Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 192 of 210
Found at i:56502149 original size:30 final size:30
Alignment explanation
Indices: 56502115--56502172 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
56502105 ACAAATCCTA
56502115 TCTCAATTTCCTTCCAAAATCCTCTCAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAAAC
56502145 TCTCAATTTCCTTCCAAAATCCTCTCAA
1 TCTCAATTTCCTTCCAAAATCCTCTCAA
56502173 TTTCCTTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAAAC
Found at i:56502172 original size:22 final size:22
Alignment explanation
Indices: 56502144--56502194 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
56502134 TCCTCTCAAA
56502144 CTCTCAATTTCCTTCC-AAAAT
1 CTCTCAATTTCCTTCCAAAAAT
56502165 CCTCTCAATTTCCTTCCAAAAAT
1 -CTCTCAATTTCCTTCCAAAAAT
56502188 CTCTCAA
1 CTCTCAA
56502195 ATCCATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAAAT
Found at i:56502266 original size:31 final size:30
Alignment explanation
Indices: 56502228--56502293 Score: 114
Period size: 31 Copynumber: 2.2 Consensus size: 30
56502218 CCTCAATTTC
56502228 ATTTTTTAAAAATAATTTTAAATAATTTTAT
1 ATTTTTTAAAAATAATTTTAAAT-ATTTTAT
*
56502259 ATTTTTTAAAAATAATTTTAAATTTTTTAT
1 ATTTTTTAAAAATAATTTTAAATATTTTAT
56502289 ATTTT
1 ATTTT
56502294 CATCAATGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.32
31 23 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTTTTTAAAAATAATTTTAAATATTTTAT
Found at i:56502273 original size:21 final size:21
Alignment explanation
Indices: 56502247--56502287 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
56502237 AAATAATTTT
*
56502247 AAATAATTTTATATTTTTTAA
1 AAATAATTTTAAATTTTTTAA
56502268 AAATAATTTTAAATTTTTTA
1 AAATAATTTTAAATTTTTTA
56502288 TATTTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATAATTTTAAATTTTTTAA
Found at i:56503388 original size:7 final size:7
Alignment explanation
Indices: 56503372--56503409 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
56503362 AGTGGATTGA
*
56503372 TATTTAG
1 TATTTTG
56503379 TATTTTG
1 TATTTTG
56503386 TATTTTG
1 TATTTTG
56503393 TATTTTG
1 TATTTTG
*
56503400 TATTATG
1 TATTTTG
56503407 TAT
1 TAT
56503410 ATAACTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (7 bp):
TATTTTG
Found at i:56504733 original size:29 final size:29
Alignment explanation
Indices: 56504674--56504991 Score: 483
Period size: 29 Copynumber: 10.9 Consensus size: 29
56504664 TAAAAAAAAT
* *
56504674 CCTAATTTAGTTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
56504704 CCTAATTTCATTAAAAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
56504733 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
56504763 CTTAATTTAATTAAAAACCCTAACCTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
56504792 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
56504821 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
56504850 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
56504879 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
56504908 CTTGATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
56504937 CCTAATTTAATTAAAAACCCTAAATCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
56504967 CTTAATTTAATTAAAAACCATAACC
1 CCTAATTTAATTAAAAACCCTAACC
56504992 ATTAACAAAA
Statistics
Matches: 266, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
29 194 0.73
30 72 0.27
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.30
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:56509597 original size:16 final size:16
Alignment explanation
Indices: 56509576--56509606 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56509566 TTTTCTACTA
56509576 ATAAAAGAAATAAAAT
1 ATAAAAGAAATAAAAT
56509592 ATAAAAGAAATAAAA
1 ATAAAAGAAATAAAA
56509607 AAACTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
ATAAAAGAAATAAAAT
Found at i:56515943 original size:18 final size:18
Alignment explanation
Indices: 56515917--56515960 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
56515907 AAATATAATA
*
56515917 AAAAG-AAATCAACAAAG
1 AAAAGTAAATAAACAAAG
*
56515934 AAAAGTAAATAAACAAAT
1 AAAAGTAAATAAACAAAG
*
56515952 AAAATTAAA
1 AAAAGTAAA
56515961 GCACTTTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.14
Consensus pattern (18 bp):
AAAAGTAAATAAACAAAG
Found at i:56516156 original size:2 final size:2
Alignment explanation
Indices: 56516149--56516205 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
56516139 GAAGCTAGAC
56516149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56516191 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
56516206 AGTAANNNNN
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56516366 original size:2 final size:2
Alignment explanation
Indices: 56516313--56516346 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56516303 NNNNNNNNAG
56516313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56516347 GTAAAACGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56516415 original size:24 final size:23
Alignment explanation
Indices: 56516388--56516432 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
56516378 ATTTAAGAAG
* *
56516388 AGATATAGATATATATACATAATA
1 AGATATAAAGATATATA-ATAATA
56516412 AGATATAAAGATATATAATAA
1 AGATATAAAGATATATAATAA
56516433 GGTATGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (23 bp):
AGATATAAAGATATATAATAATA
Found at i:56516445 original size:20 final size:20
Alignment explanation
Indices: 56516396--56516450 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
56516386 AGAGATATAG
*
56516396 ATATATATACATAATAAGAT
1 ATATATATATATAATAAGAT
* * *
56516416 ATAAAGATATATAATAAGGT
1 ATATATATATATAATAAGAT
*
56516436 ATGTATATATA-AATA
1 ATATATATATATAATA
56516451 GTTATAATAG
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.35
Consensus pattern (20 bp):
ATATATATATATAATAAGAT
Found at i:56516524 original size:17 final size:16
Alignment explanation
Indices: 56516493--56516535 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
56516483 TTTAAATTTA
56516493 AATAA-GTAAAATAAT
1 AATAATGTAAAATAAT
56516508 AATAATGTAATAATAAT
1 AATAATGTAA-AATAAT
*
56516525 AATAATATAAA
1 AATAATGTAAA
56516536 GCTAATGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 5 0.20
17 15 0.60
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AATAATGTAAAATAAT
Found at i:56517621 original size:17 final size:17
Alignment explanation
Indices: 56517599--56517638 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
56517589 ACAAATTATT
56517599 TTTGGGCTT-GTTGGGTA
1 TTTGGGCTTGGTT-GGTA
56517616 TTTGGGCTTGGTTGGTA
1 TTTGGGCTTGGTTGGTA
56517633 TTTGGG
1 TTTGGG
56517639 TTAGGCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.05, C:0.05, G:0.42, T:0.47
Consensus pattern (17 bp):
TTTGGGCTTGGTTGGTA
Found at i:56526225 original size:3 final size:3
Alignment explanation
Indices: 56526210--56526240 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
56526200 AAGAAAAATA
*
56526210 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
56526241 GGGGCAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:56526327 original size:4 final size:4
Alignment explanation
Indices: 56526318--56526348 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
56526308 AGGAATAAGC
*
56526318 AAAT AAAT AAAT ACAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
56526349 ATTCATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:56527308 original size:11 final size:11
Alignment explanation
Indices: 56527252--56527299 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
56527242 ATACCCAAAC
*
56527252 AATAACAACAA
1 AATAATAACAA
* *
56527263 AATAGTAGCAA
1 AATAATAACAA
*
56527274 TATAATAACAA
1 AATAATAACAA
56527285 AATAATAACAA
1 AATAATAACAA
56527296 AATA
1 AATA
56527300 GTGACAAAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.67, C:0.10, G:0.04, T:0.19
Consensus pattern (11 bp):
AATAATAACAA
Found at i:56527318 original size:22 final size:22
Alignment explanation
Indices: 56527259--56527333 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
56527249 AACAATAACA
* * *
56527259 ACAAAATAGTAGCAATATAATA
1 ACAAAACAGTAGCAAAATAATG
* * * *
56527281 ACAAAATAATAACAAAATAGTG
1 ACAAAACAGTAGCAAAATAATG
*
56527303 ACAAAACAGTAGCAAAACAATG
1 ACAAAACAGTAGCAAAATAATG
*
56527325 ATAAAACAG
1 ACAAAACAG
56527334 ACACAGTTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.61, C:0.12, G:0.11, T:0.16
Consensus pattern (22 bp):
ACAAAACAGTAGCAAAATAATG
Found at i:56529214 original size:53 final size:53
Alignment explanation
Indices: 56529156--56529263 Score: 171
Period size: 53 Copynumber: 2.0 Consensus size: 53
56529146 ATATTATAAA
* * *
56529156 TGTGTAATTATAAGCAATTACAAACACACGTCGTATCATATATTTTATCATAT
1 TGTGTAATTATAAACAATTACAAACACACATCGTATCATATATTTTATCACAT
* *
56529209 TGTGTAATTATAAACAATTACAAACACACATTGTTTCATATATTTTATCACAT
1 TGTGTAATTATAAACAATTACAAACACACATCGTATCATATATTTTATCACAT
56529262 TG
1 TG
56529264 ATGTTAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (53 bp):
TGTGTAATTATAAACAATTACAAACACACATCGTATCATATATTTTATCACAT
Found at i:56534290 original size:48 final size:48
Alignment explanation
Indices: 56534219--56534322 Score: 199
Period size: 48 Copynumber: 2.2 Consensus size: 48
56534209 TGGAGAAACT
56534219 ATTTCTAAGAATATTACAGGTGCAGCAAAGATACACTAACAGTGTTTA
1 ATTTCTAAGAATATTACAGGTGCAGCAAAGATACACTAACAGTGTTTA
56534267 ATTTCTAAGAATATTACAGGTGCAGCAAAGATACACTAACAGTGTTTA
1 ATTTCTAAGAATATTACAGGTGCAGCAAAGATACACTAACAGTGTTTA
*
56534315 ATCTCTAA
1 ATTTCTAA
56534323 CAAACATACA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (48 bp):
ATTTCTAAGAATATTACAGGTGCAGCAAAGATACACTAACAGTGTTTA
Found at i:56548309 original size:14 final size:14
Alignment explanation
Indices: 56548292--56548336 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
56548282 CCTAAATCCC
56548292 AAACTCCAAACTCT
1 AAACTCCAAACTCT
* *
56548306 AAACTCTAAACTTT
1 AAACTCCAAACTCT
* *
56548320 AAACCCCAAACCCT
1 AAACTCCAAACTCT
56548334 AAA
1 AAA
56548337 TATTGAACCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACTCCAAACTCT
Found at i:56552024 original size:26 final size:27
Alignment explanation
Indices: 56551984--56552040 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
56551974 ACAGAGAAGC
* *
56551984 AAAACGAAAACAGGGGA-GAAAGAAAAG
1 AAAAAGAAAACAGGGAAGGAAAG-AAAG
56552011 AAAAAGAAAA-AGGGAAGGAAAGAAAG
1 AAAAAGAAAACAGGGAAGGAAAGAAAG
56552037 AAAA
1 AAAA
56552041 TTTGGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.68, C:0.04, G:0.28, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAACAGGGAAGGAAAGAAAG
Found at i:56552988 original size:22 final size:22
Alignment explanation
Indices: 56552936--56552988 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
56552926 ATTATTAGCA
*
56552936 CTCTCTGTTTAGCACATTTGTG
1 CTCTCTGTTTAACACATTTGTG
* *
56552958 TTCTTTGTTTAACAC-TTTAGTG
1 CTCTCTGTTTAACACATTT-GTG
56552980 CTCTCTGTT
1 CTCTCTGTT
56552989 CATTAGTGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.13, C:0.21, G:0.15, T:0.51
Consensus pattern (22 bp):
CTCTCTGTTTAACACATTTGTG
Found at i:56556697 original size:98 final size:98
Alignment explanation
Indices: 56556508--56556699 Score: 233
Period size: 98 Copynumber: 2.0 Consensus size: 98
56556498 TTCATTAGGG
* *
56556508 ACATGTCAAGTTGAGTAACCCGGGTGAGGTGCTTGAGTTATCATCTCACTTCGCGTCAAAAGATT
1 ACATGTCAAGTTAAGTAACCCGGGTGAGGTGCTTGAGTTATCATCTCACTTCGCGTCAAAAGACT
* *** **
56556573 TGGCTATGTCTTGAATTCGTAAAAAAAAAAAGA
66 TGACTATGTCACAAATAAGTAAAAAAAAAAAGA
* * * * *
56556606 ACATGTCGAGTTAAGTAACCGGGGTGAGGTGCTTGGGTTGTCATCTCATTTCGTC-TCAAAAGAC
1 ACATGTCAAGTTAAGTAACCCGGGTGAGGTGCTTGAGTTATCATCTCACTTCG-CGTCAAAAGAC
**
56556670 TTGACTATGTCACAAATAAGTTTAAAAAAA
65 TTGACTATGTCACAAATAAGTAAAAAAAAA
56556700 TATAATAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
98 77 0.99
99 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (98 bp):
ACATGTCAAGTTAAGTAACCCGGGTGAGGTGCTTGAGTTATCATCTCACTTCGCGTCAAAAGACT
TGACTATGTCACAAATAAGTAAAAAAAAAAAGA
Found at i:56557282 original size:19 final size:18
Alignment explanation
Indices: 56557236--56557271 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
56557226 TTGTAAATAG
*
56557236 TTTAAATTTGATTTTTAA
1 TTTAAATTTAATTTTTAA
56557254 TTTAAATTTAATTTTTAA
1 TTTAAATTTAATTTTTAA
56557272 ATTTTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTAAATTTAATTTTTAA
Found at i:56558619 original size:105 final size:107
Alignment explanation
Indices: 56558487--56558684 Score: 260
Period size: 109 Copynumber: 1.9 Consensus size: 107
56558477 CATTATAATT
* * *
56558487 AATGTCAAGGCACGAAGTAATATTTCCCATAAAAATA-TTTTT-TAATTAATAAATCATAATATA
1 AATGTCAAGGCACGAAGTAATATTTCCCAGAAAAATATTTTTTATAAATAATAAATAATAATATA
* **
56558550 AATCAAATCAATCATCAAGATTATAAATTACCCTGGTTTGTC
66 AATAAAAAAAATCATCAAGATTATAAATTACCCTGGTTTGTC
56558592 AATGTCAATGGGCACGAA-TAATA-TTCCCAGAAAAATATTTTTTTCATAAATAATAAATAATAA
1 AATGTCAA--GGCACGAAGTAATATTTCCCAGAAAAATA-TTTTTT-ATAAATAATAAATAATAA
* *
56558655 TTTAAATAAAAAAAATCCTCAAGATTATAA
62 TATAAATAAAAAAAATCATCAAGATTATAA
56558685 CATATTATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
105 21 0.27
106 5 0.06
107 13 0.16
109 40 0.51
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (107 bp):
AATGTCAAGGCACGAAGTAATATTTCCCAGAAAAATATTTTTTATAAATAATAAATAATAATATA
AATAAAAAAAATCATCAAGATTATAAATTACCCTGGTTTGTC
Found at i:56560285 original size:16 final size:16
Alignment explanation
Indices: 56560229--56560287 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
56560219 TTTTGAAAGT
*
56560229 ATAAAA-AAGTAATAA
1 ATAAAATAAATAATAA
56560244 AT-AAATAAATAAT-A
1 ATAAAATAAATAATAA
**
56560258 ATAAAGGCAAATAATAA
1 ATAAA-ATAAATAATAA
56560275 ATAAAATAAATAA
1 ATAAAATAAATAA
56560288 AATAAACAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
14 6 0.17
15 10 0.29
16 13 0.37
17 6 0.17
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (16 bp):
ATAAAATAAATAATAA
Found at i:56560318 original size:37 final size:36
Alignment explanation
Indices: 56560242--56560319 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 36
56560232 AAAAAGTAAT
* *
56560242 AAATAAATAAATAATAATAAAGGCAAATAATAAATA
1 AAATAAATAAATAATAAAAAAGGCAAATAATAAAGA
*
56560278 AAATAAATAAAATAA-ACAAAAATGCACAATAA-AAAGA
1 AAATAAAT-AAATAATA-AAAAAGGCA-AATAATAAAGA
56560315 AAATA
1 AAATA
56560320 CAAAAACAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 9 0.25
37 22 0.61
38 5 0.14
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (36 bp):
AAATAAATAAATAATAAAAAAGGCAAATAATAAAGA
Found at i:56561962 original size:44 final size:44
Alignment explanation
Indices: 56561895--56562139 Score: 185
Period size: 44 Copynumber: 5.5 Consensus size: 44
56561885 TCTAACCCAT
* *
56561895 TGCAACTTTAGAGG-TATAGGATTTGTAGCTTTAATCTGTTTCAC
1 TGCAACTTTAG-GGAGATAAGATTTGTAGCTTTAATCTGTTTCAC
* * * * * *
56561939 TGCAACTTTAGGGAGATAAGATTTTCTATCTTCAATCTGCTCCAT
1 TGCAACTTTAGGGAGATAAGA-TTTGTAGCTTTAATCTGTTTCAC
* *
56561984 TGCAACTTCAGGGAGATAAGATTTGTAG-TTTCAATCTG-CTCTAC
1 TGCAACTTTAGGGAGATAAGATTTGTAGCTTT-AATCTGTTTC-AC
* * ** * * * *
56562028 TGTAACTTTAGAGAGATAAGATTCACTATCTTCAATTTGTTCCAC
1 TGCAACTTTAGGGAGATAAGATT-TGTAGCTTTAATCTGTTTCAC
* *
56562073 TGCAAGTTTAGGGAGATAAGATTTGTAG-TTTCAATATGCTTT-AC
1 TGCAACTTTAGGGAGATAAGATTTGTAGCTTT-AATCTG-TTTCAC
* * *
56562117 TACAACTTCAGAGAGATAAGATT
1 TGCAACTTTAGGGAGATAAGATT
56562140 CGTAATTTGT
Statistics
Matches: 154, Mismatches: 38, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
43 7 0.05
44 76 0.49
45 68 0.44
46 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (44 bp):
TGCAACTTTAGGGAGATAAGATTTGTAGCTTTAATCTGTTTCAC
Found at i:56561991 original size:45 final size:45
Alignment explanation
Indices: 56561927--56562139 Score: 200
Period size: 44 Copynumber: 4.8 Consensus size: 45
56561917 TTGTAGCTTT
* *
56561927 AATCTGTTTCACTGCAACTTTAGGGAGATAAGATTTTCTATCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTTCTATCTTC
* * *
56561972 AATCTGCTCCATTGCAACTTCAGGGAGATAAGA-TTTGTAGT-TTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTTCTA-TCTTC
* * * **
56562016 AATCTGCTCTACTGTAACTTTAGAGAGATAAGATTCACTATCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTTCTATCTTC
* * * *
56562061 AATTTGTTCCACTGCAAGTTTAGGGAGATAAGA-TTTGTAGT-TTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTTCTA-TCTTC
* ** * * *
56562105 AATATGCTTTACTACAACTTCAGAGAGATAAGATT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATT
56562140 CGTAATTTGT
Statistics
Matches: 133, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
44 68 0.51
45 65 0.49
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTTCTATCTTC
Found at i:56562035 original size:89 final size:89
Alignment explanation
Indices: 56561891--56562140 Score: 317
Period size: 89 Copynumber: 2.8 Consensus size: 89
56561881 TCATTCTAAC
* * *
56561891 CCATTGCAACTTTAGAGG-TATAGGATTTGTAGCTTT-AATCTG-TTTCACTGCAACTTTAGGGA
1 CCATTGCAACTTTAG-GGAGATAAGATTTGTAG-TTTCAATCTGCTTT-ACTGCAACTTTAGAGA
**
56561953 GATAAGATTTTCTATCTTCAATCTGCT
63 GATAAGATTCACTATCTTCAATCTGCT
* * *
56561980 CCATTGCAACTTCAGGGAGATAAGATTTGTAGTTTCAATCTGCTCTACTGTAACTTTAGAGAGAT
1 CCATTGCAACTTTAGGGAGATAAGATTTGTAGTTTCAATCTGCTTTACTGCAACTTTAGAGAGAT
* *
56562045 AAGATTCACTATCTTCAATTTGTT
66 AAGATTCACTATCTTCAATCTGCT
* * * * *
56562069 CCACTGCAAGTTTAGGGAGATAAGATTTGTAGTTTCAATATGCTTTACTACAACTTCAGAGAGAT
1 CCATTGCAACTTTAGGGAGATAAGATTTGTAGTTTCAATCTGCTTTACTGCAACTTTAGAGAGAT
56562134 AAGATTC
66 AAGATTC
56562141 GTAATTTGTA
Statistics
Matches: 140, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
88 5 0.04
89 133 0.95
90 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (89 bp):
CCATTGCAACTTTAGGGAGATAAGATTTGTAGTTTCAATCTGCTTTACTGCAACTTTAGAGAGAT
AAGATTCACTATCTTCAATCTGCT
Found at i:56562229 original size:50 final size:51
Alignment explanation
Indices: 56562119--56562230 Score: 138
Period size: 50 Copynumber: 2.2 Consensus size: 51
56562109 TGCTTTACTA
* * * * * *
56562119 CAACTTCAGAGAGATAAGATTCGTAATTTGTAGCTTTAATCCATTCCACTT
1 CAACTTCAGGGAGATAAGATTCGCAATATGTAGCTTCAATCCATCCCACTG
*
56562170 CAACTTCAGGGAGATAAGATTCGCCATAATG-A-CTTCAATCCATCCCACTG
1 CAACTTCAGGGAGATAAGATTCGCAAT-ATGTAGCTTCAATCCATCCCACTG
56562220 CAACTTCAGGG
1 CAACTTCAGGG
56562231 GTATGGGTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 26 0.49
51 25 0.47
52 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (51 bp):
CAACTTCAGGGAGATAAGATTCGCAATATGTAGCTTCAATCCATCCCACTG
Found at i:56566340 original size:30 final size:31
Alignment explanation
Indices: 56566287--56566347 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
56566277 AAATCAGGAG
56566287 ATAGGTTACAATCTCTGTCATCTCTAAAGTC
1 ATAGGTTACAATCTCTGTCATCTCTAAAGTC
*
56566318 ATAGGTTACAAT-TCTGTTATCTCTAAAGTC
1 ATAGGTTACAATCTCTGTCATCTCTAAAGTC
56566348 CCGAGGTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (31 bp):
ATAGGTTACAATCTCTGTCATCTCTAAAGTC
Found at i:56574023 original size:4 final size:4
Alignment explanation
Indices: 56574014--56574053 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
56574004 TAAAAGTTGA
56574014 AAAT AAAT AAAT AAAT AAAT AAAT AAAGT -AAT AAA- AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT A
56574054 GTTTGTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 4 0.12
4 28 0.85
5 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:56574072 original size:58 final size:58
Alignment explanation
Indices: 56573942--56574081 Score: 140
Period size: 58 Copynumber: 2.4 Consensus size: 58
56573932 TTTAAGCATA
* * * *
56573942 AAAAAATAAATGAATAATAAGTAAATAAATAAATAAACAAGTGAATAACAAAAAATTTTG
1 AAAAAA-AATTGAA-AATAAATAAATAAATAAATAAAAAAGTGAATAACAAAAAAGTTTG
** * *
56574002 ATTAAAAGTTGAAAATAAATAAATAAATAAATAAATAAAGT-AATAA-AAAATAGTTTG
1 AAAAAAAATTGAAAATAAATAAATAAATAAATAAA-AAAGTGAATAACAAAAAAGTTTG
**
56574059 TAAAAAAAATTGAAGTTAAATAA
1 -AAAAAAAATTGAAAATAAATAA
56574082 GCCAAGGACT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
57 9 0.14
58 43 0.66
59 9 0.14
60 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (58 bp):
AAAAAAAATTGAAAATAAATAAATAAATAAATAAAAAAGTGAATAACAAAAAAGTTTG
Found at i:56574961 original size:33 final size:32
Alignment explanation
Indices: 56574917--56574980 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
56574907 GATTCAAAAA
56574917 AAAAAAGAAAAAATAGTCACCTTGTGAAGTTT
1 AAAAAAGAAAAAATAGTCACCTTGTGAAGTTT
* *
56574949 AAAAAAGAAAAAATGGTCACCTTTTGAAGTTT
1 AAAAAAGAAAAAATAGTCACCTTGTGAAGTTT
56574981 TCTTTATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (32 bp):
AAAAAAGAAAAAATAGTCACCTTGTGAAGTTT
Found at i:56578834 original size:32 final size:34
Alignment explanation
Indices: 56578797--56578865 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 34
56578787 TGCAAAGTAC
* * *
56578797 AAATAAATGAGCAAA-ATAAAAAAAAT-ATGAAA
1 AAATAAATCAACAAACATAAAAAAAATAAAGAAA
*
56578829 AAATAAATCAACAAACGTAAAAAAAATAAAGAAA
1 AAATAAATCAACAAACATAAAAAAAATAAAGAAA
56578863 AAA
1 AAA
56578866 AAGTACATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 13 0.42
33 10 0.32
34 8 0.26
ACGTcount: A:0.74, C:0.06, G:0.07, T:0.13
Consensus pattern (34 bp):
AAATAAATCAACAAACATAAAAAAAATAAAGAAA
Found at i:56578991 original size:20 final size:20
Alignment explanation
Indices: 56578968--56579005 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56578958 AAATATATAT
*
56578968 ATAGAAATTATAAAATATGG
1 ATAGAAAGTATAAAATATGG
*
56578988 ATAGAAAGTATAATATAT
1 ATAGAAAGTATAAAATAT
56579006 ATTAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (20 bp):
ATAGAAAGTATAAAATATGG
Found at i:56579036 original size:3 final size:3
Alignment explanation
Indices: 56579028--56579077 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
56579018 TTGTATGTTC
56579028 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56579076 AT
1 AT
56579078 GAGGAGAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:56580354 original size:43 final size:45
Alignment explanation
Indices: 56580293--56580771 Score: 135
Period size: 44 Copynumber: 10.9 Consensus size: 45
56580283 GACTTACAAT
* * * * *
56580293 CTTCAATCTATTCAACTGTTGTC-TAGGGAAGTAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAGTAAAATCTACTAG
* *** * * *
56580336 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTACCAT
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAGTAAAATCTACTAG
* * * ** ** *
56580381 CTTCGATCTACTCTACTATTG-CTTAGGG-AGATAAAATCTAAAAT
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAG-TAAAATCTACTAG
* * *
56580425 CTTCAATCTATTCCACTGTTGTC-CAGGGAAGTAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAGTAAAATCTACTAG
* * *** * ** * *
56580468 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAGTAAAATCTACTAG
* * ** ** * * *
56580513 CTTCGATCTGCTCCACTACT-TCTTAGGG-AGATAAGATCTGA-AAT
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAG-TAAAATCT-ACTAG
* * * *
56580557 CTTCAATCTATTCCACTGTTG-CCCAGGGAAGTAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAGTAAAATCTACTAG
* * *** * ** * *
56580600 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAGTAAAATCTACTAG
* * ** ** * * *
56580645 CTTCGATCTGCTCCACTACTG-CTTAGGG-AGATAAGATCTGA-AAT
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAG-TAAAATCT-ACTAG
* * *
56580689 CTTCAATCTATTCCACTGTTGTC-CAGGGAAGTAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAGTAAAATCTACTAG
* * *** *
56580732 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCT
1 CTTCAATCTACTCCACTGTTGTCACAGGGAAGTAAAATCT
56580772 GTCATATTCG
Statistics
Matches: 299, Mismatches: 116, Indels: 40
0.66 0.25 0.09
Matches are distributed among these distances:
42 2 0.01
43 74 0.25
44 164 0.55
45 59 0.20
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (45 bp):
CTTCAATCTACTCCACTGTTGTCACAGGGAAGTAAAATCTACTAG
Found at i:56580453 original size:44 final size:45
Alignment explanation
Indices: 56580272--56580717 Score: 150
Period size: 44 Copynumber: 10.1 Consensus size: 45
56580262 ACTACAACTG
* * *
56580272 CAGGGAGATAAGA-CTTACAATCTTCAATCTATTCAACTGTTGTC-
1 CAGGGAGATAAAATC-TACAATCTTCAATCTACTCCACTGTTGTCA
* * *** * ***
56580316 TAGGGA-AGTAGAAT-TACTGGCTTCAATGTACTCCACTGTAACCA
1 CAGGGAGA-TAAAATCTACAATCTTCAATCTACTCCACTGTTGTCA
* * * * * *
56580360 CAGGGAGGTAAAATCTACCATCTTCGATCTACTCTACTATTG-CT
1 CAGGGAGATAAAATCTACAATCTTCAATCTACTCCACTGTTGTCA
* * *
56580404 TAGGGAGATAAAATCTAAAATCTTCAATCTATTCCACTGTTGTC-
1 CAGGGAGATAAAATCTACAATCTTCAATCTACTCCACTGTTGTCA
* *** * * ***
56580448 CAGGGA-AGTAGAAT-TACTGGCTTCAATGTACTCCACTATAACCA
1 CAGGGAGA-TAAAATCTACAATCTTCAATCTACTCCACTGTTGTCA
* ** * * * ** *
56580492 CAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT-TCT
1 CAGGGAGATAAAATCTACAATCTTCAATCTACTCCACTGTTGTCA
* * * *
56580536 TAGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTG-CC
1 CAGGGAGATAAAATCT-ACAATCTTCAATCTACTCCACTGTTGTCA
* *** * * ***
56580580 CAGGGA-AGTAGAAT-TACTGGCTTCAATGTACTCCACTATAACCA
1 CAGGGAGA-TAAAATCTACAATCTTCAATCTACTCCACTGTTGTCA
* ** * * * ** *
56580624 CAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG-CT
1 CAGGGAGATAAAATCTACAATCTTCAATCTACTCCACTGTTGTCA
* * *
56580668 TAGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGTC-
1 CAGGGAGATAAAATCT-ACAATCTTCAATCTACTCCACTGTTGTCA
56580712 CAGGGA
1 CAGGGA
56580718 AGTAGAATTA
Statistics
Matches: 274, Mismatches: 109, Indels: 38
0.65 0.26 0.09
Matches are distributed among these distances:
42 1 0.00
43 59 0.22
44 162 0.59
45 52 0.19
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (45 bp):
CAGGGAGATAAAATCTACAATCTTCAATCTACTCCACTGTTGTCA
Found at i:56580453 original size:132 final size:132
Alignment explanation
Indices: 56580273--56581052 Score: 1310
Period size: 132 Copynumber: 5.9 Consensus size: 132
56580263 CTACAACTGC
* * *
56580273 AGGGAGATAAGA-CTTACAATCTTCAATCTATTCAACTGTTGTCTAGGGAAGTAGAATTACTGGC
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGC
* ** * * *
56580337 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTACCATCTTCGATCTACTCTACTATTG
65 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
56580402 CTT
130 CTT
* *
56580405 AGGGAGATAAAATCTAAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
56580470 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTTC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
56580535 TT
131 TT
*
56580537 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
56580602 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
56580667 TT
131 TT
56580669 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* * *
56580734 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGTCATATTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
56580799 TT
131 TT
* * * * *
56580801 AGGGAGATAATATCTGAAATCTTTAATCTATTTCGCTGTTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
56580866 TCAATGTACTCTACTATAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
56580931 TT
131 TT
*
56580933 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTTCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
56580998 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCATCTTCGATCTGCT
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
56581053 TCGCTGTCAA
Statistics
Matches: 610, Mismatches: 37, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
132 607 1.00
133 3 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:56580772 original size:88 final size:89
Alignment explanation
Indices: 56580405--56580772 Score: 186
Period size: 88 Copynumber: 4.2 Consensus size: 89
56580395 ACTATTGCTT
* * * *
56580405 AGGGAGATAAAATCTAAAATCTTCAATCTATTCCACTGTTGTC-CAGGGAAGTAGAATTACTGGC
1 AGGGAGGTAAAATCTGAAATCTTCAATCTACTCCACTATTGTCACAGGGAAGTAGAATTACTGGC
*
56580469 TTCAATGTACTCCACTATAACCAC
66 TTCAATCTACTCCACTATAACCAC
* ** * * * **
56580493 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT-TCTTAGGG-AGATA-AGA-T-CTG
1 AGGGAGGTAAAATCTGAAATCTTCAATCTACTCCACTATTGTCACAGGGAAG-TAGA-ATTACTG
* * * **
56580553 AAATCTTCAATCTATTCCACTGTTGCC-C
64 ---GCTTCAATCTACTCCACTATAACCAC
* * * * *** * * ** *
56580581 AGGGAAGTAGAATTACTG---GCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCC
1 AGGGAGGTA-AAAT-CTGAAATCTTCAATCTACTCCACTATTGTCACAGGGAAGTAGAAT-TACT
** * * * **
56580643 ATCTTCGATCTGCTCCACTACT--GCTT
63 GGCTTCAATCTACTCCACTA-TAACCAC
* * * *
56580669 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC-CAGGGAAGTAGAATTACTGGC
1 AGGGAGGTAAAATCTGAAATCTTCAATCTACTCCACTATTGTCACAGGGAAGTAGAATTACTGGC
*
56580733 TTCAATGTACTCCACTATAACCAC
66 TTCAATCTACTCCACTATAACCAC
56580757 AGGGAGGTAAAATCTG
1 AGGGAGGTAAAATCTG
56580773 TCATATTCGA
Statistics
Matches: 194, Mismatches: 65, Indels: 42
0.64 0.22 0.14
Matches are distributed among these distances:
86 7 0.04
87 40 0.21
88 103 0.53
89 41 0.21
90 2 0.01
91 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (89 bp):
AGGGAGGTAAAATCTGAAATCTTCAATCTACTCCACTATTGTCACAGGGAAGTAGAATTACTGGC
TTCAATCTACTCCACTATAACCAC
Found at i:56582141 original size:15 final size:15
Alignment explanation
Indices: 56582121--56582150 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56582111 TTTGAAGATC
56582121 CTTCTGAGTTTGACA
1 CTTCTGAGTTTGACA
56582136 CTTCTGAGTTTGACA
1 CTTCTGAGTTTGACA
56582151 TGTGTTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
CTTCTGAGTTTGACA
Found at i:56585029 original size:24 final size:24
Alignment explanation
Indices: 56585001--56585046 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
56584991 ATCATTTTTT
* *
56585001 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
56585025 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
56585047 GGATTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:56587224 original size:18 final size:17
Alignment explanation
Indices: 56587201--56587235 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
56587191 ATATACATTG
56587201 AATTATAGGAAAAATATA
1 AATTATA-GAAAAATATA
*
56587219 AATTATATAAAAATATA
1 AATTATAGAAAAATATA
56587236 TTTATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AATTATAGAAAAATATA
Found at i:56587291 original size:20 final size:21
Alignment explanation
Indices: 56587266--56587323 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
56587256 ATGAGAATAA
56587266 AGAAATATATATATATAT-AT
1 AGAAATATATATATATATGAT
*
56587286 AGAAAT-TATA-AAATATGGAT
1 AGAAATATATATATATAT-GAT
56587306 AGAAAGTATA-ATATATAT
1 AGAAA-TATATATATATAT
56587324 TAAAAAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 4 0.13
20 13 0.42
21 2 0.06
22 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (21 bp):
AGAAATATATATATATATGAT
Found at i:56587352 original size:3 final size:3
Alignment explanation
Indices: 56587344--56587372 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
56587334 TTGTATGTTC
56587344 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
56587373 GAGGAGAAAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:56592425 original size:30 final size:31
Alignment explanation
Indices: 56592326--56592401 Score: 152
Period size: 31 Copynumber: 2.5 Consensus size: 31
56592316 TGAATCAAAT
56592326 TTAAAGTTTCATATATATGTTTGAACTACAA
1 TTAAAGTTTCATATATATGTTTGAACTACAA
56592357 TTAAAGTTTCATATATATGTTTGAACTACAA
1 TTAAAGTTTCATATATATGTTTGAACTACAA
56592388 TTAAAGTTTCATAT
1 TTAAAGTTTCATAT
56592402 GTATAAATGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (31 bp):
TTAAAGTTTCATATATATGTTTGAACTACAA
Found at i:56592556 original size:2 final size:2
Alignment explanation
Indices: 56592549--56592575 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56592539 TGGGAATAAT
56592549 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
56592576 TGTCAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56595555 original size:9 final size:9
Alignment explanation
Indices: 56595541--56595569 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
56595531 GTTAGCAATA
56595541 AATTATAAT
1 AATTATAAT
56595550 AATTATAAT
1 AATTATAAT
56595559 AATTATAAT
1 AATTATAAT
56595568 AA
1 AA
56595570 AAAATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTATAAT
Found at i:56603884 original size:18 final size:19
Alignment explanation
Indices: 56603857--56603896 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
56603847 AGACATATAT
56603857 TATTTATAACTAT-AATTA
1 TATTTATAACTATAAATTA
* *
56603875 TATTTGTAACTTTAAATTA
1 TATTTATAACTATAAATTA
56603894 TAT
1 TAT
56603897 AAATACGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (19 bp):
TATTTATAACTATAAATTA
Found at i:56607031 original size:19 final size:18
Alignment explanation
Indices: 56607004--56607043 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
56606994 CTTTTTGTAA
56607004 TTGGACTTGTAATTTTTAT
1 TTGGACTTGTAA-TTTTAT
* *
56607023 TTGGGCTTGTGATTTTAT
1 TTGGACTTGTAATTTTAT
56607041 TTG
1 TTG
56607044 TTCATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.15, C:0.05, G:0.23, T:0.57
Consensus pattern (18 bp):
TTGGACTTGTAATTTTAT
Found at i:56608806 original size:55 final size:56
Alignment explanation
Indices: 56608723--56608846 Score: 187
Period size: 55 Copynumber: 2.2 Consensus size: 56
56608713 TTACATAATG
* * *
56608723 ATCAAATTGGTAACATATAGTATCCCATAATAATATCTTATAATATCCCATTAGGA
1 ATCAAATTGCTAACAAATAGTATCCCATAATAATATCTTATAATATCCCAATAGGA
* *
56608779 ATCAAATTGCTAAGAAATA-TATCCCATAATAATATCTTATAATATCTCAATAGGA
1 ATCAAATTGCTAACAAATAGTATCCCATAATAATATCTTATAATATCCCAATAGGA
*
56608834 ATCAAACTGCTAA
1 ATCAAATTGCTAA
56608847 AAGATACTAG
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
55 46 0.74
56 16 0.26
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (56 bp):
ATCAAATTGCTAACAAATAGTATCCCATAATAATATCTTATAATATCCCAATAGGA
Found at i:56610361 original size:19 final size:19
Alignment explanation
Indices: 56610337--56610375 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
56610327 ACCTAGTGAT
56610337 TACCAAAAACAACAAGATG
1 TACCAAAAACAACAAGATG
56610356 TACCAAAAACAACAAGATG
1 TACCAAAAACAACAAGATG
56610375 T
1 T
56610376 GCTTTAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.21, G:0.10, T:0.13
Consensus pattern (19 bp):
TACCAAAAACAACAAGATG
Found at i:56612552 original size:13 final size:13
Alignment explanation
Indices: 56612534--56612559 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56612524 CTAAAAGATG
56612534 ATATCCTATAATA
1 ATATCCTATAATA
56612547 ATATCCTATAATA
1 ATATCCTATAATA
56612560 TCTCGTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATCCTATAATA
Found at i:56612580 original size:56 final size:56
Alignment explanation
Indices: 56612510--56612665 Score: 208
Period size: 56 Copynumber: 2.8 Consensus size: 56
56612500 AGTAGTCACG
** * * *
56612510 TAGGAATCGGATTGCTAAAAGATGATATCCTATAATAATATCCTATAATATCTCGT
1 TAGGAATCAAATTGCTAAAAGATAATATCCTATAATAATATCCTATAATATCCCAT
*
56612566 TAGGAATCAAATTGCTAAGAA-ATAATAT-CTCATAATAATATCATATAATATCCCAT
1 TAGGAATCAAATTGCTAA-AAGATAATATCCT-ATAATAATATCCTATAATATCCCAT
* *
56612622 TAGGAATCAAATTGATAAAAGATAATATCCCATAATAATATCCT
1 TAGGAATCAAATTGCTAAAAGATAATATCCTATAATAATATCCT
56612666 GACAGATCGT
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
55 4 0.05
56 80 0.92
57 3 0.03
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (56 bp):
TAGGAATCAAATTGCTAAAAGATAATATCCTATAATAATATCCTATAATATCCCAT
Found at i:56615397 original size:2 final size:2
Alignment explanation
Indices: 56615390--56615417 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56615380 ACCTCGGGGA
56615390 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56615418 TATAAGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56624251 original size:41 final size:41
Alignment explanation
Indices: 56624194--56624501 Score: 308
Period size: 41 Copynumber: 7.7 Consensus size: 41
56624184 TTCTATGGGC
* * *
56624194 TTTAGCGGCATTTATGAAAAAGCGTCGGTAATGCTCGGGGT
1 TTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
* * * *
56624235 TTTAGCAGCGTTTATGAAAAAGTGTCGCTAATGCTCTGGGT
1 TTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
* * *
56624276 TTTAACGGCGTTTATGAAAAAACGCCGCTAATGCTCGGGGA
1 TTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
* * * * ** *
56624317 TTTAGCGGCGTTTTTAAAAAAGCGCTGCTAATGTTCCAGGA
1 TTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
*
56624358 TTTAGCGGCATTTAT-AGAAAAGCG-C-C----GCTCGGGGT
1 TTTAGCGGCGTTTATGA-AAAAGCGCCGCTAATGCTCGGGGT
* * *
56624393 TGTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
* * *
56624434 TTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTC-GGGC
1 TTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
* * *
56624474 TTTAGCGGCGTTTTTGGAGAAGCGCCGC
1 TTTAGCGGCGTTTATGAAAAAGCGCCGC
56624502 AAAAAAACAT
Statistics
Matches: 222, Mismatches: 37, Indels: 17
0.80 0.13 0.06
Matches are distributed among these distances:
35 25 0.11
36 2 0.01
37 1 0.00
39 1 0.00
40 30 0.14
41 163 0.73
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
Found at i:56624414 original size:76 final size:76
Alignment explanation
Indices: 56624226--56624462 Score: 226
Period size: 76 Copynumber: 3.0 Consensus size: 76
56624216 CGTCGGTAAT
* * * * * * * * *
56624226 GCTCGGGGTTTTAGCAGCGTTTATGAAAAAGTGTCGCTAATGCTCTGGGTTTTAACGGCGTTTAT
1 GCTCGGGGATTTAGCGGCGTTTATAAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCATTTAT
*
56624291 GAAAAAACGCCGCTAAT
66 -AAAAAA-G-CGC---C
* * *
56624308 GCTCGGGGATTTAGCGGCGTTTTTAAAAAAGCGCTGCTAATGTTCCA-GGATTTAGCGGCATTTA
1 GCTCGGGGATTTAGCGGCGTTTATAAAAAAGCGCCGCTAATGCT-CAGGGATTTAGCGGCATTTA
*
56624372 TAGAAAAGCGCC
65 TAAAAAAGCGCC
* * * *
56624384 GCTCGGGG-TTGTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTT
1 GCTCGGGGATT-TAGCGGCGTTTATAAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCATTTA
56624448 TAAAAAAGCGCC
65 TAAAAAAGCGCC
56624460 GCT
1 GCT
56624463 AATGCTCGGG
Statistics
Matches: 130, Mismatches: 22, Indels: 12
0.79 0.13 0.07
Matches are distributed among these distances:
75 4 0.03
76 65 0.50
79 3 0.02
80 1 0.01
81 5 0.04
82 51 0.39
83 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (76 bp):
GCTCGGGGATTTAGCGGCGTTTATAAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCATTTAT
AAAAAAGCGCC
Found at i:56624438 original size:117 final size:116
Alignment explanation
Indices: 56624267--56624501 Score: 335
Period size: 117 Copynumber: 2.0 Consensus size: 116
56624257 TGTCGCTAAT
* * *
56624267 GCTCTGGGTTTTAACGGCGTTTATGAAAAAACGCCGCTAATGCTCGGGGATTTAGCGGCGTTTTT
1 GCTCGGGGTTGTAACGGCGTTTATGAAAAAACGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTT
* *
56624332 AAAAAAGCGCTGCTAATGTTCCAGGATTTAGCGGCATTTATAGAAAAGCGCC
66 AAAAAAGCGCCGCTAATGCT-CAGGATTTAGCGGCATTTATAGAAAAGCGCC
* * *
56624384 GCTCGGGGTTGTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT
1 GCTCGGGGTTGTAACGGCGTTTATGAAAAAACGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTT
* * * * * *
56624449 AAAAAAGCGCCGCTAATGCTCGGGCTTTAGCGGCGTTTTTGGAGAAGCGCC
66 AAAAAAGCGCCGCTAATGCTCAGGATTTAGCGGCATTTATAGAAAAGCGCC
56624500 GC
1 GC
56624502 AAAAAAACAT
Statistics
Matches: 104, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
116 27 0.26
117 77 0.74
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (116 bp):
GCTCGGGGTTGTAACGGCGTTTATGAAAAAACGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTT
AAAAAAGCGCCGCTAATGCTCAGGATTTAGCGGCATTTATAGAAAAGCGCC
Found at i:56624530 original size:158 final size:157
Alignment explanation
Indices: 56624226--56624510 Score: 369
Period size: 158 Copynumber: 1.8 Consensus size: 157
56624216 CGTCGGTAAT
* * * * *
56624226 GCTCGGGGTTTTAGCAGCGTTTATGAAAAAGTGTCGCTAATGCTCTGGGTTTTAACGGCGTTTAT
1 GCTCGGGGTTGTAGCAGCGTTTATGAAAAAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTTAT
* *****
56624291 GAAAAAACGCCGCTAATGCTCGGGGATTTAGCGGCGTTTTTAAAAAAGCGCTGCTAATGTTCCAG
66 GAAAAAACGCCGCTAATGCTCGGGGATTTAGCGGCGTTTTTAAAAAAGCGCCGCTAAAAAAACAG
56624356 GATTTAGCGGCATTTATAGAAAAGCGCC
131 GATTTAGCGG-ATTTATAGAAAAGCGCC
* *
56624384 GCTCGGGGTTGTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTT-T
1 GCTCGGGGTTGTAGCAGCGTTTATGAAAAAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTTAT
* * ** *
56624448 TAAAAAAGCGCCGCTAATGCTC-GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGC-AAAAAAACA
66 GAAAAAA-CGCCGCTAATGCTCGGGGATTTAGCGGCGTTTTTAAAAAAGCGCCGCTAAAAAAACA
56624511 TTTTATCTTA
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
156 4 0.04
157 34 0.31
158 70 0.65
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (157 bp):
GCTCGGGGTTGTAGCAGCGTTTATGAAAAAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTTAT
GAAAAAACGCCGCTAATGCTCGGGGATTTAGCGGCGTTTTTAAAAAAGCGCCGCTAAAAAAACAG
GATTTAGCGGATTTATAGAAAAGCGCC
Found at i:56625455 original size:18 final size:18
Alignment explanation
Indices: 56625432--56625466 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56625422 TGTATTGAAT
56625432 GGTTAACTT-AGGGTTTAA
1 GGTTAA-TTAAGGGTTTAA
56625450 GGTTAATTAAGGGTTTA
1 GGTTAATTAAGGGTTTA
56625467 GTACTTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.40
Consensus pattern (18 bp):
GGTTAATTAAGGGTTTAA
Found at i:56627510 original size:2 final size:2
Alignment explanation
Indices: 56627503--56627538 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
56627493 CTGAATATTC
56627503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56627539 TATTCCTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56629266 original size:29 final size:29
Alignment explanation
Indices: 56629216--56629289 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
56629206 CATTCTTATT
** *
56629216 ACAATTTATTT-TTAATTCAATATTTCAG
1 ACAATTTATTTATTAATTCAATAAATAAG
*
56629244 ACAATTTATTTATTAATTCAATAAATAAT
1 ACAATTTATTTATTAATTCAATAAATAAG
*
56629273 TCAATTTATTTATTAAT
1 ACAATTTATTTATTAAT
56629290 CTAAAATATC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 11 0.28
29 29 0.73
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (29 bp):
ACAATTTATTTATTAATTCAATAAATAAG
Found at i:56633848 original size:11 final size:11
Alignment explanation
Indices: 56633814--56633848 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
56633804 GTAAATATTC
56633814 TAGATTAAGTT
1 TAGATTAAGTT
* *
56633825 AAGATTAAATT
1 TAGATTAAGTT
56633836 TAGATTAAGTT
1 TAGATTAAGTT
56633847 TA
1 TA
56633849 AATTGATTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (11 bp):
TAGATTAAGTT
Found at i:56635037 original size:126 final size:126
Alignment explanation
Indices: 56634811--56635101 Score: 474
Period size: 126 Copynumber: 2.3 Consensus size: 126
56634801 TAATTTAAAA
* *
56634811 AAGCTTCCACGTGGATGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTT
* * * * *
56634876 GTGATCAAATAGTGTCAAAAACGTTTTAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
66 CTGAGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
* *
56634937 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGATGTTT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTT
* *
56635002 CTGAGCAAATAGTGTCAAAAATGCTTCAAGTAGGATGCAATGTCAGCAAAAGTACTGAAAG
66 CTGAGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
*
56635063 AAGCTCCCACATGGACGCTCTTTTGCTACAGTAGTTCCT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCT
56635102 ATTTGACCTG
Statistics
Matches: 152, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 152 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTT
CTGAGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
Found at i:56635838 original size:22 final size:22
Alignment explanation
Indices: 56635785--56635840 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
56635775 TCACCTCCGA
*
56635785 CACCAATCCACCTCCAGTCCTC
1 CACCGATCCACCTCCAGTCCTC
*
56635807 CGCCGATCCACCTCC-GATCCTC
1 CACCGATCCACCTCCAG-TCCTC
* *
56635829 CACGGCTCCACC
1 CACCGATCCACC
56635841 CATTTCCAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.18, C:0.55, G:0.11, T:0.16
Consensus pattern (22 bp):
CACCGATCCACCTCCAGTCCTC
Found at i:56640018 original size:47 final size:45
Alignment explanation
Indices: 56639914--56640019 Score: 115
Period size: 47 Copynumber: 2.3 Consensus size: 45
56639904 ATTTATATTT
* ***
56639914 TATT-AAATGAAATAATATAAAAATATTCAAAATATTGTCTTTTA
1 TATTAAAATAAAATAATATAAAAATATTCAAAATATTGTCAAATA
* *
56639958 TTTTATTACATAAAATAATATAAAAATATTCAAAATATTTGTACAAATA
1 TATTA--AAATAAAATAATATAAAAATATTCAAAATA-TTGT-CAAATA
56640007 TATTAAAATAAAA
1 TATTAAAATAAAA
56640020 ATCAATGTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
44 3 0.06
47 35 0.71
48 4 0.08
49 7 0.14
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.39
Consensus pattern (45 bp):
TATTAAAATAAAATAATATAAAAATATTCAAAATATTGTCAAATA
Found at i:56650385 original size:264 final size:265
Alignment explanation
Indices: 56649915--56650446 Score: 1021
Period size: 264 Copynumber: 2.0 Consensus size: 265
56649905 TATATATTTG
56649915 GTTTGTTTACCAAGAAGTTCACACGATAAGAACATTAAACAGCAAGCACTTAACAAGTCCAAAAA
1 GTTTGTTTACCAAGAAGTTCACACGATAAGAACATTAAACAGCAAGCACTTAACAAGTCCAAAAA
*
56649980 TTTGGATTGGCAGTTGAGAATGTGAGTAAGTAGTGGAGGTCAAAGGTTTGGTTTATGTTTTAAAA
66 TTTAGATTGGCAGTTGAGAATGTGAGTAAGTAGTGGAGGTCAAAGGTTTGGTTTATGTTTTAAAA
56650045 TTTGAATTTCTTTAATCTGCTGATTGCAAAAGTTATCTGCTGTTTTGAATATATCAGCCACATTT
131 TTTGAATTTCTTTAATCTGCTGATTGCAAAAGTTATCTGCTGTTTTGAATATATCAGCCACATTT
* *
56650110 TGGTGTTAAGTCAGTCCTTCTAAATACCTATTAGGCTAATTAGATT-GGATTGCATATTTTGCCC
196 TGGTGTTAAGTCAGTCCTCCTAAATACCTATTAGGCTAATTAGATTGGGATTGCATATTTTACCC
56650174 TCAAA
261 TCAAA
56650179 GTTTGTTTACCAAGAAGTTCACACGATAAGAACATTAAACAGCAAGCACTTAACAAGTCCAAAAA
1 GTTTGTTTACCAAGAAGTTCACACGATAAGAACATTAAACAGCAAGCACTTAACAAGTCCAAAAA
56650244 TTTAGATTGGCAGTTGAGAATGTGAGTAAGTAGTGGAGGTCAAAGGTTTGGTTTATGTTTTAAAA
66 TTTAGATTGGCAGTTGAGAATGTGAGTAAGTAGTGGAGGTCAAAGGTTTGGTTTATGTTTTAAAA
56650309 TTTGAATTTCTTTAATCTGCTGATTGCAAAAGTTATCTGCTGTTTTGAATATATCAGCCACATTT
131 TTTGAATTTCTTTAATCTGCTGATTGCAAAAGTTATCTGCTGTTTTGAATATATCAGCCACATTT
*
56650374 TGGTGTTAAGTCAGTCCTCCTAAATTCCTATTAGGCTAATTAGATTGGGATTGCATATTTTACCC
196 TGGTGTTAAGTCAGTCCTCCTAAATACCTATTAGGCTAATTAGATTGGGATTGCATATTTTACCC
56650439 TCAAA
261 TCAAA
56650444 GTT
1 GTT
56650447 GGTAACTCTT
Statistics
Matches: 263, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
264 238 0.90
265 25 0.10
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.35
Consensus pattern (265 bp):
GTTTGTTTACCAAGAAGTTCACACGATAAGAACATTAAACAGCAAGCACTTAACAAGTCCAAAAA
TTTAGATTGGCAGTTGAGAATGTGAGTAAGTAGTGGAGGTCAAAGGTTTGGTTTATGTTTTAAAA
TTTGAATTTCTTTAATCTGCTGATTGCAAAAGTTATCTGCTGTTTTGAATATATCAGCCACATTT
TGGTGTTAAGTCAGTCCTCCTAAATACCTATTAGGCTAATTAGATTGGGATTGCATATTTTACCC
TCAAA
Found at i:56651248 original size:8 final size:8
Alignment explanation
Indices: 56651235--56651261 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
56651225 GAGAATCAAT
56651235 ATTTCATA
1 ATTTCATA
56651243 ATTTCATA
1 ATTTCATA
56651251 ATTTCATA
1 ATTTCATA
56651259 ATT
1 ATT
56651262 ATGAAATACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTCATA
Found at i:56656394 original size:19 final size:18
Alignment explanation
Indices: 56656367--56656402 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
56656357 AGCAAAAGAG
56656367 AACAAAAAAAAAGTTAAAA
1 AACAAAAAAAAA-TTAAAA
*
56656386 AACACAAAAAAATTAAA
1 AACAAAAAAAAATTAAA
56656403 TTGCTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.78, C:0.08, G:0.03, T:0.11
Consensus pattern (18 bp):
AACAAAAAAAAATTAAAA
Found at i:56660365 original size:10 final size:9
Alignment explanation
Indices: 56660332--56660359 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56660322 GCGAAATTCA
56660332 TTCTTTTTT
1 TTCTTTTTT
56660341 TTCTTTTTT
1 TTCTTTTTT
56660350 TTCTTTTTT
1 TTCTTTTTT
56660359 T
1 T
56660360 CACTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:56665341 original size:9 final size:10
Alignment explanation
Indices: 56665307--56665352 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
56665297 ACTTAATGCT
*
56665307 AATTTTTTTGG
1 AATTTTTAT-G
56665318 AATTTTTATG
1 AATTTTTATG
56665328 AAATTTTTAT-
1 -AATTTTTATG
56665338 AATTTTT-TG
1 AATTTTTATG
56665347 AATTTT
1 AATTTT
56665353 AAATAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 1 0.03
9 13 0.41
10 1 0.03
11 17 0.53
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (10 bp):
AATTTTTATG
Found at i:56665343 original size:19 final size:19
Alignment explanation
Indices: 56665321--56665364 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
56665311 TTTTTGGAAT
*
56665321 TTTTATGAAATTTT-TATAA
1 TTTTATG-AATTTTAAATAA
*
56665340 TTTTTTGAATTTTAAATAA
1 TTTTATGAATTTTAAATAA
56665359 TTTTAT
1 TTTTAT
56665365 TTTTATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTATGAATTTTAAATAA
Found at i:56666241 original size:27 final size:25
Alignment explanation
Indices: 56666186--56666241 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
56666176 ATTCTAGACT
*
56666186 TTTTTAATTTTTTTAACTTATATAT
1 TTTTTAATTTTTTTAACTTATATAA
* *
56666211 TTTTTAGATTTTTTTTAATTTGTATAA
1 TTTTTA-A-TTTTTTTAACTTATATAA
56666238 TTTT
1 TTTT
56666242 AAAAAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 6 0.23
26 1 0.04
27 19 0.73
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTTAATTTTTTTAACTTATATAA
Found at i:56666287 original size:20 final size:20
Alignment explanation
Indices: 56666250--56666330 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
56666240 TTAAAAAATA
**
56666250 TATAAAT-TTTTGGGTTTTT
1 TATAAATATTTTGAATTTTT
56666269 TATAAATATTTTGAA-TTTT
1 TATAAATATTTTGAATTTTT
* *
56666288 AAAAAATCATTTTGAATTTTT
1 TATAAAT-ATTTTGAATTTTT
*
56666309 GA-AAATTATTTTGAATTATTT
1 TATAAA-TATTTTGAATT-TTT
56666330 T
1 T
56666331 GTAATTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
19 16 0.31
20 26 0.51
21 9 0.18
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.56
Consensus pattern (20 bp):
TATAAATATTTTGAATTTTT
Found at i:56666423 original size:9 final size:9
Alignment explanation
Indices: 56666409--56666439 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
56666399 CACCAATATG
56666409 TTATTTGAA
1 TTATTTGAA
56666418 TTATTTGAA
1 TTATTTGAA
*
56666427 TTATTCGAA
1 TTATTTGAA
56666436 TTAT
1 TTAT
56666440 AAAGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (9 bp):
TTATTTGAA
Found at i:56667103 original size:18 final size:18
Alignment explanation
Indices: 56667049--56667104 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
56667039 TTTAAAAATA
*
56667049 AAAAATAAAAAATTATTTT
1 AAAAATAAAAAAATA-TTT
***
56667068 AAAAATATTTTAAA-ATTT
1 AAAAATA-AAAAAATATTT
56667086 AAAAATAAAAAAATATTT
1 AAAAATAAAAAAATATTT
56667104 A
1 A
56667105 TTATATTTGG
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
17 3 0.11
18 15 0.54
19 8 0.29
20 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAATAAAAAAATATTT
Found at i:56667403 original size:20 final size:19
Alignment explanation
Indices: 56667358--56667403 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
56667348 GTTTGGTTGG
56667358 TTAATTATTGAATTAATTA
1 TTAATTATTGAATTAATTA
*
56667377 TTCAATTATTGAGTTAATTA
1 TT-AATTATTGAATTAATTA
56667397 CTTAATT
1 -TTAATT
56667404 TAGTGCTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (19 bp):
TTAATTATTGAATTAATTA
Found at i:56673441 original size:37 final size:37
Alignment explanation
Indices: 56673393--56673470 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
56673383 TACTTGAGGG
56673393 TGCATGCCACCATATAATCACATCTTACACTAGATCA
1 TGCATGCCACCATATAATCACATCTTACACTAGATCA
56673430 TGCATGCCACCATATAATCACATCTTACACTAGATCA
1 TGCATGCCACCATATAATCACATCTTACACTAGATCA
56673467 TGCA
1 TGCA
56673471 AAAGAGGACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (37 bp):
TGCATGCCACCATATAATCACATCTTACACTAGATCA
Found at i:56673833 original size:53 final size:54
Alignment explanation
Indices: 56673771--56673891 Score: 158
Period size: 54 Copynumber: 2.3 Consensus size: 54
56673761 TTGGGGGTTT
*
56673771 GGGGAAAGTAAAAGGAAAAAA-TTAAAGG-GGTTTTGGGAAAGTA-AATGTTTTAG
1 GGGGAAAGTAAAAGGAAAAAAGTT-AAGGAGGTTTGGGGAAAGTACAAT-TTTTAG
* ** *
56673824 GGGGAAAGTAAAATGAAAAAAGTTTTGGAGGTTTGGGGGAAGTACAATTTTTAG
1 GGGGAAAGTAAAAGGAAAAAAGTTAAGGAGGTTTGGGGAAAGTACAATTTTTAG
56673878 GGGGAAAGTAAAAG
1 GGGGAAAGTAAAAG
56673892 TGTTTGAAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
53 22 0.37
54 34 0.58
55 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.34, T:0.24
Consensus pattern (54 bp):
GGGGAAAGTAAAAGGAAAAAAGTTAAGGAGGTTTGGGGAAAGTACAATTTTTAG
Found at i:56674904 original size:23 final size:21
Alignment explanation
Indices: 56674878--56674919 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
56674868 TTTTGTCCTA
*
56674878 CTTTTATTTTCAAGAATTTAATC
1 CTTTTAATTTC-AG-ATTTAATC
56674901 CTTTTAATTTCAGATTTAA
1 CTTTTAATTTCAGATTTAA
56674920 AATTGTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (21 bp):
CTTTTAATTTCAGATTTAATC
Found at i:56675138 original size:30 final size:29
Alignment explanation
Indices: 56675090--56675159 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
56675080 CATTTGCACT
* * * * *
56675090 TAATTTTTAAATCCAAAAAATATAATGAC
1 TAATTCTTAAAACTAAAAAATAGAAAGAC
56675119 TAAATTCTTAAAACTAAAAAATAGAAAGAC
1 T-AATTCTTAAAACTAAAAAATAGAAAGAC
*
56675149 TAATTTTTAAA
1 TAATTCTTAAA
56675160 TATGAATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (29 bp):
TAATTCTTAAAACTAAAAAATAGAAAGAC
Found at i:56679997 original size:2 final size:2
Alignment explanation
Indices: 56679992--56680031 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
56679982 TTTCTCTCTT
56679992 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56680031 T
1 T
56680032 TTAATAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56682246 original size:21 final size:20
Alignment explanation
Indices: 56682186--56682260 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 20
56682176 AAATTAAATC
* *
56682186 TCTAAGATTACAAAATCATATA
1 TCTAAGATTGCAATATC--ATA
56682208 TTCTAAGATTGC-ATATCATA
1 -TCTAAGATTGCAATATCATA
56682228 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
56682249 TCTAAGATTGCA
1 TCTAAGATTGCA
56682261 CATCCTTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.23
20 3 0.06
21 20 0.42
22 4 0.08
23 10 0.21
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:56683234 original size:29 final size:30
Alignment explanation
Indices: 56683202--56683263 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
56683192 CATTTTTTAG
**
56683202 ATTT-TATTTTTCTAGAATTTTTATATAGA
1 ATTTCTATTTTTAAAGAATTTTTATATAGA
*
56683231 ATTTTCTATTTTTAAATAATTTTTATATAGA
1 A-TTTCTATTTTTAAAGAATTTTTATATAGA
56683262 AT
1 AT
56683264 CAATGTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.04
30 4 0.14
31 23 0.82
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (30 bp):
ATTTCTATTTTTAAAGAATTTTTATATAGA
Found at i:56684853 original size:16 final size:16
Alignment explanation
Indices: 56684822--56684858 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
56684812 ATGTGAAGAA
56684822 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
56684838 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
56684854 TATTA
1 TATTA
56684859 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:56684956 original size:13 final size:14
Alignment explanation
Indices: 56684936--56684967 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
56684926 ATAATATGAA
56684936 AATA-TAATATTTT
1 AATATTAATATTTT
56684949 -ATATTAATATTTT
1 AATATTAATATTTT
56684962 AATATT
1 AATATT
56684968 TTTAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 9 0.53
14 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTAATATTTT
Found at i:56686799 original size:29 final size:27
Alignment explanation
Indices: 56686761--56686815 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
56686751 TAGAATCCAA
*
56686761 TCTTTATATTTTTATTTTTAAAAATTTAT
1 TCTTTATATTTTT-TATTT-AAAATTTAT
*
56686790 TCTTTTTATTTTTTATTTAAAATTTA
1 TCTTTATATTTTTTATTTAAAATTTA
56686816 ATTTTAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
29 12 0.50
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (27 bp):
TCTTTATATTTTTTATTTAAAATTTAT
Found at i:56691206 original size:27 final size:28
Alignment explanation
Indices: 56691144--56691200 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
56691134 CATTGGTAGA
* *
56691144 TGAACTAACAAATTAATAAAGAAATTGG
1 TGAACCAACAAATTAATAAAGAAATTAG
*
56691172 TGAACCAACAAATTAATTAA-AAATTAG
1 TGAACCAACAAATTAATAAAGAAATTAG
56691199 TG
1 TG
56691201 CGCCAAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (28 bp):
TGAACCAACAAATTAATAAAGAAATTAG
Found at i:56692390 original size:16 final size:16
Alignment explanation
Indices: 56692369--56692402 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
56692359 AGTTAGTACT
56692369 TTAATTTTT-TTATAAA
1 TTAATTTTTGTT-TAAA
56692385 TTAATTTTTGTTTAAA
1 TTAATTTTTGTTTAAA
56692401 TT
1 TT
56692403 TTTTAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTAATTTTTGTTTAAA
Found at i:56694862 original size:31 final size:31
Alignment explanation
Indices: 56694803--56694863 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
56694793 GGGATGAACA
**
56694803 TGTTGGGTCCGTCTCCTGTACTGGGTACAAC
1 TGTTGGGTCCGTCTCCTGTACTAAGTACAAC
* *
56694834 TGTTGGGTTCGTCTCGTGTACTAAGTACAA
1 TGTTGGGTCCGTCTCCTGTACTAAGTACAA
56694864 TTATATGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.34
Consensus pattern (31 bp):
TGTTGGGTCCGTCTCCTGTACTAAGTACAAC
Found at i:56697710 original size:28 final size:28
Alignment explanation
Indices: 56697678--56697735 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
56697668 AACAAAAGAG
56697678 TTGACTTATTCTTTTGTTAGAGTTATTT
1 TTGACTTATTCTTTTGTTAGAGTTATTT
56697706 TTGACTTATTCTTTTGTTAGAGTTATTT
1 TTGACTTATTCTTTTGTTAGAGTTATTT
56697734 TT
1 TT
56697736 TATATGCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (28 bp):
TTGACTTATTCTTTTGTTAGAGTTATTT
Found at i:56715084 original size:5 final size:5
Alignment explanation
Indices: 56715074--56715103 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
56715064 AAGAAAATAA
56715074 GAGGG GAGGG GAGGG GAGGG GAGGG GAGGG
1 GAGGG GAGGG GAGGG GAGGG GAGGG GAGGG
56715104 AGAGAGATGT
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:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
GAGGG
Found at i:56719255 original size:3 final size:3
Alignment explanation
Indices: 56719247--56719282 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
56719237 CAACCGCTTG
* *
56719247 AGA AGA AGA AGC AGA AGA GGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
56719283 GAGTTGAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.03, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:56720564 original size:3 final size:3
Alignment explanation
Indices: 56720556--56720583 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
56720546 CTTTGTTTTC
56720556 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
56720584 TCTCCTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:56720816 original size:3 final size:3
Alignment explanation
Indices: 56720803--56720863 Score: 67
Period size: 3 Copynumber: 21.7 Consensus size: 3
56720793 TCTAGAAATT
* *
56720803 TTC TT- TTC TTC TTC TTA TTC -TC TTC TTC TTC TTA TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
56720848 TTC -TC TGC TTC TTC TT
1 TTC TTC TTC TTC TTC TT
56720864 TTGCTTTTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 8 0.17
3 40 0.83
ACGTcount: A:0.03, C:0.30, G:0.02, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:56720817 original size:11 final size:11
Alignment explanation
Indices: 56720803--56720865 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
56720793 TCTAGAAATT
56720803 TTCTTTTCTTC
1 TTCTTTTCTTC
56720814 TTCTTATTC-TC
1 TTCTT-TTCTTC
*
56720825 TTCTTCTTCTTA
1 TTCTT-TTCTTC
*
56720837 TTCTCTTCTTC
1 TTCTTTTCTTC
* *
56720848 TTCTCTGCTTC
1 TTCTTTTCTTC
56720859 TTCTTTT
1 TTCTTTT
56720866 GCTTTTACAG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 35 0.81
12 8 0.19
ACGTcount: A:0.03, C:0.29, G:0.02, T:0.67
Consensus pattern (11 bp):
TTCTTTTCTTC
Found at i:56720828 original size:14 final size:14
Alignment explanation
Indices: 56720809--56720863 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
56720799 AATTTTCTTT
56720809 TCTTCTTCTTATTCTC
1 TCTTCTTCTTA-T-TC
56720825 TTCTTCTTCTTATTC
1 -TCTTCTTCTTATTC
*
56720840 TCTTCTTCTT-CTC
1 TCTTCTTCTTATTC
56720853 TGCTTCTTCTT
1 T-CTTCTTCTT
56720864 TTGCTTTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
13 3 0.08
14 19 0.53
15 2 0.06
16 1 0.03
17 11 0.31
ACGTcount: A:0.04, C:0.31, G:0.02, T:0.64
Consensus pattern (14 bp):
TCTTCTTCTTATTC
Found at i:56720828 original size:17 final size:17
Alignment explanation
Indices: 56720803--56720851 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
56720793 TCTAGAAATT
*
56720803 TTCTTTTCTTCTTCTTA
1 TTCTCTTCTTCTTCTTA
56720820 TTCTCTTCTTCTTCTTA
1 TTCTCTTCTTCTTCTTA
56720837 TTCTCTTCTTCTTCT
1 TTCTCTTCTTCTTCT
56720852 CTGCTTCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCTCTTCTTCTTCTTA
Found at i:56720860 original size:17 final size:16
Alignment explanation
Indices: 56720808--56720863 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 16
56720798 AAATTTTCTT
56720808 TTCTTCTTCTTATTCTC
1 TTCTTCTTCTTA-TCTC
56720825 TTCTTCTTCTTAT-TC
1 TTCTTCTTCTTATCTC
*
56720840 -TCTTCTTCTTCTCTGC
1 TTCTTCTTCTTATCT-C
56720856 TTCTTCTT
1 TTCTTCTT
56720864 TTGCTTTTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
14 11 0.31
15 3 0.09
16 2 0.06
17 19 0.54
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.64
Consensus pattern (16 bp):
TTCTTCTTCTTATCTC
Found at i:56721469 original size:60 final size:60
Alignment explanation
Indices: 56721405--56721518 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
56721395 ATACCTATTT
* *
56721405 TTTTAAGGATT-TACAAATATTTCTAA-GTTGTTACCAAAAATTCTAAAAGTTTATTGAAAA
1 TTTTAAGG-TTATACAAAAATTTCTAATGAT-TTACCAAAAATTCTAAAAGTTTATTGAAAA
* *
56721465 TTTTAAGGTTATACAAAAATTTCTAATGATTTACCAATAATTCTAAGAGTTTAT
1 TTTTAAGGTTATACAAAAATTTCTAATGATTTACCAAAAATTCTAAAAGTTTAT
56721519 CAGTATTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 44 0.92
61 2 0.04
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (60 bp):
TTTTAAGGTTATACAAAAATTTCTAATGATTTACCAAAAATTCTAAAAGTTTATTGAAAA
Found at i:56721528 original size:20 final size:20
Alignment explanation
Indices: 56721483--56721536 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
56721473 TTATACAAAA
56721483 ATTTCTAATGATTTACCAAT
1 ATTTCTAATGATTTACCAAT
* * *
56721503 AATTCTAA-GAGTTTATCAGT
1 ATTTCTAATGA-TTTACCAAT
*
56721523 ATTTCTAAAGATTT
1 ATTTCTAATGATTT
56721537 CCTTAGTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (20 bp):
ATTTCTAATGATTTACCAAT
Found at i:56721626 original size:20 final size:20
Alignment explanation
Indices: 56721576--56721674 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
56721566 CATTTTGACA
56721576 TACCAAAATTTCTAAAGG-TT
1 TACCAAAATTTCT-AAGGATT
**
56721596 T-CTCACTATTTCTAAGGATT
1 TAC-CAAAATTTCTAAGGATT
56721616 TACCAAAATTTAC-AAGG-TT
1 TACCAAAATTT-CTAAGGATT
* *
56721635 ATACAAAAAATT-TAATGGATT
1 -TACCAAAATTTCTAA-GGATT
*
56721656 TACCAGAATTTCTAAGGAT
1 TACCAAAATTTCTAAGGAT
56721675 AATTTGGTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
19 9 0.15
20 45 0.74
21 7 0.11
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.35
Consensus pattern (20 bp):
TACCAAAATTTCTAAGGATT
Found at i:56721702 original size:20 final size:20
Alignment explanation
Indices: 56721677--56721723 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
56721667 CTAAGGATAA
* **
56721677 TTTGGTATAACCTTAGATGT
1 TTTGGTATAACCTAAGAAAT
56721697 TTTGGTATAACCTAAGAAAT
1 TTTGGTATAACCTAAGAAAT
56721717 TTTGGTA
1 TTTGGTA
56721724 GATCCTTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (20 bp):
TTTGGTATAACCTAAGAAAT
Found at i:56721828 original size:20 final size:20
Alignment explanation
Indices: 56721786--56722031 Score: 138
Period size: 20 Copynumber: 12.6 Consensus size: 20
56721776 GACACTAGGG
* *
56721786 AAATCTTTAGAAATATTT-TT
1 AAATCCTTAGAAAT-TTTGGT
56721806 AAATCCTTAGAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* * *
56721826 AAAGCCTT-CAAA--TTCGT
1 AAATCCTTAGAAATTTTGGT
* *
56721843 AAATCTTTAGATATTTTGGT
1 AAATCCTTAGAAATTTTGGT
56721863 ATAA-CCTTA-AGAATTTTGGT
1 A-AATCCTTAGA-AATTTTGGT
* * *
56721883 AAATTCTTAGATATTTTGAT
1 AAATCCTTAGAAATTTTGGT
*
56721903 ATAA-CCTTAGAAATTTTGAT
1 A-AATCCTTAGAAATTTTGGT
56721923 AAAAT-CTTAGAAA--TTGGT
1 -AAATCCTTAGAAATTTTGGT
* **
56721941 AAAACCTTAGAAATTTTAAT
1 AAATCCTTAGAAATTTTGGT
* * * *
56721961 GAAGCCTTTA-AAACTTTGGC
1 AAATCC-TTAGAAATTTTGGT
** **
56721981 AAATATTTAGATTTTTTGGT
1 AAATCCTTAGAAATTTTGGT
56722001 ATAA-CCTTAGAAATTTTGGT
1 A-AATCCTTAGAAATTTTGGT
*
56722021 AAATTCTTAGA
1 AAATCCTTAGA
56722032 TTTTTTTGTA
Statistics
Matches: 168, Mismatches: 40, Indels: 36
0.69 0.16 0.15
Matches are distributed among these distances:
17 13 0.08
18 14 0.08
19 14 0.08
20 116 0.69
21 11 0.07
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (20 bp):
AAATCCTTAGAAATTTTGGT
Found at i:56721943 original size:18 final size:18
Alignment explanation
Indices: 56721898--56721955 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
56721888 CTTAGATATT
*
56721898 TTGATATAACCTTAGAAA
1 TTGATAAAACCTTAGAAA
*
56721916 TTTTGATAAAATCTTAGAAA
1 --TTGATAAAACCTTAGAAA
*
56721936 TTGGTAAAACCTTAGAAA
1 TTGATAAAACCTTAGAAA
56721954 TT
1 TT
56721956 TTAATGAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 18 0.53
20 16 0.47
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (18 bp):
TTGATAAAACCTTAGAAA
Found at i:56722037 original size:20 final size:20
Alignment explanation
Indices: 56721987--56722037 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
56721977 TGGCAAATAT
56721987 TTAGATTTTTTGGTATAACC
1 TTAGATTTTTTGGTATAACC
** *
56722007 TTAGAAATTTTGGTA-AATTC
1 TTAGATTTTTTGGTATAA-CC
56722027 TTAGATTTTTT
1 TTAGATTTTTT
56722038 TGTAGGCCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (20 bp):
TTAGATTTTTTGGTATAACC
Found at i:56723530 original size:20 final size:21
Alignment explanation
Indices: 56723507--56723552 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
56723497 AAATTTATTT
*
56723507 AAAATT-TTAAAAAAAATATA
1 AAAATTATTAAAAAAAATAAA
**
56723527 AAAATTATTGTAAAAAATAAA
1 AAAATTATTAAAAAAAATAAA
56723548 AAAAT
1 AAAAT
56723553 GAACATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAATTATTAAAAAAAATAAA
Found at i:56724908 original size:8 final size:8
Alignment explanation
Indices: 56724895--56724923 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
56724885 CACTAGAGAC
56724895 CAGTGTTA
1 CAGTGTTA
56724903 CAGTGTTA
1 CAGTGTTA
56724911 CAGTGTTA
1 CAGTGTTA
56724919 CAGTG
1 CAGTG
56724924 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:56725037 original size:23 final size:23
Alignment explanation
Indices: 56725010--56725085 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
56725000 AGTGTTATTG
56725010 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
56725033 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
56725056 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
56725079 ATCAGTG
1 ATCAGTG
56725086 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:56726579 original size:17 final size:17
Alignment explanation
Indices: 56726554--56726600 Score: 73
Period size: 15 Copynumber: 2.9 Consensus size: 17
56726544 TTAATAAAAT
56726554 TTTTA-AATATTTTTTC
1 TTTTATAATATTTTTTC
56726570 TTTTATAATATTTTTTC
1 TTTTATAATATTTTTTC
56726587 -TTT-TAATATTTTTT
1 TTTTATAATATTTTTT
56726601 ATACTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.37
16 8 0.27
17 11 0.37
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATAATATTTTTTC
Found at i:56726593 original size:15 final size:16
Alignment explanation
Indices: 56726553--56726600 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 16
56726543 TTTAATAAAA
56726553 TTTTTAAATATTTTTTC
1 TTTTT-AATATTTTTTC
56726570 TTTTATAATATTTTTTC
1 TTTT-TAATATTTTTTC
56726587 -TTTTAATATTTTTT
1 TTTTTAATATTTTTT
56726601 ATACTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.37
16 3 0.10
17 15 0.50
18 1 0.03
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTAATATTTTTTC
Found at i:56726631 original size:18 final size:19
Alignment explanation
Indices: 56726587--56726632 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
56726577 ATATTTTTTC
* *
56726587 TTTTAATATTTTTTATACT
1 TTTTAATTTTTTTTATAAT
56726606 TTTGTAATTTTTTTTA-AAT
1 TTT-TAATTTTTTTTATAAT
56726625 TTTTAATT
1 TTTTAATT
56726633 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 8 0.33
20 11 0.46
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTAATTTTTTTTATAAT
Found at i:56726881 original size:24 final size:24
Alignment explanation
Indices: 56726817--56726881 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
56726807 ATTTTTTATA
**
56726817 AATTTTTTTTCTATATTTTATAAT
1 AATTTTTTTTCTATATTTTGCAAT
*
56726841 AA-TTTTTTAC-ATA-TTTGCAAT
1 AATTTTTTTTCTATATTTTGCAAT
56726862 AATTTTTTTTCTATATTTTG
1 AATTTTTTTTCTATATTTTG
56726882 TATTTTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 8 0.24
22 10 0.29
23 10 0.29
24 6 0.18
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (24 bp):
AATTTTTTTTCTATATTTTGCAAT
Found at i:56731894 original size:38 final size:38
Alignment explanation
Indices: 56731838--56731913 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
56731828 TCTGAAGTAA
56731838 TCATGTATGACACCCAAATTCGAGAATTATATGGAAAC
1 TCATGTATGACACCCAAATTCGAGAATTATATGGAAAC
* *
56731876 TCATGTATGACACTCAAATTTGAGAATTATATGGAAAC
1 TCATGTATGACACCCAAATTCGAGAATTATATGGAAAC
56731914 GAGCATAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (38 bp):
TCATGTATGACACCCAAATTCGAGAATTATATGGAAAC
Found at i:56736409 original size:24 final size:24
Alignment explanation
Indices: 56736358--56736409 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
56736348 TATCGGTTTT
* *
56736358 TTTTTTACTTTGATATTTAAATAT
1 TTTTTTACTTTGATACTTAAATAA
*
56736382 TTTTTTA-TTATGATACTTATATAA
1 TTTTTTACTT-TGATACTTAAATAA
56736406 TTTT
1 TTTT
56736410 ATCAGTGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (24 bp):
TTTTTTACTTTGATACTTAAATAA
Found at i:56736504 original size:11 final size:11
Alignment explanation
Indices: 56736490--56736515 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56736480 AAAAAAGTAT
56736490 AATTAATTTAA
1 AATTAATTTAA
56736501 AATTAATTTAA
1 AATTAATTTAA
56736512 AATT
1 AATT
56736516 TTCTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTAATTTAA
Found at i:56736816 original size:17 final size:18
Alignment explanation
Indices: 56736794--56736831 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
56736784 TAATTTCTAC
*
56736794 AAAAATCTT-AAAATTTA
1 AAAAATATTAAAAATTTA
56736811 AAAAATATTAAAAATTTA
1 AAAAATATTAAAAATTTA
56736829 AAA
1 AAA
56736832 GAAAATTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATATTAAAAATTTA
Done.