Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 104 of 213
Found at i:29440247 original size:18 final size:18
Alignment explanation
Indices: 29440220--29440333 Score: 125
Period size: 18 Copynumber: 6.7 Consensus size: 18
29440210 TTAGGTTAGG
29440220 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
29440238 GTTAGAGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
29440256 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
* **
29440274 ATTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
29440285 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
29440303 GTTAGGGTTTTTAAATAA
1 GTTAGGGTTTTTAATTAA
*
29440321 ATTAGGGTTTTTA
1 GTTAGGGTTTTTA
29440334 TTACATCAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
11 3 0.04
12 2 0.03
13 1 0.01
14 2 0.03
15 2 0.03
16 1 0.01
17 2 0.03
18 66 0.84
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:29440289 original size:65 final size:65
Alignment explanation
Indices: 29440207--29440333 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 65
29440197 AAATTATGTA
* *
29440207 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGAGTTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGAGTTTTTAAATAAATTAGGGTTTTTAATT
*
29440272 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAAATAAATTAGGGTTTTTA
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGAGTTTTTAAATAAATTAGGGTTTTTA
29440334 TTACATCAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (65 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGAGTTTTTAAATAAATTAGGGTTTTTAATT
Found at i:29440381 original size:25 final size:26
Alignment explanation
Indices: 29440329--29440392 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
29440319 AAATTAGGGT
*
29440329 TTTTATTACATCAAATTGAACTTCTA
1 TTTTATTACATCAAATTAAACTTCTA
* *
29440355 TTTTATTATATTAAA-TAAACTTCTA
1 TTTTATTACATCAAATTAAACTTCTA
29440380 TTTTATTACATCA
1 TTTTATTACATCA
29440393 GATAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 20 0.61
26 13 0.39
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTATTACATCAAATTAAACTTCTA
Found at i:29440828 original size:18 final size:18
Alignment explanation
Indices: 29440801--29440835 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29440791 CAGAAAAGGA
* *
29440801 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
29440819 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
29440836 AAACACACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:29441497 original size:7 final size:7
Alignment explanation
Indices: 29441487--29441511 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29441477 TTATATACAT
29441487 AATACTA
1 AATACTA
29441494 AATACTA
1 AATACTA
29441501 AATACTA
1 AATACTA
29441508 AATA
1 AATA
29441512 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:29442713 original size:51 final size:51
Alignment explanation
Indices: 29442656--29442769 Score: 194
Period size: 51 Copynumber: 2.3 Consensus size: 51
29442646 TTTAAAAAAT
*
29442656 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
* *
29442707 GGAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
29442758 GAAATTGA-AGGA
1 GAAATTGAGAGGA
29442770 TTAGAGAGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 4 0.07
51 55 0.93
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:29458472 original size:13 final size:13
Alignment explanation
Indices: 29458454--29458478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29458444 TAATGGTATA
29458454 TTGAATCCATGAC
1 TTGAATCCATGAC
29458467 TTGAATCCATGA
1 TTGAATCCATGA
29458479 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:29459059 original size:27 final size:27
Alignment explanation
Indices: 29459024--29459202 Score: 184
Period size: 27 Copynumber: 6.6 Consensus size: 27
29459014 TTAAATTGTA
29459024 TAGCACTAAGTGTGCGATATGACTATG
1 TAGCACTAAGTGTGCGATATGACTATG
* * *
29459051 TTGCACTAAGTGTGCGAAATGAATATG
1 TAGCACTAAGTGTGCGATATGACTATG
*
29459078 -ATGCACTAAGTGTGCGA-ATTGACCATG
1 TA-GCACTAAGTGTGCGATA-TGACTATG
** *
29459105 CGGCACTAAGTGTGCGAGTTTGACTATG
1 TAGCACTAAGTGTGCGA-TATGACTATG
* * *
29459133 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGATATGACTATG
* *
29459160 TAGCACTAAGTGTGCGAGT-TGATTATA
1 TAGCACTAAGTGTGCGA-TATGACTATG
*
29459187 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
29459203 GGCTCAATAT
Statistics
Matches: 130, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.01
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGATATGACTATG
Found at i:29459140 original size:82 final size:81
Alignment explanation
Indices: 29459026--29459181 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
29459016 AAATTGTATA
* *
29459026 GCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29459090 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
29459107 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29459172 TGCGAGTTGA
65 TGCGAATTGA
29459182 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29459193 original size:82 final size:81
Alignment explanation
Indices: 29459022--29459202 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
29459012 GATTAAATTG
* *
29459022 TATAGCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TATAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29459087 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
*** * ** *
29459103 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TATAGCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29459167 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
*
29459185 TATAGCACTGAGTGTGCG
1 TATAGCACTAAGTGTGCG
29459203 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 65 0.79
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TATAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29466371 original size:13 final size:13
Alignment explanation
Indices: 29466353--29466377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29466343 TAATGGTATA
29466353 TTGAATCCATGAC
1 TTGAATCCATGAC
29466366 TTGAATCCATGA
1 TTGAATCCATGA
29466378 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:29466958 original size:27 final size:27
Alignment explanation
Indices: 29466923--29467101 Score: 184
Period size: 27 Copynumber: 6.6 Consensus size: 27
29466913 TTAAATTGTA
29466923 TAGCACTAAGTGTGCGATATGACTATG
1 TAGCACTAAGTGTGCGATATGACTATG
* * *
29466950 TTGCACTAAGTGTGCGAAATGAATATG
1 TAGCACTAAGTGTGCGATATGACTATG
*
29466977 -ATGCACTAAGTGTGCGA-ATTGACCATG
1 TA-GCACTAAGTGTGCGATA-TGACTATG
** *
29467004 CGGCACTAAGTGTGCGAGTTTGACTATG
1 TAGCACTAAGTGTGCGA-TATGACTATG
* * *
29467032 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGATATGACTATG
* *
29467059 TAGCACTAAGTGTGCGAGT-TGATTATA
1 TAGCACTAAGTGTGCGA-TATGACTATG
*
29467086 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
29467102 GGCTCAATAT
Statistics
Matches: 130, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.01
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGATATGACTATG
Found at i:29467039 original size:82 final size:81
Alignment explanation
Indices: 29466925--29467080 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
29466915 AAATTGTATA
* *
29466925 GCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29466989 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
29467006 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29467071 TGCGAGTTGA
65 TGCGAATTGA
29467081 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29467092 original size:82 final size:81
Alignment explanation
Indices: 29466921--29467101 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
29466911 GATTAAATTG
* *
29466921 TATAGCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TATAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29466986 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
*** * ** *
29467002 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TATAGCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29467066 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
*
29467084 TATAGCACTGAGTGTGCG
1 TATAGCACTAAGTGTGCG
29467102 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 65 0.79
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TATAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29474348 original size:24 final size:25
Alignment explanation
Indices: 29474321--29474431 Score: 100
Period size: 25 Copynumber: 4.5 Consensus size: 25
29474311 GACACACCAC
*
29474321 AGCTCGTGTGAGCTTATCGATT-TT
1 AGCTCGTGTGAGCTTACCGATTCTT
*
29474345 AGCTCGTGAGAGCTTACCGATTCTT
1 AGCTCGTGTGAGCTTACCGATTCTT
* * * *
29474370 AGCTCGTATTAGCTTACCAATT-TCC
1 AGCTCGTGTGAGCTTACCGATTCT-T
* * * *
29474395 AGCTCGTGAGAGCATACTGATTCAT
1 AGCTCGTGTGAGCTTACCGATTCTT
*
29474420 AGCTCGTATGAG
1 AGCTCGTGTGAG
29474432 TATACATGTA
Statistics
Matches: 67, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
24 21 0.31
25 46 0.69
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (25 bp):
AGCTCGTGTGAGCTTACCGATTCTT
Found at i:29483255 original size:33 final size:33
Alignment explanation
Indices: 29483208--29483276 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
29483198 AAGGTTGTAA
*
29483208 TATAGTGCAGTAAAATAGATATAAATGAGGTGG
1 TATAGTGCAGTAAAAGAGATATAAATGAGGTGG
* *
29483241 TATATTGCAGTAAAAGATATATAAATGAGGTGG
1 TATAGTGCAGTAAAAGAGATATAAATGAGGTGG
29483274 TAT
1 TAT
29483277 CAACAAGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (33 bp):
TATAGTGCAGTAAAAGAGATATAAATGAGGTGG
Found at i:29491655 original size:31 final size:31
Alignment explanation
Indices: 29491619--29491680 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
29491609 AGATAATTTT
29491619 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
29491650 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
29491681 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:29492255 original size:19 final size:19
Alignment explanation
Indices: 29492224--29492275 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
29492214 TTCTTTAAAT
*
29492224 AAAAG-AAAAAAAACAGCAAC
1 AAAAGCAAAAAAAA-A-CAAA
*
29492244 AACAGCAAAAAAAAACAAA
1 AAAAGCAAAAAAAAACAAA
29492263 AAAAGCAAAAAAA
1 AAAAGCAAAAAAA
29492276 GCGCAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.54
20 5 0.18
21 8 0.29
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAGCAAAAAAAAACAAA
Found at i:29492285 original size:22 final size:23
Alignment explanation
Indices: 29492260--29492318 Score: 86
Period size: 22 Copynumber: 2.6 Consensus size: 23
29492250 AAAAAAAAAC
29492260 AAAAAAAGCAAAAAAAGCGC-AA
1 AAAAAAAGCAAAAAAAGCGCAAA
*
29492282 AAAAAAAG-AGTAAAAAGCGCAAA
1 AAAAAAAGCA-AAAAAAGCGCAAA
29492305 AAAAAAAGCAAAAA
1 AAAAAAAGCAAAAA
29492319 GTAAAAAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 17 0.53
23 13 0.41
24 1 0.03
ACGTcount: A:0.75, C:0.10, G:0.14, T:0.02
Consensus pattern (23 bp):
AAAAAAAGCAAAAAAAGCGCAAA
Found at i:29492311 original size:28 final size:29
Alignment explanation
Indices: 29492280--29492339 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
29492270 AAAAAAGCGC
*
29492280 AAAAA-AAAAGAGT-AAAAAGCGCAAAAA
1 AAAAAGAAAAAAGTAAAAAAGCGCAAAAA
*
29492307 AAAAAGCAAAAAGTAAAAAAGCGCAAAAA
1 AAAAAGAAAAAAGTAAAAAAGCGCAAAAA
29492336 AAAA
1 AAAA
29492340 GTTGCCTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.17
28 6 0.21
29 18 0.62
ACGTcount: A:0.75, C:0.08, G:0.13, T:0.03
Consensus pattern (29 bp):
AAAAAGAAAAAAGTAAAAAAGCGCAAAAA
Found at i:29495446 original size:31 final size:32
Alignment explanation
Indices: 29495378--29495463 Score: 156
Period size: 32 Copynumber: 2.7 Consensus size: 32
29495368 TTTTAAAGAG
*
29495378 TTATTAGGATTCAATTACTCTTTAAAGAGTTT
1 TTATTAGGATTCAATTACTCTTGAAAGAGTTT
29495410 TTATTAGGATTCAATTACTCTTGAAAGAG-TT
1 TTATTAGGATTCAATTACTCTTGAAAGAGTTT
29495441 TTATTAGGATTCAATTACTCTTG
1 TTATTAGGATTCAATTACTCTTG
29495464 TAATTTGCCT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 25 0.47
32 28 0.53
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATTAGGATTCAATTACTCTTGAAAGAGTTT
Found at i:29503177 original size:20 final size:20
Alignment explanation
Indices: 29503154--29503218 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
29503144 TAGGGGCATG
29503154 AAAGTGCAATCAGGGGTAAC
1 AAAGTGCAATCAGGGGTAAC
* * **
29503174 AAAGTACAAAT-AGGGGCATG
1 AAAGTGC-AATCAGGGGTAAC
* *
29503194 TAAGTGCAATCAGGGGTACC
1 AAAGTGCAATCAGGGGTAAC
29503214 AAAGT
1 AAAGT
29503219 ATACATAGGG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (20 bp):
AAAGTGCAATCAGGGGTAAC
Found at i:29503199 original size:40 final size:40
Alignment explanation
Indices: 29503144--29503271 Score: 175
Period size: 40 Copynumber: 3.2 Consensus size: 40
29503134 GGAGTATAAC
* *
29503144 TAGGGGCATGAAAGTGCAATCAGGGGTAACAAAGTACAAA
1 TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTACAAA
* *
29503184 TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTATACA
1 TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTACAAA
* * * *
29503224 TAGGGGCAGGTATGTGCAATCAAGCGTACCAAAGTACAAA
1 TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTACAAA
*
29503264 CAGGGGCA
1 TAGGGGCA
29503272 CAAGAGTGCA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.38, C:0.16, G:0.30, T:0.16
Consensus pattern (40 bp):
TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTACAAA
Found at i:29503281 original size:40 final size:40
Alignment explanation
Indices: 29503156--29503285 Score: 131
Period size: 40 Copynumber: 3.2 Consensus size: 40
29503146 GGGGCATGAA
* **
29503156 AGTGCAATCAGGGGTAACAAAGTACAAATAGGGGCATGTA-
1 AGTGCAATCAGGGGTACCAAAGTACAAATAGGGGCA-CAAG
* * *
29503196 AGTGCAATCAGGGGTACCAAAGTATACATAGGGG--CAGG
1 AGTGCAATCAGGGGTACCAAAGTACAAATAGGGGCACAAG
* * *
29503234 TATGTGCAATCAAGCGTACCAAAGTACAAACAGGGGCACAAG
1 -A-GTGCAATCAGGGGTACCAAAGTACAAATAGGGGCACAAG
29503276 AGTGCAATCA
1 AGTGCAATCA
29503286 TCCAATAATT
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
39 1 0.01
40 68 0.93
41 1 0.01
42 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.16
Consensus pattern (40 bp):
AGTGCAATCAGGGGTACCAAAGTACAAATAGGGGCACAAG
Found at i:29514381 original size:39 final size:39
Alignment explanation
Indices: 29514338--29514575 Score: 302
Period size: 39 Copynumber: 6.1 Consensus size: 39
29514328 GTAAATTATA
* *
29514338 CCCTGAACGCACTTACATGCCCCTGTTGTACTTCGATAC
1 CCCTGAACGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* *
29514377 CCCTGAACACACTTACGTGCCCCTATTGTACTTCGGTAC
1 CCCTGAACGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * * *
29514416 CCCTGAATGCACTTACGTGCCGCTGTTGTACATCGGTTC
1 CCCTGAACGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * *
29514455 CCCTGATCGCACTTATC-TACCCCTGTTGTACTTCAGTAC
1 CCCTGAACGCACTTA-CGTGCCCCTGTTGTACTTCGGTAC
* * *
29514494 CCC-GATCGCACTTACATGCCACTGTTGTACTTCGGTAC
1 CCCTGAACGCACTTACGTGCCCCTGTTGTACTTCGGTAC
*
29514532 CCCT-AATTGCACTTACGTGCCCCTGTTGTACTTCGGTAC
1 CCCTGAA-CGCACTTACGTGCCCCTGTTGTACTTCGGTAC
29514571 CCCTG
1 CCCTG
29514576 TTCTACTTTG
Statistics
Matches: 170, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
37 1 0.01
38 34 0.20
39 134 0.79
40 1 0.01
ACGTcount: A:0.18, C:0.35, G:0.17, T:0.30
Consensus pattern (39 bp):
CCCTGAACGCACTTACGTGCCCCTGTTGTACTTCGGTAC
Found at i:29514544 original size:77 final size:77
Alignment explanation
Indices: 29514336--29514573 Score: 293
Period size: 77 Copynumber: 3.1 Consensus size: 77
29514326 ACGTAAATTA
* * * * *
29514336 TACCCTGAACGCACTTACATGCCCCTGTTGTACTTCGATACCCCTGAA-CACACTTACGTGCCCC
1 TACCCCGATCGCACTTACATGCCACTGTTGTACTTCGGTACCCCT-AATCGCACTTACGTGCCCC
*
29514400 TATTGTACTTCGG
65 TGTTGTACTTCGG
* * * * * *
29514413 TACCCCTGAAT-GCACTTACGTGCCGCTGTTGTACATCGGTTCCCCTGATCGCACTTATC-TACC
1 TACCCC-G-ATCGCACTTACATGCCACTGTTGTACTTCGGTACCCCTAATCGCACTTA-CGTGCC
*
29514476 CCTGTTGTACTTCAG
63 CCTGTTGTACTTCGG
*
29514491 TACCCCGATCGCACTTACATGCCACTGTTGTACTTCGGTACCCCTAATTGCACTTACGTGCCCCT
1 TACCCCGATCGCACTTACATGCCACTGTTGTACTTCGGTACCCCTAATCGCACTTACGTGCCCCT
29514556 GTTGTACTTCGG
66 GTTGTACTTCGG
29514568 TACCCC
1 TACCCC
29514574 TGTTCTACTT
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
76 3 0.02
77 70 0.52
78 60 0.44
79 2 0.01
ACGTcount: A:0.18, C:0.35, G:0.17, T:0.30
Consensus pattern (77 bp):
TACCCCGATCGCACTTACATGCCACTGTTGTACTTCGGTACCCCTAATCGCACTTACGTGCCCCT
GTTGTACTTCGG
Found at i:29514558 original size:116 final size:117
Alignment explanation
Indices: 29514338--29514575 Score: 331
Period size: 116 Copynumber: 2.0 Consensus size: 117
29514328 GTAAATTATA
* * *
29514338 CCCTGAACGCACTTACATGCCCCTGTTGTACTTCGATACCCCTGAACACACTTACGTGCCCCTAT
1 CCCTGAACGCACTTACATACCCCTGTTGTACTTCGATACCCCTGAACACACTTACATGCCACTAT
* *
29514403 TGTACTTCGGTACCCCTGAATGCACTTACGTGCCGCTGTTGTACATCGGTTC
66 TGTACTTCGGTACCCCTGAATGCACTTACGTGCCCCTGTTGTACATCGGTAC
* * *
29514455 CCCTGATCGCACTTATC-TACCCCTGTTGTACTTC-AGTACCCC-GATCGCACTTACATGCCACT
1 CCCTGAACGCACTTA-CATACCCCTGTTGTACTTCGA-TACCCCTGAACACACTTACATGCCACT
* *
29514517 GTTGTACTTCGGTACCCCT-AATTGCACTTACGTGCCCCTGTTGTACTTCGGTAC
64 ATTGTACTTCGGTACCCCTGAA-TGCACTTACGTGCCCCTGTTGTACATCGGTAC
29514571 CCCTG
1 CCCTG
29514576 TTCTACTTTG
Statistics
Matches: 108, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
115 2 0.02
116 69 0.64
117 36 0.33
118 1 0.01
ACGTcount: A:0.18, C:0.35, G:0.17, T:0.30
Consensus pattern (117 bp):
CCCTGAACGCACTTACATACCCCTGTTGTACTTCGATACCCCTGAACACACTTACATGCCACTAT
TGTACTTCGGTACCCCTGAATGCACTTACGTGCCCCTGTTGTACATCGGTAC
Found at i:29514594 original size:19 final size:19
Alignment explanation
Indices: 29514515--29514594 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
29514505 TTACATGCCA
*
29514515 CTGTTGTACTTCGGTACCC
1 CTGTTCTACTTCGGTACCC
* *
29514534 CTAATTGC-ACTTAC-GTGCCC
1 CT-GTT-CTACTT-CGGTACCC
*
29514554 CTGTTGTACTTCGGTACCC
1 CTGTTCTACTTCGGTACCC
* *
29514573 CTGTTCTACTTTGGTACTC
1 CTGTTCTACTTCGGTACCC
29514592 CTG
1 CTG
29514595 ATAGCACTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
18 1 0.02
19 32 0.68
20 13 0.28
21 1 0.02
ACGTcount: A:0.12, C:0.31, G:0.19, T:0.38
Consensus pattern (19 bp):
CTGTTCTACTTCGGTACCC
Found at i:29521434 original size:25 final size:25
Alignment explanation
Indices: 29521406--29521489 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
29521396 CTTGAAAGCC
29521406 TTTGTGGCGAATTATTTGGTAAGAA
1 TTTGTGGCGAATTATTTGGTAAGAA
** * **
29521431 TTTGTGGTAAATCATTT-GTAAAGCC
1 TTTGTGGCGAATTATTTGGT-AAGAA
* * *
29521456 TTTGTGGGGGAATTGTTTGGGAAGAA
1 TTTGT-GGCGAATTATTTGGTAAGAA
29521482 TTTGTGGC
1 TTTGTGGC
29521490 AAGAACTGGG
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
24 2 0.05
25 24 0.56
26 16 0.37
27 1 0.02
ACGTcount: A:0.24, C:0.06, G:0.31, T:0.39
Consensus pattern (25 bp):
TTTGTGGCGAATTATTTGGTAAGAA
Found at i:29542307 original size:38 final size:37
Alignment explanation
Indices: 29542236--29542310 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 37
29542226 TCACCTTAAT
29542236 ATTAAATTAATATAATATTTATCAAGATAAATATTAG
1 ATTAAATTAATATAATATTTATCAAGATAAATATTAG
*
29542273 ATTAAATTTAATATTAA-ATTTTATCTAGATAATATATT
1 ATTAAA-TTAATA-TAATA-TTTATCAAGATAA-ATATT
29542311 GCTTACATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 6 0.18
38 7 0.21
39 15 0.45
40 5 0.15
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (37 bp):
ATTAAATTAATATAATATTTATCAAGATAAATATTAG
Found at i:29549472 original size:45 final size:45
Alignment explanation
Indices: 29549405--29549580 Score: 230
Period size: 45 Copynumber: 4.0 Consensus size: 45
29549395 GTGTACTGAG
* * **
29549405 TATCATTGATTATAAAAGTGGTTGCTATGTGTTGATTCCACCGGG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* *
29549450 TACCATTGATTATAAAGGTGGTTGCTATGTGCTGACTCCACCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* ** *
29549495 AATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCAGCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* *
29549540 TATAATTGATTATAAGGGTGG-TGCTATGTGCTGA-TCCACCG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCG
29549581 TGTAACGGTT
Statistics
Matches: 113, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
43 6 0.05
44 13 0.12
45 94 0.83
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (45 bp):
TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
Found at i:29550133 original size:22 final size:22
Alignment explanation
Indices: 29550105--29550148 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29550095 GATATTTCTT
29550105 TTTTAGTGAAGAGGGGTCAGAA
1 TTTTAGTGAAGAGGGGTCAGAA
29550127 TTTTAGTGAAGAGGGGTCAGAA
1 TTTTAGTGAAGAGGGGTCAGAA
29550149 CTGTCGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (22 bp):
TTTTAGTGAAGAGGGGTCAGAA
Found at i:29550274 original size:35 final size:35
Alignment explanation
Indices: 29550228--29550298 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
29550218 AAAATTTTAT
29550228 GGTAAGAAGAACGAATCTTAATTTGGAGCTCTGTA
1 GGTAAGAAGAACGAATCTTAATTTGGAGCTCTGTA
29550263 GGTAAGAAGAACGAATCTTAATTTGGAGCTCTGTA
1 GGTAAGAAGAACGAATCTTAATTTGGAGCTCTGTA
29550298 G
1 G
29550299 CGCGAGATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.28
Consensus pattern (35 bp):
GGTAAGAAGAACGAATCTTAATTTGGAGCTCTGTA
Found at i:29557005 original size:457 final size:457
Alignment explanation
Indices: 29556151--29557056 Score: 1713
Period size: 457 Copynumber: 2.0 Consensus size: 457
29556141 AAGAGAAGTT
*
29556151 ACATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAAGCTCTATTGGTAAAAATTCTTCTAT
1 ACATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAAGCTCTATTGGTAAAAATTCTTCCAT
* * *
29556216 CATTATTGAAAATGTCTTGCATGTCAATGGTCTTAAGCATATTCTTCTAATAATTAGTCAATTAT
66 CATTATTAAAAATGTCCTGCATGTCAACGGTCTTAAGCATATTCTTCTAATAATTAGTCAATTAT
* *
29556281 GTGATAAAGGTTTCAATGTCATATTTGAGTTTAAATGTTGTAAAGTTATTGACATTGCTTTTAAT
131 GTGATAAAGGTTTCAATGTCATATTTGAGTCTAAATGTTGTAAAGTTATTGACATTGCTTCTAAT
*
29556346 AAGATTATGCTTGTAGGACATAGGATAGAAAATATATATTTGGTGCATTTAGATGATATGCATAA
196 AAGATTATGCTTGTAGGACATAGGACAGAAAATATATATTTGGTGCATTTAGATGATATGCATAA
29556411 CTCTAGATTATCCCTTATTGCTAAAAATAAGAATAGCGCTTTATTATGGCATAGAAAACTAGGAC
261 CTCTAGATTATCCCTTATTGCTAAAAATAAGAATAGCGCTTTATTATGGCATAGAAAACTAGGAC
29556476 AAGGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATT
326 AAGGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATT
*
29556541 GACTTTGATGTGAATTCTATTTGTGATGCTTGTATTAAGGGTAAACATAAAAAAGTGTCCTGTAA
391 GACTTTGATGTGAATTCTATTTGTGACGCTTGTATTAAGGGTAAACATAAAAAAGTGTCCTGTAA
29556606 AA
456 AA
*
29556608 ACATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAGGCTCTATTGGTAAAAATTCTTCCAT
1 ACATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAAGCTCTATTGGTAAAAATTCTTCCAT
29556673 CATTATTAAAAATGTCCTGCATGTCAACGGTCTTAAGCATATTCTTCTAATAATTAGTCAATTAT
66 CATTATTAAAAATGTCCTGCATGTCAACGGTCTTAAGCATATTCTTCTAATAATTAGTCAATTAT
29556738 GTGATAAAGGTTTCAATGTCATATTTGAGTCTAAATGTTGTAAAGTTATTGACATTGCTTCTAAT
131 GTGATAAAGGTTTCAATGTCATATTTGAGTCTAAATGTTGTAAAGTTATTGACATTGCTTCTAAT
29556803 AAGATTATGCTTGTAGGACATAGGACAGAAAATATATATTTGGTGCATTTAGATGATATGCATAA
196 AAGATTATGCTTGTAGGACATAGGACAGAAAATATATATTTGGTGCATTTAGATGATATGCATAA
* *
29556868 CTCTAGCTTATCCCTTATTGCTAAAAATAAGAATAGCTCTTTATTATGGCATAGAAAACTAGGAC
261 CTCTAGATTATCCCTTATTGCTAAAAATAAGAATAGCGCTTTATTATGGCATAGAAAACTAGGAC
29556933 AAGGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATT
326 AAGGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATT
29556998 GACTTTGATGTGAATTCTATTTGTGACGCTTGTATTAAGGGTAAACATAAAAAAGTGTC
391 GACTTTGATGTGAATTCTATTTGTGACGCTTGTATTAAGGGTAAACATAAAAAAGTGTC
29557057 TTTTAAACCT
Statistics
Matches: 438, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
457 438 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (457 bp):
ACATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAAGCTCTATTGGTAAAAATTCTTCCAT
CATTATTAAAAATGTCCTGCATGTCAACGGTCTTAAGCATATTCTTCTAATAATTAGTCAATTAT
GTGATAAAGGTTTCAATGTCATATTTGAGTCTAAATGTTGTAAAGTTATTGACATTGCTTCTAAT
AAGATTATGCTTGTAGGACATAGGACAGAAAATATATATTTGGTGCATTTAGATGATATGCATAA
CTCTAGATTATCCCTTATTGCTAAAAATAAGAATAGCGCTTTATTATGGCATAGAAAACTAGGAC
AAGGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATT
GACTTTGATGTGAATTCTATTTGTGACGCTTGTATTAAGGGTAAACATAAAAAAGTGTCCTGTAA
AA
Found at i:29559953 original size:20 final size:20
Alignment explanation
Indices: 29559928--29559978 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
29559918 GGTAATTTGG
29559928 TATCGATACCAACT-TAAAAA
1 TATCGATACCAA-TGTAAAAA
29559948 TATCGATACTC-ATGTAAAAA
1 TATCGATAC-CAATGTAAAAA
29559968 TATCGATACCA
1 TATCGATACCA
29559979 CTGGGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (20 bp):
TATCGATACCAATGTAAAAA
Found at i:29567910 original size:28 final size:29
Alignment explanation
Indices: 29567877--29567945 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
29567867 ATTAAGTCCG
* * *
29567877 CACACTTAGTGCTATATAA-TCAAACTCT
1 CACACTTAGTGCTATACAATTCAAACCCA
* *
29567905 CACACTTAGTGCTGTACAATTTAAACCCA
1 CACACTTAGTGCTATACAATTCAAACCCA
29567934 CACACTTAGTGC
1 CACACTTAGTGC
29567946 CATGCATTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.29
Consensus pattern (29 bp):
CACACTTAGTGCTATACAATTCAAACCCA
Found at i:29572738 original size:50 final size:50
Alignment explanation
Indices: 29572630--29572822 Score: 190
Period size: 50 Copynumber: 3.7 Consensus size: 50
29572620 ATTTGGGTAA
* * * * *
29572630 AGAGATCCCATGTAAGACCATGTCTTGGACATGGAATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--CGAG---ATG
* *
29572686 AGAGGTCCCATGTAAGACCATGTCTAGGG-CATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCT-GGGACATGGCATGGGCACCGAGATG
** *
29572736 AGAGGTCCCCGGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
** * *
29572786 AGAACTCCCATGTAAGACCATTTCTGGGATATGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAT
29572823 TGGTAGTACA
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.03
50 75 0.63
53 3 0.03
55 1 0.01
56 35 0.29
57 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:29579223 original size:50 final size:50
Alignment explanation
Indices: 29579117--29579228 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
29579107 GAGAGGTCCT
* * * * **
29579117 ATGTAAGACAATGTCTGGGACATGGCGTTGGCACCGATATGAGAGGTCGC
1 ATGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAACTCGC
** *
29579167 CCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAACTCTC
1 ATGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAACTCGC
29579217 ATGTAAGACCAT
1 ATGTAAGACCAT
29579229 ATCTGGGATA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (50 bp):
ATGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAACTCGC
Found at i:29581312 original size:20 final size:19
Alignment explanation
Indices: 29581286--29581386 Score: 78
Period size: 20 Copynumber: 5.1 Consensus size: 19
29581276 AAAGATGCGT
* *
29581286 AACAGAGGCATCGAAGTGC
1 AACAGAGGCACCAAAGTGC
29581305 AGACAGAGGCA-CAAATGTGC
1 A-ACAGAGGCACCAAA-GTGC
*
29581325 AATTAGAGGCACCAAAGTGC
1 AA-CAGAGGCACCAAAGTGC
* * *
29581345 AAATAGAGGCACCGAAGTGTA
1 -AACAGAGGCACCAAAGTG-C
* *
29581366 AACAAAGGCACTAAAGTGC
1 AACAGAGGCACCAAAGTGC
29581385 AA
1 AA
29581387 TCCCGTACAA
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
19 7 0.10
20 54 0.81
21 6 0.09
ACGTcount: A:0.43, C:0.19, G:0.27, T:0.12
Consensus pattern (19 bp):
AACAGAGGCACCAAAGTGC
Found at i:29585406 original size:16 final size:16
Alignment explanation
Indices: 29585382--29585434 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
29585372 AAGACTATGA
*
29585382 ACCACTCCATTTACTT
1 ACCATTCCATTTACTT
29585398 ACCATTCCATTTACTT
1 ACCATTCCATTTACTT
29585414 ACTTTCCATTCCATTTACTT
1 A----CCATTCCATTTACTT
29585434 A
1 A
29585435 GCATAAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 16 0.50
20 16 0.50
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (16 bp):
ACCATTCCATTTACTT
Found at i:29585417 original size:20 final size:20
Alignment explanation
Indices: 29585392--29585434 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
29585382 ACCACTCCAT
29585392 TTACTTACCATTCCATTTAC
1 TTACTTACCATTCCATTTAC
*
29585412 TTACTTTCCATTCCATTTAC
1 TTACTTACCATTCCATTTAC
29585432 TTA
1 TTA
29585435 GCATAAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (20 bp):
TTACTTACCATTCCATTTAC
Found at i:29587728 original size:20 final size:20
Alignment explanation
Indices: 29587703--29587774 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
29587693 ACGGGATTTG
29587703 CACTTCGATGCCTCTGTAAA
1 CACTTCGATGCCTCTGTAAA
* * **
29587723 CACTTCGGT-CTCTCTTTTCA
1 CACTTCGATGC-CTCTGTAAA
* * **
29587743 CACTACGGTGCCTCTGTATG
1 CACTTCGATGCCTCTGTAAA
29587763 CACTTCGATGCC
1 CACTTCGATGCC
29587775 CTTTTTATGC
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (20 bp):
CACTTCGATGCCTCTGTAAA
Found at i:29595720 original size:27 final size:26
Alignment explanation
Indices: 29595690--29595749 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
29595680 TGTACTGGTG
* *
29595690 GCTTTGCCACATATTCTGTTACTGGCA
1 GCTTTGCCACA-ATACTATTACTGGCA
**
29595717 GCTTTGCTGCAATACTATTACTGGCA
1 GCTTTGCCACAATACTATTACTGGCA
29595743 GCTTTGC
1 GCTTTGC
29595750 TGCGATATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 20 0.69
27 9 0.31
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (26 bp):
GCTTTGCCACAATACTATTACTGGCA
Found at i:29595900 original size:28 final size:28
Alignment explanation
Indices: 29595859--29595919 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
29595849 ATTGTACTGT
* *
29595859 ACTGTTACTGTATTGGGATAAGGCCTAC
1 ACTGTTACTATATTGGGATAAGGCCCAC
*
29595887 ACTGTTACTATATTGGGCTAAGGCCCAC
1 ACTGTTACTATATTGGGATAAGGCCCAC
29595915 ACTGT
1 ACTGT
29595920 ACTGTTACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (28 bp):
ACTGTTACTATATTGGGATAAGGCCCAC
Found at i:29601633 original size:20 final size:19
Alignment explanation
Indices: 29601579--29601639 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
29601569 GATATCCCTA
*
29601579 TTTGCACTGCAGTGCCTCTG
1 TTTGCACTTC-GTGCCTCTG
*
29601599 CTTGCA-TAATCGTGCCTCTG
1 TTTGCACT--TCGTGCCTCTG
29601619 TTTGCACTTCGGTGCCTCTG
1 TTTGCACTTC-GTGCCTCTG
29601639 T
1 T
29601640 AATTATCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 3 0.09
20 29 0.85
21 2 0.06
ACGTcount: A:0.10, C:0.30, G:0.23, T:0.38
Consensus pattern (19 bp):
TTTGCACTTCGTGCCTCTG
Found at i:29602696 original size:28 final size:28
Alignment explanation
Indices: 29602664--29602718 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
29602654 ACAATGTCAA
*
29602664 CAATTACAAAACCATATATACATGCCAT
1 CAATTACAAAACCACATATACATGCCAT
*
29602692 CAATTATAAAACCACATATACATGCCA
1 CAATTACAAAACCACATATACATGCCA
29602719 ACATAACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (28 bp):
CAATTACAAAACCACATATACATGCCAT
Found at i:29608614 original size:17 final size:17
Alignment explanation
Indices: 29608594--29608645 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
29608584 CATAAGTACA
29608594 AATAATATAAAATTTAT
1 AATAATATAAAATTTAT
**
29608611 AAT-ATATAACTTTTAT
1 AATAATATAAAATTTAT
*
29608627 AAATAA-ATAAAAATTAT
1 -AATAATATAAAATTTAT
29608644 AA
1 AA
29608646 ATTGTCTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 13 0.46
17 14 0.50
18 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAATATAAAATTTAT
Found at i:29609309 original size:3 final size:3
Alignment explanation
Indices: 29609303--29609329 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29609293 GTAACGTTGA
29609303 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
29609330 TCAACCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29609500 original size:12 final size:12
Alignment explanation
Indices: 29609481--29609511 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29609471 TTGTTGATAC
29609481 ACAAAAATAAAA
1 ACAAAAATAAAA
*
29609493 ATAAAAATAAAA
1 ACAAAAATAAAA
29609505 ACAAAAA
1 ACAAAAA
29609512 CGTAGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (12 bp):
ACAAAAATAAAA
Found at i:29612872 original size:17 final size:16
Alignment explanation
Indices: 29612852--29612896 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
29612842 ATAAAATCTA
29612852 ATAAACTTTAAAAATTT
1 ATAAA-TTTAAAAATTT
*
29612869 ATAAATTTATAAATTT
1 ATAAATTTAAAAATTT
*
29612885 ATAAAATTAAAA
1 ATAAATTTAAAA
29612897 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAATTTAAAAATTT
Found at i:29612874 original size:8 final size:8
Alignment explanation
Indices: 29612852--29612889 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
29612842 ATAAAATCTA
29612852 ATAAACTTT
1 ATAAA-TTT
*
29612861 AAAAATTT
1 ATAAATTT
29612869 ATAAATTT
1 ATAAATTT
29612877 ATAAATTT
1 ATAAATTT
29612885 ATAAA
1 ATAAA
29612890 ATTAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 23 0.85
9 4 0.15
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (8 bp):
ATAAATTT
Found at i:29618378 original size:18 final size:18
Alignment explanation
Indices: 29618355--29618398 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
29618345 TCCTGAATAT
29618355 CTATCCAACTCAAATTTA
1 CTATCCAACTCAAATTTA
*
29618373 CTATCCAACTCAGATTTA
1 CTATCCAACTCAAATTTA
*
29618391 CTTTCCAA
1 CTATCCAA
29618399 GCCAACATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (18 bp):
CTATCCAACTCAAATTTA
Found at i:29619886 original size:22 final size:22
Alignment explanation
Indices: 29619861--29619906 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
29619851 AAATTTTAAA
29619861 ATTTCAATATAATCAT-GCATAT
1 ATTTCAATATAAT-ATAGCATAT
*
29619883 ATTTCAATCTAATATAGCATAT
1 ATTTCAATATAATATAGCATAT
29619905 AT
1 AT
29619907 CGAAACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.41
Consensus pattern (22 bp):
ATTTCAATATAATATAGCATAT
Found at i:29629185 original size:24 final size:22
Alignment explanation
Indices: 29629152--29629199 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
29629142 TTATCAAATA
29629152 TAAAAGTAAAATAAATTATATATT
1 TAAAAGTAAAAT-AATTATA-ATT
*
29629176 TAAAATTAAAATAATTATAATT
1 TAAAAGTAAAATAATTATAATT
29629198 TA
1 TA
29629200 TTTGAATCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 7 0.30
24 11 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAAAGTAAAATAATTATAATT
Found at i:29629363 original size:43 final size:43
Alignment explanation
Indices: 29629308--29629573 Score: 321
Period size: 43 Copynumber: 6.3 Consensus size: 43
29629298 TTTTTGAAAT
** *
29629308 AAACGCCGCTATAGATTAGTACCTTTAGCGGCGCTATTCCCAC
1 AAACGCCGCTATAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
**
29629351 AAACGATGCTAT--A-CA-TGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCAGT-ACCTTTAGCGGCGCTTTTCCCAC
* * *
29629391 AAACGCCGCTAAAGACCA-TGACCTTTAGCAGCACTTTTCCCAC
1 AAACGCCGCTATAGACCAGT-ACCTTTAGCGGCGCTTTTCCCAC
*
29629434 AAACGCCACTATAGACCA-TGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCAGT-ACCTTTAGCGGCGCTTTTCCCAC
* *
29629477 AAACGCCACTAAAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
* * *
29629520 AAACGCCGCTATAGACCA-TGACCTTTAACGGCGCTTTTCACAA
1 AAACGCCGCTATAGACCAGT-ACCTTTAGCGGCGCTTTTCCCAC
29629563 AAACGCCGCTA
1 AAACGCCGCTA
29629574 AAAACTTATC
Statistics
Matches: 198, Mismatches: 19, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 32 0.16
41 1 0.01
42 2 0.01
43 161 0.81
44 1 0.01
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTATAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
Found at i:29629489 original size:86 final size:86
Alignment explanation
Indices: 29629308--29629575 Score: 355
Period size: 86 Copynumber: 3.2 Consensus size: 86
29629298 TTTTTGAAAT
* ** * * * ***
29629308 AAACGCCGCTATAGATTAGTACCTTTAGCGGCGCTATTCCCACAAACGATGCTAT--A-CATGAC
1 AAACGCCGCTAAAGACCAGTACCTTTAGCAGCACTTTTCCCACAAACGCCACTATAGACCATGAC
29629370 CTTTAGCGGCGCTTTTCCCAC
66 CTTTAGCGGCGCTTTTCCCAC
29629391 AAACGCCGCTAAAGACCA-TGACCTTTAGCAGCACTTTTCCCACAAACGCCACTATAGACCATGA
1 AAACGCCGCTAAAGACCAGT-ACCTTTAGCAGCACTTTTCCCACAAACGCCACTATAGACCATGA
29629455 CCTTTAGCGGCGCTTTTCCCAC
65 CCTTTAGCGGCGCTTTTCCCAC
* * * *
29629477 AAACGCCACTAAAGACCAGTACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCATGAC
1 AAACGCCGCTAAAGACCAGTACCTTTAGCAGCACTTTTCCCACAAACGCCACTATAGACCATGAC
* * *
29629542 CTTTAACGGCGCTTTTCACAA
66 CTTTAGCGGCGCTTTTCCCAC
29629563 AAACGCCGCTAAA
1 AAACGCCGCTAAA
29629576 AACTTATCTT
Statistics
Matches: 163, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
82 1 0.01
83 44 0.27
85 1 0.01
86 116 0.71
87 1 0.01
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.23
Consensus pattern (86 bp):
AAACGCCGCTAAAGACCAGTACCTTTAGCAGCACTTTTCCCACAAACGCCACTATAGACCATGAC
CTTTAGCGGCGCTTTTCCCAC
Found at i:29629898 original size:43 final size:44
Alignment explanation
Indices: 29629850--29629947 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 44
29629840 ACATATGCAA
* * *
29629850 GGTAATAAA-ATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAGATATACAATACATTTACTTAATCAAGGAAATCTT
*
29629893 GGTAATAAAAGATATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAAT-AAAGATATACAATACATTTACTTAATCAAGGAAATCTT
29629938 GGTAATAAAG
1 GGTAATAAAG
29629948 TATCCTGAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
43 6 0.12
44 7 0.14
45 36 0.73
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (44 bp):
GGTAATAAAGATATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:29632772 original size:7 final size:7
Alignment explanation
Indices: 29632727--29632777 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
29632717 CAGGTGAAGA
29632727 AGAAAGAG
1 AGAAAG-G
29632735 AGAAAGG
1 AGAAAGG
*
29632742 -GAGAGG
1 AGAAAGG
*
29632748 GGAAAGG
1 AGAAAGG
*
29632755 ATAATAGG
1 AGAA-AGG
29632763 AGAAAGG
1 AGAAAGG
29632770 AGAAAGG
1 AGAAAGG
29632777 A
1 A
29632778 AAGGGAACGG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
6 5 0.14
7 19 0.53
8 12 0.33
ACGTcount: A:0.53, C:0.00, G:0.43, T:0.04
Consensus pattern (7 bp):
AGAAAGG
Found at i:29633774 original size:14 final size:15
Alignment explanation
Indices: 29633752--29633784 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29633742 CTTAAACTAG
*
29633752 AATCTCTAA-TCCAT
1 AATCCCTAATTCCAT
29633766 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
29633781 AATC
1 AATC
29633785 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:29634233 original size:41 final size:41
Alignment explanation
Indices: 29634180--29634441 Score: 299
Period size: 41 Copynumber: 6.1 Consensus size: 41
29634170 GAGATAAAAT
* * ** *
29634180 CTCTGAGCATTAGCGGCGCTTGTTCAAAAACGCTACTAAAT
1 CTCTGAGCATTAGCGGCGCCTCTTCAAAAACGCCGCTAAAG
29634221 CTCTGAGCATTAGCGGCGCCTCTTCAAAAACGCCGCTAAAGACGCCGCTAAAG
1 CTCTGAGCATTAGCGGCGCCTCTTC----A-------AAA-ACGCCGCTAAAG
* *
29634274 CTCTAAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAG
1 CTCTGAGCATTAGCGGCGCCTCTTCAAAAACGCCGCTAAAG
29634315 CTCTGAGCATTAGCGGCGCCTCTTCAAAAACGCCGCTAAAG
1 CTCTGAGCATTAGCGGCGCCTCTTCAAAAACGCCGCTAAAG
*
29634356 CTCTGAGGCATTAGCGGCGCCTATTCAAAAACGCCGCTAAAG
1 CTCTGA-GCATTAGCGGCGCCTCTTCAAAAACGCCGCTAAAG
* * * *
29634398 CTCTAAGCATTAGCAGCGCTTCTTCAAAAACGCCGCTAATG
1 CTCTGAGCATTAGCGGCGCCTCTTCAAAAACGCCGCTAAAG
29634439 CTC
1 CTC
29634442 ATTTTTAACG
Statistics
Matches: 193, Mismatches: 15, Indels: 26
0.82 0.06 0.11
Matches are distributed among these distances:
41 114 0.59
42 42 0.22
45 1 0.01
49 1 0.01
52 3 0.02
53 32 0.17
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (41 bp):
CTCTGAGCATTAGCGGCGCCTCTTCAAAAACGCCGCTAAAG
Found at i:29634400 original size:83 final size:82
Alignment explanation
Indices: 29634262--29634441 Score: 288
Period size: 83 Copynumber: 2.2 Consensus size: 82
29634252 GCCGCTAAAG
* * *
29634262 ACGCCGCTAAAGCTCTAAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 ACGCCGCTAAAGCTCTAAGCATTAGCGGCGCCTATTCAAAAACGCCGCTAAAGCTCTAAGCATTA
*
29634327 GCGGCGCCTCTTCAAAA
66 GCAGCGCCTCTTCAAAA
*
29634344 ACGCCGCTAAAGCTCTGAGGCATTAGCGGCGCCTATTCAAAAACGCCGCTAAAGCTCTAAGCATT
1 ACGCCGCTAAAGCTCT-AAGCATTAGCGGCGCCTATTCAAAAACGCCGCTAAAGCTCTAAGCATT
*
29634409 AGCAGCGCTTCTTCAAAA
65 AGCAGCGCCTCTTCAAAA
*
29634427 ACGCCGCTAATGCTC
1 ACGCCGCTAAAGCTC
29634442 ATTTTTAACG
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 16 0.18
83 74 0.82
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (82 bp):
ACGCCGCTAAAGCTCTAAGCATTAGCGGCGCCTATTCAAAAACGCCGCTAAAGCTCTAAGCATTA
GCAGCGCCTCTTCAAAA
Found at i:29639165 original size:20 final size:20
Alignment explanation
Indices: 29639140--29639192 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
29639130 TATTAGATTA
*
29639140 AAAAATTGTAAACA-TTTATT
1 AAAAATTGTAAA-AGTATATT
*
29639160 AAAAATCG-AAAAGTATATT
1 AAAAATTGTAAAAGTATATT
29639179 AAAAATTTGTAAAA
1 AAAAA-TTGTAAAA
29639193 AGAAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.04
19 13 0.48
20 9 0.33
21 4 0.15
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32
Consensus pattern (20 bp):
AAAAATTGTAAAAGTATATT
Found at i:29639631 original size:19 final size:19
Alignment explanation
Indices: 29639609--29639645 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29639599 TAAAAATTAA
*
29639609 ATAATATTTTATTATTTTT
1 ATAATATTTTATAATTTTT
*
29639628 ATAATTTTTTATAATTTT
1 ATAATATTTTATAATTTT
29639646 AAAGTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATAATATTTTATAATTTTT
Found at i:29640338 original size:120 final size:121
Alignment explanation
Indices: 29640197--29640441 Score: 465
Period size: 120 Copynumber: 2.0 Consensus size: 121
29640187 AAAATTTCAC
29640197 AAAAAATTGAAAAAAATATATAATGTAACACCCCTAAAATCGTAATGCTAAAAAAGTAATATTAA
1 AAAAAATTGAAAAAAATATATAATGTAACACCCCTAAAATCGTAATGCTAAAAAAGTAATATTAA
*
29640262 GCAAAAATTGTGCATAGTAGATTTCCCAGTAAAGTAAAATAAAGAATAAAAATGAT
66 GCAAAAATTGTGCATAGTAAATTTCCCAGTAAAGTAAAATAAAGAATAAAAATGAT
29640318 AAAAAATTGAAAAAAA-ATATAATGTAACACCCCTAAAATCGTAATGCTAAAAAAGTAATATTAA
1 AAAAAATTGAAAAAAATATATAATGTAACACCCCTAAAATCGTAATGCTAAAAAAGTAATATTAA
*
29640382 GCAAAAATTGTGCATAGTAAATTTCCCAGTAAAGTAAAATAAAGAATATAAATGAT
66 GCAAAAATTGTGCATAGTAAATTTCCCAGTAAAGTAAAATAAAGAATAAAAATGAT
29640438 AAAA
1 AAAA
29640442 GAAAAGGTTG
Statistics
Matches: 122, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
120 106 0.87
121 16 0.13
ACGTcount: A:0.55, C:0.10, G:0.11, T:0.24
Consensus pattern (121 bp):
AAAAAATTGAAAAAAATATATAATGTAACACCCCTAAAATCGTAATGCTAAAAAAGTAATATTAA
GCAAAAATTGTGCATAGTAAATTTCCCAGTAAAGTAAAATAAAGAATAAAAATGAT
Found at i:29646765 original size:15 final size:16
Alignment explanation
Indices: 29646745--29646778 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29646735 TTACATTGGT
29646745 TAATTCAGTT-AATGA
1 TAATTCAGTTCAATGA
*
29646760 TAATTCGGTTCAATGA
1 TAATTCAGTTCAATGA
29646776 TAA
1 TAA
29646779 CCGAATTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (16 bp):
TAATTCAGTTCAATGA
Found at i:29649342 original size:3 final size:3
Alignment explanation
Indices: 29649334--29649362 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29649324 TTATTGATAC
29649334 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29649363 ATTCAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29659437 original size:48 final size:48
Alignment explanation
Indices: 29659381--29659475 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
29659371 TGCAGATCGA
29659381 TGAACTAGATGAATGGCGAATGAAAGTTAATGAGAAACCGAGAAAACT
1 TGAACTAGATGAATGGCGAATGAAAGTTAATGAGAAACCGAGAAAACT
* *
29659429 TGAACTAGATGAATGGCGAATGAAGGTTGATGAGAAACCGAGAAAAC
1 TGAACTAGATGAATGGCGAATGAAAGTTAATGAGAAACCGAGAAAAC
29659476 ACAAGGAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.44, C:0.11, G:0.27, T:0.18
Consensus pattern (48 bp):
TGAACTAGATGAATGGCGAATGAAAGTTAATGAGAAACCGAGAAAACT
Found at i:29659876 original size:13 final size:13
Alignment explanation
Indices: 29659842--29659880 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
29659832 TGTTTTTTTG
*
29659842 TTAATTTGAAAGC
1 TTAATTTGAAAAC
29659855 TTAAGTTTGAAAAC
1 TTAA-TTTGAAAAC
29659869 TTAATTTGAAAA
1 TTAATTTGAAAA
29659881 TTTGGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (13 bp):
TTAATTTGAAAAC
Found at i:29659918 original size:29 final size:27
Alignment explanation
Indices: 29659844--29659918 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
29659834 TTTTTTTGTT
* * * *
29659844 AATTTGAAAGCTTAAGTTTGAAAACTT
1 AATTTGAAAACTTAAATTTAAAAACTA
*
29659871 AATTTGAAAATTTGGAAATTTAAAAACTA
1 AATTTGAAAACTT--AAATTTAAAAACTA
29659900 AATTTTTGAAAACTTAAAT
1 AA--TTTGAAAACTTAAAT
29659919 GTCTTGAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 11 0.29
29 17 0.45
31 10 0.26
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (27 bp):
AATTTGAAAACTTAAATTTAAAAACTA
Found at i:29660180 original size:35 final size:33
Alignment explanation
Indices: 29660141--29660332 Score: 217
Period size: 35 Copynumber: 5.7 Consensus size: 33
29660131 TTGTCTTTTC
*
29660141 TTGCAGGGAATATTTCCTGTTCACGCATTATTCTG
1 TTGCAGGGAATCTTTCCTGTTCAC-CATTATT-TG
* *
29660176 TTGCAGGGAATCTTTCCTGTTCA-CATCATTTC
1 TTGCAGGGAATCTTTCCTGTTCACCATTATTTG
*
29660208 TTGTAGGGAATCTTTCCTGTTCACACATTATTTTG
1 TTGCAGGGAATCTTTCCTGTTCAC-CATTA-TTTG
* * * *
29660243 TTACAGAGAATCTCTCTTGTTCACACATTATTTTG
1 TTGCAGGGAATCTTTCCTGTTCAC-CATTA-TTTG
* *
29660278 TTGCAGGGAATCTTTCCTGTTCA-CATAATTTC
1 TTGCAGGGAATCTTTCCTGTTCACCATTATTTG
*
29660310 TTGCAGGGAATCTCTCCTGTTCA
1 TTGCAGGGAATCTTTCCTGTTCA
29660333 TGTATTATTT
Statistics
Matches: 136, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
32 48 0.35
33 10 0.07
34 4 0.03
35 74 0.54
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (33 bp):
TTGCAGGGAATCTTTCCTGTTCACCATTATTTG
Found at i:29660342 original size:67 final size:65
Alignment explanation
Indices: 29660136--29660332 Score: 216
Period size: 67 Copynumber: 2.9 Consensus size: 65
29660126 TTCACTTGTC
* * *
29660136 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTCTTGCAGGGAATCTTTCCTGTTCA--CATAATT-TGTTGCAGGGAATCTCTCCTGTTCACA
*
29660201 TCA
63 TTA
* * * * *
29660204 -TTTCTTGTAGGGAATCTTTCCTGTTCACACATTATTTTGTTACAGAGAATCTCTCTTGTTCACA
1 TTTTCTTGCAGGGAATCTTTCCTGTT--CACA-TAATTTGTTGCAGGGAATCTCTCCTGTT--CA
29660268 CATTA
61 CATTA
* *
29660273 TTTTGTTGCAGGGAATCTTTCCTGTTCACATAATTTCTTGCAGGGAATCTCTCCTGTTCA
1 TTTTCTTGCAGGGAATCTTTCCTGTTCACATAATTTGTTGCAGGGAATCTCTCCTGTTCA
29660333 TGTATTATTT
Statistics
Matches: 107, Mismatches: 16, Indels: 15
0.78 0.12 0.11
Matches are distributed among these distances:
65 2 0.02
67 67 0.63
68 7 0.07
69 8 0.07
70 23 0.21
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.42
Consensus pattern (65 bp):
TTTTCTTGCAGGGAATCTTTCCTGTTCACATAATTTGTTGCAGGGAATCTCTCCTGTTCACATTA
Found at i:29663239 original size:14 final size:14
Alignment explanation
Indices: 29663220--29663281 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
29663210 ACTTCTCCCC
*
29663220 TTCTTTTTTTATTT
1 TTCTTTTATTATTT
*
29663234 TTCTTTTATTATTA
1 TTCTTTTATTATTT
*
29663248 TTATTATTATTTATTAT
1 TTCTT-TTA-TTATT-T
* *
29663265 TACTATTATTATTT
1 TTCTTTTATTATTT
29663279 TTC
1 TTC
29663282 CAAAAGTAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
14 19 0.51
15 8 0.22
16 8 0.22
17 2 0.05
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCTTTTATTATTT
Found at i:29663245 original size:3 final size:3
Alignment explanation
Indices: 29663239--29663277 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
29663229 TATTTTTCTT
*
29663239 TTA TTA TTA TTA TTA TTA TTTA TTA TTA CTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
29663278 TTTCCAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29663262 original size:19 final size:19
Alignment explanation
Indices: 29663238--29663278 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
29663228 TTATTTTTCT
*
29663238 TTTATTATTATTATTATTA
1 TTTATTATTACTATTATTA
29663257 TTTATTATTACTATTATTA
1 TTTATTATTACTATTATTA
29663276 TTT
1 TTT
29663279 TTCCAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTATTACTATTATTA
Found at i:29663263 original size:16 final size:16
Alignment explanation
Indices: 29663242--29663274 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29663232 TTTTCTTTTA
*
29663242 TTATTATTATTATTAT
1 TTATTATTACTATTAT
29663258 TTATTATTACTATTAT
1 TTATTATTACTATTAT
29663274 T
1 T
29663275 ATTTTTCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTACTATTAT
Found at i:29667749 original size:45 final size:46
Alignment explanation
Indices: 29667685--29667942 Score: 257
Period size: 45 Copynumber: 5.7 Consensus size: 46
29667675 GAAGGAAACA
* *
29667685 AATAAGACTATGGCTGAAAGACACTATGGCA-CTATACCG-GAACTG
1 AATAAGACCATGGTTGAAAGACACTATGGCATC-ATACCGAGAACTG
* *
29667730 AATAAGACCATAGTTGAAAGACACTATGGCATCATACCGAAAACATG
1 AATAAGACCATGGTTGAAAGACACTATGGCATCATACCGAGAAC-TG
* * ** *** *
29667777 --TAAGACCATAGCTGAAAGACGTTATGGCATCATGAATAAG-AC-A
1 AATAAGACCATGGTTGAAAGACACTATGGCATCAT-ACCGAGAACTG
*
29667820 AATAAGACCATGGTTGAAAGACACTATGGCATCA-AGGCGAGAA-TG
1 AATAAGACCATGGTTGAAAGACACTATGGCATCATA-CCGAGAACTG
* * *
29667865 TATAAGACCATGGTTGAAAGACACTATGGCATTA-AGACGAGAA-TG
1 AATAAGACCATGGTTGAAAGACACTATGGCATCATA-CCGAGAACTG
29667910 AATAAGACCATGGTTGAAAGACACTATGGCATC
1 AATAAGACCATGGTTGAAAGACACTATGGCATC
29667943 TTTCAGTCAT
Statistics
Matches: 179, Mismatches: 25, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
43 1 0.01
44 2 0.01
45 168 0.94
46 6 0.03
47 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (46 bp):
AATAAGACCATGGTTGAAAGACACTATGGCATCATACCGAGAACTG
Found at i:29667928 original size:135 final size:135
Alignment explanation
Indices: 29667682--29667942 Score: 318
Period size: 135 Copynumber: 1.9 Consensus size: 135
29667672 CTTGAAGGAA
*
29667682 ACAAATAAGACTATGGCTGAAAGACACTATGGCACTATACCGGAACTGAATAAGACCATAGTTGA
1 ACAAATAAGACCATGGCTGAAAGACACTATGGCACTATACCGGAACTGAATAAGACCATAGTTGA
* **
29667747 AAGACACTATGGCATCATACCGAAAACATGTAAGACCATAGCTGAAAGACGTTATGGCATCATGA
66 AAGACACTATGGCATCATAACGAAAACATGTAAGACCATAGCTGAAAGACACTATGGCATCATGA
29667812 ATAAG
131 ATAAG
* * * *
29667817 ACAAATAAGACCATGGTTGAAAGACACTATGGCA-TCA-AGGCGAGAA-TGTATAAGACCATGGT
1 ACAAATAAGACCATGGCTGAAAGACACTATGGCACT-ATA-CCG-GAACTGAATAAGACCATAGT
* * * *
29667879 TGAAAGACACTATGGCATTA-AGACG-AGA-ATGAATAAGACCATGGTTGAAAGACACTATGGCA
63 TGAAAGACACTATGGCATCATA-ACGAAAACATG--TAAGACCATAGCTGAAAGACACTATGGCA
29667941 TC
125 TC
29667943 TTTCAGTCAT
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
133 3 0.03
134 5 0.05
135 97 0.90
136 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (135 bp):
ACAAATAAGACCATGGCTGAAAGACACTATGGCACTATACCGGAACTGAATAAGACCATAGTTGA
AAGACACTATGGCATCATAACGAAAACATGTAAGACCATAGCTGAAAGACACTATGGCATCATGA
ATAAG
Found at i:29677718 original size:10 final size:10
Alignment explanation
Indices: 29677703--29677862 Score: 90
Period size: 10 Copynumber: 16.3 Consensus size: 10
29677693 GAAGGAGAGG
29677703 GAAAGAAGAA
1 GAAAGAAGAA
29677713 GAAAG-A-AA
1 GAAAGAAGAA
*
29677721 GAAAGAAAAA
1 GAAAGAAGAA
29677731 GAAAGAA-AA
1 GAAAGAAGAA
** *
29677740 GGAAAGGGGAG
1 -GAAAGAAGAA
29677751 GAAAGAAAGAAA
1 GAAAG-AAG-AA
29677763 GAAAGAA-AA
1 GAAAGAAGAA
29677772 GGAAAGAA-AA
1 -GAAAGAAGAA
*
29677782 GGAAAGGA-AA
1 -GAAAGAAGAA
*
29677792 G-GAGAAGAA
1 GAAAGAAGAA
29677801 -AAA-AAGAAA
1 GAAAGAAG-AA
29677810 GAAA-AAGAA
1 GAAAGAAGAA
29677819 GGAAAGAA-AA
1 -GAAAGAAGAA
*
29677829 GGAAAGGAGAA
1 -GAAAGAAGAA
* *
29677840 GAAAAAAAAA
1 GAAAGAAGAA
29677850 GAAAGAAGAA
1 GAAAGAAGAA
29677860 GAA
1 GAA
29677863 GATGAGGGAA
Statistics
Matches: 120, Mismatches: 16, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
8 13 0.11
9 14 0.12
10 79 0.66
11 8 0.07
12 6 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAGAAGAA
Found at i:29677770 original size:42 final size:42
Alignment explanation
Indices: 29677711--29677895 Score: 195
Period size: 42 Copynumber: 4.5 Consensus size: 42
29677701 GGGAAAGAAG
*
29677711 AAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAGGA
* *
29677753 AAGAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGGAAAGGA
1 AAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAGGA
* *
29677795 GAAGAAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGA
1 -AAGAAAGAAAGAAAG--AAA-AA-GAAAGAAAAGGAAAGGAGAGGA
* ** *
29677842 AA-AAA-AAAGAAAGAAGAAG-AAGATGAGGGAAGGA-AGG-
1 AAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAGGA
29677879 AA-AAAGAAAGAAA-AAAA
1 AAGAAAGAAAGAAAGAAAA
29677896 GGTAATTTTT
Statistics
Matches: 124, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
37 8 0.06
38 9 0.07
39 12 0.10
40 1 0.01
41 2 0.02
42 41 0.33
43 14 0.11
44 8 0.06
45 6 0.05
46 3 0.02
47 20 0.16
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (42 bp):
AAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAGGA
Found at i:29677807 original size:47 final size:45
Alignment explanation
Indices: 29677706--29677856 Score: 197
Period size: 42 Copynumber: 3.4 Consensus size: 45
29677696 GGAGAGGGAA
* *
29677706 AGAAG-AAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGG-GG
1 AGAAGAAAAAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGGAGG
*
29677749 AG--GAAAGAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGGAAAGG
1 AGAAGAAAAAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGG--AGG
*
29677794 AGAAGAAAAAAAGAAAGAAA-AAGAAGGAAAGAAAAGGAAAGGAGA
1 AGAAGAAAAAAAGAAAGAAAGAA-AAGGAAAGAAAAGGAAAGGAGG
29677839 AGAA-AAAAAAAGAAAGAA
1 AGAAGAAAAAAAGAAAGAA
29677857 GAAGAAGATG
Statistics
Matches: 98, Mismatches: 3, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
41 1 0.01
42 35 0.36
43 2 0.02
44 14 0.14
45 10 0.10
46 2 0.02
47 34 0.35
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (45 bp):
AGAAGAAAAAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGGAGG
Found at i:29677859 original size:47 final size:47
Alignment explanation
Indices: 29677694--29677856 Score: 171
Period size: 47 Copynumber: 3.5 Consensus size: 47
29677684 GGGGGAAGAG
* *
29677694 AAGGAG-AGGGAAAGAAGAAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGA
1 AAGGAGAAGAGAAA-AA-AAGAAAGAAAGAAA-AAAAGGAAAGAAAAGGA
* *
29677743 AAGG-GGAG-GAAAGAAAGAAAGAAAG---AAAAGGAAAGAAAAGGA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAAAAAAGGAAAGAAAAGGA
*
29677785 AAGGA-AAGGAGAAGAAAA-AAAGAAAGAAAAAGAAGGAAAGAAAAGGA
1 AAGGAGAA-GAGAAAAAAAGAAAGAAAGAAAAA-AAGGAAAGAAAAGGA
*
29677832 AAGGAGAAGAAAAAAAAAGAAAGAA
1 AAGGAGAAGAGAAAAAAAGAAAGAA
29677857 GAAGAAGATG
Statistics
Matches: 97, Mismatches: 7, Indels: 21
0.78 0.06 0.17
Matches are distributed among these distances:
42 21 0.22
43 9 0.09
44 6 0.06
46 13 0.13
47 29 0.30
48 13 0.13
49 6 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (47 bp):
AAGGAGAAGAGAAAAAAAGAAAGAAAGAAAAAAAGGAAAGAAAAGGA
Found at i:29678431 original size:157 final size:151
Alignment explanation
Indices: 29678241--29678714 Score: 497
Period size: 157 Copynumber: 3.0 Consensus size: 151
29678231 AAACACACTA
* *
29678241 AATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTATAATTATGATAT
1 AATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATAATAAAATTAAAATTATGATAT
* * *
29678306 TTTTTAAAGTAATAAAATGCGGAAAAAAAAATACGAACAAATGGCTGAAGTAAGAGTGTTTTACT
66 TTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAA-GGCCGAAGTAAGAGTCTTTTACT
29678371 AAATTATTTAGAAATTCAGAAAT
130 AAATTATTTA-AAATTCAGAAAT
* * * * * *
29678394 AATTAATATAAATAGTTCAAACAAAATATACTGAAATAATATAAAATAAGAAAATAAGAAAATAA
1 AATT-A-ATAAAT--TTCAAACATAATGTACTGAAATAATGTAAAATAATAAAAT--TAAAATTA
** * * *
29678459 T-ATATTTTTATTGAAAGTAATAAAAT-TTGAGAAAATAATACGAGCAAAGTGCAGGAA-TAAGG
60 TGATA-TTTT-TT-AAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAG-GC-CGAAGTAA-G
* * ** * *
29678521 GGTTTTTTACACTAAATTAATTTAAAAAACA-CACT
119 AGTCTTTT--ACTAAATT-ATTTAAAATTCAGAAAT
* *
29678556 AAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGAT
1 -AATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATAATAAAATTA-AAATTATGAT
*
29678621 ATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGGCCGAAGTAAGCGTCTTTTA
64 ATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAA-GGCCGAAGTAAGAGTCTTTTA
*
29678686 CTAAATTTTTTAAAAATTCAGAAAT
128 CTAAATTATTT-AAAATTCAGAAAT
29678711 AATT
1 AATT
29678715 TTTAAAAATT
Statistics
Matches: 258, Mismatches: 40, Indels: 45
0.75 0.12 0.13
Matches are distributed among these distances:
153 7 0.03
154 19 0.07
155 8 0.03
156 23 0.09
157 61 0.24
158 14 0.05
159 48 0.19
160 24 0.09
161 29 0.11
162 3 0.01
163 17 0.07
164 5 0.02
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (151 bp):
AATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATAATAAAATTAAAATTATGATAT
TTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGCCGAAGTAAGAGTCTTTTACTA
AATTATTTAAAATTCAGAAAT
Found at i:29678718 original size:21 final size:21
Alignment explanation
Indices: 29678692--29678734 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29678682 TTTACTAAAT
*
29678692 TTTTTAAAAATTCAGAAATAA
1 TTTTTAAAAATTCAAAAATAA
29678713 TTTTTAAAAATTCAAAAATAA
1 TTTTTAAAAATTCAAAAATAA
29678734 T
1 T
29678735 ATATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTTTAAAAATTCAAAAATAA
Found at i:29678845 original size:13 final size:13
Alignment explanation
Indices: 29678829--29678875 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
29678819 AAAGATAATG
29678829 TAAAATAATATAC
1 TAAAATAATATAC
* *
29678842 TAAAATGATGTAC
1 TAAAATAATATAC
29678855 TAAAATAATA-A-
1 TAAAATAATATAC
29678866 TAAAATAATA
1 TAAAATAATA
29678876 AAATACGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 10 0.33
12 1 0.03
13 19 0.63
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (13 bp):
TAAAATAATATAC
Found at i:29684154 original size:39 final size:40
Alignment explanation
Indices: 29684110--29684187 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 40
29684100 ACTAACACAA
*
29684110 TAACAATAACAA-TA-GTTTTATACTCAAAATAAT-ACTAAT
1 TAACAATAACAATTAGGGTTT-TACT-AAAATAATAACTAAT
*
29684149 TAACAATAATAATTAGGGTTTTACTAAAATAATAACTAA
1 TAACAATAACAATTAGGGTTTTACTAAAATAATAACTAA
29684188 CCATAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 19 0.56
40 11 0.32
41 4 0.12
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (40 bp):
TAACAATAACAATTAGGGTTTTACTAAAATAATAACTAAT
Found at i:29684414 original size:10 final size:10
Alignment explanation
Indices: 29684386--29684422 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
29684376 ATACCCTTTT
29684386 TTTTTCTCTTC
1 TTTTTCTC-TC
*
29684397 TATTTCTCTC
1 TTTTTCTCTC
29684407 TTTTTCTCTC
1 TTTTTCTCTC
29684417 TTTTTC
1 TTTTTC
29684423 CGGCAGTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:29684823 original size:6 final size:6
Alignment explanation
Indices: 29684812--29684849 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
29684802 GATTCTAAAA
*
29684812 AAAATT AAAATT AAAATT AAATTT AAAATT -AAATT AAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAA
29684850 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAAATT
Found at i:29684859 original size:17 final size:17
Alignment explanation
Indices: 29684816--29684852 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 17
29684806 CTAAAAAAAA
29684816 TTAAAATTAAAATTAAAT
1 TTAAAATT-AAATTAAAT
29684834 TTAAAATTAAATTAAAT
1 TTAAAATTAAATTAAAT
29684851 TT
1 TT
29684853 TTTATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAATTAAATTAAAT
Found at i:29684941 original size:46 final size:45
Alignment explanation
Indices: 29684854--29684942 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 45
29684844 ATTAAATTTT
* *
29684854 TTATTATTTATTTGAAAAATAATAATTTTAAGATATGTTTTAAAG
1 TTATTATTTATTTGAAAAATAATAATTTTAAAATATATTTTAAAG
29684899 TTATTA-TTATTTGTACCAAAA-AATAATTTTAAAATATATTTTAA
1 TTATTATTTATTTG-A--AAAATAATAATTTTAAAATATATTTTAA
29684943 TTTTAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 7 0.18
45 7 0.18
46 21 0.54
47 4 0.10
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (45 bp):
TTATTATTTATTTGAAAAATAATAATTTTAAAATATATTTTAAAG
Found at i:29684957 original size:48 final size:45
Alignment explanation
Indices: 29684858--29684958 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 45
29684848 AATTTTTTAT
* * *
29684858 TATTTATTTGAAAAATAATAATTTTAAGATATGTTTTAAAGTTAT
1 TATTTATTTGAAAAATAATAATTTTAAAATATATTTTAAAGTTAA
**
29684903 TA-TTATTTGTACCAAAA-AATAATTTTAAAATATATTTTAATTTTAAA
1 TATTTATTTG-A--AAAATAATAATTTTAAAATATATTTTAAAGTT-AA
29684950 TATTTATTT
1 TATTTATTT
29684959 ATTGAGATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
44 7 0.15
45 3 0.07
46 23 0.50
47 7 0.15
48 6 0.13
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (45 bp):
TATTTATTTGAAAAATAATAATTTTAAAATATATTTTAAAGTTAA
Found at i:29685884 original size:9 final size:9
Alignment explanation
Indices: 29685864--29685902 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
29685854 AAAACTCTTT
29685864 AAAATT-AA
1 AAAATTAAA
29685872 AAAATTAAA
1 AAAATTAAA
29685881 AAAATTAAA
1 AAAATTAAA
29685890 AAAATATAAA
1 AAAAT-TAAA
29685900 AAA
1 AAA
29685903 TTTTCAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 6 0.21
9 16 0.55
10 7 0.24
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATTAAA
Found at i:29685884 original size:17 final size:18
Alignment explanation
Indices: 29685864--29685904 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
29685854 AAAACTCTTT
*
29685864 AAAATTAAAAAATTA-AA
1 AAAATTAAAAAAATATAA
29685881 AAAATTAAAAAAATATAA
1 AAAATTAAAAAAATATAA
29685899 AAAATT
1 AAAATT
29685905 TTCAAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTAAAAAAATATAA
Found at i:29687824 original size:15 final size:17
Alignment explanation
Indices: 29687794--29687825 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
29687784 ATGAATATGG
29687794 TAAAATAATATTAAAAA
1 TAAAATAATATTAAAAA
29687811 TAAAA-AAT-TTAAAAA
1 TAAAATAATATTAAAAA
29687826 AATTCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAATAATATTAAAAA
Found at i:29687947 original size:16 final size:17
Alignment explanation
Indices: 29687927--29687972 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
29687917 CAAATATTGT
29687927 AAAAAATATTAAAAT-A
1 AAAAAATATTAAAATGA
*
29687943 TAAAAATATTAAAATGA
1 AAAAAATATTAAAATGA
29687960 AAAAAATA-TAAAA
1 AAAAAATATTAAAA
29687973 CAATTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAAATATTAAAATGA
Found at i:29687972 original size:8 final size:8
Alignment explanation
Indices: 29687928--29687972 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
29687918 AAATATTGTA
29687928 AAAAATAT
1 AAAAATAT
*
29687936 TAAAATAT
1 AAAAATAT
29687944 AAAAATAT
1 AAAAATAT
* *
29687952 TAAAATGAA
1 AAAAAT-AT
29687961 AAAAATAT
1 AAAAATAT
29687969 AAAA
1 AAAA
29687973 CAATTATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
8 24 0.80
9 6 0.20
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (8 bp):
AAAAATAT
Found at i:29688390 original size:39 final size:40
Alignment explanation
Indices: 29688330--29688405 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
29688320 CCGAATATAA
*
29688330 TAAATATATATTTTTTAA-TTTTTTAATTTTAAAATACTT
1 TAAAAATATATTTTTTAATTTTTTTAATTTTAAAATACTT
* * *
29688369 TAAAAATATTTTTTTTTATTTTTTTATTTTTAAAATA
1 TAAAAATATATTTTTTAATTTTTTTAATTTTAAAATA
29688406 TATTTTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 15 0.47
40 17 0.53
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (40 bp):
TAAAAATATATTTTTTAATTTTTTTAATTTTAAAATACTT
Found at i:29689112 original size:18 final size:18
Alignment explanation
Indices: 29689091--29689135 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
29689081 ATTTATGATA
*
29689091 TTTATAATTTTTACCATT
1 TTTATAATTTTTACAATT
*
29689109 TTTAATATTTTTTACAATT
1 TTT-ATAATTTTTACAATT
*
29689128 CTTATAAT
1 TTTATAAT
29689136 ACTTAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATAATTTTTACAATT
Found at i:29696805 original size:35 final size:35
Alignment explanation
Indices: 29696753--29696868 Score: 180
Period size: 35 Copynumber: 3.3 Consensus size: 35
29696743 ACTCTCTATT
* *
29696753 TTGGTGTGTTTCGGATGGATTAGCTCT-TATGAGCA
1 TTGGTGTGTTTCAGATGGTTTAGCT-TGTATGAGCA
*
29696788 ATGGTGTGTTTCAGATGGTTTAGCTTGTATGAGCA
1 TTGGTGTGTTTCAGATGGTTTAGCTTGTATGAGCA
*
29696823 TTGGTGTGTTTCAGATGGTTTAGCTTGTATAAGCA
1 TTGGTGTGTTTCAGATGGTTTAGCTTGTATGAGCA
29696858 TTGGTGTGTTT
1 TTGGTGTGTTT
29696869 TGGTTGGATT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
34 1 0.01
35 74 0.99
ACGTcount: A:0.17, C:0.09, G:0.31, T:0.43
Consensus pattern (35 bp):
TTGGTGTGTTTCAGATGGTTTAGCTTGTATGAGCA
Found at i:29701397 original size:20 final size:20
Alignment explanation
Indices: 29701372--29701432 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
29701362 AATTAGGTTT
29701372 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATATTAA
* *
29701392 ATTTAAATTAAAAATA-AAA
1 ATTTAAAATAAAAATATTAA
* *
29701411 ATTTATAATATTAAATATTAA
1 ATTTAAAATA-AAAATATTAA
29701432 A
1 A
29701433 AACCCACCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 10 0.30
20 20 0.61
21 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTAAAATAAAAATATTAA
Found at i:29706208 original size:12 final size:12
Alignment explanation
Indices: 29706193--29706221 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
29706183 AATTTAAATT
29706193 TTATTGTTAAGA
1 TTATTGTTAAGA
29706205 TTATTGTTAAGA
1 TTATTGTTAAGA
29706217 TTATT
1 TTATT
29706222 ATGATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (12 bp):
TTATTGTTAAGA
Found at i:29712015 original size:43 final size:43
Alignment explanation
Indices: 29711966--29712052 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
29711956 TCATATCTCA
*
29711966 TTTCTCATATCATAATCATTTCTCATATTTGCCATTTCAATAT
1 TTTCTCATATCATAATCATTTCTCATATTTACCATTTCAATAT
* * *
29712009 TTTCTCATCTCATAGTCATTTCTCATCTTTACCATTTCAATAT
1 TTTCTCATATCATAATCATTTCTCATATTTACCATTTCAATAT
29712052 T
1 T
29712053 AATCACATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.02, T:0.49
Consensus pattern (43 bp):
TTTCTCATATCATAATCATTTCTCATATTTACCATTTCAATAT
Found at i:29720938 original size:37 final size:37
Alignment explanation
Indices: 29720877--29721095 Score: 264
Period size: 37 Copynumber: 5.9 Consensus size: 37
29720867 CTGTATATCC
* * *
29720877 GTAGATTTTGCTCGTTTAAACTTCATTCAGTATAACA
1 GTAGAATTTGCTCGTTTGAGCTTCATTCAGTATAACA
* *
29720914 GTAGAAATTT-CTTGTTTGAGCTTCATTCAGTATAATA
1 GTAG-AATTTGCTCGTTTGAGCTTCATTCAGTATAACA
* *
29720951 GT-GAAATTTTCTCGTTTGAGCTTCATTTAGTATAACA
1 GTAG-AATTTGCTCGTTTGAGCTTCATTCAGTATAACA
*
29720988 GTAGAATTTGCTCGCTTGAGCTTCATTCAGTATAACA
1 GTAGAATTTGCTCGTTTGAGCTTCATTCAGTATAACA
* * *
29721025 ATAGAATTTGCTCATTTGAGCTTCATTTAGTATAAC-
1 GTAGAATTTGCTCGTTTGAGCTTCATTCAGTATAACA
* * *
29721061 GATAGAATTTGCTCATTTTAGCTCCATTCAGTATA
1 G-TAGAATTTGCTCGTTTGAGCTTCATTCAGTATA
29721096 CAACATCATA
Statistics
Matches: 159, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
36 7 0.04
37 147 0.92
38 5 0.03
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.41
Consensus pattern (37 bp):
GTAGAATTTGCTCGTTTGAGCTTCATTCAGTATAACA
Found at i:29725999 original size:100 final size:101
Alignment explanation
Indices: 29725784--29726001 Score: 296
Period size: 100 Copynumber: 2.2 Consensus size: 101
29725774 GTAGTAAAAA
* * * *
29725784 TTATGGATGAACCA-CTGATATTTTTAGTAAAAAGTTTGTAGAAAAGCTACTAGTAGGATATGGA
1 TTATGAATGAACCACCAGATATTTTCAGTAAAAAATTTGTAGAAAAGCTACTAGTAGGATATGGA
* * *
29725848 AGCAGAACATTTTTGTAGATAAAAGCTGCTAGTAAT
66 AGCACAACATTTTTGAAAATAAAAGCTGCTAGTAAT
* * * *
29725884 TTATGGATGAACCACCAGA-ATTTTCAGTAAAAAATTTGTAGACAAGCTACTAGTAGGTTGTGGA
1 TTATGAATGAACCACCAGATATTTTCAGTAAAAAATTTGTAGAAAAGCTACTAGTAGGATATGGA
* *
29725948 TGCACAACTTTTTTGAAAATAAAAGCTGCTAGTAAT
66 AGCACAACATTTTTGAAAATAAAAGCTGCTAGTAAT
*
29725984 TTGTGAATGAACCACCAG
1 TTATGAATGAACCACCAG
29726002 TGTTGCAGAT
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 101 0.97
101 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
TTATGAATGAACCACCAGATATTTTCAGTAAAAAATTTGTAGAAAAGCTACTAGTAGGATATGGA
AGCACAACATTTTTGAAAATAAAAGCTGCTAGTAAT
Found at i:29732379 original size:5 final size:5
Alignment explanation
Indices: 29732371--29732400 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
29732361 TTCGAATTTG
29732371 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
29732401 CTTGTTAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:29732456 original size:56 final size:56
Alignment explanation
Indices: 29732387--29732556 Score: 268
Period size: 56 Copynumber: 3.0 Consensus size: 56
29732377 AAATAAAATA
* * *
29732387 AAATAAAATAAAATCTTGTTAGACGGTGGGAATAAATCCTGAAACAGATTTTATTT
1 AAATCAAATAAAATCTTGTTAAACGGTGGGAATAAATCCCGAAACAGATTTTATTT
*
29732443 AAATCAAATAAAATCTTGTTAAAAGGTGGGAATAAATCCCGAAACAGATTTTATTT
1 AAATCAAATAAAATCTTGTTAAACGGTGGGAATAAATCCCGAAACAGATTTTATTT
* * **
29732499 AAATCAAATAAAATCTTGTTAAACAGCGAAAATAAATCCCGAAACAGATTTTATTT
1 AAATCAAATAAAATCTTGTTAAACGGTGGGAATAAATCCCGAAACAGATTTTATTT
29732555 AA
1 AA
29732557 TTCTATTATA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 105 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (56 bp):
AAATCAAATAAAATCTTGTTAAACGGTGGGAATAAATCCCGAAACAGATTTTATTT
Found at i:29738892 original size:84 final size:84
Alignment explanation
Indices: 29738763--29738916 Score: 200
Period size: 84 Copynumber: 1.8 Consensus size: 84
29738753 GTCTTTGTTT
* * * * *
29738763 GGAAACTAAACAATATCGAATAGAATCTTGTTAAACGGAGAGAATAAATTCCGAAACAAATTTTA
1 GGAAACAAAACAAAATCAAATAAAATCTTGTTAAACGGAGAGAATAAATCCCGAAACAAATTTTA
29738828 TTTAATTCAATTCGAATTC
66 TTTAATTCAATTCGAATTC
* * * * * * *
29738847 GGAAACAAAATAAAATCAAATAAAATTTTGTTAAGCGGTGGGAATAAATCCCGAAATAGATTTTA
1 GGAAACAAAACAAAATCAAATAAAATCTTGTTAAACGGAGAGAATAAATCCCGAAACAAATTTTA
29738912 TTTAA
66 TTTAA
29738917 ATAAAATAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 58 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.29
Consensus pattern (84 bp):
GGAAACAAAACAAAATCAAATAAAATCTTGTTAAACGGAGAGAATAAATCCCGAAACAAATTTTA
TTTAATTCAATTCGAATTC
Found at i:29739041 original size:140 final size:139
Alignment explanation
Indices: 29738781--29739055 Score: 399
Period size: 140 Copynumber: 2.0 Consensus size: 139
29738771 AACAATATCG
* * * *
29738781 AATAGAATCTTGTTAAACGGAGAGAATAAATTCCGAAACAAATTTTATTTAATTCAATTCGAATT
1 AATAAAATCTTGTTAAACGGACAGAATAAATCCCAAAACAAATTTTATTTAATTCAATTCGAATT
* * *
29738846 CGGAAACAAAATAAAATCAAATAAAATTTTGTTAAGCGGTGGGAATAAATCCCGAAATAGATTTT
66 CGAAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGTGGGAATAAATCCCGAAATAGA-TTT
29738911 ATTTAAATAA
130 ATTTAAATAA
* * * *
29738921 AATAAAATCTTGTTAAAC-GACAGCAATAAGTCCCAAAACAGATTTTATTTAATTCTATTCTAAT
1 AATAAAATCTTGTTAAACGGACAG-AATAAATCCCAAAACAAATTTTATTTAATTCAATTCGAAT
* * *
29738985 TTGAAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGTTGGAATAAATTCCGAAATAGATTT
65 TCGAAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGTGGGAATAAATCCCGAAATAGATTT
29739050 ATTTAA
130 ATTTAA
29739056 TTCTATTCTA
Statistics
Matches: 120, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
139 13 0.11
140 107 0.89
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32
Consensus pattern (139 bp):
AATAAAATCTTGTTAAACGGACAGAATAAATCCCAAAACAAATTTTATTTAATTCAATTCGAATT
CGAAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGTGGGAATAAATCCCGAAATAGATTTA
TTTAAATAA
Found at i:29739083 original size:83 final size:84
Alignment explanation
Indices: 29738915--29739224 Score: 340
Period size: 83 Copynumber: 3.7 Consensus size: 84
29738905 GATTTTATTT
* * * * *
29738915 AAATAAAATAAAATCTTGTTAAACGACAGCAATAAGTCCCAAAACAGATTTTATTTAATTCTATT
1 AAATCAAATAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCTATT
*
29738980 CTAATTTGAAAACAAAATA
66 CTAATTTGGAAACAAAATA
** * *
29738999 AAATCAAATAAAATCTTGTTAAACGGTTGGAATAAATTCCGAAATAGA-TTTATTTAATTCTATT
1 AAATCAAATAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCTATT
* *
29739063 CTAATTTGGGAACAAGATA
66 CTAATTTGGAAACAAAATA
* * *
29739082 AAATCAAATAAAATCTTGGTAAACGGCAGTAATAAATCCCGAAACAGATTTTATTTTATT-TAAT
1 AAATCAAATAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCT-A-
* *
29739146 TTCTCATTTTTGGCAACAAAATA
64 TTCT-A-ATTTGGAAACAAAATA
* * * * *
29739169 AAATCAAAT-AAATCTTTATTAAATGG-TGAGAATAAATCCCGAAATAGATTTAATTT
1 AAATCAAATAAAATC-TTGTTAAACGGCAG-GAATAAATCCCGAAACAGATTTTATTT
29739225 TATTTAATTT
Statistics
Matches: 190, Mismatches: 29, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
83 75 0.39
84 50 0.26
85 4 0.02
86 7 0.04
87 54 0.28
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (84 bp):
AAATCAAATAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCTATT
CTAATTTGGAAACAAAATA
Found at i:29739203 original size:87 final size:87
Alignment explanation
Indices: 29738915--29739312 Score: 340
Period size: 87 Copynumber: 4.7 Consensus size: 87
29738905 GATTTTATTT
* ** * * * *
29738915 AAATAAAATAAAATCTTGTTAAAC-GACAGCAATAAGTCCCAAAACAGATTTTATTTAATTCT-A
1 AAATCAAATAAAATCTTGTTAAACGGTGAG-AATAAATCCCGAAATAGATTTTATTTTATT-TAA
* **
29738978 -TTCT-A-ATTTGAAAACAAAATA
64 TTTCTCATTTTTGGCAACAAAATA
* *
29738999 AAATCAAATAAAATCTTGTTAAACGGTTG-GAATAAATTCCGAAATAGA-TTTATTTAATTCT-A
1 AAATCAAATAAAATCTTGTTAAACGG-TGAGAATAAATCCCGAAATAGATTTTATTTTATT-TAA
* * *
29739061 -TTCT-A-ATTTGGGAACAAGATA
64 TTTCTCATTTTTGGCAACAAAATA
* * *
29739082 AAATCAAATAAAATCTTGGTAAACGG-CAGTAATAAATCCCGAAACAGATTTTATTTTATTTAAT
1 AAATCAAATAAAATCTTGTTAAACGGTGAG-AATAAATCCCGAAATAGATTTTATTTTATTTAAT
29739146 TTCTCATTTTTGGCAACAAAATA
65 TTCTCATTTTTGGCAACAAAATA
* * *
29739169 AAATCAAAT-AAATCTTTATTAAATGGTGAGAATAAATCCCGAAATAGATTTAATTTTATTTAAT
1 AAATCAAATAAAATC-TTGTTAAACGGTGAGAATAAATCCCGAAATAGATTTTATTTTATTTAAT
*
29739233 TTCTCATTTTTAGCAACAAAATCA
65 TTCTCATTTTTGGCAACAAAAT-A
** * * *** * * *
29739257 AAATGTAAT-AAAT-TCGTTGAACAACGAGAATCAATCCCAAAATGGATTTTATTTTA
1 AAATCAAATAAAATCTTGTTAAACGGTGAGAATAAATCCCGAAATAGATTTTATTTTA
29739313 CTCGTTTTTG
Statistics
Matches: 264, Mismatches: 38, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
82 1 0.00
83 74 0.28
84 48 0.18
85 6 0.02
86 38 0.14
87 83 0.31
88 14 0.05
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (87 bp):
AAATCAAATAAAATCTTGTTAAACGGTGAGAATAAATCCCGAAATAGATTTTATTTTATTTAATT
TCTCATTTTTGGCAACAAAATA
Found at i:29739204 original size:170 final size:167
Alignment explanation
Indices: 29738915--29739220 Score: 420
Period size: 167 Copynumber: 1.8 Consensus size: 167
29738905 GATTTTATTT
* *
29738915 AAATAAAATAAAATCTTGTTAAACGACAGCAATAAGTCCCAAAACAGATTTTATTTAATTCTATT
1 AAATAAAATAAAATCTTGGTAAACGACAGCAATAAATCCCAAAACAGATTTTATTTAATTCTATT
* *
29738980 CTAATTTGAAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGTTGGAATAAATTCCGAAATA
66 CTAATTTGAAAACAAAATAAAATCAAATAAAATCTTATTAAACGGTTGGAATAAATCCCGAAATA
29739045 GATTTATTTAATTCTATTCTAATTTGGGAACAAGATA
131 GATTTATTTAATTCTATTCTAATTTGGGAACAAGATA
* * * * *
29739082 AAATCAAATAAAATCTTGGTAAACGGCAGTAATAAATCCCGAAACAGATTTTATTTTATT-TAAT
1 AAATAAAATAAAATCTTGGTAAACGACAGCAATAAATCCCAAAACAGATTTTATTTAATTCT-A-
* ** *
29739146 TTCTCATTTTTGGCAACAAAATAAAATCAAAT-AAATCTTTATTAAATGG-TGAGAATAAATCCC
64 TTCT-A-ATTTGAAAACAAAATAAAATCAAATAAAATC-TTATTAAACGGTTG-GAATAAATCCC
29739209 GAAATAGATTTA
125 GAAATAGATTTA
29739221 ATTTTATTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
166 1 0.01
167 54 0.45
168 4 0.03
169 8 0.07
170 53 0.44
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (167 bp):
AAATAAAATAAAATCTTGGTAAACGACAGCAATAAATCCCAAAACAGATTTTATTTAATTCTATT
CTAATTTGAAAACAAAATAAAATCAAATAAAATCTTATTAAACGGTTGGAATAAATCCCGAAATA
GATTTATTTAATTCTATTCTAATTTGGGAACAAGATA
Found at i:29739354 original size:79 final size:79
Alignment explanation
Indices: 29739263--29739438 Score: 248
Period size: 79 Copynumber: 2.2 Consensus size: 79
29739253 ATCAAAATGT
* *
29739263 AATAAATTCGTTGAAC-AACGAGAATCAATCCCAAAATGGATTTTATTTTACTCGTTTTTGGAAA
1 AATAAAATCGTTGAACGAA--AAAATCAATCCCAAAATGGATTTTATTTTACTCGTTTTTGGAAA
* *
29739327 T-AAAACAAAATTTGG
64 TAAAAAAAAAATTTAG
* *
29739342 AATAAAATCGTTGAACGGAAAAAATCAATCCCGAAATGGATTTTATTTTACTTGTTTTTGGAAAT
1 AATAAAATCGTTGAAC-GAAAAAATCAATCCCAAAATGGATTTTATTTTACTCGTTTTTGGAAAT
29739407 AAAAAAAAAATTTAG
65 AAAAAAAAAATTTAG
*
29739422 AATAAAATCGTTAAACG
1 AATAAAATCGTTGAACG
29739439 GTGGGAATAA
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
79 58 0.67
80 27 0.31
81 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (79 bp):
AATAAAATCGTTGAACGAAAAAATCAATCCCAAAATGGATTTTATTTTACTCGTTTTTGGAAATA
AAAAAAAAATTTAG
Found at i:29739457 original size:80 final size:79
Alignment explanation
Indices: 29739283--29739467 Score: 253
Period size: 80 Copynumber: 2.3 Consensus size: 79
29739273 TTGAACAACG
* * *
29739283 AGAATCAATCCCAAAATGGATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATTTGGAATAAA
1 AGAATCAATCCCGAAATGGATTTTATTTTACTCGTTTTTGGAAATAAAAAAAAATTTAGAATAAA
*
29739348 ATCGTTGAACGGAA
66 ATCGTTAAACGGAA
* *
29739362 AAAATCAATCCCGAAATGGATTTTATTTTACTTGTTTTTGGAAATAAAAAAAAAATTTAGAATAA
1 AGAATCAATCCCGAAATGGATTTTATTTTACTCGTTTTTGGAAAT-AAAAAAAAATTTAGAATAA
**
29739427 AATCGTTAAACGGTG
65 AATCGTTAAACGGAA
* * **
29739442 GGAATAAATCCCGAAACCGATTTTAT
1 AGAATCAATCCCGAAATGGATTTTAT
29739468 GTACCTTTAA
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 42 0.46
80 50 0.54
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (79 bp):
AGAATCAATCCCGAAATGGATTTTATTTTACTCGTTTTTGGAAATAAAAAAAAATTTAGAATAAA
ATCGTTAAACGGAA
Found at i:29739580 original size:88 final size:86
Alignment explanation
Indices: 29739422--29739590 Score: 187
Period size: 88 Copynumber: 1.9 Consensus size: 86
29739412 AAAAATTTAG
** * ***
29739422 AATAAAATCGTTAAACGGTGGGAATAAATCCCGAAACCGATTTTATGTACCTTTAATTCATGTTT
1 AATAAAATCGTTAAACGGCAGGAATAAATCCCAAAACCGATTTTATGTACCTTTAATTCATGAAA
*
29739487 GAAAATAAAATCAAAATAATGT
66 CAAAATAAAAT-AAAATAATGT
* * * * *
29739509 AATAAAATCTGTTGAACGGCAGGAATAAATCCCAAAACGGATTTTATTTACTTTTAATT-TTGGA
1 AATAAAATC-GTTAAACGGCAGGAATAAATCCCAAAACCGATTTTATGTACCTTTAATTCAT-GA
*
29739573 AACAAAATCAAATAAAAT
64 AACAAAATAAAATAAAAT
29739591 TTGTTAATAG
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
87 15 0.22
88 52 0.78
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (86 bp):
AATAAAATCGTTAAACGGCAGGAATAAATCCCAAAACCGATTTTATGTACCTTTAATTCATGAAA
CAAAATAAAATAAAATAATGT
Found at i:29741269 original size:139 final size:139
Alignment explanation
Indices: 29741019--29741296 Score: 556
Period size: 139 Copynumber: 2.0 Consensus size: 139
29741009 TTTCAATGAT
29741019 GGGGTTGTTTGTGAAATGAGATTAGTTAAGGTTTGGTAGTAAGAGAATGGTGAAGATAATAAAGT
1 GGGGTTGTTTGTGAAATGAGATTAGTTAAGGTTTGGTAGTAAGAGAATGGTGAAGATAATAAAGT
29741084 TGTGGGATATATGGCGTTTTGGAATAATTCATTATTTAGCATACATTTCTCTTCATTTTTCTTAT
66 TGTGGGATATATGGCGTTTTGGAATAATTCATTATTTAGCATACATTTCTCTTCATTTTTCTTAT
29741149 GGTAAATAA
131 GGTAAATAA
29741158 GGGGTTGTTTGTGAAATGAGATTAGTTAAGGTTTGGTAGTAAGAGAATGGTGAAGATAATAAAGT
1 GGGGTTGTTTGTGAAATGAGATTAGTTAAGGTTTGGTAGTAAGAGAATGGTGAAGATAATAAAGT
29741223 TGTGGGATATATGGCGTTTTGGAATAATTCATTATTTAGCATACATTTCTCTTCATTTTTCTTAT
66 TGTGGGATATATGGCGTTTTGGAATAATTCATTATTTAGCATACATTTCTCTTCATTTTTCTTAT
29741288 GGTAAATAA
131 GGTAAATAA
29741297 AAAATACGAA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 139 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (139 bp):
GGGGTTGTTTGTGAAATGAGATTAGTTAAGGTTTGGTAGTAAGAGAATGGTGAAGATAATAAAGT
TGTGGGATATATGGCGTTTTGGAATAATTCATTATTTAGCATACATTTCTCTTCATTTTTCTTAT
GGTAAATAA
Found at i:29742037 original size:28 final size:27
Alignment explanation
Indices: 29741980--29742043 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
29741970 ATTTAATATT
* * *
29741980 TTTTATATTTTATATAATTTTTTAGGA
1 TTTTATATTATAAATAATTTTTTAGAA
*
29742007 TTTATATATTATAAATAATTTTTTATAA
1 TTT-TATATTATAAATAATTTTTTAGAA
29742035 TTTTATATT
1 TTTTATATT
29742044 TTTAAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTTATATTATAAATAATTTTTTAGAA
Found at i:29742760 original size:62 final size:62
Alignment explanation
Indices: 29742663--29742788 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
29742653 ATCTGGCTAA
29742663 TTAGGGGACTAATTTGCAAAATGGTTGAAATTATAGGGTTTTTCCATGAGAGAATTTTAGTT
1 TTAGGGGACTAATTTGCAAAATGGTTGAAATTATAGGGTTTTTCCATGAGAGAATTTTAGTT
29742725 TTAGGGGACTAATTTGCAAAATGGTTGAAATTATAGGGTTTTTCCATGAGAGAATTTTAGTT
1 TTAGGGGACTAATTTGCAAAATGGTTGAAATTATAGGGTTTTTCCATGAGAGAATTTTAGTT
29742787 TT
1 TT
29742789 TCTTGAAGTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (62 bp):
TTAGGGGACTAATTTGCAAAATGGTTGAAATTATAGGGTTTTTCCATGAGAGAATTTTAGTT
Found at i:29743445 original size:25 final size:26
Alignment explanation
Indices: 29743393--29743480 Score: 96
Period size: 25 Copynumber: 3.5 Consensus size: 26
29743383 TTACCGATTC
*
29743393 CAGCTCTTATGAGCTTA-C-TTATACT
1 CAGCTCGTATGAGCTTACCGTTATA-T
29743418 CAGCTCGTATGAGCTTACCGTTAT-T
1 CAGCTCGTATGAGCTTACCGTTATAT
* * *
29743443 CAGCTTGGAGGAGCTTACCGTT-TAT
1 CAGCTCGTATGAGCTTACCGTTATAT
29743468 C-GCTCGTATGAGC
1 CAGCTCGTATGAGC
29743481 ATACATGTAC
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
24 10 0.19
25 38 0.72
26 1 0.02
27 4 0.08
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (26 bp):
CAGCTCGTATGAGCTTACCGTTATAT
Found at i:29745316 original size:25 final size:25
Alignment explanation
Indices: 29745288--29745335 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29745278 GAAATAATAA
*
29745288 TTTAAATACTAAAATGAAAAAAAGG
1 TTTAAATACCAAAATGAAAAAAAGG
* * *
29745313 TTTAGATACCATAATTAAAAAAA
1 TTTAAATACCAAAATGAAAAAAA
29745336 TATAATTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.27
Consensus pattern (25 bp):
TTTAAATACCAAAATGAAAAAAAGG
Found at i:29746987 original size:29 final size:30
Alignment explanation
Indices: 29746955--29747013 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
29746945 TCACTTGTAT
*
29746955 AATTGCATA-AAATTAAAGTTCATGTATAC
1 AATTGCATATAAATCAAAGTTCATGTATAC
*
29746984 AATTGCATATTAAATCAATGTTCATGTATA
1 AATTGCATA-TAAATCAAAGTTCATGTATA
29747014 ATTTTGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.35
31 17 0.65
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (30 bp):
AATTGCATATAAATCAAAGTTCATGTATAC
Found at i:29747016 original size:29 final size:27
Alignment explanation
Indices: 29746950--29747016 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
29746940 GAGTTTCACT
*
29746950 TGTATAATTGCATAAAATTAAAGTTCA
1 TGTATAATTGCATAAAATCAAAGTTCA
*
29746977 TGTATACAATTGCATATTAAATCAATGTTCA
1 TGTAT--AATTGCATA--AAATCAAAGTTCA
29747008 TGTATAATT
1 TGTATAATT
29747017 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 13 0.38
31 16 0.47
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.40
Consensus pattern (27 bp):
TGTATAATTGCATAAAATCAAAGTTCA
Done.