * *
28847704 TTGAGAAGAC-CTGGTATCTCGTTGAAGAGCTTGGGA
1 TTGAGAAGACTC-GATATCTCATTCAAGAGCTTGGGA
28847740 ATATATGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (36 bp):
TTGAGAAGACTCGATATCTCATTCAAGAGCTTGGGA
Found at i:28849370 original size:3 final size:3
Alignment explanation
Indices: 28849362--28849416 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
28849352 AAGTTTTCTT
*
28849362 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28849410 TTA TTA T
1 TTA TTA T
28849417 CATCTGTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28854150 original size:23 final size:22
Alignment explanation
Indices: 28854098--28854150 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
28854088 TCCACGTCTT
*
28854098 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
28854120 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
28854143 TTTCTTTT
1 TTTCTTTT
28854151 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:28862164 original size:21 final size:20
Alignment explanation
Indices: 28862130--28862168 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28862120 AAACATAAAC
28862130 AACTTCACATTTTTTAAAGT
1 AACTTCACATTTTTTAAAGT
*
28862150 AACTTTACAATTTTTTAAA
1 AACTTCAC-ATTTTTTAAA
28862169 ATTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (20 bp):
AACTTCACATTTTTTAAAGT
Found at i:28866347 original size:5 final size:5
Alignment explanation
Indices: 28866337--28866469 Score: 266
Period size: 5 Copynumber: 26.6 Consensus size: 5
28866327 AATAATTAAG
28866337 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
28866387 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
28866437 TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
28866470 TATATATAAA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 128 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:28866544 original size:31 final size:30
Alignment explanation
Indices: 28866509--28866569 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
28866499 GAAACAGAAT
*
28866509 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
28866540 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
28866570 AATAAGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:28867399 original size:39 final size:39
Alignment explanation
Indices: 28867292--28867426 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
28867282 GACCTCGAGT
* * *
28867292 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
28867333 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
28867371 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
28867410 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
28867427 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:28882326 original size:170 final size:170
Alignment explanation
Indices: 28882044--28882384 Score: 682
Period size: 170 Copynumber: 2.0 Consensus size: 170
28882034 TACTAAGTAG
28882044 TATTTTGTTCTAGGATCATAAAAACTCAAAAATTACAAGAAAATGAGCTAAATTAACTTACCAAT
1 TATTTTGTTCTAGGATCATAAAAACTCAAAAATTACAAGAAAATGAGCTAAATTAACTTACCAAT
28882109 TTAAGTTCAAACCCTTGAAATCCCTATTTTCCCTTTCCTTTTTCTTTCTTTCTTTCCTCTGTTTC
66 TTAAGTTCAAACCCTTGAAATCCCTATTTTCCCTTTCCTTTTTCTTTCTTTCTTTCCTCTGTTTC
28882174 GTTTTGTTATTCTGTTTTTGTTCTTTTTCATTTGCTTTGT
131 GTTTTGTTATTCTGTTTTTGTTCTTTTTCATTTGCTTTGT
28882214 TATTTTGTTCTAGGATCATAAAAACTCAAAAATTACAAGAAAATGAGCTAAATTAACTTACCAAT
1 TATTTTGTTCTAGGATCATAAAAACTCAAAAATTACAAGAAAATGAGCTAAATTAACTTACCAAT
28882279 TTAAGTTCAAACCCTTGAAATCCCTATTTTCCCTTTCCTTTTTCTTTCTTTCTTTCCTCTGTTTC
66 TTAAGTTCAAACCCTTGAAATCCCTATTTTCCCTTTCCTTTTTCTTTCTTTCTTTCCTCTGTTTC
28882344 GTTTTGTTATTCTGTTTTTGTTCTTTTTCATTTGCTTTGT
131 GTTTTGTTATTCTGTTTTTGTTCTTTTTCATTTGCTTTGT
28882384 T
1 T
28882385 TTATATTTAA
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 171 1.00
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (170 bp):
TATTTTGTTCTAGGATCATAAAAACTCAAAAATTACAAGAAAATGAGCTAAATTAACTTACCAAT
TTAAGTTCAAACCCTTGAAATCCCTATTTTCCCTTTCCTTTTTCTTTCTTTCTTTCCTCTGTTTC
GTTTTGTTATTCTGTTTTTGTTCTTTTTCATTTGCTTTGT
Found at i:28882448 original size:5 final size:5
Alignment explanation
Indices: 28882400--28882438 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
28882390 TTTAATGATA
28882400 ATAAT AT-AT -TAAT AATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT
28882439 GATATAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.13
5 22 0.71
6 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:28889606 original size:71 final size:69
Alignment explanation
Indices: 28889513--28889647 Score: 225
Period size: 71 Copynumber: 1.9 Consensus size: 69
28889503 TTACAATTTA
*
28889513 GTCCCTATTACACAACTTTTAACTTATTCTTCAATTTAATCATTTACCTAATTCTAACTTGAAAT
1 GTCCCTATTACACAACTTTTAACTTATTCTTCAATTTAATCATTTACCCAATTCTAACTTGAAAT
28889578 TTTT
66 TTTT
* *
28889582 GTCCCTATTACACAAAACTTTTAACTTATTCTTCAGTTTAATCCTTTACCCAATTCTAACTTGAA
1 GTCCCTATTACAC--AACTTTTAACTTATTCTTCAATTTAATCATTTACCCAATTCTAACTTGAA
28889647 A
64 A
28889648 CTCTATCAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 13 0.21
71 48 0.79
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (69 bp):
GTCCCTATTACACAACTTTTAACTTATTCTTCAATTTAATCATTTACCCAATTCTAACTTGAAAT
TTTT
Found at i:28889884 original size:18 final size:18
Alignment explanation
Indices: 28889861--28889924 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
28889851 TTCTTTCTTT
28889861 TATATT-TAATGATAATAA
1 TATATTATAAT-ATAATAA
*
28889879 TATATTATAATATAGTAA
1 TATATTATAATATAATAA
*
28889897 TAATAATATAATATAATATAA
1 T-ATATTATAATAT-A-ATAA
28889918 TATATTA
1 TATATTA
28889925 GTTATGCCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 13 0.34
19 15 0.39
20 6 0.16
21 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TATATTATAATATAATAA
Found at i:28889890 original size:10 final size:10
Alignment explanation
Indices: 28889875--28889924 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
28889865 TTTAATGATA
28889875 ATAATATATT
1 ATAATATATT
*
28889885 ATAATATAGTA
1 ATAATATA-TT
28889896 ATAATA-A-T
1 ATAATATATT
*
28889904 ATAATATAAT
1 ATAATATATT
28889914 ATAATATATT
1 ATAATATATT
28889924 A
1 A
28889925 GTTATGCCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 6 0.18
9 1 0.03
10 20 0.59
11 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
ATAATATATT
Found at i:28889892 original size:5 final size:5
Alignment explanation
Indices: 28889875--28889921 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
28889865 TTTAATGATA
* *
28889875 ATAAT ATATT ATAAT AT-A- GTAAT AATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATA
28889922 TTAGTTATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 1 0.03
4 2 0.06
5 28 0.80
6 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:28901217 original size:40 final size:40
Alignment explanation
Indices: 28901164--28901355 Score: 255
Period size: 40 Copynumber: 4.8 Consensus size: 40
28901154 GGATATAGCT
* * *
28901164 ACTCGCTCGAATGCCTTTGGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
** *
28901204 GTTCGCACAAATGCCTTCGGGACTTAGCCCGG-GTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
*
28901244 ACTCGCACAAATACCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
28901284 ACTCGCA-ACAATGCCTTCGGGACTTAGCCCGGAATTAGTC
1 ACTCGCACA-AATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
28901324 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
28901356 TTATCATCCG
Statistics
Matches: 136, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 133 0.98
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:28901270 original size:80 final size:79
Alignment explanation
Indices: 28901138--28901355 Score: 255
Period size: 80 Copynumber: 2.7 Consensus size: 79
28901128 AGACCAAGTA
* * * * * *
28901138 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCGAATGCCTTTGGGACTTAGCCCGG-ATATA
1 CCTTCGGGACTTAGCCCGGGTATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TA
**
28901201 GTAGTTCGC-ACAAATG
64 GTAACTCGCAAC-AATG
*
28901217 CCTTCGGGACTTAGCCCGGGTATAGTAACTCGCACAAATACCTTCGGGACTTAGCCCGGAATTAG
1 CCTTCGGGACTTAGCCCGGGTATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
28901282 TAACTCGCAACAATG
65 TAACTCGCAACAATG
* *
28901297 CCTTCGGGACTTAGCCC-GGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGGGTA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
28901356 TTATCATCCG
Statistics
Matches: 121, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
79 16 0.13
80 101 0.83
81 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGGTATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
AACTCGCAACAATG
Found at i:28921379 original size:79 final size:81
Alignment explanation
Indices: 28921243--28921427 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
28921233 TTGAATGATG
*
28921243 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28921307 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28921322 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28921384 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
28921402 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28921428 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:28921441 original size:40 final size:40
Alignment explanation
Indices: 28921244--28921427 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
28921234 TGAATGATGT
* * * *
28921244 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28921284 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
28921324 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28921362 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28921403 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28921428 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28921449 original size:79 final size:79
Alignment explanation
Indices: 28921296--28921460 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
28921286 GGACTAAGAT
* **
28921296 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28921361 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28921375 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28921438 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28921454 CCGAAGG
1 CCGAAGG
28921461 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28924999 original size:18 final size:18
Alignment explanation
Indices: 28924972--28925006 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28924962 AAGTCTGTTC
28924972 TGACTCAGGCTCCTATTT
1 TGACTCAGGCTCCTATTT
*
28924990 TGACTTAGGCTCCTATT
1 TGACTCAGGCTCCTATT
28925007 CTGATACAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TGACTCAGGCTCCTATTT
Found at i:28929181 original size:44 final size:44
Alignment explanation
Indices: 28929116--28929204 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
28929106 AAGTAACAGA
*
28929116 AACAGTACGACACACGAAGTGCCTCATCGACACAAAGTCGAAGT
1 AACAGTACGACACACGAAGTGCCTCATCAACACAAAGTCGAAGT
** * * *
28929160 AACAGTACGACACTA-TTAGTGCCTCATTAACTCAAGGTCGAAGT
1 AACAGTACGACAC-ACGAAGTGCCTCATCAACACAAAGTCGAAGT
28929204 A
1 A
28929205 TCCCTGTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (44 bp):
AACAGTACGACACACGAAGTGCCTCATCAACACAAAGTCGAAGT
Found at i:28930090 original size:5 final size:5
Alignment explanation
Indices: 28930088--28930162 Score: 150
Period size: 5 Copynumber: 15.0 Consensus size: 5
28930078 TGTTTTATAT
28930088 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
28930138 TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA
28930163 ATTTCTTAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 70 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:28930810 original size:18 final size:17
Alignment explanation
Indices: 28930759--28930811 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
28930749 ACGCCAAATT
**
28930759 GGGCGTGTGGATCACAC
1 GGGCGTGTGGGCCACAC
28930776 GGGCGTGTGGGCCACAC
1 GGGCGTGTGGGCCACAC
28930793 GGGCGTGTGGGCCCACAC
1 GGGCGTGTGGG-CCACAC
28930811 G
1 G
28930812 AACACGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
17 26 0.79
18 7 0.21
ACGTcount: A:0.13, C:0.28, G:0.45, T:0.13
Consensus pattern (17 bp):
GGGCGTGTGGGCCACAC
Found at i:28940602 original size:9 final size:9
Alignment explanation
Indices: 28940547--28940613 Score: 55
Period size: 9 Copynumber: 7.0 Consensus size: 9
28940537 AAATTTTAAA
28940547 AAAACTTATAT
1 AAAA-TTAT-T
*
28940558 AACATTATT
1 AAAATTATT
*
28940567 AAAATCATT
1 AAAATTATT
*
28940576 AAATACTA-T
1 AAA-ATTATT
28940585 AAATTATTATT
1 AAA--ATTATT
28940596 AAAATTATT
1 AAAATTATT
28940605 AAAATTATT
1 AAAATTATT
28940614 GCAAAAAAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
9 30 0.64
10 10 0.21
11 7 0.15
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATTATT
Found at i:28941083 original size:18 final size:18
Alignment explanation
Indices: 28941060--28941109 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
28941050 TTACAACTTA
28941060 TTAAT-ATTTTTATATTTT
1 TTAATAATTTTTA-ATTTT
28941078 TTAATAATTTTTAATTTT
1 TTAATAATTTTTAATTTT
*
28941096 TCT-ATAAATTTTAA
1 T-TAATAATTTTTAA
28941110 AAGTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAATAATTTTTAATTTT
Found at i:28941085 original size:38 final size:36
Alignment explanation
Indices: 28940989--28941088 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 36
28940979 ATATTTTACA
*
28940989 ATTTTTAATTTTATTTAATGATTTTCACAATCTTTTAAT
1 ATTTTTAA-TTT-TTTAATAATTTT-ACAATCTTTTAAT
* *
28941028 -TTGTTAAATTTTTTGATAATCTTTACAA-CTTATTAAT
1 ATT-TTTAATTTTTTAATAAT-TTTACAATCTT-TTAAT
28941065 ATTTTTATATTTTTTAATAATTTT
1 ATTTTTA-ATTTTTTAATAATTTT
28941089 TAATTTTTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
36 3 0.06
37 22 0.43
38 22 0.43
39 4 0.08
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (36 bp):
ATTTTTAATTTTTTAATAATTTTACAATCTTTTAAT
Found at i:28941107 original size:19 final size:19
Alignment explanation
Indices: 28941060--28941096 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28941050 TTACAACTTA
28941060 TTAAT-ATTTTTATATTTT
1 TTAATAATTTTTATATTTT
28941078 TTAATAATTTTTA-ATTTT
1 TTAATAATTTTTATATTTT
28941096 T
1 T
28941097 CTATAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTAATAATTTTTATATTTT
Found at i:28941771 original size:17 final size:17
Alignment explanation
Indices: 28941733--28941772 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
28941723 CTCGAATTCA
28941733 TAATAAATTAAAATCAT
1 TAATAAATTAAAATCAT
* *
28941750 AAATAAATTAAAATTAT
1 TAATAAATTAAAATCAT
28941767 TAATAA
1 TAATAA
28941773 CCCAGCCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAAATTAAAATCAT
Found at i:28942286 original size:3 final size:3
Alignment explanation
Indices: 28942242--28942267 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28942232 TATTGAAAAT
28942242 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
28942268 GAAACATCAG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28945214 original size:17 final size:17
Alignment explanation
Indices: 28945192--28945227 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
28945182 TTGAAATAAT
28945192 AAATGGATAT-GAAATGG
1 AAATGGA-ATGGAAATGG
28945209 AAATGGAATGGAAATGG
1 AAATGGAATGGAAATGG
28945226 AA
1 AA
28945228 TTGTGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (17 bp):
AAATGGAATGGAAATGG
Found at i:28945225 original size:11 final size:11
Alignment explanation
Indices: 28945193--28945228 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
28945183 TGAAATAATA
* *
28945193 AATGGATATGA
1 AATGGAAATGG
28945204 AATGGAAATGG
1 AATGGAAATGG
28945215 AATGGAAATGG
1 AATGGAAATGG
28945226 AAT
1 AAT
28945229 TGTGAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (11 bp):
AATGGAAATGG
Found at i:28945248 original size:12 final size:12
Alignment explanation
Indices: 28945231--28945255 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28945221 AATGGAATTG
28945231 TGAAATATGAAA
1 TGAAATATGAAA
28945243 TGAAATATGAAA
1 TGAAATATGAAA
28945255 T
1 T
28945256 TGTGGAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
TGAAATATGAAA
Found at i:28952027 original size:12 final size:13
Alignment explanation
Indices: 28951991--28952028 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
28951981 AAATATTTGA
28951991 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
28952004 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
28952018 CTTG-TCTTAAT
1 CTTGTTCTTAAT
28952029 ATTCCAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:28955518 original size:36 final size:36
Alignment explanation
Indices: 28955449--28955524 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
28955439 TGTTATCGGG
**
28955449 TGGACTAGCTCTTATAAGCATCTGGTATGTTTTGGA
1 TGGACTAGCTCTTATAAGCATCTGGTACATTTTGGA
* * * * *
28955485 TGGATTAGCTCTTATGAGCATCTTGTGCATTTTGGT
1 TGGACTAGCTCTTATAAGCATCTGGTACATTTTGGA
28955521 TGGA
1 TGGA
28955525 ATATCGATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (36 bp):
TGGACTAGCTCTTATAAGCATCTGGTACATTTTGGA
Found at i:28957861 original size:46 final size:46
Alignment explanation
Indices: 28957794--28957969 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
28957784 TATTTGGGCA
* *
28957794 TCCGAACTTGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
28957840 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* **
28957885 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
28957933 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28957970 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 63 0.58
47 28 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:28957949 original size:93 final size:93
Alignment explanation
Indices: 28957790--28957961 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
28957780 AGGATATTTG
* * **
28957790 GGCATCCGAACTTGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAG
28957855 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
28957883 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATACCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAG
28957948 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
28957962 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:28960301 original size:46 final size:48
Alignment explanation
Indices: 28960196--28960317 Score: 149
Period size: 46 Copynumber: 2.5 Consensus size: 48
28960186 TGTCTTCGAC
** * *
28960196 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--ATATATATCTAAT
* *
28960246 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAG-C-TATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATCTAAT
*
28960292 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
28960318 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 35 0.55
49 1 0.02
50 28 0.44
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATCTAAT
Found at i:28963568 original size:29 final size:29
Alignment explanation
Indices: 28963534--28963589 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
28963524 ATAGTATCGT
*
28963534 ATCTTGGGTTTC-TTATTCTGGGTTTCTCA
1 ATCTTGGATTTCTTTATTC-GGGTTTCTCA
*
28963563 ATCTTGGATTTCTTTATTCGGTTTTCT
1 ATCTTGGATTTCTTTATTCGGGTTTCT
28963590 TGTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.11, C:0.16, G:0.18, T:0.55
Consensus pattern (29 bp):
ATCTTGGATTTCTTTATTCGGGTTTCTCA
Found at i:28967943 original size:20 final size:20
Alignment explanation
Indices: 28967911--28967948 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28967901 GCCATTTCAC
*
28967911 AATTATAAGGAATGAAATAA
1 AATTATAAGGAATAAAATAA
28967931 AATTA-AAGAGAATAAAAT
1 AATTATAAG-GAATAAAAT
28967949 TCAGAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (20 bp):
AATTATAAGGAATAAAATAA
Found at i:28968208 original size:7 final size:7
Alignment explanation
Indices: 28968196--28968286 Score: 51
Period size: 7 Copynumber: 13.0 Consensus size: 7
28968186 AAAAGAATAT
28968196 AATTGAG
1 AATTGAG
28968203 AATTGAG
1 AATTGAG
*
28968210 GATTGA-
1 AATTGAG
28968216 AGATTGAG
1 A-ATTGAG
*
28968224 GATCT-AG
1 AAT-TGAG
* *
28968231 AAATAAG
1 AATTGAG
* *
28968238 AAATGAA
1 AATTGAG
28968245 AATTGAG
1 AATTGAG
*
28968252 GATTGAG
1 AATTGAG
*
28968259 GATTGAG
1 AATTGAG
*
28968266 TATTGAG
1 AATTGAG
*
28968273 TATTGAG
1 AATTGAG
*
28968280 TATTGAG
1 AATTGAG
28968287 TTGAAAAGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
6 1 0.01
7 67 0.97
8 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.30, T:0.30
Consensus pattern (7 bp):
AATTGAG
Found at i:28968287 original size:7 final size:7
Alignment explanation
Indices: 28968246--28968287 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
28968236 AGAAATGAAA
*
28968246 ATTGAGG
1 ATTGAGT
*
28968253 ATTGAGG
1 ATTGAGT
28968260 ATTGAGT
1 ATTGAGT
28968267 ATTGAGT
1 ATTGAGT
28968274 ATTGAGT
1 ATTGAGT
28968281 ATTGAGT
1 ATTGAGT
28968288 TGAAAAGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (7 bp):
ATTGAGT
Found at i:28977911 original size:7 final size:7
Alignment explanation
Indices: 28977899--28978018 Score: 59
Period size: 7 Copynumber: 17.0 Consensus size: 7
28977889 CTAATTAATA
28977899 TAAACCC
1 TAAACCC
28977906 TAAACCTC
1 TAAACC-C
*
28977914 TAACCCC
1 TAAACCC
*
28977921 T-ACCCC
1 TAAACCC
* *
28977927 TAAATCT
1 TAAACCC
*
28977934 TAAATCC
1 TAAACCC
*
28977941 TAAACAC
1 TAAACCC
28977948 TAAA-CC
1 TAAACCC
28977954 TATAACCC
1 TA-AACCC
* *
28977962 -CATCCC
1 TAAACCC
*
28977968 TTAACCC
1 TAAACCC
*
28977975 TTAAACAC
1 -TAAACCC
28977983 TAAACCC
1 TAAACCC
*
28977990 TTAACACC
1 TAAAC-CC
*
28977998 TAACCCC
1 TAAACCC
28978005 T-AACCC
1 TAAACCC
28978011 TTAAACCC
1 -TAAACCC
28978019 CAACACATAA
Statistics
Matches: 85, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
6 17 0.20
7 45 0.53
8 23 0.27
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:28977978 original size:42 final size:42
Alignment explanation
Indices: 28977899--28978017 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
28977889 CTAATTAATA
* * *
28977899 TAAACCCTAAACCTCTAACCCCTACCCCTAAATCTTAAATC-C
1 TAAACACTAAACCTATAACCCCTACCCCTAAACCTTAAA-CAC
* *
28977941 TAAACACTAAACCTATAACCCC-ATCCCTTAACCCTTAAACAC
1 TAAACACTAAACCTATAACCCCTA-CCCCTAAACCTTAAACAC
* *
28977983 TAAACCCTTAACACC--TAACCCCTAACCCTTAAACC
1 TAAACAC-TAA-ACCTATAACCCCT-ACCCCTAAACC
28978018 CCAACACATA
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
41 2 0.03
42 46 0.72
43 12 0.19
44 4 0.06
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (42 bp):
TAAACACTAAACCTATAACCCCTACCCCTAAACCTTAAACAC
Found at i:28978000 original size:15 final size:15
Alignment explanation
Indices: 28977970--28978018 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
28977960 CCCATCCCTT
28977970 AACCCTTAA-ACACTA
1 AACCCTTAACAC-CTA
28977985 AACCCTTAACACCT-
1 AACCCTTAACACCTA
*
28977999 AACCCCTAAC-CCTTA
1 AACCCTTAACACC-TA
28978014 AACCC
1 AACCC
28978019 CAACACATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.07
14 10 0.33
15 16 0.53
16 2 0.07
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (15 bp):
AACCCTTAACACCTA
Found at i:28978007 original size:22 final size:22
Alignment explanation
Indices: 28977965--28978142 Score: 62
Period size: 22 Copynumber: 8.2 Consensus size: 22
28977955 ATAACCCCAT
* *
28977965 CCCTTAAC-CCTTAAACACTAAA
1 CCCTTAACACC-TAACCCCTAAA
28977987 CCCTTAACACCTAACCCCT-AA
1 CCCTTAACACCTAACCCCTAAA
* * * *
28978008 CCCTTAA-ACCCCAACACATAAT
1 CCCTTAACA-CCTAACCCCTAAA
* *
28978030 CCC-TAA-ACCATAATCCATAAA
1 CCCTTAACACC-TAACCCCTAAA
* ** * *
28978051 -CCTTAAAATATTAACTCATAAA
1 CCCTTAACA-CCTAACCCCTAAA
* * * * **
28978073 CCATAAACCCCTAACCCTTCTA
1 CCCTTAACACCTAACCCCTAAA
* **
28978095 CCCTTAACGCCTAACCCCTATC
1 CCCTTAACACCTAACCCCTAAA
* *
28978117 CCCTTAACACTTAACCCCTAAT
1 CCCTTAACACCTAACCCCTAAA
28978139 CCCT
1 CCCT
28978143 AACCATTAAC
Statistics
Matches: 114, Mismatches: 34, Indels: 16
0.70 0.21 0.10
Matches are distributed among these distances:
20 5 0.04
21 30 0.26
22 73 0.64
23 6 0.05
ACGTcount: A:0.37, C:0.40, G:0.01, T:0.23
Consensus pattern (22 bp):
CCCTTAACACCTAACCCCTAAA
Found at i:28978088 original size:7 final size:7
Alignment explanation
Indices: 28978078--28978160 Score: 53
Period size: 7 Copynumber: 11.7 Consensus size: 7
28978068 ATAAACCATA
28978078 AACCCCT
1 AACCCCT
28978085 AACCCTTCT
1 AACCC--CT
*
28978094 -ACCCTT
1 AACCCCT
*
28978100 AACGCCT
1 AACCCCT
28978107 AACCCCT
1 AACCCCT
*
28978114 ATCCCCTT
1 AACCCC-T
* *
28978122 AACACTT
1 AACCCCT
28978129 AACCCCT
1 AACCCCT
*
28978136 AATCCCT
1 AACCCCT
**
28978143 AACCATT
1 AACCCCT
28978150 AACCCC-
1 AACCCCT
28978156 AACCC
1 AACCC
28978161 TTAAACCACC
Statistics
Matches: 56, Mismatches: 16, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
6 6 0.11
7 40 0.71
8 8 0.14
9 2 0.04
ACGTcount: A:0.29, C:0.48, G:0.01, T:0.22
Consensus pattern (7 bp):
AACCCCT
Found at i:28978155 original size:21 final size:22
Alignment explanation
Indices: 28978095--28978141 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
28978085 AACCCTTCTA
* *
28978095 CCCTTAACGCCTAACCCCTATC
1 CCCTTAACACTTAACCCCTATC
28978117 CCCTTAACACTTAACCCCTAATC
1 CCCTTAACACTTAACCCCT-ATC
28978140 CC
1 CC
28978142 TAACCATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.26, C:0.49, G:0.02, T:0.23
Consensus pattern (22 bp):
CCCTTAACACTTAACCCCTATC
Found at i:28978168 original size:21 final size:21
Alignment explanation
Indices: 28978106--28978155 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
28978096 CCTTAACGCC
28978106 TAACCCCT-ATCCCCTTAA-CACT
1 TAACCCCTAAT-CCC-TAACCA-T
28978128 TAACCCCTAATCCCTAACCAT
1 TAACCCCTAATCCCTAACCAT
28978149 TAACCCC
1 TAACCCC
28978156 AACCCTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 11 0.42
22 13 0.50
23 2 0.08
ACGTcount: A:0.30, C:0.46, G:0.00, T:0.24
Consensus pattern (21 bp):
TAACCCCTAATCCCTAACCAT
Found at i:28978831 original size:115 final size:114
Alignment explanation
Indices: 28978695--28978988 Score: 390
Period size: 115 Copynumber: 2.5 Consensus size: 114
28978685 CATTAGCGGT
* * *
28978695 GTTTTTAAAAAAGCGCTGCTAAAGGTGTACTTATAGCGGCGTTTTTGAAAAGCGCCGCTAAAGCT
1 GTTTTTAAAAAAACGCCGCTAAAGGTGTACTT-TAGCGGCGTTTTTGAAAAGCGCCGCTAAAGCC
*
28978760 ACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAAATTCTTTTACGGC
65 ACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAAATTCTTTTACGAC
* *
28978810 GTTTTTAAAAAAACGCCGCTAAAGGTGTACTTCTGGCGGTGTTTTTGAAAAGCGCCGCTAAAGCC
1 GTTTTTAAAAAAACGCCGCTAAAGGTGTACTT-TAGCGGCGTTTTTGAAAAGCGCCGCTAAAGCC
* * *
28978875 ACTAAAAGCTTAATACAGAACGACGTCATTTTGCAAAATTCTTTTGCTAC
65 ACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAAATTCTTTTACGAC
** * * ** * * *
28978925 GTTTTTTGAAAAACGCCACTAAAGATCAAGCATTAGCGGCGTTTTTTAAAAAGCGACGCTAAAG
1 GTTTTTAAAAAAACGCCGCTAAAGGTGTA-CTTTAGCGGCG-TTTTTGAAAAGCGCCGCTAAAG
28978989 GTGTACTTAT
Statistics
Matches: 156, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
115 134 0.86
116 22 0.14
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (114 bp):
GTTTTTAAAAAAACGCCGCTAAAGGTGTACTTTAGCGGCGTTTTTGAAAAGCGCCGCTAAAGCCA
CTAAAAGCTTAATACAAAACGACGTCATTTTGCAAAATTCTTTTACGAC
Found at i:28978854 original size:155 final size:155
Alignment explanation
Indices: 28978421--28978873 Score: 564
Period size: 155 Copynumber: 2.9 Consensus size: 155
28978411 CATTTCTTGT
* *
28978421 GGCGTTTTTCAAAAAGCGCCGCTAAAGCCACTAAAAGCTCAATACAAAACGACGTCATTTTGCAA
1 GGCGTTTTT-GAAAAGCGCCGCTAAAGCTACTAAAAGCTCAATACAAAACGACGTCATTTTGCAA
* * *
28978486 AATTCTTTTGCGGCGTTTTTTAAAAAGCACCGCTAAAGGTGTACTTATAGCGGTGTTTCTTAAAA
65 AATTCTTTTGCGGCGTTTTTTAAAAAACGCCGCTAAAGGTGTACTTCTAGCGGTGTTT-TTAAAA
*
28978551 AAACGCCT-CTAATA-CTCGATCTTTAGC
129 AAGCG-CTGCTAA-AGCTCGATCTTTAGC
* * *
28978578 -GCGTTTTTGAAAAGTGCCGCTAAAG-TCACTAAAAGCTCAATACAAAACGACGTCGTTTTGAAA
1 GGCGTTTTTGAAAAGCGCCGCTAAAGCT-ACTAAAAGCTCAATACAAAACGACGTCATTTTGCAA
* * * * * *
28978641 AATTATTTTGCGGCATTTTTTGAAAAACGCCACTAAAGAT-TA-TGCATTAGCGGTGTTTTTAAA
65 AATTCTTTTGCGGCGTTTTTTAAAAAACGCCGCTAAAGGTGTACTTC--TAGCGGTGTTTTTAAA
*
28978704 AAAGCGCTGCTAAAGGT-G-TACTTATAGC
128 AAAGCGCTGCTAAAGCTCGAT-CTT-TAGC
*
28978732 GGCGTTTTTGAAAAGCGCCGCTAAAGCTACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAA
1 GGCGTTTTTGAAAAGCGCCGCTAAAGCTACTAAAAGCTCAATACAAAACGACGTCATTTTGCAAA
* * * *
28978797 ATTCTTTTACGGCGTTTTTAAAAAAACGCCGCTAAAGGTGTACTTCTGGCGGTGTTTTT-GAAAA
66 ATTCTTTTGCGGCGTTTTTTAAAAAACGCCGCTAAAGGTGTACTTCTAGCGGTGTTTTTAAAAAA
*
28978861 GCGCCGCTAAAGC
131 GCGCTGCTAAAGC
28978874 CACTAAAAGC
Statistics
Matches: 253, Mismatches: 32, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
152 1 0.00
153 8 0.03
154 36 0.14
155 195 0.77
156 11 0.04
157 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (155 bp):
GGCGTTTTTGAAAAGCGCCGCTAAAGCTACTAAAAGCTCAATACAAAACGACGTCATTTTGCAAA
ATTCTTTTGCGGCGTTTTTTAAAAAACGCCGCTAAAGGTGTACTTCTAGCGGTGTTTTTAAAAAA
GCGCTGCTAAAGCTCGATCTTTAGC
Found at i:28979090 original size:39 final size:39
Alignment explanation
Indices: 28979013--28979090 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
28979003 GCGTTTCTTA
* * **
28979013 AAAAAGTGCCGCTAATACTCGATCTTTAGTTGTGTTTTT
1 AAAAAGCGCCGCTAATACTCGATCTTTAGTGGCATTTTT
*
28979052 AAAAAGCGCCGCTAATGCTC-ATTCTTTAGTGGCATTTTT
1 AAAAAGCGCCGCTAATACTCGA-TCTTTAGTGGCATTTTT
28979091 CATTCAAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (39 bp):
AAAAAGCGCCGCTAATACTCGATCTTTAGTGGCATTTTT
Found at i:28982572 original size:13 final size:13
Alignment explanation
Indices: 28982548--28982591 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
28982538 TTTATATCTT
*
28982548 TAAAACAATTATA
1 TAAAAAAATTATA
*
28982561 TAACAAAATTATA
1 TAAAAAAATTATA
*
28982574 -AAAAAAATTACA
1 TAAAAAAATTATA
28982586 TAAAAA
1 TAAAAA
28982592 TTAAATATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAAAAATTATA
Found at i:28984026 original size:10 final size:10
Alignment explanation
Indices: 28984001--28984089 Score: 52
Period size: 9 Copynumber: 9.4 Consensus size: 10
28983991 TAATTTTTAT
*
28984001 TATTTTAGAA
1 TATTTTATAA
*
28984011 AATTTTCATAA
1 TATTTT-ATAA
28984022 T-TTTTATAA
1 TATTTTATAA
28984031 TATTTT-TAGA
1 TATTTTATA-A
*
28984041 -ATTTTAGAA
1 TATTTTATAA
28984050 -ATTTT-TAA
1 TATTTTATAA
28984058 TTACTTTTATAA
1 -TA-TTTTATAA
28984070 -A-TTTAT-A
1 TATTTTATAA
28984077 TATTTTA-AA
1 TATTTTATAA
28984086 TATT
1 TATT
28984090 ATTTTTTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 23
0.69 0.05 0.25
Matches are distributed among these distances:
7 1 0.02
8 8 0.13
9 27 0.43
10 17 0.27
11 7 0.11
12 3 0.05
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (10 bp):
TATTTTATAA
Found at i:28984037 original size:39 final size:37
Alignment explanation
Indices: 28983976--28984083 Score: 112
Period size: 39 Copynumber: 2.9 Consensus size: 37
28983966 TTTAATAATG
*
28983976 ATTTTATTAACTTTT-T-AATTTTTATTATTTTAGAAA
1 ATTTTAATAACTTTTATAAATTTTTA-TATTTTAGAAA
* * *
28984012 ATTTTCATAATTTTTATAATATTTTTAGAATTTTAGAAA
1 ATTTTAATAACTTTTATAA-ATTTTTA-TATTTTAGAAA
* * *
28984051 TTTTTAATTACTTTTATAAATTTATATATTTTA
1 ATTTTAATAACTTTTATAAATTTTTATATTTTA
28984084 AATATTATTT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
36 12 0.21
37 7 0.12
38 7 0.12
39 32 0.55
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (37 bp):
ATTTTAATAACTTTTATAAATTTTTATATTTTAGAAA
Found at i:28984054 original size:28 final size:28
Alignment explanation
Indices: 28984023--28984089 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
28984013 TTTTCATAAT
*
28984023 TTTTATAATATTTTTAGAATTTTAGAAA
1 TTTTATAATATTTTTAGAAATTTAGAAA
* * * *
28984051 TTTT-TAATTACTTTTATAAATTTATATA
1 TTTTATAA-TATTTTTAGAAATTTAGAAA
28984079 TTTTA-AATATT
1 TTTTATAATATT
28984090 ATTTTTTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTTATAATATTTTTAGAAATTTAGAAA
Found at i:28984071 original size:20 final size:19
Alignment explanation
Indices: 28983992--28984073 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
28983982 TTAACTTTTT
28983992 AATTTTT-ATTATTTTAGA
1 AATTTTTAATTATTTTAGA
* * * *
28984010 AAATTTTCATAATTTTTATA
1 AATTTTTAATTA-TTTTAGA
28984030 ATATTTTTAGA--ATTTTAGA
1 A-ATTTTTA-ATTATTTTAGA
*
28984049 AATTTTTAATTACTTTTATA
1 AATTTTTAATTA-TTTTAGA
28984069 AATTT
1 AATTT
28984074 ATATATTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
17 1 0.02
18 13 0.26
19 11 0.22
20 19 0.38
21 5 0.10
22 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (19 bp):
AATTTTTAATTATTTTAGA
Found at i:28985051 original size:19 final size:18
Alignment explanation
Indices: 28984986--28985056 Score: 78
Period size: 19 Copynumber: 4.0 Consensus size: 18
28984976 TTTTTTAAAA
28984986 TTATAAAAAA-TAT-ATT
1 TTATAAAAAATTATAATT
28985002 TTA-AAAAAATTTATAAATT
1 TTATAAAAAA-TTAT-AATT
28985021 TT-TAAAAAATTATACATT
1 TTATAAAAAATTATA-ATT
*
28985039 TTATAAAAAATTAAAATT
1 TTATAAAAAATTATAATT
28985057 AAAATTAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
15 6 0.13
16 3 0.06
17 4 0.09
18 12 0.26
19 22 0.47
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATAAAAAATTATAATT
Found at i:28985529 original size:20 final size:21
Alignment explanation
Indices: 28985495--28985541 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
28985485 AAATTTATTT
28985495 ATATTTAA-TCATTTTATAAA
1 ATATTTAATTCATTTTATAAA
** *
28985515 ATATTTAATTTTTTTTATGAA
1 ATATTTAATTCATTTTATAAA
28985536 ATATTT
1 ATATTT
28985542 TTTATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATTTAATTCATTTTATAAA
Found at i:28987201 original size:27 final size:27
Alignment explanation
Indices: 28987143--28987243 Score: 71
Period size: 27 Copynumber: 3.7 Consensus size: 27
28987133 CTGTCCCGGT
* *
28987143 GGACTATCCTATGTTTGCTGACCCAGC
1 GGACTATCCCATGTTTACTGACCCAGC
* *
28987170 AGACTATCCCATGTTTACTG-CCCCGTC
1 GGACTATCCCATGTTTACTGACCCAG-C
** * *
28987197 GGACTA-CCTTGTGTTTACTGTCCCAAC
1 GGACTATCC-CATGTTTACTGACCCAGC
* * *
28987224 AGACTACCCCGTGTTTACTG
1 GGACTATCCCATGTTTACTG
28987244 TTGCAGACTA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
26 6 0.10
27 48 0.81
28 5 0.08
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.31
Consensus pattern (27 bp):
GGACTATCCCATGTTTACTGACCCAGC
Found at i:28987244 original size:27 final size:27
Alignment explanation
Indices: 28987154--28987244 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 27
28987144 GACTATCCTA
* * * * *
28987154 TGTTTGCTGACCCAGCAGACTATCCCA
1 TGTTTACTGTCCCAACAGACTACCCCG
* ** * **
28987181 TGTTTACTGCCCCGTCGGACTACCTTG
1 TGTTTACTGTCCCAACAGACTACCCCG
28987208 TGTTTACTGTCCCAACAGACTACCCCG
1 TGTTTACTGTCCCAACAGACTACCCCG
28987235 TGTTTACTGT
1 TGTTTACTGT
28987245 TGCAGACTAT
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.18, C:0.32, G:0.19, T:0.32
Consensus pattern (27 bp):
TGTTTACTGTCCCAACAGACTACCCCG
Found at i:28990619 original size:34 final size:34
Alignment explanation
Indices: 28990581--28990659 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
28990571 ACCTTGAGAT
* *
28990581 AATATATATATCATACCAACACATCATGTGTATA
1 AATATATATATCATACCAACACATCATGTGCACA
28990615 AATATATATATCATACCAACACATCATGTGCACA
1 AATATATATATCATACCAACACATCATGTGCACA
28990649 AATATATATAT
1 AATATATATAT
28990660 GTACAAGTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.32
Consensus pattern (34 bp):
AATATATATATCATACCAACACATCATGTGCACA
Found at i:28991700 original size:43 final size:43
Alignment explanation
Indices: 28991588--28991804 Score: 267
Period size: 43 Copynumber: 5.0 Consensus size: 43
28991578 ATATCATACA
* * * * * * *
28991588 ATGCCAACATCCTAGATGTGGTCTTACATGTAACCTCATATCA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * *
28991631 ATGCC-ACTATCCCAGACAG-GGCCTTACTCGTAAACACATATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* *
28991674 ATGCCAACGTCCTAGACGTGGTCTTACACGTAATCATATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
28991717 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* *
28991760 ATTCCAACGTCCCAGATGTGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
28991803 AT
1 AT
28991805 ATCACATATA
Statistics
Matches: 152, Mismatches: 18, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
42 3 0.02
43 146 0.96
44 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:28996076 original size:38 final size:38
Alignment explanation
Indices: 28996022--28996107 Score: 154
Period size: 38 Copynumber: 2.2 Consensus size: 38
28996012 TATCATTATG
*
28996022 TTTCAAATCCGCATATGATTTCTGTCGATCTGAAGCTGC
1 TTTCAAA-CTGCATATGATTTCTGTCGATCTGAAGCTGC
28996061 TTTCAAACTGCATATGATTTCTGTCGATCTGAAGCTGC
1 TTTCAAACTGCATATGATTTCTGTCGATCTGAAGCTGC
28996099 TTTCAAACT
1 TTTCAAACT
28996108 ATCACAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 39 0.85
39 7 0.15
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (38 bp):
TTTCAAACTGCATATGATTTCTGTCGATCTGAAGCTGC
Found at i:28999229 original size:47 final size:47
Alignment explanation
Indices: 28999177--28999488 Score: 453
Period size: 47 Copynumber: 6.6 Consensus size: 47
28999167 GATAATTGTG
* *
28999177 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28999224 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
28999273 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28999320 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
28999369 ATGTGAAAGTGTATATATGTGATGAGACCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
28999416 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28999463 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
28999489 TCCCGAAGGG
Statistics
Matches: 239, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
47 148 0.62
49 91 0.38
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:28999279 original size:96 final size:96
Alignment explanation
Indices: 28999177--28999488 Score: 475
Period size: 96 Copynumber: 3.3 Consensus size: 96
28999167 GATAATTGTG
* *
28999177 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
28999242 ATGTGATAAGGCCTAATGGCCGATGTGATGA
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
28999273 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
*
28999338 ATGTGATAAGGCCTAATAGCCGATGTGATGA
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
28999369 ATGTGAAAGTGTATATATGTGATGAGACCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* * * * * * *
28999432 ATGTGACAGGGCCGAGTGGCCAACGTGATGG
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28999463 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
28999489 TCCCGAAGGG
Statistics
Matches: 197, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
94 52 0.26
96 145 0.74
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (96 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
ATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:29004342 original size:12 final size:12
Alignment explanation
Indices: 29004325--29004353 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
29004315 CTACTCAAAG
29004325 CATTCGCGACTA
1 CATTCGCGACTA
29004337 CATTCGCGACTA
1 CATTCGCGACTA
29004349 CATTC
1 CATTC
29004354 CCTTTCCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (12 bp):
CATTCGCGACTA
Found at i:29005152 original size:5 final size:5
Alignment explanation
Indices: 29005142--29005166 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29005132 TTGATTAAAA
29005142 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
29005167 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:29005990 original size:12 final size:12
Alignment explanation
Indices: 29005970--29006000 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29005960 GTGTGTCGAA
29005970 TACTGTTACCGT
1 TACTGTTACCGT
*
29005982 TATTGTTACCGT
1 TACTGTTACCGT
29005994 TACTGTT
1 TACTGTT
29006001 TTGGATTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (12 bp):
TACTGTTACCGT
Found at i:29014636 original size:94 final size:94
Alignment explanation
Indices: 29014390--29014753 Score: 370
Period size: 94 Copynumber: 3.9 Consensus size: 94
29014380 TGGGATATAT
* * *
29014390 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAAGCGTGCTGATGCATGTCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATATAA-TG-GCCGATGCATGTCC
* * * *
29014455 CGGACATGTCTTACACT--AACACAACTCT-
64 CAGACATGTCTTACACTGGCACTCATCTCTG
* * * * *
29014483 TAGCCAATG-CGTGTCCCAGACA-CGTCTTACACTGGCTATCTCTATCAA-GACCGATGCATGTC
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATC-ATAT-AATGGCCGATGCATGTC
*
29014545 CTAGACATGTCTTACACTGGCACTCATCTCTG
63 CCAGACATGTCTTACACTGGCACTCATCTCTG
* * *
29014577 TGCCGATGTCATGTCCCAGACATGTTCTTACACTGGCTATCATAGT-ATGGCTGATGCATGTCCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATA-TAATGGCCGATGCATGTCCC
* * *
29014641 AGACATGTCTTACACTAGCCCTCGT-T-TGG
65 AGACATGTCTTACACTGGCACTCATCTCT-G
* * * *
29014670 ATGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTGGCCGAAGCATGTCC
1 -TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATATA-ATGGCCGATGCATGTCC
29014734 CAGACATGTCTTACACTGGC
64 CAGACATGTCTTACACTGGC
29014754 GCACAAATCA
Statistics
Matches: 226, Mismatches: 31, Indels: 27
0.80 0.11 0.10
Matches are distributed among these distances:
91 27 0.12
92 18 0.08
93 33 0.15
94 131 0.58
95 17 0.08
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (94 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATATAATGGCCGATGCATGTCCCA
GACATGTCTTACACTGGCACTCATCTCTG
Found at i:29014655 original size:141 final size:140
Alignment explanation
Indices: 29014391--29014753 Score: 346
Period size: 141 Copynumber: 2.6 Consensus size: 140
29014381 GGGATATATT
* * * * * *
29014391 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAAGCGTGCTGATGCATGTCCC
1 GCCGATGCCATGCCCCAGACATGGTCTTACACTGGCACTCATA-ATGTG-GCCGAAGCATGTCCC
* ** * * * ** * *
29014456 GGACATGTCTTACACTAAC-A-CA-ACTCTTAGCCAATGCGTGTCCCAGACACGTCTTACACTGG
64 AGACATGTCTTACACTGGCTATCATAGT-ATGGCTGATGCATGTCCCAGACACGTCTTACACTAG
*
29014518 CTATCTC-TAT-CAA
128 C--CCTCGTATGCAA
* * * * *
29014531 GACCGATG-CATGTCCTAGACAT-GTCTTACACTGGCACTCAT-CTCTGTGCCGATGTCATGTCC
1 G-CCGATGCCATGCCCCAGACATGGTCTTACACTGGCACTCATAATGTG-GCCGAAG-CATGTCC
*
29014593 CAGACATGTTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCAGACATGTCTTACACTA
63 CAGACATG-TCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCAGACACGTCTTACACTA
* * *
29014658 GCCCTCGTTTGGAT
127 GCCCTCGTATGCAA
*
29014672 GCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCCAG
1 GCCGATGCCATGCCCCAGACATGGTCTTACACTGGCACTCATAATGTGGCCGAAGCATGTCCCAG
29014737 ACATGTCTTACACTGGC
66 ACATGTCTTACACTGGC
29014754 GCACAAATCA
Statistics
Matches: 184, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
137 8 0.04
138 14 0.08
139 31 0.17
140 35 0.19
141 67 0.36
142 26 0.14
143 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (140 bp):
GCCGATGCCATGCCCCAGACATGGTCTTACACTGGCACTCATAATGTGGCCGAAGCATGTCCCAG
ACATGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCAGACACGTCTTACACTAGCCC
TCGTATGCAA
Found at i:29014724 original size:48 final size:46
Alignment explanation
Indices: 29014390--29014753 Score: 287
Period size: 47 Copynumber: 7.8 Consensus size: 46
29014380 TGGGATATAT
*
29014390 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAAGCG
1 TGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAT--GTG
* * ** * *
29014440 TGCTGATGCATGTCCCGGACATGTCTTACACT--AACACA-ACTCT-
1 TGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATA-TGTG
* * * **
29014483 TAGCCAATGCGTGTCCCAGACACGTCTTACACTGGCTATCTC-TATCAAG
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTGGC--TCTCATAT-GTG
* * * * *
29014532 -ACCGATGCATGTCCTAGACATGTCTTACACTGGCACTCATCTCTG
1 TGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATGTG
* *
29014577 TGCCGATGTCATGTCCCAGACATGTTCTTACACTGGCTATCATA-GTA
1 TGCCGATG-CATGTCCCAGACATG-TCTTACACTGGCTCTCATATGTG
* * * * *
29014624 TGGCTGATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTTTG-G
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATGTG
*
29014670 ATGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 -TGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-ATGTG
*
29014720 -GCCGAAGCATGTCCCAGACATGTCTTACACTGGC
1 TGCCGATGCATGTCCCAGACATGTCTTACACTGGC
29014754 GCACAAATCA
Statistics
Matches: 246, Mismatches: 48, Indels: 44
0.73 0.14 0.13
Matches are distributed among these distances:
43 1 0.00
44 26 0.11
45 5 0.02
46 45 0.18
47 89 0.36
48 57 0.23
49 15 0.06
50 8 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATGTG
Found at i:29034412 original size:29 final size:30
Alignment explanation
Indices: 29034348--29034429 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
29034338 AATATCAAAA
*
29034348 TTATATATAAATTTTGATTTAATGTGTAATG
1 TTATATATGAATTTTGATTT-ATGTGTAATG
* * * *
29034379 CTATACATGAATTTTGATTT-TGTGTTATT
1 TTATATATGAATTTTGATTTATGTGTAATG
*
29034408 TTATATATGAAAATTTGATTTA
1 TTATATATG-AATTTTGATTTA
29034430 ATTTAATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 14 0.34
30 10 0.24
31 17 0.41
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (30 bp):
TTATATATGAATTTTGATTTATGTGTAATG
Found at i:29038833 original size:22 final size:23
Alignment explanation
Indices: 29038808--29038853 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29038798 CAACCAAACC
29038808 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
29038830 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
29038853 A
1 A
29038854 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:29038859 original size:23 final size:23
Alignment explanation
Indices: 29038815--29038859 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29038805 ACCAATTCAA
*
29038815 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
29038838 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
29038860 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:29045185 original size:22 final size:22
Alignment explanation
Indices: 29045157--29045200 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29045147 AAATAAAAAG
29045157 CCATGTCCATGTTTTTCATTCT
1 CCATGTCCATGTTTTTCATTCT
29045179 CCATGTCCATGTTTTTCATTCT
1 CCATGTCCATGTTTTTCATTCT
29045201 TTCTTGCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.09, T:0.50
Consensus pattern (22 bp):
CCATGTCCATGTTTTTCATTCT
Found at i:29057647 original size:22 final size:23
Alignment explanation
Indices: 29057622--29057667 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29057612 CAACCAAACC
29057622 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
29057644 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
29057667 A
1 A
29057668 CGTCATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:29057673 original size:23 final size:22
Alignment explanation
Indices: 29057629--29057678 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
29057619 ACCAATTCAA
*
29057629 CATATTTTCAAGATAAATTCAT
1 CATATTTTCAAGATAAAGTCAT
*
29057651 GCATATTTAT-AAGATAACGTCAT
1 -CATATTT-TCAAGATAAAGTCAT
29057674 CATAT
1 CATAT
29057679 ACCCAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
CATATTTTCAAGATAAAGTCAT
Found at i:29060763 original size:20 final size:20
Alignment explanation
Indices: 29060738--29060781 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29060728 AACATACATC
*
29060738 CTCTATTTTGTTCTGTTCTG
1 CTCTATTTTATTCTGTTCTG
*
29060758 CTCTATTTTATTTTGTTCTG
1 CTCTATTTTATTCTGTTCTG
29060778 CTCT
1 CTCT
29060782 GTTCAGTTCA
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:0.07, C:0.20, G:0.11, T:0.61
Consensus pattern (20 bp):
CTCTATTTTATTCTGTTCTG
Found at i:29064352 original size:49 final size:49
Alignment explanation
Indices: 29064295--29064477 Score: 267
Period size: 49 Copynumber: 3.7 Consensus size: 49
29064285 CTGGTACCTA
*
29064295 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* * * * *
29064344 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCCGGTACACG
*
29064395 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* *
29064444 TAGTAGCCTACACTTAGTACTACACAGGTGACCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCA
29064478 CACAATAGAT
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 72 0.61
50 6 0.05
51 40 0.34
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
Found at i:29064422 original size:100 final size:100
Alignment explanation
Indices: 29064294--29064474 Score: 326
Period size: 100 Copynumber: 1.8 Consensus size: 100
29064284 TCTGGTACCT
* *
29064294 ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGATACACGTAGTAGCCTGCACTT
1 ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGATACACGTAGTAGCCTACACTT
29064359 AGTACTACACACGTGATCGAAGTTATCGGGTACGC
66 AGTACTACACACGTGATCGAAGTTATCGGGTACGC
*
29064394 ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGGTACACGTAGTAGCCTACACTT
1 ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGATACACGTAGTAGCCTACACTT
*
29064459 AGTACTACACAGGTGA
66 AGTACTACACACGTGA
29064475 CCACACAATA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 77 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (100 bp):
ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGATACACGTAGTAGCCTACACTT
AGTACTACACACGTGATCGAAGTTATCGGGTACGC
Found at i:29070424 original size:33 final size:34
Alignment explanation
Indices: 29070387--29070450 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
29070377 CTTAAAGTTT
*
29070387 TAGTATGTGAA-CCCCATATTATATAGTATGACG
1 TAGTATGCGAACCCCCATATTATATAGTATGACG
*
29070420 TAGTATGCGAACCCCCATGTTATATAGTATG
1 TAGTATGCGAACCCCCATATTATATAGTATG
29070451 TGATTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (34 bp):
TAGTATGCGAACCCCCATATTATATAGTATGACG
Found at i:29070478 original size:15 final size:15
Alignment explanation
Indices: 29070458--29070597 Score: 63
Period size: 15 Copynumber: 9.5 Consensus size: 15
29070448 ATGTGATTTA
29070458 ATATGTGTGAACCCT
1 ATATGTGTGAACCCT
* *
29070473 ATATGTGCGAACCTT
1 ATATGTGTGAACCCT
** * *
29070488 GCATGTG-CAGATCCT
1 ATATGTGTGA-ACCCT
*
29070503 ATATGTGCGAACCCT
1 ATATGTGTGAACCCT
**
29070518 ATA-GATGTGAACTAT
1 ATATG-TGTGAACCCT
* ** * *
29070533 AGATACGTAAACCTT
1 ATATGTGTGAACCCT
* *
29070548 AGATGTG-CAA-CCT
1 ATATGTGTGAACCCT
*
29070561 ATATGTGTGAACCTT
1 ATATGTGTGAACCCT
*
29070576 ATATGTGTGAACGCT
1 ATATGTGTGAACCCT
*
29070591 ACATGTG
1 ATATGTG
29070598 AACATGTCAT
Statistics
Matches: 89, Mismatches: 30, Indels: 12
0.68 0.23 0.09
Matches are distributed among these distances:
13 8 0.09
14 6 0.07
15 74 0.83
16 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (15 bp):
ATATGTGTGAACCCT
Found at i:29070573 original size:28 final size:28
Alignment explanation
Indices: 29070470--29070582 Score: 99
Period size: 28 Copynumber: 3.9 Consensus size: 28
29070460 ATGTGTGAAC
29070470 CCTATATGTGCGAACCTT-GCATGTGCAGA
1 CCTATATGTGCGAACCTTAG-ATGTGCA-A
29070499 TCCTATATGTGCGAACCCTATAGATGTG-AA
1 -CCTATATGTGCGAA-CCT-TAGATGTGCAA
*
29070529 -CTATA-GATACGTAAACCTTAGATGTGCAA
1 CCTATATG-TGCG--AACCTTAGATGTGCAA
* *
29070558 CCTATATGTGTGAACCTTATATGTG
1 CCTATATGTGCGAACCTTAGATGTG
29070583 TGAACGCTAC
Statistics
Matches: 70, Mismatches: 4, Indels: 20
0.74 0.04 0.21
Matches are distributed among these distances:
27 1 0.01
28 28 0.40
29 5 0.07
30 24 0.34
31 5 0.07
32 6 0.09
33 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (28 bp):
CCTATATGTGCGAACCTTAGATGTGCAA
Found at i:29072215 original size:43 final size:43
Alignment explanation
Indices: 29072167--29072338 Score: 165
Period size: 43 Copynumber: 4.0 Consensus size: 43
29072157 GTTATCGAGA
*
29072167 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
* * *
29072210 TGTGATTACGTGTAAGACCATGT-TTGGAACATTGGC-TTCATTAT
1 TGTGATTACATGTAAGACCATGTCTAGG-ACATTGGCATT--GTAT
* * * * *
29072254 T-TGATTTCATGTAAGACCCTGTTTAGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
* * *
29072295 ATGTGATAACATGTAAGACCATATCTAGGATA-TGGCATTGTAT
1 -TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
29072338 T
1 T
29072339 AGATATATGT
Statistics
Matches: 104, Mismatches: 17, Indels: 17
0.75 0.12 0.12
Matches are distributed among these distances:
41 2 0.02
42 14 0.13
43 80 0.77
44 8 0.08
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
Found at i:29081382 original size:26 final size:27
Alignment explanation
Indices: 29081318--29081389 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
29081308 TTAGGGTGAG
*
29081318 AAATTACTATTTTACCCCTAAGTATGA
1 AAATTACTATTATACCCCTAAGTATGA
* *
29081345 AAATTACCATTATACCCCT-AG-GTGCA
1 AAATTACTATTATACCCCTAAGTATG-A
*
29081371 AAATGACTATTATACCCCT
1 AAATTACTATTATACCCCT
29081390 TGGGTTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.05
26 20 0.51
27 17 0.44
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (27 bp):
AAATTACTATTATACCCCTAAGTATGA
Found at i:29081524 original size:27 final size:26
Alignment explanation
Indices: 29081494--29081607 Score: 156
Period size: 27 Copynumber: 4.3 Consensus size: 26
29081484 TGGAGGAAGC
29081494 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
29081521 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
29081548 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * *
29081574 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
29081601 GTTCTGG
1 GTTCTGG
29081608 CAGCTCTGCT
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
26 14 0.17
27 68 0.83
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:29082950 original size:49 final size:47
Alignment explanation
Indices: 29082813--29082987 Score: 154
Period size: 49 Copynumber: 3.6 Consensus size: 47
29082803 AGATGCCGAC
* * *
29082813 GCCATGTCCCAGACATGGTCTTATACTGGCTAGCAC-ATCAAAGTCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTATCACTATCGAA-TCGAT
* * * * * *
29082861 GTCATGTCCCACACAGGTCTTACACTGACTTTCAAATATCGAATCCAAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTATC-ACTATCGAAT-CGAT
* * * * *
29082910 CCCATGTCCCAGACAGGTCTTATACTGGCTCTCATCTATCGATGTTGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTATCA-CTATCGA-ATCGAT
*
29082959 GCCATGTCCCAGACATGTCTTACACTGGC
1 GCCATGTCCCAGACAGGTCTTACACTGGC
29082988 ACGCAACAAG
Statistics
Matches: 100, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
47 14 0.14
48 16 0.16
49 69 0.69
50 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTATCACTATCGAATCGAT
Found at i:29084816 original size:22 final size:21
Alignment explanation
Indices: 29084790--29084832 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29084780 TTACTGTTAT
29084790 TGATTGTTTGATACTGAATAAC
1 TGATTG-TTGATACTGAATAAC
* *
29084812 TGATTGTTGTTATTGAATAAC
1 TGATTGTTGATACTGAATAAC
29084833 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (21 bp):
TGATTGTTGATACTGAATAAC
Found at i:29091698 original size:21 final size:19
Alignment explanation
Indices: 29091669--29091716 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
29091659 ATAAACCGAA
*
29091669 TTTAATATTTAAATTGTTGTT
1 TTTATTATTTAAA-TG-TGTT
*
29091690 TTTATTA-TTATATGTGTT
1 TTTATTATTTAAATGTGTT
29091708 TTTATTATT
1 TTTATTATT
29091717 ATATATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.46
19 3 0.12
20 4 0.17
21 6 0.25
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTATTATTTAAATGTGTT
Found at i:29091717 original size:21 final size:20
Alignment explanation
Indices: 29091683--29091724 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
29091673 ATATTTAAAT
29091683 TGTTGTTTTTATTATTATATG
1 TGTTGTTTTTATTA-TATATG
29091704 TGTT-TTTATTATTATATATG
1 TGTTGTTT-TTATTATATATG
29091724 T
1 T
29091725 ATGGAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TGTTGTTTTTATTATATATG
Done.