Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_pilon, whole genome shotgun sequence
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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 16
Found at i:2786202 original size:8 final size:8
Alignment explanation
Indices: 2786191--2786227 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
2786181 TTATACATAC
2786191 ATTTTTAT
1 ATTTTTAT
2786199 ATTTTTAT
1 ATTTTTAT
2786207 ATTTTTTAT
1 A-TTTTTAT
2786216 ATTTTT-T
1 ATTTTTAT
2786223 ATTTT
1 ATTTT
2786228 ATTTATACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 6 0.21
8 14 0.50
9 8 0.29
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
ATTTTTAT
Found at i:2786212 original size:9 final size:9
Alignment explanation
Indices: 2786192--2786234 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
2786182 TATACATACA
2786192 TTTTTATA-
1 TTTTTATAT
2786200 TTTTTATAT
1 TTTTTATAT
2786209 TTTTTATAT
1 TTTTTATAT
2786218 TTTTTAT-T
1 TTTTTATAT
2786226 TTATTTATA
1 TT-TTTATA
2786235 CTATTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 11 0.34
9 21 0.66
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTATAT
Found at i:2786214 original size:17 final size:16
Alignment explanation
Indices: 2786192--2786227 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
2786182 TATACATACA
2786192 TTTTTATATTTTTATAT
1 TTTTTATATTTTT-TAT
2786209 TTTTTATATTTTTTAT
1 TTTTTATATTTTTTAT
2786225 TTT
1 TTT
2786228 ATTTATACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTATATTTTTTAT
Found at i:2786221 original size:18 final size:16
Alignment explanation
Indices: 2786192--2786249 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 16
2786182 TATACATACA
2786192 TTTTTATATTTTTATAT
1 TTTTTATATTTTTAT-T
2786209 TTTTTATATTTTTTATT
1 TTTTTATA-TTTTTATT
*
2786226 TTATTTATACTATTTATT
1 TT-TTTATA-TTTTTATT
2786244 TATTTT
1 T-TTTT
2786250 CATTATGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
17 11 0.31
18 24 0.67
19 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTATATTTTTATT
Found at i:2790993 original size:16 final size:15
Alignment explanation
Indices: 2790956--2791024 Score: 81
Period size: 14 Copynumber: 4.7 Consensus size: 15
2790946 AGATTCAATC
* *
2790956 AGAACAAAAAGGGAA
1 AGAACAAAAAAGAAA
2790971 A-AACAAAAAAGAAA
1 AGAACAAAAAAGAAA
2790985 AGAAGCAAAAAAGAAGA
1 AGAA-CAAAAAAGAA-A
2791002 A-AACAAAAAA-AAA
1 AGAACAAAAAAGAAA
2791015 AGAACAAAAA
1 AGAACAAAAA
2791025 TCAAAAAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
13 2 0.04
14 22 0.46
15 10 0.21
16 12 0.25
17 2 0.04
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.00
Consensus pattern (15 bp):
AGAACAAAAAAGAAA
Found at i:2791003 original size:19 final size:19
Alignment explanation
Indices: 2790969--2791038 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
2790959 ACAAAAAGGG
* *
2790969 AAAAACAAAA-AAGAAAAG
1 AAAAAAAAAAGAAGAAAAC
**
2790987 AAGCAAAAAAGAAGAAAAC
1 AAAAAAAAAAGAAGAAAAC
*
2791006 AAAAAAAAAAGAACAAAAATC
1 AAAAAAAAAAGAA-GAAAA-C
2791027 AAAAAGAAAAAG
1 AAAAA-AAAAAG
2791039 GGACAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 7 0.17
19 18 0.44
20 4 0.10
21 6 0.15
22 6 0.15
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.01
Consensus pattern (19 bp):
AAAAAAAAAAGAAGAAAAC
Found at i:2791030 original size:16 final size:14
Alignment explanation
Indices: 2790972--2791034 Score: 65
Period size: 16 Copynumber: 4.1 Consensus size: 14
2790962 AAAAGGGAAA
2790972 AACAAAAAAGAAAAG
1 AACAAAAAA-AAAAG
2790987 AAGCAAAAAAGAAGAA-
1 AA-CAAAAAA-AA-AAG
2791003 AACAAAAAAAAAAG
1 AACAAAAAAAAAAG
2791017 AACAAAAATCAAAAAG
1 AACAAAAA--AAAAAG
2791033 AA
1 AA
2791035 AAAGGGACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.05
14 10 0.23
15 9 0.21
16 20 0.47
17 2 0.05
ACGTcount: A:0.79, C:0.08, G:0.11, T:0.02
Consensus pattern (14 bp):
AACAAAAAAAAAAG
Found at i:2791672 original size:22 final size:22
Alignment explanation
Indices: 2791641--2791695 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2791631 GCTACCCCAT
2791641 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
2791663 CAAACTTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
2791685 CAAACCTTTGA
1 CAAACCTTTGA
2791696 CCAAACACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:2792770 original size:106 final size:106
Alignment explanation
Indices: 2792653--2795610 Score: 4450
Period size: 106 Copynumber: 27.9 Consensus size: 106
2792643 TGAGACATCA
* * * * * *
2792653 CAAGTTCAACTTCTCAACGAAGGGACGGCTGGTTATCAACAAACAACTTCCCAAATTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2792718 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATAG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA-CG
* * *
2792760 -AAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2792824 ATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
2792865 CAAGTTCAACTTCACAACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
2792930 ATTTCAACTTCTCAGCGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
2792971 CAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
2793036 ATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* ** * *
2793077 CAAGTTCAACTTCACGATGAAGGGACCATTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
2793142 ATTTTAACTTCACAATGAAGGATATTGGACTCCAGACAAAG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
2793183 CAATTTCAACTTCACGACGAAGAGATCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
2793248 ACTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2793289 CAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * * *
2793354 AATTCAACTTCAGAGA-AAAAGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACA-ACGAAGGATATTGGACTCCAGACAACG
* * * * *
2793395 CAAGTTCAACTTCACGATGAAAGGACAGCTGGTTGTCAAAAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
** *
2793460 ATTTCAACTTCACAGTGAAGGATATTGGACTCTAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
2793501 CAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTCAGAGCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * * *
2793566 ATTTTAACTTCACAAAGAGGGATATTGGACTCCAGACAATG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
2793607 CAAGTTCAACTTCACGATGAAGGAACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * * *
2793672 ATTTCAACTTCACAGCGAACGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
2793713 CAAGTTCAACTTCACGACGAAGAGACTGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
2793778 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2793819 CAAGTTCAATTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
2793884 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2793925 CAAGTTCAATTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2793990 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* ** * * *
2794031 CAAGTTCAACTTCAGGACGAAGGGAATGCTGGTCGTCAACAATCAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
2794096 ATTTCAACTTCACAGCGAAGGATATTGGACTCCGGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* **
2794137 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTAAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
2794202 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* **
2794243 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAACAAACAATTTCCCAATTTTGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
2794308 ATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * **
2794349 CAAGTTCAACTTCACAACGAAGGGA-TGACTGGTTGTCAACAAACAACGTCCCAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
*
2794413 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACG
65 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
2794455 CAAGTTCAACTTTACGACGAAGGGACTGCTGGTTGTCAACAAATAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
2794520 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2794561 CAAGTTCAACTTCACGACGAAGGGACCGCTTGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2794626 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
2794667 CAAGTTTAACTTCACGACGAAGGGACCGCTGGTTATCAACAAACAACTTCTCAATTTCAGAGCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
2794732 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2794773 CAAGTTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
2794838 ATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
2794879 CAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2794944 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2794985 CAAGTTCAACTTCACGACGAAGGGACTGTTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2795050 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
2795091 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2795156 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
2795197 CAAGTTC-ACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTCAAGTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* **
2795261 ATTTCAACTTCACAACGAAGAATATTGGACTAGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2795302 CAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
2795367 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
2795408 CATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * * *
2795473 ATTTCAACTTCACAACAAAGGGTATTGGACTCGAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
2795514 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGATTCCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2795579 ATTTCAACTTCACGAA-GGAGGATATTGGACTC
66 ATTTCAACTTCAC-AACGAAGGATATTGGACTC
2795611 AGAACAATTC
Statistics
Matches: 2608, Mismatches: 236, Indels: 15
0.91 0.08 0.01
Matches are distributed among these distances:
105 98 0.04
106 2506 0.96
107 4 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:2796448 original size:37 final size:37
Alignment explanation
Indices: 2796359--2796462 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
2796349 CTTTTCATCC
* *
2796359 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* *
2796396 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
2796433 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
2796463 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:2796908 original size:19 final size:18
Alignment explanation
Indices: 2796884--2796930 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2796874 AATATATATA
2796884 TATTTAATTATATT-TAATT
1 TATTT-ATT-TATTATAATT
2796903 TATTTATTTATTATAATT
1 TATTTATTTATTATAATT
2796921 T-TTT-TTTATT
1 TATTTATTTATT
2796931 TTTCTTTGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.22
17 7 0.26
18 9 0.33
19 5 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTTATTTATTATAATT
Found at i:2796921 original size:10 final size:9
Alignment explanation
Indices: 2796884--2796921 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
2796874 AATATATATA
2796884 TATTTAATT
1 TATTTAATT
2796893 ATATTTAATT
1 -TATTTAATT
2796903 TATTT-ATT
1 TATTTAATT
2796911 TATTATAATT
1 TATT-TAATT
2796921 T
1 T
2796922 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 6 0.23
10 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTAATT
Found at i:2796970 original size:2 final size:2
Alignment explanation
Indices: 2796963--2797001 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2796953 ATTTTCCTAT
2796963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2797002 TTATTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2797044 original size:13 final size:13
Alignment explanation
Indices: 2797026--2797051 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2797016 TGTTTACTTA
2797026 TTTACTATATTTT
1 TTTACTATATTTT
2797039 TTTACTATATTTT
1 TTTACTATATTTT
2797052 CCCAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:2797254 original size:29 final size:29
Alignment explanation
Indices: 2797198--2797261 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
2797188 TATACATACA
* **
2797198 TTTTTATATATTTTTTTATTTTTTTTAT-
1 TTTTTATATATTTATTTATTTTCATTATG
2797226 TTTTTATACTATTTATTTATTTTCATTATG
1 TTTTTATA-TATTTATTTATTTTCATTATG
2797256 TTTTTA
1 TTTTTA
2797262 GTTTCTTTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 8 0.26
29 17 0.55
30 6 0.19
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (29 bp):
TTTTTATATATTTATTTATTTTCATTATG
Found at i:2799107 original size:17 final size:17
Alignment explanation
Indices: 2799075--2799161 Score: 93
Period size: 17 Copynumber: 5.1 Consensus size: 17
2799065 TAAGATATAG
*
2799075 TTTAATAAATGAACTAT
1 TTTAATCAATGAACTAT
* * * *
2799092 TTTGATGAATGGACTAG
1 TTTAATCAATGAACTAT
2799109 TTTAATCAATGAACTAT
1 TTTAATCAATGAACTAT
* * * *
2799126 TTTGATGAATGGACTAG
1 TTTAATCAATGAACTAT
2799143 TTTAATCAATGAACTAT
1 TTTAATCAATGAACTAT
2799160 TT
1 TT
2799162 AGTTAAATGA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (17 bp):
TTTAATCAATGAACTAT
Found at i:2799111 original size:34 final size:34
Alignment explanation
Indices: 2799072--2799161 Score: 171
Period size: 34 Copynumber: 2.6 Consensus size: 34
2799062 AATTAAGATA
*
2799072 TAGTTTAATAAATGAACTATTTTGATGAATGGAC
1 TAGTTTAATCAATGAACTATTTTGATGAATGGAC
2799106 TAGTTTAATCAATGAACTATTTTGATGAATGGAC
1 TAGTTTAATCAATGAACTATTTTGATGAATGGAC
2799140 TAGTTTAATCAATGAACTATTT
1 TAGTTTAATCAATGAACTATTT
2799162 AGTTAAATGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.40
Consensus pattern (34 bp):
TAGTTTAATCAATGAACTATTTTGATGAATGGAC
Found at i:2801675 original size:6 final size:6
Alignment explanation
Indices: 2801661--2801694 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
2801651 ATTTTTCACT
*
2801661 TTCCTTC TTCCTC TTCCTC TGCCTC TTCCTC TTC
1 TTCC-TC TTCCTC TTCCTC TTCCTC TTCCTC TTC
2801695 ATTTTCTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (6 bp):
TTCCTC
Found at i:2803360 original size:19 final size:19
Alignment explanation
Indices: 2803336--2803377 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2803326 GAATGGTTTG
2803336 GCTCCGAGAAAAATAGAAT
1 GCTCCGAGAAAAATAGAAT
2803355 GCTCCGAGAAAAATAGAAT
1 GCTCCGAGAAAAATAGAAT
2803374 GCTC
1 GCTC
2803378 GGAGGGAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (19 bp):
GCTCCGAGAAAAATAGAAT
Found at i:2812874 original size:6 final size:6
Alignment explanation
Indices: 2812863--2812906 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
2812853 TGTCTTCAAC
2812863 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT AT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT AT
2812907 GGAATTCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:2817778 original size:2 final size:2
Alignment explanation
Indices: 2817773--2817813 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2817763 ATTGTATACA
2817773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2817814 ACAATACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2818420 original size:19 final size:19
Alignment explanation
Indices: 2818396--2818436 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2818386 GTTGAGTCAA
*
2818396 TAAATTATATTTTATTATT
1 TAAATTATATTTAATTATT
* *
2818415 TAAATTTTATTTAATTTTT
1 TAAATTATATTTAATTATT
2818434 TAA
1 TAA
2818437 TCCGAGTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TAAATTATATTTAATTATT
Found at i:2826454 original size:2 final size:2
Alignment explanation
Indices: 2826447--2826483 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2826437 TCAATCTACA
2826447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2826484 ATTTATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2833071 original size:18 final size:20
Alignment explanation
Indices: 2833048--2833084 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2833038 AAGATATAGA
2833048 ATATGAA-A-ATAAGAGATC
1 ATATGAAGAGATAAGAGATC
2833066 ATATGAAGAGATAAGAGAT
1 ATATGAAGAGATAAGAGAT
2833085 AGAAAGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.22
Consensus pattern (20 bp):
ATATGAAGAGATAAGAGATC
Found at i:2843140 original size:19 final size:20
Alignment explanation
Indices: 2843115--2843166 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
2843105 AGTATTGTAA
*
2843115 TGTATGAATAGTACCGATAT
1 TGTATGAATAGTACAGATAT
*
2843135 TG-ATGAATAGTACATATAT
1 TGTATGAATAGTACAGATAT
*
2843154 TGTGTGAATAGTA
1 TGTATGAATAGTA
2843167 ATAAACAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (20 bp):
TGTATGAATAGTACAGATAT
Found at i:2843194 original size:30 final size:30
Alignment explanation
Indices: 2843158--2843214 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2843148 ATATATTGTG
*
2843158 TGAATAGTAATAAACAATATCGATACTATA
1 TGAATAGCAATAAACAATATCGATACTATA
* **
2843188 TGAATAGCAATGAACTGTATCGATACT
1 TGAATAGCAATAAACAATATCGATACT
2843215 CAAAAATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (30 bp):
TGAATAGCAATAAACAATATCGATACTATA
Found at i:2843263 original size:20 final size:20
Alignment explanation
Indices: 2843238--2843282 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2843228 TGCGAAATGG
*
2843238 GTATCGATACTGCTATAGTA
1 GTATCGATACTGCTACAGTA
2843258 GTATCGATACTGCTACAGTA
1 GTATCGATACTGCTACAGTA
*
2843278 ATATC
1 GTATC
2843283 TAGCCCAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (20 bp):
GTATCGATACTGCTACAGTA
Found at i:2848315 original size:138 final size:137
Alignment explanation
Indices: 2848067--2848351 Score: 376
Period size: 138 Copynumber: 2.1 Consensus size: 137
2848057 TACACCTAAG
* * * *
2848067 TGTCGAAATGGAAATTCACAAACTCAATATGAATTCCATGGATGCACACATAGTGCCGAAAGTAC
1 TGTCGAAATGGAAATTCACAAACTCAATATAAATACCATGGATGCACACATAGTGCCAAAAATAC
* * * **
2848132 ATATAGTACTAATACAAAAATGCACCGTTATGCATTTAACAAAATCGATCGATAACTTTTATACA
66 ACAAAGTACTAATACAAAAATGCACCGTTATGCATTTAACAAAATCGATCAATAACCATTATACA
*
2848197 TAATTGTA
131 CAATT-TA
* * *
2848205 TGTCGAAATGGTAATTCACAAACTCATTATAAATACCATGGTTGCACATC-TAGTGCCAAAAATA
1 TGTCGAAATGGAAATTCACAAACTCAATATAAATACCATGGATGCACA-CATAGTGCCAAAAATA
* *
2848269 CGCAAAGTACTGATACAAAAATGCACCGTTATGCA-TTACACAAAATCGATCAATAACCATTATA
65 CACAAAGTACTAATACAAAAATGCACCGTTATGCATTTA-ACAAAATCGATCAATAACCATTATA
*
2848333 TACAATTTA
129 CACAATTTA
*
2848342 TGTTGAAATG
1 TGTCGAAATG
2848352 CACATATGAC
Statistics
Matches: 128, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
137 14 0.11
138 113 0.88
139 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (137 bp):
TGTCGAAATGGAAATTCACAAACTCAATATAAATACCATGGATGCACACATAGTGCCAAAAATAC
ACAAAGTACTAATACAAAAATGCACCGTTATGCATTTAACAAAATCGATCAATAACCATTATACA
CAATTTA
Found at i:2848546 original size:20 final size:21
Alignment explanation
Indices: 2848510--2848549 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2848500 ATCATTCCCA
2848510 TAAACATTATGAAAACATATC
1 TAAACATTATGAAAACATATC
*
2848531 TAAATATTAT-AAAACATAT
1 TAAACATTATGAAAACATAT
2848550 TTTTATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (21 bp):
TAAACATTATGAAAACATATC
Found at i:2849010 original size:20 final size:20
Alignment explanation
Indices: 2848987--2849036 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
2848977 CTTCCTTTTG
2848987 GTATCGATACCTAC-ACATCA
1 GTATCGATA-CTACTACATCA
*
2849007 GTATCGATACTACTTGCATCA
1 GTATCGATACTAC-TACATCA
2849028 GTATCGATA
1 GTATCGATA
2849037 TTGTTCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 9 0.33
21 14 0.52
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (20 bp):
GTATCGATACTACTACATCA
Found at i:2854892 original size:3 final size:3
Alignment explanation
Indices: 2854884--2854916 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2854874 TCGAATGTTT
2854884 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2854917 AGATGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2859879 original size:32 final size:32
Alignment explanation
Indices: 2859838--2859902 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2859828 CAAAACCATG
*
2859838 TTCAACCCAAAAGGCACCTATTTTCTTCATAC
1 TTCAACCCAAAAGGCACCTATTTGCTTCATAC
*
2859870 TTCAACCCAAAAGGCACCTATTTGCTTTATAC
1 TTCAACCCAAAAGGCACCTATTTGCTTCATAC
2859902 T
1 T
2859903 CTCATACAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.32
Consensus pattern (32 bp):
TTCAACCCAAAAGGCACCTATTTGCTTCATAC
Found at i:2860973 original size:84 final size:85
Alignment explanation
Indices: 2860826--2861019 Score: 216
Period size: 84 Copynumber: 2.3 Consensus size: 85
2860816 GAGTATGATT
* * * *
2860826 GTTCCTTGATTTGGCGTCATTTAGAAAAATGATCAGATCAACTATTAATTACGACTTGTCATCCT
1 GTTCCTTGATTTGGCGTCATTTAGAAAAAAGAGCAGATCAACTATTAATTACAACTTGGCATCCT
2860891 T-AATAGAAATGAACAAGATC
66 TCAA-AGAAATGAACAAGATC
* * *
2860911 GTTCTTTGATTTGGTGTC-TTTA-AAAAAGAGAGCAGATTAA-TCATTAATTACAACTTGGCATC
1 GTTCCTTGATTTGGCGTCATTTAGAAAAA-AGAGCAGATCAACT-ATTAATTACAACTTGGCATC
*
2860973 CTTCAAAGAAATGAGCAAGATC
64 CTTCAAAGAAATGAACAAGATC
* * * * *
2860995 ATTACTCGATTTGGCATCCTTTAGA
1 GTTCCTTGATTTGGCGTCATTTAGA
2861020 GAAAGGATAA
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
83 6 0.07
84 61 0.68
85 22 0.24
86 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (85 bp):
GTTCCTTGATTTGGCGTCATTTAGAAAAAAGAGCAGATCAACTATTAATTACAACTTGGCATCCT
TCAAAGAAATGAACAAGATC
Found at i:2862895 original size:15 final size:16
Alignment explanation
Indices: 2862864--2862896 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2862854 AGTATGTTAA
2862864 AAATTATTTTCATTTT
1 AAATTATTTTCATTTT
2862880 AAATTATTTT-ATTTT
1 AAATTATTTTCATTTT
2862895 AA
1 AA
2862897 TCATTTACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
AAATTATTTTCATTTT
Found at i:2868578 original size:32 final size:32
Alignment explanation
Indices: 2868537--2868603 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
2868527 TGAAGAGATA
2868537 AAGGCTCTAGGAATGACGCATACTATATATTT
1 AAGGCTCTAGGAATGACGCATACTATATATTT
*
2868569 AAGGCTCTAGGAATGACGCATACTATATGTTT
1 AAGGCTCTAGGAATGACGCATACTATATATTT
2868601 AAG
1 AAG
2868604 AGCTAGGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (32 bp):
AAGGCTCTAGGAATGACGCATACTATATATTT
Found at i:2873219 original size:20 final size:19
Alignment explanation
Indices: 2873178--2873219 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2873168 CGTACTGTCA
*
2873178 TTTTTAATTTATTATTATT
1 TTTTTAATTTATTATTAAT
2873197 TTTTTCAATTTCATT-TTAAT
1 TTTTT-AATTT-ATTATTAAT
2873217 TTT
1 TTT
2873220 CCTTTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 12 0.60
21 3 0.15
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTAATTTATTATTAAT
Found at i:2883407 original size:4 final size:4
Alignment explanation
Indices: 2883398--2883465 Score: 127
Period size: 4 Copynumber: 17.0 Consensus size: 4
2883388 TTACAATACA
*
2883398 TATG TATG TATG TATT TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2883446 TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG
2883466 AGGTTTTCAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2884342 original size:6 final size:6
Alignment explanation
Indices: 2884331--2884359 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2884321 TTAAAACATA
2884331 ATAATT ATAATT ATAATT ATAATT ATAAT
1 ATAATT ATAATT ATAATT ATAATT ATAAT
2884360 GAATCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:2885011 original size:31 final size:31
Alignment explanation
Indices: 2884973--2885032 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
2884963 CCGCTATCGA
2884973 CGTAAACCGTTATTCACCGTTAAATTCGTAG
1 CGTAAACCGTTATTCACCGTTAAATTCGTAG
2885004 CGTAAACCGTTATTCACCGTTAAATTCGT
1 CGTAAACCGTTATTCACCGTTAAATTCGT
2885033 CAATATAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (31 bp):
CGTAAACCGTTATTCACCGTTAAATTCGTAG
Found at i:2885078 original size:19 final size:19
Alignment explanation
Indices: 2885054--2885099 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
2885044 TCAGACAACA
2885054 TCCGCTATAGTATTTTTGT
1 TCCGCTATAGTATTTTTGT
2885073 TCCGCTATAGTATTTTTGT
1 TCCGCTATAGTATTTTTGT
2885092 TCCGCTAT
1 TCCGCTAT
2885100 TTGAAACCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (19 bp):
TCCGCTATAGTATTTTTGT
Found at i:2897776 original size:20 final size:20
Alignment explanation
Indices: 2897751--2897788 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2897741 AAAATGATCC
* *
2897751 AAATCAACCTTTTAACATCA
1 AAATCAACATTCTAACATCA
2897771 AAATCAACATTCTAACAT
1 AAATCAACATTCTAACAT
2897789 TCAATTCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATCAACATTCTAACATCA
Found at i:2898614 original size:14 final size:15
Alignment explanation
Indices: 2898591--2898623 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2898581 ATTACCATGA
2898591 CATCATTCCTCACAT
1 CATCATTCCTCACAT
*
2898606 CATCA-TCCTTACAT
1 CATCATTCCTCACAT
2898620 CATC
1 CATC
2898624 TATGAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.27, C:0.39, G:0.00, T:0.33
Consensus pattern (15 bp):
CATCATTCCTCACAT
Found at i:2900675 original size:30 final size:30
Alignment explanation
Indices: 2900638--2900728 Score: 121
Period size: 30 Copynumber: 3.1 Consensus size: 30
2900628 ACTAAATAGC
2900638 AAAAATAGAAAGTTAAAGGACTAAAACAAT
1 AAAAATAGAAAGTTAAAGGACTAAAACAAT
* * * * *
2900668 GAAAATAGAAACTTAAAGGATTAAAATAGT
1 AAAAATAGAAAGTTAAAGGACTAAAACAAT
*
2900698 AAAAACAGAAAGTTAAAGGACT-AAACAAT
1 AAAAATAGAAAGTTAAAGGACTAAAACAAT
2900727 AA
1 AA
2900729 TTTCAAATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
29 7 0.14
30 43 0.86
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.18
Consensus pattern (30 bp):
AAAAATAGAAAGTTAAAGGACTAAAACAAT
Found at i:2902319 original size:3 final size:3
Alignment explanation
Indices: 2902311--2902365 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
2902301 GTAATTGTTC
* * *
2902311 ATA ATA ATA TATA ACA ATA ACA ATA ACA ATA ATA ATA ATA ATA ATTA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
2902358 A-A ATA ATA
1 ATA ATA ATA
2902366 TATTTGTAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2903069 original size:17 final size:16
Alignment explanation
Indices: 2903025--2903073 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
2903015 AGACTCAAAC
*
2903025 ATTTTTTTCAAGAGAA
1 ATTTGTTTCAAGAGAA
* *
2903041 A-CTGTCTCAAGAGACA
1 ATTTGTTTCAAGAGA-A
2903057 ATTTGTTTCAAGAGAA
1 ATTTGTTTCAAGAGAA
2903073 A
1 A
2903074 CAACTCAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 10 0.38
16 5 0.19
17 11 0.42
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (16 bp):
ATTTGTTTCAAGAGAA
Found at i:2903082 original size:59 final size:59
Alignment explanation
Indices: 2902950--2903082 Score: 169
Period size: 61 Copynumber: 2.2 Consensus size: 59
2902940 CATTTTAAAG
* *
2902950 GAAACAACTCAAAGATTTTTTTAAAAAGAAACTGTCTCAGGAGAGACACTTGTTTCAAGT
1 GAAACAACTCAAACATTTTTTTAAAAAGAAACTGTCTCA-GAGAGACACTTGTTTCAAGA
* * * * *
2903010 GTAATAGACTCAAACATTTTTTTCAAGAGAAACTGTCTCA-AGAGACAATTTGTTTCAAGA
1 GAAACA-ACTCAAACATTTTTTTAAAAAGAAACTGTCTCAGAGAGAC-ACTTGTTTCAAGA
2903070 GAAACAACTCAAA
1 GAAACAACTCAAA
2903083 GGAGTATCAG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
59 13 0.21
60 19 0.31
61 30 0.48
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (59 bp):
GAAACAACTCAAACATTTTTTTAAAAAGAAACTGTCTCAGAGAGACACTTGTTTCAAGA
Found at i:2906913 original size:31 final size:31
Alignment explanation
Indices: 2906853--2906914 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2906843 ACGAAAAATT
* *
2906853 ACACAAACAAAAGAAAAGAAATAAGTTAGTA
1 ACACAAACAAAAGAAAAGAAACAAATTAGTA
*
2906884 ACACAAACAAAAAGAGAA-AAACAAATTAGTA
1 ACACAAAC-AAAAGAAAAGAAACAAATTAGTA
2906915 CCAGCAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.11
Consensus pattern (31 bp):
ACACAAACAAAAGAAAAGAAACAAATTAGTA
Found at i:2908676 original size:30 final size:30
Alignment explanation
Indices: 2908640--2908724 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 30
2908630 ACTAAATAGC
2908640 AAAAATAGAAAGTTAAAGGACTAAAACAAT
1 AAAAATAGAAAGTTAAAGGACTAAAACAAT
* * * *
2908670 AAAAATAGATAA-TTAATGGATTAAAATAGT
1 AAAAATAGA-AAGTTAAAGGACTAAAACAAT
2908700 AAAAATAGAAAGTTAAAGGACTAAA
1 AAAAATAGAAAGTTAAAGGACTAAA
2908725 CAGTAATTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.04
30 43 0.91
31 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.14, T:0.21
Consensus pattern (30 bp):
AAAAATAGAAAGTTAAAGGACTAAAACAAT
Found at i:2910268 original size:3 final size:3
Alignment explanation
Indices: 2910260--2910290 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2910250 GCAAAAATTG
*
2910260 TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2910291 TAAAATAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2911443 original size:27 final size:26
Alignment explanation
Indices: 2911413--2911477 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
2911403 ATAATACTTA
* *
2911413 ATAATTTATTTTTAAAATTATATTTTT
1 ATAATTT-TTTTTAAAAATAAATTTTT
**
2911440 ATAAATTGGTTTTAAAAATAAATTTTT
1 AT-AATTTTTTTTAAAAATAAATTTTT
2911467 -T-ATTTTTTTTA
1 ATAATTTTTTTTA
2911478 GATTTTAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 8 0.26
26 1 0.03
27 18 0.58
28 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (26 bp):
ATAATTTTTTTTAAAAATAAATTTTT
Found at i:2912335 original size:20 final size:21
Alignment explanation
Indices: 2912310--2912354 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
2912300 CTTTATAAGT
*
2912310 AAAAAAAAATCAT-AATTATA
1 AAAAAAAAATAATAAATTATA
* *
2912330 AAAAAACAATAATAAATTGTA
1 AAAAAAAAATAATAAATTATA
2912351 AAAA
1 AAAA
2912355 GCCAATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAAAAAAATAATAAATTATA
Found at i:2912347 original size:21 final size:19
Alignment explanation
Indices: 2912309--2912354 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
2912299 ACTTTATAAG
*
2912309 TAAAAAAAAATCATAATTA
1 TAAAAAAAAATAATAATTA
*
2912328 TAAAAAAACAATAATAAATTG
1 TAAAAAAA-AATAAT-AATTA
2912349 TAAAAA
1 TAAAAA
2912355 GCCAATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 5 0.22
21 10 0.43
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (19 bp):
TAAAAAAAAATAATAATTA
Found at i:2921986 original size:17 final size:18
Alignment explanation
Indices: 2921959--2922000 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2921949 GAAAAAGAAT
2921959 AAGCGATTCCAGAACA-TG
1 AAGC-ATTCCAGAACATTG
* *
2921977 AAGCATTCCATAATATTG
1 AAGCATTCCAGAACATTG
2921995 AAGCAT
1 AAGCAT
2922001 ATGGTCTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (18 bp):
AAGCATTCCAGAACATTG
Found at i:2922993 original size:54 final size:53
Alignment explanation
Indices: 2922930--2923058 Score: 134
Period size: 55 Copynumber: 2.4 Consensus size: 53
2922920 TTACCCAGCT
* * *
2922930 AATGTGTTTTTTAGAACCTAAGTCCGATTTTCAGAAGTTTCTTGATGACTTTCA
1 AATGAGTTTTTTAGAAACTAAGTCCGATTTTCAGAAGTTTCTTCATG-CTTTCA
* ** * ** *
2922984 AATGCGTTTTCAAAAAAACTAAGTCTTATTTTCAGAAGTTTCTTCATGTTTTCA
1 AATGAGTTTT-TTAGAAACTAAGTCCGATTTTCAGAAGTTTCTTCATGCTTTCA
*
2923038 AATGAG-ATTTTAGAAACTAAG
1 AATGAGTTTTTTAGAAACTAAG
2923059 CCTTCGGGGG
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
52 9 0.15
53 2 0.03
54 19 0.32
55 30 0.50
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (53 bp):
AATGAGTTTTTTAGAAACTAAGTCCGATTTTCAGAAGTTTCTTCATGCTTTCA
Found at i:2923187 original size:90 final size:90
Alignment explanation
Indices: 2923032--2923271 Score: 399
Period size: 90 Copynumber: 2.7 Consensus size: 90
2923022 TTTCTTCATG
* * * *
2923032 TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCATGCGGGCCA
1 TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGAGCCA
2923097 TCCATAAGACCTTCAGTGCAAGATC
66 TCCATAAGACCTTCAGTGCAAGATC
2923122 TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGAGCCA
1 TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGAGCCA
* *
2923187 TCCATAAGACCTTCAGTGCAGGATG
66 TCCATAAGACCTTCAGTGCAAGATC
* * *
2923212 TTTTCAAATGAGATTTTAGAAACTAAACCTTCAGGGGTTTCTTGATTTTTAAATCCTTCG
1 TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCG
2923272 GGTCATCAGT
Statistics
Matches: 141, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 141 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (90 bp):
TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGAGCCA
TCCATAAGACCTTCAGTGCAAGATC
Found at i:2923332 original size:42 final size:41
Alignment explanation
Indices: 2923261--2923346 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 41
2923251 TCTTGATTTT
* * *
2923261 TAAATCCTTCGGGTCATCAGTATGTCTTTCGAGCATGATGCA
1 TAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATG-A
2923303 TAAATCCTTCGGGTCAT-ATGTAAGCCTTTCGAGCAAGATGA
1 TAAATCCTTCGGGTCATCA-GTAAGCCTTTCGAGCAAGATGA
2923344 TAA
1 TAA
2923347 GAACTTCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 5 0.12
42 35 0.88
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATGA
Found at i:2923613 original size:136 final size:134
Alignment explanation
Indices: 2923370--2923707 Score: 477
Period size: 136 Copynumber: 2.5 Consensus size: 134
2923360 AATGTTTTCA
*
2923370 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAGAGGGAGAAGAAGTTCATAATG
* * * ** **
2923435 AGAAGAGCTTGTTTGATCTATCACTCGATTCACGGCATTTCGAATCAATGTTGCCTCGCTTGAGG
65 AGAAGAGCTTATTCGACCTATCACTCGATTCACAACATTTCGAATCAATGACGCCTCGCTTGAGG
2923500 GATTG
130 GATTG
*
2923505 ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-A-AGAGGGAGAAGAAGTTCATAAT
* * *
2923570 GAGAAGAGCTTATTCGACCTATCATTCGATTCACAATATTTCGAATCAATGACGCCTCGGTTGAG
64 GAGAAGAGCTTATTCGACCTATCACTCGATTCACAACATTTCGAATCAATGACGCCTCGCTTGAG
2923635 GGATTG
129 GGATTG
* * *
2923641 ACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCTAA-A-AGAG-A-AAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAGAGGGAGAAGAAGTTCATAATG
2923702 AGAAGA
65 AGAAGA
2923708 ACTCGTTCCT
Statistics
Matches: 184, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
131 18 0.10
132 1 0.01
133 3 0.02
134 1 0.01
135 41 0.22
136 120 0.65
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (134 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAGAGGGAGAAGAAGTTCATAATGA
GAAGAGCTTATTCGACCTATCACTCGATTCACAACATTTCGAATCAATGACGCCTCGCTTGAGGG
ATTG
Found at i:2923838 original size:105 final size:108
Alignment explanation
Indices: 2923654--2923930 Score: 368
Period size: 105 Copynumber: 2.6 Consensus size: 108
2923644 TTTCTAGTGG
*
2923654 AGAGTTCATAATGAGAAGAACTCATCCTAAA-AGAGAAAGTTCATAATGAGAAGAACTCGTTCCT
1 AGAGTTCATAATGAGAAGAACTCATCCTAAAGAGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
*
2923718 TTCAAATTCAACACAG-AAGTAGGTGAACCAATA-TTTCCA-GA
66 TTCAAATTCAACACAGAAAG-AGGTGAACCAATATTTTCAATGA
* *
2923759 AGAGTTCATAATGAGAAGAACTCGTCCTAAAGA-AGAAAGTTCATAATGAGAAGAGCTTGTTCCT
1 AGAGTTCATAATGAGAAGAACTCATCCTAAAGAGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
* * * * *
2923823 TTC-AAGTCTATCACAGAAAGAGGTGGATCAGTATTTTCAATGA
66 TTCAAATTC-AACACAGAAAGAGGTGAACCAATATTTTCAATGA
* *
2923866 AGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGAAGTTCATTATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCTA-AAGAGAG-A-AAGTTCATAATGAGAAGAACTTGTT
2923931 TAATCTAATG
Statistics
Matches: 150, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
104 4 0.03
105 78 0.52
106 9 0.06
107 29 0.19
108 4 0.03
109 2 0.01
110 1 0.01
111 23 0.15
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (108 bp):
AGAGTTCATAATGAGAAGAACTCATCCTAAAGAGAGAAAGTTCATAATGAGAAGAACTTGTTCCT
TTCAAATTCAACACAGAAAGAGGTGAACCAATATTTTCAATGA
Found at i:2930240 original size:25 final size:25
Alignment explanation
Indices: 2930202--2930251 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2930192 TCAGCTACAC
*
2930202 GTATGAAACAAATATATAATATATA
1 GTATGAAACAAATAAATAATATATA
* *
2930227 GTATGACACTAATAAATAATATATA
1 GTATGAAACAAATAAATAATATATA
2930252 TATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (25 bp):
GTATGAAACAAATAAATAATATATA
Found at i:2930252 original size:2 final size:2
Alignment explanation
Indices: 2930245--2930274 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2930235 CTAATAAATA
2930245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2930275 GTAACTCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2939010 original size:10 final size:10
Alignment explanation
Indices: 2938962--2938994 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
2938952 CGTTTATGTT
2938962 TGTTCATTTA
1 TGTTCATTTA
2938972 TGTTCATTTA
1 TGTTCATTTA
*
2938982 TATTCATTTA
1 TGTTCATTTA
2938992 TGT
1 TGT
2938995 CCGTTCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (10 bp):
TGTTCATTTA
Found at i:2939305 original size:23 final size:23
Alignment explanation
Indices: 2939273--2939354 Score: 119
Period size: 23 Copynumber: 3.5 Consensus size: 23
2939263 GTATTTGTGT
2939273 TGTTCGTTTATTGTGTTCGTTTA
1 TGTTCGTTTATTGTGTTCGTTTA
* *
2939296 TGTTCATTTATTATGTTCGTTTA
1 TGTTCGTTTATTGTGTTCGTTTA
* *
2939319 TATTCGTTTGTTTGTGTTCGTTTA
1 TGTTCGTTT-ATTGTGTTCGTTTA
2939343 TGTTCGTTTATT
1 TGTTCGTTTATT
2939355 ATTTAAATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
23 30 0.60
24 20 0.40
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.62
Consensus pattern (23 bp):
TGTTCGTTTATTGTGTTCGTTTA
Found at i:2944710 original size:57 final size:57
Alignment explanation
Indices: 2944622--2944739 Score: 182
Period size: 57 Copynumber: 2.1 Consensus size: 57
2944612 GATGTCAAAT
** * *
2944622 TCGAATTGGTCGTCACAACAATTTTGTTAAAATCAGATAGGTCGGTGGGATTGGGAA
1 TCGAATTGGTCACCACAACAATTTTGCTAAAATCAGATAGGTCGGTGGGATCGGGAA
* *
2944679 TCGAATTGGTCACCACAACTATTTTGCTAAAATCAGATAGGTTGGTGGGATCGGGAA
1 TCGAATTGGTCACCACAACAATTTTGCTAAAATCAGATAGGTCGGTGGGATCGGGAA
2944736 TCGA
1 TCGA
2944740 TAAGTGCAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (57 bp):
TCGAATTGGTCACCACAACAATTTTGCTAAAATCAGATAGGTCGGTGGGATCGGGAA
Found at i:2946749 original size:23 final size:23
Alignment explanation
Indices: 2946723--2946784 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
2946713 AGAGCTTTGC
* *
2946723 AGAGAGCTTTACTGTGAGATTGG
1 AGAGAGCTTTACCGTGAGACTGG
2946746 AGAGAGCTTTACCGTGAGACTGG
1 AGAGAGCTTTACCGTGAGACTGG
*
2946769 AGAGAGCTTTGCCGTG
1 AGAGAGCTTTACCGTG
2946785 GGAGGGGGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (23 bp):
AGAGAGCTTTACCGTGAGACTGG
Found at i:2959429 original size:27 final size:28
Alignment explanation
Indices: 2959377--2959430 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2959367 CTTCATTTTG
*
2959377 TTTTATTATTTTTATTTTAGTGCACTAT
1 TTTTATTATTTTTAATTTAGTGCACTAT
*
2959405 TTTTA-TATATTTTAATTTGGT-CACTA
1 TTTTATTAT-TTTTAATTTAGTGCACTA
2959431 ATGTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.61
Consensus pattern (28 bp):
TTTTATTATTTTTAATTTAGTGCACTAT
Found at i:2959909 original size:44 final size:44
Alignment explanation
Indices: 2959859--2959950 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
2959849 GTAATTTCCT
*
2959859 CTCCTTCACGGCATTCACTTGAAAATTTTGATTGCAGGTCGACC
1 CTCCTTCACGACATTCACTTGAAAATTTTGATTGCAGGTCGACC
2959903 CTCCTTCACGACATTCACTTGAAAATTTTGATTGCAGGTCGACC
1 CTCCTTCACGACATTCACTTGAAAATTTTGATTGCAGGTCGACC
2959947 CTCC
1 CTCC
2959951 CGCATCTTGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (44 bp):
CTCCTTCACGACATTCACTTGAAAATTTTGATTGCAGGTCGACC
Found at i:2961246 original size:14 final size:14
Alignment explanation
Indices: 2961227--2961256 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2961217 GGCAAGTATA
2961227 TTTTTATGGAACAT
1 TTTTTATGGAACAT
*
2961241 TTTTTATGGAATAT
1 TTTTTATGGAACAT
2961255 TT
1 TT
2961257 AGGGTTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (14 bp):
TTTTTATGGAACAT
Found at i:2964990 original size:21 final size:20
Alignment explanation
Indices: 2964964--2965021 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
2964954 TTTATATGTA
*
2964964 TTTTTAGTATATTTTTCTTT
1 TTTTTACTATATTTTTCTTT
**
2964984 TTATTTACTATATTCCTCTTT
1 TT-TTTACTATATTTTTCTTT
*
2965005 TTTTATATTATATTTTT
1 TTTT-TACTATATTTTT
2965022 ATTATATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTACTATATTTTTCTTT
Found at i:2965031 original size:15 final size:15
Alignment explanation
Indices: 2965002--2965035 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2964992 TATATTCCTC
2965002 TTTTTTTATATTATA
1 TTTTTTTATATTATA
2965017 TTTTTATTATA-TATA
1 TTTTT-TTATATTATA
2965032 TTTT
1 TTTT
2965036 ATATCGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTTATATTATA
Found at i:2968084 original size:22 final size:22
Alignment explanation
Indices: 2968055--2968107 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2968045 CAGAATGAAC
*
2968055 ACTT-GAGAATCTGGGTGGCTG
1 ACTTAGAGAATCTGGCTGGCTG
*
2968076 ACTTAGAGAATCTGGCTGGCTT
1 ACTTAGAGAATCTGGCTGGCTG
2968098 ACTTAGAGAA
1 ACTTAGAGAA
2968108 GCAACATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (22 bp):
ACTTAGAGAATCTGGCTGGCTG
Found at i:2968592 original size:21 final size:21
Alignment explanation
Indices: 2968567--2968606 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2968557 ATACTTTGCA
2968567 TTTTATATATTT-CATGTTTAT
1 TTTTATAT-TTTCCATGTTTAT
2968588 TTTTATATTTTCCATGTTT
1 TTTTATATTTTCCATGTTT
2968607 TTACATTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTATATTTTCCATGTTTAT
Found at i:2975648 original size:22 final size:22
Alignment explanation
Indices: 2975625--2975666 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2975615 TCTTAAGTCA
*
2975625 AAAAAAAGAAAAAG-GAAAAAC
1 AAAAAAACAAAAAGAGAAAAAC
*
2975646 AAAATAACAAAAAGAGAAAAA
1 AAAAAAACAAAAAGAGAAAAA
2975667 ATGTTTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAACAAAAAGAGAAAAAC
Found at i:2975741 original size:15 final size:15
Alignment explanation
Indices: 2975706--2975752 Score: 67
Period size: 16 Copynumber: 3.0 Consensus size: 15
2975696 CCTAAATTTA
*
2975706 AAAAAGGAAAAAAGAG
1 AAAAA-GAAAAAAAAG
2975722 AAAAAGAACAAAAAAG
1 AAAAAGAA-AAAAAAG
2975738 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
2975753 GTGGGTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:2979921 original size:21 final size:20
Alignment explanation
Indices: 2979897--2979946 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
2979887 ATATTTTAAG
*
2979897 TATATTTTTCTTTTTATTTAC
1 TATATTTTTCTTTTT-TATAC
** *
2979918 TATATTCCTCTTTTTTATAT
1 TATATTTTTCTTTTTTATAC
2979938 TATATTTTT
1 TATATTTTT
2979947 ATTATATATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (20 bp):
TATATTTTTCTTTTTTATAC
Found at i:2979946 original size:15 final size:15
Alignment explanation
Indices: 2979928--2979960 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2979918 TATATTCCTC
2979928 TTTT-TTATATTATAT
1 TTTTATTATA-TATAT
2979943 TTTTATTATATATAT
1 TTTTATTATATATAT
2979958 TTT
1 TTT
2979961 ATATCGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATTATATATAT
Found at i:2980114 original size:20 final size:19
Alignment explanation
Indices: 2980069--2980115 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2980059 CATTTACTTA
* *
2980069 TTTATT-TATATATATTTT
1 TTTATTGTATATATACTAT
2980087 TTTAATTGTATATATTACTAT
1 TTT-ATTGTATATA-TACTAT
2980108 TTTATTGT
1 TTTATTGT
2980116 TTTTTTCCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 11 0.46
21 7 0.29
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (19 bp):
TTTATTGTATATATACTAT
Found at i:2981908 original size:2 final size:2
Alignment explanation
Indices: 2981901--2981943 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2981891 AACCCATTAA
2981901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2981943 A
1 A
2981944 CTCGCGCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2991506 original size:23 final size:23
Alignment explanation
Indices: 2991451--2991506 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
2991441 AGAGGGAAGT
*
2991451 CGATACCCCC-TTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
2991473 CGATTCCCCCTTTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
2991496 CGATTCCCCCT
1 CGATTCCCCCT
2991507 AGTGGAATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 9 0.28
23 23 0.72
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.20
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGGGAAC
Found at i:2992414 original size:13 final size:13
Alignment explanation
Indices: 2992396--2992429 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2992386 CAAGCTATGA
*
2992396 TAGATATTGATTT
1 TAGATATCGATTT
2992409 TAGATATCGATTT
1 TAGATATCGATTT
2992422 TAGATATC
1 TAGATATC
2992430 TTCCTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (13 bp):
TAGATATCGATTT
Found at i:2993790 original size:12 final size:12
Alignment explanation
Indices: 2993773--2993798 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2993763 AAAAATGGGG
2993773 AGAAATGTTAAA
1 AGAAATGTTAAA
2993785 AGAAATGTTAAA
1 AGAAATGTTAAA
2993797 AG
1 AG
2993799 CGTTTTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (12 bp):
AGAAATGTTAAA
Found at i:3004400 original size:8 final size:8
Alignment explanation
Indices: 3004389--3004460 Score: 92
Period size: 8 Copynumber: 8.6 Consensus size: 8
3004379 AGAAAAAGAG
*
3004389 AAAAATGA
1 AAAAATAA
3004397 AAAAATGAA
1 AAAAAT-AA
3004406 AAAAATAA
1 AAAAATAA
3004414 AAAAATAA
1 AAAAATAA
3004422 AAAAATAA
1 AAAAATAA
3004430 AAAAATAA
1 AAAAATAA
3004438 AAAAA-AA
1 AAAAATAA
3004445 TGAAAAATGAA
1 --AAAAAT-AA
3004456 AAAAA
1 AAAAA
3004461 ATTGAAAAGG
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
7 2 0.03
8 37 0.64
9 17 0.29
11 2 0.03
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:3004461 original size:17 final size:17
Alignment explanation
Indices: 3004389--3004486 Score: 78
Period size: 17 Copynumber: 5.7 Consensus size: 17
3004379 AGAAAAAGAG
3004389 AAAAATGAAAAAATG-AA
1 AAAAATG-AAAAATGAAA
*
3004406 AAAAAT-AAAAA-AATAA
1 AAAAATGAAAAATGA-AA
* *
3004422 AAAAATAAAAAAATAAAA
1 AAAAAT-GAAAAATGAAA
3004440 AAAAATGAAAAATGAAA
1 AAAAATGAAAAATGAAA
*
3004457 AAAAATTG-AAAAGGAAA
1 AAAAA-TGAAAAATGAAA
*
3004474 AGAAAAAGAAAAA
1 A-AAAATGAAAAA
3004487 AAATCCGAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
15 5 0.07
16 8 0.12
17 30 0.44
18 23 0.34
19 2 0.03
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.10
Consensus pattern (17 bp):
AAAAATGAAAAATGAAA
Found at i:3004466 original size:11 final size:10
Alignment explanation
Indices: 3004396--3004468 Score: 58
Period size: 8 Copynumber: 8.2 Consensus size: 10
3004386 GAGAAAAATG
3004396 AAAAAATG-A
1 AAAAAATGAA
3004405 AAAAAAT--A
1 AAAAAATGAA
3004413 AAAAAAT--A
1 AAAAAATGAA
3004421 AAAAAAT--A
1 AAAAAATGAA
*
3004429 AAAAAATAAA
1 AAAAAATGAA
3004439 AAAAAATG--
1 AAAAAATGAA
3004447 -AAAAATGAA
1 AAAAAATGAA
3004456 AAAAAATTGAA
1 AAAAAA-TGAA
3004467 AA
1 AA
3004469 GGAAAAGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
7 7 0.12
8 24 0.42
9 7 0.12
10 13 0.23
11 6 0.11
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:3004486 original size:18 final size:17
Alignment explanation
Indices: 3004397--3004486 Score: 55
Period size: 16 Copynumber: 5.3 Consensus size: 17
3004387 AGAAAAATGA
*
3004397 AAAAATGAAAAAAATAA-
1 AAAAAGGAAAAAAA-AAG
*
3004414 AAAAA-TAAAAAAATAA-
1 AAAAAGGAAAAAAA-AAG
*
3004430 AAAAA-TAAAAAAAAATG
1 AAAAAGGAAAAAAAAA-G
* *
3004447 AAAAATGAAAAAAAATTG
1 AAAAAGGAAAAAAAA-AG
3004465 -AAAAGGAAAAGAAAAAG
1 AAAAAGGAAAA-AAAAAG
3004482 AAAAA
1 AAAAA
3004487 AAATCCGAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
15 2 0.03
16 23 0.37
17 20 0.32
18 17 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.10
Consensus pattern (17 bp):
AAAAAGGAAAAAAAAAG
Found at i:3004496 original size:29 final size:30
Alignment explanation
Indices: 3004441--3004497 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
3004431 AAAATAAAAA
*
3004441 AAAATGAAAAATGAAAAAAAATTGAAAAGG
1 AAAATGAAAAATGAAAAAAAATCGAAAAGG
3004471 AAAA-GAAAAA-GAAAAAAAATCCGAAAA
1 AAAATGAAAAATGAAAAAAAAT-CGAAAA
3004498 CGGCTTCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 11 0.44
30 4 0.16
ACGTcount: A:0.74, C:0.04, G:0.14, T:0.09
Consensus pattern (30 bp):
AAAATGAAAAATGAAAAAAAATCGAAAAGG
Found at i:3005765 original size:37 final size:36
Alignment explanation
Indices: 3005690--3005805 Score: 128
Period size: 37 Copynumber: 3.2 Consensus size: 36
3005680 AGGTTTCTTC
* * *
3005690 GAAGCAAGTCAATCTTAAGCCTTCGC-AAAGGAGAAGT
1 GAAGCAAGT-AATCTTAAGCCTTCACGGAA-GAGTAGT
*
3005727 GAAGCGAGTAAATCTTAAGCCTTCACGGAAGAGTAGT
1 GAAGCAAGT-AATCTTAAGCCTTCACGGAAGAGTAGT
* * *
3005764 GAAGCAAATTATCTT-AGCCTTCATGGAAGAGTAGT
1 GAAGCAAGTAATCTTAAGCCTTCACGGAAGAGTAGT
3005799 GAAGCAA
1 GAAGCAA
3005806 ATCGGTCTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 26 0.38
36 5 0.07
37 36 0.52
38 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (36 bp):
GAAGCAAGTAATCTTAAGCCTTCACGGAAGAGTAGT
Found at i:3005792 original size:35 final size:36
Alignment explanation
Indices: 3005738--3005807 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 36
3005728 AAGCGAGTAA
3005738 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATT
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATT
*
3005774 ATCTT-AGCCTTCATGGAAGAGTAGTGAAGCAAAT
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
3005808 CGGTCTTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 28 0.85
36 5 0.15
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATT
Found at i:3005911 original size:55 final size:55
Alignment explanation
Indices: 3005824--3006120 Score: 409
Period size: 55 Copynumber: 5.4 Consensus size: 55
3005814 TGAGTCTGAT
*
3005824 CTCCTTGAAAGAATAGGGAGCGAACCCATTTTCAGAAGATTATTCGAGTTCTATA
1 CTCCTTGAAAGAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATA
* * * *
3005879 TTCCTTGAAAGAATAGGGTGCGAACCCGTTTTCAAAAGATTGTTCGAGTTCTATA
1 CTCCTTGAAAGAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATA
* *
3005934 CT-CTCTGAAAGAATAGGGAACGAACCCATTTTCAGCAGATTGTTCGAGTTCTATA
1 CTCCT-TGAAAGAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATA
* * *
3005989 TTCTTTGAAAGAATAGGGAGCGAACTCATTTTCAGAAGATTGTTCGAG-TCTTATA
1 CTCCTTGAAAGAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTC-TATA
* * * ** *
3006044 CTCCTTGAAAGAATAGGGAGTGGACTCATTTTTTGAAGATTGTTCGAGTCCTATA
1 CTCCTTGAAAGAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATA
*
3006099 CTCCTTGAAAGAAAAGGGAGCG
1 CTCCTTGAAAGAATAGGGAGCG
3006121 GAGCCATCCT
Statistics
Matches: 213, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
54 4 0.02
55 207 0.97
56 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (55 bp):
CTCCTTGAAAGAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATA
Found at i:3007357 original size:2 final size:2
Alignment explanation
Indices: 3007350--3007382 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3007340 AAACCCATTA
3007350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3007383 CACTTGCGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3008585 original size:19 final size:20
Alignment explanation
Indices: 3008550--3008591 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3008540 AAACGAGAGA
**
3008550 TTTTTTAAATCGTATTA-TT
1 TTTTTTAAATCACATTACTT
3008569 TTTTTTAAATCACATTACTT
1 TTTTTTAAATCACATTACTT
3008589 TTT
1 TTT
3008592 AATTAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTTAAATCACATTACTT
Found at i:3009203 original size:48 final size:48
Alignment explanation
Indices: 3009132--3009226 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
3009122 TTGTTGAGAA
*
3009132 TCTTTAAAATATACACTACCTTATAATCATCCAAGATTAATAAAAAAT
1 TCTTTAAAATAGACACTACCTTATAATCATCCAAGATTAATAAAAAAT
* * * **
3009180 TCTTTAAAATAGAGATTATCTTATAATCATCCTGGATTAATAAAAAA
1 TCTTTAAAATAGACACTACCTTATAATCATCCAAGATTAATAAAAAA
3009227 AAGCTCCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (48 bp):
TCTTTAAAATAGACACTACCTTATAATCATCCAAGATTAATAAAAAAT
Found at i:3010224 original size:18 final size:17
Alignment explanation
Indices: 3010172--3010224 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
3010162 AACTATAATA
* *
3010172 TATATATATATATATAT
1 TATATGTATGTATATAT
3010189 TATATGTATG-ATGAATAT
1 TATATGTATGTAT--ATAT
3010207 TATGATGTATGTATATAT
1 TAT-ATGTATGTATATAT
3010225 AATGTACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.07
17 8 0.27
18 11 0.37
19 7 0.23
20 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (17 bp):
TATATGTATGTATATAT
Found at i:3010292 original size:12 final size:12
Alignment explanation
Indices: 3010262--3010313 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
3010252 ATACTTATAT
3010262 TATATAT-A-TA
1 TATATATAAGTA
*
3010272 TATATATAACTA
1 TATATATAAGTA
3010284 TATATATAAGTA
1 TATATATAAGTA
* *
3010296 CATAAATAAGTA
1 TATATATAAGTA
3010308 TATATA
1 TATATA
3010314 AGTAAATGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 7 0.20
11 1 0.03
12 27 0.77
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (12 bp):
TATATATAAGTA
Found at i:3016262 original size:54 final size:54
Alignment explanation
Indices: 3016177--3016724 Score: 507
Period size: 54 Copynumber: 10.2 Consensus size: 54
3016167 GTTGCACCTA
* * * * * * *
3016177 AGTGCCGAAATGGAAATTCATAAACTTATTATGAATTCCATGGATTGCGCACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGATTGCACACAT
** * *
3016231 AGTGCTAATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGCACACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGATTGCACACAT
* * ** *
3016285 AGTGCCGATACGGTAATTCACAAATTCATTTTGAA-T-AATTGAGTTGCACACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGA-TTGCACACAT
* * * ** * *
3016338 AATGCCAATACAGTAATTCACAAACTCATTATGAATTTTGT-AAGTTGCACACTT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGA-TTGCACACAT
* * * * *** * *
3016392 ACTGTCGATACAGTAATTCACAAACTAATTATGAATTATAT-AAGTTGCACACTT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGA-TTGCACACAT
* ** ** *
3016446 AGTGTCGATATAGTAATTCACAAACTCATTATGAATTATGTGGGTTGCACACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGATTGCACACAT
* * * *
3016500 AGTACCGATACGGTAATTCACAAACTAATTATGAATTTCGTGGGTTGCACACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGATTGCACACAT
* * * *
3016554 AGTGTCGATACGGTAATTCACAAACTCATTTTGAATTTCGT-GAGTTGCACACTT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGA-TTGCACACAT
* * * *
3016608 AGTGCCGATACAGTAATTCACAAACTCATTATGAATTCCGTGGGTGGCACACTT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGATTGCACACAT
* * * * *
3016662 AGTGTCGATGCGGTAATTCAC-AACTCATTATGAACTT-TGTGGGTTTCACACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAA-TTCCGTGGATTGCACACAT
3016715 AGTGCCGATA
1 AGTGCCGATA
3016725 GTACTGATAG
Statistics
Matches: 418, Mismatches: 69, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
52 2 0.00
53 75 0.18
54 339 0.81
55 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (54 bp):
AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGATTGCACACAT
Found at i:3016481 original size:108 final size:108
Alignment explanation
Indices: 3016191--3016724 Score: 603
Period size: 108 Copynumber: 5.0 Consensus size: 108
3016181 CCGAAATGGA
* * * * *
3016191 AATTCATAAACTTATTATGAATTCCATG-GA-TTGCGCACATAGTG-CTAATACGGTAATTCACA
1 AATTCACAAACTAATTATGAATT--ATGTGAGTTGCACACATAGTGTC-GATACAGTAATTCACA
* * *
3016253 AACTCATTATGAATTCTGTGGGTTGCACACATAGTGCCGATACGGT
63 AACTCATTATGAATTTTGTGAGTTGCACACATAGTGCCGATACAGT
* * * * * * *
3016299 AATTCACAAATTCATTTTGAATAAT-TGAGTTGCACACATAATGCCAATACAGTAATTCACAAAC
1 AATTCACAAACTAATTATGAATTATGTGAGTTGCACACATAGTGTCGATACAGTAATTCACAAAC
* * * *
3016363 TCATTATGAATTTTGTAAGTTGCACACTTACTGTCGATACAGT
66 TCATTATGAATTTTGTGAGTTGCACACATAGTGCCGATACAGT
* * * *
3016406 AATTCACAAACTAATTATGAATTATATAAGTTGCACACTTAGTGTCGATATAGTAATTCACAAAC
1 AATTCACAAACTAATTATGAATTATGTGAGTTGCACACATAGTGTCGATACAGTAATTCACAAAC
* * * *
3016471 TCATTATGAATTATGTGGGTTGCACACATAGTACCGATACGGT
66 TCATTATGAATTTTGTGAGTTGCACACATAGTGCCGATACAGT
* *
3016514 AATTCACAAACTAATTATGAATT-TCGTGGGTTGCACACATAGTGTCGATACGGTAATTCACAAA
1 AATTCACAAACTAATTATGAATTAT-GTGAGTTGCACACATAGTGTCGATACAGTAATTCACAAA
* * *
3016578 CTCATTTTGAATTTCGTGAGTTGCACACTTAGTGCCGATACAGT
65 CTCATTATGAATTTTGTGAGTTGCACACATAGTGCCGATACAGT
* ** * * * * *
3016622 AATTCACAAACTCATTATGAATTCCGTGGGTGGCACACTTAGTGTCGATGCGGTAATTCAC-AAC
1 AATTCACAAACTAATTATGAATTATGTGAGTTGCACACATAGTGTCGATACAGTAATTCACAAAC
* * *
3016686 TCATTATGAACTTTGTGGGTTTCACACATAGTGCCGATA
66 TCATTATGAATTTTGTGAGTTGCACACATAGTGCCGATA
3016725 GTACTGATAG
Statistics
Matches: 363, Mismatches: 57, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
106 4 0.01
107 124 0.34
108 235 0.65
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (108 bp):
AATTCACAAACTAATTATGAATTATGTGAGTTGCACACATAGTGTCGATACAGTAATTCACAAAC
TCATTATGAATTTTGTGAGTTGCACACATAGTGCCGATACAGT
Found at i:3016550 original size:162 final size:160
Alignment explanation
Indices: 3016238--3016724 Score: 618
Period size: 162 Copynumber: 3.0 Consensus size: 160
3016228 CATAGTGCTA
* * *
3016238 ATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCCGATACGGTAATT
1 ATACGGTAATTCACAAACTCATTATGAATT-TGTGAGTTGCACACTTAGTGCCGATACAGTAATT
* * * * * * *
3016303 CACAAATTCATTTTGAATAAT-TGAGTTGCACACATAATGCCAATACAGTAATTCACAAACTCAT
65 CACAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCGATACGGTAATTCACAAACTCAT
** *
3016367 TATGAATTTTGTAAGTTGCACACTTACTGTCG
130 TATGAA-TTTGTGGGTTGCACACATACTGTCG
* * * * * *
3016399 ATACAGTAATTCACAAACTAATTATGAATTATATAAGTTGCACACTTAGTGTCGATATAGTAATT
1 ATACGGTAATTCACAAACTCATTATGAATT-TGTGAGTTGCACACTTAGTGCCGATACAGTAATT
* *
3016464 CACAAACTCATTATGAATTATGTGGGTTGCACACATAGTACCGATACGGTAATTCACAAACTAAT
65 CACAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCGATACGGTAATTCACAAACTCAT
*
3016529 TATGAATTTCGTGGGTTGCACACATAGTGTCG
130 TATGAATTT-GTGGGTTGCACACATACTGTCG
*
3016561 ATACGGTAATTCACAAACTCATTTTGAATTTCGTGAGTTGCACACTTAGTGCCGATACAGTAATT
1 ATACGGTAATTCACAAACTCATTATGAATTT-GTGAGTTGCACACTTAGTGCCGATACAGTAATT
** * * * *
3016626 CACAAACTCATTATGAATTCCGTGGGTGGCACACTTAGTGTCGATGCGGTAATTCAC-AACTCAT
65 CACAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCGATACGGTAATTCACAAACTCAT
* * *
3016690 TATGAACTTTGTGGGTTTCACACATAGTGCCG
130 TATGAA-TTTGTGGGTTGCACACATACTGTCG
3016722 ATA
1 ATA
3016725 GTACTGATAG
Statistics
Matches: 282, Mismatches: 40, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
161 112 0.40
162 170 0.60
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (160 bp):
ATACGGTAATTCACAAACTCATTATGAATTTGTGAGTTGCACACTTAGTGCCGATACAGTAATTC
ACAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCGATACGGTAATTCACAAACTCATT
ATGAATTTGTGGGTTGCACACATACTGTCG
Found at i:3017093 original size:20 final size:20
Alignment explanation
Indices: 3017055--3017111 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3017045 TTCAGACTAA
3017055 ATAGTATCGATACCCCTCTT
1 ATAGTATCGATACCCCTCTT
* **
3017075 ATAGTGTCGATACTTCTCTTGT
1 ATAGTATCGATACCCCTC-T-T
*
3017097 ATGGTATCGATACCC
1 ATAGTATCGATACCC
3017112 ACTTCGGTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 15 0.54
21 1 0.04
22 12 0.43
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (20 bp):
ATAGTATCGATACCCCTCTT
Found at i:3017186 original size:19 final size:18
Alignment explanation
Indices: 3017162--3017214 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
3017152 TTTTTATTAC
3017162 GGTATCGATACTTCCTCTA
1 GGTATCGATACTTCCTC-A
3017181 GGTATCGATACCTATACCTCA
1 GGTATCGATA-CT-T-CCTCA
3017202 -GTATCGATACTTC
1 GGTATCGATACTTC
3017215 TTTAAATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.03
18 1 0.03
19 12 0.39
20 11 0.35
21 2 0.06
22 4 0.13
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (18 bp):
GGTATCGATACTTCCTCA
Found at i:3024949 original size:15 final size:15
Alignment explanation
Indices: 3024929--3024957 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3024919 ATGGTGGCAC
3024929 TGTGTATAGCAGCAA
1 TGTGTATAGCAGCAA
3024944 TGTGTATAGCAGCA
1 TGTGTATAGCAGCA
3024958 TGGAAGTTGA
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:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TGTGTATAGCAGCAA
Found at i:3026376 original size:14 final size:14
Alignment explanation
Indices: 3026335--3026376 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3026325 AATTGGGTTG
*
3026335 AATATAAAAGAACG
1 AATATAAAAGAACA
3026349 AATATAAACA-AACA
1 AATATAAA-AGAACA
*
3026363 AATATAAATGAACA
1 AATATAAAAGAACA
3026377 TAAATGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 23 0.96
15 1 0.04
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (14 bp):
AATATAAAAGAACA
Found at i:3026928 original size:11 final size:10
Alignment explanation
Indices: 3026913--3026951 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
3026903 TATTTAAAAG
3026913 TATATTTTAT
1 TATATTTTAT
3026923 TAATATTTTAT
1 T-ATATTTTAT
3026934 TATATTATTAT
1 TATATT-TTAT
3026945 T-TATTTT
1 TATATTTT
3026952 TAAAAAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.07
10 10 0.37
11 15 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATATTTTAT
Found at i:3027135 original size:29 final size:30
Alignment explanation
Indices: 3027097--3027155 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
3027087 CTATTTTACG
*
3027097 ATGACATGAATTATTTTATTAATA-TTTTT
1 ATGACATGAAGTATTTTATTAATACTTTTT
*
3027126 ATGACGTGAAGTATTTTATTAATACTTTTT
1 ATGACATGAAGTATTTTATTAATACTTTTT
3027156 GCCATATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (30 bp):
ATGACATGAAGTATTTTATTAATACTTTTT
Found at i:3027459 original size:12 final size:12
Alignment explanation
Indices: 3027442--3027468 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3027432 TTAATTGCGA
3027442 AAATTGAAATTT
1 AAATTGAAATTT
3027454 AAATTGAAATTT
1 AAATTGAAATTT
3027466 AAA
1 AAA
3027469 ATATTCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTGAAATTT
Found at i:3027622 original size:26 final size:26
Alignment explanation
Indices: 3027593--3027662 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
3027583 AAAGGTTAGT
3027593 AAAAAAATAAATAATAATAAT-AAACA
1 AAAAAAATAAATAA-AATAATAAAACA
* * *
3027619 AAAATAATACAAGAAAATAATAAAAGA
1 AAAAAAATA-AATAAAATAATAAAACA
*
3027646 AAATAAAATGAATAAAA
1 AAA-AAAATAAATAAAA
3027663 CAAAAAGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
26 14 0.40
27 17 0.49
28 4 0.11
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.17
Consensus pattern (26 bp):
AAAAAAATAAATAAAATAATAAAACA
Found at i:3027645 original size:13 final size:13
Alignment explanation
Indices: 3027608--3027651 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
3027598 AATAAATAAT
3027608 AATAATAAACA-AA
1 AATAATAAA-AGAA
*
3027621 AATAATACAAGAA
1 AATAATAAAAGAA
3027634 AATAATAAAAGAA
1 AATAATAAAAGAA
3027647 AATAA
1 AATAA
3027652 AATGAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 1 0.04
13 27 0.96
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (13 bp):
AATAATAAAAGAA
Found at i:3027661 original size:19 final size:18
Alignment explanation
Indices: 3027632--3027667 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3027622 ATAATACAAG
*
3027632 AAAATAATAAAAGAAAAT
1 AAAATAATAAAACAAAAT
3027650 AAAATGAATAAAACAAAA
1 AAAAT-AATAAAACAAAA
3027668 AGTAAAGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAATAATAAAACAAAAT
Found at i:3028058 original size:17 final size:17
Alignment explanation
Indices: 3028032--3028069 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
3028022 CGATTTCTGG
*
3028032 CCACCTGTCGCCGCCGT
1 CCACCCGTCGCCGCCGT
3028049 CCACCCGTCGCCGCCGT
1 CCACCCGTCGCCGCCGT
3028066 CCAC
1 CCAC
3028070 AGCCGCCGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.08, C:0.58, G:0.21, T:0.13
Consensus pattern (17 bp):
CCACCCGTCGCCGCCGT
Found at i:3029003 original size:36 final size:35
Alignment explanation
Indices: 3028956--3029292 Score: 240
Period size: 36 Copynumber: 9.4 Consensus size: 35
3028946 TAATATAAAT
* *
3028956 TATATAATATATATTTTAAAAATATTTTGTTTAAAC
1 TATATATTATATATTTTAAAAATATTTT-TTAAAAC
* * *
3028992 TATATATTATATTTTTTAAAAACA---ATTAAAAC
1 TATATATTATATATTTTAAAAATATTTTTTAAAAC
* * * * *
3029024 TCTATATTACATAGTTTTCAAAAAAATGTTTTAAAAA
1 TATATATTATATA-TTTT-AAAAATATTTTTTAAAAC
*
3029061 TAT-TA-TATA-AGTTTTCAAAAATGTTTTTTAAAAC
1 TATATATTATATA-TTTT-AAAAATATTTTTTAAAAC
*
3029095 TATATATTATATAATTTTTAAAAAT-GTTTTTAAAAC
1 TATATATTATAT-A-TTTTAAAAATATTTTTTAAAAC
** *
3029131 TATATATTATATAATTTCCAAAAT-CTTTTTAAAAC
1 TATATATTATAT-ATTTTAAAAATATTTTTTAAAAC
* * * *
3029166 TATATTTTATATGTATTTTCAAAATGTTTTTCAAAAAC
1 TATATATTATA--TATTTTAAAAATATTTTT-TAAAAC
* * * * *
3029204 CATATAGTATATATTTTTAAAATGTTTTTTCAAAATA
1 TATATATTATATATTTTAAAAATATTTTTT-AAAA-C
* *
3029241 TATATAATATATATATTTTCAAAATATTTTTCAAAAAC
1 TATAT-AT-TATATATTTTAAAAATATTTTT-TAAAAC
3029279 TATATATTATATAT
1 TATATATTATATAT
3029293 ATTTTTTCAA
Statistics
Matches: 245, Mismatches: 38, Indels: 36
0.77 0.12 0.11
Matches are distributed among these distances:
32 16 0.07
33 4 0.02
34 30 0.12
35 33 0.13
36 89 0.36
37 25 0.10
38 24 0.10
39 24 0.10
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (35 bp):
TATATATTATATATTTTAAAAATATTTTTTAAAAC
Found at i:3029101 original size:71 final size:70
Alignment explanation
Indices: 3029017--3029296 Score: 180
Period size: 71 Copynumber: 3.8 Consensus size: 70
3029007 TTAAAAACAA
* *
3029017 TTAAAACTCTATATTACATAGTTTTCAAAAAAATG-TTTT-AAA-A-ATATTATATAAGTTTTCA
1 TTAAAACTATATATTACATAATTTT--AAAAAATGTTTTTAAAACATATATTATATAA--TTTCA
*
3029078 AAAATGTTTT
62 AAAAT-CTTT
* * *
3029088 TTAAAACTATATATTATATAATTTTTAAAAATGTTTTTAAAACTATATATTATATAATTTCCAAA
1 TTAAAACTATATATTACATAATTTTAAAAAATGTTTTTAAAAC-ATATATTATATAATTTCAAAA
3029153 ATCTTT
65 ATCTTT
* * * * * **
3029159 TTAAAACTATATTTTATATGTATTTT-CAAAATGTTTTTCAAAAACCATATAGTATAT-ATTTTT
1 TTAAAACTATATATTACAT-AATTTTAAAAAATGTTTTT--AAAA-CATATATTATATAATTTCA
*
3029222 AAAATGTTTT
62 AAAAT-CTTT
* * *
3029232 TTCAAAA-TATATATAATATATATATTTTCAAAATAT-TTTTCAAAAACTATATATTATATATAT
1 TT-AAAACTATATAT--TACATA-ATTTT-AAAAAATGTTTT-TAAAAC-ATATATTATATA-AT
3029295 TT
58 TT
3029297 TTTCAAAATG
Statistics
Matches: 170, Mismatches: 19, Indels: 34
0.76 0.09 0.15
Matches are distributed among these distances:
69 7 0.04
70 4 0.02
71 57 0.34
72 23 0.14
73 26 0.15
74 17 0.10
75 24 0.14
76 4 0.02
77 8 0.05
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (70 bp):
TTAAAACTATATATTACATAATTTTAAAAAATGTTTTTAAAACATATATTATATAATTTCAAAAA
TCTTT
Found at i:3029277 original size:13 final size:13
Alignment explanation
Indices: 3029212--3029276 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
3029202 ACCATATAGT
*
3029212 ATATATTTTTAAA
1 ATATATTTTCAAA
* *
3029225 ATGTTTTTTCAAA
1 ATATATTTTCAAA
*
3029238 ATATA-TAT-AATA
1 ATATATTTTCAA-A
3029250 TATATATTTTCAAA
1 -ATATATTTTCAAA
3029264 ATAT-TTTTCAAA
1 ATATATTTTCAAA
3029276 A
1 A
3029277 ACTATATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
11 2 0.05
12 12 0.29
13 22 0.54
14 3 0.07
15 2 0.05
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (13 bp):
ATATATTTTCAAA
Found at i:3029315 original size:38 final size:37
Alignment explanation
Indices: 3029060--3029323 Score: 240
Period size: 36 Copynumber: 7.1 Consensus size: 37
3029050 TGTTTTAAAA
* *
3029060 ATATTATATA-AGTTTTCAAAAATGTTTTTTAAAACTAT
1 ATATTATATATATTTTTC-AAAATG-TTTTAAAAACTAT
* *
3029098 ATATTATATA-ATTTTTAAAAATGTTTTTAAAACTAT
1 ATATTATATATATTTTTCAAAATGTTTTAAAAACTAT
* * *
3029134 ATATTATATA-A-TTTCCAAAATCTTTTTAAAACTAT
1 ATATTATATATATTTTTCAAAATGTTTTAAAAACTAT
* * *
3029169 ATTTTATATGTA-TTTTCAAAATGTTTTTCAAAAACCAT
1 ATATTATATATATTTTTCAAAATG-TTTT-AAAAACTAT
* *
3029207 ATA--GTATATATTTTT-AAAATGTTTTTTCAAAA-TAT
1 ATATTATATATATTTTTCAAAATG--TTTTAAAAACTAT
* *
3029242 ATATAATATATATATTTTCAAAATATTTTTCAAAAACTAT
1 ATATTATATATAT-TTTTCAAAAT-GTTTT-AAAAACTAT
*
3029282 ATATTATATATATTTTTTCAAAATGTTTTAAAAACCAT
1 ATATTATATATA-TTTTTCAAAATGTTTTAAAAACTAT
3029320 ATAT
1 ATAT
3029324 ATAAGTTTTC
Statistics
Matches: 191, Mismatches: 22, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
35 34 0.18
36 49 0.26
37 26 0.14
38 44 0.23
39 13 0.07
40 24 0.13
41 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (37 bp):
ATATTATATATATTTTTCAAAATGTTTTAAAAACTAT
Found at i:3033895 original size:59 final size:59
Alignment explanation
Indices: 3033820--3033955 Score: 202
Period size: 59 Copynumber: 2.3 Consensus size: 59
3033810 TATGCACCGA
**
3033820 AGTGCTAAATCAAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTACCCTTT
1 AGTGCTAACCCAAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTACCCTTT
* * **
3033879 AGTGCTAA-CCAGAATATGACACATAAGGTCTTACCCACCATCTGCACTAGGTATTCTTT
1 AGTGCTAACCCA-AATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTACCCTTT
3033938 AGTGCTAACCCAAATATG
1 AGTGCTAACCCAAATATG
3033956 CAACCTGCTG
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
58 2 0.03
59 65 0.93
60 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (59 bp):
AGTGCTAACCCAAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTACCCTTT
Found at i:3043597 original size:33 final size:33
Alignment explanation
Indices: 3043560--3043622 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
3043550 GACAATAGTA
* *
3043560 TCCAAAAATACATAATAAAATAGAGTTTACGAC
1 TCCAAAAATAAATAATAAAATAAAGTTTACGAC
3043593 TCCAAAAATAAATAATAAAATAAAGTTTAC
1 TCCAAAAATAAATAATAAAATAAAGTTTAC
3043623 AACTGAACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (33 bp):
TCCAAAAATAAATAATAAAATAAAGTTTACGAC
Found at i:3053796 original size:15 final size:15
Alignment explanation
Indices: 3053772--3053805 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3053762 TCTTCCTCTC
3053772 TTAA-TTGAAAAGTT
1 TTAAGTTGAAAAGTT
3053786 TTAAGTTGAAAAGTT
1 TTAAGTTGAAAAGTT
3053801 TTAAG
1 TTAAG
3053806 GACATAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (15 bp):
TTAAGTTGAAAAGTT
Found at i:3059943 original size:31 final size:30
Alignment explanation
Indices: 3059886--3059943 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
3059876 ACTAAAATGT
* *
3059886 AACTTTTGAAAGTTTAGAGGATAAAGTATA
1 AACTTTGGAAAGTTTAGAGGACAAAGTATA
3059916 AACTTTGGAAAAGTTTAG-GGACCAAAGT
1 AACTTTGG-AAAGTTTAGAGGA-CAAAGT
3059944 GTAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (30 bp):
AACTTTGGAAAGTTTAGAGGACAAAGTATA
Found at i:3068018 original size:21 final size:20
Alignment explanation
Indices: 3067983--3068063 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 20
3067973 AAAGTAATAA
3067983 AATATATTT-TTTTATTTTTG
1 AATAT-TTTATTTTATTTTTG
3068003 AATAATTTTATTTTATTTTTG
1 AAT-ATTTTATTTTATTTTTG
*
3068024 -GTATTATTATTTTTAAGTTTTTG
1 AATATT-TTA-TTTT-A-TTTTTG
3068047 AATA-TTT-TTTTATTTTT
1 AATATTTTATTTTATTTTT
3068064 TTAAAAATCC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
18 5 0.10
19 4 0.08
20 14 0.27
21 17 0.33
22 3 0.06
23 7 0.13
24 2 0.04
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (20 bp):
AATATTTTATTTTATTTTTG
Found at i:3068429 original size:19 final size:19
Alignment explanation
Indices: 3068405--3068443 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3068395 ACACTCTAAA
*
3068405 TTAAAAGTAATTTCTTTAT
1 TTAAAAGTAATTTATTTAT
*
3068424 TTAAAAGTATTTTATTTAT
1 TTAAAAGTAATTTATTTAT
3068443 T
1 T
3068444 CTCATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
TTAAAAGTAATTTATTTAT
Found at i:3069764 original size:20 final size:20
Alignment explanation
Indices: 3069739--3069790 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3069729 AATTCGCAAC
3069739 TCGAGTTGCGAAATCCGAAT
1 TCGAGTTGCGAAATCCGAAT
*
3069759 TCGAGTTGTGAAATCCGAAT
1 TCGAGTTGCGAAATCCGAAT
3069779 TCGAGTTGCGAA
1 TCGAGTTGCGAA
3069791 TTTGAAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (20 bp):
TCGAGTTGCGAAATCCGAAT
Found at i:3069883 original size:20 final size:20
Alignment explanation
Indices: 3069834--3069908 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
3069824 CTATATTAGT
*
3069834 AATTCGCATTGCGAAAACGA
1 AATTCGCGTTGCGAAAACGA
3069854 AATTCGCGTTGCGAAAACGA
1 AATTCGCGTTGCGAAAACGA
** *
3069874 AATTTTCGTTGCGAAATCCG-
1 AATTCGCGTTGCGAAA-ACGA
*
3069894 AATTCGAGTTGCGAA
1 AATTCGCGTTGCGAA
3069909 TTTGAAAACT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 45 0.96
21 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (20 bp):
AATTCGCGTTGCGAAAACGA
Found at i:3073016 original size:2 final size:2
Alignment explanation
Indices: 3073009--3073038 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3072999 ATTTCTAACT
3073009 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3073039 AACTCATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.