Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 90 of 250
Found at i:29095380 original size:27 final size:26
Alignment explanation
Indices: 29095324--29095380 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
29095314 CAACCTTAAC
* * *
29095324 CCTAGGGGTATATTAGTAATTTTGCT
1 CCTAGGGGTAAATTAGTAATTTTCCA
29095350 CCTAGGGGTAAATCT-GTAAATTTTCCA
1 CCTAGGGGTAAAT-TAGT-AATTTTCCA
29095377 CCTA
1 CCTA
29095381 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (26 bp):
CCTAGGGGTAAATTAGTAATTTTCCA
Found at i:29097502 original size:19 final size:18
Alignment explanation
Indices: 29097471--29097514 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
29097461 ATACATACAG
29097471 TAAT-ATTTTTCTCATAA
1 TAATAATTTTTCTCATAA
29097488 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTCATAA
*
29097507 TACTAATT
1 TAATAATT
29097515 AAAATTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.21
19 15 0.62
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTCATAA
Found at i:29110067 original size:25 final size:25
Alignment explanation
Indices: 29110027--29110077 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29110017 TCCCTTGTAT
* *
29110027 TGGATAGAGATTAAGGAAAATTAGA
1 TGGATAGAGATCAAGGAAAATCAGA
*
29110052 TGGATAGAGCTCAAGGAAAATCAGA
1 TGGATAGAGATCAAGGAAAATCAGA
29110077 T
1 T
29110078 TCACGATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.27, T:0.22
Consensus pattern (25 bp):
TGGATAGAGATCAAGGAAAATCAGA
Found at i:29112246 original size:28 final size:28
Alignment explanation
Indices: 29112214--29112316 Score: 134
Period size: 28 Copynumber: 3.7 Consensus size: 28
29112204 ATTGCATGAC
**
29112214 TATGAATGTGATTCGGCCTGACAGGCCA
1 TATGAATGTGATTCGGCCTGATGGGCCA
*
29112242 TATGAAAGTGATTCGGCCTGATGGGCCA
1 TATGAATGTGATTCGGCCTGATGGGCCA
* * *
29112270 CATGAATGTGATTGGGCCCGATGGGCCA
1 TATGAATGTGATTCGGCCTGATGGGCCA
* *
29112298 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTCGGCCT
29112317 AAAGGGGCCA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (28 bp):
TATGAATGTGATTCGGCCTGATGGGCCA
Found at i:29113601 original size:17 final size:18
Alignment explanation
Indices: 29113562--29113603 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29113552 GTTTTTATTC
29113562 TAAAA-AAGGATTTTCAA
1 TAAAACAAGGATTTTCAA
*
29113579 TGAAAACAAGG-TTTTCGA
1 T-AAAACAAGGATTTTCAA
29113597 TAAAACA
1 TAAAACA
29113604 CTTCAATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 4 0.18
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (18 bp):
TAAAACAAGGATTTTCAA
Found at i:29116743 original size:28 final size:28
Alignment explanation
Indices: 29116710--29116773 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
29116700 ATTGCATGAC
* * *
29116710 TATGAATGTCATTGTGCCTGACGGGCTA
1 TATGAATGTCATTGGGCCTAACGGGCCA
* * *
29116738 TATGAAAGTGATTGGGCCTAATGGGCCA
1 TATGAATGTCATTGGGCCTAACGGGCCA
29116766 TATGAATG
1 TATGAATG
29116774 AGATTGGACC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (28 bp):
TATGAATGTCATTGGGCCTAACGGGCCA
Found at i:29116778 original size:28 final size:28
Alignment explanation
Indices: 29116732--29116786 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
29116722 TGTGCCTGAC
* * *
29116732 GGGCTATATGAAAGTGATTGGGCCTAAT
1 GGGCCATATGAAAGAGATTGGACCTAAT
*
29116760 GGGCCATATGAATGAGATTGGACCTAA
1 GGGCCATATGAAAGAGATTGGACCTAA
29116787 AGGGGTCGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (28 bp):
GGGCCATATGAAAGAGATTGGACCTAAT
Found at i:29119367 original size:48 final size:48
Alignment explanation
Indices: 29119283--29119375 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 48
29119273 CACCATGGTT
* *
29119283 AATGAGATCCCATGTAAGACCATGTCTAGGACATGGCATT-GGCATTGA
1 AATGAGATCCCATATAAGACCATATCTAGGACATGGC-TTCGGCATTGA
* *
29119331 AATGAGATCCCGTATAAGACCATATC-AGGGATATGGCTTCGGCAT
1 AATGAGATCCCATATAAGACCATATCTA-GGACATGGCTTCGGCAT
29119376 CGTTAACTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 3 0.08
48 36 0.92
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (48 bp):
AATGAGATCCCATATAAGACCATATCTAGGACATGGCTTCGGCATTGA
Found at i:29122874 original size:12 final size:13
Alignment explanation
Indices: 29122838--29122875 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
29122828 AAATATTTGA
29122838 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
29122851 ATATGTTCTTAATT
1 CT-TGTTCTTAATT
29122865 CTTG-TCTTAAT
1 CTTGTTCTTAAT
29122876 ATTCCATGAT
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:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:29139547 original size:27 final size:26
Alignment explanation
Indices: 29139477--29139590 Score: 111
Period size: 27 Copynumber: 4.2 Consensus size: 26
29139467 AGCATGGCTG
* **
29139477 CCAGAACAGATATTGTGACAGAGTAA
1 CCAGAACAGATATTGTGGCAGAGCCA
*
29139503 CCAGATATAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
* *
29139530 CTAGAACAGATATATGTGGCATAGCCA
1 CCAGAACAGATAT-TGTGGCAGAGCCA
* * *
29139557 CCAGAAACAAATATTTGTAGCATAGCCA
1 CCAG-AACAGATA-TTGTGGCAGAGCCA
29139585 CCAGAA
1 CCAGAA
29139591 TGCTTCCTCC
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 12 0.16
27 38 0.51
28 23 0.31
29 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:29139570 original size:28 final size:27
Alignment explanation
Indices: 29139513--29139590 Score: 95
Period size: 28 Copynumber: 2.9 Consensus size: 27
29139503 CCAGATATAG
* * *
29139513 ATATTGTGGCAGAGCCACTAG-AACAG
1 ATATTGTGGCATAGCCACCAGAAACAA
29139539 ATATATGTGGCATAGCCACCAGAAACAA
1 ATAT-TGTGGCATAGCCACCAGAAACAA
*
29139567 ATATTTGTAGCATAGCCACCAGAA
1 ATA-TTGTGGCATAGCCACCAGAA
29139591 TGCTTCCTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.09
27 15 0.33
28 25 0.56
29 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (27 bp):
ATATTGTGGCATAGCCACCAGAAACAA
Found at i:29147461 original size:46 final size:47
Alignment explanation
Indices: 29147357--29147470 Score: 149
Period size: 46 Copynumber: 2.4 Consensus size: 47
29147347 TGTCTTCGAC
** * *
29147357 ATGGACTTACATGAATTATTCATGTCTCCAATGCCATATATATCTAAT
1 ATGGACTTACATGGCTCATTCATGTCTCCAAAGCCA-ATATATCTAAT
* * *
29147405 ATGGGCTTACATGGCTCATTCCTGTCTCTAAAGCC-ATATATCTAAT
1 ATGGACTTACATGGCTCATTCATGTCTCCAAAGCCAATATATCTAAT
29147451 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
29147471 TCTGCCCTAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 30 0.52
48 28 0.48
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCATGTCTCCAAAGCCAATATATCTAAT
Found at i:29149784 original size:27 final size:26
Alignment explanation
Indices: 29149715--29149827 Score: 100
Period size: 27 Copynumber: 4.2 Consensus size: 26
29149705 AGCATGGCTG
* * * *
29149715 CCAGAATAGATATTGTGACAGAGTCA
1 CCAGAACAGATTTTGTGGCAGAGCCA
* *
29149741 CCAGATACGGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATTTTGTGGCAGAGCCA
*
29149768 CCAGAACAGATGTTTGTGGCATAGCCA
1 CCAGAACAGAT-TTTGTGGCAGAGCCA
* * *
29149795 CCAGAAAAAGATATTTGTGGCATAGCTA
1 CCAG-AACAGAT-TTTGTGGCAGAGCCA
29149823 CCAGA
1 CCAGA
29149828 CCGCTTCCTC
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 10 0.14
27 40 0.54
28 24 0.32
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (26 bp):
CCAGAACAGATTTTGTGGCAGAGCCA
Found at i:29149815 original size:28 final size:28
Alignment explanation
Indices: 29149750--29149827 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 28
29149740 ACCAGATACG
* *
29149750 GATA-TTGTGGCAGAGCCACCAG-AACA
1 GATATTTGTGGCATAGCCACCAGAAAAA
*
29149776 GATGTTTGTGGCATAGCCACCAGAAAAA
1 GATATTTGTGGCATAGCCACCAGAAAAA
*
29149804 GATATTTGTGGCATAGCTACCAGA
1 GATATTTGTGGCATAGCCACCAGA
29149828 CCGCTTCCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 3 0.07
27 17 0.38
28 25 0.56
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (28 bp):
GATATTTGTGGCATAGCCACCAGAAAAA
Found at i:29160425 original size:46 final size:46
Alignment explanation
Indices: 29160375--29160547 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
29160365 TGGTTGAGCA
29160375 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29160421 TCCGAACTCGTTGAGTTGAGTCCGAGTT--CGTA-AGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
29160466 CATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29160514 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29160548 GGGGCAGGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 3 0.03
45 1 0.01
46 58 0.55
47 27 0.25
48 1 0.01
49 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29160531 original size:93 final size:93
Alignment explanation
Indices: 29160372--29160542 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
29160362 GGATGGTTGA
* * * *
29160372 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
29160437 TGAGTCCGAGTTCGTAAGATGTAACTAG
66 TGAGTCCGAGTTCGTAAGATGTAACTAG
*
29160465 GCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
29160530 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29160543 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTAAGATGTAACTAG
Found at i:29163495 original size:41 final size:41
Alignment explanation
Indices: 29163433--29163515 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
29163423 AGTAGCCGTT
*
29163433 AATTTATTCGTAACAAAATAAGCATGAGTTTAATAATTCTA
1 AATTTATTCATAACAAAATAAGCATGAGTTTAATAATTCTA
*
29163474 AATTTATTCATAACAACATAAGCATGAGTTTAATAATTCTA
1 AATTTATTCATAACAAAATAAGCATGAGTTTAATAATTCTA
29163515 A
1 A
29163516 GTTAAAGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (41 bp):
AATTTATTCATAACAAAATAAGCATGAGTTTAATAATTCTA
Found at i:29174326 original size:5 final size:5
Alignment explanation
Indices: 29174316--29174344 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
29174306 TTTCTTTGAG
29174316 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
29174345 CAGTAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:29174647 original size:27 final size:27
Alignment explanation
Indices: 29174582--29174639 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
29174572 AGCATGGCTG
* * *
29174582 CCAGA-ACAGATATCGTGACAGAGTCA
1 CCAGATACAGATATTGTGGCAGAGCCA
29174608 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGATACAGATATTGTGGCAGAGCCA
29174635 CCAGA
1 CCAGA
29174640 ATTAGATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGATACAGATATTGTGGCAGAGCCA
Found at i:29174868 original size:22 final size:22
Alignment explanation
Indices: 29174820--29174878 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
29174810 GTAAATACGT
*
29174820 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
29174842 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
29174864 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
29174879 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:29175045 original size:27 final size:26
Alignment explanation
Indices: 29174966--29175048 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
29174956 TCGATCAGTC
* * *
29174966 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
29174992 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
29175019 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
29175046 AAC
1 AAC
29175049 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:29175277 original size:27 final size:27
Alignment explanation
Indices: 29175247--29175434 Score: 250
Period size: 27 Copynumber: 7.0 Consensus size: 27
29175237 GGGGCAAAAT
* * *
29175247 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
29175274 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29175301 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29175328 GATAATTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29175355 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
29175382 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29175409 GGAAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
29175435 TAGTAATTTC
Statistics
Matches: 142, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 142 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:29175477 original size:27 final size:27
Alignment explanation
Indices: 29175447--29175775 Score: 387
Period size: 27 Copynumber: 12.2 Consensus size: 27
29175437 GTAATTTCAC
* *
29175447 AATCAAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
29175474 AATCGAGAGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
29175501 AA-CTGAGGGTAAAACAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
** * * **
29175528 AATTAAGGGTAAAATGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
29175555 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
29175582 AAACGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
29175609 AA-CTGAGGGTAAAATGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* *
29175636 AATCGAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
29175663 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* ** * *
29175690 AATCAAGGGTAAAATAGTAGTTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
29175717 AATTGAGGGTAAAACGGCAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
29175744 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
29175771 AATCG
1 AATCG
29175776 GGAGTACTTT
Statistics
Matches: 253, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
26 3 0.01
27 247 0.98
28 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:29175774 original size:81 final size:81
Alignment explanation
Indices: 29175447--29175774 Score: 462
Period size: 81 Copynumber: 4.0 Consensus size: 81
29175437 GTAATTTCAC
* * * * *
29175447 AATCAAGGGTAAAACGGTAATTTTGTAAATCGAGAGTAAAACGATAATTTTGTAAACTGAGGGTA
1 AATCAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGTA
*
29175512 AAACAGTAATTCTGTA
66 AAACGGTAATTCTGTA
* * * *
29175528 AATTAAGGGTAAAATGGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAAAC-GAGGGT
1 AATCAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGT-AAACTGAGGGT
29175592 AAAACGGTAATTCTGTA
65 AAAACGGTAATTCTGTA
* * *
29175609 AA-CTGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGATAATTCTATAAACTGAGGGT
1 AATC-AAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGT
29175673 AAAACGGTAATTCTGTA
65 AAAACGGTAATTCTGTA
* * * **
29175690 AATCAAGGGTAAAATAGTAGTTCTATAAATTGAGGGTAAAACGGCAATTCTGTAAACTGAGGGTA
1 AATCAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGTA
29175755 AAACGGTAATTCTGTA
66 AAACGGTAATTCTGTA
29175771 AATC
1 AATC
29175775 GGGAGTACTT
Statistics
Matches: 220, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
80 4 0.02
81 211 0.96
82 5 0.02
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (81 bp):
AATCAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGTA
AAACGGTAATTCTGTA
Found at i:29178602 original size:40 final size:40
Alignment explanation
Indices: 29178547--29178653 Score: 187
Period size: 40 Copynumber: 2.7 Consensus size: 40
29178537 TTTTATTCAT
29178547 GGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTACATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTACATCC
*
29178587 GGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTACATCC
* *
29178627 GGGCTAAGTCCTGAAGGGCATTCGTGC
1 GGGCTAAGTCCCGAAGAGCATTCGTGC
29178654 CAGTGATGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTACATCC
Found at i:29178897 original size:28 final size:28
Alignment explanation
Indices: 29178860--29178958 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 28
29178850 ATGAATTGAG
* *
29178860 GCACTGTGTGTGTGAATTCTTTAACCGA
1 GCACTATGTGTGCGAATTCTTTAACCGA
** * ** *
29178888 GCACTATGTGTGCGAGA-TCGATCAGTGG
1 GCACTATGTGTGCGA-ATTCTTTAACCGA
*
29178916 GCACTGTGTGTGCGAATTCTTTAACCGA
1 GCACTATGTGTGCGAATTCTTTAACCGA
29178944 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
29178959 GATCGGTCAG
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
27 1 0.02
28 51 0.96
29 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (28 bp):
GCACTATGTGTGCGAATTCTTTAACCGA
Found at i:29178923 original size:56 final size:56
Alignment explanation
Indices: 29178836--29178985 Score: 227
Period size: 56 Copynumber: 2.7 Consensus size: 56
29178826 TGAATATAGA
* *
29178836 CACTATGTGTGCGA-AT-GA--ATTGAGGCACTGTGTGTGTGAATTCTTTAACCGAG
1 CACTATGTGTGCGAGATCGATCAGTG-GGCACTGTGTGTGCGAATTCTTTAACCGAG
29178889 CACTATGTGTGCGAGATCGATCAGTGGGCACTGTGTGTGCGAATTCTTTAACCGAG
1 CACTATGTGTGCGAGATCGATCAGTGGGCACTGTGTGTGCGAATTCTTTAACCGAG
* *
29178945 CACTATGTGTGCGAGATCGGTCAGTAGGCACTGTGTGTGCG
1 CACTATGTGTGCGAGATCGATCAGTGGGCACTGTGTGTGCG
29178986 GATTTCGTTT
Statistics
Matches: 89, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
53 14 0.16
54 2 0.02
55 2 0.02
56 68 0.76
57 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.29
Consensus pattern (56 bp):
CACTATGTGTGCGAGATCGATCAGTGGGCACTGTGTGTGCGAATTCTTTAACCGAG
Found at i:29178975 original size:28 final size:28
Alignment explanation
Indices: 29178888--29178985 Score: 85
Period size: 28 Copynumber: 3.5 Consensus size: 28
29178878 CTTTAACCGA
*
29178888 GCACTATGTGTGCGAGATCGATCAGTGG
1 GCACTATGTGTGCGAGATCGATCAGTAG
* * * *
29178916 GCACTGTGTGTGCGA-ATTCTTTAACCG-A-
1 GCACTATGTGTGCGAGA-TC--GATCAGTAG
*
29178944 GCACTATGTGTGCGAGATCGGTCAGTAG
1 GCACTATGTGTGCGAGATCGATCAGTAG
*
29178972 GCACTGTGTGTGCG
1 GCACTATGTGTGCG
29178986 GATTTCGTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
26 2 0.04
27 2 0.04
28 45 0.85
29 1 0.02
30 3 0.06
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGATCAGTAG
Found at i:29184820 original size:20 final size:20
Alignment explanation
Indices: 29184795--29184833 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29184785 CTAGATGTAA
*
29184795 GGATTCAGAAGGAAACTTAG
1 GGATTCAGAAAGAAACTTAG
29184815 GGATTCAGAAAGAAACTTA
1 GGATTCAGAAAGAAACTTA
29184834 ATCGACAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.21
Consensus pattern (20 bp):
GGATTCAGAAAGAAACTTAG
Found at i:29186192 original size:25 final size:25
Alignment explanation
Indices: 29186163--29186219 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
29186153 TAAGCTTTCA
29186163 AAAGCTTAGTAAGCCATATACAAAT
1 AAAGCTTAGTAAGCCATATACAAAT
29186188 AAAGCTTAGTAAGCCATATACAAAT
1 AAAGCTTAGTAAGCCATATACAAAT
29186213 AAA-CTTA
1 AAAGCTTA
29186220 TTATATATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.25
Consensus pattern (25 bp):
AAAGCTTAGTAAGCCATATACAAAT
Found at i:29190406 original size:28 final size:27
Alignment explanation
Indices: 29190373--29190464 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 27
29190363 CCCTTTAGGG
* *
29190373 CCAATCTCATTCATATGGCCCATCGGGC
1 CCAATCAC-TTCATATGGCCCATCAGGC
*
29190401 CCAATCACTTTCATATGGCCTATCAGGC
1 CCAATCAC-TTCATATGGCCCATCAGGC
* * *
29190429 CCAATCACTTCCATATGGCTCGTTAGGC
1 CCAATCACTT-CATATGGCCCATCAGGC
29190457 CCAATCAC
1 CCAATCAC
29190465 ACTCATAGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 2 0.04
28 53 0.96
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (27 bp):
CCAATCACTTCATATGGCCCATCAGGC
Found at i:29190710 original size:16 final size:16
Alignment explanation
Indices: 29190689--29190719 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29190679 AAACTTCCAG
29190689 CTTTTTGGCATTTCGA
1 CTTTTTGGCATTTCGA
29190705 CTTTTTGGCATTTCG
1 CTTTTTGGCATTTCG
29190720 GGATCTACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (16 bp):
CTTTTTGGCATTTCGA
Found at i:29193140 original size:27 final size:27
Alignment explanation
Indices: 29193101--29193172 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
29193091 CAGCGGACTT
* *
29193101 CCTCATGTTTAATGTCTCGGCGAACTA
1 CCTCATGTATAATGTCCCGGCGAACTA
* * *
29193128 CCTCGTGTATAATGTCCCGGTGGACTA
1 CCTCATGTATAATGTCCCGGCGAACTA
* *
29193155 CCTCATGTTTAGTGTCCC
1 CCTCATGTATAATGTCCC
29193173 ACGGACTCTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (27 bp):
CCTCATGTATAATGTCCCGGCGAACTA
Found at i:29194984 original size:48 final size:48
Alignment explanation
Indices: 29194915--29195091 Score: 230
Period size: 48 Copynumber: 3.7 Consensus size: 48
29194905 CCAAAGTCTA
*
29194915 AATATCATGGTCC-AAAGCCAACTCAATGAATCTCGCACCCGAAGTGCC
1 AATATCATGGCCCGAAA-CCAACTCAATGAATCTCGCACCCGAAGTGCC
* *
29194963 AATATCATGGCCCGAAACCAACTCAATGAATCTTGCACTCGAAGTGCC
1 AATATCATGGCCCGAAACCAACTCAATGAATCTCGCACCCGAAGTGCC
* * * *
29195011 AATATCATGGCCTGAAGCCAACTCAATGAATCTCGCATCTGAAGTGCC
1 AATATCATGGCCCGAAACCAACTCAATGAATCTCGCACCCGAAGTGCC
* * * *
29195059 AATATCCTAGCCCGAAGCAAACTCAATGTAATC
1 AATATCATGGCCCGAAACCAACTCAATG-AATC
29195092 CCTAATGACA
Statistics
Matches: 114, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
48 107 0.94
49 7 0.06
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (48 bp):
AATATCATGGCCCGAAACCAACTCAATGAATCTCGCACCCGAAGTGCC
Found at i:29195082 original size:96 final size:97
Alignment explanation
Indices: 29194915--29195091 Score: 268
Period size: 96 Copynumber: 1.8 Consensus size: 97
29194905 CCAAAGTCTA
*
29194915 AATATCATGGTCCAAAGCCAACTCAATGAATCTCGCACCCGAAGTGCCAATATCATGGCCCGAAA
1 AATATCATGGTCCAAAGCCAACTCAATGAATCTCGCACCCGAAGTGCCAATATCATAGCCCGAAA
*
29194980 CCAACTCAATG-AATCTTGCACTCGAAGTGCC
66 CAAACTCAATGTAATCTTGCACTCGAAGTGCC
* * * *
29195011 AATATCATGG-CCTGAAGCCAACTCAATGAATCTCGCATCTGAAGTGCCAATATCCTAGCCCGAA
1 AATATCATGGTCC-AAAGCCAACTCAATGAATCTCGCACCCGAAGTGCCAATATCATAGCCCGAA
*
29195075 GCAAACTCAATGTAATC
65 ACAAACTCAATGTAATC
29195092 CCTAATGACA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
95 2 0.03
96 66 0.92
97 4 0.06
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (97 bp):
AATATCATGGTCCAAAGCCAACTCAATGAATCTCGCACCCGAAGTGCCAATATCATAGCCCGAAA
CAAACTCAATGTAATCTTGCACTCGAAGTGCC
Found at i:29196697 original size:37 final size:37
Alignment explanation
Indices: 29196638--29196745 Score: 173
Period size: 36 Copynumber: 2.9 Consensus size: 37
29196628 AGCTCAGACG
* * *
29196638 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
29196675 AAATCTCCACACGTAGTCATCGGGTCTTA-CCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
29196711 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
29196746 ATATATTTCC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
36 35 0.53
37 31 0.47
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:29197016 original size:47 final size:47
Alignment explanation
Indices: 29196954--29197293 Score: 446
Period size: 47 Copynumber: 7.1 Consensus size: 47
29196944 ACACGTTTCG
* * *
29196954 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
29197001 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
29197048 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* **
29197095 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CAC--ATATATGCATGTTCACATTCATCA
* *
29197146 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* **
29197193 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CAC--ATATATGCATGTTCACATTCATCA
* * * *
29197244 CATTGGCCATTCGACCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
29197291 CAT
1 CAT
29197294 AAAATCCTAA
Statistics
Matches: 256, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
47 167 0.65
49 12 0.05
51 77 0.30
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:29197142 original size:145 final size:144
Alignment explanation
Indices: 29196954--29197271 Score: 480
Period size: 145 Copynumber: 2.2 Consensus size: 144
29196944 ACACGTTTCG
* *
29196954 CATTAGCCATTCGGCCTTA-C-CACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCC
1 CATTGGCCATTCGGCCTTATCACACATATATTCAGGTTCACATTCATCACATTGGCCATTCGGCC
* * * *
29197017 TTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCAT-
66 TTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATG
29197081 GTTCACATTCATCA
131 GTTCACATTCATCA
*
29197095 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATAT-T-CAGGTTCACATTCATCACATTGGCCATTCGG
* *
29197160 CCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATATA
64 CCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA
29197225 TACGGGTTCACATTCATCA
129 T---GGTTCACATTCATCA
*
29197244 CATTGGCCATTCGACCTTATCACACATA
1 CATTGGCCATTCGGCCTTATCACACATA
29197272 CGCATGTTCA
Statistics
Matches: 159, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
141 18 0.11
142 1 0.01
143 9 0.06
144 1 0.01
145 89 0.56
149 41 0.26
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (144 bp):
CATTGGCCATTCGGCCTTATCACACATATATTCAGGTTCACATTCATCACATTGGCCATTCGGCC
TTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATG
GTTCACATTCATCA
Found at i:29197163 original size:98 final size:98
Alignment explanation
Indices: 29196954--29197293 Score: 553
Period size: 98 Copynumber: 3.5 Consensus size: 98
29196944 ACACGTTTCG
* * * **
29196954 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * **
29197019 AT--CTC--ATATATGCATGTTCACATTCATCA
66 ATCACACATATATATACGGGTTCACATTCATCA
29197048 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
29197113 ATCACACATATATATACGGGTTCACATTCATCA
66 ATCACACATATATATACGGGTTCACATTCATCA
29197146 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
29197211 ATCACACATATATATACGGGTTCACATTCATCA
66 ATCACACATATATATACGGGTTCACATTCATCA
* *
29197244 CATTGGCCATTCGACCTTATCACACATACGCATGTTCACATCCATCACAT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
29197294 AAAATCCTAA
Statistics
Matches: 231, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
94 62 0.27
96 2 0.01
98 167 0.72
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.31
Consensus pattern (98 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATATATATACGGGTTCACATTCATCA
Found at i:29199604 original size:85 final size:85
Alignment explanation
Indices: 29199475--29199653 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
29199465 TATTTTATTG
*
29199475 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
29199540 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
29199560 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
29199625 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
29199645 CCCATGCTC
1 CCCATGCTC
29199654 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:29205901 original size:47 final size:47
Alignment explanation
Indices: 29205847--29206088 Score: 331
Period size: 47 Copynumber: 5.1 Consensus size: 47
29205837 TTAGGATTTT
** * *
29205847 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
*
29205894 ATGTGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG--TATATAT--GTGATAAGGCCGAATGGCCA
** *
29205945 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* *
29205992 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * *
29206039 ATGTGATGAATGTGAACATGTATATATGTGGTCAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
29206086 ATG
1 ATG
29206089 CGAAATGTGT
Statistics
Matches: 175, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
47 127 0.73
49 11 0.06
51 37 0.21
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
Found at i:29206130 original size:46 final size:46
Alignment explanation
Indices: 29206078--29206180 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
29206068 GGTCAGGCCG
*
29206078 AATGGCTAATGCGAAATGTGTATGAGATAGATATGAGGTAAAGCCA
1 AATGGCTAATGCGAAACGTGTATGAGATAGATATGAGGTAAAGCCA
* *
29206124 AATGGCTAATGCGAAACGTGTATGAGATGGATATGTGGTAAAGCCA
1 AATGGCTAATGCGAAACGTGTATGAGATAGATATGAGGTAAAGCCA
29206170 AATGGCTAATG
1 AATGGCTAATG
29206181 TGCGATATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.37, C:0.10, G:0.29, T:0.24
Consensus pattern (46 bp):
AATGGCTAATGCGAAACGTGTATGAGATAGATATGAGGTAAAGCCA
Found at i:29206192 original size:46 final size:46
Alignment explanation
Indices: 29206062--29206198 Score: 152
Period size: 46 Copynumber: 3.0 Consensus size: 46
29206052 GAACATGTAT
* * * * ** * *
29206062 ATATGTGGTCAGGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
1 ATATGTGGTAAAGCCAAATGGCTAATGTGCGATATGTATGAGATGG
* *
29206108 ATATGAGGTAAAGCCAAATGGCTAA--TGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGTGCGATA--TGTATGAGATGG
29206154 ATATGTGGTAAAGCCAAATGGCTAATGTGCGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGTGCGATATGTATGAGATG
29206199 TGTATATATA
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
44 2 0.03
46 67 0.89
48 6 0.08
ACGTcount: A:0.34, C:0.10, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGTGCGATATGTATGAGATGG
Found at i:29208306 original size:18 final size:17
Alignment explanation
Indices: 29208268--29208313 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
29208258 TAATTTAGCC
29208268 ATTTTTATTTTTGTTAT
1 ATTTTTATTTTTGTTAT
*
29208285 ATTTGTATTTTTAGTT-T
1 ATTTTTATTTTT-GTTAT
29208302 AATTTTTATTTT
1 -ATTTTTATTTT
29208314 CTAATTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (17 bp):
ATTTTTATTTTTGTTAT
Found at i:29211675 original size:23 final size:22
Alignment explanation
Indices: 29211637--29211687 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
29211627 AAGCCACCCC
*
29211637 TTTTA-TT-TTATTTTATTTAT
1 TTTTATTTGTTATATTATTTAT
29211657 TTATTATTTGTTATATTATTTAT
1 TT-TTATTTGTTATATTATTTAT
29211680 TTTTATTT
1 TTTTATTT
29211688 TACTAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 3 0.11
22 8 0.30
23 14 0.52
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTATTTGTTATATTATTTAT
Found at i:29211859 original size:23 final size:23
Alignment explanation
Indices: 29211819--29211877 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
29211809 TTTATTATTA
* *
29211819 TATTATTATTATTAATTTCAT-TT
1 TATTTTTATTTTTAATTT-ATCTT
*
29211842 TATTTTTATTTTTTATTTATCTT
1 TATTTTTATTTTTAATTTATCTT
* *
29211865 TCTTTTTAATTTT
1 TATTTTTATTTTT
29211878 GTTTTAGATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (23 bp):
TATTTTTATTTTTAATTTATCTT
Found at i:29214364 original size:45 final size:45
Alignment explanation
Indices: 29214306--29214397 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
29214296 AGATTGAGTT
* *
29214306 AATGCGACAATAGATATTTTAATTAGAAAGAGGTTTCAATTAATA
1 AATGCGACAATAGAGATTTTAATTAGAAAAAGGTTTCAATTAATA
29214351 AATGCGACAATAGAGATTTTAATTAGAAAAAGGTTTCAATTAATA
1 AATGCGACAATAGAGATTTTAATTAGAAAAAGGTTTCAATTAATA
29214396 AA
1 AA
29214398 CCTAGAATCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.32
Consensus pattern (45 bp):
AATGCGACAATAGAGATTTTAATTAGAAAAAGGTTTCAATTAATA
Found at i:29214884 original size:35 final size:35
Alignment explanation
Indices: 29214785--29214938 Score: 128
Period size: 35 Copynumber: 4.4 Consensus size: 35
29214775 GTGACCATCA
* * * * *
29214785 TCTACAGACTTTACGGAGTGACATCGTGTAAATGG
1 TCTACAGGCTCTACGGAGTGACACCATGTAAATAG
* ** **
29214820 TCTACAGGCTCTATGGAGCAACATTATGTAAATAG
1 TCTACAGGCTCTACGGAGTGACACCATGTAAATAG
* * *
29214855 TCTACAGGCTATACAGAGTGACACCATGTAAATAA
1 TCTACAGGCTCTACGGAGTGACACCATGTAAATAG
* * * * * *
29214890 TCTACAAGATTTATGGAGTGACACCATGAAAATGG
1 TCTACAGGCTCTACGGAGTGACACCATGTAAATAG
*
29214925 TCTATAGGCTCTAC
1 TCTACAGGCTCTAC
29214939 ACGATGACAC
Statistics
Matches: 90, Mismatches: 29, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
35 90 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (35 bp):
TCTACAGGCTCTACGGAGTGACACCATGTAAATAG
Found at i:29218101 original size:79 final size:81
Alignment explanation
Indices: 29217992--29218174 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
29217982 TACTCGTTCA
* *
29217992 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
29218055 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
29218072 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
29218135 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
29218151 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
29218175 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:29218174 original size:40 final size:40
Alignment explanation
Indices: 29217971--29218174 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
29217961 CGGAATTTAA
** *
29217971 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29218011 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29218051 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
29218090 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
29218130 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29218170 CCGGA
1 CCGGA
29218175 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:29239833 original size:18 final size:17
Alignment explanation
Indices: 29239801--29239834 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29239791 AAATTGGACA
29239801 GTGTGAGCCACACGGGT
1 GTGTGAGCCACACGGGT
*
29239818 GTGTGGGCCTACACGGG
1 GTGTGAGCC-ACACGGG
29239835 CAGGCCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (17 bp):
GTGTGAGCCACACGGGT
Found at i:29240575 original size:6 final size:6
Alignment explanation
Indices: 29240559--29240596 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
29240549 TGAGTATTGG
*
29240559 TTTTAT TTTTTT ATTTTAT TTTTAT TTTTA- TTTTAT TT
1 TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TT
29240597 GGTTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.18
6 18 0.64
7 5 0.18
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:29249606 original size:108 final size:108
Alignment explanation
Indices: 29249432--29249629 Score: 369
Period size: 108 Copynumber: 1.8 Consensus size: 108
29249422 AGCTTGGTAT
*
29249432 AATACAAATGCGTTCGGCACTTACGCCTATACAATGCCTCATAAGGTGCCATCTTTAAACTCGAC
1 AATACAAATGCGTTCGGCACTTACGCCTATACAACGCCTCATAAGGTGCCATCTTTAAACTCGAC
* *
29249497 TGAAAGTTGTTGTTGTAAGCAAACTACACTCTAAGCTCAGTCC
66 TGAAAGCTGTTGTTATAAGCAAACTACACTCTAAGCTCAGTCC
29249540 AATACAAATGCGTTCGGCACTTACGCCTATACAACGCCTCATAAGGTGCCATCTTTAAACTCGAC
1 AATACAAATGCGTTCGGCACTTACGCCTATACAACGCCTCATAAGGTGCCATCTTTAAACTCGAC
29249605 TGAAAGCTGTTGTTATAAGCAAACT
66 TGAAAGCTGTTGTTATAAGCAAACT
29249630 CCACCAGCGG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 87 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (108 bp):
AATACAAATGCGTTCGGCACTTACGCCTATACAACGCCTCATAAGGTGCCATCTTTAAACTCGAC
TGAAAGCTGTTGTTATAAGCAAACTACACTCTAAGCTCAGTCC
Found at i:29256863 original size:14 final size:14
Alignment explanation
Indices: 29256846--29256875 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29256836 TATTTATGTA
*
29256846 TGATTATTGTTAGT
1 TGATTACTGTTAGT
29256860 TGATTACTGTTAGT
1 TGATTACTGTTAGT
29256874 TG
1 TG
29256876 CATATAAGCA
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:0.20, C:0.03, G:0.23, T:0.53
Consensus pattern (14 bp):
TGATTACTGTTAGT
Found at i:29261189 original size:6 final size:6
Alignment explanation
Indices: 29261178--29261522 Score: 300
Period size: 6 Copynumber: 56.8 Consensus size: 6
29261168 AACCAAAATG
* *
29261178 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATTTT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* *
29261226 AGTAA-C AGAATC AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC
* *
29261275 AGAATC AGAATC AGAATC AGAATC AGTATT AGTAA-C AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC
* * *
29261323 AGAATC AAAATT ACGTGA-C AGAATC AGAATC AGAATC AGAATC AGTAA-C
1 AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC
* *
29261372 AGAATC AGAATC AGAATC A-ATTTT AGTAA-C AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGA-ATC AG-AATC AGAATC AGAATC AGAATC
* * * *
29261420 AGAATT AG-GTGAC AGAATC AGAATC AGAATC AGAATC AGAATC AGTATT
1 AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC
* * *
29261469 AGTAA-C AGAATC AGAATC AGAATC AAAATT ACGTGA-C AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
29261518 AGAAT
1 AGAAT
29261523 ATGAATGCAA
Statistics
Matches: 275, Mismatches: 36, Indels: 56
0.75 0.10 0.15
Matches are distributed among these distances:
5 18 0.07
6 239 0.87
7 12 0.04
8 6 0.02
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:29261277 original size:91 final size:91
Alignment explanation
Indices: 29261178--29261464 Score: 339
Period size: 85 Copynumber: 3.4 Consensus size: 91
29261168 AACCAAAATG
29261178 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGTAACAGAATCAGAAT
29261243 CAGAATCAGAATCAGAATTAGGTGAC
66 CAGAATCAGAATCAGAATTAGGTGAC
29261269 AGAATCAGAATCAG-A--A-T--CAGAATCAGAATCAG--T--A--TTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGTAACAGAATCAGAAT
* * * * *
29261322 CAGAATCAAAATTACG--TGACAG-AATC
66 CAGAATCAGAATCA-GAATTA-GGTGA-C
29261348 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGT-----AA-CAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGTAACAGAATCAGAAT
29261407 CAGAATCAGAATCAGAATTAGGTGAC
66 CAGAATCAGAATCAGAATTAGGTGAC
29261433 AGAATCAGAATCAGAATCAG-AATCAGAATCAG
1 AGAATCAGAATCAGAATCAGTAA-CAGAATCAG
29261465 TATTAGTAAC
Statistics
Matches: 167, Mismatches: 10, Indels: 44
0.76 0.05 0.20
Matches are distributed among these distances:
78 3 0.02
79 47 0.28
80 2 0.01
81 1 0.01
82 1 0.01
83 2 0.01
84 3 0.02
85 79 0.47
86 5 0.03
87 2 0.01
88 1 0.01
89 1 0.01
90 1 0.01
91 19 0.11
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (91 bp):
AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGTAACAGAATCAGAAT
CAGAATCAGAATCAGAATTAGGTGAC
Found at i:29261387 original size:73 final size:73
Alignment explanation
Indices: 29261201--29261390 Score: 260
Period size: 73 Copynumber: 2.6 Consensus size: 73
29261191 GAATCAGTAA
* *** * *
29261201 CAGAATCAGAATCAGAATCAATTTTAGTAA-CAGAATCAGAATCAGAATCAGAATCAGAATTAGG
1 CAGAATCAGAATCAGAATCAGTAACAG-AATCAGAATCAGAATCAGAATCAGAATCAAAATTACG
29261265 TGACAGAAT
65 TGACAGAAT
* *
29261274 CAGAATCAGAATCAGAATCAG-AATCAGTATTAGTAA-CAGAATCAGAATCAGAATCAAAATTAC
1 CAGAATCAGAATCAGAATCAGTAA-CAGAATCAG-AATCAGAATCAGAATCAGAATCAAAATTAC
29261337 GTGACAGAAT
64 GTGACAGAAT
29261347 CAGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCA
1 CAGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCA
29261391 ATTTTAGTAA
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
72 3 0.03
73 95 0.93
74 4 0.04
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (73 bp):
CAGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATCAGAATCAAAATTACGT
GACAGAAT
Found at i:29261436 original size:73 final size:73
Alignment explanation
Indices: 29261359--29261522 Score: 276
Period size: 73 Copynumber: 2.2 Consensus size: 73
29261349 GAATCAGAAT
* *
29261359 CAGAATCAGTAA-CAGAATCAGAATCAGAATCAATTTTAGTAACAGAATCAGAATCAGAATCAGA
1 CAGAATCAG-AATCAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGAATCAAA
*
29261423 ATTAGGTGA
65 ATTACGTGA
*
29261432 CAGAATCAGAATCAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAATCAGAATCAAAA
1 CAGAATCAGAATCAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGAATCAAAA
29261497 TTACGTGA
66 TTACGTGA
29261505 CAGAATCAGAATCAGAAT
1 CAGAATCAGAATCAGAAT
29261523 ATGAATGCAA
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
72 2 0.02
73 84 0.98
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.21
Consensus pattern (73 bp):
CAGAATCAGAATCAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGAATCAAAA
TTACGTGA
Found at i:29261449 original size:164 final size:166
Alignment explanation
Indices: 29261178--29261522 Score: 640
Period size: 164 Copynumber: 2.1 Consensus size: 166
29261168 AACCAAAATG
29261178 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGT---A-AATCAGAAT
29261243 CAGAATCAGAATCAGAATTAGGTGACAGAATCAGAATCAGAATCAGAATCAGAATCAGTATTAGT
62 CAGAATCAGAATCAGAATTAGGTGACAGAATCAGAATCAGAATCAGAATCAGAATCAGTATTAGT
29261308 AACAGAATCAGAATCAGAATCAAAATTACGTGACAGAATC
127 AACAGAATCAGAATCAGAATCAAAATTACGTGACAGAATC
29261348 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGT-AA-CAGAATCAGA
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGTAAATCAGAATCAGA
29261411 ATCAGAATCAGAATTAGGTGACAGAATCAGAATCAGAATCAGAATCAGAATCAGTATTAGTAACA
66 ATCAGAATCAGAATTAGGTGACAGAATCAGAATCAGAATCAGAATCAGAATCAGTATTAGTAACA
29261476 GAATCAGAATCAGAATCAAAATTACGTGACAGAATC
131 GAATCAGAATCAGAATCAAAATTACGTGACAGAATC
29261512 AGAATCAGAAT
1 AGAATCAGAAT
29261523 ATGAATGCAA
Statistics
Matches: 175, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
164 122 0.70
165 2 0.01
170 51 0.29
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (166 bp):
AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATTTTAGTAAATCAGAATCAGA
ATCAGAATCAGAATTAGGTGACAGAATCAGAATCAGAATCAGAATCAGAATCAGTATTAGTAACA
GAATCAGAATCAGAATCAAAATTACGTGACAGAATC
Found at i:29261677 original size:27 final size:26
Alignment explanation
Indices: 29261640--29261705 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
29261630 AGCATGGCTG
*
29261640 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
29261666 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
29261693 CCAGAATCAGATA
1 CCAGAA-CAGATA
29261706 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:29261710 original size:27 final size:27
Alignment explanation
Indices: 29261640--29261713 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
29261630 AGCATGGCTG
* *
29261640 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
29261666 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
29261693 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
29261714 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:29261720 original size:27 final size:27
Alignment explanation
Indices: 29261664--29261721 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
29261654 GTGACAGAGT
* * *
29261664 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
29261691 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
29261718 CACC
1 CACC
29261722 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:29262069 original size:27 final size:28
Alignment explanation
Indices: 29262025--29262105 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 28
29262015 CGATCAGTCA
*
29262025 ACAGATATTGTGACAGAGTCACCA-AAT
1 ACAGATATTGTGACAGAGCCACCAGAAT
**
29262052 ACAGATATTGTGGTAGAGCCACCAGAAT
1 ACAGATATTGTGACAGAGCCACCAGAAT
* *
29262080 --AGATATTTGTGGCATAGCCACCAGAA
1 ACAGATA-TTGTGACAGAGCCACCAGAA
29262106 CGCTTCCTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 5 0.11
27 39 0.83
28 3 0.06
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (28 bp):
ACAGATATTGTGACAGAGCCACCAGAAT
Found at i:29262335 original size:27 final size:27
Alignment explanation
Indices: 29262306--29262500 Score: 248
Period size: 27 Copynumber: 7.2 Consensus size: 27
29262296 GGGCAAAATG
* * *
29262306 GTAATTTTACCCTACAAGGGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
29262333 GTAATTCTACCCTACAAGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
*
29262360 GTATTTCTACCCTACAAGGGTATTTC-
1 GTAATTCTACCCTACAAGGGTATTTCA
*
29262386 GATAATTCTACCCTACAAGGGTATTTTA
1 G-TAATTCTACCCTACAAGGGTATTTCA
* *
29262414 GTAATTCTATCCTATAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* * **
29262441 GTAATTCTACCCTATAGGGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
29262468 GAAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
29262495 GTAATT
1 GTAATT
29262501 TCACAATCAA
Statistics
Matches: 146, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 144 0.99
28 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:29262375 original size:54 final size:54
Alignment explanation
Indices: 29262306--29262500 Score: 275
Period size: 54 Copynumber: 3.6 Consensus size: 54
29262296 GGGCAAAATG
* * *
29262306 GTAATTTTACCCTACAAGGGTATCTCGGTAATTCTACCCTACAAGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTTA
*
29262360 GTATTTCTACCCTACAAGGGTATTTC-GATAATTCTACCCTACAAGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCAG-TAATTCTACCCTACAAGGGTATTTTA
* * * * *
29262414 GTAATTCTATCCTATAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTTA
* *
29262468 GAAATTCTACCCTACAGGGGTATTTCAGTAATT
1 GTAATTCTACCCTACAAGGGTATTTCAGTAATT
29262501 TCACAATCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 124 0.98
55 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTTA
Found at i:29262535 original size:27 final size:27
Alignment explanation
Indices: 29262505--29262833 Score: 385
Period size: 27 Copynumber: 12.2 Consensus size: 27
29262495 GTAATTTCAC
* *
29262505 AATCAAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
29262532 AATCGAGAGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
29262559 AA-CTGAGGGTAAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
** * * **
29262586 AATTAAGGGTAAAATGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
29262613 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
29262640 AACCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
29262667 AACCGAGGGTAAAACGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
29262694 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
29262721 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * * *
29262748 AATCAAGGGTAAAACAGTAGTTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
29262775 AATTGAGGGTAAAACGGCAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
29262802 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
29262829 AATCG
1 AATCG
29262834 GGAGTACTTT
Statistics
Matches: 254, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.01
27 250 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:29262625 original size:81 final size:81
Alignment explanation
Indices: 29262505--29262832 Score: 485
Period size: 81 Copynumber: 4.0 Consensus size: 81
29262495 GTAATTTCAC
* * *
29262505 AATCAAGGGTAAAACGGTAATTTTGTAAATCGAGAGTAAAACGATAATTTTGTAAACTGAGGGTA
1 AATCAAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGTA
* *
29262570 AACCAGTAATTCTGTA
66 AAACGGTAATTCTGTA
* * * * * *
29262586 AATTAAGGGTAAAATGGTAATTTTACAAATCAAGGGTAAAACGGTAATTCTGTAAACCGAGGGTA
1 AATCAAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGTA
29262651 AAACGGTAATTCTGTA
66 AAACGGTAATTCTGTA
* *
29262667 AACCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGTA
1 AATCAAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGTA
29262732 AAACGGTAATTCTGTA
66 AAACGGTAATTCTGTA
* * * * **
29262748 AATCAAGGGTAAAACAGTAGTTCTATAAATTGAGGGTAAAACGGCAATTCTGTAAACTGAGGGTA
1 AATCAAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGTA
29262813 AAACGGTAATTCTGTA
66 AAACGGTAATTCTGTA
29262829 AATC
1 AATC
29262833 GGGAGTACTT
Statistics
Matches: 220, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 220 1.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (81 bp):
AATCAAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACGATAATTCTGTAAACTGAGGGTA
AAACGGTAATTCTGTA
Found at i:29265855 original size:40 final size:40
Alignment explanation
Indices: 29265811--29265926 Score: 205
Period size: 40 Copynumber: 2.9 Consensus size: 40
29265801 AGAATTGAGA
29265811 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
29265851 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
* * *
29265891 GTTATATCCGGGCTAAGTCCTGAAGGGCATTCGTGC
1 GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGC
29265927 CAGTGATGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (40 bp):
GTTACATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
Found at i:29266123 original size:25 final size:25
Alignment explanation
Indices: 29266095--29266149 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
29266085 TGTGTAATAA
29266095 CGAATGAATAT-AGACACTATGTGTG
1 CGAATGAAT-TGAGACACTATGTGTG
*
29266120 CGAATGAATTGAGGCACTATGTGTG
1 CGAATGAATTGAGACACTATGTGTG
*
29266145 TGAAT
1 CGAAT
29266150 TCTTTAACCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (25 bp):
CGAATGAATTGAGACACTATGTGTG
Found at i:29266169 original size:28 final size:28
Alignment explanation
Indices: 29266133--29266231 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
29266123 ATGAATTGAG
*
29266133 GCACTATGTGTGTGAATTCTTTAACCGA
1 GCACTATGTGTGCGAATTCTTTAACCGA
** * ** *
29266161 GCACTATGTGTGCGAGA-TCGATCAGTGG
1 GCACTATGTGTGCGA-ATTCTTTAACCGA
*
29266189 GCACTGTGTGTGCGAATTCTTTAACCGA
1 GCACTATGTGTGCGAATTCTTTAACCGA
29266217 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
29266232 GATCGGTCAG
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
27 1 0.02
28 52 0.96
29 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTATGTGTGCGAATTCTTTAACCGA
Found at i:29266199 original size:56 final size:56
Alignment explanation
Indices: 29266109--29266258 Score: 209
Period size: 56 Copynumber: 2.7 Consensus size: 56
29266099 TGAATATAGA
* * *
29266109 CACTATGTGTGCGA-AT-GA--ATTGAGGCACTATGTGTGTGAATTCTTTAACCGAG
1 CACTATGTGTGCGAGATCGATCAGTG-GGCACTGTGTGTGCGAATTCTTTAACCGAG
29266162 CACTATGTGTGCGAGATCGATCAGTGGGCACTGTGTGTGCGAATTCTTTAACCGAG
1 CACTATGTGTGCGAGATCGATCAGTGGGCACTGTGTGTGCGAATTCTTTAACCGAG
* * *
29266218 CACTATGTGTGCGAGATCGGTCAGTAGGCACTGTATGTGCG
1 CACTATGTGTGCGAGATCGATCAGTGGGCACTGTGTGTGCG
29266259 GATTTCGTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
53 14 0.16
54 2 0.02
55 2 0.02
56 66 0.76
57 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (56 bp):
CACTATGTGTGCGAGATCGATCAGTGGGCACTGTGTGTGCGAATTCTTTAACCGAG
Found at i:29266248 original size:28 final size:28
Alignment explanation
Indices: 29266161--29266258 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 28
29266151 CTTTAACCGA
*
29266161 GCACTATGTGTGCGAGATCGATCAGTGG
1 GCACTATGTGTGCGAGATCGATCAGTAG
* * * *
29266189 GCACTGTGTGTGCGA-ATTCTTTAACCG-A-
1 GCACTATGTGTGCGAGA-TC--GATCAGTAG
*
29266217 GCACTATGTGTGCGAGATCGGTCAGTAG
1 GCACTATGTGTGCGAGATCGATCAGTAG
* *
29266245 GCACTGTATGTGCG
1 GCACTATGTGTGCG
29266259 GATTTCGTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
26 2 0.04
27 2 0.04
28 44 0.85
29 1 0.02
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGATCAGTAG
Found at i:29273733 original size:25 final size:25
Alignment explanation
Indices: 29273704--29273760 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
29273694 TAAGCTTTCA
29273704 AAAGCTTAGTAAGCCATATACAAAT
1 AAAGCTTAGTAAGCCATATACAAAT
29273729 AAAGCTTAGTAAGCCATATACAAAT
1 AAAGCTTAGTAAGCCATATACAAAT
29273754 AAA-CTTA
1 AAAGCTTA
29273761 TTATATATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.25
Consensus pattern (25 bp):
AAAGCTTAGTAAGCCATATACAAAT
Found at i:29344036 original size:14 final size:14
Alignment explanation
Indices: 29344019--29344048 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29344009 TATTTATGTA
*
29344019 TGATTATTGTTAGT
1 TGATTACTGTTAGT
29344033 TGATTACTGTTAGT
1 TGATTACTGTTAGT
29344047 TG
1 TG
29344049 CATATAAGGA
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:0.20, C:0.03, G:0.23, T:0.53
Consensus pattern (14 bp):
TGATTACTGTTAGT
Found at i:29353743 original size:40 final size:40
Alignment explanation
Indices: 29353606--29353736 Score: 226
Period size: 40 Copynumber: 3.3 Consensus size: 40
29353596 AACTCGTACG
*
29353606 AATGCCTTCGGGACTTAGCCCGGACATAGTCACTAGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACA
*
29353646 AATGCCTTCGGGACTTAGCCCGAATATAGTCACTAGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACA
* *
29353686 AATGCCTTTGGGACTTAGCCCGGATATAATCACTAGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACA
29353726 AATGCCTTCGG
1 AATGCCTTCGG
29353737 ATCTTAGTCC
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACA
Found at i:29357880 original size:40 final size:39
Alignment explanation
Indices: 29357794--29357889 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 39
29357784 GTCTCAGTAT
* * *
29357794 TGCACACTTAGTGCCACATATATCCGAAGCTATTCCAAT
1 TGCACACTAAGTGCCACATATAGCCGAAGCTATTCCAAA
* * * *
29357833 TCACACACTAAGTGCTATATATAGCCGAAGCTATCTCGAAA
1 T-GCACACTAAGTGCCACATATAGCCGAAGCTAT-TCCAAA
29357874 TGCACACTAAGTGCCA
1 TGCACACTAAGTGCCA
29357890 AACATAACCG
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.02
40 40 0.87
41 5 0.11
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (39 bp):
TGCACACTAAGTGCCACATATAGCCGAAGCTATTCCAAA
Found at i:29364995 original size:21 final size:20
Alignment explanation
Indices: 29364970--29365023 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
29364960 TACTGATTTG
*
29364970 TACATAATATGCCATGATATGA
1 TACAT-ATATGCAATGATAT-A
*
29364992 -ACATGATATGTAATGATATA
1 TACAT-ATATGCAATGATATA
29365012 TACATATATGCA
1 TACATATATGCA
29365024 TGGGTTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (20 bp):
TACATATATGCAATGATATA
Found at i:29365084 original size:25 final size:25
Alignment explanation
Indices: 29365056--29365147 Score: 148
Period size: 25 Copynumber: 3.7 Consensus size: 25
29365046 GAAGAAGTGC
*
29365056 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
29365081 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* * *
29365106 AAAAGGGCTTTGCCCCAATTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
29365131 AAAAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
29365148 ATTATTAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:29365163 original size:24 final size:25
Alignment explanation
Indices: 29365055--29365163 Score: 102
Period size: 25 Copynumber: 4.4 Consensus size: 25
29365045 GGAAGAAGTG
* * *
29365055 CAAAAG-GGCTATGCCCCAGTTTAC
1 CAAAAGAGGCTTTGCCCCAATTTAT
* *
29365079 CGAAAAG-GGCTTTGCCCCAGTTTAC
1 C-AAAAGAGGCTTTGCCCCAATTTAT
29365104 CGAAAAG-GGCTTTGCCCCAATTTAT
1 C-AAAAGAGGCTTTGCCCCAATTTAT
29365129 CAAAA-AGGGCTTTGCCCCAA-TTAT
1 CAAAAGA-GGCTTTGCCCCAATTTAT
*
29365153 TAAAAGAGGCT
1 CAAAAGAGGCT
29365164 AGGCCTCCAG
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.22
25 60 0.78
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (25 bp):
CAAAAGAGGCTTTGCCCCAATTTAT
Found at i:29365406 original size:31 final size:31
Alignment explanation
Indices: 29365371--29365454 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
29365361 CGTTTACAAT
*
29365371 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCTAGTGATATGAATAATGA
* *
29365402 AAAGGCTTCGGCCTAGTGGTATGAATAATGT
1 AAAGGCTTCGGCCTAGTGATATGAATAATGA
*
29365433 AAAGGCTTCAGCCTAGT-ATATG
1 AAAGGCTTCGGCCTAGTGATATG
29365455 CTGAGATTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 4 0.08
31 44 0.92
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCTAGTGATATGAATAATGA
Found at i:29372880 original size:10 final size:10
Alignment explanation
Indices: 29372865--29372899 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
29372855 TTTGTACATA
29372865 ATATGCCATG
1 ATATGCCATG
29372875 ATATGCACATG
1 ATATGC-CATG
29372886 ATATGCCATG
1 ATATGCCATG
29372896 ATAT
1 ATAT
29372900 ATACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:29372884 original size:21 final size:21
Alignment explanation
Indices: 29372860--29372899 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29372850 ACTGATTTGT
29372860 ACATAATATGCCATGATATGC
1 ACATAATATGCCATGATATGC
*
29372881 ACATGATATGCCATGATAT
1 ACATAATATGCCATGATAT
29372900 ATACATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
ACATAATATGCCATGATATGC
Found at i:29372905 original size:21 final size:20
Alignment explanation
Indices: 29372859--29372911 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
29372849 TACTGATTTG
*
29372859 TACATAATATGCCATGATATG
1 TACAT-ATATGCCATGATATA
*
29372880 CACATGATATGCCATGATATA
1 TACAT-ATATGCCATGATATA
29372901 TACATATATGC
1 TACATATATGC
29372912 ATGGGTTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (20 bp):
TACATATATGCCATGATATA
Found at i:29372973 original size:25 final size:24
Alignment explanation
Indices: 29372945--29373038 Score: 116
Period size: 25 Copynumber: 3.8 Consensus size: 24
29372935 GAGGAAGTGC
*
29372945 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTA-CG
* *
29372970 AAAAAGGCTTTGCCCTAGTTTACG
1 AAAAGGGCTTTGCCCCAGTTTACG
* *
29372994 AAAAAGAGCTTTGCCCCAGTTTATCA
1 -AAAAGGGCTTTGCCCCAGTTTA-CG
29373020 AAAAGGGCTTTGCCCCAGT
1 AAAAGGGCTTTGCCCCAGT
29373039 GATTAAAAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.03
25 56 0.95
26 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACG
Found at i:29373052 original size:24 final size:25
Alignment explanation
Indices: 29372944--29373052 Score: 77
Period size: 25 Copynumber: 4.4 Consensus size: 25
29372934 GGAGGAAGTG
* * *
29372944 CAAAAG-GGCTATGCCCCAGTTTAC
1 CAAAAGAGGCTTTGCCCCAGTTGAT
* *
29372968 CGAAAA-AGGCTTTGCCCTAGTTTA-
1 C-AAAAGAGGCTTTGCCCCAGTTGAT
*
29372992 CGAAAA-AGAGCTTTGCCCCAGTTTAT
1 C-AAAAGAG-GCTTTGCCCCAGTTGAT
29373018 CAAAA-AGGGCTTTGCCCCAG-TGAT
1 CAAAAGA-GGCTTTGCCCCAGTTGAT
*
29373042 TAAAAGAGGCT
1 CAAAAGAGGCT
29373053 AGGCCTCCAG
Statistics
Matches: 74, Mismatches: 5, Indels: 12
0.81 0.05 0.13
Matches are distributed among these distances:
24 20 0.27
25 52 0.70
26 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (25 bp):
CAAAAGAGGCTTTGCCCCAGTTGAT
Found at i:29373295 original size:31 final size:31
Alignment explanation
Indices: 29373260--29373343 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
29373250 CGTTTGCAGT
29373260 AAAGGCTTTGGCCCAGTGATATGAATAATGA
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
* *
29373291 AAAGGCTTTGGCCCAGTGGTATGAATAATGT
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
*
29373322 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTTGGCCCAGTGATATG
29373344 CTGAGATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (31 bp):
AAAGGCTTTGGCCCAGTGATATGAATAATGA
Found at i:29380348 original size:39 final size:40
Alignment explanation
Indices: 29380303--29380470 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
29380293 CGGGGTTTAG
* * *
29380303 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
29380342 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
29380382 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
29380422 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
29380463 CCGGATAT
1 CCGGATAT
29380471 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:29380453 original size:41 final size:40
Alignment explanation
Indices: 29380326--29380470 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
29380316 CTCGCACAAG
* * * * *
29380326 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
29380366 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
29380406 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
29380447 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
29380471 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:29388289 original size:39 final size:40
Alignment explanation
Indices: 29388244--29388411 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
29388234 CGGGGTTTAG
* * *
29388244 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
29388283 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
29388323 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
29388363 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
29388404 CCGGATAT
1 CCGGATAT
29388412 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:29388394 original size:41 final size:40
Alignment explanation
Indices: 29388267--29388411 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
29388257 CTCGCACAAG
* * * * *
29388267 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
29388307 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
29388347 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
29388388 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
29388412 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:29395414 original size:21 final size:21
Alignment explanation
Indices: 29395388--29395432 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29395378 TATATGTGAG
* * *
29395388 AAATTTACTTATGTTATGGAT
1 AAATTTACCTATGTCATGAAT
29395409 AAATTTACCTATGTCATGAAT
1 AAATTTACCTATGTCATGAAT
29395430 AAA
1 AAA
29395433 CACACGGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (21 bp):
AAATTTACCTATGTCATGAAT
Found at i:29395499 original size:20 final size:20
Alignment explanation
Indices: 29395474--29395581 Score: 155
Period size: 20 Copynumber: 5.5 Consensus size: 20
29395464 AGGCTTATGC
29395474 TAAGTAAATGGAATGAAAAG
1 TAAGTAAATGGAATGAAAAG
* *
29395494 TAAGTAAATGGAACGGAAAG
1 TAAGTAAATGGAATGAAAAG
*
29395514 TAAGTAAATGAAATGAAAAG
1 TAAGTAAATGGAATGAAAAG
*
29395534 TAAGTAAATGAAATGAAAAG
1 TAAGTAAATGGAATGAAAAG
**
29395554 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGGAATGAAAAG
29395574 TAAG-AAAT
1 TAAGTAAAT
29395582 AGAGTGGTTC
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
19 4 0.05
20 76 0.95
ACGTcount: A:0.55, C:0.01, G:0.24, T:0.20
Consensus pattern (20 bp):
TAAGTAAATGGAATGAAAAG
Found at i:29398470 original size:24 final size:23
Alignment explanation
Indices: 29398414--29398472 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
29398404 ATGTTAATGT
* *
29398414 ATAATATAA-TAATTAATTTTTA
1 ATAAAATAATTAAATAATTTTTA
*
29398436 ATTACAA-AATTAAATAATTTTTTA
1 A-TAAAATAATTAAATAA-TTTTTA
29398460 ATAAAATAATTAA
1 ATAAAATAATTAA
29398473 TTTATTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
22 3 0.10
23 13 0.45
24 13 0.45
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAAAATAATTAAATAATTTTTA
Found at i:29398475 original size:20 final size:20
Alignment explanation
Indices: 29398415--29398475 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
29398405 TGTTAATGTA
*
29398415 TAATATAATAATTAA-TTTT
1 TAATAAAATAATTAATTTTT
*
29398434 TAATTACAAAATTAAATAATTTTT
1 TAA-T--AAAA-TAATTAATTTTT
29398458 TAATAAAATAATTAATTT
1 TAATAAAATAATTAATTT
29398476 ATTATTTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 4 0.12
22 3 0.09
23 7 0.21
24 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATAAAATAATTAATTTTT
Found at i:29402713 original size:40 final size:40
Alignment explanation
Indices: 29402512--29402722 Score: 216
Period size: 40 Copynumber: 5.3 Consensus size: 40
29402502 TGTTCGGATG
* * *
29402512 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCT
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGTGCAAGTGACT
* * *
29402552 A-ATTCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCT-ACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACT
* * * *
29402592 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCAAGTTATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACT
* *
29402632 AT-ACCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACT
* * *
29402671 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACT
*
29402711 ATATCC-GGCTAA
1 ATAACCGGGCTAA
29402723 ACTCTGAAGG
Statistics
Matches: 146, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
39 43 0.29
40 99 0.68
41 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACT
Found at i:29402732 original size:79 final size:80
Alignment explanation
Indices: 29402512--29402722 Score: 295
Period size: 79 Copynumber: 2.7 Consensus size: 80
29402502 TGTTCGGATG
29402512 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATTCCGGGCTAAGTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGAGCTAGTGGCTATA-TCCGGGCTAAGTCCCGAAGG
*
29402575 CATTCGTGCGAGCTACT
64 CATTCGTGCAAGCTACT
* * * * ***
29402592 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCAAGTTATTATA-CCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGGCA
*
29402656 TTCGTGCAAGTTACT
66 TTCGTGCAAGCTACT
29402671 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAA
29402723 ACTCTGAAGG
Statistics
Matches: 112, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
79 76 0.68
80 33 0.29
81 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGGCA
TTCGTGCAAGCTACT
Found at i:29405347 original size:41 final size:41
Alignment explanation
Indices: 29405282--29405361 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
29405272 TACAGGGGTT
*
29405282 TTCACACGGCATGGCACACGCCCGTGTCCATGGCCCGTGTCC
1 TTCACACGGCATGGCACACGCCCGTGTCC-TAGCCCGTGTCC
29405324 TTCACACGGCCAT-G-ACACGCCCGTGTCCTAGCCCGTGT
1 TTCACACGG-CATGGCACACGCCCGTGTCCTAGCCCGTGT
29405362 GTAAAAACGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
40 9 0.25
41 14 0.39
42 10 0.28
43 3 0.08
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (41 bp):
TTCACACGGCATGGCACACGCCCGTGTCCTAGCCCGTGTCC
Found at i:29406327 original size:47 final size:47
Alignment explanation
Indices: 29406270--29406471 Score: 175
Period size: 46 Copynumber: 4.3 Consensus size: 47
29406260 GCCGTGGCCT
* **
29406270 AGACACGGTCTTACACTGGCTCAT-ATCTC-AAGTTGAAGCCATGTCCC
1 AGACATGGTCTTACACTGGCT-ATCATCTCGAAGCCGAAG-CATGTCCC
* * *
29406317 AGACATGGTCTTACACTGACTATCATCTCGTAGCCGACGCATGTCCC
1 AGACATGGTCTTACACTGGCTATCATCTCGAAGCCGAAGCATGTCCC
* **
29406364 AGACAT-GTCTTACACTGGCT-TACATCTCGAAGCCGATGCATGTCTT
1 AGACATGGTCTTACACTGGCTAT-CATCTCGAAGCCGAAGCATGTCCC
* * * * *
29406410 AGACAT-GTCTTATACTAGC-ACTCGTCTC-AATGCCGATGCCACGTCCC
1 AGACATGGTCTTACACTGGCTA-TCATCTCGAA-GCCGAAG-CATGTCCC
29406457 AGACATGGTCTTACA
1 AGACATGGTCTTACA
29406472 GTAGCTCACA
Statistics
Matches: 129, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
45 3 0.02
46 64 0.50
47 50 0.39
48 12 0.09
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
AGACATGGTCTTACACTGGCTATCATCTCGAAGCCGAAGCATGTCCC
Found at i:29414025 original size:46 final size:46
Alignment explanation
Indices: 29413942--29414058 Score: 130
Period size: 46 Copynumber: 2.5 Consensus size: 46
29413932 AAGTGAAAGC
*
29413942 CATGTCCCAGACATGATCTTACATTGACTATCATCTCGTA-GCCGACG
1 CATGTCCCAGACATG-TCTTACACTGACTATCATCTCG-AGGCCGACG
* * * * *
29413989 CATGTCCCAGATATGTCTTACACTGGCT-TACGTCTCGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTGACTAT-CATCTCGAGGCCGACG
*
29414035 CATGTCCTAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
29414059 AGCACTTGAC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
45 2 0.03
46 44 0.73
47 14 0.23
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGACTATCATCTCGAGGCCGACG
Found at i:29416747 original size:42 final size:42
Alignment explanation
Indices: 29416640--29416803 Score: 193
Period size: 42 Copynumber: 3.9 Consensus size: 42
29416630 AGTATCGTAC
* * * * *
29416640 CAATGCCATATCCTAGATATGGTTTTACATGTAATCTCGTAT
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAT
* * * * *
29416682 CGATGGCAATAGCCCAGCTATGGTCTTACACGAAATATCATAT
1 CAAT-GCCATATCCCAGATATGGTCTTACACGAAATCTCATAT
* *
29416725 CAATGCCATATCCCAGATATGGTCTTAAACGACATCTCATAT
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAT
* *
29416767 TAATGCCATATCCCAGATATGGTCTTACACGTAATCT
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCT
29416804 TAGTAACCCT
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 68 0.68
43 32 0.32
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (42 bp):
CAATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAT
Found at i:29418589 original size:42 final size:42
Alignment explanation
Indices: 29418542--29418645 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
29418532 AAACCGACAT
*
29418542 AAAGCTTGATAGGCAATAAGCCTGATATCATACACTAGCATC
1 AAAGCTTGATAGGCAATAAGCCTGATATCATACACCAGCATC
* *
29418584 AAAGCTTGCTAGGCAATAAGCCTGATATCATACACCGGCATC
1 AAAGCTTGATAGGCAATAAGCCTGATATCATACACCAGCATC
*
29418626 AAAGCCTGCA-AGGCAATAAG
1 AAAGCTTG-ATAGGCAATAAG
29418646 TCTAATATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (42 bp):
AAAGCTTGATAGGCAATAAGCCTGATATCATACACCAGCATC
Found at i:29423825 original size:32 final size:32
Alignment explanation
Indices: 29423786--29423851 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
29423776 GAATTTTTAA
29423786 ATCATATTATATTGTTATTACACTTTAAAACT
1 ATCATATTATATTGTTATTACACTTTAAAACT
29423818 ATCATATTATATTGTTATTACACTTTAAAACT
1 ATCATATTATATTGTTATTACACTTTAAAACT
29423850 AT
1 AT
29423852 GTTTGTTGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (32 bp):
ATCATATTATATTGTTATTACACTTTAAAACT
Found at i:29424274 original size:34 final size:34
Alignment explanation
Indices: 29424222--29424286 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
29424212 AGATCCTGTT
* *
29424222 TGGGCTTGAGCCCGTTACAGTATCAGTATCAACG
1 TGGGCTTGAGCCCATTACAGTAACAGTATCAACG
*
29424256 TGGGTCTT-AGCCCATTACAGTAAGAGTATCA
1 TGGG-CTTGAGCCCATTACAGTAACAGTATCA
29424287 GTGCAGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 24 0.89
35 3 0.11
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (34 bp):
TGGGCTTGAGCCCATTACAGTAACAGTATCAACG
Found at i:29433289 original size:14 final size:14
Alignment explanation
Indices: 29433259--29433299 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
29433249 AATTAGGTAA
*
29433259 ATAATATAAATGTT
1 ATAATATAAATGAT
29433273 ATAATATAACAT-AT
1 ATAATATAA-ATGAT
29433287 ATAATA-AAATGAT
1 ATAATATAAATGAT
29433300 GTTCATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.08
13 4 0.17
14 16 0.67
15 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (14 bp):
ATAATATAAATGAT
Found at i:29447150 original size:27 final size:28
Alignment explanation
Indices: 29447120--29447209 Score: 96
Period size: 27 Copynumber: 3.3 Consensus size: 28
29447110 TTTAGTTTAC
* *
29447120 TAAAATTATTAAAATACCCTTAG-TTTG
1 TAAAATTACTGAAATACCCTTAGATTTG
* * *
29447147 TAAAAATACTGAAATGCCC-TCGATTTG
1 TAAAATTACTGAAATACCCTTAGATTTG
* *
29447174 TAAAATTACTGAAATA-CCTTCGACTTG
1 TAAAATTACTGAAATACCCTTAGATTTG
29447201 TAAAATTAC
1 TAAAATTAC
29447210 CAAAGTACCC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.08
27 49 0.92
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (28 bp):
TAAAATTACTGAAATACCCTTAGATTTG
Found at i:29447218 original size:27 final size:27
Alignment explanation
Indices: 29447144--29447218 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
29447134 TACCCTTAGT
* * * * *
29447144 TTGTAAAAATACTGAAATGCCCTCGAT
1 TTGTAAAATTACTCAAATACCTTCGAC
*
29447171 TTGTAAAATTACTGAAATACCTTCGAC
1 TTGTAAAATTACTCAAATACCTTCGAC
29447198 TTGTAAAATTAC-CAAAGTACC
1 TTGTAAAATTACTCAAA-TACC
29447219 CCCGATTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 3 0.07
27 39 0.93
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (27 bp):
TTGTAAAATTACTCAAATACCTTCGAC
Found at i:29447248 original size:27 final size:27
Alignment explanation
Indices: 29447215--29447399 Score: 212
Period size: 27 Copynumber: 6.9 Consensus size: 27
29447205 ATTACCAAAG
* *
29447215 TACCCCCGATTTACATAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
29447242 TAGCCC-CAATTTACATAATTACTGTTT
1 TA-CCCTCGATTTACAGAATTACTGTTT
*
29447269 TACCCTCGATTTATAGAATTAGC-GTTT
1 TACCCTCGATTTACAGAATTA-CTGTTT
* *
29447296 TACCCTCGATTTACAGAATTACCGTCT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
29447323 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
29447350 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
** * *
29447377 TAGTCTCGATTTATAAAATTACT
1 TACCCTCGATTTACAGAATTACT
29447400 AAAATACCCT
Statistics
Matches: 136, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.03
27 128 0.94
28 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:29447420 original size:27 final size:27
Alignment explanation
Indices: 29447386--29447625 Score: 171
Period size: 27 Copynumber: 9.0 Consensus size: 27
29447376 TTAGTCTCGA
*
29447386 TTTATAAAATTACTAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* * *
29447413 TTTTTAAAATTACCAAAATACCCCTAG
1 TTTATAAAATTACCAAAATACCCTTGG
29447440 -TT-TAAAATTACCAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* * * ***
29447465 TTTGTGAAATTACCGAAATACCCTCAA
1 TTTATAAAATTACCAAAATACCCTTGG
* * *
29447492 TTTGTAAAATTACCAAAATACCCCTGA
1 TTTATAAAATTACCAAAATACCCTTGG
* * * *
29447519 TTTACAAAGTTACAAAAATACCCTTGAC
1 TTTATAAAATTACCAAAATACCCTTG-G
* *** *
29447547 TTTCTAAAATTATGGAAA-ACCATTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* * **
29447573 TTTACAAATTTACTGAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* * * * *
29447600 TTTGTAGATTTACCAAGACACCCTTG
1 TTTATAAAATTACCAAAATACCCTTG
29447626 TAGGATGAAA
Statistics
Matches: 166, Mismatches: 43, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
25 21 0.13
26 17 0.10
27 116 0.70
28 12 0.07
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (27 bp):
TTTATAAAATTACCAAAATACCCTTGG
Found at i:29447424 original size:81 final size:81
Alignment explanation
Indices: 29447258--29447425 Score: 176
Period size: 81 Copynumber: 2.1 Consensus size: 81
29447248 CAATTTACAT
* * * ****
29447258 AATTACTGTTTTACCCTCGATTTATAGAATTAGCGTTTTACCCTCGATTTACAGAATTACCGTCT
1 AATTACTATTTTACCCTCGATTTACAGAATTAGCGTTTTACCCTCGATTTACAAAATTACCAAAA
*
29447323 TACCCTCGATTTATAG
66 TACCCTCGATTTATAA
* ** * *
29447339 AATTACTATTTTACCCTTGATTTACAGAATTA-CTGTTTTAGTCTCGATTTATAAAATTACTAAA
1 AATTACTATTTTACCCTCGATTTACAGAATTAGC-GTTTTACCCTCGATTTACAAAATTACCAAA
* * *
29447403 ATACCCTTGGTTTTTAA
65 ATACCCTCGATTTATAA
29447420 AATTAC
1 AATTAC
29447426 CAAAATACCC
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
80 1 0.01
81 69 0.99
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (81 bp):
AATTACTATTTTACCCTCGATTTACAGAATTAGCGTTTTACCCTCGATTTACAAAATTACCAAAA
TACCCTCGATTTATAA
Found at i:29447456 original size:52 final size:54
Alignment explanation
Indices: 29447390--29447542 Score: 184
Period size: 52 Copynumber: 2.9 Consensus size: 54
29447380 TCTCGATTTA
* * *
29447390 TAAAATTACTAAAATACCCTTGGTTTTTAAAATTACCAAAATACCC-CTAGTT-
1 TAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTCAAGTTG
* * * *
29447442 TAAAATTACCAAAATACCCTTGGTTTGTGAAATTACCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTCAAGTTG
* * * * *
29447496 TAAAATTACCAAAATACCCCTGATTTACAAAGTTACAAAAATACCCT
1 TAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCT
29447543 TGACTTTCTA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
52 42 0.49
53 4 0.05
54 39 0.46
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (54 bp):
TAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTCAAGTTG
Found at i:29447484 original size:79 final size:81
Alignment explanation
Indices: 29447392--29447544 Score: 213
Period size: 79 Copynumber: 1.9 Consensus size: 81
29447382 TCGATTTATA
* *** * *
29447392 AAATTACTAAAATACCCTTGGTTTTTAAAATTACCAAAATACCCCT-AGTTTA-AAA-TTACCAA
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGA-TTTACAAAGTTACAAA
29447454 AATACCCTTGGTTTGTG
65 AATACCCTTGGTTTGTG
*
29447471 AAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTACAAAA
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTACAAAA
29447536 ATACCCTTG
66 ATACCCTTG
29447545 ACTTTCTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
79 44 0.69
80 4 0.06
81 16 0.25
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (81 bp):
AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTACAAAA
ATACCCTTGGTTTGTG
Found at i:29447747 original size:27 final size:27
Alignment explanation
Indices: 29447660--29447747 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
29447650 CTATTAGGTA
*
29447660 AAAAT-ACCGTAAAGCCCCTGTAGGGT
1 AAAATGACCGTAAAGCCCCTGTATGGT
* * *
29447686 AAAGA-GACCATAAAGCCCTTGTAAGGT
1 AAA-ATGACCGTAAAGCCCCTGTATGGT
*
29447713 AAAGTGACCGTAATA-CCCCTGTATGGT
1 AAAATGACCGTAA-AGCCCCTGTATGGT
29447740 AAAATGAC
1 AAAATGAC
29447748 GAATATGCCC
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
26 3 0.06
27 46 0.92
28 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (27 bp):
AAAATGACCGTAAAGCCCCTGTATGGT
Found at i:29448796 original size:42 final size:42
Alignment explanation
Indices: 29448737--29448828 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
29448727 TAGTCTCCCC
* ** *
29448737 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
29448779 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
29448821 AAATGGGC
1 AAATGGGC
29448829 CTATAGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:29448927 original size:31 final size:31
Alignment explanation
Indices: 29448852--29448930 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
29448842 TGTTTACAGT
* *
29448852 AAAGGCTTCAGCCAAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
*
29448883 AAAGGC-TCTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTC-GGCCCAGTGAAATGATTTATGA
29448914 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
29448931 AACCGTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 2 0.05
31 39 0.91
32 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Found at i:29453863 original size:17 final size:18
Alignment explanation
Indices: 29453832--29453866 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29453822 TTTTACTTTA
*
29453832 TTTTTTATTTATTTTAAT
1 TTTTTTATGTATTTTAAT
29453850 TTTTTTATGT-TTTTAAT
1 TTTTTTATGTATTTTAAT
29453867 CACCCTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTTATGTATTTTAAT
Found at i:29457334 original size:30 final size:29
Alignment explanation
Indices: 29457280--29457343 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
29457270 CAAGTAACCG
* *
29457280 AAGCTAGCTAAATCGCACACTTAGTGCCA
1 AAGCTAGCTAAATCACACAATTAGTGCCA
*
29457309 AAGCTAGTTTAAATCACACAATTAGTGCCA
1 AAGCTAG-CTAAATCACACAATTAGTGCCA
29457339 AAGCT
1 AAGCT
29457344 TCTGATTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (29 bp):
AAGCTAGCTAAATCACACAATTAGTGCCA
Found at i:29464617 original size:30 final size:29
Alignment explanation
Indices: 29464571--29464634 Score: 119
Period size: 30 Copynumber: 2.2 Consensus size: 29
29464561 CCTTAAGTAA
29464571 CCAAAGCTAGTTAAATCGCACACTTAGTG
1 CCAAAGCTAGTTAAATCGCACACTTAGTG
29464600 CCAAAGCTAGTTTAAATCGCACACTTAGTG
1 CCAAAGCTAG-TTAAATCGCACACTTAGTG
29464630 CCAAA
1 CCAAA
29464635 TCTTCCGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (29 bp):
CCAAAGCTAGTTAAATCGCACACTTAGTG
Found at i:29469786 original size:14 final size:15
Alignment explanation
Indices: 29469762--29469790 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29469752 AGAGATGATA
29469762 ATTATTAATATATAT
1 ATTATTAATATATAT
29469777 ATTA-TAATATATAT
1 ATTATTAATATATAT
29469791 TAATTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTATTAATATATAT
Found at i:29471897 original size:15 final size:15
Alignment explanation
Indices: 29471877--29471907 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29471867 CTCTTGAGGT
29471877 GAAATCCTAGGAAGC
1 GAAATCCTAGGAAGC
29471892 GAAATCCTAGGAAGC
1 GAAATCCTAGGAAGC
29471907 G
1 G
29471908 TGGAATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.29, T:0.13
Consensus pattern (15 bp):
GAAATCCTAGGAAGC
Found at i:29480489 original size:14 final size:14
Alignment explanation
Indices: 29480470--29480496 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29480460 ACACGCGGGT
29480470 GTGTCTAAGGCCGC
1 GTGTCTAAGGCCGC
29480484 GTGTCTAAGGCCG
1 GTGTCTAAGGCCG
29480497 TGTGAGGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (14 bp):
GTGTCTAAGGCCGC
Done.