Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 52 of 117
Found at i:11844439 original size:18 final size:18
Alignment explanation
Indices: 11844416--11844457 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
11844406 GATATTTAAT
11844416 ATTTTT-GATAGAAAATA
1 ATTTTTCGATAGAAAATA
* *
11844433 GATTTTTCGGTAGACAATA
1 -ATTTTTCGATAGAAAATA
11844452 ATTTTT
1 ATTTTT
11844458 TATTATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (18 bp):
ATTTTTCGATAGAAAATA
Found at i:11848594 original size:20 final size:20
Alignment explanation
Indices: 11848569--11848633 Score: 105
Period size: 20 Copynumber: 3.2 Consensus size: 20
11848559 GGAAGTTAAA
11848569 TTTTAGTAATTTTGTGTTTG
1 TTTTAGTAATTTTGTGTTTG
11848589 TTTTAGTAATTTTGTGTTAT-
1 TTTTAGTAATTTTGTGTT-TG
*
11848609 ATTTAGTAATTTTGTGTTTG
1 TTTTAGTAATTTTGTGTTTG
11848629 TTTTA
1 TTTTA
11848634 AGTTTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.17, T:0.65
Consensus pattern (20 bp):
TTTTAGTAATTTTGTGTTTG
Found at i:11851864 original size:18 final size:17
Alignment explanation
Indices: 11851839--11851873 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11851829 AATCATTTTC
*
11851839 CAAAATATTTTTTATTT
1 CAAAATATTATTTATTT
11851856 CAAATATATTATTTATTT
1 CAAA-ATATTATTTATTT
11851874 AGTACAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (17 bp):
CAAAATATTATTTATTT
Found at i:11852000 original size:104 final size:104
Alignment explanation
Indices: 11851784--11851986 Score: 307
Period size: 104 Copynumber: 1.9 Consensus size: 104
11851774 CCAAAATAAT
*
11851784 AAATCATAAGAACCATGTACTAAATAAATCTTTTTCAAAGTCCAAAATCATTTTCCAAAATATTT
1 AAATTATAAGAACCATGTACTAAATAAATCTTTTTCAAAGTCCAAAATCATTTTCCAAAATATTT
* *
11851849 TTTATTTCAAATATATTATTTATTTAGTACAAACACAAC
66 TTCATTTCAAATATAGTATTTATTTAGTACAAACACAAC
* * * *
11851888 AAATTATAAGAACCATGTACTAAATAATTTTTTTTCAAATTCTAAAATCATTTTCCAAAATATTT
1 AAATTATAAGAACCATGTACTAAATAAATCTTTTTCAAAGTCCAAAATCATTTTCCAAAATATTT
11851953 TTCATTTCAAATGTATCTAGTATTTATTTAGTAC
66 TTCATTTCAAA--TA--TAGTATTTATTTAGTAC
11851987 TAAAAATAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
104 70 0.80
106 2 0.02
108 16 0.18
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (104 bp):
AAATTATAAGAACCATGTACTAAATAAATCTTTTTCAAAGTCCAAAATCATTTTCCAAAATATTT
TTCATTTCAAATATAGTATTTATTTAGTACAAACACAAC
Found at i:11856067 original size:17 final size:18
Alignment explanation
Indices: 11856045--11856078 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11856035 CATCACCCAT
*
11856045 ATTAT-CTTTTTTCTTTG
1 ATTATCCTTTCTTCTTTG
11856062 ATTATCCTTTCTTCTTT
1 ATTATCCTTTCTTCTTT
11856079 TGCTCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.12, C:0.18, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTATCCTTTCTTCTTTG
Found at i:11857668 original size:11 final size:11
Alignment explanation
Indices: 11857654--11857681 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
11857644 ACGAAAAATT
11857654 AAAATATTTAA
1 AAAATATTTAA
11857665 AAAATATTTAA
1 AAAATATTTAA
11857676 AAAATA
1 AAAATA
11857682 CCAAACTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATATTTAA
Found at i:11858436 original size:35 final size:35
Alignment explanation
Indices: 11858390--11858456 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
11858380 ATTTTGATTA
*
11858390 AGGCATTTCATCGAACACCTAGTATACTATATATG
1 AGGCATTTCATCAAACACCTAGTATACTATATATG
* *
11858425 AGGCATTTCATCAAAGACTTAGTATACTATAT
1 AGGCATTTCATCAAACACCTAGTATACTATAT
11858457 GCAAACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (35 bp):
AGGCATTTCATCAAACACCTAGTATACTATATATG
Found at i:11858671 original size:30 final size:31
Alignment explanation
Indices: 11858635--11858700 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
11858625 AATGAAAATT
11858635 ACTAAGATATAATCTATATGGCACTAT-AAA
1 ACTAAGATATAATCTATATGGCACTATAAAA
*
11858665 ACTAAGATGTAATCTATATGGCACTATAAAA
1 ACTAAGATATAATCTATATGGCACTATAAAA
11858696 ACTAA
1 ACTAA
11858701 TTGAACTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.76
31 8 0.24
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.29
Consensus pattern (31 bp):
ACTAAGATATAATCTATATGGCACTATAAAA
Found at i:11862690 original size:35 final size:34
Alignment explanation
Indices: 11862618--11862742 Score: 124
Period size: 34 Copynumber: 3.6 Consensus size: 34
11862608 ATAAAATGCT
** * * * * *
11862618 ACTATATTAGCGGTGTTTATATGTGGAAAATGCC
1 ACTATATTAGCGGCATTTGTATTTGAAAAACGTC
*
11862652 ACTAATATTAGTGGCATTTGTATTTGAAAAACGTC
1 ACT-ATATTAGCGGCATTTGTATTTGAAAAACGTC
*
11862687 ACTATATTAGCGGCATTTGTATTTGGAAAACGTC
1 ACTATATTAGCGGCATTTGTATTTGAAAAACGTC
** * *
11862721 GTTATTTTAGCAGCATTTGTAT
1 ACTATATTAGCGGCATTTGTAT
11862743 CTTTGAGACA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
34 50 0.66
35 26 0.34
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (34 bp):
ACTATATTAGCGGCATTTGTATTTGAAAAACGTC
Found at i:11871219 original size:162 final size:163
Alignment explanation
Indices: 11870912--11871234 Score: 375
Period size: 162 Copynumber: 2.0 Consensus size: 163
11870902 ATTTATGTAC
*
11870912 ATAATTATTGAAGCATTTTTTAAGAACAAACACCTTCAATAATTTTCTTTTAAAAATTTTTGAGA
1 ATAATTATTGAAGCATTTTTTAAGAACAAACACCTTCAATAATTTTCCTTTAAAAATTTTTGAGA
* * ***
11870977 TTATTAAATGCGTCTTCTAATGAAAAACGCCTTCAATATACCAATACTCAAATTTTAAAATGGTT
66 TTATTAAAGGCGTCTTCTAATGAAAAACACCTTCAATATACCAATACTCAAATTTTAAAACAATT
* *
11871042 AGTAAATGCGTTTATTCCAGAA-AATACCTTTA
131 ACTAAAGGCGTTTATTCCAGAATAATACCTTTA
* * **
11871074 ATAATTTATTGAAGGTATTTTTTAAGAATAAATGCCTTCAATAA-TTTCCTTTAAAAATTTTTG-
1 ATAA-TTATTGAA-GCATTTTTTAAGAACAAACACCTTCAATAATTTTCCTTTAAAAATTTTTGA
* * * * * * * *
11871137 GGTTATTAAAGGCGTCTTTTAGTGAAAAATACCTTCAATAGT-CCATTACTTAAATTTTGAGACA
64 GATTATTAAAGGCGTCTTCTAATGAAAAACACCTTCAATA-TACCAATACTCAAATTTTAAAACA
* * * *
11871201 ATTACTGAAGGTGTTTATTCTAGAATAATGCCTT
128 ATTACTAAAGGCGTTTATTCCAGAATAATACCTT
11871235 CACTAATTCC
Statistics
Matches: 133, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
162 73 0.55
163 34 0.26
164 26 0.20
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (163 bp):
ATAATTATTGAAGCATTTTTTAAGAACAAACACCTTCAATAATTTTCCTTTAAAAATTTTTGAGA
TTATTAAAGGCGTCTTCTAATGAAAAACACCTTCAATATACCAATACTCAAATTTTAAAACAATT
ACTAAAGGCGTTTATTCCAGAATAATACCTTTA
Found at i:11875488 original size:64 final size:62
Alignment explanation
Indices: 11875311--11875498 Score: 166
Period size: 64 Copynumber: 3.0 Consensus size: 62
11875301 ATTTAAGGTG
* * * * *
11875311 TTTTTACAAAAATCGCCTTCAATAATCCCACTTAAAAATATATTGTTTGGAATATTAAAGGCAT
1 TTTTTACAAAAATCGCCTTCAATAATCTC-GTTAAAAATTTATTG-TTGGATTATTGAAGGCAT
** * * * * **
11875375 TTTAGGATAAAAAT-GCTTTCTAGAAT-TCGTTCCAAATATT-TTGTATGGATTATTGAAGGCAT
1 TTT-TTACAAAAATCGCCTTCAATAATCTCGTTAAAAAT-TTATTGT-TGGATTATTGAAGGCAT
*
11875437 TTTTTACAAAAATCACCTTCAATAATCTCTGTTAAAAATTTATTGATTGGATTATTGAAGGC
1 TTTTTACAAAAATCGCCTTCAATAATCTC-GTTAAAAATTTATTG-TTGGATTATTGAAGGC
11875499 GCTTTCACCC
Statistics
Matches: 94, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
61 8 0.09
62 35 0.37
63 6 0.06
64 37 0.39
65 8 0.09
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.39
Consensus pattern (62 bp):
TTTTTACAAAAATCGCCTTCAATAATCTCGTTAAAAATTTATTGTTGGATTATTGAAGGCAT
Found at i:11875548 original size:126 final size:126
Alignment explanation
Indices: 11875311--11875562 Score: 276
Period size: 126 Copynumber: 2.0 Consensus size: 126
11875301 ATTTAAGGTG
* *
11875311 TTTTTACAAAAATCGCCTTCAATAATCCCACTTAAAAATATATTGTTTGGAATATTAAAGGCATT
1 TTTTTACAAAAATCACCTTCAATAATCCCACTTAAAAATATATTGATTGGAATATTAAAGGCATT
* * * ** * * *
11875376 TTAGGATAAAAATGCTTTCTAGAATTCGTTCCAAATATTTTGTATGGATTATTGAA-GGCAT
66 TCAGCACAAAAACACCTTCAAGAATCCGTTCCAAATATTTTGTATGGATTATT-AACGGCAT
* ** * * * *
11875437 TTTTTACAAAAATCACCTTCAATAATCTCTGTTAAAAATTTATTGATTGGATTATTGAAGGCGCT
1 TTTTTACAAAAATCACCTTCAATAATCCCACTTAAAAATATATTGATTGGAATATTAAAGGC-AT
* * *
11875502 TTCA-CCCAAAAACACCTTCAAGAATCCGTTCCATAT-TTTTCTTATGGATTATTAACGGCAT
65 TTCAGCACAAAAACACCTTCAAGAATCCGTTCCAAATATTTT-GTATGGATTATTAACGGCAT
11875563 ATTTAGCAAG
Statistics
Matches: 103, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
125 6 0.06
126 93 0.90
127 4 0.04
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (126 bp):
TTTTTACAAAAATCACCTTCAATAATCCCACTTAAAAATATATTGATTGGAATATTAAAGGCATT
TCAGCACAAAAACACCTTCAAGAATCCGTTCCAAATATTTTGTATGGATTATTAACGGCAT
Found at i:11875802 original size:304 final size:303
Alignment explanation
Indices: 11875230--11876050 Score: 909
Period size: 304 Copynumber: 2.7 Consensus size: 303
11875220 AATATCAAAA
* * * * *
11875230 ATATTTTT-TTGATGGGATTAATAAAGACATTTTTAGTAAGAAAATG-CTTGAATCATCCCTAAC
1 ATATTTTTCTT-AT-GGATTATTAAAGGCATTTTTAGCAAGAAAATGCCTTGAATAATCCATAAC
* * *
11875293 AAAATGTTATTTAAGGTGTTTTTACAAAAATCGCCTTCAATAATCCCACTTAAAAATATATTGTT
64 AAAATGTTATTTAAGAT-TTTTTACAAAAATCGCCTTCAATAATCCCACTTAAAAATTTATTGTG
* ** * * * * * * *
11875358 TGGAATATTAAAGGCATTTTAGGATAAAAATGCTTTCTAGAATTCGTTCCAAATATTTTGTATGG
128 TGGAATATTAAAGGCATTTTAAGCCAAAAACGCCTTCAAGAATCCATTCCAACTTTTTTGTATGG
** * * * *** * *
11875423 ATTATTGAAGGCATTTTTTACAAAAATCACCTTCAATAATCTCTGTTAAAAATTTATTGATTGGA
193 ATTATTGAAGGCATTTTAAAAAAAAACCACCTTCAATAATATCAACTAAAAATTAATTGAATGGA
* *
11875488 TTATTGAAGGCGCTTTCACCCAAAAACACCTTCAAGAATCCGTTCC
258 TTATTGAAGGCACTTTCAACCAAAAACACCTTCAAGAATCCGTTCC
* * * *
11875534 ATATTTTTCTTATGGATTATTAACGGCATATTTAGCAAGAAAATGCCTTGAATTATTCATAACAA
1 ATATTTTTCTTATGGATTATTAAAGGCATTTTTAGCAAGAAAATGCCTTGAATAATCCATAACAA
* * *
11875599 AATGTTATTGATAGCATTTTTTACCAAAA-CAGCATTCAATAATCCCACTTAAAAATTTATTGTG
66 AATGTTATTTA-AG-ATTTTTTACAAAAATC-GCCTTCAATAATCCCACTTAAAAATTTATTGTG
*
11875663 TGGAATATTAAAGGCATTTTAAGCCAAAAACGCCTTCAAGAATCCATTCTAACTTTTTTGTATGG
128 TGGAATATTAAAGGCATTTTAAGCCAAAAACGCCTTCAAGAATCCATTCCAACTTTTTTGTATGG
* *
11875728 ATTATTTAAGGTA-TTTAAAAAAAAACCACCTTCAATAATATCAACTAAAAATTAATTGAATGGA
193 ATTATTGAAGGCATTTTAAAAAAAAACCACCTTCAATAATATCAACTAAAAATTAATTGAATGGA
* *** * *
11875792 TTATTGAAGGCATTTTCAACCAAAAATGGCTTCAAGAATCTGTTTC
258 TTATTGAAGGCACTTTCAACCAAAAACACCTTCAAGAATCCGTTCC
* * * * * * *
11875838 ATATTTTTCCTATGGATTATTAAGGGTATTTTTCTGC-TGAAAATACCTTGAATAATCCTTAACA
1 ATATTTTTCTTATGGATTATTAAAGGCATTTTT-AGCAAGAAAATGCCTTGAATAATCCATAACA
* *
11875902 AAATGTTATTTAAGGTATTTTTTTATAAAAATCGCCTTCAATAATCTGACCA-TT-CAAATTTAT
65 AAATGTTATTTAA-G-A-TTTTTTACAAAAATCGCCTTCAATAATC---CCACTTAAAAATTTAT
* * * * * * *
11875965 TGTGTGAAATATTAAAGACTTTTTGAGCCAAAAACGCCTTTAAAAATCCATTCCAACTTTTGTGT
124 TGTGTGGAATATTAAAGGCATTTTAAGCCAAAAACGCCTTCAAGAATCCATTCCAACTTTTTTGT
*
11876030 ATGGATTATTGAAGGCGTTTT
189 ATGGATTATTGAAGGCATTTT
11876051 TGACAAAATC
Statistics
Matches: 432, Mismatches: 72, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
303 28 0.06
304 180 0.42
305 135 0.31
306 81 0.19
307 5 0.01
308 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (303 bp):
ATATTTTTCTTATGGATTATTAAAGGCATTTTTAGCAAGAAAATGCCTTGAATAATCCATAACAA
AATGTTATTTAAGATTTTTTACAAAAATCGCCTTCAATAATCCCACTTAAAAATTTATTGTGTGG
AATATTAAAGGCATTTTAAGCCAAAAACGCCTTCAAGAATCCATTCCAACTTTTTTGTATGGATT
ATTGAAGGCATTTTAAAAAAAAACCACCTTCAATAATATCAACTAAAAATTAATTGAATGGATTA
TTGAAGGCACTTTCAACCAAAAACACCTTCAAGAATCCGTTCC
Found at i:11876626 original size:61 final size:61
Alignment explanation
Indices: 11876495--11876636 Score: 173
Period size: 62 Copynumber: 2.3 Consensus size: 61
11876485 TTTTATGAGG
* * * *
11876495 GGATTATTAAAGGCATTATCTGTCAAAAATGCCTTCAGTAATTCCTTATCAATTTTTTAACA
1 GGATTATTCAAGGCATTTTCTGTCAAAAATGCCTTCAGTAATTCCTCA-CAATTTTTAAACA
* *
11876557 GGATTATTCAAGTCATTTTCTG-CTAAAAATGCCTTTAGT-ATTCACTCA-AATTTTTAAAACA
1 GGATTATTCAAGGCATTTTCTGTC-AAAAATGCCTTCAGTAATTC-CTCACAATTTTT-AAACA
11876618 GGATTATTCAAGGCATTTT
1 GGATTATTCAAGGCATTTT
11876637 AGTTGATAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
60 7 0.10
61 27 0.39
62 36 0.51
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (61 bp):
GGATTATTCAAGGCATTTTCTGTCAAAAATGCCTTCAGTAATTCCTCACAATTTTTAAACA
Found at i:11881857 original size:13 final size:14
Alignment explanation
Indices: 11881829--11881857 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11881819 ACGCAATATG
11881829 ATTTTCAAAAATGC
1 ATTTTCAAAAATGC
11881843 ATTTTCAAAAA-GC
1 ATTTTCAAAAATGC
11881856 AT
1 AT
11881858 GTTGCATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (14 bp):
ATTTTCAAAAATGC
Found at i:11885871 original size:22 final size:22
Alignment explanation
Indices: 11885843--11885886 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11885833 CTAAATCTTC
*
11885843 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
11885865 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
11885887 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:11889585 original size:23 final size:25
Alignment explanation
Indices: 11889530--11889588 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
11889520 AAAGGGTTCG
* * *
11889530 GCAATGAAGGCCTAAACAGGATTCG
1 GCAATGAAGGCCTAAACAGAAGTCA
11889555 GCAATGAAGGCCTAAA-A-AAGTCA
1 GCAATGAAGGCCTAAACAGAAGTCA
11889578 GCAATGAAGGC
1 GCAATGAAGGC
11889589 TGAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 14 0.45
24 1 0.03
25 16 0.52
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.14
Consensus pattern (25 bp):
GCAATGAAGGCCTAAACAGAAGTCA
Found at i:11889764 original size:22 final size:22
Alignment explanation
Indices: 11889736--11889779 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11889726 CTAAATCTTC
*
11889736 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
11889758 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
11889780 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:11892009 original size:19 final size:20
Alignment explanation
Indices: 11891959--11892009 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
11891949 TTTCTCAAGA
*
11891959 AAAAAGAAGA-AAGATGAAG
1 AAAAAGAAGAGAACATGAAG
* * *
11891978 AAAAAAAAAAGAACATG-GG
1 AAAAAGAAGAGAACATGAAG
11891997 AAAAAGAAGAGAA
1 AAAAAGAAGAGAA
11892010 AGGGAATGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.04
Consensus pattern (20 bp):
AAAAAGAAGAGAACATGAAG
Found at i:11893055 original size:30 final size:30
Alignment explanation
Indices: 11893020--11893088 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
11893010 ATTTATGATG
11893020 AAAATTTTTTGAATTTTTAAAATCTTACAT
1 AAAATTTTTTGAATTTTTAAAATCTTACAT
** ** *
11893050 AAAATTACTTGAATTTTTAATGTCTTACGT
1 AAAATTTTTTGAATTTTTAAAATCTTACAT
11893080 -AAATTTTTT
1 AAAATTTTTT
11893089 AAAAAAGATA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (30 bp):
AAAATTTTTTGAATTTTTAAAATCTTACAT
Found at i:11893255 original size:21 final size:21
Alignment explanation
Indices: 11893215--11893266 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
11893205 ATAATTTTTT
* * *
11893215 AAATAAGATTATTTGGTAAAC
1 AAATAAAATTATTTAGTAAAA
* *
11893236 AATTAAAATTATTTATTAAAA
1 AAATAAAATTATTTAGTAAAA
11893257 AAATAAAATT
1 AAATAAAATT
11893267 CATATTTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (21 bp):
AAATAAAATTATTTAGTAAAA
Found at i:11893616 original size:1 final size:1
Alignment explanation
Indices: 11893610--11893640 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
11893600 AATCCCTCCT
11893610 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
11893641 TCTTATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:11894403 original size:2 final size:2
Alignment explanation
Indices: 11894396--11894444 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
11894386 GCATGACGTT
* *
11894396 TA TA TA TA TA TA AA TA TA AA 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
11894438 TA -A TA TA
1 TA TA TA TA
11894445 AACTTATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:11900344 original size:32 final size:33
Alignment explanation
Indices: 11900261--11900352 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
11900251 TAATCTAATT
* *
11900261 ATCATAATTTAACCTCTTAGAAAATCTCCAAAG
1 ATCATAATATAAGCTCTTAGAAAATCTCCAAAG
*** * *
11900294 ATCATAGCCTAAGTTCTTAGAAAATCTTCAAA-
1 ATCATAATATAAGCTCTTAGAAAATCTCCAAAG
*
11900326 ATCATAATATAAGCTCTTA-AATATCTC
1 ATCATAATATAAGCTCTTAGAAAATCTC
11900353 ACATAGTTTA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 6 0.13
32 15 0.32
33 26 0.55
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (33 bp):
ATCATAATATAAGCTCTTAGAAAATCTCCAAAG
Found at i:11903018 original size:2 final size:2
Alignment explanation
Indices: 11903006--11903037 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11902996 GTTCAAATAA
11903006 AT AT A- 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
11903038 ATGGTGGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11907330 original size:29 final size:29
Alignment explanation
Indices: 11907298--11907363 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
11907288 AAACTATAGT
11907298 AAAATGATCAATATGATATCTAAACTT-TA
1 AAAATGATCAATATGATATCTAAA-TTATA
*
11907327 AAAAT-ATTTAATATGATATCTAAATTATA
1 AAAATGA-TCAATATGATATCTAAATTATA
*
11907356 AATATGAT
1 AAAATGAT
11907364 AATTAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 3 0.09
29 28 0.88
30 1 0.03
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (29 bp):
AAAATGATCAATATGATATCTAAATTATA
Found at i:11907510 original size:27 final size:28
Alignment explanation
Indices: 11907456--11907511 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
11907446 ATAGATTCAT
* *
11907456 AATTTAAATACTATATTAAAAATTTTTTA
1 AATTTAAATAATATATT-AAAATATTTTA
11907485 AATTTAAATAATATATT-AAATATTTTA
1 AATTTAAATAATATATTAAAATATTTTA
11907512 TTATAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.36
29 16 0.64
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTTAAATAATATATTAAAATATTTTA
Found at i:11910248 original size:4 final size:4
Alignment explanation
Indices: 11910212--11910269 Score: 62
Period size: 4 Copynumber: 14.5 Consensus size: 4
11910202 CATATATGTT
* * * * * *
11910212 TATA TACA TATA CATA CATA CATA CATA CATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
11910260 TATA TATA TA
1 TATA TATA TA
11910270 GATGGAATAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (4 bp):
TATA
Found at i:11910674 original size:28 final size:28
Alignment explanation
Indices: 11910634--11910690 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
11910624 GAATTTTGTA
*
11910634 ATTTTTATTATATTGATACTTAAAATTT
1 ATTTTTATCATATTGATACTTAAAATTT
*
11910662 ATTTTTATCATATTGATACTTAAACTTT
1 ATTTTTATCATATTGATACTTAAAATTT
11910690 A
1 A
11910691 AAATCATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (28 bp):
ATTTTTATCATATTGATACTTAAAATTT
Found at i:11910951 original size:9 final size:9
Alignment explanation
Indices: 11910937--11910987 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
11910927 GTTAAGATTC
11910937 TAAAAATTT
1 TAAAAATTT
*
11910946 TAAAAAATTC
1 T-AAAAATTT
11910956 TAAAAATTT
1 TAAAAATTT
*
11910965 TAAAAAATTC
1 T-AAAAATTT
11910975 TAAAAATTT
1 TAAAAATTT
11910984 TAAA
1 TAAA
11910988 CAGTTCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (9 bp):
TAAAAATTT
Found at i:11910955 original size:19 final size:19
Alignment explanation
Indices: 11910902--11911089 Score: 118
Period size: 19 Copynumber: 9.7 Consensus size: 19
11910892 CAAAAATATT
*
11910902 AAAA-TTTAAAAAAATCT-
1 AAAATTTTAAAAAATTCTA
** *
11910919 AAAATTTTGTTAAGATTCTA
1 AAAATTTT-AAAAAATTCTA
11910939 AAAATTTTAAAAAATTCTA
1 AAAATTTTAAAAAATTCTA
11910958 AAAATTTTAAAAAATTCTA
1 AAAATTTTAAAAAATTCTA
* *
11910977 AAAATTTTAAACAGTTC-A
1 AAAATTTTAAAAAATTCTA
** *
11910995 AAAA-AATAATAAAAGTTTTA
1 AAAATTTTAA-AAAA-TTCTA
* * * *
11911015 AAGAATTTTTTAGAACTTCAA
1 AA-AA-TTTTAAAAAATTCTA
*
11911036 AAAATATTAAAAAATT-TAA
1 AAAATTTTAAAAAATTCT-A
*
11911055 AAAATTCTCAAAAAATGT-TA
1 AAAATT-TTAAAAAAT-TCTA
11911075 AAAATTTTCAAAAAA
1 AAAATTTT-AAAAAA
11911090 AAAATTAGAA
Statistics
Matches: 129, Mismatches: 29, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
17 7 0.05
18 10 0.08
19 65 0.50
20 34 0.26
21 9 0.07
22 2 0.02
23 2 0.02
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (19 bp):
AAAATTTTAAAAAATTCTA
Found at i:11911054 original size:9 final size:9
Alignment explanation
Indices: 11911034--11911089 Score: 58
Period size: 10 Copynumber: 5.7 Consensus size: 9
11911024 TTAGAACTTC
11911034 AAAAAATATT
1 AAAAAAT-TT
11911044 AAAAAATTT
1 AAAAAATTT
11911053 AAAAAATTCT
1 AAAAAATT-T
11911063 CAAAAAATGTT
1 -AAAAAAT-TT
*
11911074 AAAAATTTT
1 AAAAAATTT
11911083 CAAAAAA
1 -AAAAAA
11911090 AAAATTAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 12 0.30
10 19 0.47
11 8 0.20
12 1 0.03
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAAATTT
Found at i:11911054 original size:39 final size:39
Alignment explanation
Indices: 11910957--11911057 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 39
11910947 AAAAAATTCT
*
11910957 AAAAATTTTAAAAAATTCTAAAAA--TTTTAAACAGTTCAA
1 AAAAATATTAAAAAATT-TAAAAATTTTTTAAACA-TTCAA
* **
11910996 AAAAATAATAAAAGTTTTAAAGAATTTTTTAGAAC-TTC-A
1 AAAAATATTAAAAAATTTAAA-AATTTTTTA-AACATTCAA
11911035 AAAAATATTAAAAAATTTAAAAA
1 AAAAATATTAAAAAATTTAAAAA
11911058 ATTCTCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
38 6 0.12
39 34 0.67
40 3 0.06
41 5 0.10
42 3 0.06
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (39 bp):
AAAAATATTAAAAAATTTAAAAATTTTTTAAACATTCAA
Found at i:11911066 original size:30 final size:31
Alignment explanation
Indices: 11911032--11911089 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
11911022 TTTTAGAACT
11911032 TCAAAAAATATTAAAAAATTT-AAAAAATTC
1 TCAAAAAATATTAAAAAATTTCAAAAAATTC
* *
11911062 TCAAAAAATGTTAAAAATTTTCAAAAAA
1 TCAAAAAATATTAAAAAATTTCAAAAAA
11911090 AAAATTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (31 bp):
TCAAAAAATATTAAAAAATTTCAAAAAATTC
Found at i:11911067 original size:20 final size:20
Alignment explanation
Indices: 11911044--11911089 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
11911034 AAAAAATATT
11911044 AAAAAAT-TTAAAAAATTCTC
1 AAAAAATGTT-AAAAATTCTC
*
11911064 AAAAAATGTTAAAAATTTTC
1 AAAAAATGTTAAAAATTCTC
11911084 AAAAAA
1 AAAAAA
11911090 AAAATTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAAATGTTAAAAATTCTC
Found at i:11911131 original size:17 final size:19
Alignment explanation
Indices: 11911086--11911129 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
11911076 AAATTTTCAA
*
11911086 AAAAAAAATTAGAAACATT
1 AAAAAAAATTAAAAACATT
11911105 AAAAAAAATTAAAAAC-TT
1 AAAAAAAATTAAAAACATT
11911123 AAGAAAA
1 AA-AAAA
11911130 TTCAAGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAAAAAATTAAAAACATT
Found at i:11911151 original size:22 final size:21
Alignment explanation
Indices: 11911126--11911171 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
11911116 AAAACTTAAG
11911126 AAAATTCAAGATAATTCTAAAA
1 AAAATTCAA-ATAATTCTAAAA
** *
11911148 AAAATTTTAATAATTCTGAAA
1 AAAATTCAAATAATTCTAAAA
11911169 AAA
1 AAA
11911172 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (21 bp):
AAAATTCAAATAATTCTAAAA
Found at i:11911171 original size:20 final size:20
Alignment explanation
Indices: 11911136--11911195 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
11911126 AAAATTCAAG
*
11911136 ATAATTCTAAAAAAAATTTTA
1 ATAATTCT-GAAAAAATTTTA
11911157 ATAATTCTGAAAAAATTTTA
1 ATAATTCTGAAAAAATTTTA
*
11911177 A-AATTTTCTGAAAACATTT
1 ATAA--TTCTGAAAAAATTT
11911196 AAAATTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 12 0.34
21 21 0.60
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (20 bp):
ATAATTCTGAAAAAATTTTA
Found at i:11911196 original size:20 final size:21
Alignment explanation
Indices: 11911146--11911201 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
11911136 ATAATTCTAA
11911146 AAAAAATTTTAATAA--TTCTG
1 AAAAAATTTTAA-AATTTTCTG
11911166 AAAAAATTTTAAAATTTTCTG
1 AAAAAATTTTAAAATTTTCTG
*
11911187 AAAACA-TTTAAAATT
1 AAAAAATTTTAAAATT
11911202 AATATTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 2 0.06
20 21 0.64
21 10 0.30
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (21 bp):
AAAAAATTTTAAAATTTTCTG
Found at i:11911393 original size:19 final size:18
Alignment explanation
Indices: 11911302--11911410 Score: 58
Period size: 19 Copynumber: 5.5 Consensus size: 18
11911292 CTGAAAAGAC
11911302 TTTAAAATTTTCTAAACAAT
1 TTTAAAATTTT-TAAA-AAT
* *
11911322 TCTAAACAATTATTAAAAAT
1 T-TTAA-AATTTTTAAAAAT
**
11911342 TCTTAATTTTTTTAAAAAAT
1 T-TTAAAATTTTT-AAAAAT
**
11911362 CATAAGTAATTTTTAAATAAT
1 TTTAA--AATTTTTAAA-AAT
11911383 TTTAAAA-TTTTAGAAGAAT
1 TTTAAAATTTTTA-AA-AAT
11911402 TTTAAAATT
1 TTTAAAATT
11911411 ATAAAAAAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
18 5 0.07
19 21 0.31
20 19 0.28
21 18 0.26
22 5 0.07
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (18 bp):
TTTAAAATTTTTAAAAAT
Found at i:11911556 original size:16 final size:16
Alignment explanation
Indices: 11911537--11911583 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
11911527 CTTATAGTTT
*
11911537 AAAAAATACAAAAACA
1 AAAAAATATAAAAACA
* * *
11911553 AAAAAAAATGAAAATA
1 AAAAAATATAAAAACA
11911569 AAAAAATATAAAAAC
1 AAAAAATATAAAAAC
11911584 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (16 bp):
AAAAAATATAAAAACA
Found at i:11911782 original size:19 final size:18
Alignment explanation
Indices: 11911760--11911864 Score: 72
Period size: 18 Copynumber: 5.8 Consensus size: 18
11911750 TTTTTTGAAT
11911760 TTTTTTAAATTTTCTAAAA
1 TTTTTTAAATTTT-TAAAA
* * *
11911779 -TTTTTAGAGTTTT-AGA
1 TTTTTTAAATTTTTAAAA
* *
11911795 TTCTTTTTAATTTTCAAAA
1 TT-TTTTAAATTTTTAAAA
*
11911814 GTTTTTAGAATTTTTAAAA
1 TTTTTTA-AATTTTTAAAA
* *
11911833 TTTTTCAGAATTTTT-AAG
1 TTTTTTA-AATTTTTAAAA
*
11911851 TTTTTAAAATTTTT
1 TTTTTTAAATTTTT
11911865 TTATATTTTC
Statistics
Matches: 67, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
16 2 0.03
17 9 0.13
18 30 0.45
19 26 0.39
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (18 bp):
TTTTTTAAATTTTTAAAA
Found at i:11911783 original size:30 final size:30
Alignment explanation
Indices: 11911719--11911783 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
11911709 ATTTTGGATT
* * *
11911719 TTTTTTTGAAAGTTTTTAAGTTTCCTTAAT
1 TTTTTTTGAAAGTTTTTAAATTTCCTAAAA
** *
11911749 TTTTTTTGAATTTTTTTAAATTTTCTAAAA
1 TTTTTTTGAAAGTTTTTAAATTTCCTAAAA
11911779 TTTTT
1 TTTTT
11911784 AGAGTTTTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.05, G:0.06, T:0.65
Consensus pattern (30 bp):
TTTTTTTGAAAGTTTTTAAATTTCCTAAAA
Found at i:11911865 original size:10 final size:9
Alignment explanation
Indices: 11911803--11911864 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
11911793 GATTCTTTTT
*
11911803 AATTTTCAA
1 AATTTTTAA
*
11911812 AAGTTTTTAG
1 AA-TTTTTAA
11911822 AATTTTTAA
1 AATTTTTAA
*
11911831 AATTTTTCAG
1 AATTTTT-AA
11911841 AATTTTT-A
1 AATTTTTAA
*
11911849 AGTTTTTAA
1 AATTTTTAA
11911858 AATTTTT
1 AATTTTT
11911865 TTATATTTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 6 0.14
9 22 0.51
10 15 0.35
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (9 bp):
AATTTTTAA
Found at i:11911873 original size:27 final size:28
Alignment explanation
Indices: 11911761--11911864 Score: 94
Period size: 27 Copynumber: 3.8 Consensus size: 28
11911751 TTTTTGAATT
11911761 TTTTTA-AATTTTCTAAAATTTTT-AG-A
1 TTTTTAGAATTTT-TAAAATTTTTCAGAA
* ** *
11911787 GTTTTAG-ATTCTTTTTAA-TTTTCAAAA
1 TTTTTAGAATT-TTTAAAATTTTTCAGAA
11911814 GTTTTTAGAATTTTTAAAATTTTTCAGAA
1 -TTTTTAGAATTTTTAAAATTTTTCAGAA
*
11911843 TTTTTA-AGTTTTTAAAATTTTT
1 TTTTTAGAATTTTTAAAATTTTT
11911865 TTATATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
25 4 0.06
26 12 0.19
27 18 0.29
28 17 0.27
29 11 0.18
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.58
Consensus pattern (28 bp):
TTTTTAGAATTTTTAAAATTTTTCAGAA
Found at i:11911926 original size:19 final size:19
Alignment explanation
Indices: 11911803--11911926 Score: 57
Period size: 19 Copynumber: 6.8 Consensus size: 19
11911793 GATTCTTTTT
*
11911803 AATTTTCAAAAGTTTTT-AG
1 AATTTT-AAAAATTTTTCAG
*
11911822 AATTTTTAAAATTTTTCAG
1 AATTTTAAAAATTTTTCAG
* * *
11911841 AATTTT-TAAGTTTTT-AA
1 AATTTTAAAAATTTTTCAG
***
11911858 AATTTT-TTTATATTTTC--
1 AATTTTAAAAAT-TTTTCAG
*
11911875 AATTATAAAAA-TTTTC-G
1 AATTTTAAAAATTTTTCAG
** *
11911892 AATCTTTAAATTTTTTTCAA
1 AAT-TTTAAAAATTTTTCAG
11911912 AATTTTAAAAATTTT
1 AATTTTAAAAATTTT
11911927 AACTTATTTT
Statistics
Matches: 79, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
16 5 0.06
17 17 0.22
18 25 0.32
19 29 0.37
20 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (19 bp):
AATTTTAAAAATTTTTCAG
Found at i:11911990 original size:28 final size:29
Alignment explanation
Indices: 11911940--11911999 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
11911930 TTATTTTTAC
* *
11911940 TTTTCAAAATTATTTTAGAATTTTTAGAA
1 TTTTCAAAATAATGTTAGAATTTTTAGAA
* *
11911969 TTTTCAAAA-AATGTTATAATTTTTATAA
1 TTTTCAAAATAATGTTAGAATTTTTAGAA
11911997 TTT
1 TTT
11912000 AAAAAAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTTCAAAATAATGTTAGAATTTTTAGAA
Found at i:11912004 original size:27 final size:28
Alignment explanation
Indices: 11911958--11912019 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
11911948 ATTATTTTAG
* *
11911958 AATTTTTAGAATTTTCAAAAAATGTT-A
1 AATTTTTAGAATTTTAAAAAAAAGTTCA
*
11911985 TAATTTTTATAA-TTTAAAAAAAAGTTCA
1 -AATTTTTAGAATTTTAAAAAAAAGTTCA
11912013 AATTTTT
1 AATTTTT
11912020 TAAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (28 bp):
AATTTTTAGAATTTTAAAAAAAAGTTCA
Found at i:11912041 original size:22 final size:21
Alignment explanation
Indices: 11911997--11912043 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
11911987 ATTTTTATAA
*
11911997 TTTAAAAAAAAGTTCAAATTT
1 TTTAAAAAAAAGTCCAAATTT
11912018 TTTAAAAAAAA-TCCATAATATT
1 TTTAAAAAAAAGTCCA-AAT-TT
11912040 TTTA
1 TTTA
11912044 GAATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 3 0.13
21 14 0.61
22 6 0.26
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTAAAAAAAAGTCCAAATTT
Found at i:11912078 original size:19 final size:18
Alignment explanation
Indices: 11912056--11912112 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
11912046 ATTTTTAAAA
11912056 AATTTTAGAATTTTGTTAG
1 AATTTTA-AATTTTGTTAG
* *
11912075 AATTTTTAAATTTTTTTTG
1 AA-TTTTAAATTTTGTTAG
11912094 AATTTTCAAAATTTTGTTA
1 AATTTT--AAATTTTGTTA
11912113 AAAAAGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 4 0.13
19 13 0.42
20 14 0.45
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.58
Consensus pattern (18 bp):
AATTTTAAATTTTGTTAG
Found at i:11912166 original size:11 final size:10
Alignment explanation
Indices: 11912148--11912246 Score: 73
Period size: 10 Copynumber: 10.3 Consensus size: 10
11912138 ATTTTAAAGC
*
11912148 ATTTTTTAGA
1 ATTTTTTAAA
11912158 ATTTCTTTAAA
1 ATTT-TTTAAA
11912169 ATTTTTT--A
1 ATTTTTTAAA
* *
11912177 ATCTTTT-AG
1 ATTTTTTAAA
11912186 ATTTTTTAAA
1 ATTTTTTAAA
*
11912196 A-TTTTTATA
1 ATTTTTTAAA
**
11912205 ATTTTAAAAA
1 ATTTTTTAAA
**
11912215 AAATTTT-AA
1 ATTTTTTAAA
*
11912224 ATTTTTAAAA
1 ATTTTTTAAA
11912234 ATTTTTTAAA
1 ATTTTTTAAA
11912244 ATT
1 ATT
11912247 GTTTCTTTTA
Statistics
Matches: 67, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
8 7 0.10
9 20 0.30
10 31 0.46
11 9 0.13
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:11912200 original size:9 final size:9
Alignment explanation
Indices: 11912037--11912246 Score: 66
Period size: 9 Copynumber: 21.3 Consensus size: 9
11912027 AATCCATAAT
*
11912037 ATTTTTAGA
1 ATTTTTAAA
11912046 ATTTTTAAAA
1 ATTTTT-AAA
*
11912056 AATTTTAGAA
1 ATTTTTA-AA
* *
11912066 TTTTGTTAGA
1 ATTT-TTAAA
11912076 ATTTTTAAA
1 ATTTTTAAA
* **
11912085 TTTTTTTTGA
1 -ATTTTTAAA
*
11912095 ATTTTCAAA
1 ATTTTTAAA
11912104 ATTTTGTTAAAAA
1 A-TTT-TT--AAA
11912117 AGTATTTTAGAA
1 A-T-TTTTA-AA
*
11912129 ATTTTCAAA
1 ATTTTTAAA
11912138 A-TTTTAAA
1 ATTTTTAAA
11912146 GCATTTTTTAGAA
1 --A-TTTTTA-AA
*
11912159 TTTCTTTAAA
1 ATT-TTTAAA
*
11912169 ATTTTT-TA
1 ATTTTTAAA
*
11912177 ATCTTTTAGA
1 AT-TTTTAAA
*
11912187 TTTTTTAAA
1 ATTTTTAAA
*
11912196 ATTTTTATA
1 ATTTTTAAA
*
11912205 ATTTTAAAAAA
1 ATTTT--TAAA
*
11912216 AATTTT-AA
1 ATTTTTAAA
11912224 ATTTTTAAAA
1 ATTTTT-AAA
11912234 ATTTTTTAAA
1 A-TTTTTAAA
11912244 ATT
1 ATT
11912247 GTTTCTTTTA
Statistics
Matches: 147, Mismatches: 31, Indels: 46
0.66 0.14 0.21
Matches are distributed among these distances:
8 16 0.11
9 47 0.32
10 44 0.30
11 21 0.14
12 8 0.05
13 9 0.06
14 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.53
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:11912206 original size:28 final size:29
Alignment explanation
Indices: 11912151--11912206 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 29
11912141 TTAAAGCATT
11912151 TTTTAGAATTTCTTTAAAATTTTTTAATC
1 TTTTAGAATTTCTTTAAAATTTTTTAATC
11912180 TTTTAG-ATTT-TTTAAAATTTTTATAAT
1 TTTTAGAATTTCTTTAAAATTTTT-TAAT
11912207 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 12 0.46
28 8 0.31
29 6 0.23
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (29 bp):
TTTTAGAATTTCTTTAAAATTTTTTAATC
Found at i:11912208 original size:19 final size:18
Alignment explanation
Indices: 11912037--11912239 Score: 86
Period size: 19 Copynumber: 10.3 Consensus size: 18
11912027 AATCCATAAT
*
11912037 ATTTTTAGAATTTTTAAAA
1 ATTTTTA-AATTTTTTAAA
* *
11912056 AATTTTAGAATTTTGTTAGA
1 ATTTTTA-AATTTT-TTAAA
**
11912076 ATTTTTAAATTTTTTTTGA
1 ATTTTTAAA-TTTTTTAAA
*
11912095 ATTTTCAAAATTTTGTTAAAAA
1 ATTTT-TAAATTTT-TT--AAA
* *
11912117 AGTATTTTAGAAATTTTCAAA
1 A-T-TTTTA-AATTTTTTAAA
*
11912138 ATTTTAAAGCATTTTTTAGAA
1 ATTTTTAA--ATTTTTTA-AA
*
11912159 TTTCTTTAAAATTTTTT--A
1 ATT-TTT-AAATTTTTTAAA
*
11912177 ATCTTTTAGATTTTTTAAA
1 AT-TTTTAAATTTTTTAAA
**
11912196 ATTTTTATAATTTTAAAAAA
1 ATTTTTA-AATTTT-TTAAA
* *
11912216 AATTTTAAATTTTTAAAA
1 ATTTTTAAATTTTTTAAA
11912234 ATTTTT
1 ATTTTT
11912240 TAAAATTGTT
Statistics
Matches: 141, Mismatches: 24, Indels: 39
0.69 0.12 0.19
Matches are distributed among these distances:
17 8 0.06
18 20 0.14
19 47 0.33
20 34 0.24
21 15 0.11
22 4 0.03
23 5 0.04
24 8 0.06
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTTTTAAATTTTTTAAA
Found at i:11915561 original size:21 final size:22
Alignment explanation
Indices: 11915523--11915564 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11915513 AAAAAAATAT
11915523 GAAAATGATATAAAAATGCAAG
1 GAAAATGATATAAAAATGCAAG
*
11915545 GAAAATGTTAT-AAAATGCAA
1 GAAAATGATATAAAAATGCAA
11915565 AAAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.21
Consensus pattern (22 bp):
GAAAATGATATAAAAATGCAAG
Found at i:11915571 original size:22 final size:22
Alignment explanation
Indices: 11915524--11915570 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
11915514 AAAAAATATG
**
11915524 AAAATGATATAAAAATGCAAGG
1 AAAATGATATAAAAATGCAAAA
*
11915546 AAAATGTTAT-AAAATGCAAAA
1 AAAATGATATAAAAATGCAAAA
11915567 AAAA
1 AAAA
11915571 AGAAACTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.64, C:0.04, G:0.13, T:0.19
Consensus pattern (22 bp):
AAAATGATATAAAAATGCAAAA
Found at i:11916730 original size:26 final size:28
Alignment explanation
Indices: 11916672--11916730 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
11916662 CGATTTTGAC
*
11916672 TAAGTTTAACTTTGTTTGATCAGGTTTGAT
1 TAAGTTTAACTTTG--TGATCAGGTTGGAT
*
11916702 TAAGTTTAACTTTG-GATC-GGTTGGGT
1 TAAGTTTAACTTTGTGATCAGGTTGGAT
11916728 TAA
1 TAA
11916731 ATTGATCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 9 0.33
27 4 0.15
30 14 0.52
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.46
Consensus pattern (28 bp):
TAAGTTTAACTTTGTGATCAGGTTGGAT
Found at i:11917005 original size:308 final size:305
Alignment explanation
Indices: 11916445--11917060 Score: 1054
Period size: 308 Copynumber: 2.0 Consensus size: 305
11916435 AGATATTTAA
11916445 TTATAATCTAGAAGTTTTCAAGAAAATTCAACTTCGAGAAGGCCAAATTACAAAAATACCCCTAA
1 TTATAATCTAGAAGTTTTCAAGAAAATTCAACTTCGAGAAGGCCAAATTACAAAAATACCCCTAA
*
11916510 AGGGTATTTGAATAATTTTACCTTTCTCGAAATACAATTAAAGTTTTTAATACTTTAAAATCATA
66 AGGGTATTTGAATAATTTTACCTTTCTCGAAATACAATTAAAGTTTTTAATACTTTAAAATCACA
* * *
11916575 ATTATCATTCCCATGGTTGATTAATCCTATTTGGTTATGAATTTTGAAAAACTGACCTAAGTTCA
131 ATTATCATTCCCATGATTGATTAATCCCATTTGGTTATGAATTTTGAAAAACTAACCTAAGTTCA
* *
11916640 ATATAGTTTGACTAATTTTGATCGATTTTGACTAAGTTTAACTTTGTTTGATCAGGTTTGATTAA
196 ATATAGTTTGACAAATTTTGATCGATTTTGACCAAGTTTAACTTTGTTTGATCAGGTTTGATTAA
11916705 GTTTAACTTTGGATCGGTTGGGTTAAATTGATCTCAATTTTGATT
261 GTTTAACTTTGGATCGGTTGGGTTAAATTGATCTCAATTTTGATT
* * *
11916750 TTATGATCTAGAAGTTTTCAAGAAAATTCAACTTCGAGAAGAAGGCTAAATTACAAAAATACCCT
1 TTATAATCTAGAAGTTTTCAAGAAAATTCAACTTC--G-AGAAGGCCAAATTACAAAAATACCCC
11916815 TAAAGGGTATTTCG-ATAATTTTACCTTTCTCGAAATACAATTAAAGTTTTTAATACTTTAAAAT
63 TAAAGGGTATTT-GAATAATTTTACCTTTCTCGAAATACAATTAAAGTTTTTAATACTTTAAAAT
11916879 CACAATTATCATTCCCATGATTGATTAATCCCATTTGGTTATGAATTTTGAAAAACTAACCTAAG
127 CACAATTATCATTCCCATGATTGATTAATCCCATTTGGTTATGAATTTTGAAAAACTAACCTAAG
*
11916944 TTCAATATAGTTTGACAAATTTTGTTCGATTTTGACCAAGTTTAACTTTGTTTGATCAGGTTTGA
192 TTCAATATAGTTTGACAAATTTTGATCGATTTTGACCAAGTTTAACTTTGTTTGATCAGGTTTGA
** * * *
11917009 TTAAGTTTGGCTTTGTATCGTTTGGGTTAAATTGGTCTCAATTTTGATT
257 TTAAGTTTAACTTTGGATCGGTTGGGTTAAATTGATCTCAATTTTGATT
11917058 TTA
1 TTA
11917061 GAAACTTTTC
Statistics
Matches: 292, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
305 34 0.12
307 1 0.00
308 256 0.88
309 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (305 bp):
TTATAATCTAGAAGTTTTCAAGAAAATTCAACTTCGAGAAGGCCAAATTACAAAAATACCCCTAA
AGGGTATTTGAATAATTTTACCTTTCTCGAAATACAATTAAAGTTTTTAATACTTTAAAATCACA
ATTATCATTCCCATGATTGATTAATCCCATTTGGTTATGAATTTTGAAAAACTAACCTAAGTTCA
ATATAGTTTGACAAATTTTGATCGATTTTGACCAAGTTTAACTTTGTTTGATCAGGTTTGATTAA
GTTTAACTTTGGATCGGTTGGGTTAAATTGATCTCAATTTTGATT
Found at i:11917467 original size:3 final size:3
Alignment explanation
Indices: 11917459--11917505 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
11917449 TATCTTCCTT
* *
11917459 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC CTT ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
11917506 TGTCATCTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:11921088 original size:85 final size:85
Alignment explanation
Indices: 11920939--11921107 Score: 293
Period size: 85 Copynumber: 2.0 Consensus size: 85
11920929 TTAAAAGATT
* * *
11920939 TTACTAGTATAGAATTTCGATTTAAAGAGCATTAATAGAATTATAGTTTGTCATCTGGATAACTC
1 TTACAAGTATAAAATTTCGATTTAAAGAGCATTAATAGAATTATAGTTTGTCATCTGGAGAACTC
11921004 TTGACAGAAAATTAGATAGG
66 TTGACAGAAAATTAGATAGG
* *
11921024 TTACAAGTATAAAATTTCGATTTAAAGAGCATTAATAGAATTATATTTTGTCATCTTGAGAACTC
1 TTACAAGTATAAAATTTCGATTTAAAGAGCATTAATAGAATTATAGTTTGTCATCTGGAGAACTC
11921089 TTGACAGAAAATTAGATAG
66 TTGACAGAAAATTAGATAG
11921108 AGCATTAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (85 bp):
TTACAAGTATAAAATTTCGATTTAAAGAGCATTAATAGAATTATAGTTTGTCATCTGGAGAACTC
TTGACAGAAAATTAGATAGG
Found at i:11922546 original size:2 final size:2
Alignment explanation
Indices: 11922541--11922567 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11922531 TATATATATA
11922541 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
11922568 CTTTGTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:11923204 original size:23 final size:24
Alignment explanation
Indices: 11923151--11923218 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
11923141 ATATATTTTT
11923151 TTATTAT-ATATAATTAATTATTG
1 TTATTATCATATAATTAATTATTG
* *
11923174 ATAATATCATATTAA-TAA-TATTG
1 TTATTATCATA-TAATTAATTATTG
*
11923197 TTATTATCATTTATATTAATTA
1 TTATTATCATATA-ATTAATTA
11923219 GTTATAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
22 2 0.06
23 19 0.54
24 9 0.26
25 5 0.14
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (24 bp):
TTATTATCATATAATTAATTATTG
Found at i:11924728 original size:21 final size:21
Alignment explanation
Indices: 11924688--11924728 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11924678 AAAAATGTAA
* *
11924688 TAATATTATTATCTAGAAATG
1 TAATATTATTATCCAAAAATG
11924709 TAATATTATTATCCAAAAAT
1 TAATATTATTATCCAAAAAT
11924729 TTATTTAAAA
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:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (21 bp):
TAATATTATTATCCAAAAATG
Found at i:11925282 original size:13 final size:13
Alignment explanation
Indices: 11925252--11925301 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
11925242 TCTTTTTTGT
11925252 CTAATTATTT-ATC
1 CTAATT-TTTAATC
*
11925265 TTAATTTTTAATC
1 CTAATTTTTAATC
11925278 CTAATTTTTAATC
1 CTAATTTTTAATC
*
11925291 TTTAATTTTTA
1 -CTAATTTTTA
11925302 GAAAATAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 3 0.09
13 20 0.62
14 9 0.28
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (13 bp):
CTAATTTTTAATC
Found at i:11928244 original size:51 final size:50
Alignment explanation
Indices: 11928160--11928497 Score: 279
Period size: 51 Copynumber: 6.6 Consensus size: 50
11928150 TCAAAGCATC
*
11928160 GAAACTTT-AAAAATTCTTGTTT-AAAATAGCTCCTCCAAAACAGAGGCTTT
1 GAAACTTTAAAAAATT-TTGTTTGAAAATGGCTCCTCC-AAACAGAGGCTTT
* *
11928210 GAAACTTTAAAAAATTTTATTTAAAAATGGCTCCTCTCAAACAGAGGCTTT
1 GAAACTTTAAAAAATTTTGTTTGAAAATGGCTCCTC-CAAACAGAGGCTTT
* * ** * * *
11928261 GAAACTTTAAAAAAAAAAATTAGCGTGAAAATAGCT-CTACCCATATAGAGGCTTT
1 GAAACTTT----AAAAAATTTTGTTTGAAAATGGCTCCT--CCAAACAGAGGCTTT
* ** ** * *
11928316 GAAACTTTAAAAAA-TTGGTGCGAAAATGGCTTATCCTAAACAAAGGTTTT
1 GAAACTTTAAAAAATTTTGTTTGAAAATGGCTCCTCC-AAACAGAGGCTTT
* * * *
11928366 GAAACTTTTAAAAAATTTGGTGTGAAAATGGCTCCTCCCAAATATAGGCTTT
1 GAAAC-TTTAAAAAATTTTGTTTGAAAATGGCTCCT-CCAAACAGAGGCTTT
* * * *
11928418 GAAACTTTAAAAAATTTTGTTTGAAAATGACTCTTTTCAAACAAAGGCTTT
1 GAAACTTTAAAAAATTTTGTTTGAAAATGGCTC-CTCCAAACAGAGGCTTT
* * *
11928469 GAAGCTTTACAAAATCTTGTTTGAAAATG
1 GAAACTTTAAAAAATTTTGTTTGAAAATG
11928498 ACTTGAGGGT
Statistics
Matches: 237, Mismatches: 36, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
49 2 0.01
50 40 0.17
51 119 0.50
52 34 0.14
53 2 0.01
54 2 0.01
55 37 0.16
56 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (50 bp):
GAAACTTTAAAAAATTTTGTTTGAAAATGGCTCCTCCAAACAGAGGCTTT
Found at i:11929427 original size:10 final size:10
Alignment explanation
Indices: 11929414--11929485 Score: 54
Period size: 10 Copynumber: 6.8 Consensus size: 10
11929404 TTTTTATTCA
*
11929414 TTTTTTCTTT
1 TTTTTTGTTT
*
11929424 TTTTTAGTTT
1 TTTTTTGTTT
*
11929434 TCTCTTATGTTT
1 T-T-TTTTGTTT
*
11929446 TCTTTTGTTT
1 TTTTTTGTTT
*
11929456 TTTTTCTCTCTT
1 TTTTT-TGT-TT
*
11929468 TTTATTGTTT
1 TTTTTTGTTT
11929478 TTTTTTGT
1 TTTTTTGT
11929486 CTCTTTCTCA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
10 29 0.62
11 5 0.11
12 13 0.28
ACGTcount: A:0.04, C:0.10, G:0.07, T:0.79
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:11929434 original size:27 final size:28
Alignment explanation
Indices: 11929399--11929456 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
11929389 TGAGTCTTCC
* *
11929399 TTTA-TTTTTTATTCATTTTTTCTTTT-T
1 TTTAGTTTTCTATT-ATGTTTTCTTTTGT
*
11929426 TTTAGTTTTCTCTTATGTTTTCTTTTGT
1 TTTAGTTTTCTATTATGTTTTCTTTTGT
11929454 TTT
1 TTT
11929457 TTTTCTCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.78
Consensus pattern (28 bp):
TTTAGTTTTCTATTATGTTTTCTTTTGT
Found at i:11937125 original size:15 final size:15
Alignment explanation
Indices: 11937075--11937141 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
11937065 ATTGCAAAAT
*
11937075 AAATAAAATAAATGAA
1 AAATAAAATCAAT-AA
* *
11937091 AAA-AAAAAC-TTAA
1 AAATAAAATCAATAA
*
11937104 AATATAAAATGAATAA
1 AA-ATAAAATCAATAA
11937120 AAATAAAATCAA-AA
1 AAATAAAATCAATAA
11937134 AAATAAAA
1 AAATAAAA
11937142 ATAAAAAAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
13 4 0.10
14 12 0.29
15 17 0.41
16 8 0.20
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (15 bp):
AAATAAAATCAATAA
Found at i:11937142 original size:15 final size:14
Alignment explanation
Indices: 11937102--11937149 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
11937092 AAAAAAACTT
11937102 AAAATATAAAATGAATA
1 AAAATA-AAAAT-AA-A
11937119 AAAAT-AAAATCAAA
1 AAAATAAAAAT-AAA
11937133 AAAATAAAAATAAA
1 AAAATAAAAATAAA
11937147 AAA
1 AAA
11937150 GAAAATATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.41
15 12 0.41
17 5 0.17
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:11937154 original size:20 final size:20
Alignment explanation
Indices: 11937075--11937147 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
11937065 ATTGCAAAAT
11937075 AAATAAAATAAATGAAAAA-AA
1 AAATAAAATAAA--AAAAATAA
*
11937096 AAACTTAAAATATAAAATGAATAA
1 AAA--TAAAATA-AAAA-AAATAA
*
11937120 AAATAAAATCAAAAAAATAA
1 AAATAAAATAAAAAAAATAA
11937140 AAATAAAA
1 AAATAAAA
11937148 AAGAAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
20 13 0.30
21 7 0.16
22 8 0.18
23 9 0.20
24 7 0.16
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
AAATAAAATAAAAAAAATAA
Found at i:11939894 original size:15 final size:16
Alignment explanation
Indices: 11939874--11939903 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11939864 TTCTAGGAGT
11939874 CTCAAATTCT-TTTTC
1 CTCAAATTCTCTTTTC
11939889 CTCAAATTCTCTTTT
1 CTCAAATTCTCTTTT
11939904 TTTTGCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (16 bp):
CTCAAATTCTCTTTTC
Found at i:11942070 original size:16 final size:15
Alignment explanation
Indices: 11942051--11942087 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
11942041 TATTATTATT
11942051 ATTAGAAAAAATTAAA
1 ATTA-AAAAAATTAAA
*
11942067 ATTAAGAAAATTAAA
1 ATTAAAAAAATTAAA
11942082 ATTAAA
1 ATTAAA
11942088 TACCAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (15 bp):
ATTAAAAAAATTAAA
Found at i:11942078 original size:15 final size:15
Alignment explanation
Indices: 11942058--11942086 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11942048 ATTATTAGAA
11942058 AAAATTAAAATTAAG
1 AAAATTAAAATTAAG
11942073 AAAATTAAAATTAA
1 AAAATTAAAATTAA
11942087 ATACCAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATTAAAATTAAG
Found at i:11943734 original size:3 final size:3
Alignment explanation
Indices: 11943728--11943774 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
11943718 GAGATTTCAT
**
11943728 TTA TTA TTA TTA ACA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11943775 TATATATTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:11943830 original size:17 final size:16
Alignment explanation
Indices: 11943806--11943855 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
11943796 GCTAGTGTGC
11943806 ATAAAAAATAAATTGA
1 ATAAAAAATAAATTGA
* *
11943822 ATCAAAAAATAATTTACA
1 AT-AAAAAATAAATT-GA
11943840 ATAATAAAATAAATTG
1 ATAA-AAAATAAATTG
11943856 CACAGAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 2 0.07
17 13 0.48
18 12 0.44
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (16 bp):
ATAAAAAATAAATTGA
Found at i:11951035 original size:20 final size:21
Alignment explanation
Indices: 11951003--11951044 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
11950993 GTTTGGATTG
11951003 AGGAAAGAGAAAGTGAGGGAA
1 AGGAAAGAGAAAGTGAGGGAA
*
11951024 AGGAAA-AGAAAGTTAGGGAA
1 AGGAAAGAGAAAGTGAGGGAA
11951044 A
1 A
11951045 TGAGGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (21 bp):
AGGAAAGAGAAAGTGAGGGAA
Found at i:11954835 original size:21 final size:20
Alignment explanation
Indices: 11954769--11954836 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
11954759 TTTATTATAA
*
11954769 TATTTATAAA-ATATTATTT
1 TATTTATAAATATATTTTTT
* *
11954788 TATTAAAATAAATTATATTTTAAT
1 TATT--TATAAA-TATATTTT-TT
11954812 TATTTATAAATATATTGTTTT
1 TATTTATAAATATATT-TTTT
11954833 TATT
1 TATT
11954837 AAGTTAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 4 0.11
21 16 0.42
22 7 0.18
23 6 0.16
24 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (20 bp):
TATTTATAAATATATTTTTT
Found at i:11954856 original size:13 final size:13
Alignment explanation
Indices: 11954833--11954911 Score: 56
Period size: 13 Copynumber: 6.0 Consensus size: 13
11954823 ATATTGTTTT
*
11954833 TATTAAGTTAATA
1 TATTAAATTAATA
* *
11954846 TTTTAAATTAAAA
1 TATTAAATTAATA
11954859 TATTAAA-TAATAA
1 TATTAAATTAAT-A
11954872 TATTATTAATATAATA
1 TATTA--AAT-TAATA
*
11954888 TATAAAATTAA-A
1 TATTAAATTAATA
*
11954900 -ATTAAATAAATA
1 TATTAAATTAATA
11954912 ATAAAAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
11 8 0.15
12 5 0.10
13 25 0.48
14 3 0.06
15 2 0.04
16 5 0.10
17 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (13 bp):
TATTAAATTAATA
Found at i:11954878 original size:42 final size:41
Alignment explanation
Indices: 11954832--11954914 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 41
11954822 TATATTGTTT
* *
11954832 TTATTAAGT-TAATATTTTAAATTAAAATATTAAAT-AATAATA
1 TTATTAA-TATAATATATAAAATT-AAA-ATTAAATAAATAATA
11954874 TTATTAATATAATATATAAAATTAAAATTAAATAAATAATA
1 TTATTAATATAATATATAAAATTAAAATTAAATAAATAATA
11954915 AAAATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
40 7 0.19
41 11 0.30
42 19 0.51
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (41 bp):
TTATTAATATAATATATAAAATTAAAATTAAATAAATAATA
Found at i:11954931 original size:41 final size:41
Alignment explanation
Indices: 11954850--11954935 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 41
11954840 TTAATATTTT
* * *
11954850 AAATTAAAATATTAAATAATAATATTATTAATATAATATATA
1 AAATTAAAATAATAAATAATAAAAATATTAATAT-ATATATA
11954892 AAATTAAAATTAAATAAATAATAAAAATATTATATTATATATAT
1 AAATTAAAA-T-AATAAATAATAAAAATATTA-A-TATATATAT
11954936 TTTGGATTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 9 0.24
43 1 0.03
44 17 0.46
45 7 0.19
46 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (41 bp):
AAATTAAAATAATAAATAATAAAAATATTAATATATATATA
Found at i:11955023 original size:17 final size:19
Alignment explanation
Indices: 11955001--11955036 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
11954991 GATCCAAACC
11955001 TAATTTTA-AAAA-TAAAT
1 TAATTTTATAAAATTAAAT
11955018 TAATTTTATAAAATTAAAT
1 TAATTTTATAAAATTAAAT
11955037 CGAGTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATTTTATAAAATTAAAT
Found at i:11956556 original size:20 final size:20
Alignment explanation
Indices: 11956518--11956557 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11956508 TATAATAAGA
*
11956518 TATTTTTATTTATTAATTTT
1 TATTTTTATTAATTAATTTT
11956538 TATTTTTATTCAATT-ATTTT
1 TATTTTTATT-AATTAATTTT
11956558 CAATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTTATTAATTAATTTT
Found at i:11962792 original size:17 final size:16
Alignment explanation
Indices: 11962758--11962806 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 16
11962748 AAGTTGAGTG
*
11962758 TTTATCTTTTTCAACTT
1 TTTATCTTTTTC-TCTT
11962775 TGTTATCTTTTTCTCTT
1 T-TTATCTTTTTCTCTT
*
11962792 TTTTTCTTTTT-TCTT
1 TTTATCTTTTTCTCTT
11962807 ATTCGGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 4 0.14
16 9 0.31
17 5 0.17
18 11 0.38
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTATCTTTTTCTCTT
Found at i:11966231 original size:2 final size:2
Alignment explanation
Indices: 11966224--11966259 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11966214 GATGACATAC
11966224 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
11966260 GGTTAGAGGG
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):
AT
Found at i:11969675 original size:68 final size:67
Alignment explanation
Indices: 11969571--11969715 Score: 172
Period size: 68 Copynumber: 2.2 Consensus size: 67
11969561 ATGATATCGT
11969571 GAGTCA-AAAAAT-AAGGTGACCAAGATCGAGTCGAGGTTGAAAATAAAATGACC-AGGATGAAA
1 GAGTCATAAAAATGAAGGTGACCAAGATCGAGTCGAGGTTGAAAAT-AAATGACCGA-GATGAAA
11969633 CCAC
64 CCAC
* * * * *
11969637 GAGTCATAAGAAATGAA-GTGACTAATATCGAGTTGAGGTTGAAAATAAATGATCGAGATGAAAT
1 GAGTCATAA-AAATGAAGGTGACCAAGATCGAGTCGAGGTTGAAAATAAATGACCGAGATGAAAC
11969701 CAC
65 CAC
* *
11969704 AACTCATAAAAA
1 GAGTCATAAAAA
11969716 ATGATTTGGA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
66 9 0.13
67 26 0.38
68 31 0.46
69 2 0.03
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.19
Consensus pattern (67 bp):
GAGTCATAAAAATGAAGGTGACCAAGATCGAGTCGAGGTTGAAAATAAATGACCGAGATGAAACC
AC
Found at i:11969919 original size:51 final size:51
Alignment explanation
Indices: 11969853--11969983 Score: 163
Period size: 51 Copynumber: 2.6 Consensus size: 51
11969843 GATTCAAAAG
* *** * ** *
11969853 TTTCAGATTCACAAGAATGGAAGATTCACAAGATGCAAAATTTGTAAGGAT
1 TTTCAGGTTCACAAGAAAAAAAGATTCACAAAATGCAAAATTCATAAAGAT
* * *
11969904 TTTCAGGTTCGCAAGAAAAAAAGATTTACAAAATGCAAGATTCATAAAGAT
1 TTTCAGGTTCACAAGAAAAAAAGATTCACAAAATGCAAAATTCATAAAGAT
11969955 TTTCAGGTTCACAAGAAAAAAAGATTCAC
1 TTTCAGGTTCACAAGAAAAAAAGATTCAC
11969984 CAACTCTAAG
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (51 bp):
TTTCAGGTTCACAAGAAAAAAAGATTCACAAAATGCAAAATTCATAAAGAT
Found at i:11969929 original size:25 final size:25
Alignment explanation
Indices: 11969901--11969980 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
11969891 AATTTGTAAG
11969901 GATTTTCAGGTTCGCAAGAAAAAAA
1 GATTTTCAGGTTCGCAAGAAAAAAA
* *** * *
11969926 GATTTACAAAAT-GCAAGATTCATAAA
1 GATTTTCAGGTTCGCAAGA--AAAAAA
*
11969952 GATTTTCAGGTTCACAAGAAAAAAA
1 GATTTTCAGGTTCGCAAGAAAAAAA
11969977 GATT
1 GATT
11969981 CACCAACTCT
Statistics
Matches: 39, Mismatches: 13, Indels: 6
0.67 0.22 0.10
Matches are distributed among these distances:
24 6 0.15
25 16 0.41
26 12 0.31
27 5 0.13
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.26
Consensus pattern (25 bp):
GATTTTCAGGTTCGCAAGAAAAAAA
Found at i:11970879 original size:120 final size:120
Alignment explanation
Indices: 11970175--11970910 Score: 547
Period size: 120 Copynumber: 6.1 Consensus size: 120
11970165 ATTTGCATTG
* * ** * *
11970175 AGCCAAGATTGGATGATCGAAATGAAATCATTAGTCAAAAAAATAAAACGA-CAAGGATCGAGTC
1 AGCCAAGATCGGATGATCGAGATGAAATCACGAGTC--AAAAATAAAGCGACCAA-GATTGAGTC
* * * * * * * * *
11970239 AAAGTAGAAAATAAATGATCAAGA-CAAAATCACGAGTCATAAGAAATGATCTAGATTG
63 AAGGTAAAAAATAAATGATTAGGATGAAACT-ACGAGTCATAAGAAATGATCTGGACTA
* * * * * * ** *
11970297 AGCCAAGATTGGATG-TCTGA-ACGAAA-CAATGAATTGAAAAATAAGGTAACCAGGATTGAGTC
1 AGCCAAGATCGGATGATC-GAGATGAAATC-ACG-AGTCAAAAATAAAGCGACCAAGATTGAGTC
* * * * * *
11970359 AAGGTAAACAATAAATGACT-GAAATGAAAC-ATCAAGTCATAAGAAATGATCTAGATTA
63 AAGGTAAAAAATAAATGATTAG-GATGAAACTA-CGAGTCATAAGAAATGATCTGGACTA
* ** * * *
11970417 AGCCAAGATCGGATGATCGAAATGAAA-CAATAGGTCAAAAATAAAGCAACCAAGATCGAGTTAA
1 AGCCAAGATCGGATGATCGAGATGAAATCACGA-GTCAAAAATAAAGCGACCAAGATTGAGTCAA
** * ** * *
11970481 GGTCTAAAATAAACGACCAAGATGAAA-TCACGAGTCATAAGAAATGATCTGGACTG
65 GGTAAAAAATAAATGATTAGGATGAAACT-ACGAGTCATAAGAAATGATCTGGACTA
* * * *
11970537 AGCCAAGATCGGGTGATCGGGATAAAATCACGAGTCAAAAA-ACAAGGCGACCAGGATTGAGTCA
1 AGCCAAGATCGGATGATCGAGATGAAATCACGAGTCAAAAATA-AA-GCGACCAAGATTGAGTCA
** ** ** *
11970601 AGGTCTAAAATGTATGATCGGGATGAAACTATGAGTCATAAGAAATGATCTGGACTA
64 AGGTAAAAAATAAATGATTAGGATGAAACTACGAGTCATAAGAAATGATCTGGACTA
* ** * * * * ** *
11970658 AGCTAAGATTAGATGATTGGGATGAAATCATGAGTCAAAAAATGAAGCGATTAAGATTGAGTCGA
1 AGCCAAGATCGGATGATCGAGATGAAATCACGAGTC-AAAAATAAAGCGACCAAGATTGAGTCAA
* * * * * *
11970723 GGTAAAAAATAAATGATTGGGATGAAACCACTAGTCATAAGAAATGATTTGGATTG
65 GGTAAAAAATAAATGATTAGGATGAAACTACGAGTCATAAGAAATGATCTGGACTA
* ** * * **
11970779 AGCCAAGATCGGGTGATCGAGACAAAATCACGAGTCAAAAATAAAGTGACCAAGATCGAGTTGAG
1 AGCCAAGATCGGATGATCGAGATGAAATCACGAGTCAAAAATAAAGCGACCAAGATTGAGTCAAG
* * *
11970844 GTAAAAAATAAATGATTAGGATGAAACTACGAGTCATAAAAAATAATTTGGACTA
66 GTAAAAAATAAATGATTAGGATGAAACTACGAGTCATAAGAAATGATCTGGACTA
*
11970899 AACCAAGATCGG
1 AGCCAAGATCGG
11970911 GTGAGTGATA
Statistics
Matches: 488, Mismatches: 107, Indels: 40
0.77 0.17 0.06
Matches are distributed among these distances:
119 3 0.01
120 255 0.52
121 203 0.42
122 27 0.06
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.21
Consensus pattern (120 bp):
AGCCAAGATCGGATGATCGAGATGAAATCACGAGTCAAAAATAAAGCGACCAAGATTGAGTCAAG
GTAAAAAATAAATGATTAGGATGAAACTACGAGTCATAAGAAATGATCTGGACTA
Found at i:11971682 original size:17 final size:17
Alignment explanation
Indices: 11971662--11971713 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
11971652 CCTTTGTCTC
11971662 TTTTT-CTTTTTTCTTT
1 TTTTTGCTTTTTTCTTT
* *
11971678 TTTTTGCCTTTTGCTTT
1 TTTTTGCTTTTTTCTTT
11971695 TTTTTGCTTTTTT-TTT
1 TTTTTGCTTTTTTCTTT
11971711 TTT
1 TTT
11971714 CTTTTTGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 11 0.35
17 20 0.65
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTTGCTTTTTTCTTT
Found at i:11971689 original size:16 final size:15
Alignment explanation
Indices: 11971670--11971718 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 15
11971660 TCTTTTTCTT
11971670 TTTTCTTTTTTTTGCC
1 TTTTCTTTTTTTTG-C
11971686 TTTTGCTTTTTTTTGC
1 TTTT-CTTTTTTTTGC
11971702 TTTT-TTTTTTTT-C
1 TTTTCTTTTTTTTGC
11971715 TTTT
1 TTTT
11971719 TGTACACCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.16
14 8 0.25
16 9 0.28
17 10 0.31
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTTTTGC
Found at i:11972018 original size:13 final size:13
Alignment explanation
Indices: 11971990--11972023 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11971980 TCCCAATCTA
11971990 TTTCTTT-TTCTT
1 TTTCTTTGTTCTT
*
11972002 TTTCTTTGTTTTT
1 TTTCTTTGTTCTT
11972015 TTTCTTTGT
1 TTTCTTTGT
11972024 GTTAGCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTCTTTGTTCTT
Found at i:11979394 original size:21 final size:21
Alignment explanation
Indices: 11979362--11979408 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
11979352 TAGAAGATAG
*
11979362 AAAAT-ATAATTTTTATTGAAA
1 AAAATGATAATTTCTA-TGAAA
*
11979383 AAAATGAT-ATTTCTATGATA
1 AAAATGATAATTTCTATGAAA
11979403 AAAATG
1 AAAATG
11979409 TGATTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 10 0.43
21 11 0.48
22 2 0.09
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (21 bp):
AAAATGATAATTTCTATGAAA
Found at i:11979607 original size:114 final size:115
Alignment explanation
Indices: 11979464--11979737 Score: 349
Period size: 112 Copynumber: 2.4 Consensus size: 115
11979454 AAAACTAATA
11979464 TTTCTAAGATAAAAAAATACAATTTTTGTTAAAAATATGAAAAAAATATAGTTTTCAAAATTCAA
1 TTTCTAAGAT--AAAAATACAATTTTTGTTAAAAATATGAAAAAAATATAGTTTTCAAAATTCAA
** * * * *
11979529 TAAAAATGGTGTTTCTAAAATAAAAACTTAGTTTTTGTTGAAAAGACGA-TT
64 TAAAAATGACGTTTCTAAAATAAAAACATAATTTTTATTGAAAAGACAACTT
** * * *
11979580 TTTCTAAGATAAAAATGTAATTTTTGTTAAAAATATG--AAAAATATATTTTTTAGAATTCAATA
1 TTTCTAAGATAAAAATACAATTTTTGTTAAAAATATGAAAAAAATATAGTTTTCAAAATTCAATA
* * *
11979643 AAGATGACGTTTCTAAGATAAAAACATAATTTTTATTGAAAATACAACTT
66 AAAATGACGTTTCTAAAATAAAAACATAATTTTTATTGAAAAGACAACTT
* * *
11979693 TTT-TAAGATAAAAATACAGTCTTTGTTGAAAATATGAAAAAAATA
1 TTTCTAAGATAAAAATACAATTTTTGTTAAAAATATGAAAAAAATA
11979738 AAACGTAAAA
Statistics
Matches: 136, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
112 89 0.65
113 5 0.04
114 32 0.24
116 10 0.07
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (115 bp):
TTTCTAAGATAAAAATACAATTTTTGTTAAAAATATGAAAAAAATATAGTTTTCAAAATTCAATA
AAAATGACGTTTCTAAAATAAAAACATAATTTTTATTGAAAAGACAACTT
Found at i:11979784 original size:37 final size:38
Alignment explanation
Indices: 11979735--11979815 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
11979725 TATGAAAAAA
* **
11979735 ATAAAA-CGTAAAATACT-TTTTTTTAATATTATTACTT
1 ATAAAATCGTAAAATA-TATTTATTTAATATTATTACAC
11979772 ATAAAATC-TAAAATATATTTATTTAATATTATTACAC
1 ATAAAATCGTAAAATATATTTATTTAATATTATTACAC
11979809 ATAAAAT
1 ATAAAAT
11979816 TTGTTCTATG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
36 1 0.03
37 37 0.95
38 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (38 bp):
ATAAAATCGTAAAATATATTTATTTAATATTATTACAC
Found at i:11980411 original size:36 final size:36
Alignment explanation
Indices: 11980371--11980448 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
11980361 TAAAAGAATT
*
11980371 GATTATTTATTATAAAAATCCTAACATGTAATAAAA
1 GATTATTTATTATAAAAATCCTAACATATAATAAAA
11980407 GATTATTTATTATAAAAATCCTAACATATAATAAAA
1 GATTATTTATTATAAAAATCCTAACATATAATAAAA
11980443 GATTAT
1 GATTAT
11980449 AATTAAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (36 bp):
GATTATTTATTATAAAAATCCTAACATATAATAAAA
Found at i:11980442 original size:19 final size:19
Alignment explanation
Indices: 11980382--11980442 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
11980372 ATTATTTATT
*
11980382 ATAAAAATCCTAACATGTA
1 ATAAAAATCCTAACATATA
** *
11980401 ATAAAAGAT--T-ATTTATT
1 ATAAAA-ATCCTAACATATA
11980418 ATAAAAATCCTAACATATA
1 ATAAAAATCCTAACATATA
11980437 ATAAAA
1 ATAAAA
11980443 GATTATAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
16 2 0.06
17 9 0.29
18 2 0.06
19 16 0.52
20 2 0.06
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (19 bp):
ATAAAAATCCTAACATATA
Found at i:11980992 original size:24 final size:24
Alignment explanation
Indices: 11980964--11981014 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
11980954 AAATTAATTT
*
11980964 AATAAAACTAATAAATATAACACA
1 AATAAAAATAATAAATATAACACA
*
11980988 AATAAAAATAATAAATATAACATA
1 AATAAAAATAATAAATATAACACA
11981012 AAT
1 AAT
11981015 GATAACTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.24
Consensus pattern (24 bp):
AATAAAAATAATAAATATAACACA
Found at i:11985864 original size:13 final size:12
Alignment explanation
Indices: 11985847--11985879 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
11985837 TTTTATCGAG
11985847 TAAAATTAATAT
1 TAAAATTAATAT
11985859 TGAAAATTAATAT
1 T-AAAATTAATAT
11985872 TAAAATTA
1 TAAAATTA
11985880 CTCTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
TAAAATTAATAT
Found at i:11986405 original size:14 final size:15
Alignment explanation
Indices: 11986372--11986406 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
11986362 GCTACGTTTG
11986372 TTTTGCGAAAAATGAC
1 TTTT-CGAAAAATGAC
11986388 TTTTCGAAAAATGA-
1 TTTTCGAAAAATGAC
11986402 TTTTC
1 TTTTC
11986407 ACATTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 10 0.53
16 4 0.21
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (15 bp):
TTTTCGAAAAATGAC
Found at i:11986623 original size:22 final size:22
Alignment explanation
Indices: 11986592--11986637 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
11986582 AAATTTACTT
* *
11986592 ATAAAAAATATTATATTAATAA
1 ATAAAAAATAGTATATCAATAA
*
11986614 ATAAATAATAGTATATCAATAA
1 ATAAAAAATAGTATATCAATAA
11986636 AT
1 AT
11986638 CATACATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
ATAAAAAATAGTATATCAATAA
Found at i:11986779 original size:15 final size:15
Alignment explanation
Indices: 11986736--11986779 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
11986726 GAAAAATATT
11986736 ATAATA-TATAATAA
1 ATAATATTATAATAA
* *
11986750 ACTATTATTACAATAA
1 A-TAATATTATAATAA
11986766 ATAATATTATAATA
1 ATAATATTATAATA
11986780 TCTTAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 1 0.04
15 15 0.62
16 8 0.33
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATATTATAATAA
Found at i:11987213 original size:26 final size:26
Alignment explanation
Indices: 11987184--11987233 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
11987174 TTTTTGAGAA
*
11987184 AAATTAATTAAGAT-AAAATTTAAATC
1 AAATAAATTAA-ATAAAAATTTAAATC
11987210 AAATAAATTAAATAAAAATTTAAA
1 AAATAAATTAAATAAAAATTTAAA
11987234 AAAATTACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AAATAAATTAAATAAAAATTTAAATC
Found at i:11987505 original size:2 final size:2
Alignment explanation
Indices: 11987498--11987528 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11987488 CAAAAGCCTT
11987498 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11987529 TTCTTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11988225 original size:30 final size:28
Alignment explanation
Indices: 11988204--11988286 Score: 88
Period size: 26 Copynumber: 3.1 Consensus size: 28
11988194 AATCAATATA
11988204 AATAAATAAAATAAAGATAAAAATAAAAT
1 AATAAA-AAAATAAAGATAAAAATAAAAT
11988233 AATAAAAAAATAATAG-T--AAATAAAA-
1 AATAAAAAAATAA-AGATAAAAATAAAAT
*
11988258 AAT--AAAGATAAAGATAAAAATATAAAT
1 AATAAAAAAATAAAGATAAAAATA-AAAT
11988285 AA
1 AA
11988287 ATGTGAAGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
22 2 0.04
23 8 0.17
25 8 0.17
26 11 0.23
27 2 0.04
28 8 0.17
29 8 0.17
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (28 bp):
AATAAAAAAATAAAGATAAAAATAAAAT
Found at i:11988229 original size:17 final size:16
Alignment explanation
Indices: 11988207--11988287 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 16
11988197 CAATATAAAT
11988207 AAATAAAATAAAGATAA
1 AAATAAAATAAAGA-AA
11988224 AAATAAAATAATA-AAA
1 AAATAAAATAA-AGAAA
* *
11988240 AAATAATAGTAAATAAA
1 AAATAA-AATAAAGAAA
11988257 AAATAAAGATAAAGATAA
1 AAATAAA-ATAAAGA-AA
11988275 AAATATAAATAAA
1 AAATA-AAATAAA
11988288 TGTGAAGATA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
16 10 0.18
17 30 0.55
18 13 0.24
19 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (16 bp):
AAATAAAATAAAGAAA
Found at i:11988350 original size:7 final size:7
Alignment explanation
Indices: 11988303--11988368 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
11988293 AGATAAAGAC
11988303 AAATATA
1 AAATATA
*
11988310 AAACA-A
1 AAATATA
11988316 AAATA-A
1 AAATATA
11988322 TAAATA-A
1 -AAATATA
*
11988329 ATAA-ATG
1 A-AATATA
11988336 AAATATA
1 AAATATA
*
11988343 AGATATA
1 AAATATA
11988350 AAATATA
1 AAATATA
11988357 AAATATA
1 AAATATA
11988364 TAAAT
1 -AAAT
11988369 CAGTCATTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
6 10 0.21
7 34 0.71
8 4 0.08
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.26
Consensus pattern (7 bp):
AAATATA
Found at i:11989983 original size:11 final size:11
Alignment explanation
Indices: 11989959--11990141 Score: 70
Period size: 11 Copynumber: 15.7 Consensus size: 11
11989949 AAAAAGAATA
*
11989959 AAAATAAAGGT
1 AAAATAAAGAT
*
11989970 AAAATCAAGAT
1 AAAATAAAGAT
11989981 AAATAAATAAA-AT
1 --A-AAATAAAGAT
*
11989994 AAAGATAAAGGT
1 AAA-ATAAAGAT
11990006 -AAATAAAGAT
1 AAAATAAAGAT
11990016 AATAATAAAGTAAT
1 AA-AATAAAG--AT
*
11990030 AAAATAAAAAT
1 AAAATAAAGAT
11990041 AAAATAATA-A-
1 AAAATAA-AGAT
* *
11990051 ATAATAAATAT
1 AAAATAAAGAT
*
11990062 AAAAGATAAATAT
1 -AAA-ATAAAGAT
11990075 AAAAATATAA-AT
1 -AAAATA-AAGAT
* *
11990087 AAATGTGAAGAT
1 AAA-ATAAAGAT
* *
11990099 AAAGATCAATAT
1 AAA-ATAAAGAT
* *
11990111 AAAACAAAAAT
1 AAAATAAAGAT
*
11990122 AATAATAAATAT
1 AA-AATAAAGAT
11990134 AAAATAAA
1 AAAATAAA
11990142 AATTTAAAAT
Statistics
Matches: 135, Mismatches: 19, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
9 1 0.01
10 16 0.12
11 46 0.34
12 39 0.29
13 23 0.17
14 10 0.07
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (11 bp):
AAAATAAAGAT
Found at i:11989993 original size:19 final size:20
Alignment explanation
Indices: 11989969--11990090 Score: 85
Period size: 19 Copynumber: 6.0 Consensus size: 20
11989959 AAAATAAAGG
*
11989969 TAAAATCAAGATAAA-TAAA
1 TAAAATAAAGATAAAGTAAA
11989988 TAAAATAAAGATAAAGGTAAA
1 TAAAATAAAGATAAA-GTAAA
11990009 TAAAGATAATA-ATAAAGT-AA
1 TAAA-ATAA-AGATAAAGTAAA
* *
11990029 TAAAATAAAAATAAAAT-AA
1 TAAAATAAAGATAAAGTAAA
*
11990048 TAAATAATAAATATAAAAGATAAA
1 T-AA-AATAAAGAT-AAAG-TAAA
* *
11990072 TATAA-AAATATAAA-TAAA
1 TAAAATAAAGATAAAGTAAA
11990090 T
1 T
11990091 GTGAAGATAA
Statistics
Matches: 88, Mismatches: 5, Indels: 21
0.77 0.04 0.18
Matches are distributed among these distances:
18 6 0.07
19 27 0.31
20 11 0.12
21 24 0.27
22 14 0.16
23 3 0.03
24 3 0.03
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.24
Consensus pattern (20 bp):
TAAAATAAAGATAAAGTAAA
Found at i:11990031 original size:8 final size:7
Alignment explanation
Indices: 11990016--11990088 Score: 59
Period size: 7 Copynumber: 10.7 Consensus size: 7
11990006 AAATAAAGAT
11990016 AATAATA
1 AATAATA
11990023 AAGTAAT-
1 AA-TAATA
11990030 AA-AATA
1 AATAATA
11990036 AA-AATAA
1 AATAAT-A
11990043 AATAATA
1 AATAATA
11990050 AATAATA
1 AATAATA
11990057 AAT-ATA
1 AATAATA
11990063 AA-AGATA
1 AATA-ATA
11990070 AAT-ATA
1 AATAATA
*
11990076 AAAATATA
1 AATA-ATA
11990084 AATAA
1 AATAA
11990089 ATGTGAAGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
5 3 0.05
6 15 0.27
7 24 0.44
8 13 0.24
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.25
Consensus pattern (7 bp):
AATAATA
Found at i:11990063 original size:27 final size:28
Alignment explanation
Indices: 11990016--11990087 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 28
11990006 AAATAAAGAT
11990016 AATAATAAAGTAATAAA-ATAAAA-ATAA
1 AATAATAAA-TAATAAATATAAAAGATAA
11990043 AATAATAAATAATAAATATAAAAGATAA
1 AATAATAAATAATAAATATAAAAGATAA
11990071 ATATAA-AAAT-ATAAATA
1 A-ATAATAAATAATAAATA
11990088 AATGTGAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
26 7 0.17
27 22 0.52
28 9 0.21
29 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (28 bp):
AATAATAAATAATAAATATAAAAGATAA
Found at i:11990071 original size:34 final size:34
Alignment explanation
Indices: 11990016--11990088 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 34
11990006 AAATAAAGAT
11990016 AATAATAAAGTAATAAAATAAAAAT-AAAATAATA
1 AATAATAAAGTAATAAAATAAAAATAAAAAT-ATA
*
11990050 AATAATAAA-T-ATAAAAGATAAATATAAAAATATA
1 AATAATAAAGTAAT-AAA-ATAAAAATAAAAATATA
11990084 AATAA
1 AATAA
11990089 ATGTGAAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
32 2 0.06
33 4 0.11
34 24 0.69
35 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.25
Consensus pattern (34 bp):
AATAATAAAGTAATAAAATAAAAATAAAAATATA
Found at i:11990143 original size:6 final size:6
Alignment explanation
Indices: 11990006--11990144 Score: 68
Period size: 6 Copynumber: 22.7 Consensus size: 6
11989996 AGATAAAGGT
* *
11990006 AAATAA AGATAA TAATAA AGTAAT-A AAATAA AAATAAA ATAATAA ATAATAA
1 AAATAA AAATAA AAATAA A--AATAA AAATAA AAAT-AA A-AATAA A-AATAA
* * * ** * * * *
11990058 ATATAA AAGATAA ATATAA AAATAT AAATAA ATGTGA AGATAA AGATCA
1 AAATAA AA-ATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * * *
11990107 ATAT-A AAACAA AAATAA TAATAA ATAT-A AAATAA AAAT
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAAT
11990145 TTAAAATATA
Statistics
Matches: 100, Mismatches: 25, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
5 10 0.10
6 64 0.64
7 20 0.20
8 6 0.06
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (6 bp):
AAATAA
Found at i:11997107 original size:34 final size:34
Alignment explanation
Indices: 11997006--11997116 Score: 104
Period size: 33 Copynumber: 3.3 Consensus size: 34
11996996 CAATCTTTGC
* * * * *
11997006 TAAA-TTAATGACGTTTGTATCAAAAAAATACCAA
1 TAAATTTAGTGACATTTGTAT-AGAAAAATACTAT
**
11997040 TAAA-TTAGCAACATTTGTATAGAAAAATACTAT
1 TAAATTTAGTGACATTTGTATAGAAAAATACTAT
11997073 T-AATTTAGTGACATTTGTATAGAAAAA-ACGCTAT
1 TAAATTTAGTGACATTTGTATAGAAAAATA--CTAT
11997107 TAAATTTAGT
1 TAAATTTAGT
11997117 AGCATTTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
32 3 0.05
33 32 0.50
34 21 0.33
35 8 0.12
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (34 bp):
TAAATTTAGTGACATTTGTATAGAAAAATACTAT
Found at i:11997489 original size:15 final size:15
Alignment explanation
Indices: 11997469--11997502 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
11997459 TAGTGTGCTC
11997469 AATAACTTACTAAAT
1 AATAACTTACTAAAT
11997484 AATAACTTACTAAAT
1 AATAACTTACTAAAT
11997499 AATA
1 AATA
11997503 TCATACAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAACTTACTAAAT
Found at i:11998806 original size:161 final size:159
Alignment explanation
Indices: 11998420--11998881 Score: 554
Period size: 161 Copynumber: 2.9 Consensus size: 159
11998410 CATTTTGGCC
* * * * *
11998420 TTTCACAAATATCAATCATA-G-AAACCAAATTCAATCATTTGGACAAGTTTAATATCATGTATT
1 TTTCACATATATCAA-C-TACGAAAACCAAGTTCAATCATTCGAAAAAGTTTAATATCATGTATT
* * * * *
11998483 AAAGCTATCTAAACTGTTAAAATAGAACAATAATAACGACTTTTTATTTTTGACTTTTAACAGCA
64 GAAGCTATCTAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTT-ACTTTTAACAGCA
* *
11998548 AAAAAGTCCTTAACAGAGGTAAGCAACAACTT
128 AAAAAGTCCTAAACAGAGGTAAACAACAACTT
* * *
11998580 TTTCACATATATCAACTACGAAAACTAAGTTTAATCATTCGAAAAAGTTTAATATCATATATTGA
1 TTTCACATATATCAACTACGAAAACCAAGTTCAATCATTCGAAAAAGTTTAATATCATGTATTGA
* *
11998645 AGCTATCCAAACTGTTAAAATAGAACAATAATAGTAAATTTGTATTTTTACCTTTTAACAGCCTA
66 AGCTATCTAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTA-CTTTTAACAG-C-A
* **
11998710 AAAAA-TCCTAAATAGAGGTAAACAGTAACTT
128 AAAAAGTCCTAAACAGAGGTAAACAACAACTT
* * *
11998741 TTTCACATATATTAACTACGAAAACCAAGTTCAATCATTCAAAAAAGTTTAATATTATGTATTGA
1 TTTCACATATATCAACTACGAAAACCAAGTTCAATCATTCGAAAAAGTTTAATATCATGTATTGA
* * * * * *
11998806 AACCATCTAAACTGTTAAAATAAAATAATAATAGCACATTTGTATTTTTGTCTTTTAAC-GTCAA
66 AGCTATCTAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTT-ACTTTTAACAG-CAA
*
11998870 AATAGTCCTAAA
129 AAAAGTCCTAAA
11998882 TTTTTTGACA
Statistics
Matches: 259, Mismatches: 36, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
158 2 0.01
159 8 0.03
160 112 0.43
161 131 0.51
162 6 0.02
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (159 bp):
TTTCACATATATCAACTACGAAAACCAAGTTCAATCATTCGAAAAAGTTTAATATCATGTATTGA
AGCTATCTAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTACTTTTAACAGCAAAA
AAGTCCTAAACAGAGGTAAACAACAACTT
Found at i:11999024 original size:28 final size:30
Alignment explanation
Indices: 11998954--11999024 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
11998944 AAGAAACAAG
11998954 GAAAAAAAAAGCATAAAATAAAAAGCCAAAA
1 GAAAAAAAAAG-ATAAAATAAAAAGCCAAAA
** * *
11998985 GAAAAATCAAGA-AAACTAAAAATCCAAAA
1 GAAAAAAAAAGATAAAATAAAAAGCCAAAA
11999014 -AAAAAAAAAGA
1 GAAAAAAAAAGA
11999025 GAAGAAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 9 0.26
29 15 0.44
30 1 0.03
31 9 0.26
ACGTcount: A:0.75, C:0.10, G:0.08, T:0.07
Consensus pattern (30 bp):
GAAAAAAAAAGATAAAATAAAAAGCCAAAA
Found at i:11999423 original size:27 final size:28
Alignment explanation
Indices: 11999392--11999462 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 28
11999382 AAAGGTGAAG
**
11999392 AAAAAGAGAAAAAAA-AGGGAAAAATTA
1 AAAAAGAGAAAAAAAGAAAGAAAAATTA
11999419 AAAAA-A-AAAGAAAAGAAAGAAAAATTA
1 AAAAAGAGAAA-AAAAGAAAGAAAAATTA
11999446 AAAAATGAAGAAAAAAA
1 AAAAA-G-AGAAAAAAA
11999463 TGAATGGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 20 0.56
30 5 0.14
31 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (28 bp):
AAAAAGAGAAAAAAAGAAAGAAAAATTA
Found at i:12011955 original size:26 final size:24
Alignment explanation
Indices: 12011903--12011958 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
12011893 AATTAACTAC
*
12011903 AAAAATAAAAGTAAATAAAGCATA
1 AAAAATAAAAGTAAATAAAGCAAA
*
12011927 AAAAATATAAAGCTAAATAAATGAAAA
1 AAAAATA-AAAG-TAAATAAA-GCAAA
12011954 AAAAA
1 AAAAA
12011959 AGAATAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 7 0.26
25 4 0.15
26 8 0.30
27 8 0.30
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (24 bp):
AAAAATAAAAGTAAATAAAGCAAA
Found at i:12020318 original size:12 final size:12
Alignment explanation
Indices: 12020301--12020330 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
12020291 TGTTTAAAAC
12020301 ATTATCAACTTA
1 ATTATCAACTTA
12020313 ATTATCAACTTA
1 ATTATCAACTTA
12020325 ACTTAT
1 A-TTAT
12020331 GTGTGATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTATCAACTTA
Found at i:12020429 original size:2 final size:2
Alignment explanation
Indices: 12020411--12020447 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
12020401 GCGTGTTGTG
* *
12020411 TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12020448 TCTTAACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Done.