Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 184 of 214
Found at i:54039730 original size:3 final size:3
Alignment explanation
Indices: 54039661--54039710 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
54039651 ATAAAAGAGA
54039661 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54039709 AA
1 AA
54039711 ACTAATTAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54045919 original size:11 final size:11
Alignment explanation
Indices: 54045903--54045941 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
54045893 ATGCGCATGA
54045903 ATATTTTTTAT
1 ATATTTTTTAT
*
54045914 ATATTTTATAT
1 ATATTTTTTAT
54045925 A-ATTTTTTAT
1 ATATTTTTTAT
*
54045935 CTATTTT
1 ATATTTT
54045942 CTTCTTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
ATATTTTTTAT
Found at i:54046372 original size:107 final size:110
Alignment explanation
Indices: 54046166--54046473 Score: 468
Period size: 107 Copynumber: 2.8 Consensus size: 110
54046156 TCAAAAAACA
*
54046166 AAAAATTTTATAAATAAGGCAATGTTTTACGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAAA-TTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
*
54046231 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCC-TTTT
65 GGGTGTCGATTTTTCTCGTTCAACCAAATAGCTTAATATCCTTTTT
*
54046276 AAAAATTT-TAAAT-AGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
54046339 GGTGTCGATTTTTCTCGTTCAACCAAATAGCTTAATATCCTTTTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATAGCTTAATATCCTTTTT
** * *
54046384 AAAAATTTCA-AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GGACGTGCCCTTAGGTGCT
1 AAAAATTT-ATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* *
54046447 GGGTTTCGA--TTTCTCGTTTAACCAAAT
65 GGGTGTCGATTTTTCTCGTTCAACCAAAT
54046474 TGCCAAATAT
Statistics
Matches: 184, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
107 104 0.57
108 17 0.09
109 30 0.16
110 33 0.18
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (110 bp):
AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCGTTCAACCAAATAGCTTAATATCCTTTTT
Found at i:54048259 original size:125 final size:125
Alignment explanation
Indices: 54048033--54048279 Score: 286
Period size: 125 Copynumber: 2.0 Consensus size: 125
54048023 TAGAAATTTC
* * ** *
54048033 TGCTTGTAAAGTCTTCATGGCCATAACTTGAGCTGCCGAACTTGAAATTAAGTGATTCAAAGTGC
1 TGCTTGCAAAGTCTTCATGGCCATAACTTGAGCTGCCAAACTCAAAATCAAGTGATTCAAAGTGC
* * * *
54048098 ATTCTGAAACTAAAAGATAGCTCTTTCATTAGTTTGAAGATATTTTTGCTCAAAATTTTT
66 ATTCTAAAACTAAAAGATAGCTCTTTCATTACTTTGAAGACATTTTCGCTCAAAATTTTT
* *
54048158 TGCTTGCAAAGTCTTCA-GGACCATAACTTGAGCTTCTAAACTCAAAATCAAGTGATTC-AA-TG
1 TGCTTGCAAAGTCTTCATGG-CCATAACTTGAGCTGCCAAACTCAAAATCAAGTGATTCAAAGTG
* * * * *
54048220 CGTGTTTCAAAATTAAGAGATAGCTCTTTTATCT-CTTTGAAGACATTTTCGCTCAAAATT
65 CAT-TCT-AAAACTAAAAGATAGCTCTTTCAT-TACTTTGAAGACATTTTCGCTCAAAATT
54048280 ACTTAGATCC
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
123 4 0.04
124 6 0.06
125 91 0.89
126 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (125 bp):
TGCTTGCAAAGTCTTCATGGCCATAACTTGAGCTGCCAAACTCAAAATCAAGTGATTCAAAGTGC
ATTCTAAAACTAAAAGATAGCTCTTTCATTACTTTGAAGACATTTTCGCTCAAAATTTTT
Found at i:54052011 original size:103 final size:102
Alignment explanation
Indices: 54051884--54052073 Score: 283
Period size: 103 Copynumber: 1.9 Consensus size: 102
54051874 ATGAATTTCG
* * * * * *
54051884 ACTACCCATTCAATTCTACACTCTACATAATTCTAAGGTATCATTATTTTTATTTAAGA-TAATT
1 ACTACCCATCCAATTATACACTCTACATAATCCTAAGGTACCATTATTTATATCTAAGATTAA-T
54051948 AAATATATATATATTCATGTATTTATCAATGAATTTATT
65 AAA-ATATATATATTCATGTATTTATCAATGAATTTATT
* *
54051987 ACTACCCATCCAATTATACGCTCTACATAATCCTAAGGTACCATTATTTATATCTAAGATTAATC
1 ACTACCCATCCAATTATACACTCTACATAATCCTAAGGTACCATTATTTATATCTAAGATTAATA
54052052 AAATATATATATTCATGTATTT
66 AAATATATATATTCATGTATTT
54052074 GGATCATGTT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 20 0.26
103 55 0.71
104 3 0.04
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (102 bp):
ACTACCCATCCAATTATACACTCTACATAATCCTAAGGTACCATTATTTATATCTAAGATTAATA
AAATATATATATTCATGTATTTATCAATGAATTTATT
Found at i:54052262 original size:14 final size:15
Alignment explanation
Indices: 54052240--54052269 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54052230 TCATATACAT
54052240 TAAGTTATATTTTTA
1 TAAGTTATATTTTTA
54052255 TAAG-TATATTTTTA
1 TAAGTTATATTTTTA
54052269 T
1 T
54052270 TTTTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TAAGTTATATTTTTA
Found at i:54053344 original size:15 final size:15
Alignment explanation
Indices: 54053299--54053344 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
54053289 ATTTAATAAA
54053299 AATAATATTTTAT-T
1 AATAATATTTTATGT
*
54053313 AATATATATAATT-TGT
1 AATA-ATAT-TTTATGT
54053329 AATAATATTTTATGT
1 AATAATATTTTATGT
54053344 A
1 A
54053345 TTGCTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.23
15 13 0.50
16 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (15 bp):
AATAATATTTTATGT
Found at i:54053953 original size:27 final size:28
Alignment explanation
Indices: 54053923--54053983 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
54053913 AAAGAAATAT
* * *
54053923 ATAAAATACATAAA-TATTTAAAAAA-AA
1 ATAAAATA-AAAAATTATATAAAAATAAA
54053950 ATAAAATAAAAAATTATATAAAAATAAA
1 ATAAAATAAAAAATTATATAAAAATAAA
54053978 A-AAAAT
1 ATAAAAT
54053984 GATTATTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 4 0.14
27 22 0.76
28 3 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (28 bp):
ATAAAATAAAAAATTATATAAAAATAAA
Found at i:54058489 original size:18 final size:18
Alignment explanation
Indices: 54058447--54058489 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54058437 ATATAAAAAT
*
54058447 ATTTTTAAAATAAATTTT
1 ATTTTTAAAATAAATTTG
**
54058465 AGATTTAAAATAAATTTG
1 ATTTTTAAAATAAATTTG
54058483 ATTTTTA
1 ATTTTTA
54058490 TTACTTAAGT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTTAAAATAAATTTG
Found at i:54059006 original size:51 final size:51
Alignment explanation
Indices: 54058922--54059019 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
54058912 AATTATTTTT
54058922 TCAATTTCCTCTCAATTTCCTTCCAAATCTCTCTCAAA-CCCATATTTAATC
1 TCAATTTCCTCTCAATTTCCTTCCAAATCTCTCTCAAATCCC-TATTTAATC
* * * * *
54058973 TCAATTTGCTCTCAGTTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTCCTCTCAATTTCCTTC-CAAATCTCTCTCAAATCCCTATTT
54059020 TTAATTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 2 0.05
51 35 0.88
52 3 0.08
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAATCTCTCTCAAATCCCTATTTAATC
Found at i:54060664 original size:30 final size:30
Alignment explanation
Indices: 54060598--54060665 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
54060588 GAAAACGACG
54060598 CAGGCCCATCAACGAGGCCCAAAAATTCAC
1 CAGGCCCATCAACGAGGCCCAAAAATTCAC
* * * * *
54060628 CCGGCCCATCATC-AGCGCCCATAACTTCAT
1 CAGGCCCATCAACGAG-GCCCAAAAATTCAC
54060658 CAGGCCCA
1 CAGGCCCA
54060666 GCAAATGTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.29, C:0.41, G:0.16, T:0.13
Consensus pattern (30 bp):
CAGGCCCATCAACGAGGCCCAAAAATTCAC
Found at i:54060772 original size:18 final size:18
Alignment explanation
Indices: 54060749--54060791 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54060739 TGTCAGGTGC
* *
54060749 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
54060767 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
54060785 GTTTCCT
1 GTATCCT
54060792 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:54064552 original size:124 final size:124
Alignment explanation
Indices: 54064332--54064617 Score: 491
Period size: 124 Copynumber: 2.3 Consensus size: 124
54064322 CCCAAACATA
* *
54064332 CTACTGTAGCAAAAGCCCGTCCACGTGGGAGCGATTTAAAAAATTCTTCTGATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTAC
* *
54064397 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAAGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTACTTTTTCAAGAC
*
54064456 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTAC
* *
54064521 TTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTACTTTTTCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTACTTTTTCAAGAC
* *
54064580 CTACTGTATCAAAAACGCGTCCACGTGGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
54064618 CTTAATAAAT
Statistics
Matches: 153, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 153 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTAC
TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTACTTTTTCAAGAC
Found at i:54071140 original size:68 final size:68
Alignment explanation
Indices: 54071031--54071170 Score: 280
Period size: 68 Copynumber: 2.1 Consensus size: 68
54071021 TGTAATTGAG
54071031 ATCTATATATTCAGATTCTATCCAAGTGATGATATAAATATGTATTGAATAATCATACTTTTATA
1 ATCTATATATTCAGATTCTATCCAAGTGATGATATAAATATGTATTGAATAATCATACTTTTATA
54071096 CTC
66 CTC
54071099 ATCTATATATTCAGATTCTATCCAAGTGATGATATAAATATGTATTGAATAATCATACTTTTATA
1 ATCTATATATTCAGATTCTATCCAAGTGATGATATAAATATGTATTGAATAATCATACTTTTATA
54071164 CTC
66 CTC
54071167 ATCT
1 ATCT
54071171 CACTCCTCAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 72 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (68 bp):
ATCTATATATTCAGATTCTATCCAAGTGATGATATAAATATGTATTGAATAATCATACTTTTATA
CTC
Found at i:54073639 original size:16 final size:17
Alignment explanation
Indices: 54073615--54073647 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54073605 GGATTTATAT
*
54073615 AATTTTAAA-ATTTTAA
1 AATTATAAATATTTTAA
54073631 AATTATAAATATTTTAA
1 AATTATAAATATTTTAA
54073648 TTTTAGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTATAAATATTTTAA
Found at i:54078446 original size:57 final size:59
Alignment explanation
Indices: 54078335--54078482 Score: 194
Period size: 57 Copynumber: 2.5 Consensus size: 59
54078325 AATTGACGGT
*
54078335 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCTGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-G
54078398 AAAAAGATCTAGCCTGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCTGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
* * *
54078454 AAAATGAATTTAGCCTGGACGGGTAATCC
1 AAAAAG-ATCTAGCCTGGACGGGTGATCC
54078483 GAATTAGGGT
Statistics
Matches: 79, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
56 6 0.08
57 45 0.57
58 1 0.01
59 1 0.01
61 1 0.01
62 20 0.25
63 5 0.06
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (59 bp):
AAAAAGATCTAGCCTGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:54078710 original size:66 final size:66
Alignment explanation
Indices: 54078604--54078729 Score: 243
Period size: 66 Copynumber: 1.9 Consensus size: 66
54078594 GTTTATATTA
*
54078604 CAGGGGATTTAGCTTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCGGGAGTGTGCTATCTT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCGGGAGTGTGCTATCTT
54078669 G
66 G
54078670 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCGGGAGTGTGCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCGGGAGTGTGCT
54078730 CTCTGAAATG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.18, C:0.17, G:0.37, T:0.27
Consensus pattern (66 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCGGGAGTGTGCTATCTT
G
Found at i:54084722 original size:6 final size:6
Alignment explanation
Indices: 54084708--54084740 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
54084698 AAGACAGTAA
*
54084708 AAGAAG AAGATG AAGATG AAGATG AAGA-G AAGA
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGA
54084741 GGAGGAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (6 bp):
AAGATG
Found at i:54093974 original size:38 final size:38
Alignment explanation
Indices: 54093930--54094006 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
54093920 TTGAACTATC
54093930 TCACTTAGTTCTTTTTGCTCAAAATCTATCTCACTTAG
1 TCACTTAGTTCTTTTTGCTCAAAATCTATCTCACTTAG
54093968 TCACTTAGTTCTTTTTGCTCAAAATCTATCTCACTTAG
1 TCACTTAGTTCTTTTTGCTCAAAATCTATCTCACTTAG
54094006 T
1 T
54094007 TACCCGGCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.45
Consensus pattern (38 bp):
TCACTTAGTTCTTTTTGCTCAAAATCTATCTCACTTAG
Found at i:54095279 original size:31 final size:31
Alignment explanation
Indices: 54095215--54095280 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
54095205 AAAAAATATT
* *
54095215 AATTTAACTCTTTCTAAAACATTAATAGTTA
1 AATTCAACTCTTTCTAAAACATTAATAGCTA
* *
54095246 AATTCAACTCTTTTTAAAATATTGAATA-CTA
1 AATTCAACTCTTTCTAAAACATT-AATAGCTA
54095277 AATT
1 AATT
54095281 TAGCTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (31 bp):
AATTCAACTCTTTCTAAAACATTAATAGCTA
Found at i:54095608 original size:27 final size:28
Alignment explanation
Indices: 54095578--54095650 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
54095568 GACTAGTTGC
54095578 GCCTATCTCGA-AGGCGCCAATGGTGGA
1 GCCTATCTCGACAGGCGCCAATGGTGGA
*
54095605 GCCTAT-TTGACAGGCGCCAATGGTGGA
1 GCCTATCTCGACAGGCGCCAATGGTGGA
*
54095632 GCCTATCT-GACAGGTGCCA
1 GCCTATCTCGACAGGCGCCA
54095651 CTGCTGCTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.07
27 38 0.90
28 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.32, T:0.21
Consensus pattern (28 bp):
GCCTATCTCGACAGGCGCCAATGGTGGA
Found at i:54095858 original size:12 final size:12
Alignment explanation
Indices: 54095841--54095865 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54095831 GGTGTTCATT
54095841 CGGTTAACCGAC
1 CGGTTAACCGAC
54095853 CGGTTAACCGAC
1 CGGTTAACCGAC
54095865 C
1 C
54095866 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:54097584 original size:3 final size:3
Alignment explanation
Indices: 54097578--54097612 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
54097568 CATTACCTTT
54097578 TTC TTC TTC TTC -TC TTC TTC TTC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
54097613 CCTTTCTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:54097595 original size:8 final size:8
Alignment explanation
Indices: 54097582--54097613 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
54097572 ACCTTTTTCT
54097582 TCTTCTTC
1 TCTTCTTC
54097590 TCTTC-T-
1 TCTTCTTC
54097596 TCTTCTTC
1 TCTTCTTC
54097604 TCTTCTTC
1 TCTTCTTC
54097612 TC
1 TC
54097614 CTTTCTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.23
7 2 0.09
8 15 0.68
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (8 bp):
TCTTCTTC
Found at i:54097595 original size:11 final size:11
Alignment explanation
Indices: 54097579--54097634 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
54097569 ATTACCTTTT
54097579 TCTTCTTCTTC
1 TCTTCTTCTTC
54097590 TCTTCTTCTTC
1 TCTTCTTCTTC
54097601 T-TCTCTTCTTC
1 TCT-TCTTCTTC
*
54097612 TCCT-TTC-TC
1 TCTTCTTCTTC
54097621 TCTT-TTCTTTC
1 TCTTCTTC-TTC
54097632 TCT
1 TCT
54097635 CTCCCGTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 8 0.21
10 4 0.10
11 27 0.69
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:54097597 original size:14 final size:14
Alignment explanation
Indices: 54097578--54097634 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
54097568 CATTACCTTT
54097578 TTCTTCTTCTTCTC
1 TTCTTCTTCTTCTC
54097592 TTCTTCTTCTTCTC
1 TTCTTCTTCTTCTC
*
54097606 TTCTTCTCCTT-TC
1 TTCTTCTTCTTCTC
54097619 TCTCTT-TTCTTTCTC
1 T-TCTTCTTC-TTCTC
54097634 T
1 T
54097635 CTCCCGTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
13 5 0.13
14 30 0.79
15 3 0.08
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (14 bp):
TTCTTCTTCTTCTC
Found at i:54097600 original size:17 final size:17
Alignment explanation
Indices: 54097578--54097629 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
54097568 CATTACCTTT
54097578 TTCTTCTTCT-TCTCTTC
1 TTCTTCTTCTCT-TCTTC
54097595 TTCTTCTTCTCTTCTTC
1 TTCTTCTTCTCTTCTTC
*
54097612 TCCTT-TCTCTCTT-TTC
1 TTCTTCT-TCTCTTCTTC
54097628 TT
1 TT
54097630 TCTCTCTCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 5 0.16
17 25 0.81
18 1 0.03
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTTCTTCTCTTCTTC
Found at i:54098894 original size:5 final size:5
Alignment explanation
Indices: 54098886--54098910 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54098876 TTAAAATAAA
54098886 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
54098911 GTGAGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:54102491 original size:10 final size:10
Alignment explanation
Indices: 54102476--54102500 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54102466 GTCACTAGGC
54102476 TGATTGACTG
1 TGATTGACTG
54102486 TGATTGACTG
1 TGATTGACTG
54102496 TGATT
1 TGATT
54102501 CCTTTGTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.28, T:0.44
Consensus pattern (10 bp):
TGATTGACTG
Found at i:54102772 original size:18 final size:19
Alignment explanation
Indices: 54102749--54102789 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
54102739 TAATGGACTT
54102749 TATAGGATAA-TTTATTGG
1 TATAGGATAATTTTATTGG
54102767 TATAGGATAATTTTTATTGG
1 TATAGGATAA-TTTTATTGG
54102787 TAT
1 TAT
54102790 TTTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.49
Consensus pattern (19 bp):
TATAGGATAATTTTATTGG
Found at i:54106980 original size:91 final size:90
Alignment explanation
Indices: 54106879--54107050 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 90
54106869 AAGTAAATTA
54106879 TAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGA-TT-TTA
1 TAAATTATATTTAATAATAATTATTTTAAATTATA-TTT-TAGTA-T-TATATTATGATTTATTA
54106941 GTAAATTCATATAAGAATAAGAATTTTAT
62 GTAAATTCATATAAGAATAAGAATTTTAT
*
54106970 TAAATTATATTTAATAATTATTATTTTAAATTATATTTTAGTATTATATTATGATTTTATTAGTA
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATTATATTATGA-TTTATTAGTA
54107035 AATTCATATAAGAATA
65 AATTCATATAAGAATA
54107051 TTTATTAACA
Statistics
Matches: 76, Mismatches: 1, Indels: 8
0.89 0.01 0.09
Matches are distributed among these distances:
88 10 0.13
89 1 0.01
90 7 0.09
91 47 0.62
92 11 0.14
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (90 bp):
TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATTATATTATGATTTATTAGTAA
ATTCATATAAGAATAAGAATTTTAT
Found at i:54107099 original size:15 final size:17
Alignment explanation
Indices: 54107061--54107094 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54107051 TTTATTAACA
54107061 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
54107078 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
54107095 TTTATAACAA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:54107108 original size:16 final size:15
Alignment explanation
Indices: 54107061--54107108 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
54107051 TTTATTAACA
*
54107061 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
54107078 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
54107093 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
54107109 GTTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:54107294 original size:39 final size:43
Alignment explanation
Indices: 54107251--54107342 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 43
54107241 CTATTATACC
*
54107251 TCTATTC-A-ATTCAACCAAACACAAGAA-TA-CTATTACGCA
1 TCTATTCTACATTCAACCAAACAAAAGAATTACCTATTACGCA
*
54107290 TCTATTCCATTACATTCAACCAAACAAAAGAATTACCTATTACGCC
1 TCTATT-C--TACATTCAACCAAACAAAAGAATTACCTATTACGCA
54107336 TCTATTC
1 TCTATTC
54107343 CATTACGCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
39 6 0.14
40 1 0.02
43 1 0.02
44 18 0.41
45 3 0.07
46 15 0.34
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.29
Consensus pattern (43 bp):
TCTATTCTACATTCAACCAAACAAAAGAATTACCTATTACGCA
Found at i:54107322 original size:44 final size:46
Alignment explanation
Indices: 54107259--54107348 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
54107249 CCTCTATTCA
*
54107259 ATTCAACCAAACACAAGAA-TA-CTATTACGCATCTATTCCATTAC
1 ATTCAACCAAACAAAAGAATTACCTATTACGCATCTATTCCATTAC
*
54107303 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACAAAAGAATTACCTATTACGCATCTATTCCATTAC
54107349 GCCTCTATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 18 0.43
45 2 0.05
46 22 0.52
ACGTcount: A:0.40, C:0.28, G:0.04, T:0.28
Consensus pattern (46 bp):
ATTCAACCAAACAAAAGAATTACCTATTACGCATCTATTCCATTAC
Found at i:54107349 original size:16 final size:16
Alignment explanation
Indices: 54107328--54107364 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
54107318 AGAATTACCT
54107328 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
54107344 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
54107360 ATTAC
1 ATTAC
54107365 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:54109161 original size:21 final size:21
Alignment explanation
Indices: 54109137--54109183 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
54109127 CAGCTTCTTG
*
54109137 GCAGTGATGACAAACTGTTCT
1 GCAGCGATGACAAACTGTTCT
54109158 GCAGCGATGACAAACTGTTCT
1 GCAGCGATGACAAACTGTTCT
54109179 GCAGC
1 GCAGC
54109184 CTTTAAGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
GCAGCGATGACAAACTGTTCT
Found at i:54116305 original size:25 final size:25
Alignment explanation
Indices: 54116226--54116305 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 25
54116216 AAGCAATTTT
*
54116226 TCAAAATCTATTCCATGGATCATTC
1 TCAAAATCTACTCCATGGATCATTC
* *** *
54116251 TCAAGA--T-C-CCAAACATC-TTT
1 TCAAAATCTACTCCATGGATCATTC
*
54116271 TCAATATCTACTCCATGGATCATTC
1 TCAAAATCTACTCCATGGATCATTC
54116296 TCAAAATCTA
1 TCAAAATCTA
54116306 TTCCCCTGTA
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
20 7 0.18
21 6 0.16
22 1 0.03
23 2 0.05
24 6 0.16
25 16 0.42
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (25 bp):
TCAAAATCTACTCCATGGATCATTC
Found at i:54120766 original size:24 final size:24
Alignment explanation
Indices: 54120734--54120779 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
54120724 TCATTCAATC
*
54120734 GAAGGGCGA-GAGAGAAGGAGAAAA
1 GAAGAGCGATGAGAG-AGGAGAAAA
*
54120758 GAAGAGCGATGGGAGAGGAGAA
1 GAAGAGCGATGAGAGAGGAGAA
54120780 GCGACACGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.46, C:0.04, G:0.48, T:0.02
Consensus pattern (24 bp):
GAAGAGCGATGAGAGAGGAGAAAA
Found at i:54127763 original size:23 final size:23
Alignment explanation
Indices: 54127737--54127788 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
54127727 TATTGAAATT
54127737 TATTTCAAATATATAATA-TTATA
1 TATTT-AAATATATAATAGTTATA
* *
54127760 TATTTAAATTTGTAATAGTTATA
1 TATTTAAATATATAATAGTTATA
54127783 T-TTTAA
1 TATTTAA
54127789 TGTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
TATTTAAATATATAATAGTTATA
Found at i:54130238 original size:19 final size:18
Alignment explanation
Indices: 54130205--54130266 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
54130195 GGGATACAAA
*
54130205 TTTTAGTAATTTTTTTGCAT
1 TTTTA-TAA-TTTTTTGTAT
* *
54130225 TTTTATATTGTTTTTGTAA
1 TTTTATAAT-TTTTTGTAT
54130244 TTTTATAATTTTTTGTAT
1 TTTTATAATTTTTTGTAT
54130262 TTTTA
1 TTTTA
54130267 AATATATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.39
19 17 0.47
20 5 0.14
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTTATAATTTTTTGTAT
Found at i:54130246 original size:20 final size:19
Alignment explanation
Indices: 54130213--54130286 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
54130203 AATTTTAGTA
*
54130213 ATTTTTTTG-CATTTTTAT
1 ATTTTTTTGTAATTTTTAT
54130231 ATTGTTTTTGTAA-TTTTAT
1 ATT-TTTTTGTAATTTTTAT
*
54130250 AATTTTTTGT-ATTTTTAAAT
1 ATTTTTTTGTAATTTTT--AT
* *
54130270 ATATTTTTATAATTTTT
1 ATTTTTTTGTAATTTTT
54130287 TTTGTAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
17 1 0.02
18 14 0.31
19 14 0.31
20 10 0.22
21 6 0.13
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.69
Consensus pattern (19 bp):
ATTTTTTTGTAATTTTTAT
Found at i:54130255 original size:38 final size:39
Alignment explanation
Indices: 54130203--54130285 Score: 107
Period size: 37 Copynumber: 2.2 Consensus size: 39
54130193 AGGGGATACA
* * *
54130203 AATTTTAGTAATTTTTTTGCATTTTTATAT-TGTTTTTGT
1 AATTTTAGTAA-TTTTTTGCATTTTTAAATATATTTTTAT
*
54130242 AATTTTA-TAATTTTTTGTATTTTTAAATATATTTTTAT
1 AATTTTAGTAATTTTTTGCATTTTTAAATATATTTTTAT
54130280 AATTTT
1 AATTTT
54130286 TTTTGTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
37 16 0.41
38 16 0.41
39 7 0.18
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (39 bp):
AATTTTAGTAATTTTTTGCATTTTTAAATATATTTTTAT
Found at i:54132065 original size:7 final size:7
Alignment explanation
Indices: 54132053--54132087 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
54132043 TTTTGGTACT
54132053 CTTTCCA
1 CTTTCCA
54132060 CTTTCCA
1 CTTTCCA
54132067 CTTTCCA
1 CTTTCCA
54132074 CTTTCCA
1 CTTTCCA
54132081 CTTTCCA
1 CTTTCCA
54132088 ATCCTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
CTTTCCA
Found at i:54135900 original size:14 final size:15
Alignment explanation
Indices: 54135876--54135911 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
54135866 TATTATTGAA
54135876 AAATA-TTCAAT-AT
1 AAATATTTCAATAAT
54135889 AAATATTTCAATAAT
1 AAATATTTCAATAAT
54135904 AAATATTT
1 AAATATTT
54135912 ATTATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 6 0.29
15 10 0.48
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTTCAATAAT
Found at i:54136862 original size:14 final size:15
Alignment explanation
Indices: 54136831--54136868 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
54136821 ATTTGCCATT
54136831 AAAAT-ATTTTTCAG
1 AAAATAATTTTTCAG
*
54136845 AAAATAATTTTTGA-
1 AAAATAATTTTTCAG
54136859 AAAATAATTT
1 AAAATAATTT
54136869 ATTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (15 bp):
AAAATAATTTTTCAG
Found at i:54136898 original size:19 final size:20
Alignment explanation
Indices: 54136860--54136898 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54136850 AATTTTTGAA
*
54136860 AAATAATTTATTTTTTTTAG
1 AAATAATTTATTTATTTTAG
*
54136880 AAATGATTTA-TTATTTTAG
1 AAATAATTTATTTATTTTAG
54136899 TGTTTGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
AAATAATTTATTTATTTTAG
Found at i:54137743 original size:18 final size:18
Alignment explanation
Indices: 54137720--54137756 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
54137710 GGTTTATGCA
54137720 AAACCAAATATAGCATCT
1 AAACCAAATATAGCATCT
54137738 AAACCAAATATAGCATCT
1 AAACCAAATATAGCATCT
54137756 A
1 A
54137757 TTGATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (18 bp):
AAACCAAATATAGCATCT
Found at i:54142705 original size:5 final size:5
Alignment explanation
Indices: 54142695--54142734 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
54142685 TTCTTCGTGT
*
54142695 TTTTA TTTTA TTTTA -TTTA TTTTA TCTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
54142735 ATATATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:54142719 original size:19 final size:19
Alignment explanation
Indices: 54142695--54142731 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54142685 TTCTTCGTGT
*
54142695 TTTTATTTTATTTTATTTA
1 TTTTATCTTATTTTATTTA
54142714 TTTTATCTTATTTTATTT
1 TTTTATCTTATTTTATTT
54142732 TATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATCTTATTTTATTTA
Found at i:54143601 original size:16 final size:18
Alignment explanation
Indices: 54143570--54143604 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
54143560 AGAAGAAAAG
54143570 AAGGAGGAAGGAAGGAGA
1 AAGGAGGAAGGAAGGAGA
54143588 AAGG-GGAA-GAAGGAGA
1 AAGGAGGAAGGAAGGAGA
54143604 A
1 A
54143605 GAAGAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (18 bp):
AAGGAGGAAGGAAGGAGA
Found at i:54143902 original size:26 final size:26
Alignment explanation
Indices: 54143867--54143925 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
54143857 AGCAGGCCAG
* *
54143867 CCAGCAGGCCCAGATTCG-GCAGCAGC
1 CCAGCAGGCCCAG-TCCGCCCAGCAGC
54143893 CCAGCAGGCCCAGTCCGCCCAGCAGC
1 CCAGCAGGCCCAGTCCGCCCAGCAGC
54143919 CCAGCAG
1 CCAGCAG
54143926 TGCAGCAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.22, C:0.44, G:0.29, T:0.05
Consensus pattern (26 bp):
CCAGCAGGCCCAGTCCGCCCAGCAGC
Found at i:54143905 original size:9 final size:8
Alignment explanation
Indices: 54143886--54143925 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
54143876 CCAGATTCGG
54143886 CAGCAGCC
1 CAGCAGCC
54143894 CAGCAGGCC
1 CAGCA-GCC
*
54143903 CAGTCCGCC
1 CAG-CAGCC
54143912 CAGCAGCC
1 CAGCAGCC
54143920 CAGCAG
1 CAGCAG
54143926 TGCAGCAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 15 0.54
9 12 0.43
10 1 0.04
ACGTcount: A:0.23, C:0.47, G:0.28, T:0.03
Consensus pattern (8 bp):
CAGCAGCC
Found at i:54144519 original size:17 final size:17
Alignment explanation
Indices: 54144475--54144522 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
54144465 AAAAAAAAAA
*
54144475 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTC
*
54144492 TCATGTCTTCAAAAATTC
1 TCGTGT-TTCAAAAATTC
54144510 TCGTGTTTCAAAA
1 TCGTGTTTCAAAA
54144523 CAATAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTC
Found at i:54144638 original size:35 final size:35
Alignment explanation
Indices: 54144598--54144691 Score: 125
Period size: 35 Copynumber: 2.6 Consensus size: 35
54144588 TATTATTGTG
54144598 TTTCAAAAATTCTCGTGAATAAAAAAATTTCGTGT
1 TTTCAAAAATTCTCGTGAATAAAAAAATTTCGTGT
* ** *
54144633 TTTCAAAAATTCCCGTGTTTAAAAAATTTTCGTGT
1 TTTCAAAAATTCTCGTGAATAAAAAAATTTCGTGT
54144668 TTTCACAAAAAATTCTCGTGAATA
1 TTT--C-AAAAATTCTCGTGAATA
54144692 TTTTTTTGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 34 0.69
37 1 0.02
38 14 0.29
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (35 bp):
TTTCAAAAATTCTCGTGAATAAAAAAATTTCGTGT
Found at i:54144640 original size:17 final size:17
Alignment explanation
Indices: 54144620--54144677 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
54144610 TCGTGAATAA
54144620 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
* *
54144637 AAAAATTCCCGTG-TTTA
1 AAAAATT-TCGTGTTTTC
54144654 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
54144672 ACAAAA
1 A-AAAA
54144678 AATTCTCGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 19 0.58
18 10 0.30
19 4 0.12
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:54144788 original size:18 final size:17
Alignment explanation
Indices: 54144767--54144815 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
54144757 AAAAAATTCG
54144767 TGTTTCCAAAAATTTTCA
1 TGTTTCC-AAAATTTTCA
* *
54144785 TGTTTTCAAAATTTTCG
1 TGTTTCCAAAATTTTCA
*
54144802 TGTTT-TAAAATTTT
1 TGTTTCCAAAATTTT
54144816 TTTCGTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 8 0.29
17 14 0.50
18 6 0.21
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (17 bp):
TGTTTCCAAAATTTTCA
Found at i:54144795 original size:17 final size:16
Alignment explanation
Indices: 54144775--54144865 Score: 83
Period size: 17 Copynumber: 5.2 Consensus size: 16
54144765 CGTGTTTCCA
*
54144775 AAAATTTTCATGTTTT
1 AAAATTTTCGTGTTTT
54144791 CAAAATTTTCGTGTTTT
1 -AAAATTTTCGTGTTTT
54144808 AAAATTTTTTTCGTGTTATT
1 AAAA---TTTTCGTGTT-TT
* * *
54144828 AAAATTCTCATGTATTG
1 AAAATTTTCGTGT-TTT
54144845 AAAATTTTCGTGTTTT
1 AAAATTTTCGTGTTTT
54144861 CAAAA
1 -AAAA
54144866 AAATTCTGTG
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.10
17 38 0.62
18 1 0.02
19 10 0.16
20 6 0.10
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (16 bp):
AAAATTTTCGTGTTTT
Found at i:54144820 original size:19 final size:20
Alignment explanation
Indices: 54144796--54144833 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
54144786 GTTTTCAAAA
54144796 TTTTCGTGTT-TTAAAATTT
1 TTTTCGTGTTATTAAAATTT
54144815 TTTTCGTGTTATTAAAATT
1 TTTTCGTGTTATTAAAATT
54144834 CTCATGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTTCGTGTTATTAAAATTT
Found at i:54144832 original size:36 final size:37
Alignment explanation
Indices: 54144779--54144852 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
54144769 TTTCCAAAAA
* * *
54144779 TTTTCATGTTTTCAAAATTTTCGTGT-TTTAAAATTT
1 TTTTCATGTTTTCAAAATTCTCATGTATTGAAAATTT
*
54144815 TTTTCGTGTTATT-AAAATTCTCATGTATTGAAAATTT
1 TTTTCATGTT-TTCAAAATTCTCATGTATTGAAAATTT
54144852 T
1 T
54144853 CGTGTTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55
Consensus pattern (37 bp):
TTTTCATGTTTTCAAAATTCTCATGTATTGAAAATTT
Found at i:54144870 original size:20 final size:20
Alignment explanation
Indices: 54144845--54144923 Score: 119
Period size: 19 Copynumber: 4.1 Consensus size: 20
54144835 TCATGTATTG
54144845 AAAATTTTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTCAAA
*
54144865 AAAATTCT-GTGTTTTCAAA
1 AAAATTTTCGTGTTTTCAAA
54144884 AAAA-TTTCGTG-TTTCAAA
1 AAAATTTTCGTGTTTTCAAA
*
54144902 AAAATCTTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTCAAA
54144922 AA
1 AA
54144924 TTATTATTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 13 0.25
19 24 0.45
20 16 0.30
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (20 bp):
AAAATTTTCGTGTTTTCAAA
Found at i:54144877 original size:53 final size:53
Alignment explanation
Indices: 54144738--54144942 Score: 141
Period size: 53 Copynumber: 3.7 Consensus size: 53
54144728 TTGTTTGACG
* *
54144738 AATTTTCGTGTTTTCAAAAAAAAAATTC-GTGTTTCCAAAAATTTTCATGTTTTCAA
1 AATTTTCGTGTTTTC---AAAAAAATTCTGTGTTT-CAAAAATTCTCATGTATTCAA
*** * * *
54144794 AATTTTCGTGTTTT-AAAATTTTTTTCGTGTTAT-TAAAATTCTCATGTATTGAA
1 AATTTTCGTGTTTTCAAAAAAATTCT-GTGTT-TCAAAAATTCTCATGTATTCAA
*
54144847 AATTTTCGTGTTTTCAAAAAAATTCTGTGTTTTCAAAAAAATT-TCGTGT-TTCAAAAA
1 AATTTTCGTGTTTTCAAAAAAATTCTGTG-TTTC--AAAAATTCTCATGTATTC---AA
* * *
54144904 AATCTTCGTGTTTTCAAAAATTATTATTGTGTTTCAAAA
1 AATTTTCGTGTTTTCAAAAA-AATT-CTGTGTTTCAAAA
54144943 TCTCGTGTTT
Statistics
Matches: 118, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
52 6 0.05
53 34 0.29
54 16 0.14
55 6 0.05
56 24 0.20
57 21 0.18
58 7 0.06
59 4 0.03
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (53 bp):
AATTTTCGTGTTTTCAAAAAAATTCTGTGTTTCAAAAATTCTCATGTATTCAA
Found at i:54144895 original size:38 final size:38
Alignment explanation
Indices: 54144845--54144942 Score: 119
Period size: 38 Copynumber: 2.5 Consensus size: 38
54144835 TCATGTATTG
*
54144845 AAAATTTTCGTGTTTTCAAAAAAA--TTCTGTGTTTTCAA
1 AAAAATTTCGTG-TTTCAAAAAAATCTTC-GTGTTTTCAA
54144883 AAAAATTTCGTGTTTCAAAAAAATCTTCGTGTTTTCAA
1 AAAAATTTCGTGTTTCAAAAAAATCTTCGTGTTTTCAA
* *
54144921 AAATTATTATTGTGTTTCAAAA
1 AAA-AATT-TCGTGTTTCAAAA
54144943 TCTCGTGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
37 11 0.21
38 24 0.45
39 6 0.11
40 12 0.23
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (38 bp):
AAAAATTTCGTGTTTCAAAAAAATCTTCGTGTTTTCAA
Found at i:54146374 original size:18 final size:18
Alignment explanation
Indices: 54146334--54146371 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54146324 ATAATAAATT
54146334 TAAA-ATTTATATTAATA
1 TAAATATTTATATTAATA
*
54146351 TTAATATTTATATTAA-A
1 TAAATATTTATATTAATA
54146368 TAAA
1 TAAA
54146372 ATAAAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATATTTATATTAATA
Found at i:54147459 original size:6 final size:6
Alignment explanation
Indices: 54147443--54147493 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
54147433 TTTTTTTTTT
**
54147443 TTAATA TTTAATA TTAATA -TAATCA TTTTTA CTTAATA TTAATA TTAATA
1 TTAATA -TTAATA TTAATA TTAAT-A TTAATA -TTAATA TTAATA TTAATA
54147493 T
1 T
54147494 ACAATTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.11
6 21 0.57
7 12 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAATA
Found at i:54147591 original size:50 final size:49
Alignment explanation
Indices: 54147498--54147597 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 49
54147488 TAATATACAA
* * * *
54147498 TTTAAATTTATTATCAGTGTTTGAAAATATCTATCTATTTTTATCTATT
1 TTTAAATCTATTATCAGTGTTTGAAAATATCTATATATATTTATATATT
* * *
54147547 TTTAAATCTATTATTATGTTTTTGAAAATATTTATATATATTTATATATT
1 TTTAAATCTATTATCA-GTGTTTGAAAATATCTATATATATTTATATATT
54147597 T
1 T
54147598 ATTTGATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 14 0.33
50 29 0.67
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (49 bp):
TTTAAATCTATTATCAGTGTTTGAAAATATCTATATATATTTATATATT
Found at i:54159624 original size:16 final size:18
Alignment explanation
Indices: 54159591--54159641 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
54159581 ATTCTCTTTC
54159591 ATCCTCTTTCTCAACAAA
1 ATCCTCTTTCTCAACAAA
*
54159609 ATCCT-TTTCTC-CCAAA
1 ATCCTCTTTCTCAACAAA
**
54159625 ATTTATCTTTCTCAACA
1 A-TCCTCTTTCTCAACA
54159642 GTATTCTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 5 0.19
17 8 0.31
18 11 0.42
19 2 0.08
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.39
Consensus pattern (18 bp):
ATCCTCTTTCTCAACAAA
Found at i:54175251 original size:27 final size:28
Alignment explanation
Indices: 54175221--54175273 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
54175211 TTTTAATTTT
*
54175221 TTTTAAATTACTTTTTATA-ATTTTTAA
1 TTTTAAAATACTTTTTATATATTTTTAA
*
54175248 TTTTAAAATATTTTTTATATATTTTT
1 TTTTAAAATACTTTTTATATATTTTT
54175274 TTAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTAAAATACTTTTTATATATTTTTAA
Found at i:54178745 original size:29 final size:30
Alignment explanation
Indices: 54178690--54178751 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
54178680 GTTATATATA
*
54178690 AACTTTGATTTAATGTGTAATGTCATACATG
1 AACTTTGATTT-ATGTGTAATGTCATAAATG
* *
54178721 AACTTTGATTT-TGTGTGATTTCATAAATG
1 AACTTTGATTTATGTGTAATGTCATAAATG
54178750 AA
1 AA
54178752 ATTTTGCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.61
31 11 0.39
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (30 bp):
AACTTTGATTTATGTGTAATGTCATAAATG
Found at i:54201890 original size:19 final size:20
Alignment explanation
Indices: 54201863--54201904 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
54201853 ATTAGAAATG
* *
54201863 AAATAATCATAAA-CTTTTA
1 AAATAATCACAAATCTATTA
*
54201882 AAATTATCACAAATCTATTA
1 AAATAATCACAAATCTATTA
54201902 AAA
1 AAA
54201905 ACAAATATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATCACAAATCTATTA
Found at i:54202019 original size:14 final size:14
Alignment explanation
Indices: 54202000--54202027 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54201990 GAAAAAGAAA
54202000 GGATTCCACTGTTT
1 GGATTCCACTGTTT
54202014 GGATTCCACTGTTT
1 GGATTCCACTGTTT
54202028 TTCCACCGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
GGATTCCACTGTTT
Found at i:54203299 original size:18 final size:18
Alignment explanation
Indices: 54203276--54203334 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
54203266 TTTGATATGC
54203276 TTTTATTTCCTTTTGTGT
1 TTTTATTTCCTTTTGTGT
** * *
54203294 TTTTATGTT--TGATATGC
1 TTTTAT-TTCCTTTTGTGT
54203311 TTTTATTTCCTTTTGTGT
1 TTTTATTTCCTTTTGTGT
54203329 TTTTAT
1 TTTTAT
54203335 GTTATTTCAT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 2 0.07
17 10 0.33
18 16 0.53
19 2 0.07
ACGTcount: A:0.10, C:0.08, G:0.12, T:0.69
Consensus pattern (18 bp):
TTTTATTTCCTTTTGTGT
Found at i:54203309 original size:35 final size:35
Alignment explanation
Indices: 54203263--54203337 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
54203253 AGAGTCTTTC
54203263 ATGTTTGATATGCTTTTATTTCCTTTTGTGTTTTT
1 ATGTTTGATATGCTTTTATTTCCTTTTGTGTTTTT
54203298 ATGTTTGATATGCTTTTATTTCCTTTTGTGTTTTT
1 ATGTTTGATATGCTTTTATTTCCTTTTGTGTTTTT
54203333 ATGTT
1 ATGTT
54203338 ATTTCATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.12, C:0.08, G:0.15, T:0.65
Consensus pattern (35 bp):
ATGTTTGATATGCTTTTATTTCCTTTTGTGTTTTT
Found at i:54214273 original size:18 final size:19
Alignment explanation
Indices: 54214238--54214276 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
54214228 ACAAAAATTA
*
54214238 TAAAAATTATTATAATTTT
1 TAAAAAATATTATAATTTT
54214257 TAAAAAATA-TATAATTTT
1 TAAAAAATATTATAATTTT
54214275 TA
1 TA
54214277 GATTGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAAAATATTATAATTTT
Found at i:54214484 original size:11 final size:10
Alignment explanation
Indices: 54214470--54214532 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
54214460 TTTTTACTCA
54214470 TTTTTATAAT
1 TTTTTATAAT
* *
54214480 GTTTTACAA-
1 TTTTTATAAT
*
54214489 GTTTTATAAT
1 TTTTTATAAT
*
54214499 TTTTT-TACAA
1 TTTTTATA-AT
54214509 TTTTTATAAAT
1 TTTTTAT-AAT
54214520 TTTTTAT-AT
1 TTTTTATAAT
54214529 TTTT
1 TTTT
54214533 AAATAATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
9 16 0.37
10 17 0.40
11 9 0.21
12 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:54214502 original size:9 final size:9
Alignment explanation
Indices: 54214469--54214611 Score: 61
Period size: 9 Copynumber: 15.8 Consensus size: 9
54214459 TTTTTTACTC
54214469 ATTTTTATA
1 ATTTTTATA
*
54214478 ATGTTTTACA
1 AT-TTTTATA
*
54214488 AGTTTTATA
1 ATTTTTATA
*
54214497 ATTTTTTTACA
1 A--TTTTTATA
54214508 ATTTTTATAA
1 ATTTTTAT-A
54214518 ATTTTT-TA
1 ATTTTTATA
54214526 TATTTTTA-A
1 -ATTTTTATA
**
54214535 A-TAATAT-
1 ATTTTTATA
*
54214542 ATATTTATA
1 ATTTTTATA
54214551 CATTTTTAATA
1 -ATTTTT-ATA
*
54214562 AATTTTA-A
1 ATTTTTATA
54214570 ATTTTTA-A
1 ATTTTTATA
*
54214578 ATGGTCTT-T-
1 AT--TTTTATA
54214587 -TTTTTACTA
1 ATTTTTA-TA
54214596 ATTTTTATA
1 ATTTTTATA
54214605 ATTTTTA
1 ATTTTTA
54214612 CAAGTTTCTT
Statistics
Matches: 100, Mismatches: 16, Indels: 36
0.66 0.11 0.24
Matches are distributed among these distances:
6 3 0.03
7 4 0.04
8 17 0.17
9 33 0.33
10 33 0.33
11 10 0.10
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (9 bp):
ATTTTTATA
Found at i:54214511 original size:124 final size:124
Alignment explanation
Indices: 54214375--54214618 Score: 350
Period size: 124 Copynumber: 2.0 Consensus size: 124
54214365 TTTTCATATA
* *
54214375 TTTTTTAAAATTTTTAGAACTTTTTAATATTTTTAAATAGTATATATTTATACATTTTTTAAATA
1 TTTTTTAAAATTTTTAGAAATTTTTAATATTTTTAAATAATATATATTTATACA-TTTTT-AATA
*
54214440 AATTCTAAA-TTTTAAAT-G-ATTTTTTACTCATTTTTATAATGTTTTACAAGTTTTATAAT
64 AATTCTAAATTTTTAAATGGTATTTTTTACTAATTTTTATAAT-TTTTACAAGTTTTATAAT
* * *
54214499 TTTTTTACAATTTTTATAAATTTTTTATATTTTTAAATAATATATATTTATACATTTTTAATAAA
1 TTTTTTAAAATTTTTAGAAATTTTTAATATTTTTAAATAATATATATTTATACATTTTTAATAAA
* *
54214564 TTTTAAATTTTTAAATGGTCTTTTTTTTACTAATTTTTATAATTTTTACAAGTTT
66 TTCTAAATTTTTAAATGG--TATTTTTTACTAATTTTTATAATTTTTACAAGTTT
54214619 CTTTTTACAT
Statistics
Matches: 107, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
122 12 0.11
123 13 0.12
124 50 0.47
126 12 0.11
127 20 0.19
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (124 bp):
TTTTTTAAAATTTTTAGAAATTTTTAATATTTTTAAATAATATATATTTATACATTTTTAATAAA
TTCTAAATTTTTAAATGGTATTTTTTACTAATTTTTATAATTTTTACAAGTTTTATAAT
Found at i:54214532 original size:20 final size:20
Alignment explanation
Indices: 54214458--54214525 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
54214448 ATTTTAAATG
*
54214458 ATTTTTTACTCATTTTTAT-A
1 ATTTTTTAC-AATTTTTATAA
* *
54214478 ATGTTTTACAAGTTTTATAA
1 ATTTTTTACAATTTTTATAA
*
54214498 TTTTTTTACAATTTTTATAA
1 ATTTTTTACAATTTTTATAA
54214518 ATTTTTTA
1 ATTTTTTA
54214526 TATTTTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 7 0.17
20 33 0.82
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTTTTACAATTTTTATAA
Found at i:54214611 original size:19 final size:19
Alignment explanation
Indices: 54214460--54214612 Score: 64
Period size: 19 Copynumber: 8.4 Consensus size: 19
54214450 TTTAAATGAT
*
54214460 TTTTTACTCATTTTTATAA
1 TTTTTACTAATTTTTATAA
*
54214479 TGTTTTAC-AAGTTTTATAA
1 T-TTTTACTAATTTTTATAA
54214498 TTTTTTTAC-AATTTTTATAAA
1 --TTTTTACTAATTTTTAT-AA
54214519 TTTTT--TATATTTTTA-AA
1 TTTTTACTA-ATTTTTATAA
** *
54214536 -TAATA-T-ATATTTATACA
1 TTTTTACTAATTTTTATA-A
* *
54214553 TTTTTAATAAATTTTA-AA
1 TTTTTACTAATTTTTATAA
*
54214571 TTTTTA--AATGGTCTT-T--
1 TTTTTACTAAT--TTTTATAA
54214587 TTTTTACTAATTTTTATAA
1 TTTTTACTAATTTTTATAA
54214606 TTTTTAC
1 TTTTTAC
54214613 AAGTTTCTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 40
0.66 0.08 0.26
Matches are distributed among these distances:
15 6 0.06
16 14 0.14
17 5 0.05
18 17 0.17
19 31 0.31
20 25 0.25
21 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTTTACTAATTTTTATAA
Found at i:54214611 original size:43 final size:42
Alignment explanation
Indices: 54214370--54214611 Score: 121
Period size: 43 Copynumber: 5.7 Consensus size: 42
54214360 AGATTTTTTC
* *
54214370 ATATATTTTTTA-AAATTTTTAGAACTTTTTAATATTTTTAAATA
1 ATAT-TTTTTTACTAATTTTTATAA-TTTTTAA-ATTTTTAAATA
* * * * *
54214414 GTATATATTTATAC-ATTTTTTAAATAAATTCTAAA-TTTTAAAT-
1 --ATATTTTTTTACTAATTTTT--ATAATTTTTAAATTTTTAAATA
* * *
54214457 -GA-TTTTTTACTCATTTTTATAATGTTTTACAAGTTTT--AT-
1 ATATTTTTTTACTAATTTTTATAAT-TTTTA-AATTTTTAAATA
*
54214496 A-ATTTTTTTAC-AATTTTTATAAATTTTTTATATTTTTAAATA
1 ATATTTTTTTACTAATTTTTAT-AA-TTTTTAAATTTTTAAATA
* * * *
54214538 ATATATATTTA-TACATTTTTAATAAATTTTAAATTTTTAAATG
1 ATATTTTTTTACTA-ATTTTT-ATAATTTTTAAATTTTTAAATA
* *
54214581 GTCTTTTTTTTACTAATTTTTATAATTTTTA
1 AT-ATTTTTTTACTAATTTTTATAATTTTTA
54214612 CAAGTTTCTT
Statistics
Matches: 150, Mismatches: 26, Indels: 43
0.68 0.12 0.20
Matches are distributed among these distances:
38 4 0.03
39 26 0.17
40 23 0.15
41 7 0.05
42 1 0.01
43 33 0.22
44 28 0.19
45 16 0.11
46 9 0.06
47 3 0.02
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (42 bp):
ATATTTTTTTACTAATTTTTATAATTTTTAAATTTTTAAATA
Found at i:54214624 original size:33 final size:33
Alignment explanation
Indices: 54214553--54214626 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 33
54214543 TATTTATACA
* *
54214553 TTTTTAATAAATTTTAAATTTTTAAATGGTCTTT
1 TTTTTACTAAATTTTAAATTTTTAAA-GGTCTTC
*
54214587 TTTTTACTAATTTTTATAATTTTTACAA-GT-TTC
1 TTTTTACTAAATTTTA-AATTTTTA-AAGGTCTTC
54214620 TTTTTAC
1 TTTTTAC
54214627 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 9 0.26
34 16 0.46
35 8 0.23
36 2 0.06
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (33 bp):
TTTTTACTAAATTTTAAATTTTTAAAGGTCTTC
Found at i:54215088 original size:18 final size:18
Alignment explanation
Indices: 54215065--54215099 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54215055 AAATACAATA
54215065 ATATTTTAATTTTAAAAC
1 ATATTTTAATTTTAAAAC
*
54215083 ATATTTTATTTTTAAAA
1 ATATTTTAATTTTAAAA
54215100 TATAATTATA
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:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTTAATTTTAAAAC
Found at i:54234993 original size:19 final size:18
Alignment explanation
Indices: 54234966--54235005 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
54234956 TATTATCAAA
* *
54234966 AAAATAAATCCAATTACT
1 AAAATAAATCAAAATACT
54234984 AAAATGAAATCAAAATACT
1 AAAAT-AAATCAAAATACT
54235003 AAA
1 AAA
54235006 CCGAAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATAAATCAAAATACT
Found at i:54238279 original size:23 final size:23
Alignment explanation
Indices: 54238253--54238305 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
54238243 AAATTAAAAC
54238253 AAATATTCAT-ATTTATATTATTA
1 AAATATTCATCATTTATATTA-TA
* *
54238276 AAATCTTCATCTTTTATATTATA
1 AAATATTCATCATTTATATTATA
54238299 AAATATT
1 AAATATT
54238306 TATAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATTCATCATTTATATTATA
Found at i:54240213 original size:20 final size:20
Alignment explanation
Indices: 54240188--54240225 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54240178 GGTAAAATGA
*
54240188 TTTCTGGAAAATGTTTTATT
1 TTTCTGGAAAATGATTTATT
*
54240208 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
54240226 CTAGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTATT
Found at i:54240217 original size:34 final size:35
Alignment explanation
Indices: 54240173--54240239 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54240163 CAGTAAAAAG
* *
54240173 TTTTCGGTAAAATGATTT-CTGGAAAATGTTTTAT
1 TTTTCGGTAAAATGATTTACTAGAAAATATTTTAT
*
54240207 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCGGTAAAATGATTTACTAGAAAATATTTT
54240240 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCGGTAAAATGATTTACTAGAAAATATTTTAT
Found at i:54242806 original size:25 final size:25
Alignment explanation
Indices: 54242767--54242818 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
54242757 AAAATGTCTG
54242767 CTGCTTAGAAGAGAATGGAAAATGT
1 CTGCTTAGAAGAGAATGGAAAATGT
54242792 CTGCTTAG-AGAAGAATGGAAAATGT
1 CTGCTTAGAAG-AGAATGGAAAATGT
54242817 CT
1 CT
54242819 TACCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (25 bp):
CTGCTTAGAAGAGAATGGAAAATGT
Found at i:54243707 original size:11 final size:11
Alignment explanation
Indices: 54243704--54243771 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
54243694 TTTTTTTAAA
54243704 TTTTAAAATTT
1 TTTTAAAATTT
54243715 TTTTAAAATACTT
1 TTTTAAAAT--TT
54243728 TTTT--AATTT
1 TTTTAAAATTT
54243737 TTTT--AA---
1 TTTTAAAATTT
*
54243743 TTTTAAAATAT
1 TTTTAAAATTT
54243754 TTTTAAAATATT
1 TTTTAAAAT-TT
54243766 TTTTAA
1 TTTTAA
54243772 TTTTTGTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
6 4 0.08
8 2 0.04
9 8 0.17
11 21 0.44
12 7 0.15
13 6 0.12
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:54243718 original size:22 final size:22
Alignment explanation
Indices: 54243661--54243718 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
54243651 CCGAATATAA
*
54243661 TAAATATTTTTATTTTTTTAATTT
1 TAAA-ATTTTT-TTTTTTAAATTT
**
54243685 TAAAATACTTTTTTTTAAATTT
1 TAAAATTTTTTTTTTTAAATTT
54243707 TAAAATTTTTTT
1 TAAAATTTTTTT
54243719 AAAATACTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 21 0.72
23 4 0.14
24 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TAAAATTTTTTTTTTTAAATTT
Found at i:54243738 original size:39 final size:38
Alignment explanation
Indices: 54243695--54243776 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 38
54243685 TAAAATACTT
*
54243695 TTTTTTAAATTTTAAAATTTTTTTAAAATACTTTTTTAA
1 TTTTTTAAATTTTAAAATATTTTTAAAATA-TTTTTTAA
*
54243734 TTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTAA
1 TTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTAA
54243772 TTTTT
1 TTTTT
54243777 GTTTTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 13 0.32
39 28 0.68
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (38 bp):
TTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTAA
Found at i:54249441 original size:22 final size:22
Alignment explanation
Indices: 54249396--54249441 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54249386 AAAATATTAA
* *
54249396 TTTTTTATTTCAAAAATTAATT
1 TTTTTTATTCCAAAAACTAATT
*
54249418 TTTTTTATTCCAAAACCT-ATT
1 TTTTTTATTCCAAAAACTAATT
54249439 TTT
1 TTT
54249442 AAAAGCATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTTTATTCCAAAAACTAATT
Found at i:54255819 original size:41 final size:40
Alignment explanation
Indices: 54255751--54255838 Score: 131
Period size: 41 Copynumber: 2.2 Consensus size: 40
54255741 GGTGCCAATT
54255751 TACTTCGGTTTAACCGATGAGACACTGGGTATCAATTTAC
1 TACTTCGGTTTAACCGATGAGACACTGGGTATCAATTTAC
** * *
54255791 TACTTCGGATTTATTCGATGAGATACTGGGTGTCAATTTAC
1 TACTTCGG-TTTAACCGATGAGACACTGGGTATCAATTTAC
54255832 TACTTCG
1 TACTTCG
54255839 AATTATCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 8 0.19
41 35 0.81
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (40 bp):
TACTTCGGTTTAACCGATGAGACACTGGGTATCAATTTAC
Found at i:54256902 original size:17 final size:17
Alignment explanation
Indices: 54256873--54256916 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
54256863 GAATTTGGAA
54256873 GAATTTT-TGAATTAGT
1 GAATTTTGTGAATTAGT
*
54256889 GAATTTTGTGAATTATT
1 GAATTTTGTGAATTAGT
54256906 GAATTTTGTGA
1 GAATTTTGTGA
54256917 TTTAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (17 bp):
GAATTTTGTGAATTAGT
Found at i:54257784 original size:46 final size:46
Alignment explanation
Indices: 54257667--54257988 Score: 538
Period size: 46 Copynumber: 7.0 Consensus size: 46
54257657 CATGGCAAAG
* * *
54257667 TGTGAAATGTAGGTATGATATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
54257713 TGTG-AAAGTATGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
54257758 TGTGAAAAGTAAGTATGGTGTTTCAGTGAAGAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
54257804 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
54257850 TGTGAAAAGTAAGTATGGTGTTTCAGTGAAGAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
54257896 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACTATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
54257942 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
54257988 T
1 T
54257989 ATAGCAATGT
Statistics
Matches: 259, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
45 41 0.16
46 218 0.84
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
Found at i:54260784 original size:20 final size:20
Alignment explanation
Indices: 54260761--54260807 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
54260751 GGGTTAAGAT
*
54260761 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
54260781 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
54260801 TGAGCTG
1 TGAGCTG
54260808 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:54265921 original size:11 final size:10
Alignment explanation
Indices: 54265885--54265923 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
54265875 AATAAAAAGG
54265885 AAAGAAAGAA
1 AAAGAAAGAA
*
54265895 AAGAGAAAGAG
1 AA-AGAAAGAA
54265906 AAAGAAAGAA
1 AAAGAAAGAA
54265916 AGAAGAAA
1 A-AAGAAA
54265924 CGCAAGGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:54265921 original size:17 final size:17
Alignment explanation
Indices: 54265878--54265919 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
54265868 AAAACGAAAT
*
54265878 AAAAAGGAA-AGAAAGA
1 AAAAAGAAAGAGAAAGA
*
54265894 AAAGAGAAAGAGAAAGA
1 AAAAAGAAAGAGAAAGA
54265911 AAGAAAGAA
1 AA-AAAGAA
54265920 GAAACGCAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 7 0.33
17 9 0.43
18 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAGAAAGA
Found at i:54266843 original size:37 final size:40
Alignment explanation
Indices: 54266801--54266931 Score: 117
Period size: 41 Copynumber: 3.3 Consensus size: 40
54266791 GTTGATTAGG
54266801 CACTAGGTGTCAA-TT-TACTTCGG-TTTAACCGATGAGA
1 CACTAGGTGTCAATTTATACTTCGGATTTAACCGATGAGA
* **
54266838 CACTAGGTATCAATTTACTACTTCGGATTTATTCGATGAGA
1 CACTAGGTGTCAATTTA-TACTTCGGATTTAACCGATGAGA
* * * * * * *
54266879 CACTCGGTGTTATTTTAGTACTTC-GAATTATCCAATGAGG
1 CACTAGGTGTCAATTTA-TACTTCGGATTTAACCGATGAGA
*
54266919 CACTGGGTGTCAA
1 CACTAGGTGTCAA
54266932 ACTGGTGTGT
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
37 12 0.16
38 2 0.03
40 30 0.40
41 31 0.41
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
CACTAGGTGTCAATTTATACTTCGGATTTAACCGATGAGA
Found at i:54276658 original size:20 final size:20
Alignment explanation
Indices: 54276633--54276670 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54276623 TTAATTTTAT
54276633 TTAATTTTCA-TTTTTTTAAA
1 TTAATTTT-AGTTTTTTTAAA
54276653 TTAATTTTAGTTTTTTTA
1 TTAATTTTAGTTTTTTTA
54276671 TTTTATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTAATTTTAGTTTTTTTAAA
Found at i:54278716 original size:17 final size:18
Alignment explanation
Indices: 54278696--54278734 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
54278686 ATGTTTTTTT
54278696 TCTTTTTC-ATTTTAATA
1 TCTTTTTCTATTTTAATA
54278713 TC-TTTTCTATTTTAATA
1 TCTTTTTCTATTTTAATA
54278730 -CTTTT
1 TCTTTT
54278735 CATATCCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTTTCTATTTTAATA
Found at i:54278718 original size:16 final size:15
Alignment explanation
Indices: 54278699--54278737 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
54278689 TTTTTTTTCT
54278699 TTTTCATTTTAATATC
1 TTTTCATTTTAATA-C
54278715 TTTTCTATTTTAATAC
1 TTTTC-ATTTTAATAC
54278731 TTTTCAT
1 TTTTCAT
54278738 ATCCATGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTCATTTTAATAC
Found at i:54284006 original size:21 final size:21
Alignment explanation
Indices: 54283916--54284017 Score: 82
Period size: 21 Copynumber: 5.0 Consensus size: 21
54283906 CAATTACGCA
54283916 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * ** *
54283935 AGCAGAAGATTATAAAAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * *
54283956 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTG
* *
54283977 AACAAAAGCTCGTAAGAGCTT
1 AACAGAAGCTCGTAAGAGCTG
* *
54283998 AACAGAAGCTTGAAAGAGCT
1 AACAGAAGCTCGTAAGAGCT
54284018 AAAGAAAAAG
Statistics
Matches: 63, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
19 8 0.13
20 2 0.03
21 53 0.84
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:54285500 original size:31 final size:33
Alignment explanation
Indices: 54285438--54285500 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
54285428 ATAACAATAT
*
54285438 AGTGACTTAAATAAAAAAATATTTGAATAGTTC
1 AGTGACTTAAATAAAAAAATATTCGAATAGTTC
* *
54285471 AGTGACTTAAAT-GAAAACT-TTCGAATAGTT
1 AGTGACTTAAATAAAAAAATATTCGAATAGTT
54285501 TAATGACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 10 0.37
32 5 0.19
33 12 0.44
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (33 bp):
AGTGACTTAAATAAAAAAATATTCGAATAGTTC
Found at i:54287737 original size:20 final size:21
Alignment explanation
Indices: 54287707--54287755 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
54287697 CATGTTTTTA
54287707 AAATG-ATTTGA-TTTATATC-
1 AAATGTATTTGAGTTTAT-TCT
54287726 AAATGTATTTGAGTTTATTCT
1 AAATGTATTTGAGTTTATTCT
54287747 AAAT-TATTT
1 AAATGTATTT
54287756 TAAAGAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
21 9 0.33
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (21 bp):
AAATGTATTTGAGTTTATTCT
Found at i:54289666 original size:21 final size:21
Alignment explanation
Indices: 54289620--54289677 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
54289610 CTAGGAGGGT
* *
54289620 AAAGTGTCAATACTTGATCTT
1 AAAGTATCAATACTTGATCTA
*
54289641 GAAGTATCAATACTT-ACTCTA
1 AAAGTATCAATACTTGA-TCTA
**
54289662 AAAGTATTTATACTTG
1 AAAGTATCAATACTTG
54289678 CCTTAAAGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (21 bp):
AAAGTATCAATACTTGATCTA
Found at i:54296881 original size:20 final size:20
Alignment explanation
Indices: 54296858--54296898 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
54296848 ACAAAAAGTG
54296858 GGAAAACAACAACAAAACAT
1 GGAAAACAACAACAAAACAT
*
54296878 GGAAAACAACATCAAAACAT
1 GGAAAACAACAACAAAACAT
54296898 G
1 G
54296899 AAGGGGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.20, G:0.12, T:0.07
Consensus pattern (20 bp):
GGAAAACAACAACAAAACAT
Found at i:54301208 original size:167 final size:162
Alignment explanation
Indices: 54300911--54301241 Score: 563
Period size: 167 Copynumber: 2.0 Consensus size: 162
54300901 ATGACATTAA
*
54300911 CAACCTCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
1 CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
* *
54300976 TATATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATTTGCAGAACCCAATGAT
66 TAGATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCAATGAT
*
54301041 CCACCCACCATTATGATCTCGCACTAATCCTT
131 CCACCCACCATTATGATCCCGCACTAATCCTT
54301073 CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
1 CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAA-C
* *
54301138 CATCCAAGATGCCCCAAAGCTCAACTTTCGTCACCGTGCAATTTCCTAAGTATCTGCAGAACCCA
65 C-T---AGATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCA
54301203 ATGATCCACCCACCATTATGATCCCGCACTAATCCTT
126 ATGATCCACCCACCATTATGATCCCGCACTAATCCTT
54301240 CA
1 CA
54301242 GCAGCAGTGA
Statistics
Matches: 158, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
162 62 0.39
163 2 0.01
164 1 0.01
167 93 0.59
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.27
Consensus pattern (162 bp):
CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
TAGATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCAATGAT
CCACCCACCATTATGATCCCGCACTAATCCTT
Found at i:54302844 original size:31 final size:31
Alignment explanation
Indices: 54302785--54302844 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
54302775 AGTCACAAAT
* * ***
54302785 GTTTTCGATCATTTCTATTTTGGTCACTCAC
1 GTTTTAGATCATTTCTAGTTTAACCACTCAC
54302816 GTTTTAGATCATTTCTAGTTTAACCACTC
1 GTTTTAGATCATTTCTAGTTTAACCACTC
54302845 TCCTTTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.47
Consensus pattern (31 bp):
GTTTTAGATCATTTCTAGTTTAACCACTCAC
Found at i:54308506 original size:39 final size:39
Alignment explanation
Indices: 54308454--54308534 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
54308444 AGTTTGATGA
* * * *
54308454 AATAATGCGAATACATAGTTGAGCGAGAGATATAGCAAT
1 AATAATGCAAATACATAGATAAGCAAGAGATATAGCAAT
*
54308493 AATAATGTAAATACATAGATAAGCAAGAGATATAGCAAT
1 AATAATGCAAATACATAGATAAGCAAGAGATATAGCAAT
54308532 AAT
1 AAT
54308535 TAAATTAGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (39 bp):
AATAATGCAAATACATAGATAAGCAAGAGATATAGCAAT
Found at i:54314700 original size:19 final size:19
Alignment explanation
Indices: 54314676--54314713 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54314666 GTCAAATCTA
54314676 TTTAATTTTATATTTAATT
1 TTTAATTTTATATTTAATT
54314695 TTTAATTTTATATTTAATT
1 TTTAATTTTATATTTAATT
54314714 ATTGTTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTTTATATTTAATT
Found at i:54321731 original size:15 final size:15
Alignment explanation
Indices: 54321711--54321758 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
54321701 TGGGTCTTTT
54321711 ACAAAAATAATACAA
1 ACAAAAATAATACAA
*
54321726 ACAAAAATAAAACAAA
1 ACAAAAATAATAC-AA
* *
54321742 ACTAAAATAATATAA
1 ACAAAAATAATACAA
54321757 AC
1 AC
54321759 TTTTTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (15 bp):
ACAAAAATAATACAA
Found at i:54328231 original size:17 final size:17
Alignment explanation
Indices: 54328201--54328234 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54328191 TTTGTCACCC
*
54328201 ACCATATGGGTCTCATT
1 ACCATATGGATCTCATT
*
54328218 ACCATTTGGATCTCATT
1 ACCATATGGATCTCATT
54328235 GGTTTTTGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (17 bp):
ACCATATGGATCTCATT
Found at i:54330086 original size:20 final size:19
Alignment explanation
Indices: 54330063--54330106 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
54330053 ATATGCTTTC
*
54330063 AAAATTAAATTTTGATATGA
1 AAAATCAAATTTTGATAT-A
* *
54330083 AAAATCAATTTTTGGTATA
1 AAAATCAAATTTTGATATA
54330102 AAAAT
1 AAAAT
54330107 ACCATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (19 bp):
AAAATCAAATTTTGATATA
Found at i:54332094 original size:13 final size:13
Alignment explanation
Indices: 54332078--54332107 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
54332068 AGTGCTGCAA
54332078 AAAAATGCTTTTG
1 AAAAATGCTTTTG
54332091 AAAAATGCTTTTG
1 AAAAATGCTTTTG
54332104 AAAA
1 AAAA
54332108 GCTTGGTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (13 bp):
AAAAATGCTTTTG
Found at i:54333705 original size:16 final size:18
Alignment explanation
Indices: 54333668--54333702 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54333658 AATACTAAGA
54333668 ATTT-TATTAAATTATAT
1 ATTTATATTAAATTATAT
54333685 ATTTATATTAAATTATAT
1 ATTTATATTAAATTATAT
54333703 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATTAAATTATAT
Found at i:54333714 original size:16 final size:17
Alignment explanation
Indices: 54333675--54333720 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
54333665 AGAATTTTAT
* *
54333675 TAAATTATATATTTATAT
1 TAAATTATAT-TTAATAA
54333693 TAAATTATATTTAATAA
1 TAAATTATATTTAATAA
54333710 T-AATTAT-TTTA
1 TAAATTATATTTA
54333721 GATTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 4 0.15
16 6 0.23
17 6 0.23
18 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTATATTTAATAA
Found at i:54333716 original size:26 final size:25
Alignment explanation
Indices: 54333687--54333743 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
54333677 AATTATATAT
54333687 TTATATTAAATTATATTTAATAATAA
1 TTATATTAAATTATATTTAATAAT-A
* * * *
54333713 TTATTTTAGATTATATTTTATAGTA
1 TTATATTAAATTATATTTAATAATA
54333738 TTATAT
1 TTATAT
54333744 ATTATGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TTATATTAAATTATATTTAATAATA
Found at i:54333748 original size:120 final size:119
Alignment explanation
Indices: 54333591--54333897 Score: 526
Period size: 120 Copynumber: 2.6 Consensus size: 119
54333581 CCACAAAATC
*
54333591 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCGTATAAGAATAT
1 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
54333656 TTAATACTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAAT
66 TTAATACTAAGAATTTTATTAAATTATAT-TTTATATTAAATTATATTTAATAAT
54333711 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
1 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-
* *
54333776 TTTAATATTAAGAATTTTATTAAATTATATTTTTTATTAAATTATATTTAATAAT
65 TTTAATACTAAGAATTTTATTAAATTATATTTTATATTAAATTATATTTAATAAT
* * * *
54333831 TATTATTTTAAATTATATTTTATACTATTATATATTATAATTTTAGTAAATTCATATAAGAAT-T
1 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
54333895 TTA
66 TTA
54333898 TTAAATTATA
Statistics
Matches: 179, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
118 4 0.02
120 146 0.82
121 29 0.16
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (119 bp):
AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
TTAATACTAAGAATTTTATTAAATTATATTTTATATTAAATTATATTTAATAAT
Found at i:54333805 original size:22 final size:21
Alignment explanation
Indices: 54333788--54333952 Score: 82
Period size: 22 Copynumber: 8.0 Consensus size: 21
54333778 TAATATTAAG
54333788 AATTTTATTAAATTATA-T-T
1 AATTTTATTAAATTATATTAT
54333807 --TTTTATTAAATTATATTTAAT
1 AATTTTATTAAATTATA-TT-AT
54333828 AATTATTATTTTAAATTATATT-T
1 AATT-TTA--TTAAATTATATTAT
* **
54333851 TATACTATT--A-TATATTAT
1 AATTTTATTAAATTATATTAT
* * *
54333869 AATTTTAGTAAATTCATATAAG
1 AATTTTATTAAATT-ATATTAT
*
54333891 AATTTTATTAAATTATAATAT
1 AATTTTATTAAATTATATTAT
* *
54333912 -ATTTAATTATAATTATGTT-T
1 AATTTTATTA-AATTATATTAT
* *
54333932 AAATATGATTAAATTAT-TTAT
1 -AATTTTATTAAATTATATTAT
54333953 TATTGATAAT
Statistics
Matches: 110, Mismatches: 18, Indels: 34
0.68 0.11 0.21
Matches are distributed among these distances:
17 21 0.19
18 7 0.06
19 1 0.01
20 14 0.13
21 20 0.18
22 27 0.25
23 5 0.05
24 3 0.03
25 2 0.02
26 10 0.09
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (21 bp):
AATTTTATTAAATTATATTAT
Found at i:54333810 original size:17 final size:17
Alignment explanation
Indices: 54333790--54333824 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
54333780 ATATTAAGAA
54333790 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
54333807 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
54333824 T
1 T
54333825 AATAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Done.