Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 172 of 172
Found at i:56364637 original size:132 final size:131
Alignment explanation
Indices: 56364486--56364903 Score: 469
Period size: 132 Copynumber: 3.2 Consensus size: 131
56364476 AGCTGTCACG
* * * * * * *
56364486 TCCTTCGCTTCCTTCGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTTCCATTGTAGT
1 TCCTTTGC-TCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTTCCATTGTAGC
* * * * *
56364551 ATCTTTTGCTTCCTTAGCTTTCTGTGCTGCGTAGTCTGTAAACTCGGAAGCCTTCTGCGCTGTCG
65 ATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCGGAAGCCTTCTGCGCTGTAG
56364616 TA
130 TA
**
56364618 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGC-TTTTCCAATTGCGG
1 TCCTTTGCT-CCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTTCC-ATTGTAG
* * * * * *
56364682 CATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTGTACTCAGAAGCTTTTTGGGCTGTA
64 CATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCGGAAGCCTTCTGCGCTGTA
56364747 GTA
129 GTA
* * * * * **
56364750 TCTCTTTCCTCCTTGGCTTTCTGAGCTGTATAATCCTTATATTCAGCCGCTTTCCCCATTGTAGC
1 TC-CTTTGCTCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTTCCATTGTAGC
* * * * *
56364815 ATCCTTTGCATCCTTAGTTTTCTGTGCTGCATAGCCTGTATACTCGGAAGCCTTCTGTGCAGTGG
65 ATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCGGAAGCCTTCTGCGCTGTAG
*
56364880 TG
130 TA
* *
56364882 TCTTTTGCGTCCTTAGCTTTCT
1 TCCTTTGC-TCCTTGGCTTTCT
56364904 GGGTAGCGTA
Statistics
Matches: 238, Mismatches: 43, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
131 11 0.05
132 217 0.91
133 10 0.04
ACGTcount: A:0.13, C:0.27, G:0.19, T:0.41
Consensus pattern (131 bp):
TCCTTTGCTCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTTCCATTGTAGCA
TCCTTTGCATCCTTAGCTTTCTGTGCTGCATAGTCTGTATACTCGGAAGCCTTCTGCGCTGTAGT
A
Found at i:56364822 original size:198 final size:199
Alignment explanation
Indices: 56364684--56365129 Score: 643
Period size: 198 Copynumber: 2.3 Consensus size: 199
56364674 AATTGCGGCA
* *
56364684 TCCTTTGCATCCTTAGCTTTCTGTGCT-GCATAATCTGTGTACTCAGAAGCTTTTTGGGCTGTAG
1 TCCTTTGCATCCTTAGCTTTCTG-GCTAGCATAATCTGTATACTCAGAAGCCTTTTGGGCTGTAG
* *
56364748 TATCTCTTTCCTCCTTGGCTTTCT-GAGCTGTATAATCCTTATATTCAGCCGCTTTCCCCATTGT
65 TATCTCTTGCCTCCTTGGCTTTCTCG-GCGGTATAATCCTTATATTCAGCCGCTTTCCCCATTGT
* *
56364812 AGCATCCTTTGCAT-CCTTAGTTTTCTGTGCTGCATAG-CCTGTATACTCGGAAGCCTTCTGTGC
129 AGCATCCTTTGC-TCCCTTAGTTTTCTGTGCTGCATAGTCCTGTATACTCAGAAGCCTTCTGTCC
56364875 AGTGGTG
193 AGTGGTG
* * * * *
56364882 TCTTTTGCGTCCTTAGCTTTCTGGGTAGCGTAATCTGTATACTCAGAAGCCTTTTGGGCTGTGGT
1 TCCTTTGCATCCTTAGCTTTCTGGCTAGCATAATCTGTATACTCAGAAGCCTTTTGGGCTGTAGT
*
56364947 ATCTCTTGCCTCCTTGGCTTTCTCGGCGGTATAATCCTTATATTCAGTCGCTTTCCCCATTGTAG
66 ATCTCTTGCCTCCTTGGCTTTCTCGGCGGTATAATCCTTATATTCAGCCGCTTTCCCCATTGTAG
* * * * *
56365012 CATCCTTTGCACCCTTAGTTTTCTGTGCTGCATAGT-CTGTATACTCGGAAGCCTTTTGTGCTGT
131 CATCCTTTGCTCCCTTAGTTTTCTGTGCTGCATAGTCCTGTATACTCAGAAGCCTTCTGTCCAGT
56365076 GGTG
196 GGTG
* *
56365080 TCTTTTGCGTCCTTAGCTTTCTGGGC-AGCATAATCTGTATACTCAGAAGC
1 TCCTTTGCATCCTTAGCTTTCT-GGCTAGCATAATCTGTATACTCAGAAGC
56365130 TTTACCTGTT
Statistics
Matches: 228, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
197 2 0.01
198 223 0.98
199 3 0.01
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (199 bp):
TCCTTTGCATCCTTAGCTTTCTGGCTAGCATAATCTGTATACTCAGAAGCCTTTTGGGCTGTAGT
ATCTCTTGCCTCCTTGGCTTTCTCGGCGGTATAATCCTTATATTCAGCCGCTTTCCCCATTGTAG
CATCCTTTGCTCCCTTAGTTTTCTGTGCTGCATAGTCCTGTATACTCAGAAGCCTTCTGTCCAGT
GGTG
Found at i:56364903 original size:66 final size:65
Alignment explanation
Indices: 56364687--56365129 Score: 247
Period size: 66 Copynumber: 6.7 Consensus size: 65
56364677 TGCGGCATCC
* * * * * *
56364687 TTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTGTACTCAGAAGCTTTTTGGGCTGTAGTATC
1 TTTGCATCCTTAGCTTTCTG-GCTGCATAATCTGTATACTCAGAAGCCTTTTGTGCAGTGGTGTC
56364752 T
65 T
* * * * ** *** *
56364753 CTTT-CCTCCTTGGCTTTCTGAGCTGTATAATCCT-TATATTCAGCCG-C-TTTCCCCA-TTGTA
1 -TTTGCATCCTTAGCTTTCTG-GCTGCATAAT-CTGTATACTCAGAAGCCTTTTGTGCAGTGGT-
*
56364813 GCATCC
62 G--TCT
* ** * *
56364819 TTTGCATCCTTAGTTTTCTGTGCTGCATAGCCTGTATACTCGGAAGCCTTCTGTGCAGTGGTGTC
1 TTTGCATCCTTAGCTTTCTG-GCTGCATAATCTGTATACTCAGAAGCCTTTTGTGCAGTGGTGTC
56364884 T
65 T
* * * * * *
56364885 TTTGCGTCCTTAGCTTTCTGGGTAGCGTAATCTGTATACTCAGAAGCCTTTTGGGCTGTGGTATC
1 TTTGCATCCTTAGCTTTCTGGCT-GCATAATCTGTATACTCAGAAGCCTTTTGTGCAGTGGTGTC
56364950 T
65 T
* * * * * * ** *** *
56364951 CTTGCCTCCTTGGCTTTCTCGGCGGTATAATCCT-TATATTCAGTCG-C-TTTCCCCA-TTGTAG
1 TTTGCATCCTTAGCTTTCT-GGCTGCATAAT-CTGTATACTCAGAAGCCTTTTGTGCAGTGGT-G
*
56365012 CATCC
63 --TCT
* * * * *
56365017 TTTGCACCCTTAGTTTTCTGTGCTGCATAGTCTGTATACTCGGAAGCCTTTTGTGCTGTGGTGTC
1 TTTGCATCCTTAGCTTTCTG-GCTGCATAATCTGTATACTCAGAAGCCTTTTGTGCAGTGGTGTC
56365082 T
65 T
* *
56365083 TTTGCGTCCTTAGCTTTCTGGGCAGCATAATCTGTATACTCAGAAGC
1 TTTGCATCCTTAGCTTTCT-GGCTGCATAATCTGTATACTCAGAAGC
56365130 TTTACCTGTT
Statistics
Matches: 270, Mismatches: 85, Indels: 43
0.68 0.21 0.11
Matches are distributed among these distances:
63 6 0.02
64 8 0.03
65 11 0.04
66 217 0.80
67 12 0.04
68 10 0.04
69 6 0.02
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (65 bp):
TTTGCATCCTTAGCTTTCTGGCTGCATAATCTGTATACTCAGAAGCCTTTTGTGCAGTGGTGTCT
Found at i:56383223 original size:33 final size:33
Alignment explanation
Indices: 56383181--56383249 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
56383171 TTGCTTTAAG
*
56383181 AATGTTAATGTAGGTATTGATTAGTTATGTTGT
1 AATGTTAATGCAGGTATTGATTAGTTATGTTGT
56383214 AATGTTAATGCAGGTATTGATTAGTTATGTTGT
1 AATGTTAATGCAGGTATTGATTAGTTATGTTGT
56383247 AAT
1 AAT
56383250 AGCTTATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.46
Consensus pattern (33 bp):
AATGTTAATGCAGGTATTGATTAGTTATGTTGT
Found at i:56384628 original size:31 final size:31
Alignment explanation
Indices: 56384593--56384656 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
56384583 TTCATCATAG
56384593 AGTAAATTACACCCAAGGTCACTCAAATATT
1 AGTAAATTACACCCAAGGTCACTCAAATATT
* * *
56384624 AGTAAATTGCGCCCAAGGTCACTCAACTATT
1 AGTAAATTACACCCAAGGTCACTCAAATATT
56384655 AG
1 AG
56384657 CAAGTTGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (31 bp):
AGTAAATTACACCCAAGGTCACTCAAATATT
Found at i:56398395 original size:32 final size:32
Alignment explanation
Indices: 56398343--56398423 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 32
56398333 AAAAGAAATT
* *
56398343 AATAAAATTAAATTTTAAAAATTAAAAA-AATA
1 AATAAAAATAAATTTTAAAAAATAAAAATAA-A
56398375 AA-AAAAATAAATTTTAAAAAATAAAAATAAA
1 AATAAAAATAAATTTTAAAAAATAAAAATAAA
*
56398406 AATAAAAA-GAATTTTAAA
1 AATAAAAATAAATTTTAAA
56398424 TTTTATTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
31 35 0.80
32 9 0.20
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (32 bp):
AATAAAAATAAATTTTAAAAAATAAAAATAAA
Found at i:56408647 original size:46 final size:47
Alignment explanation
Indices: 56408567--56408689 Score: 142
Period size: 46 Copynumber: 2.6 Consensus size: 47
56408557 GTAGACGATG
* * * *
56408567 CATGTCCCAGACGTATCTTATACTGGCTTACGTCTCGAGGCCGA-AA
1 CATGTCCCAGACATATCTTACACTAGCTTACGTCTCAAGGCCGATAA
* **
56408613 CATGTCCCAGACATATCTTACACTAGCATT-CGTCTCAATGCCGATGC
1 CATGTCCCAGACATATCTTACACTAGC-TTACGTCTCAAGGCCGATAA
*
56408660 CATGTCCCAGACATGGTCTTACACTAGCTT
1 CATGTCCCAGACAT-ATCTTACACTAGCTT
56408690 TCAAAATGTG
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 36 0.55
47 18 0.27
48 12 0.18
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (47 bp):
CATGTCCCAGACATATCTTACACTAGCTTACGTCTCAAGGCCGATAA
Found at i:56410274 original size:7 final size:7
Alignment explanation
Indices: 56410262--56410294 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
56410252 TCAACTAAAT
56410262 AAATTCC
1 AAATTCC
56410269 AAATTCC
1 AAATTCC
56410276 AAATTCC
1 AAATTCC
56410283 AAATTCC
1 AAATTCC
56410290 AAATT
1 AAATT
56410295 TATTTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATTCC
Found at i:56419267 original size:10 final size:10
Alignment explanation
Indices: 56419254--56419303 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
56419244 TAATTACCCC
56419254 CTCTCTCTTT
1 CTCTCTCTTT
56419264 CTCTCTC--T
1 CTCTCTCTTT
**
56419272 CTCTCTCTCC
1 CTCTCTCTTT
56419282 CTCTCTCTTT
1 CTCTCTCTTT
*
56419292 CTTTCTCTTT
1 CTCTCTCTTT
56419302 CT
1 CT
56419304 TTGGATTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 8 0.24
10 26 0.76
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (10 bp):
CTCTCTCTTT
Found at i:56419270 original size:4 final size:4
Alignment explanation
Indices: 56419254--56419299 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
56419244 TAATTACCCC
* * * *
56419254 CTCT CTCT TTCT CTCT CTCT CTCT CTCC CTCT CTCT TTCT TTCT CT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CT
56419300 TTCTTTGGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (4 bp):
CTCT
Found at i:56427742 original size:20 final size:20
Alignment explanation
Indices: 56427697--56427748 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
56427687 ATTTTTACAA
56427697 TTTAATTTTTTAATAAAAAT
1 TTTAATTTTTTAATAAAAAT
** **
56427717 GATAATTTTTTAATAAGTAT
1 TTTAATTTTTTAATAAAAAT
56427737 TTTAATTATTTT
1 TTTAATT-TTTT
56427749 TTATTAAGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTAATTTTTTAATAAAAAT
Found at i:56432668 original size:35 final size:35
Alignment explanation
Indices: 56432629--56432724 Score: 149
Period size: 35 Copynumber: 2.8 Consensus size: 35
56432619 CGTTCGTGAC
* *
56432629 CCCTTTGAGAATTGGAGCTAGTGACGTGTATTCAA
1 CCCTTTGAGAATTAGAGCTAGTGACATGTATTCAA
*
56432664 CCCTTTGAGAATTAGAGCTAGTGATATGTATTCAA
1 CCCTTTGAGAATTAGAGCTAGTGACATGTATTCAA
*
56432699 CTCTTTGAGAATTAGAG-TAGTGACAT
1 CCCTTTGAGAATTAGAGCTAGTGACAT
56432725 ATCTAGAGGG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 8 0.14
35 48 0.86
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (35 bp):
CCCTTTGAGAATTAGAGCTAGTGACATGTATTCAA
Found at i:56439056 original size:22 final size:21
Alignment explanation
Indices: 56439031--56439071 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56439021 CATAAGACAA
*
56439031 AAGAAGACTCAATAACAAATAT
1 AAGAAGAC-CAAAAACAAATAT
*
56439053 AAGAATACCAAAAACAAAT
1 AAGAAGACCAAAAACAAAT
56439072 TAAATTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (21 bp):
AAGAAGACCAAAAACAAATAT
Found at i:56445115 original size:30 final size:30
Alignment explanation
Indices: 56445048--56445124 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
56445038 GGGAATCTTG
* * * * *
56445048 ACCTATCTAATACATTAATGATCTCAAGAA
1 ACCTATCTAATACATGAATAAGCCCAACAA
*
56445078 ACTTATCTAATACATGAATAAGCCCAACAA
1 ACCTATCTAATACATGAATAAGCCCAACAA
*
56445108 GCCTATCTAATACATGA
1 ACCTATCTAATACATGA
56445125 TGGATAGCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (30 bp):
ACCTATCTAATACATGAATAAGCCCAACAA
Found at i:56448445 original size:88 final size:88
Alignment explanation
Indices: 56448285--56448455 Score: 229
Period size: 88 Copynumber: 1.9 Consensus size: 88
56448275 GAAGATAACA
* * *
56448285 AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAACCTTGTCTCCCTGAATATG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAATATG
* *
56448350 TAGTAGAGTAGGAT-GAAGTTACT
66 CAATAGAGT-GGATCGAAGTTACT
* ** *
56448373 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAGTCTTATCTCTCTGAAGT-T
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAA-TAT
56448437 GCAATAGAGTGGATCGAAG
65 GCAATAGAGTGGATCGAAG
56448456 CAACAATTCC
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
87 4 0.06
88 67 0.93
89 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (88 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAATATG
CAATAGAGTGGATCGAAGTTACT
Found at i:56448456 original size:44 final size:44
Alignment explanation
Indices: 56448282--56448445 Score: 170
Period size: 44 Copynumber: 3.7 Consensus size: 44
56448272 ACTGAAGATA
* * *
56448282 ACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGCT
* * * * * *
56448326 ATAAACCTTGTCTCCCTGAA-TATGTAGTAGAGTAGGA-TGAAGTT
1 ACAAATCTTATCTCCCTGAAGT-TGCAGTAGAGCA-GATTGAAGCT
* *
56448370 ACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGCT
* * *
56448414 ACAAGTCTTATCTCTCTGAAGTTGCAATAGAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAG
56448446 TGGATCGAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
43 3 0.03
44 88 0.94
45 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGCT
Found at i:56448477 original size:88 final size:88
Alignment explanation
Indices: 56448285--56448487 Score: 209
Period size: 88 Copynumber: 2.3 Consensus size: 88
56448275 GAAGATAACA
* * *
56448285 AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAACCTTGTCTCCCTGAATATG
1 AATCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAATATG
* * **
56448350 TAGTAGAGTAGGATGAAGTTACT
66 CAATAGAGTAGGATGAAGCAACT
* * * ** *
56448373 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAGTCTTATCTCTCTGAAGT-T
1 AATCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAA-TAT
56448437 GCAATAGAGT-GGATCGAAGCAAC-
65 GCAATAGAGTAGGAT-GAAGCAACT
56448460 AATTCCTATAC-CTCTGAA-TATGCAGTGG
1 AA-TCCTAT-CTCTCTGAAGT-TGCAGTGG
56448488 TTTGGAATGG
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
87 7 0.07
88 88 0.91
89 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (88 bp):
AATCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAATATG
CAATAGAGTAGGATGAAGCAACT
Found at i:56449851 original size:4 final size:4
Alignment explanation
Indices: 56449832--56449933 Score: 73
Period size: 4 Copynumber: 25.5 Consensus size: 4
56449822 CTTTAATCAT
* * * * *
56449832 TTTA TTTA CTTC TTTA TTTA TTCA CTTGA -TTA TTTA TTTA TTTA CTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
* * ** * *
56449880 TTTA TTTA TTCA CTTGA -TTA TTTA TTCC TTTA TTTG TTTG TTTA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
56449928 TTTA TT
1 TTTA TT
56449934 CACATATCAT
Statistics
Matches: 76, Mismatches: 18, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
3 4 0.05
4 66 0.87
5 6 0.08
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:56449869 original size:20 final size:20
Alignment explanation
Indices: 56449844--56449905 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
56449834 TATTTACTTC
56449844 TTTATTTATTCACTTGATTA
1 TTTATTTATTCACTTGATTA
*
56449864 TTTATTTATTTAC----TTA
1 TTTATTTATTCACTTGATTA
56449880 TTTATTTATTCACTTGATTA
1 TTTATTTATTCACTTGATTA
56449900 TTTATT
1 TTTATT
56449906 CCTTTATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 15 0.42
20 21 0.58
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTATTTATTCACTTGATTA
Found at i:56449872 original size:36 final size:36
Alignment explanation
Indices: 56449832--56449905 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
56449822 CTTTAATCAT
*
56449832 TTTATTTACTTCTTTATTTATTCACTTGATTATTTA
1 TTTATTTACTTATTTATTTATTCACTTGATTATTTA
56449868 TTTATTTACTTATTTATTTATTCACTTGATTATTTA
1 TTTATTTACTTATTTATTTATTCACTTGATTATTTA
56449904 TT
1 TT
56449906 CCTTTATTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.65
Consensus pattern (36 bp):
TTTATTTACTTATTTATTTATTCACTTGATTATTTA
Found at i:56449924 original size:36 final size:36
Alignment explanation
Indices: 56449835--56449925 Score: 128
Period size: 36 Copynumber: 2.5 Consensus size: 36
56449825 TAATCATTTT
* *
56449835 ATTTACTTCTTTATTTATTCACTTGATTATTTATTT
1 ATTTACTTATTTATTTATTCACTTGATTATTTATTC
56449871 ATTTACTTATTTATTTATTCACTTGATTATTTATTC
1 ATTTACTTATTTATTTATTCACTTGATTATTTATTC
* * * *
56449907 CTTTATTTGTTTGTTTATT
1 ATTTACTTATTTATTTATT
56449926 TATTTATTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.21, C:0.10, G:0.04, T:0.65
Consensus pattern (36 bp):
ATTTACTTATTTATTTATTCACTTGATTATTTATTC
Found at i:56450026 original size:3 final size:3
Alignment explanation
Indices: 56450018--56450043 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56450008 TGTTTGTGCC
56450018 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
56450044 CAATAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:56450160 original size:4 final size:4
Alignment explanation
Indices: 56450151--56450189 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
56450141 TTTTTCTTAA
* *
56450151 TATT TATT TATT GTATC TATT TATT TATT CATT TATT TA
1 TATT TATT TATT -TATT TATT TATT TATT TATT TATT TA
56450190 CACATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:56450212 original size:6 final size:6
Alignment explanation
Indices: 56450201--56450234 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
56450191 ACATTTTTTA
*
56450201 TTATTC TTATTC TTATTC TTATTC TTATTG TTAT
1 TTATTC TTATTC TTATTC TTATTC TTATTC TTAT
56450235 ATTTTTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.68
Consensus pattern (6 bp):
TTATTC
Found at i:56450317 original size:25 final size:25
Alignment explanation
Indices: 56450284--56450392 Score: 218
Period size: 25 Copynumber: 4.4 Consensus size: 25
56450274 ATTAAAATTT
56450284 TTTTACTTAACATTATGAATATCTA
1 TTTTACTTAACATTATGAATATCTA
56450309 TTTTACTTAACATTATGAATATCTA
1 TTTTACTTAACATTATGAATATCTA
56450334 TTTTACTTAACATTATGAATATCTA
1 TTTTACTTAACATTATGAATATCTA
56450359 TTTTACTTAACATTATGAATATCTA
1 TTTTACTTAACATTATGAATATCTA
56450384 TTTTACTTA
1 TTTTACTTA
56450393 CTTATTTATT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 84 1.00
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTTACTTAACATTATGAATATCTA
Found at i:56452054 original size:46 final size:46
Alignment explanation
Indices: 56452002--56452448 Score: 824
Period size: 46 Copynumber: 9.7 Consensus size: 46
56451992 TGTCATAGTG
* * * *
56452002 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
56452048 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
56452094 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
56452140 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
56452186 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
56452232 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
56452278 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
56452324 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
56452370 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATAGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
56452416 TCTTTCAACCATAGTCTTACACATTTCATATCA
1 TCTTTCAACCATGGTCTTACACATTTCATATCA
56452449 AAAAGCACAC
Statistics
Matches: 394, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
45 4 0.01
46 390 0.99
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
Found at i:56452549 original size:54 final size:54
Alignment explanation
Indices: 56452483--56452618 Score: 272
Period size: 54 Copynumber: 2.5 Consensus size: 54
56452473 TCCTTACAGT
56452483 GGGATTACCAGTCCAGGCTAAATCCCCTATAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTATAATATAAACTCATAGAGTATTGTC
56452537 GGGATTACCAGTCCAGGCTAAATCCCCTATAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTATAATATAAACTCATAGAGTATTGTC
56452591 GGGATTACCAGTCCAGGCTAAATCCCCT
1 GGGATTACCAGTCCAGGCTAAATCCCCT
56452619 GCAACAACAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (54 bp):
GGGATTACCAGTCCAGGCTAAATCCCCTATAATATAAACTCATAGAGTATTGTC
Found at i:56453371 original size:21 final size:21
Alignment explanation
Indices: 56453323--56453371 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
56453313 AAATAATAAT
* *
56453323 ATATAAGTGACAATAATGAAA
1 ATATGAGTGACAAAAATGAAA
56453344 ATAATGAGT-ACAAAAATGAATA
1 AT-ATGAGTGACAAAAATGAA-A
56453366 ATATGA
1 ATATGA
56453372 CATACGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.14, T:0.24
Consensus pattern (21 bp):
ATATGAGTGACAAAAATGAAA
Found at i:56453598 original size:27 final size:27
Alignment explanation
Indices: 56453559--56453619 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
56453549 AATTTTGTGC
* * *
56453559 AAGA-TATATATATATAATATGATGTT
1 AAGAGTATACATATAAAATATAATGTT
56453585 AAGAGTATACATATAAAATATAATGTT
1 AAGAGTATACATATAAAATATAATGTT
*
56453612 AAAAGTAT
1 AAGAGTAT
56453620 GTATGCATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (27 bp):
AAGAGTATACATATAAAATATAATGTT
Found at i:56454134 original size:40 final size:37
Alignment explanation
Indices: 56454052--56454130 Score: 124
Period size: 40 Copynumber: 2.1 Consensus size: 37
56454042 ACAAATATAT
56454052 ATAATAATAATAATAAATATAACAACAATATTGAAAATAC
1 ATAATAATAATAATAAATATAACAAC---ATTGAAAATAC
56454092 ATAATAATAATAATAAATATAACAAC-TTGAAAATAC
1 ATAATAATAATAATAAATATAACAACATTGAAAATAC
56454128 ATA
1 ATA
56454131 CATATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 13 0.33
40 26 0.67
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (37 bp):
ATAATAATAATAATAAATATAACAACATTGAAAATAC
Found at i:56454205 original size:18 final size:17
Alignment explanation
Indices: 56454184--56454217 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
56454174 ATACATTTAA
56454184 TATAACAAATATAAATAT
1 TATAACAAATA-AAATAT
56454202 TATAACAAATAAAATA
1 TATAACAAATAAAATA
56454218 CAGAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
TATAACAAATAAAATAT
Found at i:56456574 original size:55 final size:56
Alignment explanation
Indices: 56456493--56456667 Score: 273
Period size: 57 Copynumber: 3.1 Consensus size: 56
56456483 TAAAAGCAGA
* * *
56456493 TTTTGAAAAATA-GAAATTAAAGGGCTCAACTCACCTTTCGCAATATGAGTTGA-T
1 TTTTGAAAAACATGAATTTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATT
*
56456547 TTTTGAAAAACATGAATTTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 TTTTGAAAAACATGAATTTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
* *
56456604 TTTTGAAAAACATAAATTGAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 TTTTGAAAAACATGAATTTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATT
56456660 TTTTGAAA
1 TTTTGAAA
56456668 GGTAGAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
54 11 0.10
55 38 0.34
56 10 0.09
57 52 0.47
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (56 bp):
TTTTGAAAAACATGAATTTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATT
Found at i:56456816 original size:170 final size:167
Alignment explanation
Indices: 56456604--56456922 Score: 451
Period size: 167 Copynumber: 1.9 Consensus size: 167
56456594 GAGTTGATTT
* * * *
56456604 TTTTGAAAAACATAAATTGAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAG
1 TTTTGAAAAACAGAAATTGAAAAGCCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA
* * * * * * *
56456669 GTAGAAATTGAAAAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATCTCTCG
65 ATAGAAACTG--AAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCA
* * *
56456734 CAATGTGAGTTGATTTTTTGAAACTTGATTTGAAAAGTAGA
128 CAATATGAATTGA-CTTTTGAAACTTGATTTGAAAAGTAGA
56456775 TTTTGAAAAACAGAAATT-AAAAGCCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 TTTTGAAAAACAGAAATTGAAAAGCCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
* *
56456839 TAGAAACTGAAAACAGAAATTGAAAATACTTCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAA
66 TAGAAACTGAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAA
56456904 TATGAATTGACTTTTGAAA
131 TATGAATTGACTTTTGAAA
56456923 AACAGAAATT
Statistics
Matches: 132, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
166 8 0.06
167 57 0.43
169 17 0.13
170 33 0.25
171 17 0.13
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (167 bp):
TTTTGAAAAACAGAAATTGAAAAGCCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
TAGAAACTGAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAA
TATGAATTGACTTTTGAAACTTGATTTGAAAAGTAGA
Found at i:56456862 original size:81 final size:83
Alignment explanation
Indices: 56456606--56456864 Score: 213
Period size: 81 Copynumber: 3.1 Consensus size: 83
56456596 GTTGATTTTT
* * * **
56456606 TTGAAAAACATAAATTGAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGGT
1 TTGAAAAACAGAAATTCAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAT
*
56456671 AGAAATTGAAAAAACAAAAA
66 AGAAATTG--AAAACAGAAA
* ** *** * *
56456691 TTGAAATTACCTCAG-CGTGTCCTGAGGCTCAACTCATCTCTCGCAATGTGAGTTGATTTTTTG-
1 TTGAAA--A--ACAGAAAT-TCAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA
* * * * **
56456754 AAACTTG-ATTTGAAAAGTAGATT
61 AAAATAGAAATTGAAAA-CAGAAA
*
56456777 TTGAAAAACAGAAATT-AAAAGCCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAT
1 TTGAAAAACAGAAATTCAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAT
*
56456840 AGAAACTGAAAACAGAAA
66 AGAAATTGAAAACAGAAA
56456858 TTGAAAA
1 TTGAAAA
56456865 TACTTCAGCG
Statistics
Matches: 130, Mismatches: 35, Indels: 22
0.70 0.19 0.12
Matches are distributed among these distances:
80 6 0.05
81 44 0.34
82 11 0.08
83 1 0.01
84 1 0.01
85 10 0.08
86 8 0.06
87 5 0.04
88 5 0.04
89 39 0.30
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (83 bp):
TTGAAAAACAGAAATTCAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAT
AGAAATTGAAAACAGAAA
Found at i:56456905 original size:86 final size:85
Alignment explanation
Indices: 56456627--56456936 Score: 260
Period size: 86 Copynumber: 3.7 Consensus size: 85
56456617 AAATTGAAAG
** *
56456627 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGGTAGAAATTGAAAAAACAAAAAT
1 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTG--AAAACAGAAAT
* *
56456692 TGAAATTACCTCAGCGTGTCCTGA
64 TGAAAATA-CTCAGCGTG-CCAGA
* * * * * * **
56456716 GGCTCAACTCATCTCTCGCAATGTGAGTTGATTTTTTG-AAACTTG-ATTTGAAAAGTAGATTTT
1 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTGAAAA-CAGAAATT
** ** *
56456779 GAAAA-A--CAGAAAT-TAAAA
65 GAAAATACTCAG-CGTGCCAGA
* *
56456797 GCCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAACTGAAAACAGAAATTG
1 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTGAAAACAGAAATTG
*
56456861 AAAATACTTCAGCGTGCCCCGA
66 AAAATAC-TCAGCGTG-CCAGA
* * * *
56456883 GGCTCAACTCACCTCTCACAATATGAATTGA-CTTTTGAAAAACAGAAATT-AAAA
1 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTGAAAA
56456937 GGCTCAACTC
Statistics
Matches: 172, Mismatches: 39, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
80 6 0.03
81 44 0.26
82 11 0.06
83 1 0.01
84 1 0.01
85 12 0.07
86 53 0.31
87 4 0.02
88 4 0.02
89 36 0.21
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (85 bp):
GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTGAAAACAGAAATTG
AAAATACTCAGCGTGCCAGA
Found at i:56456945 original size:54 final size:54
Alignment explanation
Indices: 56456882--56456989 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
56456872 GCGTGCCCCG
56456882 AGGCTCAACTCACCTCTCACAATATGAATTGACTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCACAATATGAATTGACTTTTGAAAAACAGAAATTAAA
* * *
56456936 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCACAATATGAATTGACTTTTGAAAAACAGAAATTAAA
56456990 GACAGAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (54 bp):
AGGCTCAACTCACCTCTCACAATATGAATTGACTTTTGAAAAACAGAAATTAAA
Found at i:56456962 original size:140 final size:140
Alignment explanation
Indices: 56456775--56457218 Score: 617
Period size: 140 Copynumber: 3.1 Consensus size: 140
56456765 GAAAAGTAGA
*
56456775 TTTTGAAAAACAGAAATTAAAAGCCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAT
* * * * *
56456840 AGAAACTGAAAACAGAAATTGAAAATACTTCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAAT
66 AGAAACTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
* *
56456905 ATGAATTGAC
131 ATGAGTTGAT
*
56456915 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAT
* * ** *
56456980 AGAAA-TTAAAGACAGAAATTGAAATTACCTCAGCGTATATTGAGGCTCAACTCACCTCTCGTAA
66 AGAAACTGAAA-ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
56457044 TATGAGTTGAT
130 TATGAGTTGAT
* *
56457055 TTTTGACAAACAGAAATTAAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAGAA
1 TTTTGAAAAACAGAAATT-AAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
*
56457119 TAAAAACACAATTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCT
65 T-AGAA-AC----TG-AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCT
56457184 CTCGCAATATGAGTCT-AT
123 CTCGCAATATGAGT-TGAT
56457202 TTTTG-AAAACAGAAATT
1 TTTTGAAAAACAGAAATT
56457219 TGAAAAATAG
Statistics
Matches: 269, Mismatches: 24, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
139 4 0.01
140 147 0.55
141 38 0.14
142 1 0.00
146 11 0.04
147 64 0.24
148 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (140 bp):
TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAT
AGAAACTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGAT
Found at i:56457250 original size:87 final size:88
Alignment explanation
Indices: 56457077--56457304 Score: 334
Period size: 87 Copynumber: 2.6 Consensus size: 88
56457067 GAAATTAAAA
* * *
56457077 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAGAATAAAAACACAATTTGAAAAACAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT--TGAA-AAACAGA-AATTTGAAAAACAG
*
56457142 AAATTGAAATTACCTCAGCGTGTCCTG
62 AAATTGAAAATACCTCAGCGTGTCCTG
*
56457169 AGGCTCAACTCACCTCTCGCAATATGAGTCT-ATTTTTG-AAAACAGAAATTTGAAAAATAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGT-TGATTTTTGAAAAACAGAAATTTGAAAAACAGAAA
**
56457232 TTGAAAATACCTCAGCGTGTGTTG
65 TTGAAAATACCTCAGCGTGTCCTG
56457256 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
56457305 CTAAAACATC
Statistics
Matches: 126, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
86 1 0.01
87 73 0.58
88 15 0.12
89 1 0.01
90 1 0.01
92 34 0.27
93 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (88 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTGAAAAACAGAAAT
TGAAAATACCTCAGCGTGTCCTG
Found at i:56469414 original size:18 final size:17
Alignment explanation
Indices: 56469393--56469426 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
56469383 ATACATTTAA
56469393 TATAACAAATATAAATAT
1 TATAACAAATA-AAATAT
56469411 TATAACAAATAAAATA
1 TATAACAAATAAAATA
56469427 CAAAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
TATAACAAATAAAATAT
Found at i:56472574 original size:27 final size:26
Alignment explanation
Indices: 56472544--56472596 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
56472534 TATATACTAA
*
56472544 TAAAATAATAATAATATAATATCTTAT
1 TAAAATAATAATAAAATAATAT-TTAT
**
56472571 TAAAATTTTAATAAAATAATATTTAT
1 TAAAATAATAATAAAATAATATTTAT
56472597 CTAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAAATAATAATAAAATAATATTTAT
Found at i:56473164 original size:25 final size:25
Alignment explanation
Indices: 56473135--56473188 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
56473125 ACAAGATGCA
*
56473135 CATATATAAATATCACCACCTAATG
1 CATATACAAATATCACCACCTAATG
*
56473160 CATATGCAAATATCACCACCTAATG
1 CATATACAAATATCACCACCTAATG
56473185 CATA
1 CATA
56473189 GGCATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.26
Consensus pattern (25 bp):
CATATACAAATATCACCACCTAATG
Found at i:56473370 original size:23 final size:23
Alignment explanation
Indices: 56473339--56473383 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
56473329 CATTTATTCA
*
56473339 TTATTTATACATA-AAACACCAAT
1 TTATATATA-ATACAAACACCAAT
*
56473362 TTATATATAATACTAACACCAA
1 TTATATATAATACAAACACCAA
56473384 ACACATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (23 bp):
TTATATATAATACAAACACCAAT
Done.