Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 94 of 344
Found at i:31392406 original size:46 final size:46
Alignment explanation
Indices: 31392379--31392553 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 46
31392369 TCATCTCTTA
*
31392379 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACGTCTCGAG
1 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATCTCGAG
* * ** *
31392425 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTCACGTCTTAAT
1 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATCTCGAG
* * * * *
31392471 GCCGATGCCATGTCCCATACATGGTCTTACACTGGCTCT-CATAAT-GTG
1 GCCGATG-CATGTCCTAGACAT-GTCTTACACTAGCT-TACAT-CTCGAG
* *
31392519 GTCGATGCATGTCCTAGACATTTCTTACACTAGCT
1 GCCGATGCATGTCCTAGACATGTCTTACACTAGCT
31392554 CACACACAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
46 61 0.57
47 24 0.22
48 21 0.20
49 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.30
Consensus pattern (46 bp):
GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATCTCGAG
Found at i:31394756 original size:18 final size:18
Alignment explanation
Indices: 31394733--31394769 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31394723 TTTTAAAGAT
31394733 ATATTTAATTGCTTAACA
1 ATATTTAATTGCTTAACA
31394751 ATATTTAATTGCTTAACA
1 ATATTTAATTGCTTAACA
31394769 A
1 A
31394770 GGACTTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (18 bp):
ATATTTAATTGCTTAACA
Found at i:31403344 original size:93 final size:93
Alignment explanation
Indices: 31403231--31403402 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
31403221 CGCCCATAAG
* *
31403231 CGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
31403296 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
31403324 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
31403389 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
31403403 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:31403399 original size:46 final size:46
Alignment explanation
Indices: 31403224--31403399 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
31403214 TGTAACCCGC
* * * *
31403224 CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
31403270 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
31403320 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
31403363 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
31403400 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:31403418 original size:46 final size:46
Alignment explanation
Indices: 31403273--31403411 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 46
31403263 TTCGCATCCA
31403273 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
31403321 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
31403366 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
31403412 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:31406059 original size:26 final size:26
Alignment explanation
Indices: 31406030--31406117 Score: 61
Period size: 26 Copynumber: 3.3 Consensus size: 26
31406020 TTTGTACTTG
31406030 TTTTAAATCTCTTCATATATTATTTA
1 TTTTAAATCTCTTCATATATTATTTA
* * * * * *
31406056 TTTTGAACCATTTTTAT-TATTACTTG
1 TTTTAAATC-TCTTCATATATTATTTA
* *
31406082 TTTTAAATTTTCTTCCATATATTATTTC
1 TTTTAAA-TCTCTT-CATATATTATTTA
*
31406110 TTTAAAAT
1 TTTTAAAT
31406118 TTATATTATT
Statistics
Matches: 44, Mismatches: 14, Indels: 7
0.68 0.22 0.11
Matches are distributed among these distances:
26 23 0.52
27 8 0.18
28 13 0.30
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTAAATCTCTTCATATATTATTTA
Found at i:31406127 original size:54 final size:52
Alignment explanation
Indices: 31406024--31406127 Score: 133
Period size: 52 Copynumber: 2.0 Consensus size: 52
31406014 TGCAAATTTG
* *
31406024 TACTTGTTTTAAATCTCTTCATATATTATTTATTTTGAACCATTTTTATTAT
1 TACTTGTTTTAAATCTCTTCATATATTATTTACTTTGAACAATTTTTATTAT
* *
31406076 TACTTGTTTTAAATTTTCTTCCATATATTATTT-CTTT-AA-AATTTATATTAT
1 TACTTGTTTTAAA-TCTCTT-CATATATTATTTACTTTGAACAATTTTTATTAT
31406127 T
1 T
31406128 TCATGCCGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
51 11 0.24
52 15 0.33
53 8 0.17
54 12 0.26
ACGTcount: A:0.28, C:0.11, G:0.03, T:0.59
Consensus pattern (52 bp):
TACTTGTTTTAAATCTCTTCATATATTATTTACTTTGAACAATTTTTATTAT
Found at i:31416694 original size:24 final size:24
Alignment explanation
Indices: 31416650--31416695 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
31416640 AAGCTCATGT
* *
31416650 GAGCCAATAACGAGTAGCTCTGAA
1 GAGCCAATAACGAGAAACTCTGAA
*
31416674 GAGCCATTAACGAGAAACTCTG
1 GAGCCAATAACGAGAAACTCTG
31416696 GATAACCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (24 bp):
GAGCCAATAACGAGAAACTCTGAA
Found at i:31417159 original size:21 final size:21
Alignment explanation
Indices: 31417134--31417175 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31417124 TAAATTTAGC
*
31417134 TCAATTTAATAAAATTCATAT
1 TCAATTCAATAAAATTCATAT
**
31417155 TCAATTCAATTCAATTCATAT
1 TCAATTCAATAAAATTCATAT
31417176 CTTAGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (21 bp):
TCAATTCAATAAAATTCATAT
Found at i:31417166 original size:10 final size:11
Alignment explanation
Indices: 31417146--31417175 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
31417136 AATTTAATAA
31417146 AATTCATATTC
1 AATTCATATTC
31417157 AATTCA-ATTC
1 AATTCATATTC
31417167 AATTCATAT
1 AATTCATAT
31417176 CTTAGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (11 bp):
AATTCATATTC
Found at i:31418606 original size:46 final size:47
Alignment explanation
Indices: 31418542--31418755 Score: 192
Period size: 47 Copynumber: 4.6 Consensus size: 47
31418532 AAAGCCAGTA
* *
31418542 TAAGACCATGTCTGGGACATGGCATCGGAATTGAGACAAGAGCTAGT-
1 TAAGACCATGTCTGGGACATGGCATCGGACTCGAGACAAGAG-TAGTG
* *
31418589 TAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAGACGTAAG-GTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGACTCGAGAC--AAGAGTAGTG
* * ** *
31418635 AAAGA-CATGTCTGGGACAT-GCATTGG-CTACGAGATGATAGTCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGACT-CGAGACAAGAGT-AGTG
* ** * *
31418681 TAAGACCATGTTTGGGACATGGCATC-GACTTAAGATATGAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGACTCGAGACAAGAG-TAGTG
31418728 TAAGACCATGTCTGGGACATGGCATCGG
1 TAAGACCATGTCTGGGACATGGCATCGG
31418756 CACCTTACCC
Statistics
Matches: 137, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
44 1 0.01
45 21 0.15
46 50 0.36
47 57 0.42
48 8 0.06
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (47 bp):
TAAGACCATGTCTGGGACATGGCATCGGACTCGAGACAAGAGTAGTG
Found at i:31425776 original size:20 final size:19
Alignment explanation
Indices: 31425740--31425790 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
31425730 AAGGGCTATT
*
31425740 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
31425759 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
31425779 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
31425791 GTTGTTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:31426643 original size:49 final size:46
Alignment explanation
Indices: 31426584--31426756 Score: 204
Period size: 49 Copynumber: 3.6 Consensus size: 46
31426574 TGTTGTGTGT
*
31426584 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTGATA-ATGA-AGC
* *
31426633 CAGTGTAAGACCTGTCTGGGACACGGCATCGACCTTGATATATGAATCC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACC-TGATA-ATGAA-GC
* * *
31426682 CAGTGTAAGACCTGTCTGGGACATGACATCGACTTTGAT-ATGCTAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTGATAATG-AAGC
31426729 CAGTGTAAGACCATGTCTGGGACATGGC
1 CAGTGTAAGACC-TGTCTGGGACATGGC
31426757 GTTGGCATCT
Statistics
Matches: 109, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
47 16 0.15
48 17 0.16
49 76 0.70
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.23
Consensus pattern (46 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTGATAATGAAGC
Found at i:31438010 original size:27 final size:27
Alignment explanation
Indices: 31437979--31438156 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31437969 TAAATTGTAC
*
31437979 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
31438006 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
31438032 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
*
31438060 GGCACTAAGTGTGCGAGATTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
31438088 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
31438115 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
31438142 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31438157 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:31438093 original size:82 final size:81
Alignment explanation
Indices: 31437980--31438135 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
31437970 AAATTGTACA
* * *
31437980 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31438044 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
31438061 GCACTAAGTGTGCGAGATTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
31438126 TGCGAGTTGA
65 TGCGAATTGA
31438136 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:31438147 original size:82 final size:81
Alignment explanation
Indices: 31437976--31438156 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
31437966 GATTAAATTG
* * *
31437976 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31438041 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
31438057 TGCGGCACTAAGTGTGCGAGATTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
31438121 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
31438139 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31438157 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:31442418 original size:15 final size:15
Alignment explanation
Indices: 31442398--31442427 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31442388 ATAATCATAA
*
31442398 TAATTATCTTAATAT
1 TAATTATCCTAATAT
31442413 TAATTATCCTAATAT
1 TAATTATCCTAATAT
31442428 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:31445107 original size:23 final size:23
Alignment explanation
Indices: 31445050--31445112 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
31445040 GATTAAAAGC
*
31445050 TATTTACAAATCAAATC-TCTAA
1 TATTTACAAATCATATCTTCTAA
*
31445072 GA-TTACAAAATCATATCTTCTAA
1 TATTTAC-AAATCATATCTTCTAA
*
31445095 TATTTACATATCATATCT
1 TATTTACAAATCATATCT
31445113 AAGGTTGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.12
22 10 0.29
23 16 0.47
24 4 0.12
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.40
Consensus pattern (23 bp):
TATTTACAAATCATATCTTCTAA
Found at i:31467393 original size:23 final size:23
Alignment explanation
Indices: 31467367--31467413 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
31467357 ATTGTTTAAG
* *
31467367 TTAAATGAACATGTTTGTAAACA
1 TTAAATGAACATGTTCGAAAACA
31467390 TTAAATGAACATGTTCGAAAACA
1 TTAAATGAACATGTTCGAAAACA
31467413 T
1 T
31467414 CTTCATAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (23 bp):
TTAAATGAACATGTTCGAAAACA
Found at i:31467537 original size:12 final size:12
Alignment explanation
Indices: 31467520--31467544 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31467510 TCAAATACAA
31467520 ATATTATAAATT
1 ATATTATAAATT
31467532 ATATTATAAATT
1 ATATTATAAATT
31467544 A
1 A
31467545 ATAAACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATTATAAATT
Found at i:31472231 original size:48 final size:48
Alignment explanation
Indices: 31472164--31472440 Score: 455
Period size: 48 Copynumber: 5.8 Consensus size: 48
31472154 TACAAGATAA
* * * *
31472164 ATATATATATGTGGTAAAGCCGAATGACGAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
31472212 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* *
31472260 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* * *
31472308 ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATATGTGTG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* *
31472356 ATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
31472404 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
31472441 TGTTGTAACA
Statistics
Matches: 216, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 216 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
Found at i:31481951 original size:27 final size:27
Alignment explanation
Indices: 31481917--31482116 Score: 276
Period size: 27 Copynumber: 7.4 Consensus size: 27
31481907 TTGTTAAGTT
*
31481917 GTAGAATTACCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
31481944 GTAGAATTACCAAAAGACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
31481971 GTAGAATTACCGAAAGACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
31481998 GTAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
31482025 GTAGAATTACCGAGATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
31482052 GTAGAAATACTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
31482079 GTAGAATTACCGAGATACCCTTGT-GG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
31482105 AGTAAAATTACC
1 -GTAGAATTACC
31482117 ATTTTGCCCC
Statistics
Matches: 154, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
26 2 0.01
27 152 0.99
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:31482849 original size:67 final size:67
Alignment explanation
Indices: 31482741--31482983 Score: 351
Period size: 67 Copynumber: 3.6 Consensus size: 67
31482731 GAGGAAGCAT
* **
31482741 TCTGGTAGCCTCACTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTTACAA
1 TCTGGCAGCCTCGTTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTTACAA
31482806 TA
66 TA
*
31482808 TCTGGCAGCCTCGTTGCAATATGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTTACAA
1 TCTGGCAGCCTCGTTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTTACAA
31482873 TA
66 TA
* * * * * *
31482875 TCTAGCAGCCTCGTTGCAATTTGGTGGCCTCGCCACATATGTCTATTTTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGTTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTTACAA
31482940 TA
66 TA
* ** * *
31482942 TTTTCCAGCCTCGTTGTAATCTGGTGGCTTCGCCACATATAT
1 TCTGGCAGCCTCGTTGCAATCTGGTGGCCTCGCCACATATAT
31482984 ATATCTGTTC
Statistics
Matches: 159, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 159 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (67 bp):
TCTGGCAGCCTCGTTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTTACAA
TA
Found at i:31483013 original size:26 final size:27
Alignment explanation
Indices: 31482984--31483043 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
31482974 CCACATATAT
*
31482984 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
31483010 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
31483037 ATATCTG
1 ATATCTG
31483044 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:31486957 original size:15 final size:15
Alignment explanation
Indices: 31486934--31486994 Score: 77
Period size: 15 Copynumber: 4.1 Consensus size: 15
31486924 GTATCGTATC
*
31486934 TTGGGTTTCTTTATT
1 TTGGATTTCTTTATT
31486949 TTGGATTTCTTTATT
1 TTGGATTTCTTTATT
* * * *
31486964 CTGGGTTTCTCTATC
1 TTGGATTTCTTTATT
31486979 TTGGATTTCTTTATT
1 TTGGATTTCTTTATT
31486994 T
1 T
31486995 GATTTTCTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.10, C:0.11, G:0.16, T:0.62
Consensus pattern (15 bp):
TTGGATTTCTTTATT
Found at i:31486971 original size:30 final size:30
Alignment explanation
Indices: 31486935--31486993 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
31486925 TATCGTATCT
* *
31486935 TGGGTTTCTTTATTTTGGATTTCTTTATTC
1 TGGGTTTCTCTATCTTGGATTTCTTTATTC
31486965 TGGGTTTCTCTATCTTGGATTTCTTTATT
1 TGGGTTTCTCTATCTTGGATTTCTTTATT
31486994 TGATTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.10, C:0.12, G:0.17, T:0.61
Consensus pattern (30 bp):
TGGGTTTCTCTATCTTGGATTTCTTTATTC
Found at i:31489536 original size:46 final size:46
Alignment explanation
Indices: 31489478--31489641 Score: 158
Period size: 46 Copynumber: 3.5 Consensus size: 46
31489468 CATCCGACTC
* *
31489478 GAGTTGAGTCCGAGTTCACTTATGAATGCGAATGCCCTAACTCGTT
1 GAGTTGAGTCCGAGTTCACTTATGAATGCGAACGCCCGAACTCGTT
* * * *
31489524 GAGTTGAGTCCGAGTTC-GTGA-G-ATG-TAACTAGGCATCCGAGCTCGTT
1 GAGTTGAGTCCGAGTTCACTTATGAATGCGAAC---GC--CCGAACTCGTT
* *
31489571 GAGTTGAGTCCGAGTTCATTTATGGATGCGAACG-CCGAAGCTCGTT
1 GAGTTGAGTCCGAGTTCACTTATGAATGCGAACGCCCGAA-CTCGTT
*
31489617 GGGTTGAGTCCGAGTTCACTTATGA
1 GAGTTGAGTCCGAGTTCACTTATGA
31489642 GCGGGTTACA
Statistics
Matches: 95, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 8 0.08
46 45 0.47
47 26 0.27
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
GAGTTGAGTCCGAGTTCACTTATGAATGCGAACGCCCGAACTCGTT
Found at i:31496186 original size:40 final size:40
Alignment explanation
Indices: 31496139--31496342 Score: 295
Period size: 40 Copynumber: 5.1 Consensus size: 40
31496129 CGGGCTTTAA
** *
31496139 CCGGATATAGCCACTCGCTCAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
**
31496179 CCGGATATAGTAGTTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
31496219 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
31496259 CCGGA-ATTAGTAACTCGCACAAATGCCTTCGGGACTTAG-
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
31496298 CCTGAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
31496339 CCGG
1 CCGG
31496343 TTATCATCCG
Statistics
Matches: 150, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 5 0.03
40 142 0.95
41 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:31498697 original size:31 final size:31
Alignment explanation
Indices: 31498659--31498722 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
31498649 CCTTTCCATA
*
31498659 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCAGAACACTGGGCCGAAGCCT
**
31498690 TTTCATATTTCAGATTACTGGGCCGAAGCCT
1 TTTCATATTTCAGAACACTGGGCCGAAGCCT
31498721 TT
1 TT
31498723 ACTGTAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (31 bp):
TTTCATATTTCAGAACACTGGGCCGAAGCCT
Found at i:31499014 original size:46 final size:47
Alignment explanation
Indices: 31498937--31499058 Score: 212
Period size: 49 Copynumber: 2.6 Consensus size: 47
31498927 CCTAGCCTCT
31498937 TTTAATAACTGGGGCA-AAGCCCTTTTAATAACTGGGGCA-AAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
31498982 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
31499029 TTTATCATAACTGGGGCATAAGCCCTTTTA
1 TTTA--ATAACTGGGGCATAAGCCCTTTTA
31499059 CACTTCTTCC
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
45 16 0.22
46 23 0.32
47 10 0.14
49 24 0.33
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
Found at i:31499044 original size:25 final size:24
Alignment explanation
Indices: 31498930--31499058 Score: 210
Period size: 24 Copynumber: 5.4 Consensus size: 24
31498920 CTGGAGGCCT
31498930 AGCCTCTTTTAATAACTGGGGCA-A
1 AGCC-CTTTTAATAACTGGGGCATA
31498954 AGCCCTTTTAATAACTGGGGCA-A
1 AGCCCTTTTAATAACTGGGGCATA
31498977 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
31499000 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
31499024 AGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTT-TAATAACTGGGGCATA
31499049 AGCCCTTTTA
1 AGCCCTTTTA
31499059 CACTTCTTCC
Statistics
Matches: 100, Mismatches: 2, Indels: 6
0.93 0.02 0.06
Matches are distributed among these distances:
22 16 0.16
23 30 0.30
24 31 0.31
25 23 0.23
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:31499136 original size:20 final size:20
Alignment explanation
Indices: 31499108--31499146 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31499098 TACGAATACA
*
31499108 TCATGTGCATATCATACATG
1 TCATATGCATATCATACATG
31499128 TCATATGCATATCATACAT
1 TCATATGCATATCATACAT
31499147 ACCATGTTTA
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:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (20 bp):
TCATATGCATATCATACATG
Found at i:31499673 original size:8 final size:8
Alignment explanation
Indices: 31499660--31499687 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
31499650 AAATGCCAGA
31499660 ATTTCGGC
1 ATTTCGGC
31499668 ATTTCGGC
1 ATTTCGGC
31499676 ATTTCGGC
1 ATTTCGGC
31499684 ATTT
1 ATTT
31499688 ACCGCTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (8 bp):
ATTTCGGC
Found at i:31514797 original size:24 final size:24
Alignment explanation
Indices: 31514724--31514829 Score: 162
Period size: 23 Copynumber: 4.4 Consensus size: 24
31514714 CTGGAGGCCT
31514724 AGCCTCTTTTAATAACTGGGGCA-A
1 AGCC-CTTTTAATAACTGGGGCATA
31514748 AGCCCTTTTAATAAC-GGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
31514771 AGCCCTTTTAATAACTGAGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
31514795 AGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTT-TAATAACTGGGGCATA
31514820 AGCCCTTTTA
1 AGCCCTTTTA
31514830 CACTTCCTCC
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
22 6 0.08
23 27 0.36
24 20 0.27
25 22 0.29
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:31514900 original size:9 final size:9
Alignment explanation
Indices: 31514886--31514938 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
31514876 ACATCATGTG
31514886 CATATCATA
1 CATATCATA
*
31514895 CATATCATGTG
1 CATATCA--TA
31514906 CATATCATA
1 CATATCATA
*
31514915 CATGTCATA
1 CATATCATA
31514924 TGCATATCATA
1 --CATATCATA
31514935 CATA
1 CATA
31514939 CCATGTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 20 0.56
11 16 0.44
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (9 bp):
CATATCATA
Found at i:31514903 original size:20 final size:20
Alignment explanation
Indices: 31514878--31514944 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
31514868 TTACGAATAC
31514878 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
31514898 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
31514918 GTCATATGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31514938 ACCATGT
1 ATCATGT
31514945 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31514918 original size:15 final size:15
Alignment explanation
Indices: 31514890--31514933 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
31514880 CATGTGCATA
31514890 TCATA-CATATCATG
1 TCATATCATATCATG
31514904 TGCATATCATA-CATG
1 T-CATATCATATCATG
31514919 TCATATGCATATCAT
1 TCATAT-CATATCAT
31514934 ACATACCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.23
15 13 0.50
16 7 0.27
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (15 bp):
TCATATCATATCATG
Found at i:31519434 original size:16 final size:16
Alignment explanation
Indices: 31519415--31519445 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31519405 CTTCTTCACT
31519415 TACTCACTTACTTAAG
1 TACTCACTTACTTAAG
*
31519431 TACTTACTTACTTAA
1 TACTCACTTACTTAA
31519446 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAG
Found at i:31519799 original size:55 final size:53
Alignment explanation
Indices: 31519673--31519806 Score: 169
Period size: 53 Copynumber: 2.5 Consensus size: 53
31519663 CTTACCATTT
* * *
31519673 CCATGTCTCGACATGGTCTTACATGGTATCTTTGCCTTATGAACTCACCAATG
1 CCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATGAACTCACCAATG
* * * * * *
31519726 CCATGCCTTGGCATGGTCTTATATGGGACCTTTGGCTTATAGTAACTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTAT-G-AACTCACCAATG
31519781 CCATGTCTTGACATGGTCTTACATGG
1 CCATGTCTTGACATGGTCTTACATGG
31519807 TATCCTTACC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
53 33 0.49
54 1 0.01
55 33 0.49
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATGAACTCACCAATG
Found at i:31519855 original size:54 final size:53
Alignment explanation
Indices: 31519614--31519864 Score: 208
Period size: 55 Copynumber: 4.8 Consensus size: 53
31519604 ACACGGGTAC
* * * * *
31519614 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCCTT---TT-GAAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTAAAAA
* * * * * * **
31519663 CTTACCATTTCCATGTCTCGACATGGTCTTACATGGTATCTTTGCCTTATGAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTAAAAA
* * * * *
31519716 CTCACCAATGCCATGCCTTGGCATGGTCTTATATGGGA-CCTTTGGCTTATAGTAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCC-TTGCCTTA-A-AAA
* * * *
31519771 CTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTACCTTAAAAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTAAAAA
*
31519824 CCTTACCAATTGTCAT-CCTTGGCATGGTCTTACATGGTATC
1 -CTTACCAA-TGCCATGCCTTGGCATGGTCTTACATGGTATC
31519865 GTTAAACCCT
Statistics
Matches: 159, Mismatches: 33, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
49 37 0.23
52 3 0.02
53 41 0.26
54 31 0.19
55 45 0.28
56 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (53 bp):
CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTAAAAA
Found at i:31527506 original size:108 final size:110
Alignment explanation
Indices: 31527360--31527560 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
31527350 ATCCTTTTGA
* * * *
31527360 AACTTACCATTGCCATGTCTCGACGTGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCATCAA
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTACCTTA-GAAACCTCACCAA
31527423 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGGCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGGCTTATAGT
* * *
31527468 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTACCTTAGAAACCTCACCAAT
31527533 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
31527561 TATCCTTAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.58
109 6 0.07
110 28 0.34
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTACCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGGCTTATAGT
Found at i:31527568 original size:55 final size:54
Alignment explanation
Indices: 31527313--31527568 Score: 226
Period size: 55 Copynumber: 4.8 Consensus size: 54
31527303 ACACAGGTAC
* * * * *
31527313 CTTA-CAATTTCCATGACTTGTCATGGTCATACGTGGTATCCTT---TT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
* * * *
31527362 CTTACC-ATTGCCATGTCTCGACGTGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTA-GAAA
* * * * * * *
31527415 CTCATCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGGCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCC-TT-ACCT-TAGAAA
* *
31527470 CTTATCAA-TGCCATGTCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
*
31527523 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTTA
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTA
31527569 AACCCTAATG
Statistics
Matches: 168, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
49 34 0.20
50 1 0.01
52 4 0.02
53 38 0.23
54 15 0.09
55 74 0.44
56 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
Found at i:31538152 original size:19 final size:20
Alignment explanation
Indices: 31538110--31538153 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
31538100 CCATATTAAC
** *
31538110 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
31538130 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
31538149 ACAGT
1 ACAGT
31538154 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:31538766 original size:8 final size:8
Alignment explanation
Indices: 31538753--31538791 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
31538743 CACAAATGCA
31538753 GGCTTTTC
1 GGCTTTTC
31538761 GGCTTTTC
1 GGCTTTTC
31538769 GGCTTTTC
1 GGCTTTTC
31538777 GGCTTTTC
1 GGCTTTTC
*
31538785 GACTTTT
1 GGCTTTT
31538792 ACCGATCTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.03, C:0.23, G:0.23, T:0.51
Consensus pattern (8 bp):
GGCTTTTC
Found at i:31545538 original size:28 final size:28
Alignment explanation
Indices: 31545506--31545633 Score: 166
Period size: 29 Copynumber: 4.5 Consensus size: 28
31545496 ATAGTAAGTC
*
31545506 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
31545534 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
31545563 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * ** * *
31545591 TGCAAACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
31545620 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31545634 CAATCTCATG
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 43 0.49
29 44 0.51
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:31545573 original size:57 final size:57
Alignment explanation
Indices: 31545505--31545633 Score: 179
Period size: 57 Copynumber: 2.3 Consensus size: 57
31545495 TATAGTAAGT
* *
31545505 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCAAACTTAGTGCTATACA-AATCAAAC
* * * * *
31545562 TCGCACACTTAGTGCTATATAATCAAACTTGCAAACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCAAACTTAGTGCTATACAAATCAAAC
31545619 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
31545634 CAATCTCATG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 60 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCAAACTTAGTGCTATACAAATCAAAC
Found at i:31545728 original size:51 final size:51
Alignment explanation
Indices: 31545669--31545770 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
31545659 ACCCGCACAC
31545669 TTAGTGCCGAAATCAACATCTCAATACACCTCACCTCTTTTCTTTTTCATT
1 TTAGTGCCGAAATCAACATCTCAATACACCTCACCTCTTTTCTTTTTCATT
31545720 TTAGTGCCGAAATCAACATCTCAATACACCTCACCTCTTTTCTTTTTCATT
1 TTAGTGCCGAAATCAACATCTCAATACACCTCACCTCTTTTCTTTTTCATT
31545771 CAATACTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.25, C:0.29, G:0.06, T:0.39
Consensus pattern (51 bp):
TTAGTGCCGAAATCAACATCTCAATACACCTCACCTCTTTTCTTTTTCATT
Found at i:31551258 original size:6 final size:6
Alignment explanation
Indices: 31551247--31551272 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31551237 GTAAATAAAT
31551247 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
31551273 CTTTACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:31556876 original size:46 final size:46
Alignment explanation
Indices: 31556744--31556950 Score: 169
Period size: 46 Copynumber: 4.5 Consensus size: 46
31556734 AAGGGGTGTT
* *
31556744 ACATGTCTGGGACATGCATCGACCATATTCTA-A-G-AGCCAGTGTAAG
1 ACATGTCTGGGACATGCATCGACC-TA--CGAGATGTAGCTAGTGTAAG
* * * * * * * *
31556790 ACCATGTCTAGGTCATGGCATCGGCAT-TGAGACGAGAGCTAGCGTAAG
1 A-CATGTCTGGGACAT-GCATCGACCTACGAGATG-TAGCTAGTGTAAG
31556838 ACATGTCTGGGACATGCATCGACCT-CGAGATGTAAGCTAGTGTAAG
1 ACATGTCTGGGACATGCATCGACCTACGAGATGT-AGCTAGTGTAAG
*
31556884 ACATGTCTGGGACATGCATC-AGCTACGAGATGT-G-TCAGTGTAAG
1 ACATGTCTGGGACATGCATCGACCTACGAGATGTAGCT-AGTGTAAG
31556928 ACCATGTCTGGGACATGGCATCG
1 A-CATGTCTGGGACAT-GCATCG
31556951 GCACAGAGAT
Statistics
Matches: 132, Mismatches: 17, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
43 1 0.01
44 11 0.08
45 18 0.14
46 59 0.45
47 25 0.19
48 18 0.14
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (46 bp):
ACATGTCTGGGACATGCATCGACCTACGAGATGTAGCTAGTGTAAG
Found at i:31556960 original size:46 final size:45
Alignment explanation
Indices: 31556781--31557086 Score: 183
Period size: 46 Copynumber: 6.5 Consensus size: 45
31556771 TTCTAAGAGC
* * * * *
31556781 CAGTGTAAGACCATGTCTAGGTCATGGCATCGGCATTGAGACGAGAG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGAGATG-TAG
* * *
31556828 CTAGCGTAAGA-CATGTCTGGGACAT-GCATCGACCTCGAGATGTAAG
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCG-GCACGAGATGT-AG
*
31556874 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTACGAGATGT-G
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGAGATGTAG
31556918 TCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGATGTAAGAG
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GAGATGT---AG
* * ** * **
31556968 CCAATGTAAGACCATGTTTGGGACATGGTGTCGGCCTCGATTTTGATAG
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGA-GATG-TAG
* * * * **
31557017 CCAGTGTAAGATCATGTATGGAACATGGCATCGACTTGATGGATG-AG
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGA--GATGTAG
*
31557064 CCAATGTAAGACCATGTCTGGGA
1 -CAGTGTAAGACCATGTCTGGGA
31557087 TGTGGCATTG
Statistics
Matches: 207, Mismatches: 36, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
44 10 0.05
45 18 0.09
46 64 0.31
47 35 0.17
48 12 0.06
49 31 0.15
50 32 0.15
51 4 0.02
52 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (45 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGTAG
Found at i:31557263 original size:131 final size:131
Alignment explanation
Indices: 31557029--31557419 Score: 746
Period size: 131 Copynumber: 3.0 Consensus size: 131
31557019 AGTGTAAGAT
*
31557029 CATGTATGGAACATGGCATCGACTTGATGGATGAGCCAATGTAAGACCATGTCTGGGATGTGGCA
1 CATGTATGGGACATGGCATCGACTTGATGGATGAGCCAATGTAAGACCATGTCTGGGATGTGGCA
* *
31557094 TTGCACCTTATGTTTGAGGCTTAATGAATACTTGATAGCATTCCAAATGGTCTAATGGTGAGAGA
66 TTACACCTTATGTTTGAGGCTTAATGAATACTCGATAGCATTCCAAATGGTCTAATGGTGAGAGA
31557159 C
131 C
31557160 CATGTATGGGACATGGCATCGACTTGATGGATGAGCCAATGTAAGACCATGTCTGGGATGTGGCA
1 CATGTATGGGACATGGCATCGACTTGATGGATGAGCCAATGTAAGACCATGTCTGGGATGTGGCA
*
31557225 TTACACCTTATGTTTGAGGCTTAATGAATACTCGATAGCACTCCAAATGGTCTAATGGTGAGAGA
66 TTACACCTTATGTTTGAGGCTTAATGAATACTCGATAGCATTCCAAATGGTCTAATGGTGAGAGA
31557290 C
131 C
31557291 CATGTATGGGACATGGCATCGACTTGATGGATGAGCCAATGTAAGACCATGTCTGGGATGTGGCA
1 CATGTATGGGACATGGCATCGACTTGATGGATGAGCCAATGTAAGACCATGTCTGGGATGTGGCA
31557356 TTACACCTTATGTTTGAGGCTTAATGAATACTCGATAGCATTCCAAATGGTCTAATGGTGAGAG
66 TTACACCTTATGTTTGAGGCTTAATGAATACTCGATAGCATTCCAAATGGTCTAATGGTGAGAG
31557420 TTACAGTTTA
Statistics
Matches: 255, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 255 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (131 bp):
CATGTATGGGACATGGCATCGACTTGATGGATGAGCCAATGTAAGACCATGTCTGGGATGTGGCA
TTACACCTTATGTTTGAGGCTTAATGAATACTCGATAGCATTCCAAATGGTCTAATGGTGAGAGA
C
Found at i:31564337 original size:13 final size:13
Alignment explanation
Indices: 31564319--31564344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31564309 GTTGTTGTGT
31564319 TTATTGATGACGA
1 TTATTGATGACGA
31564332 TTATTGATGACGA
1 TTATTGATGACGA
31564345 GTCTGAGCAT
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:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TTATTGATGACGA
Found at i:31574018 original size:51 final size:51
Alignment explanation
Indices: 31573963--31574075 Score: 199
Period size: 51 Copynumber: 2.2 Consensus size: 51
31573953 AACTGGGGCA
*
31573963 AAGCCCTTTTCGGTAAACTGGGGCAAATCCCTTTTCAATAAACTAGGACAT
1 AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTAGGACAT
* *
31574014 AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCAT
1 AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTAGGACAT
31574065 AAGCCCTTTTC
1 AAGCCCTTTTC
31574076 ACTTCCTCCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (51 bp):
AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTAGGACAT
Found at i:31574023 original size:26 final size:25
Alignment explanation
Indices: 31573945--31574076 Score: 169
Period size: 25 Copynumber: 5.3 Consensus size: 25
31573935 GGCCCAACCT
31573945 CTTTT-AAT-AACTGGGGCAAAGCC
1 CTTTTCAATAAACTGGGGCAAAGCC
** *
31573968 CTTTTCGGTAAACTGGGGCAAATCC
1 CTTTTCAATAAACTGGGGCAAAGCC
* *
31573993 CTTTTCAATAAACTAGGACATAAGCC
1 CTTTTCAATAAACTGGGGCA-AAGCC
**
31574019 CTTTTCGGTAAACTGGGGCAAAGCC
1 CTTTTCAATAAACTGGGGCAAAGCC
31574044 CTTTTCAATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCA-AAGCC
31574070 CTTTTCA
1 CTTTTCA
31574077 CTTCCTCCAT
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
23 5 0.05
24 1 0.01
25 53 0.58
26 32 0.35
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (25 bp):
CTTTTCAATAAACTGGGGCAAAGCC
Found at i:31574161 original size:16 final size:15
Alignment explanation
Indices: 31574133--31574162 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
31574123 ATCATGTGTA
31574133 TTTCATACATATCAT
1 TTTCATACATATCAT
31574148 TTTCATATCATATCA
1 TTTCATA-CATATCA
31574163 ATCATGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTCATACATATCAT
Found at i:31574248 original size:25 final size:24
Alignment explanation
Indices: 31574205--31574252 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
31574195 ATAATTAAAC
* * *
31574205 CCTAGGGGTATAATGGTCAGTTTTA
1 CCTAGGGGCAAAATAGTCA-TTTTA
31574230 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
31574253 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (24 bp):
CCTAGGGGCAAAATAGTCATTTTA
Found at i:31578329 original size:39 final size:39
Alignment explanation
Indices: 31578219--31578400 Score: 197
Period size: 40 Copynumber: 4.6 Consensus size: 39
31578209 GCTACTCGTT
* *
31578219 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTTGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATT-TAGTAACTCGCA
*
31578259 CAAATGCCTTCGGGGCTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGGCTTAGCCCGGATTTAGTAACTCGCA
* *
31578299 CCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
31578338 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGATTTAGTAAC-TCGCA
31578379 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGG-CTTAGCCC
31578401 AGACATCATT
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 38 0.31
40 70 0.58
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
Found at i:31578363 original size:79 final size:80
Alignment explanation
Indices: 31578221--31578400 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 80
31578211 TACTCGTTCA
* * * *
31578221 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGGCTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGAGCTTAACCCGGAT
* *
31578286 TTAGTAAC-TCGCACC
66 ATAGTAACTTAGCA-C
* **
31578301 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGAGCTTAACCCGGA
* *
31578364 TATGGTCACTTAGCAC
65 TATAGTAACTTAGCAC
*
31578380 AAAGCCTTCGGGACTTAGCCC
1 AATGCCTTCGGGACTTAGCCC
31578401 AGACATCATT
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
78 1 0.01
79 60 0.71
80 24 0.28
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGAGCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:31580295 original size:12 final size:12
Alignment explanation
Indices: 31580278--31580303 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31580268 TCCACAATTA
31580278 CCCAAACCGAAT
1 CCCAAACCGAAT
31580290 CCCAAACCGAAT
1 CCCAAACCGAAT
31580302 CC
1 CC
31580304 TTCTTAGAAG
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:0.38, C:0.46, G:0.08, T:0.08
Consensus pattern (12 bp):
CCCAAACCGAAT
Found at i:31585377 original size:51 final size:51
Alignment explanation
Indices: 31585299--31585434 Score: 215
Period size: 51 Copynumber: 2.7 Consensus size: 51
31585289 CTGGAGGCCT
*
31585299 AGCCTCTTTT-AAT-AACTGGGGCA-AAGCCCTTTTTGGTAAACTGGGGCAA
1 AGCC-CTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
* *
31585348 ATCCCTTTTCAATAAACTAGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
31585399 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTC
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTC
31585435 ACTTCCTCCA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
48 5 0.06
49 6 0.08
50 9 0.11
51 59 0.75
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (51 bp):
AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
Found at i:31585389 original size:26 final size:25
Alignment explanation
Indices: 31585299--31585435 Score: 170
Period size: 25 Copynumber: 5.4 Consensus size: 25
31585289 CTGGAGGCCT
31585299 AGCCTCTTTT-AAT-AACTGGGGCAA
1 AGCC-CTTTTCAATAAACTGGGGCAA
***
31585323 AGCCCTTTTTGGTAAACTGGGGCAA
1 AGCCCTTTTCAATAAACTGGGGCAA
* *
31585348 ATCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCA-A
**
31585374 AGCCCTTTTCGGTAAACTGGGGCAA
1 AGCCCTTTTCAATAAACTGGGGCAA
31585399 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCA-A
31585425 AGCCCTTTTCA
1 AGCCCTTTTCA
31585436 CTTCCTCCAT
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
23 5 0.05
24 5 0.05
25 53 0.55
26 33 0.34
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTCAATAAACTGGGGCAA
Found at i:31585507 original size:20 final size:20
Alignment explanation
Indices: 31585482--31585556 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
31585472 TTATGAATAC
* *
31585482 ATCATGTGTATTTCATACAT
1 ATCATGTGCATATCATACAT
31585502 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31585522 ATCATGTGCATATCGTATCA-
1 ATCATGTGCATATCATA-CAT
31585542 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
31585557 TCCCACGTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.14
20 41 0.82
21 2 0.04
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31585513 original size:11 final size:11
Alignment explanation
Indices: 31585499--31585535 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31585489 GTATTTCATA
31585499 CATATCATGTG
1 CATATCATGTG
*
31585510 CATATCA--TA
1 CATATCATGTG
31585519 CATATCATGTG
1 CATATCATGTG
31585530 CATATC
1 CATATC
31585536 GTATCAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (11 bp):
CATATCATGTG
Found at i:31586155 original size:14 final size:14
Alignment explanation
Indices: 31586124--31586164 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
31586114 ATACCTGTTT
31586124 CACGATAT-TCCT-
1 CACGATATCTCCTA
31586136 CGACGATATCTCCTA
1 C-ACGATATCTCCTA
*
31586151 CACGATTTCTCCTA
1 CACGATATCTCCTA
31586165 TAATCAACCG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 7 0.28
14 16 0.64
15 1 0.04
ACGTcount: A:0.24, C:0.34, G:0.10, T:0.32
Consensus pattern (14 bp):
CACGATATCTCCTA
Found at i:31587940 original size:5 final size:5
Alignment explanation
Indices: 31587932--31587957 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31587922 AAAAAAAGAA
31587932 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
31587958 CATGTATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:31593710 original size:46 final size:48
Alignment explanation
Indices: 31593566--31593916 Score: 273
Period size: 46 Copynumber: 7.4 Consensus size: 48
31593556 TGTGCACTAG
* * *
31593566 TGTAAGA-CATGTTTGGGACATGCATCGGCCAC-ATTATG-AGAGCCAA
1 TGTAAGACCATGTCTGGGACATGCATCGGCCTCGA-GATGTAGAGCCAA
* * * * ** * *
31593612 TGTAAGACCATGTCTAGGACATGGCATCGACATTGAGA-CAAGAGCTAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGTAGAGCCAA
*
31593660 TGTAAGA-CATGTCTGGGACATGCATCGGCCTCGAGATGTA-AGCCAG
1 TGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCCAA
*
31593706 TGTAAGA-CATGTCTGGGACATGCATCGG-CTACGAGATGT---GTCAA
1 TGTAAGACCATGTCTGGGACATGCATCGGCCT-CGAGATGTAGAGCCAA
* * * *
31593750 TGTAAGACCATGTCTGGGACATGGCATCGACATAGAGATGTGAGAGCCAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGT-AGAGCCAA
* * * * * *
31593800 TGTAAGACCATGTTTTGGGACATGGCATAGGCCTCGA-TTTTGATAGTCAA
1 TGTAAGACCATG-TCTGGGACAT-GCATCGGCCTCGAGATGT-AGAGCCAA
* * *
31593850 TGTAAGACCATGTCTGGGACATGCCATC-GACT--TGATGGATGAGCCAA
1 TGTAAGACCATGTCTGGGACATG-CATCGGCCTCGAGATGTA-GAGCCAA
31593897 TGTAAGACCATGTCTGGGAC
1 TGTAAGACCATGTCTGGGAC
31593917 GTGGCATTAG
Statistics
Matches: 245, Mismatches: 43, Indels: 33
0.76 0.13 0.10
Matches are distributed among these distances:
44 10 0.04
45 16 0.07
46 74 0.30
47 53 0.22
48 25 0.10
49 13 0.05
50 35 0.14
51 19 0.08
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCCAA
Found at i:31593858 original size:100 final size:94
Alignment explanation
Indices: 31593660--31593923 Score: 294
Period size: 100 Copynumber: 2.8 Consensus size: 94
31593650 CAAGAGCTAG
*
31593660 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGT-A-AGCCAGTGTAAGA-CATGTCT
1 TGTAAGACCATGTCTGGGACATGGCATC-GACT-GAGATGTGAGAGCCAGTGTAAGACCATGTCT
*
31593720 GGGACAT-GCATCGGCTACGAGATGTGTCAA
64 GGGACATGGCATAGGCTACGAGATGTGTCAA
*
31593750 TGTAAGACCATGTCTGGGACATGGCATCGACATAGAGATGTGAGAGCCAGTGTAAGACCATGTTT
1 TGTAAGACCATGTCTGGGACATGGCATCGAC-T-GAGATGTGAGAGCCAGTGTAAGACCATG-TC
**
31593815 TGGGACATGGCATAGGCCT-CGATTTTGATAGTCAA
63 TGGGACATGGCATAGG-CTACGA-GATG-T-GTCAA
* * *
31593850 TGTAAGACCATGTCTGGGACATGCCATCGACT-TGATG-GATGAGCCAATGTAAGACCATGTCTG
1 TGTAAGACCATGTCTGGGACATGGCATCGACTGAGATGTGA-GAGCCAGTGTAAGACCATGTCTG
*
31593913 GGACGTGGCAT
65 GGACATGGCAT
31593924 TAGCATTACA
Statistics
Matches: 150, Mismatches: 11, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
90 7 0.05
91 16 0.11
92 13 0.09
93 1 0.01
94 13 0.09
95 4 0.03
96 24 0.16
97 31 0.21
98 4 0.03
99 2 0.01
100 35 0.23
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (94 bp):
TGTAAGACCATGTCTGGGACATGGCATCGACTGAGATGTGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATAGGCTACGAGATGTGTCAA
Found at i:31597425 original size:22 final size:22
Alignment explanation
Indices: 31597397--31597447 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
31597387 AATATATATG
31597397 TAACATAGCTTGTCTAACATTT
1 TAACATAGCTTGTCTAACATTT
31597419 TAACATAGCTTGTCTAACATTT
1 TAACATAGCTTGTCTAACATTT
31597441 TAACATA
1 TAACATA
31597448 CCATAACCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (22 bp):
TAACATAGCTTGTCTAACATTT
Found at i:31599427 original size:15 final size:15
Alignment explanation
Indices: 31599404--31599434 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31599394 TCAAAAATTC
31599404 CAATACAAAACATAT
1 CAATACAAAACATAT
*
31599419 CAATCCAAAACATAT
1 CAATACAAAACATAT
31599434 C
1 C
31599435 TTTCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:31604210 original size:7 final size:7
Alignment explanation
Indices: 31604197--31604226 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
31604187 ACGCTACCTT
31604197 ATATCAC
1 ATATCAC
*
31604204 TTATCAC
1 ATATCAC
31604211 ATATCAC
1 ATATCAC
31604218 ATATCAC
1 ATATCAC
31604225 AT
1 AT
31604227 GTTGCTCGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (7 bp):
ATATCAC
Found at i:31604426 original size:20 final size:20
Alignment explanation
Indices: 31604401--31604438 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31604391 GTAACATATA
31604401 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
31604421 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
31604439 TAGTTCCTAT
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:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:31611222 original size:13 final size:14
Alignment explanation
Indices: 31611198--31611229 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
31611188 CAAACCTTAC
31611198 AACATACATGACAT
1 AACATACATGACAT
31611212 AACAT-CATGACAT
1 AACATACATGACAT
31611225 AACAT
1 AACAT
31611230 TATCAACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (14 bp):
AACATACATGACAT
Found at i:31613910 original size:93 final size:93
Alignment explanation
Indices: 31613751--31613923 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
31613741 CGCCCATAAG
* * * *
31613751 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
31613816 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCAGATGCCTAGTTACATCTCA
*
31613844 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
31613909 ACGAGTTCAGATGCC
66 ACGAGTTCAGATGCC
31613924 CAAATATCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCAGATGCCTAGTTACATCTCA
Found at i:31613912 original size:46 final size:46
Alignment explanation
Indices: 31613744--31613916 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
31613734 TGTAACCCGC
* * * *
31613744 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
31613790 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
31613840 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
31613883 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC
31613917 AGATGCCCAA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 58 0.55
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:31613938 original size:46 final size:45
Alignment explanation
Indices: 31613795--31613938 Score: 109
Period size: 46 Copynumber: 3.1 Consensus size: 45
31613785 CGCATCCATG
* * *
31613795 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGT-TACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCA-TAT-C--CTA
* * * *
31613843 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGTTC--AGATGCCCATATCC-TA
31613888 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCAAATATCCT-
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCC--ATATCCTA
31613934 AGTGA
1 AGTGA
31613939 CATGTCACTT
Statistics
Matches: 76, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
44 6 0.08
45 2 0.03
46 32 0.42
47 28 0.37
48 5 0.07
49 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCATATCCTA
Found at i:31616906 original size:23 final size:23
Alignment explanation
Indices: 31616879--31616930 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
31616869 CAAGTTACAC
31616879 AGCCAAATACCACATCAAACCCT
1 AGCCAAATACCACATCAAACCCT
* *
31616902 GGCCAAATACCACATCAAAGCCT
1 AGCCAAATACCACATCAAACCCT
31616925 AGCCAA
1 AGCCAA
31616931 TTACAACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.42, C:0.37, G:0.10, T:0.12
Consensus pattern (23 bp):
AGCCAAATACCACATCAAACCCT
Found at i:31625685 original size:25 final size:25
Alignment explanation
Indices: 31625633--31625686 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
31625623 GACATTTGGG
* * *
31625633 AAGCCTTTGTGGCGAGTTGTCTATA
1 AAGCCTTTGTGGCGAATTATCTAGA
* *
31625658 AAGCCTTTGTGGTGAATTATCTGGA
1 AAGCCTTTGTGGCGAATTATCTAGA
31625683 AAGC
1 AAGC
31625687 ACTTATGGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (25 bp):
AAGCCTTTGTGGCGAATTATCTAGA
Found at i:31629399 original size:14 final size:15
Alignment explanation
Indices: 31629380--31629412 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
31629370 AAATTGTAAC
31629380 AAACC-ATTTTGCTA
1 AAACCAATTTTGCTA
31629394 AAACCATATTTTGCTA
1 AAACCA-ATTTTGCTA
31629410 AAA
1 AAA
31629413 ATCAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
16 12 0.71
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (15 bp):
AAACCAATTTTGCTA
Found at i:31633355 original size:46 final size:44
Alignment explanation
Indices: 31633267--31633442 Score: 165
Period size: 46 Copynumber: 3.8 Consensus size: 44
31633257 GGGTAGGATA
31633267 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTCGTA-G
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCATCTCG-AGG
*
31633313 TCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGC-T-CATCTCGAGG
* ** * * * *
31633359 CCGATACATGTCTTAGACATGTCTTACACTAGCTCTCGTCTCAATG
1 CCGATGCATGTCCCAGACATGTCTTACACT-G-GCTCATCTCGAGG
* * *
31633405 CCGGTGCCATGTCCCAGACGTGGTCTTACACTAGCTCA
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCA
31633443 CAATAACCCA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
44 13 0.12
45 16 0.15
46 53 0.50
47 13 0.12
48 11 0.10
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (44 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTCATCTCGAGG
Found at i:31636756 original size:46 final size:46
Alignment explanation
Indices: 31636698--31636915 Score: 242
Period size: 46 Copynumber: 4.7 Consensus size: 46
31636688 ATTCGTGTGT
* *
31636698 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGA
* * * * * *
31636744 GAGCCAGTGTAAGACCATGTCTAGGACATGACATCGTCATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCTCGAGATGA
* * * *
31636792 GGGCTAGTGTAAAACATGTCTGAGACATGCATCGGCCTCGAGACGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
* *
31636838 GGGCTAGTGTAAGACATGTCTGGAACATGCATCGGCCTCGAGATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-A
* *
31636885 -AGCTAGTGTAAGACATCTCTCGGACATGCAT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCAT
31636916 TAGCTACAAG
Statistics
Matches: 144, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
46 95 0.66
47 28 0.19
48 20 0.14
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
Found at i:31636847 original size:94 final size:92
Alignment explanation
Indices: 31636700--31636871 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 92
31636690 TCGTGTGTGA
* * * *
31636700 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAAACATGTCTGAGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGA-CATGTC
31636765 TAGG-ACATGACATCGTCATTGAGACGAGG
65 T-GGAACATG-CATCGTCATTGAGACGAGG
* * *
31636794 GCTAGTGTAAAACATGTCTGAGACATGCATCGGCCTCGA-GACGAGGGCTAGTGTAAGACATGTC
1 GCTAGTGTAAAACATGTCTGAGACATGCATCGGCCAC-ATGACGAGAGCCAGTGTAAGACATGTC
31636858 TGGAACATGCATCG
65 TGGAACATGCATCG
31636872 GCCTCGAGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
92 7 0.10
93 12 0.17
94 49 0.71
95 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.22
Consensus pattern (92 bp):
GCTAGTGTAAAACATGTCTGAGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGACATGTCT
GGAACATGCATCGTCATTGAGACGAGG
Found at i:31636928 original size:46 final size:46
Alignment explanation
Indices: 31636699--31636944 Score: 128
Period size: 46 Copynumber: 5.3 Consensus size: 46
31636689 TTCGTGTGTG
* * * * ** *
31636699 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAG
1 AGCTAGTGTAAGACATCTCTGGAACATGCATCAGCCTCAAGATGAT
* * * ** * *
31636745 AGCCAGTGTAAGACCATGTCTAGG-ACATGACATC-GTCATTGAGACGAG
1 AGCTAGTGTAAGA-CATCTCT-GGAACATG-CATCAG-CCTCAAGATGAT
* * * * * * *
31636793 GGCTAGTGTAAAACATGTCT-GAGACATGCATCGGCCTCGAGACGAG
1 AGCTAGTGTAAGACATCTCTGGA-ACATGCATCAGCCTCAAGATGAT
* * * *
31636839 GGCTAGTGTAAGACATGTCTGGAACATGCATCGGCCTCGAGATG-T
1 AGCTAGTGTAAGACATCTCTGGAACATGCATCAGCCTCAAGATGAT
*
31636884 AAGCTAGTGTAAGACATCTCTCGG-ACATGCATTAG-CTACAAGATGAT
1 -AGCTAGTGTAAGACATCTCT-GGAACATGCATCAGCCT-CAAGATGAT
31636931 AGTCT-GTGTAAGAC
1 AG-CTAGTGTAAGAC
31636945 CATGTCTAGG
Statistics
Matches: 166, Mismatches: 21, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
45 3 0.02
46 109 0.66
47 33 0.20
48 21 0.13
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
AGCTAGTGTAAGACATCTCTGGAACATGCATCAGCCTCAAGATGAT
Found at i:31636973 original size:92 final size:91
Alignment explanation
Indices: 31636698--31637005 Score: 243
Period size: 92 Copynumber: 3.3 Consensus size: 91
31636688 ATTCGTGTGT
* ** *
31636698 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATG
1 GAGCTAGTGTAAGACATGTCT-GGACATGCATCGGCTACAAGATGA-AGCCTGTGTAAGACCATG
* * *
31636763 TCTAGGACATGACATCGTCATTGAGACGA
64 TCTAGGACATGGCATCGAC-TTGAGATGA
* * * * * *
31636792 GGGCTAGTGTAAAACATGTCTGAGACATGCATCGGCCT-CGAGACGAGGGCTAGTGTAAGA-CAT
1 GAGCTAGTGTAAGACATGTCTG-GACATGCATCGG-CTACAAGATGAAGCCT-GTGTAAGACCAT
* *
31636855 GTCT-GGAACAT-GCATCGGCCTCGAGATGTA
63 GTCTAGG-ACATGGCATC-GACTTGAGATG-A
* ** *
31636885 -AGCTAGTGTAAGACATCTCTCGGACATGCATTAGCTACAAGATGATAGTCTGTGTAAGACCATG
1 GAGCTAGTGTAAGACATGTCT-GGACATGCATCGGCTACAAGATGA-AGCCTGTGTAAGACCATG
31636949 TCTAGGA-ATGGCATCGACTTGAGAT-A
64 TCTAGGACATGGCATCGACTTGAGATGA
* * *
31636975 TGAGCCAGAGTAAGACCGTGTCTAGGACATG
1 -GAGCTAGTGTAAGA-CATGTCT-GGACATG
31637006 GCATTGGCAC
Statistics
Matches: 169, Mismatches: 30, Indels: 31
0.73 0.13 0.13
Matches are distributed among these distances:
90 1 0.01
91 2 0.01
92 74 0.44
93 46 0.27
94 45 0.27
95 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (91 bp):
GAGCTAGTGTAAGACATGTCTGGACATGCATCGGCTACAAGATGAAGCCTGTGTAAGACCATGTC
TAGGACATGGCATCGACTTGAGATGA
Found at i:31648942 original size:40 final size:40
Alignment explanation
Indices: 31648887--31649031 Score: 247
Period size: 40 Copynumber: 3.6 Consensus size: 40
31648877 CGGATGATAA
* *
31648887 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
31648927 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
31648967 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
31649007 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31649032 AGCAAGTAGT
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
40 100 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:31649046 original size:80 final size:80
Alignment explanation
Indices: 31648887--31649063 Score: 243
Period size: 80 Copynumber: 2.2 Consensus size: 80
31648877 CGGATGATAA
* *
31648887 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCATTTG
* *
31648952 TGCGAGTTACTATAT
66 AGCAAGTTACTATAT
*
31648967 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAGTCCCGAAGGCATTT
*
31649031 GAGCAAG-TAGTTATAT
65 GAGCAAGTTA-CTATAT
* *
31649047 TC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
31649064 ATGCTTGGGT
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
79 18 0.21
80 69 0.79
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCATTTG
AGCAAGTTACTATAT
Found at i:31649331 original size:22 final size:21
Alignment explanation
Indices: 31649290--31649333 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
31649280 GAATGTGCAT
31649290 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
31649312 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
31649334 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:31656901 original size:40 final size:40
Alignment explanation
Indices: 31656846--31657030 Score: 309
Period size: 40 Copynumber: 4.6 Consensus size: 40
31656836 CGGATGATAA
* * *
31656846 CCGGGCTAAGTCCCGAAGGAATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
31656886 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
31656926 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
31656966 CCGGGCTAAGTCACGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
31657006 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31657031 AGCAAGTAGT
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
40 137 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:31657045 original size:80 final size:79
Alignment explanation
Indices: 31656842--31657062 Score: 302
Period size: 80 Copynumber: 2.8 Consensus size: 79
31656832 TATTCGGATG
* * *
31656842 ATAACCGGGCTAAGTCCCGAAGGAATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ATTATA-TCCGGGCTAAGTCCCGAAGGC
31656906 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTTACT
* * * *
31656922 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCACGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TATTATATCCGGGCTAAGTCCCGAAGGCA
31656987 TTTGTGCGAGTTACT
65 TTTGTGCGAGTTACT
* * *
31657002 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGTTATATTC-GGCTAAATCCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTA-TTATATCCGGGCTAAGTCCCGAAG
31657063 ATGCTTGGGT
Statistics
Matches: 127, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
79 15 0.12
80 110 0.87
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTATTATATCCGGGCTAAGTCCCGAAGGCAT
TTGTGCGAGTTACT
Found at i:31659170 original size:46 final size:47
Alignment explanation
Indices: 31659081--31659251 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 47
31659071 AGGGTAGGAT
* *
31659081 GCCGATGCCATGTCCTAGACATGGTTTTACACTGGC-TCATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCTCGTA
*
31659127 GTCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCG-A
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATCTCGTA
* * * *
31659172 GGCTGATG-CATGTCTCAGACAT-GTCTTACACTAGCTCTCGTCTCAGTA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATCTC-GTA
*
31659220 -CCAATGCCATGTCCCAGACATGGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
31659252 AGCTCACAAT
Statistics
Matches: 106, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
44 12 0.11
45 15 0.14
46 53 0.50
47 15 0.14
48 11 0.10
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCTCGTA
Found at i:31661032 original size:25 final size:26
Alignment explanation
Indices: 31660982--31661040 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
31660972 CATTTTGACC
*
31660982 CACAGCTTGTGTGAGCAAACCTATTT
1 CACAGCTCGTGTGAGCAAACCTATTT
31661008 CACAGCTCGTGTG-GCAAA-CTCATTT
1 CACAGCTCGTGTGAGCAAACCT-ATTT
31661033 CACAGCTC
1 CACAGCTC
31661041 CTATGAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 2 0.06
25 17 0.55
26 12 0.39
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAAACCTATTT
Found at i:31662478 original size:14 final size:15
Alignment explanation
Indices: 31662459--31662487 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31662449 TGGTTGAATA
31662459 GAAATTGGTC-TTTT
1 GAAATTGGTCATTTT
31662473 GAAATTGGTCATTTT
1 GAAATTGGTCATTTT
31662488 ATGCATGTTT
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:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
GAAATTGGTCATTTT
Found at i:31665989 original size:19 final size:19
Alignment explanation
Indices: 31665965--31666003 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31665955 GAGAGCATGT
31665965 TGTGCTACTTTTCACTCTA
1 TGTGCTACTTTTCACTCTA
*
31665984 TGTGCTACTTTTTACTCTA
1 TGTGCTACTTTTCACTCTA
31666003 T
1 T
31666004 CTTTTCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.10, T:0.51
Consensus pattern (19 bp):
TGTGCTACTTTTCACTCTA
Found at i:31667283 original size:2 final size:2
Alignment explanation
Indices: 31667271--31667300 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
31667261 GGCACCCAAA
31667271 AT AT A- 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 A
31667301 AAAGAGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31668430 original size:30 final size:30
Alignment explanation
Indices: 31668396--31668458 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
31668386 ACTTAATAAG
31668396 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
31668426 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
31668456 CAA
1 CAA
31668459 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:31671124 original size:49 final size:49
Alignment explanation
Indices: 31671071--31671302 Score: 284
Period size: 49 Copynumber: 4.7 Consensus size: 49
31671061 CTGGTACGCA
*
31671071 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
* * * ** ** * *
31671120 TAGTAGCCTACACTTTGTACTACACAAGTGACCTAACCATTTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * *
31671170 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACG
* * *
31671221 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATTCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
31671270 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
31671303 TCACAATAGA
Statistics
Matches: 150, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
49 71 0.47
50 43 0.29
51 36 0.24
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:31675667 original size:21 final size:21
Alignment explanation
Indices: 31675642--31675728 Score: 67
Period size: 20 Copynumber: 4.3 Consensus size: 21
31675632 CTTCATAAAA
*
31675642 TTTTATAAATTTTTTTATGAT
1 TTTTATAAATTTTTATATGAT
* * *
31675663 TTTTAT-AATTTTTTTCTAAT
1 TTTTATAAATTTTTATATGAT
* *
31675683 TTTT-TCTAATTTGTATAT--T
1 TTTTAT-AAATTTTTATATGAT
31675702 TTTTATTAAATTTTTAT-TGAT
1 TTTTA-TAAATTTTTATATGAT
31675723 TTTTAT
1 TTTTAT
31675729 TTTTTATTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
19 7 0.13
20 25 0.47
21 21 0.40
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.69
Consensus pattern (21 bp):
TTTTATAAATTTTTATATGAT
Found at i:31675686 original size:30 final size:29
Alignment explanation
Indices: 31675642--31675744 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
31675632 CTTCATAAAA
*
31675642 TTTTATAAATTTTTTTATGATTTTTATAATT
1 TTTTATTAA-TTTTTTATGATTTTTAT-ATT
* * *
31675673 TTTT-TCTAATTTTTTCTAATTTGTATATT
1 TTTTAT-TAATTTTTTATGATTTTTATATT
*
31675702 TTTTATTAAATTTTTATTGA-TTTT-TATT
1 TTTTATTAATTTTTTA-TGATTTTTATATT
*
31675730 TTTTATTATTTTTTT
1 TTTTATTAATTTTTT
31675745 CACATGTCAC
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
28 17 0.29
29 18 0.31
30 18 0.31
31 6 0.10
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (29 bp):
TTTTATTAATTTTTTATGATTTTTATATT
Found at i:31675717 original size:11 final size:10
Alignment explanation
Indices: 31675642--31675729 Score: 58
Period size: 11 Copynumber: 8.7 Consensus size: 10
31675632 CTTCATAAAA
*
31675642 TTTTATAAAT
1 TTTTATTAAT
31675652 TTTT-TTATGAT
1 TTTTATTA--AT
31675663 TTTTA-TAAT
1 TTTTATTAAT
*
31675672 TTTTTTCTAAT
1 TTTTAT-TAAT
31675683 TTTT-TCTAAT
1 TTTTAT-TAAT
* *
31675693 TTGTA-TATT
1 TTTTATTAAT
31675702 TTTTATTAAAT
1 TTTTATT-AAT
*
31675713 TTTTATTGAT
1 TTTTATTAAT
31675723 TTTTATT
1 TTTTATT
31675730 TTTTATTATT
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
9 15 0.24
10 23 0.37
11 25 0.40
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.69
Consensus pattern (10 bp):
TTTTATTAAT
Found at i:31676278 original size:19 final size:18
Alignment explanation
Indices: 31676247--31676291 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
31676237 TTTATGATTT
* *
31676247 TTTTATATTTTATCAGTA
1 TTTTATATATTATCAATA
*
31676265 TTTTATATAATTATGAATA
1 TTTTATAT-ATTATCAATA
31676284 TTTTATAT
1 TTTTATAT
31676292 TTAAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTATATATTATCAATA
Found at i:31677456 original size:31 final size:31
Alignment explanation
Indices: 31677421--31677480 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
31677411 GGTGCAAGTA
31677421 TATACCTGAAACTCTAATTGTGAATTAATTG
1 TATACCTGAAACTCTAATTGTGAATTAATTG
* * * * *
31677452 TATACTTGAAATTTTAATTTTGATTTAAT
1 TATACCTGAAACTCTAATTGTGAATTAAT
31677481 CATGCACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (31 bp):
TATACCTGAAACTCTAATTGTGAATTAATTG
Found at i:31682233 original size:16 final size:16
Alignment explanation
Indices: 31682212--31682242 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31682202 GACTATTTAT
*
31682212 AAATATTTTAAAATAA
1 AAATATTATAAAATAA
31682228 AAATATTATAAAATA
1 AAATATTATAAAATA
31682243 TTTTATTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATTATAAAATAA
Found at i:31682452 original size:32 final size:31
Alignment explanation
Indices: 31682416--31682507 Score: 76
Period size: 32 Copynumber: 3.2 Consensus size: 31
31682406 TTTCTTACAG
31682416 TAATTTGATATACTTTTTATTCTTTATTGCAA
1 TAATTTGATATA-TTTTTATTCTTTATTGCAA
* * *
31682448 TAA-TT--T-TA--GTTA---TTTCTTCCAA
1 TAATTTGATATATTTTTATTCTTTATTGCAA
31682470 TAATTTGATATATTTTTTATTCTTTATTGCAA
1 TAATTTGATATA-TTTTTATTCTTTATTGCAA
31682502 TAATTT
1 TAATTT
31682508 TAGTTATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 20
0.63 0.09 0.29
Matches are distributed among these distances:
22 11 0.25
23 2 0.05
25 4 0.09
26 2 0.05
28 2 0.05
29 4 0.09
31 2 0.05
32 17 0.39
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (31 bp):
TAATTTGATATATTTTTATTCTTTATTGCAA
Found at i:31682476 original size:54 final size:54
Alignment explanation
Indices: 31682394--31682514 Score: 215
Period size: 54 Copynumber: 2.2 Consensus size: 54
31682384 AAAGTCAACT
*
31682394 TAATTTTAGTTATTTCTTACAGTAATTTGATATACTTTTTATTCTTTATTGCAA
1 TAATTTTAGTTATTTCTTACAATAATTTGATATACTTTTTATTCTTTATTGCAA
* *
31682448 TAATTTTAGTTATTTCTTCCAATAATTTGATATATTTTTTATTCTTTATTGCAA
1 TAATTTTAGTTATTTCTTACAATAATTTGATATACTTTTTATTCTTTATTGCAA
31682502 TAATTTTAGTTAT
1 TAATTTTAGTTAT
31682515 AAAACTGAGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.28, C:0.08, G:0.07, T:0.57
Consensus pattern (54 bp):
TAATTTTAGTTATTTCTTACAATAATTTGATATACTTTTTATTCTTTATTGCAA
Found at i:31692227 original size:35 final size:34
Alignment explanation
Indices: 31692115--31692228 Score: 113
Period size: 35 Copynumber: 3.3 Consensus size: 34
31692105 CATAGGTAAG
* *
31692115 TACATGTAAGCTTATATTGAACTTGTATATTTGGC
1 TACATGTGAGCTTATATTGAACTTGTATA-TTGGT
* * * * *
31692150 TGCATATGAGGTTATATTGAA-TTTTAGTATTCGAT
1 TACATGTGAGCTTATATTGAACTTGTA-TATT-GGT
31692185 TACATGTGAGCTTATATTGAACTTGTATACTTGGT
1 TACATGTGAGCTTATATTGAACTTGTATA-TTGGT
*
31692220 TATATGTGA
1 TACATGTGA
31692229 AGTTATCTTA
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
34 6 0.10
35 50 0.81
36 6 0.10
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (34 bp):
TACATGTGAGCTTATATTGAACTTGTATATTGGT
Found at i:31699418 original size:35 final size:35
Alignment explanation
Indices: 31699309--31699419 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 35
31699299 AGGTAAGTAC
* * *
31699309 ATGTAAGCTTATATTGAACTTGTATATTCGGCTGT
1 ATGTGAGCTTATATTGAACTTGTATATTCGGTTAT
* * * * *
31699344 ATTTGAGGTTATATTGAA-TTTTAGTATTCGATTAC
1 ATGTGAGCTTATATTGAACTTGTA-TATTCGGTTAT
*
31699379 ATGTGAGCTTATATTGAACTTGTATACTCGGTTAT
1 ATGTGAGCTTATATTGAACTTGTATATTCGGTTAT
31699414 ATGTGA
1 ATGTGA
31699420 AGTTATCTTG
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
34 4 0.07
35 52 0.87
36 4 0.07
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (35 bp):
ATGTGAGCTTATATTGAACTTGTATATTCGGTTAT
Found at i:31711708 original size:28 final size:28
Alignment explanation
Indices: 31711668--31711722 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
31711658 GAAGGGCATC
31711668 ACTTTGAGCATGTTTAAGCGAGTTTTTT
1 ACTTTGAGCATGTTTAAGCGAGTTTTTT
31711696 ACTTTGAGCATGTTTAAGCGAGTTTTT
1 ACTTTGAGCATGTTTAAGCGAGTTTTT
31711723 CTTACAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.45
Consensus pattern (28 bp):
ACTTTGAGCATGTTTAAGCGAGTTTTTT
Found at i:31716289 original size:26 final size:26
Alignment explanation
Indices: 31716260--31716310 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
31716250 AAATCAAATA
31716260 GTTTAAAATAAATAATATATAAAAGG
1 GTTTAAAATAAATAATATATAAAAGG
* * *
31716286 GTTTGAGATAAATAATATGTAAAAG
1 GTTTAAAATAAATAATATATAAAAG
31716311 AAATATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (26 bp):
GTTTAAAATAAATAATATATAAAAGG
Found at i:31718643 original size:39 final size:39
Alignment explanation
Indices: 31718586--31718873 Score: 274
Period size: 39 Copynumber: 7.3 Consensus size: 39
31718576 AACCACGATA
* * *
31718586 ATGAGCCACCCCAACACCCTGGACCTAGTGGTAGGGGGG
1 ATGAGCCACCACACCACCCTGGACCTGGTGGTAGGGGGG
* * * *
31718625 ATGAGCCACCACACCACCCTGAACCTAGTGGTATGGGGA
1 ATGAGCCACCACACCACCCTGGACCTGGTGGTAGGGGGG
* * * * * *
31718664 ATGAACCACTACATCACCCCGGACCTGGTGGTAGGAGAG
1 ATGAGCCACCACACCACCCTGGACCTGGTGGTAGGGGGG
** * *
31718703 A-GAAGCCACCACACCACCCCAGACCTAGTGGTATGGGGG
1 ATG-AGCCACCACACCACCCTGGACCTGGTGGTAGGGGGG
* * *
31718742 ATGAGCCACCACATCA-CCTCGGACCTGGTGGTAGAGGAG
1 ATGAGCCACCACACCACCCT-GGACCTGGTGGTAGGGGGG
* * *
31718781 AGGAGCCACCACATCACCCCGGACCTGGTGGTAGGAGGGAG
1 ATGAGCCACCACACCACCCTGGACCTGGTGGTAGG-GGG-G
* * *
31718822 AGGAGCCACCACACCACCCTGGACCCGGTGGTAGGGGAG
1 ATGAGCCACCACACCACCCTGGACCTGGTGGTAGGGGGG
* *
31718861 AGGAACCACCACA
1 ATGAGCCACCACA
31718874 TGGGGAAACA
Statistics
Matches: 204, Mismatches: 39, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
38 3 0.01
39 161 0.79
40 7 0.03
41 33 0.16
ACGTcount: A:0.27, C:0.31, G:0.31, T:0.12
Consensus pattern (39 bp):
ATGAGCCACCACACCACCCTGGACCTGGTGGTAGGGGGG
Found at i:31718795 original size:117 final size:118
Alignment explanation
Indices: 31718589--31718873 Score: 342
Period size: 117 Copynumber: 2.4 Consensus size: 118
31718579 CACGATAATG
* * **
31718589 AGCCACCCCAACACCCTGGACCTAGTGGTAGGGGGGATGAGCCACCACACCACCCTGAACCTAGT
1 AGCCACCACACCACCCCAGACCTAGTGGTAGGGGGGATGAGCCACCACACCACCCTGAACCTAGT
* * *
31718654 GGTATGGGGAATGAACCACTACATCACCCCGGACCTGGTGGTAGGA-GAGAGA
66 GGTATGAGGAAGGAACCACCACATCACCCCGGACCTGGTGGTAGGAGGAGAGA
* * * *
31718706 AGCCACCACACCACCCCAGACCTAGTGGTATGGGGGATGAGCCACCACATCA-CCTCGGACCTGG
1 AGCCACCACACCACCCCAGACCTAGTGGTAGGGGGGATGAGCCACCACACCACCCT-GAACCTAG
* *
31718770 TGGTA-GAGGAGAGGAGCCACCACATCACCCCGGACCTGGTGGTAGGAGGGAGAGG
65 TGGTATGAGGA-AGGAACCACCACATCACCCCGGACCTGGTGGTAGGA-GGAGAGA
** ** * * *
31718825 AGCCACCACACCACCCTGGACCCGGTGGTAGGGGAGAGGAACCACCACA
1 AGCCACCACACCACCCCAGACCTAGTGGTAGGGGGGATGAGCCACCACA
31718874 TGGGGAAACA
Statistics
Matches: 143, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
116 7 0.05
117 90 0.63
119 46 0.32
ACGTcount: A:0.27, C:0.31, G:0.31, T:0.12
Consensus pattern (118 bp):
AGCCACCACACCACCCCAGACCTAGTGGTAGGGGGGATGAGCCACCACACCACCCTGAACCTAGT
GGTATGAGGAAGGAACCACCACATCACCCCGGACCTGGTGGTAGGAGGAGAGA
Found at i:31725023 original size:40 final size:40
Alignment explanation
Indices: 31724953--31725030 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
31724943 GCCATATATA
* * * *
31724953 TATATAGCCGAAGCTATTTTGATTCACACACTATGTGCTT
1 TATATAGCCGAAGCTATCTCGATACACACACTAAGTGCTT
*
31724993 TATATAGCCGAAGCTATCTCGATACGCACACTAAGTGC
1 TATATAGCCGAAGCTATCTCGATACACACACTAAGTGC
31725031 CAAACATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (40 bp):
TATATAGCCGAAGCTATCTCGATACACACACTAAGTGCTT
Found at i:31731524 original size:23 final size:23
Alignment explanation
Indices: 31731307--31731528 Score: 261
Period size: 23 Copynumber: 9.7 Consensus size: 23
31731297 GGAATCTATA
*
31731307 GGCTACAATACAGTGGTAGCTTC
1 GGCTACATTACAGTGGTAGCTTC
31731330 GGCTACATCT-CAGTGGTAGCTTC
1 GGCTACAT-TACAGTGGTAGCTTC
* * *
31731353 AGCTACAATATAGTGGTAGCTTC
1 GGCTACATTACAGTGGTAGCTTC
*
31731376 AGCTACATCT-CAGTGGTAGCTTC
1 GGCTACAT-TACAGTGGTAGCTTC
* *
31731399 GGCTACAATACAGTGGTAGCTTT
1 GGCTACATTACAGTGGTAGCTTC
*
31731422 GGCTATATCT-CAGTGGTAGCTTC
1 GGCTACAT-TACAGTGGTAGCTTC
* *
31731445 GGCTACAATACAGTGGTAGCTTT
1 GGCTACATTACAGTGGTAGCTTC
*
31731468 GGCTACAATACAGTGGTAGCTTC
1 GGCTACATTACAGTGGTAGCTTC
* *
31731491 GGCTACGTTACAGTGATAGCTTC
1 GGCTACATTACAGTGGTAGCTTC
* *
31731514 AGCTATATTACAGTG
1 GGCTACATTACAGTG
31731529 TGGCACTTTG
Statistics
Matches: 171, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
22 3 0.02
23 165 0.96
24 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCTACATTACAGTGGTAGCTTC
Found at i:31731528 original size:46 final size:46
Alignment explanation
Indices: 31731307--31731518 Score: 309
Period size: 46 Copynumber: 4.6 Consensus size: 46
31731297 GGAATCTATA
31731307 GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTC
* * *
31731353 AGCTACAATATAGTGGTAGCTTCAGCTACATCTCAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTC
* *
31731399 GGCTACAATACAGTGGTAGCTTTGGCTATATCTCAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTC
* *
31731445 GGCTACAATACAGTGGTAGCTTTGGCTACAAT-ACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTCGGCTAC-ATCTCAGTGGTAGCTTC
** * *
31731491 GGCTACGTTACAGTGATAGCTTCAGCTA
1 GGCTACAATACAGTGGTAGCTTCGGCTA
31731519 TATTACAGTG
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 148 0.99
47 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (46 bp):
GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTC
Found at i:31736509 original size:30 final size:30
Alignment explanation
Indices: 31736473--31736538 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
31736463 ATAGTGTGAT
31736473 CGTGTGTCACACACGGCCTAGACACACGCC
1 CGTGTGTCACACACGGCCTAGACACACGCC
31736503 CGTGTGTCACACACGGCCTAGACACACGCC
1 CGTGTGTCACACACGGCCTAGACACACGCC
*
31736533 CATGTG
1 CGTGTG
31736539 GCTATCCATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.38, G:0.24, T:0.15
Consensus pattern (30 bp):
CGTGTGTCACACACGGCCTAGACACACGCC
Found at i:31738135 original size:43 final size:43
Alignment explanation
Indices: 31738002--31738136 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 43
31737992 TGGCAATAAG
* *
31738002 CCTGCTAGACCTTTAAGTCTGATATCATTTCACTGGCATTACG
1 CCTGCTAGACCTTTAAGTCTGATATCATTTCACCGGCATTACA
* *** * *
31738045 CCTGCTAG-GCTCGGAG-CTTGATA--ATATTCACCAGC-TTAAA
1 CCTGCTAGACCTTTAAGTC-TGATATCAT-TTCACCGGCATTACA
* *
31738085 GCTTGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACA
1 -CCTGCTAGACCTTTAAGTCTGATATCATTTCACCGGCATTACA
31738129 CCTGCTAG
1 CCTGCTAG
31738137 GCTCAAAGCC
Statistics
Matches: 67, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
40 5 0.07
41 15 0.22
42 17 0.25
43 24 0.36
44 6 0.09
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (43 bp):
CCTGCTAGACCTTTAAGTCTGATATCATTTCACCGGCATTACA
Found at i:31738176 original size:84 final size:84
Alignment explanation
Indices: 31737984--31738177 Score: 223
Period size: 84 Copynumber: 2.3 Consensus size: 84
31737974 ATAACCTGAT
* * * *
31737984 TTCATCACTGGCAATAAGCCTGCTAGACCTTTAAGTCTGATATCATTTCACTGGCATTACGCCTG
1 TTCATCACCGGCAA-AAGCCTGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACACCTG
** **
31738049 CTAGGCTCGGAGCTTGATAA
65 CTAGGCTCAAAGCCCGATAA
* * *
31738069 -T-ATTCACCAGCTTAAAGCTTGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACACCT
1 TTCA-TCACCGGC-AAAAGCCTGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACACCT
31738132 GCTAGGCTCAAAGCCCGA-AA
64 GCTAGGCTCAAAGCCCGATAA
*
31738152 TTCATCACCGGCACAAGGCCTGCTAG
1 TTCATCACCGGCA-AAAGCCTGCTAG
31738178 GTTTGAAACC
Statistics
Matches: 89, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
83 3 0.03
84 84 0.94
85 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (84 bp):
TTCATCACCGGCAAAAGCCTGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACACCTGC
TAGGCTCAAAGCCCGATAA
Found at i:31740055 original size:14 final size:15
Alignment explanation
Indices: 31740026--31740055 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31740016 CAAAATTAAG
31740026 ACATGATACTTTCAC
1 ACATGATACTTTCAC
31740041 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
31740055 A
1 A
31740056 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:31741741 original size:23 final size:23
Alignment explanation
Indices: 31741633--31741808 Score: 203
Period size: 23 Copynumber: 7.7 Consensus size: 23
31741623 GGAATCTATA
31741633 GGCTACAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* *
31741656 GACTAC-ATCTCAGTGGTAGCTTC
1 GGCTACAAT-ACAGTGGTAGCTTC
*
31741679 AGCTACAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
*
31741702 GGCTAC-ATCTCAGTGGTAGCTTC
1 GGCTACAAT-ACAGTGGTAGCTTC
* *
31741725 GGCTACAATACAATGGTAGCTTT
1 GGCTACAATACAGTGGTAGCTTC
*
31741748 GGCTGCAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
** *
31741771 GGCTACGTTACAGTGATAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* * *
31741794 AGCTATATTACAGTG
1 GGCTACAATACAGTG
31741809 TAGTACTTTG
Statistics
Matches: 129, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
22 4 0.03
23 121 0.94
24 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCTACAATACAGTGGTAGCTTC
Found at i:31741808 original size:46 final size:46
Alignment explanation
Indices: 31741633--31741798 Score: 226
Period size: 46 Copynumber: 3.6 Consensus size: 46
31741623 GGAATCTATA
*
31741633 GGCTACAATACAGTGGTAGCTTCGACTACATCTCAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTC
*
31741679 AGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTC
* * * *
31741725 GGCTACAATACAATGGTAGCTTTGGCTGCAAT-ACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTCGGCTAC-ATCTCAGTGGTAGCTTC
** * *
31741771 GGCTACGTTACAGTGATAGCTTCAGCTA
1 GGCTACAATACAGTGGTAGCTTCGGCTA
31741799 TATTACAGTG
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
46 103 0.98
47 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (46 bp):
GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTC
Found at i:31746925 original size:57 final size:57
Alignment explanation
Indices: 31746837--31747048 Score: 194
Period size: 57 Copynumber: 3.7 Consensus size: 57
31746827 GTATTACAGG
* *
31746837 ATTACCAGTCCAGGCTAAATCCTTTATGTAACGTATGCTCAGAAGAACTAAATTAGT
1 ATTACCAGTCCAGGCTAAATCCTATATGTAACATATGCTCAGAAGAACTAAATTAGT
* * * * * * * ** *
31746894 ATTACTAGTCTAGGTTAAATCCTA-ATTGTAACATATACTCAAGAGGAATTATACCAGG
1 ATTACCAGTCCAGGCTAAATCCTATA-TGTAACATATGCTC-AGAAGAACTAAATTAGT
* * * * ** *
31746952 ATTACCCGTTCGGGCTAAATCCTTTATGTAATGTATGCTCAGAAGAACTCAATTAGT
1 ATTACCAGTCCAGGCTAAATCCTATATGTAACATATGCTCAGAAGAACTAAATTAGT
* *
31747009 ATTACTAGTCCAAGCTAAATCCTA-ATTGTAACATATGCTC
1 ATTACCAGTCCAGGCTAAATCCTATA-TGTAACATATGCTC
31747049 GAGAGAAATT
Statistics
Matches: 114, Mismatches: 37, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
56 2 0.02
57 72 0.63
58 39 0.34
59 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (57 bp):
ATTACCAGTCCAGGCTAAATCCTATATGTAACATATGCTCAGAAGAACTAAATTAGT
Found at i:31746973 original size:58 final size:57
Alignment explanation
Indices: 31746909--31747089 Score: 177
Period size: 58 Copynumber: 3.1 Consensus size: 57
31746899 TAGTCTAGGT
* *
31746909 TAAATCCTAATTGTAACATATACTCAAGAGGAATTATACCAGGATTACCCGTTCGGGC
1 TAAATCCTAATTGTAACATATGCTC-AGAGGAATTATATCAGGATTACCCGTTCGGGC
* ** * * * * ** * **
31746967 TAAATCCT-TTATGTAATGTATGCTCAGAAGAACTCA-ATTAGTATTACTAGTCCAAGC
1 TAAATCCTAAT-TGTAACATATGCTCAGAGGAA-TTATATCAGGATTACCCGTTCGGGC
*
31747024 TAAATCCTAATTGTAACATATGCTCGAGAGAAATTATATCAGGATTACCCGTTCGGGC
1 TAAATCCTAATTGTAACATATGCTC-AGAGGAATTATATCAGGATTACCCGTTCGGGC
31747082 TAAATCCT
1 TAAATCCT
31747090 TTCTATAATG
Statistics
Matches: 91, Mismatches: 27, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
57 42 0.46
58 49 0.54
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (57 bp):
TAAATCCTAATTGTAACATATGCTCAGAGGAATTATATCAGGATTACCCGTTCGGGC
Done.