Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 114 of 132
Found at i:34681517 original size:29 final size:30
Alignment explanation
Indices: 34681436--34681521 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 30
34681426 TTTAACCCCG
*
34681436 ATTTCACCAAAAATTACCATTTTACACCCAA
1 ATTTTACCAAAAATTACCATTTTAC-CCCAA
* * *
34681467 ACTTT-CC-AAAATT-TCATTTTTTACCTC-A
1 ATTTTACCAAAAATTACCA--TTTTACCCCAA
34681495 ATTTTACCAAAAATTACCATTTTACCC
1 ATTTTACCAAAAATTACCATTTTACCC
34681522 TCGGATGTCC
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
28 7 0.16
29 17 0.40
30 14 0.33
31 5 0.12
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.37
Consensus pattern (30 bp):
ATTTTACCAAAAATTACCATTTTACCCCAA
Found at i:34682960 original size:23 final size:20
Alignment explanation
Indices: 34682933--34682982 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 20
34682923 AACACTAGTC
34682933 TTTAAATAAATAAATTAGTAATA
1 TTTAAATAAATAAA--A-TAATA
*
34682956 TTTAAA-CAATAAAATAATA
1 TTTAAATAAATAAAATAATA
34682975 TTTAAATA
1 TTTAAATA
34682983 TAGGGTGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 11 0.46
20 1 0.04
22 6 0.25
23 6 0.25
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAAATAAATAAAATAATA
Found at i:34694697 original size:41 final size:41
Alignment explanation
Indices: 34694647--34694850 Score: 320
Period size: 41 Copynumber: 5.0 Consensus size: 41
34694637 TAAAAAGTAG
* *
34694647 AGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGATCAT
1 AGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAA
* *
34694688 AGCAATAGCGGGGCTTATGGGAAAGCGCCACTAAAGGTCAA
1 AGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAA
34694729 AGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAA
1 AGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAA
*
34694770 AGCAATAGCGGCGCTTATGGGCAAA-CGCCGTTAAAGGTCAA
1 AGCAATAGCGGCGCTTATGGG-AAAGCGCCGCTAAAGGTCAA
** *
34694811 AGCAATAGCGGCGCTTATGAAAAAGCGCCACTAAAGGTCA
1 AGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCA
34694851 GTGTAATAAT
Statistics
Matches: 150, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 3 0.02
41 144 0.96
42 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.29, T:0.16
Consensus pattern (41 bp):
AGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAA
Found at i:34697755 original size:19 final size:18
Alignment explanation
Indices: 34697727--34697789 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
34697717 TAAAATAGAG
*
34697727 AAAATTATAAAAATAATA
1 AAAAATATAAAAATAATA
34697745 AAAAATCATAAATATATACATA
1 AAAAAT-ATAAA-A-ATA-ATA
* * *
34697767 AAACATAAAAAAATTATA
1 AAAAATATAAAAATAATA
34697785 AAAAA
1 AAAAA
34697790 AATTAACAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 12 0.33
19 7 0.19
20 2 0.06
21 7 0.19
22 8 0.22
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATATAAAAATAATA
Found at i:34699459 original size:43 final size:43
Alignment explanation
Indices: 34699398--34699493 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
34699388 ATTTGTTAAT
* *
34699398 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGAACATGTTC
1 TTTAGCGGCGATTGTGGGAAAAGCGCCGCTAAAGAACATGTTC
*
34699441 TTTAGCGGCGATTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGATTGTGGGAAAAGCGCCGCTAAAGAACATGTTC
34699484 TTTAGCGGCG
1 TTTAGCGGCG
34699494 TTTTTTCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (43 bp):
TTTAGCGGCGATTGTGGGAAAAGCGCCGCTAAAGAACATGTTC
Found at i:34708945 original size:16 final size:17
Alignment explanation
Indices: 34708890--34708945 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
34708880 ATATTATAAA
*
34708890 AATTATAAATTAATT-T
1 AATTTTAAATTAATTAT
34708906 AATTTATAAA-TAA-TAT
1 AATTT-TAAATTAATTAT
*
34708922 AATATTAAATTAATTAT
1 AATTTTAAATTAATTAT
34708939 -ATTTTAA
1 AATTTTAA
34708946 CAATTATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 5 0.15
16 21 0.64
17 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTTAAATTAATTAT
Found at i:34708960 original size:33 final size:33
Alignment explanation
Indices: 34708895--34708971 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
34708885 ATAAAAATTA
34708895 TAAATTAATT-TAATTTATAAATAATATAATAT
1 TAAATTAATTATAATTTATAAATAATATAATAT
* *
34708927 TAAATTAATTATATTTTA-ACAATTATATAATAT
1 TAAATTAATTATAATTTATA-AATAATATAATAT
34708960 T-AATTGAATTAT
1 TAAATT-AATTAT
34708972 TGTTTTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 15 0.38
33 25 0.62
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
TAAATTAATTATAATTTATAAATAATATAATAT
Found at i:34735739 original size:80 final size:80
Alignment explanation
Indices: 34735609--34735777 Score: 311
Period size: 80 Copynumber: 2.1 Consensus size: 80
34735599 TATACGGAAG
*
34735609 TGTGGTTTTTAACATGGCATTAACATTGGGGCAATTAGTTTTAAAGGGGGACTTTCTATAGGATG
1 TGTGGTTTTTAACATGGCATTAACATTGGGGCAATTAGTTTTAAAAGGGGACTTTCTATAGGATG
34735674 ACGGGATCATTTGGA
66 ACGGGATCATTTGGA
*
34735689 TGTGGTTTTTAACATGGCATTAACATTGGGGCAATTAGTTTTAAAAGGGGATTTTCTATAGGATG
1 TGTGGTTTTTAACATGGCATTAACATTGGGGCAATTAGTTTTAAAAGGGGACTTTCTATAGGATG
*
34735754 GCGGGATCATTTGGA
66 ACGGGATCATTTGGA
34735769 TGTGGTTTT
1 TGTGGTTTT
34735778 AAAAAGTTAT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 86 1.00
ACGTcount: A:0.25, C:0.09, G:0.29, T:0.37
Consensus pattern (80 bp):
TGTGGTTTTTAACATGGCATTAACATTGGGGCAATTAGTTTTAAAAGGGGACTTTCTATAGGATG
ACGGGATCATTTGGA
Found at i:34736073 original size:80 final size:80
Alignment explanation
Indices: 34735940--34736108 Score: 302
Period size: 80 Copynumber: 2.1 Consensus size: 80
34735930 TATACGGAAG
* *
34735940 TGTGGTTTTTAACATGGCATTAATATTGGGGCAATTAGTTTTAAAAGGGGACTTTCTATAGGATG
1 TGTGGTTTTTAACATGGCATTAACATTGGGGCAATTAGTTTTAAAAGAGGACTTTCTATAGGATG
*
34736005 GCGGGATCATTTGGA
66 GCAGGATCATTTGGA
*
34736020 TGTGGTTTTTTACATGGCATTAACATTGGGGCAATTAGTTTTAAAAGAGGACTTTCTATAGGATG
1 TGTGGTTTTTAACATGGCATTAACATTGGGGCAATTAGTTTTAAAAGAGGACTTTCTATAGGATG
34736085 GCAGGATCATTTGGA
66 GCAGGATCATTTGGA
34736100 TGTGGTTTT
1 TGTGGTTTT
34736109 AAAAAGTTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 85 1.00
ACGTcount: A:0.25, C:0.09, G:0.28, T:0.38
Consensus pattern (80 bp):
TGTGGTTTTTAACATGGCATTAACATTGGGGCAATTAGTTTTAAAAGAGGACTTTCTATAGGATG
GCAGGATCATTTGGA
Found at i:34736182 original size:331 final size:331
Alignment explanation
Indices: 34735580--34736243 Score: 1238
Period size: 331 Copynumber: 2.0 Consensus size: 331
34735570 AAAATTAGTA
34735580 CTCGTCATATGGAACGGGTTATACGGAAGTGTGGTTTTTAACATGGCATTAACATTGGGGCAATT
1 CTCGTCATATGGAACGGGTTATACGGAAGTGTGGTTTTTAACATGGCATTAACATTGGGGCAATT
*
34735645 AGTTTTAAAGGGGGACTTTCTATAGGATGACGGGATCATTTGGATGTGGTTTTTAACATGGCATT
66 AGTTTTAAAAGGGGACTTTCTATAGGATGACGGGATCATTTGGATGTGGTTTTTAACATGGCATT
* * *
34735710 AACATTGGGGCAATTAGTTTTAAAAGGGGATTTTCTATAGGATGGCGGGATCATTTGGATGTGGT
131 AACATTGGGGCAATTAGTTTTAAAAGAGGACTTTCTATAGGATGGCAGGATCATTTGGATGTGGT
*
34735775 TTTAAAAAGTTATTCTCAGCATCATATTGATGTTGAGATCAATGATATCGAAGATGGGCATTCTT
196 TTTAAAAAGTTATTCTCAGCATCATATTAATGTTGAGATCAATGATATCGAAGATGGGCATTCTT
34735840 GGCGTTACACTGGGTTCTATGGTCATCTAGAAGATCATTTGAGGGACAGATCATGGGATTTATTG
261 GGCGTTACACTGGGTTCTATGGTCATCTAGAAGATCATTTGAGGGACAGATCATGGGATTTATTG
34735905 AGAGTT
326 AGAGTT
* *
34735911 CTCGTCATATGGAATGGGTTATACGGAAGTGTGGTTTTTAACATGGCATTAATATTGGGGCAATT
1 CTCGTCATATGGAACGGGTTATACGGAAGTGTGGTTTTTAACATGGCATTAACATTGGGGCAATT
* *
34735976 AGTTTTAAAAGGGGACTTTCTATAGGATGGCGGGATCATTTGGATGTGGTTTTTTACATGGCATT
66 AGTTTTAAAAGGGGACTTTCTATAGGATGACGGGATCATTTGGATGTGGTTTTTAACATGGCATT
34736041 AACATTGGGGCAATTAGTTTTAAAAGAGGACTTTCTATAGGATGGCAGGATCATTTGGATGTGGT
131 AACATTGGGGCAATTAGTTTTAAAAGAGGACTTTCTATAGGATGGCAGGATCATTTGGATGTGGT
*
34736106 TTTAAAAAGTTATTCTCAGCATCATATTAATGTTGAGATTAATGATATCGAAGATGGGCATTCTT
196 TTTAAAAAGTTATTCTCAGCATCATATTAATGTTGAGATCAATGATATCGAAGATGGGCATTCTT
34736171 GGCGTTACACTGGGTTCTATGGTCATCTAGAAGATCATTTGAGGGACAGATCATGGGATTTATTG
261 GGCGTTACACTGGGTTCTATGGTCATCTAGAAGATCATTTGAGGGACAGATCATGGGATTTATTG
34736236 AGAGTT
326 AGAGTT
34736242 CT
1 CT
34736244 TGGAAGGGAT
Statistics
Matches: 323, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
331 323 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (331 bp):
CTCGTCATATGGAACGGGTTATACGGAAGTGTGGTTTTTAACATGGCATTAACATTGGGGCAATT
AGTTTTAAAAGGGGACTTTCTATAGGATGACGGGATCATTTGGATGTGGTTTTTAACATGGCATT
AACATTGGGGCAATTAGTTTTAAAAGAGGACTTTCTATAGGATGGCAGGATCATTTGGATGTGGT
TTTAAAAAGTTATTCTCAGCATCATATTAATGTTGAGATCAATGATATCGAAGATGGGCATTCTT
GGCGTTACACTGGGTTCTATGGTCATCTAGAAGATCATTTGAGGGACAGATCATGGGATTTATTG
AGAGTT
Found at i:34738667 original size:70 final size:70
Alignment explanation
Indices: 34738580--34738719 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
34738570 GGGTCTTACC
34738580 CTTCTTTTACCTGGAGAAGTATTGTGGCAGCCAAGGGGCTGATTGAGAGTGGTCTGGGGTGGCAC
1 CTTCTTTTACCTGGAGAAGTATTGTGGCAGCCAAGGGGCTGATTGAGAGTGGTCTGGGGTGGCAC
34738645 GTGGG
66 GTGGG
34738650 CTTCTTTTACCTGGAGAAGTATTGTGGCAGCCAAGGGGCTGATTGAGAGTGGTCTGGGGTGGCAC
1 CTTCTTTTACCTGGAGAAGTATTGTGGCAGCCAAGGGGCTGATTGAGAGTGGTCTGGGGTGGCAC
34738715 GTGGG
66 GTGGG
34738720 AGATGGTTTG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.17, C:0.16, G:0.40, T:0.27
Consensus pattern (70 bp):
CTTCTTTTACCTGGAGAAGTATTGTGGCAGCCAAGGGGCTGATTGAGAGTGGTCTGGGGTGGCAC
GTGGG
Found at i:34739084 original size:93 final size:93
Alignment explanation
Indices: 34738925--34739120 Score: 365
Period size: 93 Copynumber: 2.1 Consensus size: 93
34738915 TTTACCCCAA
* *
34738925 ACACAAATAGTCTGATGCCAAGGTGTGGAGGTTCGATGCCAAAAGGGAGTATACATTTAAGAGTG
1 ACACAAACAGTCTGATGCCAAGGTGTGGAGGTTCGATGCCAAAAGGGAGTATACAGTTAAGAGTG
34738990 GCTACAAAACTCTCCTACTGTCTAGACT
66 GCTACAAAACTCTCCTACTGTCTAGACT
*
34739018 ACACAAACAGTCTGATGCTAAGGTGTGGAGGTTCGATGCCAAAAGGGAGTATACAGTTAAGAGTG
1 ACACAAACAGTCTGATGCCAAGGTGTGGAGGTTCGATGCCAAAAGGGAGTATACAGTTAAGAGTG
34739083 GCTACAAAACTCTCCTACTGTCTAGACT
66 GCTACAAAACTCTCCTACTGTCTAGACT
34739111 ACACAAACAG
1 ACACAAACAG
34739121 ATTCCTAATT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 100 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (93 bp):
ACACAAACAGTCTGATGCCAAGGTGTGGAGGTTCGATGCCAAAAGGGAGTATACAGTTAAGAGTG
GCTACAAAACTCTCCTACTGTCTAGACT
Found at i:34741436 original size:73 final size:73
Alignment explanation
Indices: 34741317--34741461 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 73
34741307 ACAAATTAAA
34741317 GATCAAATTAAATCATGTTTCAAACCGAATAGACTTCAATACAAAATATCCCCAAAGTCAAGAGT
1 GATCAAATTAAATCATGTTTCAAACCGAATAGACTTCAATACAAAATATCCCCAAAGTCAAGAGT
34741382 TCAATAAG
66 TCAATAAG
*
34741390 GATCAAATTAAATCATGTTTCAAACCTAATAGACTTCAATACAAAATATCCCCAAAGTCAAGAGT
1 GATCAAATTAAATCATGTTTCAAACCGAATAGACTTCAATACAAAATATCCCCAAAGTCAAGAGT
34741455 TCAATAA
66 TCAATAA
34741462 TTCACCCCCC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.26
Consensus pattern (73 bp):
GATCAAATTAAATCATGTTTCAAACCGAATAGACTTCAATACAAAATATCCCCAAAGTCAAGAGT
TCAATAAG
Found at i:34743392 original size:24 final size:24
Alignment explanation
Indices: 34743356--34743404 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
34743346 TTGTCGCCGA
34743356 TGCAAAGTACGTGGGTTCGAGTGT
1 TGCAAAGTACGTGGGTTCGAGTGT
*
34743380 TGCAAAGTTCGTGGGTTCGAGTGT
1 TGCAAAGTACGTGGGTTCGAGTGT
34743404 T
1 T
34743405 CTGAATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.12, G:0.37, T:0.33
Consensus pattern (24 bp):
TGCAAAGTACGTGGGTTCGAGTGT
Found at i:34746400 original size:30 final size:30
Alignment explanation
Indices: 34746364--34746425 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
34746354 CAATTAGTCT
* *
34746364 TGTGGTGGGGTTACAAACAACTCCTGGATA
1 TGTGGTGGCGTTACAAACAACTCCTCGATA
* * *
34746394 TGTGGTGGCGTTACTAGCAGCTCCTCGATA
1 TGTGGTGGCGTTACAAACAACTCCTCGATA
34746424 TG
1 TG
34746426 AAATTGAGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (30 bp):
TGTGGTGGCGTTACAAACAACTCCTCGATA
Found at i:34748728 original size:21 final size:19
Alignment explanation
Indices: 34748677--34748754 Score: 57
Period size: 21 Copynumber: 3.8 Consensus size: 19
34748667 GGAATAGTAC
*
34748677 AGACTTGTACCGATACATG
1 AGACTTCTACCGATACATG
*
34748696 AGACAGTACTACCGATACAAGTG
1 AGAC--TTCTACCGATAC-A-TG
* *
34748719 AGACTTCTACCGAAATATG
1 AGACTTCTACCGATACATG
**
34748738 TCATCTTCTACCGATAC
1 AGA-CTTCTACCGATAC
34748755 TAAAAACTCC
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
19 7 0.16
20 12 0.27
21 19 0.42
22 1 0.02
23 6 0.13
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (19 bp):
AGACTTCTACCGATACATG
Found at i:34749491 original size:24 final size:24
Alignment explanation
Indices: 34749463--34749518 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
34749453 ACAGAAAACA
*
34749463 TTAGCTCTCAT-AAGCCCAGGATGG
1 TTAGCTCT-ATCAAGCCCAGAATGG
* *
34749487 TTAGCTCTTTCGAGCCCAGAATGG
1 TTAGCTCTATCAAGCCCAGAATGG
34749511 TTAGCTCT
1 TTAGCTCT
34749519 TACGAGCCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TTAGCTCTATCAAGCCCAGAATGG
Found at i:34749519 original size:24 final size:24
Alignment explanation
Indices: 34749475--34749537 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
34749465 AGCTCTCATA
* *
34749475 AGCCCAGGATGGTTAGCTCTTTCG
1 AGCCCAGAATGGTTAGCTCTTACG
34749499 AGCCCAGAATGGTTAGCTCTTACG
1 AGCCCAGAATGGTTAGCTCTTACG
* *
34749523 AGCCCGGAATAGTTA
1 AGCCCAGAATGGTTA
34749538 ACCAGTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (24 bp):
AGCCCAGAATGGTTAGCTCTTACG
Found at i:34764195 original size:2 final size:2
Alignment explanation
Indices: 34764188--34764222 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34764178 TAAAATTTCA
34764188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34764223 ACTTATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34770044 original size:15 final size:15
Alignment explanation
Indices: 34770024--34770055 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
34770014 TTGTTGATAA
*
34770024 TAATAGCGTCAAAAG
1 TAATAGCATCAAAAG
34770039 TAATAGCATCAAAAG
1 TAATAGCATCAAAAG
34770054 TA
1 TA
34770056 TAATAGTAGT
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:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (15 bp):
TAATAGCATCAAAAG
Found at i:34770061 original size:17 final size:16
Alignment explanation
Indices: 34770023--34770061 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
34770013 TTTGTTGATA
*
34770023 ATAATAGCGTCAAAAG
1 ATAATAGCATCAAAAG
34770039 -TAATAGCATCAAAAG
1 ATAATAGCATCAAAAG
34770054 TATAATAG
1 -ATAATAG
34770062 TAGTGCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 14 0.70
17 6 0.30
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (16 bp):
ATAATAGCATCAAAAG
Found at i:34772682 original size:120 final size:120
Alignment explanation
Indices: 34772539--34772784 Score: 492
Period size: 120 Copynumber: 2.0 Consensus size: 120
34772529 CTAAGTGTTC
34772539 CATTGTAACTATTGTATTACAATTTGACATTGTCATGCTTGTAGTAATGTTGTGCTTATATTGTT
1 CATTGTAACTATTGTATTACAATTTGACATTGTCATGCTTGTAGTAATGTTGTGCTTATATTGTT
34772604 AAAGTTATTTGTATGTTTTTTATTAATCATATACGAACGATCAAGTTGTTAGTGT
66 AAAGTTATTTGTATGTTTTTTATTAATCATATACGAACGATCAAGTTGTTAGTGT
34772659 CATTGTAACTATTGTATTACAATTTGACATTGTCATGCTTGTAGTAATGTTGTGCTTATATTGTT
1 CATTGTAACTATTGTATTACAATTTGACATTGTCATGCTTGTAGTAATGTTGTGCTTATATTGTT
34772724 AAAGTTATTTGTATGTTTTTTATTAATCATATACGAACGATCAAGTTGTTAGTGT
66 AAAGTTATTTGTATGTTTTTTATTAATCATATACGAACGATCAAGTTGTTAGTGT
34772779 CATTGT
1 CATTGT
34772785 CAGGGTTTGT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 126 1.00
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (120 bp):
CATTGTAACTATTGTATTACAATTTGACATTGTCATGCTTGTAGTAATGTTGTGCTTATATTGTT
AAAGTTATTTGTATGTTTTTTATTAATCATATACGAACGATCAAGTTGTTAGTGT
Found at i:34776558 original size:30 final size:30
Alignment explanation
Indices: 34776524--34776618 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
34776514 GTGAAGGATT
*
34776524 AAATTTATTAAATTATTTAAAATTAGGATC
1 AAATTTATTAAATTATTTAAAATTAAGATC
* * * *
34776554 AAATTGA-TAGAATT-TATAAATATGAAGATT
1 AAATTTATTA-AATTATTTAAA-ATTAAGATC
* *
34776584 AAATTTATTGAATTATTTAGAATTAAGATC
1 AAATTTATTAAATTATTTAAAATTAAGATC
34776614 AAATT
1 AAATT
34776619 GATAAAATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
29 7 0.14
30 38 0.76
31 5 0.10
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.41
Consensus pattern (30 bp):
AAATTTATTAAATTATTTAAAATTAAGATC
Found at i:34776561 original size:61 final size:61
Alignment explanation
Indices: 34776490--34776648 Score: 232
Period size: 60 Copynumber: 2.6 Consensus size: 61
34776480 AAGTTTGAAT
* *
34776490 ATCAAATTGATAAAATTTATAAATGTGAAGGATTAAATTTATTAAATTATTTAAAATTAGG
1 ATCAAATTGATAAAATTTATAAATATGAAGGATTAAATTTATTAAATTATTTAAAATTAAG
* * *
34776551 ATCAAATTGATAGAATTTATAAATATGAA-GATTAAATTTATTGAATTATTTAGAATTAAG
1 ATCAAATTGATAAAATTTATAAATATGAAGGATTAAATTTATTAAATTATTTAAAATTAAG
* *
34776611 ATCAAATTGATAAAATATGTAAATATCG-AGGATTAAAT
1 ATCAAATTGATAAAATTTATAAATAT-GAAGGATTAAAT
34776649 AGTTATTATA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
60 52 0.59
61 36 0.41
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.38
Consensus pattern (61 bp):
ATCAAATTGATAAAATTTATAAATATGAAGGATTAAATTTATTAAATTATTTAAAATTAAG
Found at i:34784935 original size:11 final size:11
Alignment explanation
Indices: 34784921--34784989 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 11
34784911 TAAATATTTT
*
34784921 TAAAATAGTAA
1 TAAAATAATAA
34784932 TAAAATTAATAA
1 TAAAA-TAATAA
* *
34784944 TAAAATAAGAG
1 TAAAATAATAA
* *
34784955 TTATATAAT-A
1 TAAAATAATAA
34784965 TACAAATAATAA
1 TA-AAATAATAA
34784977 TAATAATAA-AA
1 TAA-AATAATAA
34784988 TA
1 TA
34784990 GCATCAAAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
10 1 0.02
11 26 0.58
12 18 0.40
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:34786565 original size:41 final size:41
Alignment explanation
Indices: 34786508--34786590 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
34786498 CTATGAAAAC
* *
34786508 TTAAATTTCAGCTCAAACTTATCATCTTTCTCTCGAGGATA
1 TTAAATTTCAACTCAAACTTATCATCTTTCTCTCAAGGATA
*
34786549 TTAAATTTCAACTCAAACTTATCATTTTTCTCTCAAGGATA
1 TTAAATTTCAACTCAAACTTATCATCTTTCTCTCAAGGATA
34786590 T
1 T
34786591 GCAACAATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41
Consensus pattern (41 bp):
TTAAATTTCAACTCAAACTTATCATCTTTCTCTCAAGGATA
Found at i:34787086 original size:28 final size:28
Alignment explanation
Indices: 34787053--34787108 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
34787043 GTTGCGAATA
34787053 GTATTGAATTACATCTGAGATCAACATT
1 GTATTGAATTACATCTGAGATCAACATT
34787081 GTATTGAATTACATCTGAGATCAACATT
1 GTATTGAATTACATCTGAGATCAACATT
34787109 CATGTTTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (28 bp):
GTATTGAATTACATCTGAGATCAACATT
Found at i:34789734 original size:2 final size:2
Alignment explanation
Indices: 34789727--34789778 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
34789717 ACCACAAGAA
34789727 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34789769 AG AG AG AG AG
1 AG AG AG AG AG
34789779 GTAGCTGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34791624 original size:25 final size:23
Alignment explanation
Indices: 34791596--34791641 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
34791586 GTTGGATTTA
34791596 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
34791621 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
34791642 TCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:34797058 original size:22 final size:22
Alignment explanation
Indices: 34797033--34797179 Score: 105
Period size: 22 Copynumber: 6.7 Consensus size: 22
34797023 CTGATGTGTT
*
34797033 TTTTTTGTTATTTTGGTTGCTA
1 TTTTTTGTTATTTTTGTTGCTA
* *
34797055 TTTTTTATTA-TTTTGGTGCTA
1 TTTTTTGTTATTTTTGTTGCTA
*
34797076 CTTTTGTTGTTA--TTT-TT-ATA
1 -TTTT-TTGTTATTTTTGTTGCTA
34797096 TTTTTTGCTGCTATTTTTGTTG-T-
1 TTTTTTG-T--TATTTTTGTTGCTA
34797119 TTTTTGCTGTTATTTTTGTTGCTA
1 TTTTT--TGTTATTTTTGTTGCTA
34797143 TTTTGATTGTTATTTTTGTTG-T-
1 TTTT--TTGTTATTTTTGTTGCTA
*
34797165 TTTTGTGTTATTTTT
1 TTTTTTGTTATTTTT
34797180 TTATGTGTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 32
0.73 0.05 0.23
Matches are distributed among these distances:
18 3 0.03
19 5 0.05
20 12 0.12
21 12 0.12
22 31 0.30
23 15 0.15
24 22 0.21
25 2 0.02
26 1 0.01
ACGTcount: A:0.10, C:0.05, G:0.16, T:0.70
Consensus pattern (22 bp):
TTTTTTGTTATTTTTGTTGCTA
Found at i:34797164 original size:12 final size:12
Alignment explanation
Indices: 34797031--34797165 Score: 81
Period size: 12 Copynumber: 11.9 Consensus size: 12
34797021 TTCTGATGTG
*
34797031 TTTTTTTTGTTA
1 TTTTTGTTGTTA
* *
34797043 TTTTGGTTGCTA
1 TTTTTGTTGTTA
*
34797055 -TTTT-TTATTA
1 TTTTTGTTGTTA
* *
34797065 -TTTTGGTGCTA
1 TTTTTGTTGTTA
*
34797076 CTTTTGTTGTTA
1 TTTTTGTTGTTA
* *
34797088 TTTTT-AT-AT-
1 TTTTTGTTGTTA
* *
34797097 TTTTTGCTGCTA
1 TTTTTGTTGTTA
34797109 TTTTTGTTG-T-
1 TTTTTGTTGTTA
*
34797119 TTTTTGCTGTTA
1 TTTTTGTTGTTA
*
34797131 TTTTTGTTGCTA
1 TTTTTGTTGTTA
34797143 -TTTTGATTGTTA
1 TTTTTG-TTGTTA
34797155 TTTTTGTTGTT
1 TTTTTGTTGTT
34797166 TTTGTGTTAT
Statistics
Matches: 93, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.05
10 18 0.19
11 15 0.16
12 50 0.54
13 5 0.05
ACGTcount: A:0.10, C:0.05, G:0.16, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:34797168 original size:33 final size:32
Alignment explanation
Indices: 34797031--34797178 Score: 119
Period size: 33 Copynumber: 4.5 Consensus size: 32
34797021 TTCTGATGTG
* *
34797031 TTTTTT-TTGTTATTTTGGTTGCTATTTTT-TA
1 TTTTTTGTTGCTATTTT-GTTGTTATTTTTGTA
* *
34797062 TTATTTTGGTGCTACTTTTGTTGTTATTTTTATA
1 TT-TTTTGTTGCTA-TTTTGTTGTTATTTTTGTA
*
34797096 TTTTTTGCTGCTATTTTTGTTGTT-TTTTGCTGT-
1 TTTTTTGTTGCTA-TTTTGTTGTTATTTT--TGTA
34797129 TATTTTTGTTGCTATTTTGATTGTTATTTTTGT-
1 T-TTTTTGTTGCTATTTTG-TTGTTATTTTTGTA
*
34797162 TGTTTTTG-TGTTATTTT
1 T-TTTTTGTTGCTATTTT
34797179 TTTATGTGTT
Statistics
Matches: 99, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
31 2 0.02
32 16 0.16
33 51 0.52
34 26 0.26
35 4 0.04
ACGTcount: A:0.09, C:0.05, G:0.16, T:0.70
Consensus pattern (32 bp):
TTTTTTGTTGCTATTTTGTTGTTATTTTTGTA
Found at i:34799197 original size:4 final size:4
Alignment explanation
Indices: 34799183--34799314 Score: 104
Period size: 4 Copynumber: 32.0 Consensus size: 4
34799173 TTTTGTGATG
* * * *
34799183 TAAA AAAA TAAA TAAC TAAA AAAA GTAAA TAAA TAAC TAAA TAAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA -TAAA TAAA TAAA TAAA T-AAA TAAA
* * * * * *
34799233 CAAA T-AA TTAA TTAA TGAAAA TAAA TAAA TAAC TAAA TATA TAAA TAAT
1 TAAA TAAA TAAA TAAA T--AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* *
34799282 TAAA TAAAA TAAA TAAA TAAT TAAT TAAA TAAA
1 TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA
34799315 AATATTTTTA
Statistics
Matches: 103, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
3 3 0.03
4 86 0.83
5 11 0.11
6 3 0.03
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:34799213 original size:21 final size:20
Alignment explanation
Indices: 34799184--34799315 Score: 104
Period size: 21 Copynumber: 6.2 Consensus size: 20
34799174 TTTGTGATGT
34799184 AAAA-AAATAAATAACTAAA
1 AAAATAAATAAATAACTAAA
34799203 AAAAGTAAATAAATAACTAAA
1 AAAA-TAAATAAATAACTAAA
* *
34799224 TAAAATAAACAAATAATTAATTAA
1 -AAAATAAATAAATAACT-A--AA
34799248 TGAAAATAAATAAATAACTAAA
1 --AAAATAAATAAATAACTAAA
* * * *
34799270 TATATAAATAATTAAATAAA
1 AAAATAAATAAATAACTAAA
* *
34799290 ATAAATAAATAATTAATTAAA
1 A-AAATAAATAAATAACTAAA
34799311 TAAAA
1 -AAAA
34799316 ATATTTTTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.04
20 16 0.17
21 46 0.50
22 8 0.09
24 3 0.03
25 15 0.16
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAATAAATAAATAACTAAA
Found at i:34799216 original size:25 final size:24
Alignment explanation
Indices: 34799183--34799314 Score: 104
Period size: 25 Copynumber: 5.2 Consensus size: 24
34799173 TTTTGTGATG
*
34799183 TAAAAAAATAAATAACTAAAA-AAA
1 TAAATAAATAAATAA-TAAAATAAA
*
34799207 GTAAATAAATAACTAAATAAAATAAA
1 -TAAATAAATAAAT-AATAAAATAAA
* * *
34799233 CAAATAATTAATTAATGAAAATAAA
1 TAAATAAATAAATAAT-AAAATAAA
*
34799258 TAAATAACTAAATATATAAATAATTAAA
1 TAAATAAATAAATA-AT-AA-AA-TAAA
* *
34799286 TAAAATAAATAAATAATTAATTAAA
1 T-AAATAAATAAATAATAAAATAAA
34799311 TAAA
1 TAAA
34799315 AATATTTTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
24 6 0.07
25 50 0.57
26 10 0.11
27 3 0.03
28 7 0.08
29 12 0.14
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (24 bp):
TAAATAAATAAATAATAAAATAAA
Found at i:34803091 original size:17 final size:17
Alignment explanation
Indices: 34803069--34803103 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
34803059 TTATTTGTGC
34803069 ATATATAAATAGAACAT
1 ATATATAAATAGAACAT
*
34803086 ATATATAAATATAACAT
1 ATATATAAATAGAACAT
34803103 A
1 A
34803104 AAGTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
ATATATAAATAGAACAT
Found at i:34803338 original size:33 final size:33
Alignment explanation
Indices: 34803277--34803343 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
34803267 TCGTTGAACC
*
34803277 TGCAAGGAAAGGATGGACCAAGTGGTGTTTGAG
1 TGCAAGGAAAGGATGGACCAAGTGGTGTTGGAG
*
34803310 TGCAAGGAAAGGATGGACTAAG-GAGTGTTGGAG
1 TGCAAGGAAAGGATGGACCAAGTG-GTGTTGGAG
34803343 T
1 T
34803344 TTACACTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.31, C:0.07, G:0.40, T:0.21
Consensus pattern (33 bp):
TGCAAGGAAAGGATGGACCAAGTGGTGTTGGAG
Found at i:34817375 original size:10 final size:10
Alignment explanation
Indices: 34817360--34817426 Score: 52
Period size: 9 Copynumber: 7.0 Consensus size: 10
34817350 ATTAAAATTA
34817360 AAAAATATAT
1 AAAAATATAT
**
34817370 AAAAAT-TCG
1 AAAAATATAT
*
34817379 AAAATTAT-T
1 AAAAATATAT
34817388 AAAAAT-TAT
1 AAAAATATAT
*
34817397 AAAATATAAAT
1 AAAA-ATATAT
*
34817408 AATAATA-AT
1 AAAAATATAT
34817417 AAAAATATAT
1 AAAAATATAT
34817427 TTAGAAATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
8 1 0.02
9 24 0.55
10 14 0.32
11 5 0.11
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAAATATAT
Found at i:34817391 original size:17 final size:18
Alignment explanation
Indices: 34817340--34817427 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 18
34817330 AAAAATTAAG
*
34817340 AAAAACATAAATTAAAATT
1 AAAAA-ATATATTAAAATT
*
34817359 AAAAAATATATAAAAATT
1 AAAAAATATATTAAAATT
**
34817377 CGAAAAT-TATTAAAAATT
1 AAAAAATATATT-AAAATT
* * *
34817395 ATAAAATATAAATAATAATA
1 AAAAAATAT-ATTAA-AATT
34817415 ATAAAAATATATT
1 A-AAAAATATATT
34817428 TAGAAATTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
17 3 0.06
18 27 0.51
19 8 0.15
20 8 0.15
21 7 0.13
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (18 bp):
AAAAAATATATTAAAATT
Found at i:34818444 original size:17 final size:16
Alignment explanation
Indices: 34818422--34818465 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
34818412 AGTTTTTATA
34818422 AATTTTAATAATTTTTG
1 AATTTTAATAA-TTTTG
*
34818439 AATTTTTATGTAATTTTG
1 AA-TTTTA-ATAATTTTG
34818457 AATTTTAAT
1 AATTTTAAT
34818466 TTAGTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 1 0.04
17 7 0.30
18 12 0.52
19 3 0.13
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (16 bp):
AATTTTAATAATTTTG
Found at i:34818445 original size:18 final size:18
Alignment explanation
Indices: 34818424--34818462 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34818414 TTTTTATAAA
34818424 TTTTA-ATAATTTTTGAAT
1 TTTTATATAA-TTTTGAAT
*
34818442 TTTTATGTAATTTTGAAT
1 TTTTATATAATTTTGAAT
34818460 TTT
1 TTT
34818463 AATTTAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (18 bp):
TTTTATATAATTTTGAAT
Found at i:34818468 original size:22 final size:21
Alignment explanation
Indices: 34818443--34818483 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34818433 TTTTTGAATT
34818443 TTTATGTAATTTTGAATTTTAA
1 TTTA-GTAATTTTGAATTTTAA
* *
34818465 TTTAGTTATTTTTAATTTT
1 TTTAGTAATTTTGAATTTT
34818484 TTAAAACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (21 bp):
TTTAGTAATTTTGAATTTTAA
Found at i:34818757 original size:21 final size:21
Alignment explanation
Indices: 34818731--34818770 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34818721 AACGGGACCG
34818731 CTGATGTGACAAGTTAACTAA
1 CTGATGTGACAAGTTAACTAA
* *
34818752 CTGATGTGGCCAGTTAACT
1 CTGATGTGACAAGTTAACT
34818771 TGCCACGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (21 bp):
CTGATGTGACAAGTTAACTAA
Found at i:34819739 original size:14 final size:14
Alignment explanation
Indices: 34819722--34819748 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34819712 TCTTTTCTCC
34819722 TTCTTCTTCTTTTT
1 TTCTTCTTCTTTTT
34819736 TTCTTCTTCTTTT
1 TTCTTCTTCTTTT
34819749 ACTGAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTCTTCTTTTT
Found at i:34820078 original size:21 final size:22
Alignment explanation
Indices: 34820054--34820098 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
34820044 CAAATTAATT
*
34820054 TTAACAAC-AGAGTGACTAAAA
1 TTAACAACGAGAATGACTAAAA
*
34820075 TTAACAACGAGAATGATTAAAA
1 TTAACAACGAGAATGACTAAAA
34820097 TT
1 TT
34820099 GAGAACTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.24
Consensus pattern (22 bp):
TTAACAACGAGAATGACTAAAA
Found at i:34823799 original size:30 final size:30
Alignment explanation
Indices: 34823744--34823800 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
34823734 TTTAAATCCA
* *
34823744 AAAAATAAAAAATTTAATATTTTTTAAATT
1 AAAAATAAAAAATTAAATATATTTTAAATT
34823774 AAAAAT-AAAAATTAAGATATATTTTAA
1 AAAAATAAAAAATTAA-ATATATTTTAA
34823801 CATTCAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAAATAAAAAATTAAATATATTTTAAATT
Found at i:34829227 original size:9 final size:8
Alignment explanation
Indices: 34829213--34829283 Score: 54
Period size: 9 Copynumber: 8.1 Consensus size: 8
34829203 AAATATATTA
34829213 ATTTTTACT
1 ATTTTTA-T
34829222 ATTTTTAT
1 ATTTTTAT
*
34829230 AATATTTA-
1 -ATTTTTAT
*
34829238 ATATTTAAT
1 AT-TTTTAT
34829247 ATTTTTAAT
1 ATTTTT-AT
34829256 AATTTTTAT
1 -ATTTTTAT
34829265 AGTTTTTATT
1 A-TTTTTA-T
34829275 ATTTTTAT
1 ATTTTTAT
34829283 A
1 A
34829284 AAATTTTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
7 2 0.04
8 10 0.20
9 31 0.61
10 8 0.16
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (8 bp):
ATTTTTAT
Found at i:34829237 original size:18 final size:18
Alignment explanation
Indices: 34829211--34829284 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 18
34829201 TCAAATATAT
*
34829211 TAATTTTTACTATTTTTA
1 TAATTTTTAATATTTTTA
* *
34829229 TAATATTTAATA-TTTAA
1 TAATTTTTAATATTTTTA
34829246 T-ATTTTTAATAATTTTTA
1 TAATTTTTAAT-ATTTTTA
* *
34829264 TAGTTTTTATTATTTTTA
1 TAATTTTTAATATTTTTA
34829282 TAA
1 TAA
34829285 AATTTTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 8 0.18
17 6 0.13
18 24 0.53
19 7 0.16
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (18 bp):
TAATTTTTAATATTTTTA
Found at i:34837642 original size:85 final size:85
Alignment explanation
Indices: 34837535--34837699 Score: 215
Period size: 87 Copynumber: 1.9 Consensus size: 85
34837525 TACATGCATA
* *
34837535 AGGTTGAGCTATTACTCTTAATGAGTTCATATCC-CAAGTTGGGTGGTCCTATTGAGACGGACTT
1 AGGTTGAGCTATTACTCTTAATGAATTCATATCCAAAAGTTGGGTGGTCCTATTGAGACGGACTT
*
34837599 AATAAATTTACCGACATGAG
66 AATAAATTCACCGACATGAG
* * * * *
34837619 AGGTTGAGTTTATTACTTTTAATGAATTCATATCCTAAAATTTGGTTGGTCCTATTGCGACGGAC
1 AGGTTGAG-CTATTACTCTTAATGAATTCATATCC-AAAAGTTGGGTGGTCCTATTGAGACGGAC
* *
34837684 TTGATGAATTCACCGA
64 TTAATAAATTCACCGA
34837700 ACTTAATTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 8 0.12
85 23 0.34
87 37 0.54
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (85 bp):
AGGTTGAGCTATTACTCTTAATGAATTCATATCCAAAAGTTGGGTGGTCCTATTGAGACGGACTT
AATAAATTCACCGACATGAG
Found at i:34839623 original size:3 final size:3
Alignment explanation
Indices: 34839615--34839647 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
34839605 TACATCCAAA
*
34839615 AAT AAT AAT AAT AAT GAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
34839648 GAATAGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:34840714 original size:13 final size:13
Alignment explanation
Indices: 34840692--34840746 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
34840682 GTTTTTCAAA
34840692 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
34840705 AAAGTTAACGGTC
1 AAAGTCAACGGTC
34840718 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
34840731 AACGGTCAACGGTC
1 AA-AGTCAACGGTC
34840745 AA
1 AA
34840747 TCAACACCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
13 26 0.68
14 12 0.32
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:34840733 original size:7 final size:7
Alignment explanation
Indices: 34840695--34840746 Score: 63
Period size: 7 Copynumber: 7.7 Consensus size: 7
34840685 TTTCAAAAAA
34840695 GTCAACG
1 GTCAACG
*
34840702 GTCAA-A
1 GTCAACG
*
34840708 GTTAACG
1 GTCAACG
*
34840715 GTCAA-A
1 GTCAACG
34840721 GTCAACG
1 GTCAACG
34840728 GTCAACG
1 GTCAACG
34840735 GTCAACG
1 GTCAACG
34840742 GTCAA
1 GTCAA
34840747 TCAACACCTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
6 9 0.24
7 28 0.76
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:34840771 original size:21 final size:21
Alignment explanation
Indices: 34840735--34840791 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
34840725 ACGGTCAACG
** *
34840735 GTCAACGGTCAATCAACACCT
1 GTCAACGGTCGGTCAACACCA
*
34840756 GTCAACGGTCGGTCAACGCCA
1 GTCAACGGTCGGTCAACACCA
*
34840777 GTCAA-TGTCGGTCAA
1 GTCAACGGTCGGTCAA
34840792 TGGTTTGACT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
GTCAACGGTCGGTCAACACCA
Found at i:34841263 original size:11 final size:11
Alignment explanation
Indices: 34841230--34841304 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
34841220 AAGTGTGATT
*
34841230 AAAAGAGGAAG
1 AAAAGAGAAAG
*
34841241 AAAATAGAAAAG
1 AAAAGAG-AAAG
34841253 AAAAGAGAAAG
1 AAAAGAGAAAG
34841264 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
34841276 AATGAGAAAAAG
1 AA-AAGAGAAAG
34841288 AAAAGAGAAAG
1 AAAAGAGAAAG
*
34841299 GAAAGA
1 AAAAGA
34841305 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:34841272 original size:23 final size:23
Alignment explanation
Indices: 34841230--34841302 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
34841220 AAGTGTGATT
*
34841230 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
34841253 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
34841276 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
34841300 AAA
1 AAA
34841303 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:34843490 original size:2 final size:2
Alignment explanation
Indices: 34843483--34843518 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34843473 ACCAATTTCC
34843483 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
34843519 GGGTGGTTTT
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:34855555 original size:46 final size:46
Alignment explanation
Indices: 34855503--34855595 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
34855493 AATACTTCGA
34855503 TCCTGCAATATCAAAGCATCCTAACACTAGTAATGACAAAGGCTGT
1 TCCTGCAATATCAAAGCATCCTAACACTAGTAATGACAAAGGCTGT
34855549 TCCTGCAATATCAAAGCATCCTAACACTAGTAATGACAAAGGCTGT
1 TCCTGCAATATCAAAGCATCCTAACACTAGTAATGACAAAGGCTGT
34855595 T
1 T
34855596 AAAAATCTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.25
Consensus pattern (46 bp):
TCCTGCAATATCAAAGCATCCTAACACTAGTAATGACAAAGGCTGT
Found at i:34857183 original size:11 final size:11
Alignment explanation
Indices: 34857167--34857206 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
34857157 GATTCGACAC
34857167 TCATAACTCTT
1 TCATAACTCTT
34857178 TCATAACTCTT
1 TCATAACTCTT
34857189 TCATAACTCTT
1 TCATAACTCTT
*
34857200 TCGTAAC
1 TCATAAC
34857207 ATCTCATAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.42
Consensus pattern (11 bp):
TCATAACTCTT
Found at i:34858925 original size:4 final size:4
Alignment explanation
Indices: 34858916--34858943 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
34858906 GAAGTGTGTG
34858916 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
34858944 ATATACATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:34862927 original size:23 final size:23
Alignment explanation
Indices: 34862890--34862998 Score: 73
Period size: 23 Copynumber: 4.7 Consensus size: 23
34862880 TATATTGTTA
*
34862890 TTTTGG-TGCTGTTTTTTTGCTG
1 TTTTGGTTGCTATTTTTTTGCTG
**
34862912 TTTTGGTTGCTATTTTGGTGCTG
1 TTTTGGTTGCTATTTTTTTGCTG
** * *
34862935 TTTTTATTGTTATTTTTGTTGCTA
1 TTTTGGTTGCTATTTTT-TTGCTG
34862959 TTTT--TT-CTATTATTTTTGCTGCTG
1 TTTTGGTTGCTA-T-TTTTT--TGCTG
*
34862983 TTTTGGTTGTTATTTT
1 TTTTGGTTGCTATTTT
34862999 GGTTATTTAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
21 2 0.03
22 10 0.15
23 30 0.45
24 16 0.24
25 3 0.05
26 3 0.05
27 2 0.03
ACGTcount: A:0.06, C:0.07, G:0.20, T:0.66
Consensus pattern (23 bp):
TTTTGGTTGCTATTTTTTTGCTG
Found at i:34862939 original size:12 final size:12
Alignment explanation
Indices: 34862890--34862939 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
34862880 TATATTGTTA
34862890 TTTTGGTGCTGT
1 TTTTGGTGCTGT
*
34862902 TTTT-TTGCTG-
1 TTTTGGTGCTGT
*
34862912 TTTTGGTTGCT-A
1 TTTTGG-TGCTGT
34862924 TTTTGGTGCTGT
1 TTTTGGTGCTGT
34862936 TTTT
1 TTTT
34862940 ATTGTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 4 0.13
11 9 0.29
12 18 0.58
ACGTcount: A:0.02, C:0.08, G:0.26, T:0.64
Consensus pattern (12 bp):
TTTTGGTGCTGT
Found at i:34862951 original size:24 final size:24
Alignment explanation
Indices: 34862907--34862998 Score: 89
Period size: 24 Copynumber: 3.9 Consensus size: 24
34862897 GCTGTTTTTT
* *
34862907 TGCTGTTTTGGTTGCTA-TTTTGG
1 TGCTGTTTTGGTTGTTATTTTTGC
** *
34862930 TGCTGTTTTTATTGTTATTTTTGT
1 TGCTGTTTTGGTTGTTATTTTTGC
* * *
34862954 TGCTATTTT-TTCTATTATTTTTGC
1 TGCTGTTTTGGT-TGTTATTTTTGC
34862978 TGCTGTTTTGGTTGTTATTTT
1 TGCTGTTTTGGTTGTTATTTT
34862999 GGTTATTTAC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
23 15 0.27
24 39 0.71
25 1 0.02
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.65
Consensus pattern (24 bp):
TGCTGTTTTGGTTGTTATTTTTGC
Found at i:34872267 original size:3 final size:3
Alignment explanation
Indices: 34872259--34872288 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34872249 CTCTATTTTC
34872259 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34872289 ATATAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:34875598 original size:40 final size:38
Alignment explanation
Indices: 34875530--34875664 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
34875520 ACTAGAATGG
* *
34875530 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
34875570 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
34875607 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
34875648 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
34875665 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:34875662 original size:41 final size:38
Alignment explanation
Indices: 34875562--34875665 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
34875552 TTCGAAGCAA
* *
34875562 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
34875599 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
34875637 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
34875666 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:34875793 original size:12 final size:13
Alignment explanation
Indices: 34875770--34875807 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
34875760 AATTCATATC
*
34875770 ACTTTCAATTTCA
1 ACTTTCACTTTCA
34875783 AC-TTCACTTTC-
1 ACTTTCACTTTCA
34875794 ACTTTCACTTTCA
1 ACTTTCACTTTCA
34875807 A
1 A
34875808 TTTTGATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 2 0.09
12 17 0.77
13 3 0.14
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:34875985 original size:22 final size:22
Alignment explanation
Indices: 34875957--34876002 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
34875947 TAAACGTATA
34875957 ATATTTCACATATACATTATTC
1 ATATTTCACATATACATTATTC
*
34875979 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTATTC
34876001 AT
1 AT
34876003 CACATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATTTCACATATACATTATTC
Found at i:34877841 original size:52 final size:52
Alignment explanation
Indices: 34877757--34878062 Score: 353
Period size: 52 Copynumber: 5.7 Consensus size: 52
34877747 TAAATGAAAA
* *
34877757 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATG
*
34877809 AGGTCCGATGACTATGTGTCATCATGAATATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATG
* * * * *** *
34877861 AGGTCCGGTGGCTATGTGTCATCATGAGTATATGGATGAAATGAAATCCATTGCAGATTA-A
1 AGGTCCGATGACTATGTGTCATC--GTG-A-AT--AT---ATG-AATCCTTTATGGATTATG
* *
34877922 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATG
34877974 AGGTCCGATGACTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATG
* * * * *
34878026 AGGTCCGGTGGCTATGTGTTATTGTGAGTATATGAAT
1 AGGTCCGATGACTATGTGTCATCGTGAATATATGAAT
34878063 GAAATGAAAT
Statistics
Matches: 214, Mismatches: 29, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
51 11 0.05
52 155 0.72
54 1 0.00
55 3 0.01
56 2 0.01
57 1 0.00
58 3 0.01
59 2 0.01
61 24 0.11
62 12 0.06
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATG
Found at i:34878027 original size:165 final size:165
Alignment explanation
Indices: 34877755--34878117 Score: 609
Period size: 165 Copynumber: 2.2 Consensus size: 165
34877745 CGTAAATGAA
34877755 AAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGA
1 AAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGA
34877820 CTATGTGTCATCATGAATATATGAATCCTTTATGGATTATGAGGTCCGGTGGCTATGTGTCATCA
66 CTATGTGTCATCATGAATATATGAATCCTTTATGGATTATGAGGTCCGGTGGCTATGTGTCATCA
*
34877885 TGAGTATATGGATGAAATGAAATCCATTGCAGATT
131 TGAGTATATGAATGAAATGAAATCCATTGCAGATT
* *
34877920 AAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTATGGATTATGAGGTCCGATGA
1 AAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGA
* * **
34877985 CTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATGAGGTCCGGTGGCTATGTGTTATTG
66 CTATGTGTCATCATGAATATATGAATCCTTTATGGATTATGAGGTCCGGTGGCTATGTGTCATCA
**
34878050 TGAGTATATGAATGAAATGAAATCCATTGTGGATT
131 TGAGTATATGAATGAAATGAAATCCATTGCAGATT
* * * *
34878085 AAAGGTCTGATGACTCTATGTCATTGTGAGTAT
1 AAAGGTCCGATGACTATGTGTCATCGTGAGTAT
34878118 CAAATGTGAA
Statistics
Matches: 185, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
165 185 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (165 bp):
AAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGA
CTATGTGTCATCATGAATATATGAATCCTTTATGGATTATGAGGTCCGGTGGCTATGTGTCATCA
TGAGTATATGAATGAAATGAAATCCATTGCAGATT
Found at i:34879278 original size:17 final size:18
Alignment explanation
Indices: 34879256--34879294 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
34879246 AAATTTTTAT
*
34879256 TTTTATAT-AAATATATA
1 TTTTATATAAAAAATATA
34879273 TTTTATATAAAAAATATA
1 TTTTATATAAAAAATATA
34879291 TTTT
1 TTTT
34879295 GTAAAGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTATATAAAAAATATA
Found at i:34894685 original size:63 final size:62
Alignment explanation
Indices: 34894490--34894683 Score: 196
Period size: 63 Copynumber: 3.1 Consensus size: 62
34894480 CGATGATGGT
* * *
34894490 TATGTCGGTGCAGGGAATAAATGCGCGTGATG-TGATACTTGTGTGTAATAAACCT-GTGATGAA
1 TATGTCGGTGCAGGGAA-AATTGCGCGTGATGTTG-TGCTTGTGTGAAATAAA-CTGGTGATGAA
* * * * *
34894553 TGTGTCGGTGCAGGGAAAGATTGCGCATG-TAGTGGTGCTTGTGTGAAATACAGTGGTGATGAA
1 TATGTCGGTGCAGGGAAA-ATTGCGCGTGAT-GTTGTGCTTGTGTGAAATAAACTGGTGATGAA
* * * * *
34894616 TATGTTGGTGCAGGGAACAATTGCACGTGATGTTGTGCTCGTGTAAAATAAACTGGTGATGTA
1 TATGTCGGTGCAGGGAA-AATTGCGCGTGATGTTGTGCTTGTGTGAAATAAACTGGTGATGAA
34894679 TATGT
1 TATGT
34894684 TGATGCAAAG
Statistics
Matches: 107, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
62 3 0.03
63 101 0.94
64 3 0.03
ACGTcount: A:0.26, C:0.10, G:0.32, T:0.31
Consensus pattern (62 bp):
TATGTCGGTGCAGGGAAAATTGCGCGTGATGTTGTGCTTGTGTGAAATAAACTGGTGATGAA
Found at i:34897604 original size:11 final size:12
Alignment explanation
Indices: 34897588--34897616 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
34897578 TTACTTGGAG
34897588 TTTAAATTTAT-
1 TTTAAATTTATA
34897599 TTTAAATTTATA
1 TTTAAATTTATA
34897611 TTTAAA
1 TTTAAA
34897617 AAGTTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTAAATTTATA
Found at i:34897608 original size:17 final size:17
Alignment explanation
Indices: 34897529--34897614 Score: 64
Period size: 17 Copynumber: 5.1 Consensus size: 17
34897519 CCAATTTTAG
* *
34897529 ATTTTAAATTTTAATTC
1 ATTTTAAATTTAAATTT
**
34897546 ATTTTACGTTTAAATTT
1 ATTTTAAATTTAAATTT
* **
34897563 ATTATAAATTTAAGCTT
1 ATTTTAAATTTAAATTT
* ** *
34897580 ACTTGGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
34897597 ATTTTAAATTTATATTT
1 ATTTTAAATTTAAATTT
34897614 A
1 A
34897615 AAAAGTTCAA
Statistics
Matches: 48, Mismatches: 21, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:34898314 original size:3 final size:3
Alignment explanation
Indices: 34898306--34898372 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
34898296 CCATTATCAT
34898306 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
34898354 TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TT
34898373 TAAGAAAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:34899667 original size:30 final size:30
Alignment explanation
Indices: 34899633--34899841 Score: 114
Period size: 30 Copynumber: 7.0 Consensus size: 30
34899623 TCATACTTAG
* *
34899633 ACCCCTGAAGTTTTTAAAAATTACATTTTA
1 ACCCCTGAAATTTCTAAAAATTACATTTTA
*
34899663 ACCCCT-AAACTTTCAAAAAATTACATTTTTA
1 ACCCCTGAAA-TTTCTAAAAATTACA-TTTTA
* *
34899694 A-CCCTGAAACTTCCAAAAATTACCATTTT-
1 ACCCCTGAAATTTCTAAAAATTA-CATTTTA
* *
34899723 ACCCCCG-AATATCTAAAAATT-CTATTTTTA
1 ACCCCTGAAATTTCTAAAAATTAC-A-TTTTA
* *
34899753 A-CCCTTAAACTTT-TGAAAATTACCATTTT-
1 ACCCCTGAAA-TTTCTAAAAATTA-CATTTTA
* ** * * *
34899782 ACCCC-CAAACGTCCAAAAATTCCATTTTTG
1 ACCCCTGAAATTTCTAAAAATTACA-TTTTA
* *
34899812 ACCCC-AAAACTTCTAAAAATTACCATTTTA
1 ACCCCTGAAATTTCTAAAAATTA-CATTTTA
34899842 CCCTTAGATG
Statistics
Matches: 138, Mismatches: 24, Indels: 34
0.70 0.12 0.17
Matches are distributed among these distances:
27 1 0.01
28 4 0.03
29 35 0.25
30 81 0.59
31 16 0.12
32 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (30 bp):
ACCCCTGAAATTTCTAAAAATTACATTTTA
Found at i:34899855 original size:59 final size:59
Alignment explanation
Indices: 34899647--34899900 Score: 249
Period size: 59 Copynumber: 4.3 Consensus size: 59
34899637 CTGAAGTTTT
* * * * *
34899647 TAAAAATTA-CATTTTAACCCCTAAACTTTCAAAAAATTACATTTTTAACCCTGAAACTTC
1 TAAAAATTACCATTTT-ACCCCCAAA-TGTCCAAAAATTCCATTTTTAACCCCGAAACTTC
* * * * * ** *
34899707 CAAAAATTACCATTTTACCCCCGAATATCTAAAAATTCTATTTTTAACCCTTAAACTTT
1 TAAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTAACCCCGAAACTTC
* * * *
34899766 TGAAAATTACCATTTTACCCCCAAACGTCCAAAAATTCCATTTTTGACCCCAAAACTTC
1 TAAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTAACCCCGAAACTTC
** * * * * *
34899825 TAAAAATTACCATTTTACCCTTAGATGTCCAAAAATTCCATTTTTGACCTCGAAATTTT
1 TAAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTAACCCCGAAACTTC
* *
34899884 TGAAAATTACCGTTTTA
1 TAAAAATTACCATTTTA
34899901 TCCTGGGGTA
Statistics
Matches: 162, Mismatches: 31, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
59 141 0.87
60 15 0.09
61 6 0.04
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.35
Consensus pattern (59 bp):
TAAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTAACCCCGAAACTTC
Found at i:34899858 original size:29 final size:28
Alignment explanation
Indices: 34899768--34899868 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
34899758 TAAACTTTTG
* *
34899768 AAAATTACCATTTTACCCCCAAACGTCCA
1 AAAATT-CCATTTTACCCCAAAATGTCCA
*
34899797 AAAATTCCATTTTTGACCCCAAAACT-TCTA
1 AAAATTCCA-TTTT-ACCCCAAAA-TGTCCA
** *
34899827 AAAATTACCATTTTACCCTTAGATGTCCA
1 AAAATT-CCATTTTACCCCAAAATGTCCA
34899856 AAAATTCCATTTT
1 AAAATTCCATTTT
34899869 TGACCTCGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
28 11 0.18
29 25 0.42
30 21 0.35
31 3 0.05
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCAAAATGTCCA
Found at i:34899859 original size:118 final size:119
Alignment explanation
Indices: 34899644--34899900 Score: 297
Period size: 118 Copynumber: 2.2 Consensus size: 119
34899634 CCCCTGAAGT
* * * **
34899644 TTTTAAAAATTA-CATTTTAACCCCTAAACTTTCAAAAAATTACATTTTTAACCCTGAAACTTCC
1 TTTTGAAAATTACCATTTT-ACCCCCAAACTGTCAAAAAATTACATTTTTAACCCCAAAACTTCC
* * * *
34899708 AAAAATTACCATTTTACCCCCGAATATCTAAAAATTCTATTTTTAACC-CTTAAAC
65 AAAAATTACCATTTTACCCCAGAATATCCAAAAATTCCATTTTTAACCTC-GAAAC
* * * *
34899763 TTTTGAAAATTACCATTTTACCCCCAAAC-GTCCAAAAATTCCATTTTTGACCCCAAAACTTCTA
1 TTTTGAAAATTACCATTTTACCCCCAAACTGTCAAAAAATTACATTTTTAACCCCAAAACTTCCA
* * * *
34899827 AAAATTACCATTTTACCCTTAG-ATGTCCAAAAATTCCATTTTTGACCTCGAAAT
66 AAAATTACCATTTTACCC-CAGAATATCCAAAAATTCCATTTTTAACCTCGAAAC
*
34899881 TTTTGAAAATTACCGTTTTA
1 TTTTGAAAATTACCATTTTA
34899901 TCCTGGGGTA
Statistics
Matches: 117, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
118 89 0.76
119 22 0.19
120 6 0.05
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (119 bp):
TTTTGAAAATTACCATTTTACCCCCAAACTGTCAAAAAATTACATTTTTAACCCCAAAACTTCCA
AAAATTACCATTTTACCCCAGAATATCCAAAAATTCCATTTTTAACCTCGAAAC
Found at i:34899869 original size:29 final size:31
Alignment explanation
Indices: 34899648--34899873 Score: 109
Period size: 30 Copynumber: 7.6 Consensus size: 31
34899638 TGAAGTTTTT
* * * * *
34899648 AAAAATTACA-TTTTAACCCCTAAACTTTCA
1 AAAAATTCCATTTTTGACCCCAAAACTGTCC
* * **
34899678 AAAAATTACATTTTTAACCCTGAAACT-TCC
1 AAAAATTCCATTTTTGACCCCAAAACTGTCC
** * *
34899708 AAAAATTACCA-TTTT-ACCCCCGAA-TATCT
1 AAAAATT-CCATTTTTGACCCCAAAACTGTCC
* * ** **
34899737 AAAAATTCTATTTTTAACCCTTAAACT-TTT
1 AAAAATTCCATTTTTGACCCCAAAACTGTCC
* *
34899767 GAAAATTACCA-TTTT-ACCCCCAAAC-GTCC
1 AAAAATT-CCATTTTTGACCCCAAAACTGTCC
*
34899796 AAAAATTCCATTTTTGACCCCAAAACT-TCT
1 AAAAATTCCATTTTTGACCCCAAAACTGTCC
** *
34899826 AAAAATTACCA-TTTT-ACCCTTAGA-TGTCC
1 AAAAATT-CCATTTTTGACCCCAAAACTGTCC
34899855 AAAAATTCCATTTTTGACC
1 AAAAATTCCATTTTTGACC
34899874 TCGAAATTTT
Statistics
Matches: 155, Mismatches: 26, Indels: 30
0.73 0.12 0.14
Matches are distributed among these distances:
28 10 0.06
29 57 0.37
30 66 0.43
31 22 0.14
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.34
Consensus pattern (31 bp):
AAAAATTCCATTTTTGACCCCAAAACTGTCC
Found at i:34901948 original size:39 final size:39
Alignment explanation
Indices: 34901869--34901958 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
34901859 TTCCCTCAAT
* * ** * *
34901869 TTTCAATCATTTCAACAATTAACAGTAAGTTACTTCCCA
1 TTTCAACCATTACAACAATTAACAGTAAGAAAATTACCA
*
34901908 TTTCAACCATTACAATAATTAACAGTAAGAAAATTACCA
1 TTTCAACCATTACAACAATTAACAGTAAGAAAATTACCA
*
34901947 TTTCAACAATTA
1 TTTCAACCATTA
34901959 GTAGTAAGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (39 bp):
TTTCAACCATTACAACAATTAACAGTAAGAAAATTACCA
Found at i:34902835 original size:30 final size:29
Alignment explanation
Indices: 34902789--34902846 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
34902779 CAGTTTGTAC
*
34902789 CTTTTTTTCTCTGTGATCTGGAGCATGAG
1 CTTTTTTTCGCTGTGATCTGGAGCATGAG
*
34902818 CTTTTTCTTCGCTGTGATTTGGAGCATGA
1 CTTTTT-TTCGCTGTGATCTGGAGCATGA
34902847 ACCTTCACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (29 bp):
CTTTTTTTCGCTGTGATCTGGAGCATGAG
Found at i:34904531 original size:6 final size:6
Alignment explanation
Indices: 34904522--34904582 Score: 113
Period size: 6 Copynumber: 10.2 Consensus size: 6
34904512 TATACATACT
34904522 CCTATC CCTATC CCTATC CCTATC CCTATC CCTATC CCTATC CCTATC
1 CCTATC CCTATC CCTATC CCTATC CCTATC CCTATC CCTATC CCTATC
*
34904570 GCTATC CCTATC C
1 CCTATC CCTATC C
34904583 AAAATGTGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.16, C:0.49, G:0.02, T:0.33
Consensus pattern (6 bp):
CCTATC
Found at i:34906841 original size:18 final size:18
Alignment explanation
Indices: 34906820--34906857 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
34906810 TGAATTTTCG
*
34906820 AATTTGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
34906838 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
34906856 AA
1 AA
34906858 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:34911976 original size:314 final size:314
Alignment explanation
Indices: 34911407--34912034 Score: 1148
Period size: 314 Copynumber: 2.0 Consensus size: 314
34911397 ATGATGCCAA
* *
34911407 CTTGAGAGACTTGATAAATACATCAGGAACTTGGTCCTCACTTCTACAATACTCTAGTTCAATTG
1 CTTGAGAGACTTGATAAATACATCAGCAACTTGGTCCTCACTTCTACAATACTCTAGCTCAATTG
*
34911472 CTCCTTTATTGCTAAGATCTCGTATAAAATAATATTTTACATCAATATGCTTGTTTCTTCCATGC
66 CTCCTTTATTGCTAAGATCTCGCATAAAATAATATTTTACATCAATATGCTTGTTTCTTCCATGC
*
34911537 AGCACAAAATTCTTTGACAACTTGATGGATAAGTTGTTATCACAGAAAATTGTAGTGGCAGTTTC
131 AGCACAAAATTCTTTGACAACTTGATGGATAAGTTATTATCACAGAAAATTGTAGTGGCAGTTTC
*
34911602 TAGCTTGAATTGTAATTGTTCAAGGATTCTCCTAAGCCAAATAACTTGACAAGCACAATATATTA
196 AAGCTTGAATTGTAATTGTTCAAGGATTCTCCTAAGCCAAATAACTTGACAAGCACAATATATTA
*
34911667 CAACAACAAATTCAGCTTCTTTGCTTTATAATGTGACAATGGATTGCTTTTTAG
261 CAACAACAAATTCAGCTTCTGTGCTTTATAATGTGACAATGGATTGCTTTTTAG
* *
34911721 CTTGAGAGGCTTGATAAATACATCAGCAACTTGGTCCTCACTTCTGCAATACTCTAGCTCAATTG
1 CTTGAGAGACTTGATAAATACATCAGCAACTTGGTCCTCACTTCTACAATACTCTAGCTCAATTG
34911786 CTCCTTTATTGCTAAGATCTCGCATAAAATAATATTTTACATCAATATGCTTGTTTCTTCCATGC
66 CTCCTTTATTGCTAAGATCTCGCATAAAATAATATTTTACATCAATATGCTTGTTTCTTCCATGC
* *
34911851 AGCACAAAATTCTTTGACAACTTGATGGATGAGTTATTATCACAGAAAATTGTAGTGGCATTTTC
131 AGCACAAAATTCTTTGACAACTTGATGGATAAGTTATTATCACAGAAAATTGTAGTGGCAGTTTC
* *
34911916 AAGCTTGAATTGTAATTGTTCAAGGATTCTCCTAGGCCAAATAGCTTGACAAGCACAATATATTA
196 AAGCTTGAATTGTAATTGTTCAAGGATTCTCCTAAGCCAAATAACTTGACAAGCACAATATATTA
34911981 CAACAACAAATTCAGCTTCTGTGCTTTATAATGTGACAATGGATTGCTTTTTAG
261 CAACAACAAATTCAGCTTCTGTGCTTTATAATGTGACAATGGATTGCTTTTTAG
34912035 ATGACCATGA
Statistics
Matches: 302, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
314 302 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (314 bp):
CTTGAGAGACTTGATAAATACATCAGCAACTTGGTCCTCACTTCTACAATACTCTAGCTCAATTG
CTCCTTTATTGCTAAGATCTCGCATAAAATAATATTTTACATCAATATGCTTGTTTCTTCCATGC
AGCACAAAATTCTTTGACAACTTGATGGATAAGTTATTATCACAGAAAATTGTAGTGGCAGTTTC
AAGCTTGAATTGTAATTGTTCAAGGATTCTCCTAAGCCAAATAACTTGACAAGCACAATATATTA
CAACAACAAATTCAGCTTCTGTGCTTTATAATGTGACAATGGATTGCTTTTTAG
Found at i:34913386 original size:20 final size:20
Alignment explanation
Indices: 34913361--34913421 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
34913351 TAAGGTATTT
34913361 AAATTTATGGAAGTATTTTG
1 AAATTTATGGAAGTATTTTG
*** *
34913381 AAATTT-TAGCTTGT-TCTTG
1 AAATTTAT-GGAAGTATTTTG
34913400 AAAGTTTATGGAAGTATTTTG
1 AAA-TTTATGGAAGTATTTTG
34913421 A
1 A
34913422 GCTTGGTTGT
Statistics
Matches: 29, Mismatches: 8, Indels: 7
0.66 0.18 0.16
Matches are distributed among these distances:
19 8 0.28
20 15 0.52
21 6 0.21
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (20 bp):
AAATTTATGGAAGTATTTTG
Found at i:34914106 original size:60 final size:59
Alignment explanation
Indices: 34913942--34914157 Score: 276
Period size: 60 Copynumber: 3.7 Consensus size: 59
34913932 AAATGCAAAA
*
34913942 AAGGTCCGATGACTTTATGTCATCGTGAGTATTAAATGCAATGAATCCAATTACGGATT
1 AAGGTCCGATGACTTTATGTCATCGTGAGTATTAAATGCAATGAATCCAATTATGGATT
* *
34914001 AAAGGTCTGATGAC--T-TGTCATCGTGAGTATTAAATGCAATGAATCCAATCATGGATT
1 -AAGGTCCGATGACTTTATGTCATCGTGAGTATTAAATGCAATGAATCCAATTATGGATT
* * * *
34914058 AAGGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAAATTAATCCTATTATGGATT
1 AA-GGTCCGATGACTTTATGTCATCGTGAGTATTAAATGCAATGAATCCAATTATGGATT
* * * * *
34914118 ATATGTCCGATAACTCTATGTCATCATGAGTATCAAATGC
1 A-AGGTCCGATGACTTTATGTCATCGTGAGTATTAAATGC
34914158 GAATTAAAAC
Statistics
Matches: 136, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
56 2 0.01
57 50 0.37
58 1 0.01
59 1 0.01
60 81 0.60
61 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (59 bp):
AAGGTCCGATGACTTTATGTCATCGTGAGTATTAAATGCAATGAATCCAATTATGGATT
Found at i:34924530 original size:24 final size:25
Alignment explanation
Indices: 34924469--34924532 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
34924459 TCAAGCACTA
34924469 AAAATTAACATAATTTTTATAAATATC
1 AAAA-TAA-ATAATTTTTATAAATATC
*
34924496 AAAATATATAATTTTTATCAAATA-C
1 AAAATAAATAATTTTTAT-AAATATC
*
34924521 -AAGTAAATAATT
1 AAAATAAATAATT
34924533 ATACCAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 10 0.30
25 12 0.36
26 7 0.21
27 4 0.12
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
AAAATAAATAATTTTTATAAATATC
Found at i:34927373 original size:17 final size:19
Alignment explanation
Indices: 34927347--34927385 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
34927337 GTAAGATATT
*
34927347 AGAAATAAAAAA-AA-AAA
1 AGAAAGAAAAAACAATAAA
34927364 AGAAAGAAAAAACAATAAA
1 AGAAAGAAAAAACAATAAA
34927383 AGA
1 AGA
34927386 CAAGGAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (19 bp):
AGAAAGAAAAAACAATAAA
Found at i:34928193 original size:1 final size:1
Alignment explanation
Indices: 34928187--34928214 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
34928177 CTATAACCCT
34928187 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
34928215 TCTCAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:34930004 original size:19 final size:19
Alignment explanation
Indices: 34929982--34930090 Score: 50
Period size: 19 Copynumber: 5.7 Consensus size: 19
34929972 AAAATTGTAA
34929982 AGAAAATTATAAAATATAT
1 AGAAAATTATAAAATATAT
* * *
34930001 AGAAATTTAGAAAA-AAATT
1 AGAAAATTATAAAATATA-T
* * *
34930020 ATAAAATT-TAATAAATTTGT
1 AGAAAATTAT-A-AAATATAT
* *
34930040 AAGAAAATTATAAAAAAGTAA
1 -AGAAAATTATAAAATA-TAT
34930061 AG-AAA-TATAAAAT-TCAT
1 AGAAAATTATAAAATAT-AT
34930078 A-AAAATTATAAAA
1 AGAAAATTATAAAA
34930091 ATTATCATAC
Statistics
Matches: 64, Mismatches: 16, Indels: 21
0.63 0.16 0.21
Matches are distributed among these distances:
16 1 0.02
17 5 0.08
18 16 0.25
19 23 0.36
20 9 0.14
21 9 0.14
22 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.29
Consensus pattern (19 bp):
AGAAAATTATAAAATATAT
Found at i:34930007 original size:30 final size:30
Alignment explanation
Indices: 34929972--34930054 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
34929962 ACTTTTATTA
34929972 AAAATTGTAAAGAAAATTATAAAATAT-AT
1 AAAATTGTAAAGAAAATTATAAAATATAAT
* *
34930001 AGAAATT-TAGAAAAAAATTATAAAATTTAAT
1 A-AAATTGTA-AAGAAAATTATAAAATATAAT
*
34930032 AAATTTGT-AAGAAAATTATAAAA
1 AAAATTGTAAAGAAAATTATAAAA
34930055 AAGTAAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 17 0.37
30 25 0.54
31 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (30 bp):
AAAATTGTAAAGAAAATTATAAAATATAAT
Found at i:34930036 original size:29 final size:30
Alignment explanation
Indices: 34929976--34930054 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
34929966 TTATTAAAAA
34929976 TTGTAAAGAAAATTATAAAATATATAGAAAT
1 TTGTAAA-AAAATTATAAAATATATAGAAAT
* *
34930007 TTAG-AAAAAAATTATAAAATTTA-ATAAAT
1 TT-GTAAAAAAATTATAAAATATATAGAAAT
*
34930036 TTGTAAGAAAATTATAAAA
1 TTGTAAAAAAATTATAAAA
34930055 AAGTAAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
28 1 0.02
29 21 0.49
30 15 0.35
31 5 0.12
32 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (30 bp):
TTGTAAAAAAATTATAAAATATATAGAAAT
Found at i:34930055 original size:9 final size:9
Alignment explanation
Indices: 34930013--34930095 Score: 50
Period size: 9 Copynumber: 9.0 Consensus size: 9
34930003 AAATTTAGAA
34930013 AAAAATTAT
1 AAAAATTAT
34930022 -AAAATT-T
1 AAAAATTAT
*
34930029 AATAAATTTGT
1 AA-AAA-TTAT
34930040 AAGAAAATTAT
1 -A-AAAATTAT
34930051 AAAAA--AGT
1 AAAAATTA-T
*
34930059 AAAGAAATAT
1 AAA-AATTAT
34930069 -AAAATTCAT
1 AAAAATT-AT
34930078 AAAAATTAT
1 AAAAATTAT
34930087 AAAAATTAT
1 AAAAATTAT
34930096 CATACCGATA
Statistics
Matches: 60, Mismatches: 2, Indels: 24
0.70 0.02 0.28
Matches are distributed among these distances:
7 2 0.03
8 14 0.23
9 24 0.40
10 10 0.17
11 5 0.08
12 4 0.07
13 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:34933227 original size:17 final size:17
Alignment explanation
Indices: 34933205--34933238 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34933195 AAGGGACATA
34933205 ATAATTAAAAATTTAAT
1 ATAATTAAAAATTTAAT
*
34933222 ATAATTATAAATTTAAT
1 ATAATTAAAAATTTAAT
34933239 TTTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATTAAAAATTTAAT
Found at i:34934298 original size:21 final size:21
Alignment explanation
Indices: 34934257--34934298 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
34934247 TGATTAGAAA
* *
34934257 AATTATAAAAATATATTTTTT
1 AATTAAAAAAATATATATTTT
34934278 AATTAAAATAAAT-TATATTTT
1 AATTAAAA-AAATATATATTTT
34934299 TCGATGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTAAAAAAATATATATTTT
Found at i:34935011 original size:25 final size:23
Alignment explanation
Indices: 34934967--34935016 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
34934957 ACCAATTGTA
34934967 TTAGTAAAATATTTAATTTATCAT
1 TTAGTAAAATATTTAATTTAT-AT
*
34934991 TTAGCTAAAAT-TTTATTTTTATAT
1 TTAG-TAAAATATTTA-ATTTATAT
34935015 TT
1 TT
34935017 TTATACATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (23 bp):
TTAGTAAAATATTTAATTTATAT
Found at i:34935237 original size:10 final size:9
Alignment explanation
Indices: 34935221--34935259 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
34935211 TAATTTTAAG
34935221 TTATATTTA
1 TTATATTTA
34935230 TTATTATTTA
1 TTA-TATTTA
34935240 TTATATGTTA
1 TTATAT-TTA
*
34935250 TTACATTTA
1 TTATATTTA
34935259 T
1 T
34935260 ATTTTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 10 0.37
10 17 0.63
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (9 bp):
TTATATTTA
Found at i:34935257 original size:19 final size:19
Alignment explanation
Indices: 34935221--34935259 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34935211 TAATTTTAAG
*
34935221 TTATATTTATTATTATTTA
1 TTATATTTATTATCATTTA
34935240 TTATATGTTATTA-CATTTA
1 TTATAT-TTATTATCATTTA
34935259 T
1 T
34935260 ATTTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTATATTTATTATCATTTA
Found at i:34935743 original size:17 final size:18
Alignment explanation
Indices: 34935723--34935756 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34935713 ACAATTCAAT
*
34935723 AAAAAAGAAAAG-ACAAA
1 AAAAAAAAAAAGCACAAA
34935740 AAAAAAAAAAAGCACAA
1 AAAAAAAAAAAGCACAA
34935757 GCCTAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGCACAAA
Found at i:34937092 original size:15 final size:16
Alignment explanation
Indices: 34937072--34937102 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
34937062 ATATAGATGC
34937072 AATGTAGATAA-AAAA
1 AATGTAGATAATAAAA
34937087 AATGTAGATAATAAAA
1 AATGTAGATAATAAAA
34937103 GAATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23
Consensus pattern (16 bp):
AATGTAGATAATAAAA
Found at i:34937134 original size:12 final size:12
Alignment explanation
Indices: 34937117--34937143 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
34937107 AATTTAAAAA
34937117 TATAAAAATATT
1 TATAAAAATATT
34937129 TATAAAAATATT
1 TATAAAAATATT
34937141 TAT
1 TAT
34937144 TAATTTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAAAAATATT
Found at i:34937380 original size:6 final size:6
Alignment explanation
Indices: 34937360--34937418 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
34937350 TTAAAAGGGT
* * *
34937360 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTCA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
34937408 TTTAAG TTTAA
1 TTTAAA TTTAA
34937419 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:34937395 original size:14 final size:14
Alignment explanation
Indices: 34937376--34937402 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34937366 TTTATTTTAA
34937376 ATTTAAATTTACTC
1 ATTTAAATTTACTC
34937390 ATTTAAATTTACT
1 ATTTAAATTTACT
34937403 TTAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAATTTACTC
Found at i:34937507 original size:28 final size:28
Alignment explanation
Indices: 34937475--34937577 Score: 179
Period size: 28 Copynumber: 3.7 Consensus size: 28
34937465 TTACAAATGT
34937475 CCAATTACAAACAAACCCAAATTGGGGC
1 CCAATTACAAACAAACCCAAATTGGGGC
*
34937503 CCAATTACAAACAAACCCAAATCGGGGC
1 CCAATTACAAACAAACCCAAATTGGGGC
* *
34937531 CCAATTACAAGCAAACCCAAATTGGAGC
1 CCAATTACAAACAAACCCAAATTGGGGC
34937559 CCAATTACAAACAAACCCA
1 CCAATTACAAACAAACCCA
34937578 TCGGCCCAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 70 1.00
ACGTcount: A:0.45, C:0.31, G:0.12, T:0.13
Consensus pattern (28 bp):
CCAATTACAAACAAACCCAAATTGGGGC
Found at i:34939282 original size:29 final size:29
Alignment explanation
Indices: 34939240--34939458 Score: 144
Period size: 29 Copynumber: 7.5 Consensus size: 29
34939230 GGACTGTTCA
*
34939240 AAAATTACCATTTTACCCCCAAACTTCCC
1 AAAATTACCATTTTACCCCCGAACTTCCC
* *
34939269 AAAATT-CCATTTTTAACCCCG-ATTTCACC
1 AAAATTACCA-TTTTACCCCCGAACTTC-CC
* * *
34939298 AAAATTATCATTTTACCCTCGAACTTTCC
1 AAAATTACCATTTTACCCCCGAACTTCCC
** * ** **
34939327 AAAATT-CCATTTTTGGCCTCGATTTTATC
1 AAAATTACCA-TTTTACCCCCGAACTTCCC
*
34939356 AAAATTACCATTTTACCCCCGAACTTTCC
1 AAAATTACCATTTTACCCCCGAACTTCCC
* * *
34939385 AAAATT-CCATTTTTAACCTCG-ATTTCACC
1 AAAATTACCA-TTTTACCCCCGAACTTC-CC
* * *
34939414 AAAAATTACCCTTTTATCCCCTAGACTTTCCC
1 -AAAATTACCATTTTACCCCCGA-AC-TTCCC
34939446 AAAATT-CCATTTT
1 AAAATTACCATTTT
34939459 GACCTCGATT
Statistics
Matches: 145, Mismatches: 32, Indels: 25
0.72 0.16 0.12
Matches are distributed among these distances:
28 15 0.10
29 88 0.61
30 28 0.19
31 8 0.06
32 3 0.02
33 3 0.02
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAACTTCCC
Found at i:34939310 original size:58 final size:59
Alignment explanation
Indices: 34939238--34939529 Score: 322
Period size: 58 Copynumber: 5.0 Consensus size: 59
34939228 TTGGACTGTT
*
34939238 CAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTCCATTTTTAACCTCGATTTCAC
* * * * ** * *
34939297 C-AAAATTATCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGGCCTCGATTTTAT
1 CAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTCCATTTTTAACCTCGATTTCAC
* *
34939355 C-AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTCCATTTTTAACCTCGATTTCAC
* * * *
34939413 CAAAAATTACCCTTTTATCCCCTAGACTTTCCCAAAATTCCA-TTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTA-CCCCCAAAC-TTCCCAAAATTCCATTTTTAACCTCGATTTCAC
* * * * * * * *
34939473 CAAAAATTATCATTTTTCCCCC-GAGTACCCAAAAGTCCCGTTTTCAACCTCGATTTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCCAAAA-TTCCATTTTTAACCTCGATTTC
34939530 GTCGTTTCTT
Statistics
Matches: 197, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
57 8 0.04
58 106 0.54
59 33 0.17
60 37 0.19
61 13 0.07
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTCCATTTTTAACCTCGATTTCAC
Found at i:34939429 original size:30 final size:30
Alignment explanation
Indices: 34939238--34939488 Score: 129
Period size: 29 Copynumber: 8.5 Consensus size: 30
34939228 TTGGACTGTT
* * * *
34939238 CAAAAATTACCATTTTACCCCCAAACTTC-C
1 CAAAAATTACCATTTTAACCTC-GATTTCAC
*
34939268 C-AAAATT-CCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCA-TTTTAACCTCGATTTCAC
* *
34939297 C-AAAATTATCATTTTACCCTCGAACTTT--C
1 CAAAAATTACCATTTTAACCTCG-A-TTTCAC
** * *
34939326 C-AAAATT-CCATTTTTGGCCTCGATTTTAT
1 CAAAAATTACCA-TTTTAACCTCGATTTCAC
* *
34939355 C-AAAATTACCATTTTACCCCCGAACTTT--C
1 CAAAAATTACCATTTTAACCTCG-A-TTTCAC
34939384 C-AAAATT-CCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCA-TTTTAACCTCGATTTCAC
* * *
34939413 CAAAAATTACCCTTTTATCCCCTAGACTTTC-C
1 CAAAAATTACCATTTTA--ACCTCGA-TTTCAC
*
34939445 C-AAAATT-CCATTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTAACCTCGATTTCAC
*
34939473 CAAAAATTATCATTTT
1 CAAAAATTACCATTTT
34939489 TCCCCCGAGT
Statistics
Matches: 175, Mismatches: 24, Indels: 44
0.72 0.10 0.18
Matches are distributed among these distances:
27 10 0.06
28 21 0.12
29 88 0.50
30 31 0.18
31 14 0.08
32 7 0.04
33 4 0.02
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (30 bp):
CAAAAATTACCATTTTAACCTCGATTTCAC
Found at i:34939596 original size:15 final size:16
Alignment explanation
Indices: 34939570--34939615 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
34939560 GTTACTTGCA
*
34939570 TCTGCATTTTATATTT
1 TCTGCATATTATATTT
*
34939586 TC-GCATATTAT-TTA
1 TCTGCATATTATATTT
*
34939600 TCTGCTTATTATATTT
1 TCTGCATATTATATTT
34939616 CTTCGTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.59
Consensus pattern (16 bp):
TCTGCATATTATATTT
Found at i:34941316 original size:18 final size:18
Alignment explanation
Indices: 34941293--34941327 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34941283 ACTAAAACGA
34941293 AAATTTATCATAATTTTG
1 AAATTTATCATAATTTTG
*
34941311 AAATTTATCCTAATTTT
1 AAATTTATCATAATTTT
34941328 TAACTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATTTATCATAATTTTG
Found at i:34942721 original size:2 final size:2
Alignment explanation
Indices: 34942714--34942740 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34942704 ATAGATGCCT
34942714 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 T
34942741 ATGTGGAAAA
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:34948171 original size:10 final size:10
Alignment explanation
Indices: 34948139--34948164 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
34948129 ATTTTCTAAC
34948139 AAAATATAAA
1 AAAATATAAA
34948149 AAAATATAAA
1 AAAATATAAA
34948159 AAAATA
1 AAAATA
34948165 AAGAAAATGA
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATATAAA
Found at i:34953114 original size:26 final size:26
Alignment explanation
Indices: 34953085--34953134 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
34953075 CTTAATATAT
*
34953085 ATTTTAATATAATTTAAAATAATAAC
1 ATTTTAATATAAATTAAAATAATAAC
* * *
34953111 ATTTTATTTTAAATTAAATTAATA
1 ATTTTAATATAAATTAAAATAATA
34953135 TTTTATATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTTAATATAAATTAAAATAATAAC
Found at i:34953138 original size:18 final size:18
Alignment explanation
Indices: 34953115--34953149 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34953105 AATAACATTT
34953115 TATTTTAAATTAAATTAA
1 TATTTTAAATTAAATTAA
*
34953133 TATTTTATATTAAATTA
1 TATTTTAAATTAAATTA
34953150 TTTCAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTTAAATTAAATTAA
Found at i:34953776 original size:17 final size:18
Alignment explanation
Indices: 34953740--34953784 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
34953730 TGAAATTGAT
**
34953740 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTCATAAA
34953758 TTTAAATTTA-TCATAAA
1 TTTAAATTTATTCATAAA
34953775 TTTAAATTTA
1 TTTAAATTTA
34953785 ATTAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATTCATAAA
Found at i:34953797 original size:17 final size:16
Alignment explanation
Indices: 34953753--34953793 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
34953743 AAATTTATTT
34953753 TTAAATTTAAATTT-A
1 TTAAATTTAAATTTAA
34953768 TCATAAATTTAAATTTAA
1 T--TAAATTTAAATTTAA
34953786 TTAAATTT
1 TTAAATTT
34953794 TAAACAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 7 0.30
17 13 0.57
18 2 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAATTTAAATTTAA
Found at i:34955465 original size:59 final size:59
Alignment explanation
Indices: 34955353--34955517 Score: 201
Period size: 59 Copynumber: 2.8 Consensus size: 59
34955343 TAAATTGTCT
** * * * *
34955353 AAAAATTACATTTTTACCCC-GAACTTTCTGAAATTCTATATTTAACCTTGATTTTTCC
1 AAAAATTACATTTTTACCCCTGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCC
* *
34955411 AAAATTTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCC
1 AAAAATTACATTTTTACCCCTGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCC
* *
34955470 AAAAATTACCA-TTTTACCCCTGAA-TGTCCAAAAACTCCATTTTTGACC
1 AAAAATTA-CATTTTTACCCCTGAACTTTCC-AAAATTCCATTTTTGACC
34955518 CCGAAACTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 23 0.25
59 67 0.73
60 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCCTGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCC
Found at i:34955475 original size:30 final size:30
Alignment explanation
Indices: 34955353--34955519 Score: 103
Period size: 29 Copynumber: 5.7 Consensus size: 30
34955343 TAAATTGTCT
* **
34955353 AAAAATTACATTTTTACCCC-GAACTTT-C
1 AAAAATTCCATTTTTACCCCTGATTTTTCC
** * * * *
34955381 TGAAATTCTATATTTAACCTTGATTTTTCC
1 AAAAATTCCATTTTTACCCCTGATTTTTCC
* * * **
34955411 AAAATTTACATTTTTACCCCTAAACTTTCC
1 AAAAATTCCATTTTTACCCCTGATTTTTCC
*
34955441 -AAAATTCCATTTTTGACCTC-GATTTTTCC
1 AAAAATTCCATTTTT-ACCCCTGATTTTTCC
* *
34955470 AAAAATTACCA-TTTTACCCCTGA-ATGTCC
1 AAAAATT-CCATTTTTACCCCTGATTTTTCC
*
34955499 AAAAACTCCATTTTTGACCCC
1 AAAAATTCCATTTTT-ACCCC
34955520 GAAACTTTTG
Statistics
Matches: 101, Mismatches: 30, Indels: 14
0.70 0.21 0.10
Matches are distributed among these distances:
28 16 0.16
29 41 0.41
30 41 0.41
31 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (30 bp):
AAAAATTCCATTTTTACCCCTGATTTTTCC
Found at i:34955713 original size:30 final size:30
Alignment explanation
Indices: 34955618--34955722 Score: 113
Period size: 30 Copynumber: 3.5 Consensus size: 30
34955608 TCGAATGTCC
*
34955618 AAAATTCCATTTTTAACCCCAAACCTTTTAA
1 AAAATTCCATTTTTAACCCCAAACC-TTCAA
** * *
34955649 AAAATTATATTTTT-ACCCCCAAGCTTCAA
1 AAAATTCCATTTTTAACCCCAAACCTTCAA
* * *
34955678 AAAATTCCATTTTTAACCTCGAACCTTCCA
1 AAAATTCCATTTTTAACCCCAAACCTTCAA
34955708 AAAATTACCATTTTT
1 AAAATT-CCATTTTT
34955723 TCGTCGAGTG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
29 16 0.26
30 25 0.41
31 20 0.33
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCAAACCTTCAA
Found at i:34955720 original size:118 final size:117
Alignment explanation
Indices: 34955441--34955749 Score: 304
Period size: 118 Copynumber: 2.6 Consensus size: 117
34955431 TAAACTTTCC
* *** *
34955441 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCC-CTGAATGTCCAAAAAC
1 AAAATTCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCTC-GAATGTCC-AAAAT
* * * **
34955505 TCCATTTTTGACCCCGAAACTTTTGAAAATTACCATTTTATGCCTGAATGTTCA
64 TCCATTTTTAACCCCGAAACTTTTAAAAATTACCATTTTATCCCCCAATGTTCA
* * * * * * *
34955559 AAAACTCCATTTTTTTACCTTGAAGCTTTCGAAAATTATCATTTTACCCTCGAATGTCCAAAATT
1 AAAATTCCA-TTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAATT
*
34955624 CCATTTTTAACCCC-AAACCTTTTAAAAAATTA-TATTTT-TACCCCCAA-GCTTCAA
65 CCATTTTTAACCCCGAAA-CTTTT-AAAAATTACCATTTTAT-CCCCCAATG-TTC-A
** * *
34955678 AAAATTCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTTTCGTCGAGTGTCCAAAATTA
1 AAAATTCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAATT-
34955743 CCATTTT
65 CCATTTT
34955750 ACCCCTAAGA
Statistics
Matches: 156, Mismatches: 27, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
117 5 0.03
118 88 0.56
119 62 0.40
120 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (117 bp):
AAAATTCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAATTC
CATTTTTAACCCCGAAACTTTTAAAAATTACCATTTTATCCCCCAATGTTCA
Found at i:34955722 original size:60 final size:56
Alignment explanation
Indices: 34955353--34955721 Score: 186
Period size: 59 Copynumber: 6.3 Consensus size: 56
34955343 TAAATTGTCT
** * * * ***
34955353 AAAAATTA-CATTTTTACCCCGAACTTTCTGAAATTCTATATTTAACCTTGATTTTTCC
1 AAAAATTACCA-TTTTACCCCGAA--TTCAAAAATTCCATTTTTAACCTCGAACCTTCC
* * * * ***
34955411 AAAATTTA-CATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCC
1 AAAAATTACCA-TTTTACCCC-GAA--TTCAAAAATTCCATTTTTAACCTCGAACCTTCC
* * * * **
34955470 AAAAATTACCATTTTACCCCTGAATGTCCAAAAACTCCATTTTTGACCCCGAAACTTTT
1 AAAAATTACCATTTTACCCC-GAAT-T-CAAAAATTCCATTTTTAACCTCGAACCTTCC
* * * * * * * *
34955529 GAAAATTACCATTTTATGCCTGAATGTTCAAAAACTCCATTTTTTTACCTTGAAGCTTTC
1 AAAAATTACCATTTTA-CCCCGAA--TTCAAAAATTCCA-TTTTTAACCTCGAACCTTCC
* * * * * **
34955589 GAAAATTATCATTTTACCCTCGAATGTCCAAAATTCCATTTTTAACCCCAAACCTTTTA
1 AAAAATTACCATTTTACCC-CGAAT-TCAAAAATTCCATTTTTAACCTCGAACC-TTCC
* *
34955648 AAAAATTA-TATTTTTACCCCCAAGCTTCAAAAAATTCCATTTTTAACCTCGAACCTTCC
1 AAAAATTACCA-TTTTACCCCGAA--TTC-AAAAATTCCATTTTTAACCTCGAACCTTCC
34955707 AAAAATTACCATTTT
1 AAAAATTACCATTTT
34955722 TTCGTCGAGT
Statistics
Matches: 249, Mismatches: 46, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
57 1 0.00
58 36 0.14
59 148 0.59
60 63 0.25
61 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (56 bp):
AAAAATTACCATTTTACCCCGAATTCAAAAATTCCATTTTTAACCTCGAACCTTCC
Done.