Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 162 of 284
Found at i:54373408 original size:16 final size:16
Alignment explanation
Indices: 54373369--54373410 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
54373359 ATCGACAAAA
*
54373369 GCTGAAATGCTGAAAT
1 GCTGAAAAGCTGAAAT
**
54373385 GCCAAAAAGCTGAAAT
1 GCTGAAAAGCTGAAAT
54373401 GCTGAAAAGC
1 GCTGAAAAGC
54373411 CAAAAGTTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (16 bp):
GCTGAAAAGCTGAAAT
Found at i:54373679 original size:29 final size:29
Alignment explanation
Indices: 54373637--54373736 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 29
54373627 TGAATGTTAC
* *
54373637 TGGGCCCAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
54373666 TGGGCCTAATGGGCCATA-AACAGGTGGTT
1 TGGGCCTAATGGGCCATATAA-ATGTGATT
* * *
54373695 TGGGCCTAATTGGCCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
54373723 TGGGCTTAATGGGC
1 TGGGCCTAATGGGC
54373737 AAGATACAGG
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
28 15 0.26
29 42 0.72
30 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:54377328 original size:27 final size:26
Alignment explanation
Indices: 54377284--54377335 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
54377274 CTCACTGCAA
*
54377284 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
54377311 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
54377336 GCAGCCTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:54384453 original size:47 final size:49
Alignment explanation
Indices: 54384384--54384604 Score: 214
Period size: 46 Copynumber: 4.7 Consensus size: 49
54384374 TAAGGTGCCA
* * * *
54384384 ATGCCATGTCCTAGACACGGTCTTATACTGGCTCAT-ATCT-TAAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCGTCTCTAAGCCG
* *
54384431 ATGCCATGTCCCAAACATGGTCTTACACTGACT-ATCGTCTCGT-AGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCGTCTC-TAAGCCG
* * *
54384479 ATG-CATGTCCCAGACAT-GTCTTACACTGGCT-AACGTCTCGAGGCC-
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCGTCTCTAAGCCG
* * * *
54384524 ATTG-CATATCCCAAACAT-GTCTTACACTAGC-CCTCGTCTC-AATGCCG
1 A-TGCCATGTCCCAGACATGGTCTTACACTGGCTCATCGTCTCTAA-GCCG
54384571 ATGCCATGTCCCAGACATGGTCTTACACTGGCTC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTC
54384605 TCATAATATG
Statistics
Matches: 143, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
45 2 0.01
46 62 0.43
47 57 0.40
48 20 0.14
49 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCGTCTCTAAGCCG
Found at i:54397852 original size:30 final size:31
Alignment explanation
Indices: 54397774--54397852 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
54397764 CATAGTATCA
* *
54397774 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCCTGGATCTCTC
* *
54397804 TAT-TCTGGATTTCTTTATTCC-GGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCTGGATCTCTC
54397834 TATCTTGGATTTCTTTATT
1 TATCTTGGATTTCTTTATT
54397853 TGGTTTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 37 0.88
31 4 0.10
ACGTcount: A:0.11, C:0.18, G:0.15, T:0.56
Consensus pattern (31 bp):
TATCTTGGATTTCTTTATTCCTGGATCTCTC
Found at i:54397860 original size:14 final size:15
Alignment explanation
Indices: 54397783--54397862 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
54397773 ATATCTTGGG
*
54397783 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
54397798 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
54397813 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
54397828 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
54397843 TTTCTTTATT-TGGT
1 TTTCTTTATTCTGGA
54397857 TTTCTT
1 TTTCTT
54397863 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 11 0.21
15 41 0.77
16 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.14, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:54403068 original size:50 final size:50
Alignment explanation
Indices: 54402955--54403189 Score: 260
Period size: 50 Copynumber: 4.7 Consensus size: 50
54402945 CTGGTACGCA
* **
54402955 TAGTAGCCTGCACTTAGTACTACACATGTGACC-AAAAATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGATACACG
* * *
54403004 TAGTAGGCTACACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGATACACG
* * * * * * ** *
54403054 TAGTAGACTGCACTTAGTACTACACACGTGA-TTGAAGTTGTCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT-AA-CTATCTGATACACG
* *
54403105 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGATACACG
* *
54403155 TAGTATCCTGAACTTAGTACTACACACGTG-CCTAA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
54403190 AACCATCTTA
Statistics
Matches: 154, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
49 36 0.23
50 80 0.52
51 37 0.24
52 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGATACACG
Found at i:54403208 original size:101 final size:99
Alignment explanation
Indices: 54402942--54403234 Score: 293
Period size: 101 Copynumber: 2.9 Consensus size: 99
54402932 TAACTGAAGT
* * * *
54402942 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACC-AAAAATCTGATACACGTA
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTG-CCTAAAAATCTGATACACATA
* * *
54403006 GTAGGCTACACTTAGTACTACACACGTGACCTAAC
65 GTAGCCTGCACTTAGTACTACACATGTGACCTAAC
* * * ** *** * * **
54403041 CATCTGATACACGTAGTAGACTGCACTTAGTACTACACACGTGATTGAAGTTGTCGGGTATGCAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGCCT-AA-AAATCTGATACACAT
54403106 AGTAGCCTGCACTTAGTACTACACATGTGACCTAAC
64 AGTAGCCTGCACTTAGTACTACACATGTGACCTAAC
* * * *
54403142 TATCTGGTACACGTAGTATCCTGAACTTAGTACTACACACGTGCCTAAAACCATCTTAAACACAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGCCTAAAA--ATCTGATACACAT
* * *
54403207 AG-CGCCTGCACATAGTACTATACATGTG
64 AGTAGCCTGCACTTAGTACTACACATGTG
54403235 TTCTCACAAT
Statistics
Matches: 151, Mismatches: 38, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
99 37 0.25
100 27 0.18
101 87 0.58
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (99 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGCCTAAAAATCTGATACACATAG
TAGCCTGCACTTAGTACTACACATGTGACCTAAC
Found at i:54405951 original size:101 final size:99
Alignment explanation
Indices: 54405768--54405963 Score: 275
Period size: 101 Copynumber: 2.0 Consensus size: 99
54405758 AGCCGAAGCT
* * * * *
54405768 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTATACATGCGACCAATTATCCGGTACACGTAGT
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGGTACACATAGT
*
54405833 AGCCTACACTTAGTACTACACACGTGACCTAACC
66 AGCCTACACTTAGTACTACACACATGACCTAACC
* * * *
54405867 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATA
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCAGGTACACATA
*
54405932 GTAGCCTGCACTTAGTACTACACACATGACCT
64 GTAGCCTACACTTAGTACTACACACATGACCT
54405964 CACAATAGCT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 38 0.45
100 3 0.04
101 43 0.51
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (99 bp):
ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGGTACACATAGT
AGCCTACACTTAGTACTACACACATGACCTAACC
Found at i:54415951 original size:21 final size:19
Alignment explanation
Indices: 54415913--54415951 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
54415903 CTGTAATTTG
*
54415913 AAAATTTTCTATGTTTTCC
1 AAAATTTTCTAAGTTTTCC
54415932 AAAATTTTTCCTAAGTTTTC
1 AAAA-TTTT-CTAAGTTTTC
54415952 AGTTTAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.51
Consensus pattern (19 bp):
AAAATTTTCTAAGTTTTCC
Found at i:54418477 original size:40 final size:39
Alignment explanation
Indices: 54418426--54418572 Score: 215
Period size: 39 Copynumber: 3.8 Consensus size: 39
54418416 TAAAAACATG
* * * * *
54418426 TATTAAAGATGTCCAAACTATGACATAATTAAAAAAATCC
1 TATTAATGATGTTCAAATTATGACATAATT-AAAAACTCA
* *
54418466 TATTAATGATGTTTAAATTATGACATAATTAAAAACTCT
1 TATTAATGATGTTCAAATTATGACATAATTAAAAACTCA
54418505 TATTAATGATGTTCAAATTATGACATAATTAAAAACTCA
1 TATTAATGATGTTCAAATTATGACATAATTAAAAACTCA
54418544 TATTAATGATGTT-AAATTATGACATAATT
1 TATTAATGATGTTCAAATTATGACATAATT
54418573 TGTAACACCC
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 16 0.16
39 57 0.58
40 26 0.26
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (39 bp):
TATTAATGATGTTCAAATTATGACATAATTAAAAACTCA
Found at i:54418498 original size:79 final size:77
Alignment explanation
Indices: 54418415--54418572 Score: 228
Period size: 79 Copynumber: 2.0 Consensus size: 77
54418405 TTAAACACAC
*
54418415 TTAAAAACAT-GTATTAAAGATGTCCAAACTATGACATAATTAAAAAAATCCTATTAATGATGTT
1 TTAAAAAC-TCGTATTAAAGATGTCCAAACTATGACATAATT-AAAAAATCATATTAATGATG-T
54418479 TAAATTATGACATAA
63 TAAATTATGACATAA
* * * * *
54418494 TTAAAAACTCTTATTAATGATGTTCAAATTATGACATAATTAAAAACTCATATTAATGATGTTAA
1 TTAAAAACTCGTATTAAAGATGTCCAAACTATGACATAATTAAAAAATCATATTAATGATGTTAA
54418559 ATTATGACATAA
66 ATTATGACATAA
54418571 TT
1 TT
54418573 TGTAACACCC
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
77 18 0.25
78 19 0.26
79 35 0.49
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.36
Consensus pattern (77 bp):
TTAAAAACTCGTATTAAAGATGTCCAAACTATGACATAATTAAAAAATCATATTAATGATGTTAA
ATTATGACATAA
Found at i:54420607 original size:29 final size:27
Alignment explanation
Indices: 54420589--54420658 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
54420579 ATATTAAGTC
54420589 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
54420616 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
54420644 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
54420659 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:54420652 original size:28 final size:28
Alignment explanation
Indices: 54420589--54420686 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
54420579 ATATTAAGTC
*
54420589 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
54420616 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
54420644 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
54420673 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54420687 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54430479 original size:14 final size:14
Alignment explanation
Indices: 54430460--54430488 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54430450 CGACTTTAAC
54430460 ACATATTTATATAT
1 ACATATTTATATAT
54430474 ACATATTTATATAT
1 ACATATTTATATAT
54430488 A
1 A
54430489 TATCCCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ACATATTTATATAT
Found at i:54434043 original size:39 final size:40
Alignment explanation
Indices: 54433946--54434127 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 40
54433936 AATGATGTCT
* * * * *
54433946 GGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATTC
* *
54433986 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATTTC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATTC
* *
54434026 GGGCTAAG-CCTGAAGGCATTGGTGCGAGTTACTAAATTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATTC
* *
54434065 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATTC
*
54434105 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
54434128 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
39 34 0.28
40 76 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATTC
Found at i:54434149 original size:79 final size:77
Alignment explanation
Indices: 54433977--54434160 Score: 183
Period size: 79 Copynumber: 2.3 Consensus size: 77
54433967 GTGCTAAGTG
* ** *
54433977 ACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAATTTCGGGCTAAGCCTGAAGG
1 ACTATATCCGG-TTAAG-TCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGG
**
54434042 CATTGGTGCGAGTT
64 CATTGGAACGAGTT
* * *
54434056 ACTAAATTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAA
1 ACTATA-TCCGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAA
*
54434120 GGCATTTGAACGAG-T
62 GGCATTGGAACGAGTT
*
54434135 AGCTATATCCGGTTAAATTCCGAAGG
1 A-CTATATCCGGTT-AAGTCCGAAGG
54434161 TACGTGATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
78 3 0.03
79 56 0.65
80 27 0.31
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (77 bp):
ACTATATCCGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCA
TTGGAACGAGTT
Found at i:54447838 original size:54 final size:54
Alignment explanation
Indices: 54447773--54448223 Score: 353
Period size: 54 Copynumber: 8.4 Consensus size: 54
54447763 TTAGTTTACC
* *
54447773 AAATTACCAAAATACCCCTAGTTTGAAAAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTC-GATTTGTA
* *
54447827 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTC-GATTTGTA
** ** *** *
54447881 AAATTACTGAAATA-CCCTCAACTTGTAAAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCTCGATTTGTA
* * * * *
54447935 AAATTACCAAAGTACCCC-CGATTTTTAAAATTACCTAAATATCCTCGATTTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCTCGATTTGTA
* * * **
54447989 AAATTATCGAAATA-CCCTCAGTTTGCAAAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCTCGATTTGTA
** * ** * *** * *
54448043 AAATTACTGAAATACTCCT-GTAAGATAGAATTACCATTTTACCCTCAATTTATA
1 AAATTACCAAAATACCCCTAGTTTG-TAAAATTACCAAAATACCCTCGATTTGTA
* *** * * * * * *
54448097 GAATTACCATTTTA-CCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACT-
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCTCGATTT-GTA
* *
54448151 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACTCCT-GGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATAC-CCTCGATTTGTA
54448205 AAATTACCAAAATACCCCT
1 AAATTACCAAAATACCCCT
54448224 GTAGGGTAGA
Statistics
Matches: 307, Mismatches: 76, Indels: 28
0.75 0.18 0.07
Matches are distributed among these distances:
53 14 0.05
54 275 0.90
55 18 0.06
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTCGATTTGTA
Found at i:54448224 original size:27 final size:27
Alignment explanation
Indices: 54447773--54448305 Score: 307
Period size: 27 Copynumber: 19.7 Consensus size: 27
54447763 TTAGTTTACC
* *
54447773 AAATTACCAAAATACCCCTAGTTTGAA
1 AAATTACCAAAATACCCCTGGTTTGTA
54447800 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
54447827 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
54447854 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
** ***
54447881 AAATTACTGAAATA-CCCTCAACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*** **
54447908 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
* * * *
54447935 AAATTACCAAAGTACCCCCGATTTTTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
54447962 AAATTACCTAAATA-TCCTCGATTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
* * * *
54447989 AAATTATCGAAATA-CCCTCAGTTTGCA
1 AAATTACCAAAATACCCCT-GGTTTGTA
** *
54448016 AAATTACTGAAATA-CCCTCGATTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
** * **
54448043 AAATTACTGAAATACTCCT-GTAAGATA
1 AAATTACCAAAATACCCCTGGTTTG-TA
* *** ** *
54448070 GAATTACCATTTTA-CCCTCAATTTATA
1 AAATTACCAAAATACCCCT-GGTTTGTA
* *** * *
54448097 GAATTACCATTTTA-CCCTCGATTTATA
1 AAATTACCAAAATACCCCT-GGTTTGTA
* * *
54448124 AAATTACTAAAATACCCTTGGTTTACT-
1 AAATTACCAAAATACCCCTGGTTT-GTA
54448151 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
54448178 AAATTACCAAAATACTCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
**
54448205 AAATTACCAAAATACCCCT-GTAGGGTA
1 AAATTACCAAAATACCCCTGGT-TTGTA
* * **
54448232 GAATTACCGAAATACCCCT-GTAAGGTA
1 AAATTACCAAAATACCCCTGGT-TTGTA
* **
54448259 GAATTACCAAAATACCCCT-GTAGGGTA
1 AAATTACCAAAATACCCCTGGT-TTGTA
* *
54448286 GAATTACTAAAATACCCCTG
1 AAATTACCAAAATACCCCTG
54448306 TAGGGTGGAA
Statistics
Matches: 419, Mismatches: 75, Indels: 23
0.81 0.15 0.04
Matches are distributed among these distances:
26 14 0.03
27 394 0.94
28 11 0.03
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:54448224 original size:54 final size:53
Alignment explanation
Indices: 54447773--54448277 Score: 342
Period size: 54 Copynumber: 9.4 Consensus size: 53
54447763 TTAGTTTACC
* *
54447773 AAATTACCAAAATACCCCTAGTTTGAAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATA-CCCTGATTTGTA
* *
54447827 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATA-CCCTGATTTGTA
** ** *** *
54447881 AAATTACTGAAATA-CCCTCAACTTGTAAAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCT-GATTTGTA
* * * * *
54447935 AAATTACCAAAGTACCCC-CGATTTTTAAAATTACCTAAATATCCTCGATTTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCT-GATTTGTA
* * * **
54447989 AAATTATCGAAATA-CCCTCAGTTTGCAAAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCT-GATTTGTA
** * ** * *** * *
54448043 AAATTACTGAAATACTCCT-GTAAGATAGAATTACCATTTTACCCTCAATTTATA
1 AAATTACCAAAATACCCCTAGTTTG-TAAAATTACCAAAATACCCT-GATTTGTA
* *** * * * * *
54448097 GAATTACCATTTTA-CCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACT-
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCC-TGATTT-GTA
* *
54448151 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACTCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATAC-CCTGATTTGTA
** * * **
54448205 AAATTACCAAAATACCCCT-GTAGGGTAGAATTACCGAAATACCCCTG-TAAGGTA
1 AAATTACCAAAATACCCCTAGT-TTGTAAAATTACCAAAATA-CCCTGAT-TTGTA
*
54448259 GAATTACCAAAATACCCCT
1 AAATTACCAAAATACCCCT
54448278 GTAGGGTAGA
Statistics
Matches: 351, Mismatches: 82, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
53 21 0.06
54 312 0.89
55 18 0.05
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (53 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTGATTTGTA
Found at i:54448237 original size:81 final size:81
Alignment explanation
Indices: 54447773--54448307 Score: 342
Period size: 81 Copynumber: 6.6 Consensus size: 81
54447763 TTAGTTTACC
* * * *
54447773 AAATTACCAAAATACCCCT-AGTTTGAAAAATTACCAAAATACCCCTGGT-TTGTAAAATTATCA
1 AAATTACCAAAATACCCCTGA-TTTGTAAAATTACTAAAATACCCCT-GTATGGTAAAATTACCA
54447836 AAATACCC-CTAGTTTGTA
64 AAATACCCTC-AGTTTGTA
* * ** * ***
54447854 AAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATA-CCCTCAACTTGTAAAATTATTGA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTACTAAAATACCCCTGTA-TGGTAAAATTACCAA
*
54447918 AATACCCTC-GACTTGTA
65 AATACCCTCAG-TTTGTA
* * * * * *
54447935 AAATTACCAAAGTACCCCCGATTTTTAAAATTACCT-AAATA-TCCTCG-ATTTGTAAAATTATC
1 AAATTACCAAAATACCCCTGATTTGTAAAATTA-CTAAAATACCCCT-GTA-TGGTAAAATTACC
* *
54447997 GAAATACCCTCAGTTTGCA
63 AAAATACCCTCAGTTTGTA
** * * * * * *
54448016 AAATTACTGAAATA-CCCTCGATTTGTAAAATTACTGAAATACTCCTGTAAGATAGAATTACCAT
1 AAATTACCAAAATACCCCT-GATTTGTAAAATTACTAAAATACCCCTGTATGGTAAAATTACCAA
** * *
54448080 TTTACCCTCAATTTATA
65 AATACCCTCAGTTTGTA
* *** * * * **
54448097 GAATTACCATTTTA-CCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACT-AAATTACCA
1 AAATTACCAAAATACCCCT-GATTTGTAAAATTACTAAAATACCCCT-GTATGGTAAAATTACCA
*
54448160 AAATACCC-CTGGTTTGTA
64 AAATACCCTC-AGTTTGTA
* * * * * *
54448178 AAATTACCAAAATACTCCTGGTTTGTAAAATTACCAAAATACCCCTGTAGGGTAGAATTACCGAA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTACTAAAATACCCCTGTATGGTAAAATTACCAAA
* **
54448243 ATACCC-CTGTAAGGTA
66 ATACCCTCAGT-TTGTA
* ** *
54448259 GAATTACCAAAATACCCCTG-TAGGGTAGAATTACTAAAATACCCCTGTA
1 AAATTACCAAAATACCCCTGAT-TTGTAAAATTACTAAAATACCCCTGTA
54448308 GGGTGGAATT
Statistics
Matches: 355, Mismatches: 81, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
80 17 0.05
81 322 0.91
82 16 0.05
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (81 bp):
AAATTACCAAAATACCCCTGATTTGTAAAATTACTAAAATACCCCTGTATGGTAAAATTACCAAA
ATACCCTCAGTTTGTA
Found at i:54448308 original size:81 final size:81
Alignment explanation
Indices: 54448152--54448328 Score: 223
Period size: 81 Copynumber: 2.2 Consensus size: 81
54448142 TGGTTTACTA
* ** * **
54448152 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACTCCTGGTTTGTAAAATTACCAAAA
1 AATTACCGAAATACCCCTGGTAGGTAAAATTACCAAAATACCCCTGGTGGGTAAAATTACCAAAA
54448217 TACCCCTGTAGGGTAG
66 TACCCCTGTAGGGTAG
* * *
54448233 AATTACCGAAATACCCCT-GTAAGGTAGAATTACCAAAATACCCCT-GTAGGGTAGAATTACTAA
1 AATTACCGAAATACCCCTGGT-AGGTAAAATTACCAAAATACCCCTGGT-GGGTAAAATTACCAA
*
54448296 AATACCCCTGTAGGGTGG
64 AATACCCCTGTAGGGTAG
*
54448314 AATTACCGAGATACC
1 AATTACCGAAATACC
54448329 TTGTGGGGTA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
80 4 0.05
81 79 0.95
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.25
Consensus pattern (81 bp):
AATTACCGAAATACCCCTGGTAGGTAAAATTACCAAAATACCCCTGGTGGGTAAAATTACCAAAA
TACCCCTGTAGGGTAG
Found at i:54448328 original size:54 final size:54
Alignment explanation
Indices: 54448152--54448347 Score: 200
Period size: 54 Copynumber: 3.6 Consensus size: 54
54448142 TGGTTTACTA
** * * * ** *
54448152 AATTACCAAAATACCCCTGGT-TTGTAAAATTACCAAAATACTCCTGGT-TTGTAA
1 AATTACCAAAATACCCCT-GTAGGGTAGAATTACTAAAATACCCCT-GTAAGGTAG
**
54448206 AATTACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
* *
54448260 AATTACCAAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
* * * * *
54448314 AATTACCGAGATA-CCTTGTGGGGTAAAATTACTA
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACTA
54448348 TTTTACCCCT
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
53 22 0.18
54 101 0.82
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (54 bp):
AATTACCAAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
Found at i:54448826 original size:22 final size:22
Alignment explanation
Indices: 54448770--54448834 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
54448760 TTAAAGCCTT
* *
54448770 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
54448792 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
54448814 CTGATTATTGCTCTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
54448835 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:54449025 original size:27 final size:27
Alignment explanation
Indices: 54448994--54449087 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 27
54448984 CTGTTAAGTG
* *
54448994 GCCACATTATCTGTTTCTGGTGGCTAT
1 GCCACAATATCTGTTTCTGGTGGCTCT
54449021 GCCACAAATATCTG-TTCTGGTGGCTCT
1 GCCAC-AATATCTGTTTCTGGTGGCTCT
* *
54449048 GCCACAATATCTGTATCTGGTGACTCT
1 GCCACAATATCTGTTTCTGGTGGCTCT
*
54449075 GTCACAATATCTG
1 GCCACAATATCTG
54449088 ATAACTGAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
26 8 0.13
27 45 0.75
28 7 0.12
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (27 bp):
GCCACAATATCTGTTTCTGGTGGCTCT
Found at i:54449262 original size:6 final size:6
Alignment explanation
Indices: 54449247--54449343 Score: 65
Period size: 6 Copynumber: 15.8 Consensus size: 6
54449237 ATTCTATTAC
* * * *
54449247 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTAATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * *
54449296 CTGATT CTG-TCAC CTAATT CTGATT TTGATT CTGATT CT-AGTT CTGAT
1 CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
54449344 AATGTTTCTT
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
5 4 0.06
6 58 0.83
7 6 0.09
8 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (6 bp):
CTGATT
Found at i:54449278 original size:31 final size:31
Alignment explanation
Indices: 54449237--54449359 Score: 133
Period size: 31 Copynumber: 4.0 Consensus size: 31
54449227 CTCATTTTTT
* *
54449237 ATTCTATTACCTGATACTGATTCTGATTTTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
*
54449268 ATTCTGTTACCTGATACTAATTCTGATTCTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
* * * *
54449299 ATTCTGTCACCTAATTCTGATTTTGATTCTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
* * *
54449330 ATTCTAGTT--CTGATAATGTTTCTTATTCTG
1 ATTCT-GTTACCTGATACTGATTCTGATTCTG
54449360 TAATGAGTTA
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
30 15 0.20
31 59 0.78
32 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (31 bp):
ATTCTGTTACCTGATACTGATTCTGATTCTG
Found at i:54451047 original size:43 final size:42
Alignment explanation
Indices: 54451000--54451098 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 42
54450990 TCCTAGACGT
* *
54451000 GGTCTTACATGTAATCAAACATTGATGCC-ACTGTCCCAGACAG
1 GGTCTTACATGTAATCAAACA-CGATGCCGA-TGTCCCAAACAG
* * * *
54451043 GGTCTTACATGAAATCAGATACGATGCCGATGTCCCAAACAT
1 GGTCTTACATGTAATCAAACACGATGCCGATGTCCCAAACAG
54451085 GGTCTTACATGTAA
1 GGTCTTACATGTAA
54451099 AACAGAAGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 29 0.60
43 19 0.40
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
GGTCTTACATGTAATCAAACACGATGCCGATGTCCCAAACAG
Found at i:54451089 original size:42 final size:41
Alignment explanation
Indices: 54450989--54451145 Score: 136
Period size: 43 Copynumber: 3.7 Consensus size: 41
54450979 CAATGCCAAC
* * * * *
54450989 GTCCTAGACGTGGTCTTACATGTAATCAAACATTGATGCCACT
1 GTCCCAGACATGGTCTTACATGAAATCAGA-ATCGATGCCA-T
*
54451032 GTCCCAGACAGGGTCTTACATGAAATCAG-ATACGATGCCGAT
1 GTCCCAGACATGGTCTTACATGAAATCAGAAT-CGATGCC-AT
* * *
54451074 GTCCCAAACATGGTCTTACATGTAAAACAGAAGTCGATGCCAAC
1 GTCCCAGACATGGTCTTACATG-AAATCAGAA-TCGATGCC-AT
* * *
54451118 GTCCCAGACGTGGTTTTACACGAAATCA
1 GTCCCAGACATGGTCTTACATGAAATCA
54451146 CATATCAGAT
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
41 2 0.02
42 27 0.29
43 36 0.39
44 27 0.29
45 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (41 bp):
GTCCCAGACATGGTCTTACATGAAATCAGAATCGATGCCAT
Found at i:54454079 original size:63 final size:63
Alignment explanation
Indices: 54454006--54454796 Score: 1582
Period size: 63 Copynumber: 12.6 Consensus size: 63
54453996 AGCAGTGAAA
54454006 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454069 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454132 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454195 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454258 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454321 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454384 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454447 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454510 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454573 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454636 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454699 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
54454762 CAGGGGTAACTTCAATGAATAAAATGTACTAATTG
1 CAGGGGTAACTTCAATGAATAAAATGTACTAATTG
54454797 GCTAGACCAA
Statistics
Matches: 728, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 728 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (63 bp):
CAGGGGTAACTTCAATGAATAAAATGTACTAATTGAAGTTAACCCTGATCCACCTGGCCAGAT
Found at i:54458973 original size:17 final size:17
Alignment explanation
Indices: 54458951--54458984 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54458941 CAAAAAAAGT
54458951 AGAAATTGAATCAGAGA
1 AGAAATTGAATCAGAGA
54458968 AGAAATTGAATCAGAGA
1 AGAAATTGAATCAGAGA
54458985 CTGAATGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (17 bp):
AGAAATTGAATCAGAGA
Found at i:54466855 original size:42 final size:42
Alignment explanation
Indices: 54466753--54466866 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 42
54466743 AACATATACA
* *
54466753 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAACATTG
1 ATGCC-ATGTCCCAGACATGGTCTTACACGAAATCAAACATTG
* * *
54466796 ATGCCACTGTCCGAGACAGGGTCTTACACGAAATCAAATA-TG
1 ATGCCA-TGTCCCAGACATGGTCTTACACGAAATCAAACATTG
* *
54466838 ATGCTGATGTCCTAGACATGGTCTTACAC
1 ATGC-CATGTCCCAGACATGGTCTTACAC
54466867 ATAAAACAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 27 0.44
43 34 0.56
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGCCATGTCCCAGACATGGTCTTACACGAAATCAAACATTG
Found at i:54468024 original size:13 final size:13
Alignment explanation
Indices: 54468006--54468040 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
54467996 ACAAACGATT
54468006 AAATTTTCATACG
1 AAATTTTCATACG
54468019 AAATTTTCATACG
1 AAATTTTCATACG
54468032 AAATTTTCA
1 AAATTTTCA
54468041 CACATACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (13 bp):
AAATTTTCATACG
Found at i:54485087 original size:43 final size:43
Alignment explanation
Indices: 54485019--54485182 Score: 129
Period size: 43 Copynumber: 3.8 Consensus size: 43
54485009 AAAGCTCGTA
* * *
54485019 CAATGCCAACGTCCCAAACATGGTCTTACATGTAATCAAATAC
1 CAATGCCAACGTCCCAAACAGGGTCTTACACGAAATCAAATAC
*
54485062 CAATGCC-ACTGTCCCAGACAGGGTCTTACACGAAATCAAATA-
1 CAATGCCAAC-GTCCCAAACAGGGTCTTACACGAAATCAAATAC
** * ** * *
54485104 TGATACTGATGTCCCAAACATGGTCTTACACGTAAATCATAAGT--
1 CAATGCCAACGTCCCAAACAGGGTCTTACACG-AAATCA-AA-TAC
* * * *
54485148 CGATGCCAATGTCCCAGACATGGTCTTACACGAAA
1 CAATGCCAACGTCCCAAACAGGGTCTTACACGAAA
54485183 ACACATATCA
Statistics
Matches: 100, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 25 0.25
43 45 0.45
44 29 0.29
45 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (43 bp):
CAATGCCAACGTCCCAAACAGGGTCTTACACGAAATCAAATAC
Found at i:54486227 original size:45 final size:45
Alignment explanation
Indices: 54486119--54486294 Score: 214
Period size: 45 Copynumber: 4.0 Consensus size: 45
54486109 CCGAATTCAT
* *
54486119 TCACTGGCATT-TCGCCTGCTAGGCTTC-AAGCCCA-AATAGTATC
1 TCACTGGCATTATAGCCTGCTAGGC-TCAAAGGCCAGAATAGTATC
* * * * * *
54486162 TCACCGGTATTATAGCCTGCTAGGCTTAAAGGCCAGAGTGGTATT
1 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCAGAATAGTATC
*
54486207 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCAGAATAGTATC
* * *
54486252 TCACGGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTA
1 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCAGAATAGTA
54486295 CTGAGCGATA
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
43 10 0.09
44 18 0.16
45 85 0.75
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (45 bp):
TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCAGAATAGTATC
Found at i:54486268 original size:90 final size:88
Alignment explanation
Indices: 54486118--54486285 Score: 248
Period size: 90 Copynumber: 1.9 Consensus size: 88
54486108 CCCGAATTCA
* * *
54486118 TTCACTGGCATTTCGCCTGCTAGGCTTCAAGCCCAAATAGTATCTCACCGGTATTATAGCCTGCT
1 TTCACTGGCATTTAGCCTGCTAGGCTTCAAGCCCAAATAGTATCTCACCGGCATTATAGCCTACT
*
54486183 AGGCTTAAAGGCCAGAGTGGTAT
66 AGGCTCAAAGGCCAGAGTGGTAT
* *
54486206 TTCACTGGCATTATAGCCTGCTAGGC-TCAAAGGCCCGAATAGTATCTCACGGGCATTATAGCCT
1 TTCACTGGCATT-TAGCCTGCTAGGCTTC-AA-GCCCAAATAGTATCTCACCGGCATTATAGCCT
54486270 ACTAGGCTCAAAGGCC
63 ACTAGGCTCAAAGGCC
54486286 CGAATAGTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
88 14 0.20
89 14 0.20
90 43 0.61
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (88 bp):
TTCACTGGCATTTAGCCTGCTAGGCTTCAAGCCCAAATAGTATCTCACCGGCATTATAGCCTACT
AGGCTCAAAGGCCAGAGTGGTAT
Found at i:54490078 original size:21 final size:20
Alignment explanation
Indices: 54490054--54490095 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
54490044 AAACTTGTAT
*
54490054 ATCTATCAACAAGCATTCAAA
1 ATCTATCAACAAACA-TCAAA
*
54490075 ATCTATCATCAAACATCAAA
1 ATCTATCAACAAACATCAAA
54490095 A
1 A
54490096 CACACATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (20 bp):
ATCTATCAACAAACATCAAA
Found at i:54493668 original size:13 final size:13
Alignment explanation
Indices: 54493650--54493674 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54493640 CCAAGCACAT
54493650 GCCCATGTCCTTG
1 GCCCATGTCCTTG
54493663 GCCCATGTCCTT
1 GCCCATGTCCTT
54493675 CACACGGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.40, G:0.20, T:0.32
Consensus pattern (13 bp):
GCCCATGTCCTTG
Found at i:54507378 original size:20 final size:20
Alignment explanation
Indices: 54507353--54507395 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
54507343 ACTACTTGAC
54507353 ACTTTGACTATCTCCTCTGG
1 ACTTTGACTATCTCCTCTGG
54507373 ACTTTGACTATCTCCTCTGG
1 ACTTTGACTATCTCCTCTGG
54507393 ACT
1 ACT
54507396 CCAAGTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.30, G:0.14, T:0.40
Consensus pattern (20 bp):
ACTTTGACTATCTCCTCTGG
Found at i:54509291 original size:48 final size:48
Alignment explanation
Indices: 54509225--54509449 Score: 288
Period size: 48 Copynumber: 4.7 Consensus size: 48
54509215 TGTGTAACCA
* * * * * * *
54509225 TGTAAGACCATATCTGGGATATGGAATCGGTATTGTTATGTGATCCCG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGCCAG
* * * *
54509273 TATAAGACCATGTTTGGGACATGGCATCGGCATTGTTTCGTGAGCCAA
1 TGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGCCAG
** *
54509321 TGTAAGACCATGTCTAAGACATGGCATCGGTATTGTTACGTGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGCCAG
* * *
54509369 TGTAAAACCATGTCTGGGACATGGCATCTGCATTGTTACCTGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGCCAG
*
54509417 TGTAAGACCATGTCTGGGACATGGCATCTGCAT
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAT
54509450 GAGGCATCGT
Statistics
Matches: 152, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 152 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGCCAG
Found at i:54511364 original size:20 final size:18
Alignment explanation
Indices: 54511339--54511382 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
54511329 CAGGTGGGGG
54511339 ACACGGACGTGTCCTGAGCC
1 ACACGGACGTGT-CTGA-CC
* *
54511359 ACACGGGCGTGTGTGACC
1 ACACGGACGTGTCTGACC
54511377 ACACGG
1 ACACGG
54511383 CCTGCCCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 11 0.50
ACGTcount: A:0.20, C:0.32, G:0.34, T:0.14
Consensus pattern (18 bp):
ACACGGACGTGTCTGACC
Found at i:54513451 original size:93 final size:93
Alignment explanation
Indices: 54513338--54513508 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54513328 GCCCATAAGT
* *
54513338 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54513403 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
54513431 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54513496 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54513509 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54513505 original size:46 final size:46
Alignment explanation
Indices: 54513330--54513505 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
54513320 TGTAACCCGC
* * *
54513330 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54513376 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
54513426 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
54513469 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54513506 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54514370 original size:52 final size:52
Alignment explanation
Indices: 54514292--54514395 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
54514282 ATAGGGATCT
*
54514292 CAAAAACGTAAAAATCATTAAAAACGGGGCTTGGAATCACTTACTATGGAGC
1 CAAAAACGTAAAAATCATAAAAAACGGGGCTTGGAATCACTTACTATGGAGC
54514344 CAAAAACGTAAAAATCATAAAAAACGGGGCTTGGAATCACTTACTATGGAGC
1 CAAAAACGTAAAAATCATAAAAAACGGGGCTTGGAATCACTTACTATGGAGC
54514396 TTGGAAGCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.20
Consensus pattern (52 bp):
CAAAAACGTAAAAATCATAAAAAACGGGGCTTGGAATCACTTACTATGGAGC
Found at i:54519948 original size:50 final size:50
Alignment explanation
Indices: 54519873--54519971 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
54519863 TTTTTTATAG
* **
54519873 AATTTTTGGTTGGGCCAATTAGTACATTTTATTAGTTATTGTTACCCCTA
1 AATTTTTGGTTGGGCCAATTAGTACAGTTTATTAGTTAAAGTTACCCCTA
*
54519923 AATTTTTTGTTGGGCCAATTAGTACAGTTTATTAGTTAAAGTTACCCCT
1 AATTTTTGGTTGGGCCAATTAGTACAGTTTATTAGTTAAAGTTACCCCT
54519972 GTTTCAGGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.44
Consensus pattern (50 bp):
AATTTTTGGTTGGGCCAATTAGTACAGTTTATTAGTTAAAGTTACCCCTA
Found at i:54526248 original size:45 final size:45
Alignment explanation
Indices: 54526158--54526248 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 45
54526148 GTAGGATTCT
* * * * *
54526158 GATATATGTGTTTTCGAGTAAGACCACATCTGGGACGTTGGCATC
1 GATATATGTGGTTACGAGTAAGACCACATCTGGGACATCGACATC
**
54526203 GATATATGTGGTTAC-ATGTAAGACCATGTCTGGGACATCGACATC
1 GATATATGTGGTTACGA-GTAAGACCACATCTGGGACATCGACATC
54526248 G
1 G
54526249 TATTTGATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (45 bp):
GATATATGTGGTTACGAGTAAGACCACATCTGGGACATCGACATC
Found at i:54530432 original size:49 final size:49
Alignment explanation
Indices: 54530004--54530430 Score: 732
Period size: 49 Copynumber: 8.8 Consensus size: 49
54529994 AAATGATAGT
54530004 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
54530053 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
54530102 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
54530151 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
54530200 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
54530249 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
*
54530298 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAC--ATATGTGAT
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
* * * * *
54530345 AAGGCCTAACGGCCGAGGTGATGAATGTGGAAGTGTATATATATGTGAC
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
* * * * * *
54530394 AGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTA
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
54530431 TAAATGTGAT
Statistics
Matches: 362, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 42 0.12
49 320 0.88
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (49 bp):
AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATGTGAA
Found at i:54530540 original size:37 final size:37
Alignment explanation
Indices: 54530484--54530562 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54530474 CCGAGCTCTA
* * *
54530484 AAGACCCGATGACTACGTGTGAGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGAAGATTATGTCCGGGT
*
54530521 AAGACCCGATAACTTCGTGTGAAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGAAGATTATGTCCGGGT
54530558 AAGAC
1 AAGAC
54530563 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGAAGATTATGTCCGGGT
Found at i:54532425 original size:40 final size:40
Alignment explanation
Indices: 54532370--54533690 Score: 2381
Period size: 40 Copynumber: 33.0 Consensus size: 40
54532360 ATTCGAATGA
*
54532370 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
**
54532410 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
*
54532450 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532490 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532530 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532570 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532610 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532650 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532690 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532730 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532770 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532810 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532850 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532890 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532930 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54532970 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54533010 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54533050 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54533090 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54533130 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54533170 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54533210 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
*
54533250 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
*
54533290 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
*
54533330 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
* *
54533370 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGCGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
* * *
54533410 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGCGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
*
54533450 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
* *
54533490 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
* **
54533530 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
* * *
54533570 TATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
* **
54533610 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
* * * * *
54533650 TATCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGACG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
54533690 T
1 T
54533691 GTATTCGGGC
Statistics
Matches: 1255, Mismatches: 26, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 1255 1.00
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.24
Consensus pattern (40 bp):
TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGACG
Found at i:54536700 original size:35 final size:35
Alignment explanation
Indices: 54536656--54536727 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
54536646 AGTAACGTGA
54536656 TTTTAGAAAATCACCATAAATTTATGGATTTGAAT
1 TTTTAGAAAATCACCATAAATTTATGGATTTGAAT
54536691 TTTTAGAAAATCACCATAAATTTATGGATTTGAAT
1 TTTTAGAAAATCACCATAAATTTATGGATTTGAAT
54536726 TT
1 TT
54536728 GAGGCTGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (35 bp):
TTTTAGAAAATCACCATAAATTTATGGATTTGAAT
Found at i:54537761 original size:22 final size:22
Alignment explanation
Indices: 54537731--54537773 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
54537721 ACACCAAAAC
* *
54537731 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGACGCTTTTTT
54537753 AGGCCTTTAGCGACGCTTTTT
1 AGGCCTTTAGCGACGCTTTTT
54537774 AGCGCCGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGACGCTTTTTT
Found at i:54537906 original size:43 final size:43
Alignment explanation
Indices: 54537845--54538090 Score: 287
Period size: 43 Copynumber: 5.7 Consensus size: 43
54537835 GCGTCGCTAA
* **
54537845 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGCCAGGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
* * *
54537888 CTTTAACGGCGCTTTTCCCACAAACGCCGCTATAGATTAGAAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
* *
54537931 CTTTAGCGACACTTTTCCCACAAACGCCGCTATAGATCAGGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
* * *
54537974 CTTTAGCGGCACTTTT-ACACAAACGCCGCTATAGATCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
*** * *
54538016 CTTTAGCGGCGCTTTTTTTATAAACGCCGCTATAGATCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
* * * ** *
54538059 TTTTAGCGACGTTTTTTTCGCAAACGCCGCTA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
54538091 AAAGTGCCAT
Statistics
Matches: 177, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 39 0.22
43 138 0.78
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
Found at i:54538041 original size:85 final size:86
Alignment explanation
Indices: 54537845--54538066 Score: 286
Period size: 85 Copynumber: 2.6 Consensus size: 86
54537835 GCGTCGCTAA
* ** * * *
54537845 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGCCAGGACCTTTAACGGCGCTTTTCCCACA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCACTTTTCACACA
*
54537910 AACGCCGCTATAGATTAGAAC
66 AACGCCGCTATAGATAAGAAC
* *
54537931 CTTTAGCGACACTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCACTTTT-ACACA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCACTTTTCACACA
54537995 AACGCCGCTATAGATCAAG-AC
66 AACGCCGCTATAGAT-AAGAAC
*** * * *
54538016 CTTTAGCGGCGCTTTTTTTATAAACGCCGCTATAGATCATGACTTTTAGCG
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCG
54538067 ACGTTTTTTT
Statistics
Matches: 118, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
85 64 0.54
86 54 0.46
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCACTTTTCACACA
AACGCCGCTATAGATAAGAAC
Found at i:54542672 original size:21 final size:21
Alignment explanation
Indices: 54542648--54542688 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54542638 AACCCTAAAT
*
54542648 CCCTAACTCTTAACCCCTAAC
1 CCCTAACTATTAACCCCTAAC
*
54542669 CCCTAACTATTAATCCCTAA
1 CCCTAACTATTAACCCCTAA
54542689 ACCTTAAATC
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:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (21 bp):
CCCTAACTATTAACCCCTAAC
Found at i:54542684 original size:35 final size:34
Alignment explanation
Indices: 54542645--54542723 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 34
54542635 TGAAACCCTA
* *
54542645 AATCCCTAACTCTTAACCCCTAACCCCT-AACTATT
1 AATCCCTAAC-CTTAAACCCTAACACCTAAACTA-T
* *
54542680 AATCCCTAAACCTTAAATCCTAACACTTAAACTAT
1 AATCCCT-AACCTTAAACCCTAACACCTAAACTAT
54542715 AATCCCTAA
1 AATCCCTAA
54542724 ATCCATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
34 2 0.05
35 28 0.74
36 8 0.21
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (34 bp):
AATCCCTAACCTTAAACCCTAACACCTAAACTAT
Found at i:54542925 original size:23 final size:24
Alignment explanation
Indices: 54542886--54542939 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
54542876 TATATGAAAT
*
54542886 TATTTAATATATAAATTAAAAAAA
1 TATTTAATAAATAAATTAAAAAAA
54542910 TATTTAA-AAATAAATT-AAAAAA
1 TATTTAATAAATAAATTAAAAAAA
*
54542932 TAATTAAT
1 TATTTAAT
54542940 CTAAACCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 12 0.44
23 8 0.30
24 7 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TATTTAATAAATAAATTAAAAAAA
Found at i:54543012 original size:22 final size:22
Alignment explanation
Indices: 54542969--54543031 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
54542959 TTGACCCATG
* *
54542969 AACTCATAAACCCTAAATCCCT
1 AACTCATAAACCCCAAACCCCT
* *
54542991 AACTCTTAACCCCCAAACCCCT
1 AACTCATAAACCCCAAACCCCT
54543013 AAC-CACT-AACCCCTAAACC
1 AACTCA-TAAACCCC-AAACC
54543032 TTAAATCTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 6 0.18
22 27 0.82
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.17
Consensus pattern (22 bp):
AACTCATAAACCCCAAACCCCT
Found at i:54543044 original size:21 final size:20
Alignment explanation
Indices: 54543020--54543100 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 20
54543010 CCTAACCACT
*
54543020 AACCCCTAAACCTTAAATCTC
1 AACCCATAAACCTTAAATC-C
*
54543041 AACCCATAAACCAT-AATCCC
1 AACCCATAAACCTTAAAT-CC
* *
54543061 TAATCCATAATCCTTAAATCC
1 -AACCCATAAACCTTAAATCC
54543082 ATACTCCATAAACCTTAAA
1 A-AC-CCATAAACCTTAAA
54543101 ACAGTAACTC
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 5 0.10
21 27 0.56
22 16 0.33
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (20 bp):
AACCCATAAACCTTAAATCC
Found at i:54543082 original size:15 final size:15
Alignment explanation
Indices: 54543047--54543084 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
54543037 TCTCAACCCA
54543047 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
54543061 T-AATCCATAATCCT
1 TAAATCCATAATCCC
54543075 TAAATCCATA
1 TAAATCCATA
54543085 CTCCATAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:54543089 original size:22 final size:22
Alignment explanation
Indices: 54543026--54543100 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
54543016 CACTAACCCC
54543026 TAAACCTTAAATCTCA-AC-CCA
1 TAAACCTTAAATC-CATACTCCA
* * *
54543047 TAAACCAT-AATCCCTAATCCA
1 TAAACCTTAAATCCATACTCCA
*
54543068 TAATCCTTAAATCCATACTCCA
1 TAAACCTTAAATCCATACTCCA
54543090 TAAACCTTAAA
1 TAAACCTTAAA
54543101 ACAGTAACTC
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 16 0.37
22 21 0.49
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAACCTTAAATCCATACTCCA
Found at i:54543093 original size:15 final size:15
Alignment explanation
Indices: 54543044--54543093 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
54543034 AAATCTCAAC
54543044 CCATAAA-CCATAAT
1 CCATAAATCCATAAT
*
54543058 CCCT-AATCCATAAT
1 CCATAAATCCATAAT
* *
54543072 CCTTAAATCCATACT
1 CCATAAATCCATAAT
54543087 CCATAAA
1 CCATAAA
54543094 CCTTAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 2 0.07
14 13 0.43
15 15 0.50
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
CCATAAATCCATAAT
Found at i:54543376 original size:41 final size:41
Alignment explanation
Indices: 54543317--54543432 Score: 180
Period size: 41 Copynumber: 2.8 Consensus size: 41
54543307 TAAAATGTTT
*
54543317 TTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCCTA-CCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCC-AGCCA
* *
54543358 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCAGGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAGCCA
*
54543399 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAGCC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCC
54543433 ACGAAATGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 68 0.99
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAGCCA
Found at i:54543512 original size:39 final size:39
Alignment explanation
Indices: 54543468--54543546 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
54543458 TAGGCTAAGG
* * *
54543468 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCATTTTTTT-AAAAACGCCACTAATGCTCA
54543508 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
54543547 ATCTTTAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 19 0.53
40 17 0.47
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
Found at i:54543518 original size:40 final size:40
Alignment explanation
Indices: 54543468--54543605 Score: 127
Period size: 40 Copynumber: 3.5 Consensus size: 40
54543458 TAGGCTAAGG
*
54543468 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
* *
54543508 TTTTTAGCGGCATTTTTTT-AAAAACGCCACTAATGCTCAA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTC-A
* * * *** * * *
54543548 TCTTTAGTGGCGATTTCCAG-AAAGCGCCGCCAATGCTTGA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGC-TCA
*
54543588 TTTTTACCGGCGTTTTTT
1 TTTTTAGCGGCGTTTTTT
54543606 GTCCAAACGC
Statistics
Matches: 75, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
39 18 0.24
40 56 0.75
41 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
Found at i:54547469 original size:37 final size:37
Alignment explanation
Indices: 54547427--54547501 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
54547417 ACTTCTTTTC
54547427 TCTGAAGAATTATCGAGATCATTCATATTTTTTCTTA
1 TCTGAAGAATTATCGAGATCATTCATATTTTTTCTTA
54547464 TCTGAAGAATTATCGAGATCATTCATATTTTTTCTTA
1 TCTGAAGAATTATCGAGATCATTCATATTTTTTCTTA
54547501 T
1 T
54547502 GAGCTTTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (37 bp):
TCTGAAGAATTATCGAGATCATTCATATTTTTTCTTA
Found at i:54550868 original size:23 final size:23
Alignment explanation
Indices: 54550814--54550932 Score: 220
Period size: 23 Copynumber: 5.1 Consensus size: 23
54550804 CCTAGCCTCT
*
54550814 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54550837 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
54550861 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54550884 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54550907 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54550930 TTT
1 TTT
54550933 TACACTTCCT
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
23 72 0.77
24 22 0.23
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:54551008 original size:20 final size:20
Alignment explanation
Indices: 54550983--54551049 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
54550973 TTATGAATAC
54550983 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54551003 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54551023 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54551043 ACCATGT
1 ATCATGT
54551050 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54551014 original size:11 final size:11
Alignment explanation
Indices: 54550983--54551038 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
54550973 TTATGAATAC
54550983 ATCATGTGCAT
1 ATCATGTGCAT
*
54550994 ATCA--TACAT
1 ATCATGTGCAT
54551003 ATCATGTGCAT
1 ATCATGTGCAT
*
54551014 ATCA--TACAT
1 ATCATGTGCAT
*
54551023 GTCATGTGCAT
1 ATCATGTGCAT
54551034 ATCAT
1 ATCAT
54551039 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:54551118 original size:25 final size:25
Alignment explanation
Indices: 54551086--54551133 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54551076 ATACATAAAC
* * *
54551086 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
54551111 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
54551134 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:54557109 original size:48 final size:48
Alignment explanation
Indices: 54557034--54557309 Score: 326
Period size: 48 Copynumber: 5.8 Consensus size: 48
54557024 ACCGTGCTAA
* *
54557034 ATGTGCCTGTGTAAGACCATGTCCGGGAGATGGCATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * *
54557082 ATATGCCTGTGTAAGACCATGT-TCGGGACATGGCATCAGTGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCT-GGGACATGGCATCGGCGATGATAT
* *
54557130 ATGTGCCTGTGTAAGACCATGTCTAGGACACGGCATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * *
54557178 ATGCGCCTGTGTAA-AGCCATGTCTGGAACATGGCATCAGCGATGATAT
1 ATGTGCCTGTGTAAGA-CCATGTCTGGGACATGGCATCGGCGATGATAT
* * * *
54557226 GTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCGGTGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* ** *
54557274 GTG-GATTCATGTAAGACCATGTC-GAGGACATGGCAT
1 ATGTGCCT-GTGTAAGACCATGTCTG-GGACATGGCAT
54557310 TAGTACTTTT
Statistics
Matches: 196, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
47 3 0.02
48 191 0.97
49 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (48 bp):
ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
Found at i:54561200 original size:17 final size:18
Alignment explanation
Indices: 54561166--54561203 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
54561156 TACTCATCCA
*
54561166 TTCATTTTTTTTCATTCT
1 TTCATTTTTCTTCATTCT
*
54561184 TTCA-TTTTCTTCTTTCT
1 TTCATTTTTCTTCATTCT
54561201 TTC
1 TTC
54561204 CACTCCTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (18 bp):
TTCATTTTTCTTCATTCT
Found at i:54563639 original size:18 final size:19
Alignment explanation
Indices: 54563616--54563654 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54563606 TATAAGAATT
*
54563616 TTTATTCAT-TTTTTAGAA
1 TTTATTCATATTTTTACAA
*
54563634 TTTATTTATATTTTTACAA
1 TTTATTCATATTTTTACAA
54563653 TT
1 TT
54563655 ATTGTTAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTATTCATATTTTTACAA
Found at i:54564596 original size:18 final size:19
Alignment explanation
Indices: 54564562--54564601 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
54564552 CTCACCACAC
*
54564562 ATCTACTTTTTAAAAAAAA
1 ATCTACTTTTAAAAAAAAA
54564581 ATCTAC-TTTAAAAAAAAA
1 ATCTACTTTTAAAAAAAAA
54564599 ATC
1 ATC
54564602 GCTACTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCTACTTTTAAAAAAAAA
Found at i:54567415 original size:20 final size:20
Alignment explanation
Indices: 54567337--54567408 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
54567327 AAAAATATAA
* *
54567337 ATTTTGAAAATTTTATAAA-T
1 ATTTTGAATA-TTTAAAAATT
54567357 ATTTTGAAT-TTTAAAAATT
1 ATTTTGAATATTTAAAAATT
54567376 ATTTTGAATATTTAAAAATT
1 ATTTTGAATATTTAAAAATT
*
54567396 ATTTTGATTATTT
1 ATTTTGAATATTT
54567409 TGTAATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
18 7 0.15
19 10 0.21
20 30 0.64
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
ATTTTGAATATTTAAAAATT
Found at i:54568471 original size:22 final size:20
Alignment explanation
Indices: 54568438--54568477 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54568428 TTTGTTTGGA
54568438 AATTTTAGGAATTCTTTTTGC
1 AATTTTAGGAATT-TTTTTGC
*
54568459 AATTTTAATGAATTTTTTT
1 AATTTT-AGGAATTTTTTT
54568478 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (20 bp):
AATTTTAGGAATTTTTTTGC
Found at i:54572339 original size:18 final size:18
Alignment explanation
Indices: 54572298--54572332 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54572288 GCCAGGTGTG
*
54572298 TATCCTAGCCCTTATATA
1 TATCCTAACCCTTATATA
54572316 TATCCTAACCCTTATAT
1 TATCCTAACCCTTATAT
54572333 GTTTCCTTTT
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:0.29, C:0.29, G:0.03, T:0.40
Consensus pattern (18 bp):
TATCCTAACCCTTATATA
Found at i:54572623 original size:20 final size:22
Alignment explanation
Indices: 54572590--54572630 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
54572580 ACAACTAGAA
54572590 CAACCACAAACCCC-GCCGGAG
1 CAACCACAAACCCCTGCCGGAG
54572611 CAACCAC-AACCCCTGCCGGA
1 CAACCACAAACCCCTGCCGGA
54572631 AGCTGAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.32, C:0.49, G:0.17, T:0.02
Consensus pattern (22 bp):
CAACCACAAACCCCTGCCGGAG
Found at i:54596035 original size:26 final size:26
Alignment explanation
Indices: 54595999--54596051 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
54595989 GACATCTTCA
54595999 ATAGATACTATATGCCCAAGAAAACT
1 ATAGATACTATATGCCCAAGAAAACT
54596025 ATAGATACTATATGCCCAAGAAAACT
1 ATAGATACTATATGCCCAAGAAAACT
54596051 A
1 A
54596052 ACTTCCTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (26 bp):
ATAGATACTATATGCCCAAGAAAACT
Found at i:54608832 original size:38 final size:38
Alignment explanation
Indices: 54608781--54608942 Score: 171
Period size: 38 Copynumber: 4.0 Consensus size: 38
54608771 GGAATGAAAA
*
54608781 AACGTGGTGCTAAGTGGATATACCACGATTATACGTGT
1 AACGTGGTGCTAAGTGGATATACCACGATTATACATGT
* *
54608819 AACGTGGTGCTAAGTGGTTATACCATGATTACACATATTGATACATGT
1 AACGTGGTGCTAAGTGG--AT---AT-A--CCAC-GATT-ATACATGT
* *
54608867 AACGTGGTGCTAAGTGGATATACCACGGTTAAACATGT
1 AACGTGGTGCTAAGTGGATATACCACGATTATACATGT
* *
54608905 AACGTGGTGCTAAGTGGATATGCCACGGTTATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGATTATACATGT
54608943 TAATTTGAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
38 60 0.57
39 2 0.02
40 5 0.05
42 1 0.01
43 4 0.04
44 1 0.01
46 5 0.05
47 3 0.03
48 24 0.23
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (38 bp):
AACGTGGTGCTAAGTGGATATACCACGATTATACATGT
Found at i:54610606 original size:20 final size:20
Alignment explanation
Indices: 54610581--54610623 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
54610571 CTATCCCGAC
54610581 GTTGGATATGGGTGAGGGGT
1 GTTGGATATGGGTGAGGGGT
54610601 GTTGGATATGGGTGAGGGGT
1 GTTGGATATGGGTGAGGGGT
54610621 GTT
1 GTT
54610624 ACATAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.53, T:0.33
Consensus pattern (20 bp):
GTTGGATATGGGTGAGGGGT
Found at i:54615809 original size:56 final size:58
Alignment explanation
Indices: 54615734--54615880 Score: 140
Period size: 56 Copynumber: 2.6 Consensus size: 58
54615724 CCTATAACAA
* *
54615734 GATTACTAGTCCAAGCTAAATCCTTTATATAACGTATGCTCAAAGA-GT-TCA-ATTAG
1 GATTACCAGTCCAGGCTAAATCCTTTATATAACGTATGCT-AAAGAGGTATCATATTAG
* *** * ** *
54615790 GGTTACCAGTCCAGGCTAAA-CCCCAATCATAACGTATTCTTGAGAGGTATTATATTAG
1 GATTACCAGTCCAGGCTAAATCCTTTAT-ATAACGTATGCTAAAGAGGTATCATATTAG
* *
54615848 GATTACCCGTCCAGGCTAAATCCTTTCTATAAC
1 GATTACCAGTCCAGGCTAAATCCTTTATATAAC
54615881 AAGGTTGATA
Statistics
Matches: 70, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
55 7 0.10
56 30 0.43
57 2 0.03
58 28 0.40
59 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Consensus pattern (58 bp):
GATTACCAGTCCAGGCTAAATCCTTTATATAACGTATGCTAAAGAGGTATCATATTAG
Found at i:54621027 original size:40 final size:40
Alignment explanation
Indices: 54620971--54621173 Score: 277
Period size: 40 Copynumber: 5.1 Consensus size: 40
54620961 CGGAATTCAA
* * *
54620971 CCGGATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
54621011 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54621051 CCGGATATAGTAACTCGCACGAATGCCTTCAGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54621091 CCGGATATAATAACTCGCACAATTGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54621130 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
54621170 CCGG
1 CCGG
54621174 TTATCATCTG
Statistics
Matches: 145, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
38 1 0.01
39 34 0.23
40 110 0.76
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54625041 original size:50 final size:50
Alignment explanation
Indices: 54624966--54625065 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
54624956 ATAAGTTTTT
54624966 AGTTGGTCAAAACTTTTCAGACATTTTTCCGTCCATTCGAACTTAACATC
1 AGTTGGTCAAAACTTTTCAGACATTTTTCCGTCCATTCGAACTTAACATC
54625016 AGTTGGTCAAAACTTTTCAGACATTTTTCCGTCCATTCGAACTTAACATC
1 AGTTGGTCAAAACTTTTCAGACATTTTTCCGTCCATTCGAACTTAACATC
54625066 TTTTTGAAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (50 bp):
AGTTGGTCAAAACTTTTCAGACATTTTTCCGTCCATTCGAACTTAACATC
Found at i:54629279 original size:40 final size:40
Alignment explanation
Indices: 54629235--54629425 Score: 242
Period size: 40 Copynumber: 4.8 Consensus size: 40
54629225 GGATATAGCT
* * * * *
54629235 ACTCGCTCGAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
**
54629275 ACTCGCACAAATGCCTTCGGGACTTAGCCTAGATATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
*
54629315 ACTCGCACGAATGCCTTCGGGACTTAGCCCGGATATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
* * * *
54629355 ACTCGCACAATTGCCTTCGGG-CTTAGCCC-GAAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAATA
*
54629394 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
54629426 TTATCATCCG
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
38 3 0.02
39 30 0.23
40 97 0.74
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
Found at i:54634086 original size:89 final size:89
Alignment explanation
Indices: 54633984--54634161 Score: 320
Period size: 89 Copynumber: 2.0 Consensus size: 89
54633974 TGCAACTGAG
* * *
54633984 CTTTTAACTCTTTTAACTCGGTTGGTGCCATACGATACGGAGCTATCGAAATCGGCGTAGTCCCA
1 CTTTTAACTCTTTTAACTCGATTGGTGCCATACGATACGGAGCTATCGAAATCAGCATAGTCCCA
*
54634049 GGTACAGGCTCAATTCCAAACTCT
66 GGTACAAGCTCAATTCCAAACTCT
54634073 CTTTTAACTCTTTTAACTCGATTGGTGCCATACGATACGGAGCTATCGAAATCAGCATAGTCCCA
1 CTTTTAACTCTTTTAACTCGATTGGTGCCATACGATACGGAGCTATCGAAATCAGCATAGTCCCA
54634138 GGTACAAGCTCAATTCCAAACTCT
66 GGTACAAGCTCAATTCCAAACTCT
54634162 ACCTCCCGAA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (89 bp):
CTTTTAACTCTTTTAACTCGATTGGTGCCATACGATACGGAGCTATCGAAATCAGCATAGTCCCA
GGTACAAGCTCAATTCCAAACTCT
Found at i:54636886 original size:40 final size:40
Alignment explanation
Indices: 54636842--54637032 Score: 242
Period size: 40 Copynumber: 4.8 Consensus size: 40
54636832 GGATATAGCT
* * * * *
54636842 ACTCGCTCGAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
**
54636882 ACTCGCACAAATGCCTTCGGGACTTAGCCTAGATATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
*
54636922 ACTCGCACGAATGCCTTCGGGACTTAGCCCGGATATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
* * * *
54636962 ACTCGCACAATTGCCTTCGGG-CTTAGCCC-GAAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAATA
*
54637001 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
54637033 TTATCATCCG
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
38 3 0.02
39 30 0.23
40 97 0.74
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
Found at i:54639774 original size:132 final size:132
Alignment explanation
Indices: 54639532--54639795 Score: 492
Period size: 132 Copynumber: 2.0 Consensus size: 132
54639522 TAATGATTGA
*
54639532 CTGAAAACTATTGTTGTAAGCGAACTCCATCAAAGGTAGATACCGTTCCCATGAACCACTAAACT
1 CTGAAAACTATTGTTGTAAGCGAACTCCATCAAAGGTAGATACCGTTCCCATGAACCAATAAACT
* *
54639597 CAAGGATGTAGCATCTCAACATATCCTCGAGTATCTGAATAATCCGCTCGGATTGACCATCGGTT
66 CAAGGATGTAGCATCTCAACATAACCTCGAGTATCTGAATAATCCGCTCGGATTGACCATCAGTT
54639662 TG
131 TG
54639664 CTGAAAACTATTGTTGTAAGCGAACTCCATCAAAGGTAGATACCGTTCCCATGAACCAATAAACT
1 CTGAAAACTATTGTTGTAAGCGAACTCCATCAAAGGTAGATACCGTTCCCATGAACCAATAAACT
*
54639729 CAAGGATGTAGCATCTCAACATAACCTCGAGTATCTGAATTATCCGCTCGGATTGACCATCAGTT
66 CAAGGATGTAGCATCTCAACATAACCTCGAGTATCTGAATAATCCGCTCGGATTGACCATCAGTT
54639794 TG
131 TG
54639796 GGGATGAAAC
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (132 bp):
CTGAAAACTATTGTTGTAAGCGAACTCCATCAAAGGTAGATACCGTTCCCATGAACCAATAAACT
CAAGGATGTAGCATCTCAACATAACCTCGAGTATCTGAATAATCCGCTCGGATTGACCATCAGTT
TG
Found at i:54644534 original size:40 final size:40
Alignment explanation
Indices: 54644490--54644680 Score: 242
Period size: 40 Copynumber: 4.8 Consensus size: 40
54644480 GGATATAGCT
* * * * *
54644490 ACTCGCTCGAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
**
54644530 ACTCGCACAAATGCCTTCGGGACTTAGCCTAGATATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
*
54644570 ACTCGCACGAATGCCTTCGGGACTTAGCCCGGATATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
* * * *
54644610 ACTCGCACAATTGCCTTCGGG-CTTAGCCC-GAAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAATA
*
54644649 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
54644681 TTATCATCCG
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
38 3 0.02
39 30 0.23
40 97 0.74
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATA
Found at i:54646214 original size:83 final size:83
Alignment explanation
Indices: 54646027--54646193 Score: 327
Period size: 83 Copynumber: 2.0 Consensus size: 83
54646017 AAGAACCAAA
54646027 GAACACAACTTGTTTTCATCACCGAAAGCTCTCTTTTTTTTGTTTTCTTTCTTCAATTCACGGCA
1 GAACACAACTTGTTTTCATCACCGAAAGCTCTCTTTTTTTTGTTTTCTTTCTTCAATTCACGGCA
54646092 AAGGGGGGGGGAAACATG
66 AAGGGGGGGGGAAACATG
54646110 GAACACAACTTGTTTTCATCACCGAAAGCTCTCTTTTTTTTGTTTTCTTTCTTCAATTCACGGCA
1 GAACACAACTTGTTTTCATCACCGAAAGCTCTCTTTTTTTTGTTTTCTTTCTTCAATTCACGGCA
54646175 AA-GGGGGGGGAAACATG
66 AAGGGGGGGGGAAACATG
54646192 GA
1 GA
54646194 TGAGACAATT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 17 0.20
83 67 0.80
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (83 bp):
GAACACAACTTGTTTTCATCACCGAAAGCTCTCTTTTTTTTGTTTTCTTTCTTCAATTCACGGCA
AAGGGGGGGGGAAACATG
Found at i:54651583 original size:30 final size:30
Alignment explanation
Indices: 54651549--54651609 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54651539 TCCTTAACTC
54651549 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
54651579 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
54651609 A
1 A
54651610 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:54656548 original size:18 final size:18
Alignment explanation
Indices: 54656525--54656559 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
54656515 TTTGGCCCAT
54656525 TGCAGTAACAGTAAACAG
1 TGCAGTAACAGTAAACAG
54656543 TGCAGTAACAGTAAACA
1 TGCAGTAACAGTAAACA
54656560 ATATGCAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (18 bp):
TGCAGTAACAGTAAACAG
Found at i:54656746 original size:22 final size:22
Alignment explanation
Indices: 54656716--54656766 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
54656706 ATAATAGGCT
*
54656716 TAGAACCATCAGTGATTTACAG
1 TAGAGCCATCAGTGATTTACAG
*
54656738 TAGAGCCATCAGTGATTTGCAG
1 TAGAGCCATCAGTGATTTACAG
*
54656760 CAGAGCC
1 TAGAGCC
54656767 GCCAGTACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (22 bp):
TAGAGCCATCAGTGATTTACAG
Found at i:54656772 original size:22 final size:22
Alignment explanation
Indices: 54656725--54656772 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
54656715 TTAGAACCAT
* *
54656725 CAGTGATTTACAGTAGAGCCAT
1 CAGTGATTTACAGCAGAGCCAC
* *
54656747 CAGTGATTTGCAGCAGAGCCGC
1 CAGTGATTTACAGCAGAGCCAC
54656769 CAGT
1 CAGT
54656773 ACAGTACACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (22 bp):
CAGTGATTTACAGCAGAGCCAC
Found at i:54657000 original size:54 final size:54
Alignment explanation
Indices: 54656912--54657091 Score: 252
Period size: 54 Copynumber: 3.3 Consensus size: 54
54656902 ATCACATAGG
* * * * *
54656912 GGTAAAACAGTCATCTTACCATAAAAGGGAAAAACAGTCATTTTACCTCCTAAA
1 GGTAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAA
* *
54656966 GGCAAAACAGTCATTTTACTACATAAGGGCAAAACAGTCATTTTACCTCATAAA
1 GGTAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAA
* * * *
54657020 GGTAAAATAGTCATTTCACCACATAAGGGCAAAACAATCATTTTACCTCATAAG
1 GGTAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAA
*
54657074 GGTAAAATAGTCATTTTA
1 GGTAAAACAGTCATTTTA
54657092 TCGATTAAGG
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 112 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (54 bp):
GGTAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAA
Found at i:54657088 original size:81 final size:81
Alignment explanation
Indices: 54656905--54657091 Score: 227
Period size: 81 Copynumber: 2.3 Consensus size: 81
54656895 AGCATACATC
* * * * *
54656905 ACATAGGGGTAAAACAGTCATCTTACCATAAAAGGGAAAAACAGTCATTTTACCTCCTAAAGGCA
1 ACATAAGGGTAAAACAGTCATTTTACCATAAAAGGGAAAAACAGTCATTTCACCACATAAAGGCA
*
54656970 AAACAGTCATTTTACT
66 AAACAATCATTTTACT
* * * *
54656986 ACATAAGGGCAAAACAGTCATTTTACC-TCATAAA-GGTAAAATAGTCATTTCACCACATAAGGG
1 ACATAAGGGTAAAACAGTCATTTTACCAT-A-AAAGGGAAAAACAGTCATTTCACCACATAAAGG
54657049 CAAAACAATCATTTTACCT
64 CAAAACAATCATTTTA-CT
*
54657068 -CATAAGGGTAAAATAGTCATTTTA
1 ACATAAGGGTAAAACAGTCATTTTA
54657092 TCGATTAAGG
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
80 1 0.01
81 85 0.93
82 5 0.05
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (81 bp):
ACATAAGGGTAAAACAGTCATTTTACCATAAAAGGGAAAAACAGTCATTTCACCACATAAAGGCA
AAACAATCATTTTACT
Found at i:54657103 original size:27 final size:26
Alignment explanation
Indices: 54656906--54657091 Score: 176
Period size: 27 Copynumber: 6.9 Consensus size: 26
54656896 GCATACATCA
* *
54656906 CATAGGGGTAAAACAGTCATCTTAC-
1 CATAAGGGTAAAACAGTCATTTTACT
*
54656931 CATAAAAGGGAAAAACAGTCATTTTACCT
1 CAT--AAGGGTAAAACAGTCATTTTA-CT
* * *
54656960 CCTAAAGGCAAAACAGTCATTTTACT
1 CATAAGGGTAAAACAGTCATTTTACT
*
54656986 ACATAAGGGCAAAACAGTCATTTTACCT
1 -CATAAGGGTAAAACAGTCATTTTA-CT
* * * *
54657014 CATAAAGGTAAAATAGTCATTTCACCA
1 CATAAGGGTAAAACAGTCATTTTA-CT
* *
54657041 CATAAGGGCAAAACAATCATTTTACCT
1 CATAAGGGTAAAACAGTCATTTTA-CT
*
54657068 CATAAGGGTAAAATAGTCATTTTA
1 CATAAGGGTAAAACAGTCATTTTA
54657092 TCGATTAAGG
Statistics
Matches: 133, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
25 3 0.02
26 2 0.02
27 123 0.92
28 3 0.02
29 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (26 bp):
CATAAGGGTAAAACAGTCATTTTACT
Found at i:54672147 original size:54 final size:54
Alignment explanation
Indices: 54672077--54672253 Score: 248
Period size: 54 Copynumber: 3.3 Consensus size: 54
54672067 ACATAGGGGT
* *
54672077 AAAACAGTCATCTTACCATAAAAGGGCAAAATAGTCATTTTACCTTATAAGGGC
1 AAAACAGTCATTTTACCATATAAGGGCAAAATAGTCATTTTACCTTATAAGGGC
* * *
54672131 AAAACAATCATTTTACC-TCATAAGGGAAAAATAGTCATTTTACTTTATAAGGGC
1 AAAACAGTCATTTTACCAT-ATAAGGGCAAAATAGTCATTTTACCTTATAAGGGC
* * * *
54672185 AAAACAGTCATTTCACCACATAAGGGCAAAATAATCATTTTACCTCATAAGGGC
1 AAAACAGTCATTTTACCATATAAGGGCAAAATAGTCATTTTACCTTATAAGGGC
*
54672239 AAAATAGTCATTTTA
1 AAAACAGTCATTTTA
54672254 TCGTTTAAGG
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 106 0.99
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (54 bp):
AAAACAGTCATTTTACCATATAAGGGCAAAATAGTCATTTTACCTTATAAGGGC
Found at i:54672221 original size:81 final size:81
Alignment explanation
Indices: 54672098--54672253 Score: 258
Period size: 81 Copynumber: 1.9 Consensus size: 81
54672088 CTTACCATAA
* * **
54672098 AAGGGCAAAATAGTCATTTTACCTTATAAGGGCAAAACAATCATTTTACCTCATAAGGGAAAAAT
1 AAGGGCAAAACAGTCATTTCACCACATAAGGGCAAAACAATCATTTTACCTCATAAGGGAAAAAT
54672163 AGTCATTTTACTTTAT
66 AGTCATTTTACTTTAT
* *
54672179 AAGGGCAAAACAGTCATTTCACCACATAAGGGCAAAATAATCATTTTACCTCATAAGGGCAAAAT
1 AAGGGCAAAACAGTCATTTCACCACATAAGGGCAAAACAATCATTTTACCTCATAAGGGAAAAAT
54672244 AGTCATTTTA
66 AGTCATTTTA
54672254 TCGTTTAAGG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (81 bp):
AAGGGCAAAACAGTCATTTCACCACATAAGGGCAAAACAATCATTTTACCTCATAAGGGAAAAAT
AGTCATTTTACTTTAT
Found at i:54672263 original size:27 final size:26
Alignment explanation
Indices: 54672077--54672253 Score: 201
Period size: 27 Copynumber: 6.6 Consensus size: 26
54672067 ACATAGGGGT
* * *
54672077 AAAACAGTCATCTTACCATAAAAGGGC
1 AAAATAGTCATTTTACC-TATAAGGGC
54672104 AAAATAGTCATTTTACCTTATAAGGGC
1 AAAATAGTCATTTTACC-TATAAGGGC
* * *
54672131 AAAACAATCATTTTACCTCATAAGGGA
1 AAAATAGTCATTTTACCT-ATAAGGGC
*
54672158 AAAATAGTCATTTTACTTTATAAGGGC
1 AAAATAGTCATTTTAC-CTATAAGGGC
* * *
54672185 AAAACAGTCATTTCACCACATAAGGGC
1 AAAATAGTCATTTTACC-TATAAGGGC
*
54672212 AAAATAATCATTTTACCTCATAAGGGC
1 AAAATAGTCATTTTACCT-ATAAGGGC
54672239 AAAATAGTCATTTTA
1 AAAATAGTCATTTTA
54672254 TCGTTTAAGG
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.01
27 124 0.98
28 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (26 bp):
AAAATAGTCATTTTACCTATAAGGGC
Found at i:54677993 original size:21 final size:21
Alignment explanation
Indices: 54677967--54678008 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
54677957 TAAGTCAGTA
*
54677967 TCGCACACGGCCTGTGGACAC
1 TCGCACACGGCCTATGGACAC
54677988 TCGCACACGGCCTATGGACAC
1 TCGCACACGGCCTATGGACAC
54678009 ACCCATGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.14
Consensus pattern (21 bp):
TCGCACACGGCCTATGGACAC
Found at i:54680707 original size:25 final size:25
Alignment explanation
Indices: 54680646--54680709 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
54680636 TATTTTGAAG
* *
54680646 TTTTTATAT-TATATTATTTTAACA
1 TTTTTATATATATTTTATTTAAACA
* *
54680670 TTATGTATA-ATATTTTATTTAAATA
1 TT-TTTATATATATTTTATTTAAACA
54680695 TTTTTATATATATTT
1 TTTTTATATATATTT
54680710 GTACATATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTATATATATTTTATTTAAACA
Found at i:54685016 original size:19 final size:19
Alignment explanation
Indices: 54684992--54685038 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54684982 TGATGCCTCC
*
54684992 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
54685011 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
54685030 TATGCATTA
1 TTTGCATTA
54685039 AAGACTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:54690068 original size:13 final size:13
Alignment explanation
Indices: 54690050--54690074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54690040 GAGACCTTAA
54690050 AAAAAATCAAAAT
1 AAAAAATCAAAAT
54690063 AAAAAATCAAAA
1 AAAAAATCAAAA
54690075 CCAAAACAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATCAAAAT
Found at i:54690084 original size:24 final size:25
Alignment explanation
Indices: 54690052--54690114 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
54690042 GACCTTAAAA
**
54690052 AAAATCAAAATAAAAAATCAAAA-CC
1 AAAA-CAAAATAAAAAAGAAAAATCC
* *
54690077 AAAACAAAACAAAAAAGAAAAATTC
1 AAAACAAAATAAAAAAGAAAAATCC
54690102 AAAA-AAAATAAAA
1 AAAACAAAATAAAA
54690115 TCAAAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.78, C:0.11, G:0.02, T:0.10
Consensus pattern (25 bp):
AAAACAAAATAAAAAAGAAAAATCC
Found at i:54690120 original size:30 final size:28
Alignment explanation
Indices: 54690048--54690128 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 28
54690038 CTGAGACCTT
*
54690048 AAAAAAAATCAAAATAAAAAATCAAAACC
1 AAAAAAAATCAAAAAAAAAAATCAAAA-C
54690077 AAAACAAAA-CAAAAAAGAAAAATTCAAAA-
1 AAAA-AAAATCAAAAAA-AAAAA-TCAAAAC
54690106 AAAATAAAATCAAAAAAATAAAA
1 AAAA-AAAATCAAAAAAA-AAAA
54690129 AAAGAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
29 19 0.42
30 20 0.44
31 6 0.13
ACGTcount: A:0.79, C:0.10, G:0.01, T:0.10
Consensus pattern (28 bp):
AAAAAAAATCAAAAAAAAAAATCAAAAC
Found at i:54691276 original size:64 final size:64
Alignment explanation
Indices: 54691203--54691331 Score: 190
Period size: 64 Copynumber: 2.0 Consensus size: 64
54691193 TATCATCCAT
*
54691203 AACACATCTAGTTAGGAGA-A-TTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAG
1 AACACATCTAATTAGGA-ACAGTTT-ATTCATTTCGATCATAGCATCCTAATTATTTGACATAAG
54691266 C
64 C
* **
54691267 AACACATCTAATTAGGAACAGTTTATTCATTTTGATCATAGCATCCTAATTATTTTCCATAAGC
1 AACACATCTAATTAGGAACAGTTTATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGC
54691331 A
1 A
54691332 TAGATACATG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
63 1 0.02
64 55 0.93
65 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (64 bp):
AACACATCTAATTAGGAACAGTTTATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGC
Found at i:54693157 original size:40 final size:39
Alignment explanation
Indices: 54693113--54693310 Score: 247
Period size: 40 Copynumber: 5.0 Consensus size: 39
54693103 GAATTTAACC
*
54693113 GGATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCA
1 GGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCA
* ** *
54693153 GGATATAGTAGTTCATACAAATGCCTTCGGGACTTAGCCC
1 GGATATAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCA
* *
54693193 GGATATAGTAACTCGCACAAATGCCTTCGGGACCTAGCCC
1 GGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCA
54693233 GGA-ATTAGTACTCGCACAAATGCCTTCGGGACTTAGCCCA
1 GGATA-TAGTACTCGCACAAATGCCTTCGGGACTTAG-CCA
* *
54693273 GAAT-TAGTCACTAGCACAAATGCCTTCGGGACTTAGCC
1 GGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCC
54693311 CCGTTATCAT
Statistics
Matches: 139, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
39 35 0.25
40 103 0.74
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (39 bp):
GGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCA
Found at i:54693290 original size:79 final size:80
Alignment explanation
Indices: 54693130--54693311 Score: 253
Period size: 79 Copynumber: 2.3 Consensus size: 80
54693120 GCTACTCGCT
* * * *
54693130 CAAATGCCTTCGGGACTTAGCCAGGATATAGTAGTTCATACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCACACAAATGCCTTCGGGACTTAGCCCGA
*
54693195 ATATAGTAACTCGCA
66 ATATAGTAACTAGCA
* *
54693210 CAAATGCCTTCGGGACCTAGCCCGGA-ATTAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAGCTCACACAAATGCCTTCGGGACTTAGCCC-
*
54693273 GAAT-TAGTCACTAGCA
64 GAATATAGTAACTAGCA
54693289 CAAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
54693312 CGTTATCATC
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
79 59 0.65
80 32 0.35
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCACACAAATGCCTTCGGGACTTAGCCCGA
ATATAGTAACTAGCA
Found at i:54702969 original size:46 final size:47
Alignment explanation
Indices: 54702886--54703047 Score: 154
Period size: 46 Copynumber: 3.5 Consensus size: 47
54702876 GATGAGTGCT
* *
54702886 AGTGTAAGA-CATGTCTAGGACATGCATCAGC-GTCGAGACATAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTG-CGAGACATAAGCC
* * *
54702932 AGTGTAAGA-CATGTCTGGGACATGCGTCGGCTGCGAGATGAT-AGGC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTGCGAGA-CATAAGCC
* * * * **
54702978 AATGTAAGACCATGTCTGGGACATGGCTTCGACT-TGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCTGCGAGACATAAGCC
*
54703025 AGTGTAAGACCGTGTCTGGGACA
1 AGTGTAAGACCATGTCTGGGACA
54703048 CGGTATCGGC
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
46 45 0.46
47 45 0.46
48 7 0.07
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCTGCGAGACATAAGCC
Found at i:54703002 original size:47 final size:47
Alignment explanation
Indices: 54702888--54703047 Score: 143
Period size: 47 Copynumber: 3.4 Consensus size: 47
54702878 TGAGTGCTAG
* * ** *
54702888 TGTAAGA-CATGTCTAGGACAT-GCATC-AGCGTCGAGACATAAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCGTCGA-C-TCGAGATGTAAGCCAA
* *
54702934 TGTAAGA-CATGTCTGGGACAT-GCGTCGGCTGCGAGATG-ATAGGCAA
1 TGTAAGACCATGTCTGGGACATGGCGTCGACT-CGAGATGTA-AGCCAA
* * *
54702980 TGTAAGACCATGTCTGGGACATGGCTTCGACTTGAGATGTAAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCGTCGACTCGAGATGTAAGCCAA
*
54703027 TGTAAGACCGTGTCTGGGACA
1 TGTAAGACCATGTCTGGGACA
54703048 CGGTATCGGC
Statistics
Matches: 95, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
45 2 0.02
46 41 0.43
47 44 0.46
48 8 0.08
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (47 bp):
TGTAAGACCATGTCTGGGACATGGCGTCGACTCGAGATGTAAGCCAA
Found at i:54703193 original size:71 final size:71
Alignment explanation
Indices: 54703077--54703218 Score: 221
Period size: 71 Copynumber: 2.0 Consensus size: 71
54703067 CACGTTCGAG
* * *
54703077 GCTATGGTATATCTGATAGCACTCCGAATGGTTCAACGTGGAAGTTCTGATTTCTAGTTAATGAG
1 GCTATGGTATATCCGATAACACTCCGAATGGTTCAACGTGGAAGTTCTGATTTCCAGTTAATGAG
54703142 GAAAGT
66 GAAAGT
* * * *
54703148 GCTATGGTATATCCGATAACATTCTGAATGGTTCAATGTGGAAGTTTTGATTTCCAGTTAATGAG
1 GCTATGGTATATCCGATAACACTCCGAATGGTTCAACGTGGAAGTTCTGATTTCCAGTTAATGAG
54703213 GAAAGT
66 GAAAGT
54703219 ATAACCGTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.34
Consensus pattern (71 bp):
GCTATGGTATATCCGATAACACTCCGAATGGTTCAACGTGGAAGTTCTGATTTCCAGTTAATGAG
GAAAGT
Found at i:54704275 original size:22 final size:22
Alignment explanation
Indices: 54704250--54704304 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
54704240 TTGGAATGGT
* *
54704250 CACACGGGTGTGTTTCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
54704272 CACACGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
54704294 CACACGGGCGT
1 CACACGGGCGT
54704305 ATGCCTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.11, C:0.42, G:0.27, T:0.20
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTCC
Found at i:54710682 original size:47 final size:46
Alignment explanation
Indices: 54710566--54710682 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
54710556 GATGAGTGCT
*
54710566 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCAAGACATAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACATAAGCC
* * * * *
54710612 AGTGAAAGACATGTCTGGGACATGCGTCGG-CT-ATGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACAT-A-AGCC
54710658 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
54710683 GCTTTGACTT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
44 5 0.08
45 3 0.05
46 38 0.62
47 15 0.25
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACATAAGCC
Found at i:54710696 original size:47 final size:47
Alignment explanation
Indices: 54710606--54710727 Score: 133
Period size: 47 Copynumber: 2.6 Consensus size: 47
54710596 CCTCAAGACA
* *
54710606 TAAGCCAGTGAAAGA-CATGTCTGGGACATGCGTCGGCTATGAGATG
1 TAAGCCAGTGTAAGACCATGTCTGGGACATGCGTCGACTATGAGATG
* * *
54710652 -ATAGTCAGTGTAAGACCATGTCTGGGACATGGCTTTGACT-TGAGATG
1 TA-AGCCAGTGTAAGACCATGTCTGGGACAT-GCGTCGACTATGAGATG
* **
54710699 TAAGCCAGTATAAGACTGTGTCTGGGACA
1 TAAGCCAGTGTAAGACCATGTCTGGGACA
54710728 CAACATCGGC
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 1 0.02
46 11 0.17
47 44 0.70
48 7 0.11
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (47 bp):
TAAGCCAGTGTAAGACCATGTCTGGGACATGCGTCGACTATGAGATG
Found at i:54717334 original size:16 final size:17
Alignment explanation
Indices: 54717304--54717338 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
54717294 TATATGTGGT
54717304 AAGGAAATATGACATGA
1 AAGGAAATATGACATGA
*
54717321 AAGG-AATATTACATGA
1 AAGGAAATATGACATGA
54717337 AA
1 AA
54717339 TACAAGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (17 bp):
AAGGAAATATGACATGA
Found at i:54718958 original size:35 final size:35
Alignment explanation
Indices: 54718837--54718960 Score: 126
Period size: 35 Copynumber: 3.5 Consensus size: 35
54718827 TCCCAATCTT
* *
54718837 TCTATCCCAACCTTTTT-GAGGTTACCTTAGACTTA-
1 TCTATCCCAACCTTTTTAG-GGTTGCCTTAGAC-GAG
***
54718872 TCTATCCCAACCTTTTTAAAATTGCCTTAGACGAG
1 TCTATCCCAACCTTTTTAGGGTTGCCTTAGACGAG
* ** *
54718907 TATATCTTAACCTTTTTAGGGTTGCCTTAGACGGG
1 TCTATCCCAACCTTTTTAGGGTTGCCTTAGACGAG
*
54718942 TCTATCCCAACTTTTTTAG
1 TCTATCCCAACCTTTTTAG
54718961 AGTCATCTTT
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
34 1 0.01
35 70 0.99
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (35 bp):
TCTATCCCAACCTTTTTAGGGTTGCCTTAGACGAG
Found at i:54719116 original size:28 final size:28
Alignment explanation
Indices: 54719084--54719137 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
54719074 TGGCCTTGAC
54719084 TATGTTTTTGCCAACCCTTTAATAAAGG
1 TATGTTTTTGCCAACCCTTTAATAAAGG
54719112 TATGTTTTTGCCAACCCTTTAATAAA
1 TATGTTTTTGCCAACCCTTTAATAAA
54719138 AGTCGACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (28 bp):
TATGTTTTTGCCAACCCTTTAATAAAGG
Found at i:54720372 original size:5 final size:6
Alignment explanation
Indices: 54720355--54720379 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54720345 TGGTGTATAA
54720355 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
54720380 TGTGAGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:54724220 original size:17 final size:17
Alignment explanation
Indices: 54724198--54724234 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
54724188 TGGGATATGT
54724198 GTAAAAGATGATG-TGGA
1 GTAAAAGAT-ATGATGGA
54724215 GTAAAAGATATGATGGA
1 GTAAAAGATATGATGGA
54724232 GTA
1 GTA
54724235 TCATTGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.24
Consensus pattern (17 bp):
GTAAAAGATATGATGGA
Found at i:54724410 original size:34 final size:34
Alignment explanation
Indices: 54724367--54724481 Score: 119
Period size: 34 Copynumber: 3.4 Consensus size: 34
54724357 CTACGGTGCC
54724367 TTGGTGTGGTGTAGTTATTGCTCTATCT-A-TCCAT
1 TTGGTGTGGTGTAGTTATTGCTCTAT-TAAGT-CAT
* * *
54724401 TTGGTGTGGTGTACTTATCGCTTTATTAAGTCAT
1 TTGGTGTGGTGTAGTTATTGCTCTATTAAGTCAT
* *
54724435 TTGATATGGTGTAGTTATTGCTCTATTAAG-CTAT
1 TTGGTGTGGTGTAGTTATTGCTCTATTAAGTC-AT
* *
54724469 CTAGTGTGGTGTA
1 TTGGTGTGGTGTA
54724482 CTACCTGTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
33 2 0.03
34 63 0.95
35 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.46
Consensus pattern (34 bp):
TTGGTGTGGTGTAGTTATTGCTCTATTAAGTCAT
Done.