Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 78 of 226
Found at i:28546503 original size:15 final size:14
Alignment explanation
Indices: 28546483--28546530 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
28546473 TTTTAAAATA
28546483 TTTTTAAAATACTTT
1 TTTTTAAAATA-TTT
** *
28546498 TTTTTAATTTTTTT
1 TTTTTAAAATATTT
28546512 ATTTTTAAAATATTT
1 -TTTTTAAAATATTT
28546527 TTTT
1 TTTT
28546531 AATGTTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTAAAATATTT
Found at i:28546515 original size:30 final size:28
Alignment explanation
Indices: 28546481--28546538 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
28546471 AATTTTAAAA
*
28546481 TATTTTTAAAATACTTTTTTTTAATTTTTT
1 TATTTTTAAAATA--TTTTTTTAATGTTTT
28546511 TATTTTTAAAATATTTTTTTAATGTTTT
1 TATTTTTAAAATATTTTTTTAATGTTTT
28546539 ATTAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 14 0.52
30 13 0.48
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTTTAAAATATTTTTTTAATGTTTT
Found at i:28550516 original size:29 final size:29
Alignment explanation
Indices: 28550484--28550542 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
28550474 ATAAAATAAA
*
28550484 ATCCTAAAATTAGATAATCCTTA-ATAATT
1 ATCCTAAAATTA-ATAATCCTAACATAATT
* *
28550513 ATCCTAATATTAATTATCCTAACATAATT
1 ATCCTAAAATTAATAATCCTAACATAATT
28550542 A
1 A
28550543 AAATAGAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (29 bp):
ATCCTAAAATTAATAATCCTAACATAATT
Found at i:28555766 original size:14 final size:15
Alignment explanation
Indices: 28555747--28555775 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28555737 ATTTAAGTTT
28555747 AAAAAATC-TTTTAA
1 AAAAAATCATTTTAA
28555761 AAAAAATCATTTTAA
1 AAAAAATCATTTTAA
28555776 TAGCCTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAATCATTTTAA
Found at i:28562975 original size:174 final size:175
Alignment explanation
Indices: 28562657--28562977 Score: 414
Period size: 174 Copynumber: 1.8 Consensus size: 175
28562647 AATCCTAATA
* * *
28562657 TCTAAACCAACTCAGAGAATATCAAACTAAACAAGTGCACTACTAGCAAGTTAAATTTCACCTTT
1 TCTAAACCAACTCAAAGAATATCAAACTAAACAAGTGCACTAATAGCAAATTAAATTTCACCTTT
* * * * * *
28562722 CCAGCATTTCTCAAGCATCTAAATAAACTAATTAAGAGATTCAAATCTCACAACCAATTTTCCTA
66 CCAGCATTTCTCAAGCAGCCAAATAAACTAATTAAGAGATCCAAATCTCACAACCAATCTTACAA
* *
28562787 GACCTAATGCTAAAATGAGATTCACAGAAAACAAATTTCTTAGCC
131 AACCTAAAGCTAAAATGAGATTCACAGAAAACAAATTTCTTAGCC
* * * ** *
28562832 TCTAAACCAACTCAAAGAA-ATCAAAGTAAAC-AGCTTCATTAATAGCAAATTGCATTTCACTTT
1 TCTAAACCAACTCAAAGAATATCAAACTAAACAAG-TGCACTAATAGCAAATTAAATTTCACCTT
* * * *
28562895 TCCATCATTTCTCAAGCAGCCAAATAAACTGATTAAAGAGATCCTAATCTCACTACCAA-CTTAC
65 TCCAGCATTTCTCAAGCAGCCAAATAAACTAATT-AAGAGATCCAAATCTCACAACCAATCTTAC
28562959 AAAACCTAAAGCTAAAATG
129 AAAACCTAAAGCTAAAATG
28562978 TAATTTTTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
173 2 0.02
174 82 0.67
175 39 0.32
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (175 bp):
TCTAAACCAACTCAAAGAATATCAAACTAAACAAGTGCACTAATAGCAAATTAAATTTCACCTTT
CCAGCATTTCTCAAGCAGCCAAATAAACTAATTAAGAGATCCAAATCTCACAACCAATCTTACAA
AACCTAAAGCTAAAATGAGATTCACAGAAAACAAATTTCTTAGCC
Found at i:28571526 original size:61 final size:61
Alignment explanation
Indices: 28571461--28571587 Score: 166
Period size: 61 Copynumber: 2.1 Consensus size: 61
28571451 ATCCTAAATA
* ** *
28571461 TAAAATATTCAACAAAATTAGCCTTCAATGTTTACAA-AATTTGTCATTTTAGTTCGAATTC
1 TAAAAAATTCAACAAAATTAGCCTTCAAAATTTACAATAATTT-TCAATTTAGTTCGAATTC
** * *
28571522 TAAAAAATTCAGTAAATTTAGCCTTCAAAATTTACAATAATTTTCAATTTAGTTCTAATTC
1 TAAAAAATTCAACAAAATTAGCCTTCAAAATTTACAATAATTTTCAATTTAGTTCGAATTC
28571583 TAAAA
1 TAAAA
28571588 CAATAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 52 0.91
62 5 0.09
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.39
Consensus pattern (61 bp):
TAAAAAATTCAACAAAATTAGCCTTCAAAATTTACAATAATTTTCAATTTAGTTCGAATTC
Found at i:28571599 original size:61 final size:61
Alignment explanation
Indices: 28571478--28571600 Score: 160
Period size: 61 Copynumber: 2.0 Consensus size: 61
28571468 TTCAACAAAA
** * * *
28571478 TTAGCCTTCAATGTTTACAAAATTTGTCATTTTAGTTCGAATTCTAAAAAATTCAGTAAAT
1 TTAGCCTTCAAAATTTACAAAATTTGTCAATTTAGTTCGAATTCTAAAAAATTAAATAAAT
*
28571539 TTAGCCTTCAAAATTTACAATAATTT-TCAATTTAGTTCTAATTCTAAAACAA-TAAATAAAT
1 TTAGCCTTCAAAATTTACAA-AATTTGTCAATTTAGTTCGAATTCTAAAA-AATTAAATAAAT
28571600 T
1 T
28571601 ATTTTTGACC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
61 47 0.87
62 7 0.13
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.41
Consensus pattern (61 bp):
TTAGCCTTCAAAATTTACAAAATTTGTCAATTTAGTTCGAATTCTAAAAAATTAAATAAAT
Found at i:28572778 original size:33 final size:33
Alignment explanation
Indices: 28572669--28572763 Score: 82
Period size: 36 Copynumber: 2.8 Consensus size: 33
28572659 GTCTCAAAAA
* * * * *
28572669 ATAATAGCAAAATTAACAATAAAATAAGAATTAT
1 ATAATAGCAAAA-TGACAATAAAATAATAGTAAC
* *
28572703 ATAATATTCAAACAATAACAATAAAATAATAGTAAC
1 ATAATA-GC-AA-AATGACAATAAAATAATAGTAAC
*
28572739 ATAATAGTAAAATGACAATAAAATA
1 ATAATAGCAAAATGACAATAAAATA
28572764 GTGAGAAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
33 14 0.28
34 8 0.16
35 1 0.02
36 25 0.50
37 2 0.04
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (33 bp):
ATAATAGCAAAATGACAATAAAATAATAGTAAC
Found at i:28574695 original size:16 final size:15
Alignment explanation
Indices: 28574667--28574696 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
28574657 AAATATACAT
28574667 ATTAAAATAATTATA
1 ATTAAAATAATTATA
28574682 ATTAAAATTAATTAT
1 ATTAAAA-TAATTAT
28574697 TATCATACGC
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTAAAATAATTATA
Found at i:28579489 original size:3 final size:3
Alignment explanation
Indices: 28579477--28579558 Score: 155
Period size: 3 Copynumber: 27.0 Consensus size: 3
28579467 AAAAGGTTAT
28579477 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28579523 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28579559 TGGTATCATT
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
3 75 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28581245 original size:17 final size:17
Alignment explanation
Indices: 28581225--28581257 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28581215 GGCGCGGCAT
28581225 CAGAACGGTGGCGGCGA
1 CAGAACGGTGGCGGCGA
*
28581242 CAGAATGGTGGCGGCG
1 CAGAACGGTGGCGGCG
28581258 CCGGGCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.48, T:0.09
Consensus pattern (17 bp):
CAGAACGGTGGCGGCGA
Found at i:28589808 original size:17 final size:18
Alignment explanation
Indices: 28589786--28589825 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
28589776 TGTAATCATC
28589786 ATAATT-TTTATTAAAT-T
1 ATAATTATTT-TTAAATAT
28589803 ATAATTATTTTTAAATAT
1 ATAATTATTTTTAAATAT
28589821 ATAAT
1 ATAAT
28589826 CATCACACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATAATTATTTTTAAATAT
Found at i:28589961 original size:87 final size:89
Alignment explanation
Indices: 28589864--28590038 Score: 221
Period size: 87 Copynumber: 2.0 Consensus size: 89
28589854 TTTAAATAAA
* * * * * * * * *
28589864 AATTTTAAATGTTAATTTAGTAATA-AGATTAAAAATATAGGGTATTTTTGTTGGTTCAAAT-CT
1 AATTTTAAATGTCAACTTAGTAATATA-ATGAAAAATAAAGAGTATTCTCGTCGATTCAAATACT
28589927 TTTCTAAACTCAT-ATTTTATAATT
65 TTTCTAAACTCATGATTTTATAATT
*
28589951 AATTTTAAATGTCAACTTAGTAATATAATGAAAAATAAAGAGTATTCTCGTCGATTCAAATATTT
1 AATTTTAAATGTCAACTTAGTAATATAATGAAAAATAAAGAGTATTCTCGTCGATTCAAATACTT
*
28590016 TTTTAAACTCATGATTTTATAAT
66 TTCTAAACTCATGATTTTATAAT
28590039 ATATATTATA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
87 50 0.68
88 14 0.19
89 10 0.14
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (89 bp):
AATTTTAAATGTCAACTTAGTAATATAATGAAAAATAAAGAGTATTCTCGTCGATTCAAATACTT
TTCTAAACTCATGATTTTATAATT
Found at i:28590606 original size:43 final size:43
Alignment explanation
Indices: 28590558--28590841 Score: 381
Period size: 43 Copynumber: 6.6 Consensus size: 43
28590548 TTATTTTTAA
** ** *
28590558 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTCTCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAC
**
28590601 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAC
* * * ** *
28590644 AAACGTCGCGAAAGATCATGTTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAC
* * *
28590687 AAACGCTGCTAAAGACCTTGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAC
*
28590730 AAACGCCGCTAAAGACCTTGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAC
*
28590773 AAACGCCGCTAAAGACCTTGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAC
* *
28590816 AAACGCCGCTAAA-AACATAACCTTTA
1 AAACGCCGCTAAAGACCATGACCTTTA
28590842 AAAATACATA
Statistics
Matches: 222, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
42 10 0.05
43 212 0.95
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAC
Found at i:28590873 original size:20 final size:19
Alignment explanation
Indices: 28590850--28590896 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
28590840 TAAAAATACA
28590850 TATTTTAAT-CAAATAATATT
1 TATTTTAATACAAAT-AT-TT
*
28590870 TATTTTTATGACAAATATTT
1 TATTTTAAT-ACAAATATTT
28590890 TATTTTA
1 TATTTTA
28590897 TTTTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 16 0.70
21 2 0.09
22 5 0.22
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (19 bp):
TATTTTAATACAAATATTT
Found at i:28592108 original size:19 final size:20
Alignment explanation
Indices: 28592072--28592120 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
28592062 TAAAATTATA
*
28592072 ATTTTTATTTATTTTATTTC
1 ATTTTTATTTATTGTATTTC
*
28592092 ATTTTTATTT-TTGTATTTT
1 ATTTTTATTTATTGTATTTC
*
28592111 AATTTTATTT
1 ATTTTTATTT
28592121 CTTATAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (20 bp):
ATTTTTATTTATTGTATTTC
Found at i:28592860 original size:22 final size:22
Alignment explanation
Indices: 28592835--28592899 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
28592825 CTTAACCCCA
28592835 TAACCTCTAACCCTTAAACCAT
1 TAACCTCTAACCCTTAAACCAT
* *
28592857 TAACCCCTAACCCCTAAACC-T
1 TAACCTCTAACCCTTAAACCAT
** *
28592878 TAAATTCCAACCCTTAAACCAT
1 TAACCTCTAACCCTTAAACCAT
28592900 AATCCATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.37, C:0.38, G:0.00, T:0.25
Consensus pattern (22 bp):
TAACCTCTAACCCTTAAACCAT
Found at i:28592951 original size:297 final size:286
Alignment explanation
Indices: 28592415--28592999 Score: 736
Period size: 297 Copynumber: 2.0 Consensus size: 286
28592405 TTCAATATAT
28592415 TAAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAACTA
1 TAAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAACTA
* * * *
28592480 ATTAATCTAAACCCAAAACCCCGACCCCTGAGGCCTAAACCTTAAATCTCTAACTATTAACCCCA
66 ATTAATCTAAACCCAAAACCCCGACCCCTGAGCCCTAAACCTTAAACCCCTAACTACTAACCCCA
28592545 AAACATCTAACCCCTAAACAACTAAACCTTAAATCTCAACCCTTAAACCATGTTCCCTAATCCAT
131 AAACATCTAACCCCTAAACAACTAAACCTTAAATCTCAACCCTTAAACCA------CTAATCCAT
*
28592610 AATCCCTAAATCTATACCCCCTAAACCTTAAAATAGTAACTCCTAAATCGGCCTTAAATCTTAAA
190 AATCCCTAAATCTATACCCCCTAAACCTTAAAATAGTAACTCCTAAACCGGCCTTAAATCTTAAA
* *
28592675 TTAATCATATACCTTAAACTAAAAACCCTAAA
255 TTAATCATATACCCTAAACCAAAAACCCTAAA
*
28592707 TAAATTTATTATTATTTCTTTTACAATTATATATATATAAGAACATATTTAAAATATAAATTAAA
1 TAAATTTATTATTATCTCTTTTAC----A-AT-TATATAAGAACATATTTAAAATATAAATT-AA
* * *
28592772 AAAACTAATTAATCTACACCCAAAAACCTAACCCGACCCTTGAATCCCT-AACTCTT-AACCCCA
59 AAAACTAATTAATCTAAACCC-AAAA-C---CCCGACCCCTG-AGCCCTAAAC-CTTAAACCCC-
* * **
28592835 TAACCT-CTAACCCTTAAACCAT-TAACCCCT-AACCCCTAAACCTTAAAT-TCCAACCCTTAAA
116 TAA-CTACTAACCC-CAAAACATCTAACCCCTAAACAACTAAACCTTAAATCT-CAACCCTTAAA
* *
28592896 CCA-TAATCCATAATCCTTAAAT-TCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGGC
178 CCACTAATCCATAATCCCTAAATCT-ATACCCCCTAAACCTTAAAATAGTAACTCCTAAACCGGC
28592959 CTTAAATCTTAAATTAATCATATACCCTAAACCAAAAACCC
242 CTTAAATCTTAAATTAATCATATACCCTAAACCAAAAACCC
28593000 AAAACCCTAA
Statistics
Matches: 257, Mismatches: 17, Indels: 33
0.84 0.06 0.11
Matches are distributed among these distances:
292 23 0.09
296 2 0.01
297 96 0.37
298 29 0.11
299 22 0.09
300 4 0.02
301 1 0.00
303 1 0.00
304 47 0.18
305 24 0.09
306 8 0.03
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.29
Consensus pattern (286 bp):
TAAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAACTA
ATTAATCTAAACCCAAAACCCCGACCCCTGAGCCCTAAACCTTAAACCCCTAACTACTAACCCCA
AAACATCTAACCCCTAAACAACTAAACCTTAAATCTCAACCCTTAAACCACTAATCCATAATCCC
TAAATCTATACCCCCTAAACCTTAAAATAGTAACTCCTAAACCGGCCTTAAATCTTAAATTAATC
ATATACCCTAAACCAAAAACCCTAAA
Found at i:28593397 original size:41 final size:41
Alignment explanation
Indices: 28593156--28593399 Score: 335
Period size: 41 Copynumber: 5.9 Consensus size: 41
28593146 TAGTATTTTA
* **
28593156 CATTAGCGGCGCTTTTGCAAAAACGCCGCTAAAGAATAGAG
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
* *
28593197 CATTAGCGGCGCTTTTCCAAAAAACGCCGCTAAAGGCAAGAG
1 CATTAGCGGCGCTTTTCC-AAAAACGCCGCTAAAGACCAGAG
* * ** * * * *
28593239 CATTAGCGACCCTTTTTTAAAAATGCCACTAAAGGCAAGAG
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
28593280 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
* *
28593321 CATTAGCGGCGCTTTTACAAAAAGGCCGCTAAAGACCAGAG
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
*
28593362 CATTAGCGGCGCTTTTCCAAAAATGCCGCTAAAGACCA
1 CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCA
28593400 CGAAAGGTCC
Statistics
Matches: 180, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
41 146 0.81
42 34 0.19
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (41 bp):
CATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAG
Found at i:28593517 original size:55 final size:56
Alignment explanation
Indices: 28593440--28593545 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 56
28593430 TAAGTTTTTT
*
28593440 GTGGCGTTTTTCAAAAAACGCCGCTAATGCT-CATTTTTAGCGGCGTTTTTCTTTA
1 GTGGCGATTTTCAAAAAACGCCGCTAATGCTCCATTTTTAGCGGCGTTTTTCTTTA
* * * *
28593495 GTGGCGATTTTCATAGAGCGCCGCTAATGTTCCATTTTTAGCGGCGTTTTT
1 GTGGCGATTTTCAAAAAACGCCGCTAATGCTCCATTTTTAGCGGCGTTTTT
28593546 TTGTCCAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 26 0.58
56 19 0.42
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.40
Consensus pattern (56 bp):
GTGGCGATTTTCAAAAAACGCCGCTAATGCTCCATTTTTAGCGGCGTTTTTCTTTA
Found at i:28595781 original size:13 final size:13
Alignment explanation
Indices: 28595734--28595786 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
28595724 AGTTTGACAA
28595734 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
28595747 TGCTGTGGAAAAT
1 TGCTTTTGAAAAG
*
28595760 TGTTTTTGAGAAA-
1 TGCTTTTGA-AAAG
28595773 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
28595786 T
1 T
28595787 TTGGTTTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
12 3 0.10
13 25 0.81
14 3 0.10
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:28596465 original size:13 final size:13
Alignment explanation
Indices: 28596412--28596467 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
28596402 TAGCAAAAGC
*
28596412 TTTACTTAATTTT
1 TTTACATAATTTT
* *
28596425 TATATATAATTTT
1 TTTACATAATTTT
* *
28596438 TTATAAAT-ATATT
1 TT-TACATAATTTT
28596451 TTTACATAATTTT
1 TTTACATAATTTT
28596464 TTTA
1 TTTA
28596468 AGAAAAATCA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
12 4 0.12
13 25 0.76
14 4 0.12
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTACATAATTTT
Found at i:28596722 original size:19 final size:19
Alignment explanation
Indices: 28596683--28596722 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28596673 ATTCATGCAA
* *
28596683 AATTCATGTACGTTGATTG
1 AATTCATGTACGTCGAATG
*
28596702 AATTCATGTGCGTCGAATG
1 AATTCATGTACGTCGAATG
28596721 AA
1 AA
28596723 GAAGAACACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (19 bp):
AATTCATGTACGTCGAATG
Found at i:28601716 original size:31 final size:31
Alignment explanation
Indices: 28601673--28601742 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
28601663 TTACAAAATG
*
28601673 GTCACTGAACTATTCGAAAA-TTTTCATTTAA
1 GTCATTGAACTATT-GAAAAGTTTTCATTTAA
* * *
28601704 GTTATTGAACTATTTAAAAGTTTTTATTTAA
1 GTCATTGAACTATTGAAAAGTTTTCATTTAA
28601735 GTCATTGA
1 GTCATTGA
28601743 GTTGCTAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (31 bp):
GTCATTGAACTATTGAAAAGTTTTCATTTAA
Found at i:28601798 original size:13 final size:13
Alignment explanation
Indices: 28601780--28601806 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28601770 AGTCTGGCTA
28601780 GTTAGCTCTAAAT
1 GTTAGCTCTAAAT
28601793 GTTAGCTCTAAAT
1 GTTAGCTCTAAAT
28601806 G
1 G
28601807 ACGATTCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (13 bp):
GTTAGCTCTAAAT
Found at i:28604807 original size:7 final size:7
Alignment explanation
Indices: 28604797--28604870 Score: 78
Period size: 7 Copynumber: 10.7 Consensus size: 7
28604787 CAGGTTTAAT
*
28604797 GTTTATG
1 GTTTAGG
28604804 GTTTAGG
1 GTTTAGG
*
28604811 GTTTAGA
1 GTTTAGG
*
28604818 GTTTATG
1 GTTTAGG
*
28604825 GTTTACG
1 GTTTAGG
*
28604832 ATTTAGG
1 GTTTAGG
*
28604839 GTTTAAG
1 GTTTAGG
28604846 G-TTAGG
1 GTTTAGG
*
28604852 GTTTAGA
1 GTTTAGG
28604859 GTTTAGG
1 GTTTAGG
28604866 GTTTA
1 GTTTA
28604871 ATTTAAGATT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
6 5 0.09
7 49 0.91
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:28604815 original size:21 final size:21
Alignment explanation
Indices: 28604789--28604870 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 21
28604779 GTAGTTTACA
28604789 GGTTTA-ATGTTTATGGTTTAG
1 GGTTTAGA-GTTTATGGTTTAG
*
28604810 GGTTTAGAGTTTATGGTTTAC
1 GGTTTAGAGTTTATGGTTTAG
* * *
28604831 GATTTAGGGTTTAAGG-TTAG
1 GGTTTAGAGTTTATGGTTTAG
*
28604851 GGTTTAGAGTTTAGGGTTTA
1 GGTTTAGAGTTTATGGTTTA
28604871 ATTTAAGATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.31
21 34 0.67
22 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (21 bp):
GGTTTAGAGTTTATGGTTTAG
Found at i:28605133 original size:27 final size:25
Alignment explanation
Indices: 28605087--28605141 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 25
28605077 CATCATTTTT
28605087 TATTTATATATTGCATATATACATAAA
1 TATTTATATATTGCATATATA-A-AAA
28605114 TATTTATATTTATT-CA-ATATAAAAA
1 TATTTATA--TATTGCATATATAAAAA
28605139 TAT
1 TAT
28605142 AAAAATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
25 6 0.23
26 1 0.04
27 13 0.50
28 2 0.08
29 4 0.15
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (25 bp):
TATTTATATATTGCATATATAAAAA
Found at i:28605142 original size:8 final size:8
Alignment explanation
Indices: 28605129--28605158 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
28605119 ATATTTATTC
28605129 AATATAAA
1 AATATAAA
28605137 AATATAAA
1 AATATAAA
28605145 AATATAAA
1 AATATAAA
28605153 AATATA
1 AATATA
28605159 TTGATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AATATAAA
Found at i:28605486 original size:148 final size:150
Alignment explanation
Indices: 28605189--28605822 Score: 550
Period size: 148 Copynumber: 4.3 Consensus size: 150
28605179 TTTTTCTAAA
* * * * *
28605189 TTTCCATGTTCTTAGTGGCGTTTTATGCCAAAACGCCA-CAAAA-TTGTCCTAATTATGAGGGAA
1 TTTCCATGTACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGAA
* * * * *
28605252 ACGACTGT-GTTTC-ACGGTTATTTAGTGGCAC-ATACGTATTAACGCCGCAGACA--GGTTAAT
66 ACGAC-GTCATTTCTACGGTTATTTAGTGGCGCTA-ATGTATAAACGCCGC-GA-ATGGGTTCAT
* * * *
28605312 TTAATCCTGGAAAACGACGACATT
127 TTAGTCATGGAAAACGTCGTCATT
* *
28605336 TTTCTATGTACTTAGTGGCGTTTTATGCCAAAACGCCAGAAAAATTT-TCATAATTATGTGGGAA
1 TTTCCATGTACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGAA
* * *
28605400 ACGACGTCATTTCTGCGGTTATTTAGTGGCGCACAAT-TATAAACTCCGCGAATGGGTTCATTTA
66 ACGACGTCATTTCTACGGTTATTTAGTGGCGC-TAATGTATAAACGCCGCGAATGGGTTCATTTA
* *
28605464 GTCAT-GAATACGTCGTCGTT
130 GTCATGGAAAACGTCGTCATT
* * * * * * *
28605484 TTTCTATGTTCTTAGTGGCGTTTTATACCAAAACACC--AAAAATTTGTCCTAATTGTTTTGGAA
1 TTTCCATGTACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGAA
* ** * * ** *
28605547 ACGACTTCATTTCTACAATTAATTTAGTGGCGCTTATGTATAAACGCCGC-AAAGTTCTTCGTTT
66 ACGACGTCATTTCTACGGTT-ATTTAGTGGCGCTAATGTATAAACGCCGCGAATG-GGTTCATTT
*
28605611 AGTCATGGAATACGTCGTCATT
129 AGTCATGGAAAACGTCGTCATT
* * * * *
28605633 TTTCCAGGTTA-GTAGTGGCGTTTTATACCAAAACGCCAG--AAATTTGTCATAACTGTTTGGGA
1 TTTCCATG-TACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGA
** * * * ** *
28605695 AACGAAATCGTTT-T-CGGGGTTATTTAGTGGCGCTTATGTATAAACGCCGCTAATTTGTTCGTT
65 AACGACGTCATTTCTAC--GGTTATTTAGTGGCGCTAATGTATAAACGCCGCGAATGGGTTCATT
* *
28605758 TAGTCATGGAAAACGTCATCGTT
128 TAGTCATGGAAAACGTCGTCATT
* *
28605781 TTTCAATGTTA-TGAGTGGCGTTTTATACCAAAACGCCAGAAA
1 TTTCCATG-TACTTAGTGGCGTTTTATACCAAAACGCCAGAAA
28605823 TAAGACTATT
Statistics
Matches: 406, Mismatches: 60, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
146 8 0.02
147 74 0.18
148 202 0.50
149 118 0.29
150 3 0.01
151 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (150 bp):
TTTCCATGTACTTAGTGGCGTTTTATACCAAAACGCCAGAAAAATTTGTCATAATTATGTGGGAA
ACGACGTCATTTCTACGGTTATTTAGTGGCGCTAATGTATAAACGCCGCGAATGGGTTCATTTAG
TCATGGAAAACGTCGTCATT
Found at i:28606361 original size:14 final size:14
Alignment explanation
Indices: 28606344--28606378 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28606334 GTAGTGTTGA
*
28606344 GTTATTCGGATTTT
1 GTTATTCGAATTTT
28606358 GTTATTCGAATTTT
1 GTTATTCGAATTTT
28606372 GTTATTC
1 GTTATTC
28606379 AGGTTTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (14 bp):
GTTATTCGAATTTT
Found at i:28607421 original size:9 final size:9
Alignment explanation
Indices: 28607405--28607470 Score: 77
Period size: 9 Copynumber: 7.8 Consensus size: 9
28607395 CATAATAAAC
28607405 AACTTACAT
1 AACTTACAT
*
28607414 AGCTTACAT
1 AACTTACAT
28607423 AA--TACAT
1 AACTTACAT
28607430 AACTTACAT
1 AACTTACAT
*
28607439 AACTTATAT
1 AACTTACAT
28607448 AA--TACAT
1 AACTTACAT
28607455 AACTTACAT
1 AACTTACAT
*
28607464 AATTTAC
1 AACTTAC
28607471 CTAATACATA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
7 13 0.27
9 35 0.73
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:28607428 original size:16 final size:16
Alignment explanation
Indices: 28607394--28607466 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
28607384 TGTTTTTCTG
* *
28607394 ACATAATAAACAACTT
1 ACATAATACATAACTT
*
28607410 ACATAGCTTACATAA--T
1 ACATA--ATACATAACTT
28607426 ACATAACTTACATAACTT
1 ACATAA--TACATAACTT
*
28607444 ATATAATACATAACTT
1 ACATAATACATAACTT
28607460 ACATAAT
1 ACATAAT
28607467 TTACCTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
16 34 0.76
18 11 0.24
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (16 bp):
ACATAATACATAACTT
Found at i:28607433 original size:25 final size:25
Alignment explanation
Indices: 28607394--28607481 Score: 122
Period size: 25 Copynumber: 3.5 Consensus size: 25
28607384 TGTTTTTCTG
* * *
28607394 ACATAATAAACAACTTACATAGCTT
1 ACATAATACATAACTTACATAACTT
28607419 ACATAATACATAACTTACATAACTT
1 ACATAATACATAACTTACATAACTT
* *
28607444 ATATAATACATAACTTACATAATTT
1 ACATAATACATAACTTACATAACTT
*
28607469 ACCTAATACATAA
1 ACATAATACATAA
28607482 ATATATATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (25 bp):
ACATAATACATAACTTACATAACTT
Found at i:28607734 original size:39 final size:39
Alignment explanation
Indices: 28607680--28607760 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
28607670 AAGCCAAGAG
28607680 AACATGATTCTTTGCCCGTGTAAGAAGTGTGTCAACATA
1 AACATGATTCTTTGCCCGTGTAAGAAGTGTGTCAACATA
*
28607719 AACATGATTCTTTGCCCGTGTAAGATGTGTGTCAACATA
1 AACATGATTCTTTGCCCGTGTAAGAAGTGTGTCAACATA
28607758 AAC
1 AAC
28607761 TGACATTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (39 bp):
AACATGATTCTTTGCCCGTGTAAGAAGTGTGTCAACATA
Found at i:28613384 original size:43 final size:43
Alignment explanation
Indices: 28613333--28613577 Score: 334
Period size: 43 Copynumber: 5.7 Consensus size: 43
28613323 TATAAAAAAA
*
28613333 CGCCGCTAAAAGTCATGTTCTATAGCGGCGTTTGTGGGAGAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
* *
28613376 CACCGCTAAAAGTCATGATCTATAACGGCGTTTGTGGGAGAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
*
28613419 CGCTGCT-AAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
* *** *
28613461 CGCCGCTAAAAGTCATGACCTATAGCGGCGTTTGTTAAAAAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
* * *
28613504 TGCCGCTAAAAGTCATGACCTATAGCGGCATTTGTGGGAGAAG
1 CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
*
28613547 CGCCGCT-AAAGATCATGA-CATTTAGCGGCGT
1 CGCCGCTAAAAG-TCATGATC-TATAGCGGCGT
28613578 GTATTTCTAA
Statistics
Matches: 178, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 45 0.25
43 133 0.75
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAG
Found at i:28613460 original size:85 final size:86
Alignment explanation
Indices: 28613317--28613565 Score: 342
Period size: 85 Copynumber: 2.9 Consensus size: 86
28613307 TAAAATTAGT
* * * *
28613317 GGCGTTTAT-AAAAAAACGCCGCTAAAAGTCATGTTCTATAGCGGCGTTTGTGGGAGAAGCACCG
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
*
28613381 CTAAAAGTCATGATCTATAAC
66 CTAAAAGTCATGACCTATAAC
** * *
28613402 GGCGTTTGTGGGAGAAGCGCTGCT-AAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
*
28613466 CTAAAAGTCATGACCTATAGC
66 CTAAAAGTCATGACCTATAAC
* * * *
28613487 GGCGTTTGTTAAAAAAGTGCCGCTAAAAGTCATGACCTATAGCGGCATTTGTGGGAGAAGCGCCG
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
28613552 CT-AAAGATCATGAC
66 CTAAAAG-TCATGAC
28613566 ATTTAGCGGC
Statistics
Matches: 143, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
85 87 0.61
86 56 0.39
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (86 bp):
GGCGTTTGTGAAAAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCG
CTAAAAGTCATGACCTATAAC
Found at i:28622146 original size:25 final size:25
Alignment explanation
Indices: 28622118--28622239 Score: 79
Period size: 25 Copynumber: 4.9 Consensus size: 25
28622108 TCCGAGATAT
*
28622118 ATAACGGGAAGCTCATGTGAGCTAA
1 ATAACGGGAAGCTCATGCGAGCTAA
* **
28622143 ATAATGGGAAGCTCATGCGAGCTGT
1 ATAACGGGAAGCTCATGCGAGCTAA
* ** ** *
28622168 ATATCGAAAAGCTCATAAGAGTTGAA
1 ATAACGGGAAGCTCATGCGAGCT-AA
* *
28622194 ATCAA---AAAGTTCATGCGAGCTAA
1 AT-AACGGGAAGCTCATGCGAGCTAA
* *
28622217 ATATCGGGAAGCTCATGAGAGCT
1 ATAACGGGAAGCTCATGCGAGCT
28622240 GTGGTGTGTC
Statistics
Matches: 70, Mismatches: 22, Indels: 10
0.69 0.22 0.10
Matches are distributed among these distances:
22 1 0.01
23 4 0.06
24 12 0.17
25 50 0.71
26 2 0.03
27 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (25 bp):
ATAACGGGAAGCTCATGCGAGCTAA
Found at i:28627272 original size:43 final size:43
Alignment explanation
Indices: 28627205--28627587 Score: 523
Period size: 43 Copynumber: 8.9 Consensus size: 43
28627195 TTTTAGAAAT
* * * * *
28627205 AAACACCGCTATAGGCCATAACCTTTAGCGACACTTTACCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
28627248 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCATTACCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
28627291 AAACGCTGCTATAGGCCATGACCTTTAGCGGCGCCTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
28627334 AAACGCCGCTATAGGCCATGACCTTTAGCGGTGCTTTTCTCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
28627377 AAACCCCGCTATAGGCCACGACCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
28627420 AAACGCCGCTATAGGCCACGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
*
28627463 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* * *** *
28627506 AAACGCCGCTATAGGCCATGACTTTTAGCGACGCTTTTTTAAA
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
28627549 AAACGCCGCTAAAGACAATGACTTTTAGCGGCGCTTTTC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTC
28627588 TAAAAACGCC
Statistics
Matches: 306, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 306 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:28630486 original size:16 final size:16
Alignment explanation
Indices: 28630449--28630488 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28630439 ATTTACCCTA
* *
28630449 GCGACGGCAGAGGAGT
1 GCGACGGTAGAGGACT
28630465 GCGACGGTAGAGGACT
1 GCGACGGTAGAGGACT
*
28630481 GTGACGGT
1 GCGACGGT
28630489 CGACGAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.47, T:0.12
Consensus pattern (16 bp):
GCGACGGTAGAGGACT
Found at i:28635685 original size:21 final size:22
Alignment explanation
Indices: 28635641--28635694 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
28635631 ACAAAAGTTA
* *
28635641 AATAACAATAAACATATGATTT
1 AATAAAAATAAACATATAATTT
*
28635663 AATAAAAATAAA-ATCTAATTT
1 AATAAAAATAAACATATAATTT
*
28635684 AATACAAATAA
1 AATAAAAATAA
28635695 TTATTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAAAAATAAACATATAATTT
Found at i:28644136 original size:90 final size:89
Alignment explanation
Indices: 28643943--28644151 Score: 249
Period size: 90 Copynumber: 2.3 Consensus size: 89
28643933 ACTACTATTC
** * * *
28643943 AAAATGTTTGTATTATTTTTGTATCCGTAAATCAAATTTAGTTTGTATTATTTGGTGGTCGAATT
1 AAAATGTTTGTATTA-TTTTGTATATGTAAATAAAAATTAGTCTGTATTATTTGGTGGTCGAATT
* *
28644008 TTATATTTTTGTATATCAAGTTTCT
65 ATATATTTTCGTATATCAAGTTTCT
* * *
28644033 AAAATATTTGTATTAATTTTGTATATGTAAATAAAAATTAGTCTGTGTTATTTGTTGGTCGAATT
1 AAAATGTTTGTATT-ATTTTGTATATGTAAATAAAAATTAGTCTGTATTATTTGGTGGTCGAATT
* *
28644098 ATATATTTTCGTATATTAATTTTCT
65 ATATATTTTCGTATATCAAGTTTCT
** *
28644123 AGGATGTTCGTATT-TTCTTGTATATGTAA
1 AAAATGTTTGTATTATT-TTGTATATGTAA
28644152 TTTTTGTTGG
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
88 2 0.02
89 12 0.12
90 86 0.85
91 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (89 bp):
AAAATGTTTGTATTATTTTGTATATGTAAATAAAAATTAGTCTGTATTATTTGGTGGTCGAATTA
TATATTTTCGTATATCAAGTTTCT
Found at i:28644612 original size:42 final size:42
Alignment explanation
Indices: 28644556--28644642 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
28644546 GTGTGAGAAC
28644556 AATCCGGAGAGTGCTGAGTGTTGAAGCTCAAGGTCGTCGCCA
1 AATCCGGAGAGTGCTGAGTGTTGAAGCTCAAGGTCGTCGCCA
* *
28644598 AATCCGGAGTGTGCTGAGTGTTGAGGCTCAAGGTCGTCGCCA
1 AATCCGGAGAGTGCTGAGTGTTGAAGCTCAAGGTCGTCGCCA
28644640 AAT
1 AAT
28644643 ATGTCTTCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (42 bp):
AATCCGGAGAGTGCTGAGTGTTGAAGCTCAAGGTCGTCGCCA
Found at i:28645841 original size:15 final size:15
Alignment explanation
Indices: 28645830--28645861 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28645820 ATCTATACTT
*
28645830 TAATTGGTTATAATC
1 TAATTGGCTATAATC
28645845 TAATTGGCTATAATC
1 TAATTGGCTATAATC
28645860 TA
1 TA
28645862 TTCTATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (15 bp):
TAATTGGCTATAATC
Found at i:28645983 original size:19 final size:19
Alignment explanation
Indices: 28645940--28645977 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28645930 AATTCAATTA
*
28645940 AATT-TTAATTTAAACTTT
1 AATTATTAAGTTAAACTTT
28645958 AATTATTAAGTTAAACTTT
1 AATTATTAAGTTAAACTTT
28645977 A
1 A
28645978 TGTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (19 bp):
AATTATTAAGTTAAACTTT
Found at i:28646135 original size:173 final size:174
Alignment explanation
Indices: 28645845--28646458 Score: 820
Period size: 173 Copynumber: 3.5 Consensus size: 174
28645835 GGTTATAATC
* * * *
28645845 TAATTGGCTATAATCTATTCTATTGAAATGTATTAAATTATTTTTTATTTAATCTTGAAATTGTT
1 TAATTGGTTATAATCTATTCAATTGAAATGTATTAAATTATTTTTTATTTAATCTTTAAATTGAT
*
28645910 TTTTTAAATTAAAATTAAAAAATTCAATTAAATTTTAATTTAAACTTTAATTATTAAGTTAAACT
66 TTTTTAAATTAAAATTAAGAAATTCAATTAAATTTTAATTTAAACTTTAATTATTAAGTTAAACT
*
28645975 TTATGTATTTAATTTTTATTTTTTAACTGAAATTATCTATACTT
131 TTATGTATTTAATTTTTATTTTTTAATTGAAATTATCTATACTT
*
28646019 TAATTGGTTATAATCTATTCAATTGAAATGTATTAAATTA-TTTTTATTTAATCTTTAAATGGAT
1 TAATTGGTTATAATCTATTCAATTGAAATGTATTAAATTATTTTTTATTTAATCTTTAAATTGAT
*
28646083 TTTTTAAATTAAAATTAAGAAATTAAATTAAATTTTAATTTAAACTTTAATTATTAAGTTAAACT
66 TTTTTAAATTAAAATTAAGAAATTCAATTAAATTTTAATTTAAACTTTAATTATTAAGTTAAACT
28646148 TTATGTATTTAATTTTTA-TTTTTAATTGAAATTATCTATACTT
131 TTATGTATTTAATTTTTATTTTTTAATTGAAATTATCTATACTT
* *
28646191 TAATTGG------T-TATTCAATTGAAACGTATTAAATTATTTTTTATTTAACCTTTAAATTGAT
1 TAATTGGTTATAATCTATTCAATTGAAATGTATTAAATTATTTTTTATTTAATCTTTAAATTGAT
* * * * *
28646249 TTTGT-AATTAAAATTAAGGAATCCAATTAATTTTTAATTTAAACTTTAATTATCAAGTTAAACT
66 TTTTTAAATTAAAATTAAGAAATTCAATTAAATTTTAATTTAAACTTTAATTATTAAGTTAAACT
* *
28646313 TAATGTATTTAATATTTTATGTTTTAATTGAAATTATCTATACTT
131 TTATGTATTTAAT-TTTTATTTTTTAATTGAAATTATCTATACTT
*
28646358 TAATTGGTTTATTAGTTGGTTTTAATCT-TTCAATTGAAATGTTTTAAATTATTATTATTTATTT
1 TAATTGG----TTA--------TAATCTATTCAATTGAAATGTATTAAATTA-T-TT-TTTATTT
* *
28646422 AATCTTTAAATTGATTTTGT-AATTGAAATTAAGAAAT
51 AATCTTTAAATTGATTTTTTAAATTAAAATTAAGAAAT
28646459 CATGGGAAAT
Statistics
Matches: 391, Mismatches: 24, Indels: 36
0.87 0.05 0.08
Matches are distributed among these distances:
165 90 0.23
166 32 0.08
167 31 0.08
172 31 0.08
173 102 0.26
174 38 0.10
185 22 0.06
186 2 0.01
187 2 0.01
188 41 0.10
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (174 bp):
TAATTGGTTATAATCTATTCAATTGAAATGTATTAAATTATTTTTTATTTAATCTTTAAATTGAT
TTTTTAAATTAAAATTAAGAAATTCAATTAAATTTTAATTTAAACTTTAATTATTAAGTTAAACT
TTATGTATTTAATTTTTATTTTTTAATTGAAATTATCTATACTT
Found at i:28646156 original size:19 final size:19
Alignment explanation
Indices: 28646113--28646150 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28646103 AATTAAATTA
*
28646113 AATT-TTAATTTAAACTTT
1 AATTATTAAGTTAAACTTT
28646131 AATTATTAAGTTAAACTTT
1 AATTATTAAGTTAAACTTT
28646150 A
1 A
28646151 TGTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (19 bp):
AATTATTAAGTTAAACTTT
Found at i:28650344 original size:15 final size:15
Alignment explanation
Indices: 28650309--28650347 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28650299 TCACTATCGA
* *
28650309 ACCCTTTATTATCGG
1 ACCCTTCATTATCAG
*
28650324 AACCTTCATTATCAG
1 ACCCTTCATTATCAG
28650339 ACCCTTCAT
1 ACCCTTCAT
28650348 CACCATCTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.08, T:0.36
Consensus pattern (15 bp):
ACCCTTCATTATCAG
Found at i:28651197 original size:108 final size:110
Alignment explanation
Indices: 28651083--28651279 Score: 249
Period size: 108 Copynumber: 1.8 Consensus size: 110
28651073 AGTTGATGTC
* * * *
28651083 GGCCATCTAGCT-CCCCCAATCCAAAAT-TTTTTTATCTAATAAAGTGAGTGTCGACCATTACTG
1 GGCCATCTAG-TACCCCCAA-CCAAAATATTATTTATCTAATAAAGCGAGTGCCGACCATCACTG
*
28651146 TGCTAGCA-C-AAAAAAATTATTTTTTTAATCTGAAAAGCTGATGCT
64 TGCCAGCACCTAAAAAAATTATTTTTTTAATCTGAAAAGCTGATGCT
* * * * * *
28651191 GGCCATCTAGTACTCCCAACCCAAATATTATTTATCTGATAAAGCGGGTGCCGGCCATCAGTGTG
1 GGCCATCTAGTACCCCCAACCAAAATATTATTTATCTAATAAAGCGAGTGCCGACCATCACTGTG
28651256 CCAGCACCTAAAAAAATTATTTTT
66 CCAGCACCTAAAAAAATTATTTTT
28651280 AAAAAATTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
107 7 0.09
108 51 0.69
109 1 0.01
110 15 0.20
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (110 bp):
GGCCATCTAGTACCCCCAACCAAAATATTATTTATCTAATAAAGCGAGTGCCGACCATCACTGTG
CCAGCACCTAAAAAAATTATTTTTTTAATCTGAAAAGCTGATGCT
Found at i:28655249 original size:29 final size:30
Alignment explanation
Indices: 28655196--28655252 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
28655186 GAATTGAATT
*
28655196 AAATCAAAATTTCATATATAAAATTACATA
1 AAATCAAAATTCCATATATAAAATTACATA
* *
28655226 AAATCAAAA-TCCATGTATACAATTACA
1 AAATCAAAATTCCATATATAAAATTACA
28655253 CATTAGACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (30 bp):
AAATCAAAATTCCATATATAAAATTACATA
Found at i:28668162 original size:45 final size:45
Alignment explanation
Indices: 28668066--28668172 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
28668056 TTGTAACAAG
* *
28668066 CTTTTTGCTGCTGTTTTTGTAGAGTAAATGCGGCATATGTGTGCA
1 CTTTTTGTTGCTGTTTTTGTAGAGTAAATGCGGCATATGTGCGCA
* *
28668111 CTTTTTGTTGCTGTTTTTGTCGAGTGAATGTC-GCATATGTGCGCA
1 CTTTTTGTTGCTGTTTTTGTAGAGTAAATG-CGGCATATGTGCGCA
*
28668156 -TATTTTGTTGTTGTTTT
1 CT-TTTTGTTGCTGTTTT
28668173 CGGATGAGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 1 0.02
45 53 0.96
46 1 0.02
ACGTcount: A:0.14, C:0.12, G:0.25, T:0.49
Consensus pattern (45 bp):
CTTTTTGTTGCTGTTTTTGTAGAGTAAATGCGGCATATGTGCGCA
Found at i:28675229 original size:5 final size:5
Alignment explanation
Indices: 28675219--28675247 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28675209 TTTAATAACA
28675219 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
28675248 AAATGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:28676032 original size:21 final size:21
Alignment explanation
Indices: 28676008--28676055 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
28675998 TGTGTCCCCG
*
28676008 TCACACAGCCGTGTGCCTCTT
1 TCACACAGCCGTGTACCTCTT
* *
28676029 TCACACGGGCGTGTACCTCTT
1 TCACACAGCCGTGTACCTCTT
*
28676050 CCACAC
1 TCACAC
28676056 GGCTATGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.40, G:0.19, T:0.25
Consensus pattern (21 bp):
TCACACAGCCGTGTACCTCTT
Found at i:28676056 original size:21 final size:21
Alignment explanation
Indices: 28676017--28676057 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28676007 GTCACACAGC
* *
28676017 CGTGTGCCTCTTTCACACGGG
1 CGTGTACCTCTTCCACACGGG
28676038 CGTGTACCTCTTCCACACGG
1 CGTGTACCTCTTCCACACGG
28676058 CTATGTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.37, G:0.24, T:0.27
Consensus pattern (21 bp):
CGTGTACCTCTTCCACACGGG
Found at i:28678896 original size:5 final size:5
Alignment explanation
Indices: 28678886--28678913 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28678876 TTTAATGAAA
28678886 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
28678914 GAAATGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:28679024 original size:29 final size:30
Alignment explanation
Indices: 28678968--28679024 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
28678958 CTCACATTCC
* *
28678968 TTTTTTCTCTCCCTCTTTTCCATGTCAATT
1 TTTTTTCTCTCCCTCTTTCCCATATCAATT
28678998 TTTTTTCTCT-CCT-TTTCCCGATATCAA
1 TTTTTTCTCTCCCTCTTTCCC-ATATCAA
28679025 GCTTTTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 9 0.38
30 10 0.42
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (30 bp):
TTTTTTCTCTCCCTCTTTCCCATATCAATT
Found at i:28682350 original size:5 final size:5
Alignment explanation
Indices: 28682340--28682367 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28682330 TTTAATGAAA
28682340 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
28682368 GAAATGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:28682477 original size:28 final size:29
Alignment explanation
Indices: 28682422--28682477 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
28682412 CTCACATTCC
* *
28682422 TTTTTTCTCTCCCTCTTTTCCATGTCAAT
1 TTTTTTCTCTCCCTCTTTCCCATATCAAT
28682451 TTTTTTCTCT-CCT-TTTCCCGATATCAA
1 TTTTTTCTCTCCCTCTTTCCC-ATATCAA
28682478 GCTTTTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 9 0.38
29 10 0.42
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTTTTCTCTCCCTCTTTCCCATATCAAT
Found at i:28682483 original size:29 final size:29
Alignment explanation
Indices: 28682421--28682488 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
28682411 TCTCACATTC
* *
28682421 CTTTTTTCTCTCCCTCTTTTCCATGTCAA
1 CTTTTTTCTCTCCCTCTTTCCCATATCAA
*
28682450 TTTTTTTCTCT-CCT-TTTCCCGATATCAA
1 CTTTTTTCTCTCCCTCTTTCCC-ATATCAA
28682478 GCTTTTGTTCT
1 -CTTTT-TTCT
28682489 AGTCACTTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 5 0.16
28 9 0.28
29 14 0.44
30 4 0.12
ACGTcount: A:0.10, C:0.29, G:0.06, T:0.54
Consensus pattern (29 bp):
CTTTTTTCTCTCCCTCTTTCCCATATCAA
Found at i:28684559 original size:18 final size:18
Alignment explanation
Indices: 28684536--28684572 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28684526 ACATACTAGA
28684536 GTGTTTTGAAAATGATTT
1 GTGTTTTGAAAATGATTT
*
28684554 GTGTTTTGAAAATGTTTT
1 GTGTTTTGAAAATGATTT
28684572 G
1 G
28684573 CGAAAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (18 bp):
GTGTTTTGAAAATGATTT
Found at i:28684973 original size:39 final size:39
Alignment explanation
Indices: 28684918--28685004 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
28684908 TCAAAATCTA
* *
28684918 AAATAATTTGAAAATGGGTGAG-GATTGTTGGAGCATTTTC
1 AAAT-ATTTGAAAATGGG-GAGAGATTGTTGGAACATTTAC
*
28684958 AAATATTTGAAAATGGGGGGAGATTGTTGGAACATTTAC
1 AAATATTTGAAAATGGGGAGAGATTGTTGGAACATTTAC
28684997 AAATATTT
1 AAATATTT
28685005 ATAGTGTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 2 0.05
39 37 0.86
40 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (39 bp):
AAATATTTGAAAATGGGGAGAGATTGTTGGAACATTTAC
Found at i:28688618 original size:68 final size:68
Alignment explanation
Indices: 28688538--28688686 Score: 181
Period size: 68 Copynumber: 2.2 Consensus size: 68
28688528 TAAGGTTTTG
* * * * * **
28688538 CAGACCGTGTGAGAATAAGCAGCTCGTGTGGCTGGACCATGTGAGGCACACGGCCATGTGGAAAG
1 CAGACCGTGTGAGAATAAACAACCCATGTGGCTAGACCATGTGAGGCACACGGCCACATGGAAAG
28688603 GTT
66 GTT
* * * * *
28688606 CAGACCGTGTGAGAATAAACAACCCATGTGGCTAGATCGTGTGAGGCACATGGCCGCATGGAAAT
1 CAGACCGTGTGAGAATAAACAACCCATGTGGCTAGACCATGTGAGGCACACGGCCACATGGAAAG
28688671 GTT
66 GTT
*
28688674 CAAACCGTGTGAG
1 CAGACCGTGTGAG
28688687 TGGCCCATGT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.28, C:0.21, G:0.32, T:0.19
Consensus pattern (68 bp):
CAGACCGTGTGAGAATAAACAACCCATGTGGCTAGACCATGTGAGGCACACGGCCACATGGAAAG
GTT
Found at i:28695300 original size:14 final size:15
Alignment explanation
Indices: 28695276--28695304 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28695266 TTATGCATGT
28695276 TATGATTTGATATGA
1 TATGATTTGATATGA
28695291 TATG-TTTGATATGA
1 TATGATTTGATATGA
28695305 CCTAGCATGA
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:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
TATGATTTGATATGA
Found at i:28696375 original size:21 final size:21
Alignment explanation
Indices: 28696349--28696391 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28696339 TTCTTGATAT
28696349 GTTAGTGAAGGGAAATAAGAG
1 GTTAGTGAAGGGAAATAAGAG
28696370 GTTAGTGAAGGGAAATAAGAG
1 GTTAGTGAAGGGAAATAAGAG
28696391 G
1 G
28696392 AAGTGATAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.19
Consensus pattern (21 bp):
GTTAGTGAAGGGAAATAAGAG
Found at i:28696403 original size:20 final size:21
Alignment explanation
Indices: 28696352--28696405 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
28696342 TTGATATGTT
*
28696352 AGTGAAGGGAAATAAGAGGTT
1 AGTGAAGGGAAATAAGAGGTA
28696373 AGTGAAGGGAAATAAGAGG-A
1 AGTGAAGGGAAATAAGAGGTA
28696393 AGTGATA-GGAAAT
1 AGTGA-AGGGAAAT
28696406 GTTGTAGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (21 bp):
AGTGAAGGGAAATAAGAGGTA
Found at i:28699601 original size:11 final size:11
Alignment explanation
Indices: 28699585--28699613 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
28699575 TACTGCATAC
28699585 AATAATTACTT
1 AATAATTACTT
28699596 AATAATTACTT
1 AATAATTACTT
28699607 AATAATT
1 AATAATT
28699614 TCGAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (11 bp):
AATAATTACTT
Found at i:28706432 original size:30 final size:30
Alignment explanation
Indices: 28706387--28706444 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28706377 CACGGGCTGG
* *
28706387 CACATGGGCGTGTGGCTAGCCCGTGTGGCT
1 CACACGGGCGTGTGGCCAGCCCGTGTGGCT
*
28706417 CACACGGGTGTGTGGCCAGCCCGTGTGG
1 CACACGGGCGTGTGGCCAGCCCGTGTGG
28706445 AAATTTTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.10, C:0.28, G:0.41, T:0.21
Consensus pattern (30 bp):
CACACGGGCGTGTGGCCAGCCCGTGTGGCT
Found at i:28708378 original size:19 final size:19
Alignment explanation
Indices: 28708349--28708388 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
28708339 ATCAAAATTT
28708349 TTAATATATTAATAGTAAAA
1 TTAATATATTAA-AGTAAAA
*
28708369 TTAA-ATATTAAATTAAAA
1 TTAATATATTAAAGTAAAA
28708387 TT
1 TT
28708389 TATTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAATATATTAAAGTAAAA
Found at i:28711701 original size:13 final size:14
Alignment explanation
Indices: 28711670--28711703 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
28711660 TTGTTTTACT
28711670 AAAAATAATTTTCG
1 AAAAATAATTTTCG
28711684 AAAAATAATTTTCG
1 AAAAATAATTTTCG
28711698 AAAAAT
1 AAAAAT
28711704 GACTTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (14 bp):
AAAAATAATTTTCG
Found at i:28716968 original size:42 final size:42
Alignment explanation
Indices: 28716898--28716985 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
28716888 GCACAGAAAG
* *
28716898 AGGACATGAGCACATGCCCAAGTCGTGTGTGTCACACGGGTA
1 AGGACATGAGCACATGCCCAAGTCGTGTGAGTCACACGGGAA
* * *
28716940 AGGACATGAGCATATGTCC-AGGCTGTGTGAGTCACACGGGAA
1 AGGACATGAGCACATGCCCAAGTC-GTGTGAGTCACACGGGAA
28716982 AGGA
1 AGGA
28716986 TATGGCCGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 3 0.08
42 37 0.93
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.18
Consensus pattern (42 bp):
AGGACATGAGCACATGCCCAAGTCGTGTGAGTCACACGGGAA
Found at i:28723120 original size:35 final size:35
Alignment explanation
Indices: 28723036--28723110 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 35
28723026 ATTATGGCTG
28723036 AATCTAGGAGTGTTACGAAAAAGGTTTTTGAAATC
1 AATCTAGGAGTGTTACGAAAAAGGTTTTTGAAATC
28723071 AATCTAGGAGTGTTACGAAAAATGG-TTTTGAAATC
1 AATCTAGGAGTGTTACGAAAAA-GGTTTTTGAAATC
28723106 AATCT
1 AATCT
28723111 TATTATGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 37 0.95
36 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.32
Consensus pattern (35 bp):
AATCTAGGAGTGTTACGAAAAAGGTTTTTGAAATC
Found at i:28727668 original size:20 final size:20
Alignment explanation
Indices: 28727643--28727705 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
28727633 AGTCCAAACA
*
28727643 GGGCACAGATGTGCATCCAG
1 GGGCACAGATGTGCATACAG
* * * * * *
28727663 GGGCACCGAAGAGCAAAAAA
1 GGGCACAGATGTGCATACAG
*
28727683 GGGCACAGATGTGCATTCAG
1 GGGCACAGATGTGCATACAG
28727703 GGG
1 GGG
28727706 TACCGAAGTA
Statistics
Matches: 29, Mismatches: 14, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.37, T:0.11
Consensus pattern (20 bp):
GGGCACAGATGTGCATACAG
Found at i:28727735 original size:40 final size:39
Alignment explanation
Indices: 28727620--28727862 Score: 220
Period size: 40 Copynumber: 6.1 Consensus size: 39
28727610 GAATGTGTGA
* * *
28727620 TTAGGGGTACTGAAGTCCAAACAGGGCACAGATGTGCAT
1 TTAGGGGTACCGAAGTACAAACAGGGCACATATGTGCAT
** * * *
28727659 CCAGGGGCACCGAAG-AGCAAAAAAGGGCACAGATGTGCAT
1 TTAGGGGTACCGAAGTA-C-AAACAGGGCACATATGTGCAT
* * *
28727699 TCAGGGGTACCGAAGTACAAATAGGGACATATATGTGCAT
1 TTAGGGGTACCGAAGTACAAACAGGG-CACATATGTGCAT
* * *
28727739 TTTGGGGTACCAAACTACAAACAGGGGCA-AGTATGTGCAT
1 TTAGGGGTACCGAAGTACAAACA-GGGCACA-TATGTGCAT
* * *
28727779 TTAAGGGTACCAAAGTACAAACAGGGGCACGTATGTGCAT
1 TTAGGGGTACCGAAGTACAAACA-GGGCACATATGTGCAT
* * * *
28727819 TTAAGGGTACCGAAATACAAACAAAGGCACGTATGTGCAT
1 TTAGGGGTACCGAAGTACAAAC-AGGGCACATATGTGCAT
28727859 TTAG
1 TTAG
28727863 TAACATTTTC
Statistics
Matches: 172, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
39 20 0.12
40 147 0.85
41 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (39 bp):
TTAGGGGTACCGAAGTACAAACAGGGCACATATGTGCAT
Found at i:28728372 original size:20 final size:19
Alignment explanation
Indices: 28728336--28728391 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
28728326 TAGCAAAAAA
*
28728336 CAAATAGAACAGGACAGAG
1 CAAATAGAACAGAACAGAG
* *
28728355 CAAAGTAGAACATAACAGAA
1 CAAA-TAGAACAGAACAGAG
*
28728375 CAGAATAGAGCAGAACA
1 CA-AATAGAACAGAACA
28728392 AAACTAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.13
20 24 0.80
21 2 0.07
ACGTcount: A:0.55, C:0.16, G:0.21, T:0.07
Consensus pattern (19 bp):
CAAATAGAACAGAACAGAG
Found at i:28735306 original size:43 final size:43
Alignment explanation
Indices: 28735245--28735397 Score: 179
Period size: 43 Copynumber: 3.6 Consensus size: 43
28735235 CGCTATAAAT
*
28735245 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACA
1 AACGCCGCTAAAGATCATGACCTTTAGCGACGCTTCTACCACA
*
28735288 AACGCCGCTAAAGATCATGACCTTTAGCAACGCTTCTACCACA
1 AACGCCGCTAAAGATCATGACCTTTAGCGACGCTTCTACCACA
* * ***
28735331 AACGCCACTATAAAGA--ATGACTTTTAGCGACGCTT-TTTGACA
1 AACGCCGC--TAAAGATCATGACCTTTAGCGACGCTTCTACCACA
* *
28735373 AACGCCGCTAAA-AACATGACTTTTA
1 AACGCCGCTAAAGATCATGACCTTTA
28735398 AAAAAATATT
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
39 1 0.01
40 4 0.04
41 10 0.10
42 11 0.11
43 65 0.67
45 6 0.06
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
AACGCCGCTAAAGATCATGACCTTTAGCGACGCTTCTACCACA
Found at i:28739283 original size:2 final size:2
Alignment explanation
Indices: 28739278--28739310 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28739268 TACACACAAC
28739278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28739311 CACACCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28740256 original size:17 final size:16
Alignment explanation
Indices: 28740212--28740258 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
28740202 TTTTGTCTGC
*
28740212 TAAAATTATTAATTAAG
1 TAAAATTATT-TTTAAG
28740229 TAAAATTATTTTTAAAG
1 TAAAATTATTTTT-AAG
28740246 TAAAATTATTTTT
1 TAAAATTATTTTT
28740259 TGTGGCGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 2 0.07
17 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (16 bp):
TAAAATTATTTTTAAG
Found at i:28740769 original size:41 final size:41
Alignment explanation
Indices: 28740712--28740798 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
28740702 TTATATGGAT
*
28740712 AAAATTTTTATATGGATAAGCCCGTATAACAAAGTCGGCCC
1 AAAATTTTTATATGGATAAGCCCGTATAAAAAAGTCGGCCC
*
28740753 AAAATTTTTATATGGATATGCCCGTATAAAAAAGTCGGCCC
1 AAAATTTTTATATGGATAAGCCCGTATAAAAAAGTCGGCCC
28740794 AAAAT
1 AAAAT
28740799 CGTAGAACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (41 bp):
AAAATTTTTATATGGATAAGCCCGTATAAAAAAGTCGGCCC
Found at i:28741289 original size:41 final size:41
Alignment explanation
Indices: 28741183--28741376 Score: 184
Period size: 41 Copynumber: 5.0 Consensus size: 41
28741173 TAAATTATTT
* * * *
28741183 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCTGC
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCTAAAACGCCGC
*
28741224 TAAAG-CC---GCATTAGCGGCGCTTTCTCTAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCTAAAACGCCGC
* *
28741261 TAAAGCCCTGACCATTAGCAGCGCTTTCTCAAAAACG-C-C
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCTAAAACGCCGC
*
28741300 T-------TGAGCATTAGCAGCGCTTTCT-TAAAAACGCCGT
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCT-AAAACGCCGC
*
28741334 TAAAGCCCTGAGCATTAGCAGCGCTTTCT-TAAAAACGTCGC
1 TAAAGCCCTGAGCATTAGCAGCGCTTTCTCT-AAAACGCCGC
28741375 TA
1 TA
28741377 GTTGGGCTTA
Statistics
Matches: 128, Mismatches: 11, Indels: 28
0.77 0.07 0.17
Matches are distributed among these distances:
32 26 0.20
33 1 0.01
34 1 0.01
37 33 0.26
38 2 0.02
39 2 0.02
40 3 0.02
41 60 0.47
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCAGCGCTTTCTCTAAAACGCCGC
Found at i:28741338 original size:73 final size:76
Alignment explanation
Indices: 28741182--28741376 Score: 254
Period size: 73 Copynumber: 2.6 Consensus size: 76
28741172 TTAAATTATT
* * * *
28741182 TTAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCTGCTAAAGCCGCATTAGCGGCGCTTT
1 TTAAAGCCCTGAGCATTAGCAGCGCTTTCTCAAAAACGC-GCT-AAGCAGCATTAGCAGCGCTTT
28741247 CTCTAAAACGCCG
64 CTCTAAAACGCCG
* * *
28741260 CTAAAGCCCTGACCATTAGCAGCGCTTTCTCAAAAACGC-CT-TG-AGCATTAGCAGCGCTTTCT
1 TTAAAGCCCTGAGCATTAGCAGCGCTTTCTCAAAAACGCGCTAAGCAGCATTAGCAGCGCTTTCT
28741322 -TAAAAACGCCG
66 CT-AAAACGCCG
*
28741333 TTAAAGCCCTGAGCATTAGCAGCGCTTTCTTAAAAACGTCGCTA
1 TTAAAGCCCTGAGCATTAGCAGCGCTTTCTCAAAAACG-CGCTA
28741377 GTTGGGCTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
72 1 0.01
73 61 0.59
74 2 0.02
75 2 0.02
76 2 0.02
78 35 0.34
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (76 bp):
TTAAAGCCCTGAGCATTAGCAGCGCTTTCTCAAAAACGCGCTAAGCAGCATTAGCAGCGCTTTCT
CTAAAACGCCG
Found at i:28741891 original size:3 final size:3
Alignment explanation
Indices: 28741883--28741924 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
28741873 ATATGCATAT
28741883 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28741925 TCAAGCCAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28742122 original size:2 final size:2
Alignment explanation
Indices: 28742115--28742143 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28742105 ATTGTAGCTC
28742115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28742144 AACTATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28746412 original size:31 final size:30
Alignment explanation
Indices: 28746377--28746436 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28746367 GGAGGTGGGA
*
28746377 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
28746408 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
28746437 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:28746660 original size:9 final size:9
Alignment explanation
Indices: 28746646--28746682 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28746636 TATAGTTTGA
28746646 TATTCGAAT
1 TATTCGAAT
28746655 TATTCGAAT
1 TATTCGAAT
*
28746664 TATTCGAGT
1 TATTCGAAT
28746673 TATTCGAAT
1 TATTCGAAT
28746682 T
1 T
28746683 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28746759 original size:14 final size:14
Alignment explanation
Indices: 28746740--28746775 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
28746730 TTGATTTGAA
28746740 TAACTCGATCCGTT
1 TAACTCGATCCGTT
*
28746754 TAACTCGATTCGTT
1 TAACTCGATCCGTT
28746768 TAACTCGA
1 TAACTCGA
28746776 AATTCGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (14 bp):
TAACTCGATCCGTT
Found at i:28749064 original size:22 final size:22
Alignment explanation
Indices: 28749036--28749104 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
28749026 AATAGAAATG
28749036 ATGGCTAACGTACTAAGCTCTC
1 ATGGCTAACGTACTAAGCTCTC
28749058 ATGGCTAACGTACTAAGCTCTC
1 ATGGCTAACGTACTAAGCTCTC
** *
28749080 ATGTTTCACGTACTAAGCTCTC
1 ATGGCTAACGTACTAAGCTCTC
28749102 ATG
1 ATG
28749105 TTTGAACAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
ATGGCTAACGTACTAAGCTCTC
Found at i:28752601 original size:24 final size:26
Alignment explanation
Indices: 28752558--28752607 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
28752548 AAAAAAAATT
*
28752558 AATAGTATTTAAAAAATTTAATTTTA
1 AATAGTATTTAAAAAATTTAAATTTA
*
28752584 AATAG-ATTT-AAAATTTTAAATTTA
1 AATAGTATTTAAAAAATTTAAATTTA
28752608 GAAACAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 4 0.18
26 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AATAGTATTTAAAAAATTTAAATTTA
Found at i:28752816 original size:15 final size:15
Alignment explanation
Indices: 28752796--28752825 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28752786 ATGTTATGGC
28752796 CAGATCATGAAGTGT
1 CAGATCATGAAGTGT
28752811 CAGATCATGAAGTGT
1 CAGATCATGAAGTGT
28752826 TATGTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
CAGATCATGAAGTGT
Found at i:28756567 original size:4 final size:4
Alignment explanation
Indices: 28756515--28756548 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
28756505 ATAATATATC
28756515 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
28756549 AATATAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:28756792 original size:3 final size:3
Alignment explanation
Indices: 28756784--28756877 Score: 161
Period size: 3 Copynumber: 31.3 Consensus size: 3
28756774 AAATCGATAT
* *
28756784 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
28756832 ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28756878 AGTAACTAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28758246 original size:22 final size:22
Alignment explanation
Indices: 28758199--28758240 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28758189 AGGATAAGAA
*
28758199 TCTGCATCTGTACCTGATATGT
1 TCTGCATCTATACCTGATATGT
*
28758221 TCTGCATCTATATCTGATAT
1 TCTGCATCTATACCTGATAT
28758241 TCTCTGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (22 bp):
TCTGCATCTATACCTGATATGT
Found at i:28759781 original size:25 final size:27
Alignment explanation
Indices: 28759752--28759801 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
28759742 AAAACCAAAG
*
28759752 TTTAATTTTAATAT-AATA-TTTATAT
1 TTTAATTGTAATATGAATACTTTATAT
*
28759777 TTTAATTGTATTATGAATACTTTAT
1 TTTAATTGTAATATGAATACTTTAT
28759802 TATCTCCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 4 0.19
27 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTAATTGTAATATGAATACTTTATAT
Found at i:28760791 original size:17 final size:18
Alignment explanation
Indices: 28760761--28760795 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
28760751 TTAGATCCCA
28760761 TTTGAAGAAATTTTATTT
1 TTTGAAGAAATTTTATTT
28760779 TTTGAAG-AATTTTATTT
1 TTTGAAGAAATTTTATTT
28760796 ATTTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTGAAGAAATTTTATTT
Found at i:28762934 original size:32 final size:33
Alignment explanation
Indices: 28762898--28762967 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
28762888 TGTGCCAGGC
* *
28762898 CGTGTGGG-CTACATGGGCAAGGCCATTTTGGG-
1 CGTGTGGGCCCACATAGGCAA-GCCATTTTGGGT
28762930 CGTGTGGGCCCACATAGGCAAGCCATTTTGGGT
1 CGTGTGGGCCCACATAGGCAAGCCATTTTGGGT
28762963 CGTGT
1 CGTGT
28762968 AGACCCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.16, C:0.21, G:0.37, T:0.26
Consensus pattern (33 bp):
CGTGTGGGCCCACATAGGCAAGCCATTTTGGGT
Found at i:28764469 original size:14 final size:14
Alignment explanation
Indices: 28764450--28764477 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28764440 CTCATGGGTA
28764450 CGGCGAAATCGTAG
1 CGGCGAAATCGTAG
28764464 CGGCGAAATCGTAG
1 CGGCGAAATCGTAG
28764478 AGGGACTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.36, T:0.14
Consensus pattern (14 bp):
CGGCGAAATCGTAG
Found at i:28766593 original size:20 final size:21
Alignment explanation
Indices: 28766547--28766593 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
28766537 ATTCCAAATT
*
28766547 TTTTATATAGTATTGATTTTC
1 TTTTATATAGTATTGATTTTA
* * *
28766568 TCTTAT-TATTATTTATTTTA
1 TTTTATATAGTATTGATTTTA
28766588 TTTTAT
1 TTTTAT
28766594 GATAAGATGT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTATATAGTATTGATTTTA
Found at i:28766831 original size:2 final size:2
Alignment explanation
Indices: 28766824--28766879 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
28766814 CTTATACTTT
28766824 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28766866 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
28766880 CACACACATC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28777943 original size:255 final size:255
Alignment explanation
Indices: 28777492--28778001 Score: 826
Period size: 255 Copynumber: 2.0 Consensus size: 255
28777482 TTATCCACAG
*
28777492 GAACAAAGATGGTTATGGTCAATCTCTAGGAGAAAATGTAAAAGAACTAGCGTGTGTGTTGGCTA
1 GAACAAAGATGGTTATGGTCAATCTCTAGGAGAAAATGTAAAAGAACCAGCGTGTGTGTTGGCTA
**
28777557 AAAAGGTAAAAGACCAGCCCAAAAGTACTTTTTGGCTAAAAAAGTTAAAAAATTTTGCATTTTCA
66 AAAAGGTAAAAGACCAGCCCAAAAACACTTTTTGGCTAAAAAAGTTAAAAAATTTTGCATTTTCA
* * * *
28777622 TCTGTCCAAAAATACTTTAAATAAGTTAAAAATTTACTACCACCGAAGTTTGTTCTTTATTACTT
131 TCTGCCCAAAAACACTTTAAAAAAGTTAAAAATCTACTACCACCGAAGTTTGTTCTTTATTACTT
* *
28777687 TTCACTCAAAAGCACTTTTATATGTAAAAATACTTTCCAAACACCCAAAATAACACAGCC
196 TTCACCCAAAAGCACTTTTATATGTAAAAATACTTTCCAAACACCCAAAAGAACACAGCC
28777747 GAACAAAGATGGTTATGGTCAATCT-TCAGGAGAAAATGTAAAAGAACCAGCGTGTGTGTTGGCT
1 GAACAAAGATGGTTATGGTCAATCTCT-AGGAGAAAATGTAAAAGAACCAGCGTGTGTGTTGGCT
* * * *
28777811 AAAAAGGTAAAAGACCAGTCCAAAAACACTTTTTGGCTGAAAAAGTTAAAAATTTTTGCGTTTTC
65 AAAAAGGTAAAAGACCAGCCCAAAAACACTTTTTGGCTAAAAAAGTTAAAAAATTTTGCATTTTC
*
28777876 ATCTGCCCAAAAGCACTTTAAAAAAGTTAAAAATCTA-TCACCACCGAAGTTTGTTCTTTATTAC
130 ATCTGCCCAAAAACACTTTAAAAAAGTTAAAAATCTACT-ACCACCGAAGTTTGTTCTTTATTAC
* * * *
28777940 TTTTCACCCAAAAGCACTTTTATATGTAAAAATATTTTTCAAACGCCCAAAAGAACTCAGCC
194 TTTTCACCCAAAAGCACTTTTATATGTAAAAATACTTTCCAAACACCCAAAAGAACACAGCC
28778002 TTAGTATAAC
Statistics
Matches: 235, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
254 2 0.01
255 233 0.99
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (255 bp):
GAACAAAGATGGTTATGGTCAATCTCTAGGAGAAAATGTAAAAGAACCAGCGTGTGTGTTGGCTA
AAAAGGTAAAAGACCAGCCCAAAAACACTTTTTGGCTAAAAAAGTTAAAAAATTTTGCATTTTCA
TCTGCCCAAAAACACTTTAAAAAAGTTAAAAATCTACTACCACCGAAGTTTGTTCTTTATTACTT
TTCACCCAAAAGCACTTTTATATGTAAAAATACTTTCCAAACACCCAAAAGAACACAGCC
Found at i:28786518 original size:23 final size:23
Alignment explanation
Indices: 28786489--28786535 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
28786479 TATTTATCAG
28786489 ATTTTAATTTATA-ATAAAGTGTA
1 ATTTTAATTTATATATAAA-TGTA
28786512 ATTTTAATTTATATATAAATGTA
1 ATTTTAATTTATATATAAATGTA
28786535 A
1 A
28786536 CATTAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (23 bp):
ATTTTAATTTATATATAAATGTA
Found at i:28786541 original size:23 final size:23
Alignment explanation
Indices: 28786492--28786550 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
28786482 TTATCAGATT
**
28786492 TTAATTTATAATAAAGTGTAATT
1 TTAATTTATAATAAAGTGTAACA
28786515 TTAATTTATATATAAA-TGTAACA
1 TTAATTTATA-ATAAAGTGTAACA
28786538 TTAA-TTA-AATAAA
1 TTAATTTATAATAAA
28786551 AATTAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 5 0.15
21 1 0.03
22 3 0.09
23 19 0.58
24 5 0.15
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
TTAATTTATAATAAAGTGTAACA
Found at i:28790344 original size:21 final size:19
Alignment explanation
Indices: 28790320--28790373 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 19
28790310 TTCAACATAA
28790320 TTAAAATATATTAACTATTTC
1 TTAAAAT-TA-TAACTATTTC
28790341 TTAAAATTA-AA-TATTTC
1 TTAAAATTATAACTATTTC
28790358 TTAAAATTATAACTAT
1 TTAAAATTATAACTAT
28790374 GTTTATCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 15 0.48
18 4 0.13
19 3 0.10
20 2 0.06
21 7 0.23
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAAATTATAACTATTTC
Found at i:28791624 original size:29 final size:29
Alignment explanation
Indices: 28791592--28791659 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
28791582 TATGTGATAA
* *
28791592 AAATTATAATACTGAATAATTGAATAATT
1 AAATTGTAATACTGAATAATTGAATAATC
** * *
28791621 AAATTGTAATTTTGTATAATTGAGTAATC
1 AAATTGTAATACTGAATAATTGAATAATC
28791650 AAATTGTAAT
1 AAATTGTAAT
28791660 TTTACGCATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (29 bp):
AAATTGTAATACTGAATAATTGAATAATC
Found at i:28791660 original size:29 final size:29
Alignment explanation
Indices: 28791607--28791662 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
28791597 ATAATACTGA
*
28791607 ATAATTGAATAATTAAATTGTAATTTTGT
1 ATAATTGAATAATCAAATTGTAATTTTGT
*
28791636 ATAATTGAGTAATCAAATTGTAATTTT
1 ATAATTGAATAATCAAATTGTAATTTT
28791663 ACGCATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (29 bp):
ATAATTGAATAATCAAATTGTAATTTTGT
Found at i:28794635 original size:2 final size:2
Alignment explanation
Indices: 28794628--28794663 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28794618 AAAAATATTT
28794628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28794664 ATAATAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28813319 original size:3 final size:3
Alignment explanation
Indices: 28813311--28813371 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
28813301 TTCTGTAGTT
28813311 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28813359 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
28813372 ATTGTATGCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28815948 original size:2 final size:2
Alignment explanation
Indices: 28815941--28815977 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
28815931 TACACGTACG
*
28815941 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28815978 CATGTACATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:28821275 original size:11 final size:10
Alignment explanation
Indices: 28821254--28821279 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28821244 AGGGGACTTC
28821254 TTTTGTTTTT
1 TTTTGTTTTT
28821264 TTTTGTTTTT
1 TTTTGTTTTT
28821274 TTTTGT
1 TTTTGT
28821280 GCTGTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:28821789 original size:30 final size:30
Alignment explanation
Indices: 28821732--28821789 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
28821722 TATATGCACA
*
28821732 TACATATTCTTTTTATAATTTATATACATG
1 TACATATTCTTTTTATAATTTAAATACATG
*
28821762 TACATATTCTTTATT-TATTTTAAATACA
1 TACATATTCTTT-TTATAATTTAAATACA
28821790 CATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.53
Consensus pattern (30 bp):
TACATATTCTTTTTATAATTTAAATACATG
Found at i:28821826 original size:12 final size:12
Alignment explanation
Indices: 28821809--28821847 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28821799 TATTTCATAT
*
28821809 TATATATATGCA
1 TATATATATACA
*
28821821 TATATATATACT
1 TATATATATACA
*
28821833 TATATATTTACA
1 TATATATATACA
28821845 TAT
1 TAT
28821848 TTTAATTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (12 bp):
TATATATATACA
Found at i:28825370 original size:17 final size:18
Alignment explanation
Indices: 28825340--28825373 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28825330 CAGTGGAGGT
*
28825340 AAAAATAAATAAAAAATA
1 AAAAACAAATAAAAAATA
28825358 AAAAACAAA-AAAAAAT
1 AAAAACAAATAAAAAAT
28825374 CTACCGGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAACAAATAAAAAATA
Found at i:28825829 original size:18 final size:19
Alignment explanation
Indices: 28825806--28825853 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
28825796 CTTCATTTGA
*
28825806 AAAAAAGAAACGAA-AAAG
1 AAAAAAGAAAAGAAGAAAG
*
28825824 AAAAAAGAAAAGAAGAACG
1 AAAAAAGAAAAGAAGAAAG
28825843 AAAAAAGAAAA
1 AAAAAAGAAAA
28825854 AGGAGAGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAGAAGAAAG
Found at i:28825840 original size:26 final size:26
Alignment explanation
Indices: 28825804--28825854 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
28825794 TACTTCATTT
28825804 GAAAAAAAGAAACG-AAAAAGAAAAAA
1 GAAAAAAAG-AACGAAAAAAGAAAAAA
*
28825830 GAAAAGAAGAACGAAAAAAGAAAAA
1 GAAAAAAAGAACGAAAAAAGAAAAA
28825855 GGAGAGGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (26 bp):
GAAAAAAAGAACGAAAAAAGAAAAAA
Found at i:28826380 original size:108 final size:108
Alignment explanation
Indices: 28826191--28826386 Score: 286
Period size: 108 Copynumber: 1.8 Consensus size: 108
28826181 TTTGTATTCT
*
28826191 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAACAAATTTCCATCTT
1 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTACTCTCAACAAATTTCCATCTT
28826256 ATCCATTGTGATAATCTTTTTCATCTTATACATCTCGTATCTC
66 ATCCATTGTGATAATCTTTTTCATCTTATACATCTCGTATCTC
* * ** * * *
28826299 AGCAAAATTTGCTGTCTTGATTGATTTGTTTGTTTAGATCTTTACTCTCAACAAAATTT-TATTT
1 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTACTCTCAAC-AAATTTCCATCT
* *
28826363 TGTCCATTTTGATAATCTTTTTCA
65 TATCCATTGTGATAATCTTTTTCA
28826387 AGCATTTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 71 0.92
109 6 0.08
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (108 bp):
AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTACTCTCAACAAATTTCCATCTT
ATCCATTGTGATAATCTTTTTCATCTTATACATCTCGTATCTC
Found at i:28826938 original size:45 final size:45
Alignment explanation
Indices: 28826809--28826948 Score: 178
Period size: 45 Copynumber: 3.1 Consensus size: 45
28826799 TTCCCCAGAG
* * *
28826809 AGCAGACTAAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGA
1 AGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGA
* *
28826854 AGCAGA-TCGAAGA-AACTAG-TCTTGCCTTCCTGTACTGACAGCGG
1 AGCAGACT-GAAGATAGC-AGATCTTGCCTTCCTGTACTGACAGCGA
* *
28826898 AGCAGACTGAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGA
1 AGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGA
28826943 AGCAGA
1 AGCAGA
28826949 TCAAAGATGG
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
44 38 0.47
45 43 0.53
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (45 bp):
AGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGA
Found at i:28827252 original size:134 final size:132
Alignment explanation
Indices: 28826905--28827308 Score: 618
Period size: 134 Copynumber: 3.0 Consensus size: 132
28826895 CGGAGCAGAC
* *
28826905 TGAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGATGGCAGATTTTACC
1 TGAAGATTGCAGATCTTGCCTTCCTG-ATTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
* *
28826970 TCCCTGTGACTACAGTGGAGTACATTGAAGCTGATAACTCTATCTCCCTG--GTTGGCAGTGGAA
65 TCCC--TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
28827033 TAGAT
128 TAGAT
* *
28827038 TGAAGATTGCGGAACTTGCC-TCCTGATTGGCAGCGAAGCAGATCGAAA-ATGGCAGATTTTACC
1 TGAAGATTGCAGATCTTGCCTTCCTGATTGGCAGCGAAGCAGATC-AAAGATGGCAGATTTTACC
* *
28827101 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAGTA
65 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
28827166 GAT
130 GAT
* *
28827169 TGAAGATTGCAGATCTTGCCTTCCTGTATTTGGTAGCGAAGCAGATCAAAGATGACAGATTTTAC
1 TGAAGATTGCAGATCTTGCCTTCCTG-A-TTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTAC
*
28827234 CTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTAGAAT
64 CTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAAT
*
28827299 AGAG
129 AGAT
28827303 TGAAGA
1 TGAAGA
28827309 AACCACAGAT
Statistics
Matches: 248, Mismatches: 16, Indels: 13
0.90 0.06 0.05
Matches are distributed among these distances:
129 42 0.17
131 71 0.29
132 13 0.05
133 21 0.08
134 101 0.41
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (132 bp):
TGAAGATTGCAGATCTTGCCTTCCTGATTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCT
CCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAG
AT
Found at i:28827362 original size:40 final size:40
Alignment explanation
Indices: 28827318--28827551 Score: 274
Period size: 40 Copynumber: 5.8 Consensus size: 40
28827308 AAACCACAGA
*
28827318 TCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAG
1 TCTTATCTCCCTAAGCAATAGCGGAGCGGATCGCATCAAG
* * ** *
28827358 TCTTATCTCCCTAAGCAGTAGCGGAGCAGA-CAAAACCACAG
1 TCTTATCTCCCTAAGCAATAGCGGAGCGGATC-GCATCA-AG
*
28827399 ATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAATAGCGGAGCGGATCGCATCAAG
* * ** *
28827440 TCTTATCTCCCTAAGCAGTAGCGGAGCTGA-CAAAACCACAG
1 TCTTATCTCCCTAAGCAATAGCGGAGCGGATC-GCATCA-AG
*
28827481 ATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAATAGCGGAGCGGATCGCATCAAG
*
28827522 TCTTATCTCCCTAAGCAGTAGCGGAGCGGA
1 TCTTATCTCCCTAAGCAATAGCGGAGCGGA
28827552 CAAAACCACA
Statistics
Matches: 160, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
39 2 0.01
40 88 0.55
41 8 0.05
42 60 0.38
43 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAATAGCGGAGCGGATCGCATCAAG
Found at i:28827416 original size:82 final size:82
Alignment explanation
Indices: 28827308--28827569 Score: 506
Period size: 82 Copynumber: 3.2 Consensus size: 82
28827298 TAGAGTGAAG
28827308 AAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAGTCTTATCTCCCTAAG
1 AAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAGTCTTATCTCCCTAAG
28827373 CAGTAGCGGAGCAGACA
66 CAGTAGCGGAGCAGACA
28827390 AAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAGTCTTATCTCCCTAAG
1 AAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAGTCTTATCTCCCTAAG
*
28827455 CAGTAGCGGAGCTGACA
66 CAGTAGCGGAGCAGACA
28827472 AAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAGTCTTATCTCCCTAAG
1 AAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAGTCTTATCTCCCTAAG
*
28827537 CAGTAGCGGAGCGGACA
66 CAGTAGCGGAGCAGACA
28827554 AAACCACAGATCTTAT
1 AAACCACAGATCTTAT
28827570 TTTTGTTGCT
Statistics
Matches: 178, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 178 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (82 bp):
AAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAGTCTTATCTCCCTAAG
CAGTAGCGGAGCAGACA
Found at i:28830056 original size:89 final size:90
Alignment explanation
Indices: 28829956--28830120 Score: 219
Period size: 89 Copynumber: 1.8 Consensus size: 90
28829946 TTAGGGCTTG
* * * * *
28829956 AATTTGATTGTGATAATGGT-GGCAATGTGTTCA-TCGTTTAAAAGTATGATTGTGATTAG-TAT
1 AATTTGATTGTGACAATGGTAGGAAAT-TGTGCAGT-GTTTAAAAGTATGACTGTGATCAGTTAT
28830018 ATTGTTTAAAAGTGTGATTTAGACTCA
64 ATTGTTTAAAAGTGTGATTTAGACTCA
* * *
28830045 AATTTGATTGTGACAGTGGTAGTAAATTGTGCAGTGTTTAAAAGTGTGACTGTGATCAGTTATAT
1 AATTTGATTGTGACAATGGTAGGAAATTGTGCAGTGTTTAAAAGTATGACTGTGATCAGTTATAT
28830110 TGTTTAAAAGT
66 TGTTTAAAAGT
28830121 ACGATTTGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
89 44 0.68
90 21 0.32
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (90 bp):
AATTTGATTGTGACAATGGTAGGAAATTGTGCAGTGTTTAAAAGTATGACTGTGATCAGTTATAT
TGTTTAAAAGTGTGATTTAGACTCA
Found at i:28830155 original size:90 final size:87
Alignment explanation
Indices: 28830061--28830343 Score: 244
Period size: 90 Copynumber: 3.3 Consensus size: 87
28830051 ATTGTGACAG
* *
28830061 TGGTAGTAAATTGTGCAGTGTTTAAAAGTGTGACTGTGATCAGTTATATTGTTTAAAAGTACGAT
1 TGGTAGCAAATTGTGCATTGTTT-AAAG-GTGA-TGTGATCAGTTATATTGTTTAAAAGTACGAT
*
28830126 TTGGGATTGAATTC-AATCATGATAA
63 TTGGGATTGAATTCGAA-CACGATAA
* * * * * *
28830151 TGGTAGCGAATTGTGCATTATTTAAAGGT-ATG-GATGCA--AATAGTGATT---GGTACGATTT
1 TGGTAGCAAATTGTGCATTGTTTAAAGGTGATGTGAT-CAGTTATATTGTTTAAAAGTACGATTT
28830209 GGGATTGAATTCGAACACGATAA
65 GGGATTGAATTCGAACACGATAA
* * * * *
28830232 TGGTAGCAAATTATGCATTGTTTGAAGGCATGGTTGTGATTAGTTATATTGTTTAAAAGTAAGAT
1 TGGTAGCAAATTGTGCATTGTTTAAAGG--T-GATGTGATCAGTTATATTGTTTAAAAGTACGAT
* *
28830297 TTGGGATTGAATAT-GATCATTGAT-A
63 TTGGGATTGAAT-TCGAACA-CGATAA
* *
28830322 TGGTGGCGAATTGTGCATTGTT
1 TGGTAGCAAATTGTGCATTGTT
28830344 GATTCGTTAT
Statistics
Matches: 154, Mismatches: 25, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
81 52 0.34
82 2 0.01
83 1 0.01
84 7 0.05
85 6 0.04
86 7 0.05
87 8 0.05
88 2 0.01
89 4 0.03
90 61 0.40
91 4 0.03
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (87 bp):
TGGTAGCAAATTGTGCATTGTTTAAAGGTGATGTGATCAGTTATATTGTTTAAAAGTACGATTTG
GGATTGAATTCGAACACGATAA
Found at i:28836315 original size:2 final size:2
Alignment explanation
Indices: 28836308--28836358 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
28836298 CCACATTGAG
28836308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28836350 AT AT A- AT AT
1 AT AT AT AT AT
28836359 CATACGTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.