Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 38 of 203
Found at i:12458472 original size:55 final size:54
Alignment explanation
Indices: 12458406--12458676 Score: 269
Period size: 55 Copynumber: 4.8 Consensus size: 54
12458396 TCTTTTTTGA
* * * * *
12458406 GTTTTTGTTGCCTTTTGACTTGATGGGTACTTTTAATTTCATTGTTATTTTGCGG
1 GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTC-TTGTTAGTTTGTGG
*
12458461 GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATATCTTGTTTAGTTTGTGG
1 GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTCTTG-TTAGTTTGTGG
* * * *
12458516 GTTTTTCTTCTTGCCCTTCGGCTTGATGTGTAG--TTAATTTCTTTGTTATTTTGTGG
1 G--TTT-TTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTC-TTGTTAGTTTGTGG
** *
12458572 GTTTTTTATTTCTTGCCTTTTGATTTGATGGGTAATTTTAATTTCTTTGTTAGTTTGTAGG
1 G----TT-TTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTC-TTGTTAGTTTGT-GG
* *
12458633 GTTCTT-TTGCCTTTTGGCTTGATGGGTAGTTTTAGTTTCTTGTT
1 GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTCTTGTT
12458677 TAATTTGAGG
Statistics
Matches: 182, Mismatches: 23, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
54 8 0.04
55 75 0.41
56 20 0.11
57 8 0.04
58 47 0.26
59 1 0.01
60 20 0.11
61 3 0.02
ACGTcount: A:0.11, C:0.10, G:0.23, T:0.56
Consensus pattern (54 bp):
GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTCTTGTTAGTTTGTGG
Found at i:12466416 original size:151 final size:151
Alignment explanation
Indices: 12466142--12466448 Score: 535
Period size: 151 Copynumber: 2.0 Consensus size: 151
12466132 GTATCCAAAA
* **
12466142 CTACTAGGTTTAGTGATGATAATATCAGATCTAGATGGATTGATCCATTGTGAATGGTTGGGATT
1 CTACTAGGTCTAGTGATGATAATATCAGATCTAGATGGATTGATCCAGGGTGAATGGTTGGGATT
*
12466207 CCATGATTGTAGATGATAAGTTGTAGACAAAACGAACCAATGCTCTAGACCTAGAATAAGACCGA
66 CCATGATTGTAGATGATAAGTTGTAGACAAAACGAACCAATGCTCAAGACCTAGAATAAGACCGA
12466272 TTGAACTACGGTTATATAACT
131 TTGAACTACGGTTATATAACT
* *
12466293 CTACTAGGTCTAGTGATGATAATATTAGATTTAGATGGATTGATCCAGGGTGAATGGTTGGGATT
1 CTACTAGGTCTAGTGATGATAATATCAGATCTAGATGGATTGATCCAGGGTGAATGGTTGGGATT
*
12466358 CCATGATTGTAGATGATAAGTTGTAGACAAAAC-AAGCCAATGCTCAAGACCTAGAATAAGACTG
66 CCATGATTGTAGATGATAAGTTGTAGACAAAACGAA-CCAATGCTCAAGACCTAGAATAAGACCG
12466422 ATTGAACTACGGTTATATAACT
130 ATTGAACTACGGTTATATAACT
12466444 CTACT
1 CTACT
12466449 GTAACTACAA
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
150 2 0.01
151 146 0.99
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (151 bp):
CTACTAGGTCTAGTGATGATAATATCAGATCTAGATGGATTGATCCAGGGTGAATGGTTGGGATT
CCATGATTGTAGATGATAAGTTGTAGACAAAACGAACCAATGCTCAAGACCTAGAATAAGACCGA
TTGAACTACGGTTATATAACT
Found at i:12468177 original size:23 final size:22
Alignment explanation
Indices: 12468147--12468250 Score: 107
Period size: 23 Copynumber: 5.0 Consensus size: 22
12468137 TCTATGCTGC
12468147 AATATTCGGATTTACTAAGCTCA
1 AATATTCGGATTTACTAAGCT-A
12468170 AATATTCGGATTTACTAAGCTA
1 AATATTCGGATTTACTAAGCTA
* *
12468192 AATCA-TC---TATGCT--GC--
1 AAT-ATTCGGATTTACTAAGCTA
12468207 AATATTCGGATTTACTAAGCTCA
1 AATATTCGGATTTACTAAGCT-A
12468230 AATATTCGGATTTACTAAGCT
1 AATATTCGGATTTACTAAGCT
12468251 CAAAACCTGG
Statistics
Matches: 67, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.01
15 5 0.07
17 2 0.03
18 4 0.06
19 4 0.06
20 2 0.03
22 6 0.09
23 43 0.64
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (22 bp):
AATATTCGGATTTACTAAGCTA
Found at i:12468223 original size:60 final size:60
Alignment explanation
Indices: 12468130--12468250 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
12468120 CATTTCCTTT
12468130 TAAATCATCTATGCTGCAATATTCGGATTTACTAAGCTCAAATATTCGGATTTACTAAGC
1 TAAATCATCTATGCTGCAATATTCGGATTTACTAAGCTCAAATATTCGGATTTACTAAGC
12468190 TAAATCATCTATGCTGCAATATTCGGATTTACTAAGCTCAAATATTCGGATTTACTAAGC
1 TAAATCATCTATGCTGCAATATTCGGATTTACTAAGCTCAAATATTCGGATTTACTAAGC
12468250 T
1 T
12468251 CAAAACCTGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (60 bp):
TAAATCATCTATGCTGCAATATTCGGATTTACTAAGCTCAAATATTCGGATTTACTAAGC
Found at i:12469340 original size:28 final size:28
Alignment explanation
Indices: 12469300--12469357 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
12469290 ATGAATGGTG
12469300 GCCTTTTCCTTTGTAAAATGTTTCAAAT
1 GCCTTTTCCTTTGTAAAATGTTTCAAAT
12469328 GCCTTTTCCTTTGTAAAATGTTTCAAAT
1 GCCTTTTCCTTTGTAAAATGTTTCAAAT
12469356 GC
1 GC
12469358 AACTACCATC
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:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (28 bp):
GCCTTTTCCTTTGTAAAATGTTTCAAAT
Found at i:12469466 original size:246 final size:245
Alignment explanation
Indices: 12469085--12469575 Score: 777
Period size: 246 Copynumber: 2.0 Consensus size: 245
12469075 GAATGACGGA
* * * * * *
12469085 CTTTTCCTTGTAAAATGTTTTAAATACAACTACCATCCCTATTGGAGACAAACACAACTTTACGC
1 CTTTTCCTTGTAAAATGTTTCAAATACAACTACCATCCATATCGAAGACAAAAACAACTTCACGC
* * *
12469150 AAAAGAATTGCAAAAAGCAAACCCTCCAAGGCCAAGGAGCTTACACTAGTTTACAGGTCTTTTGT
66 AAAAGAATTACAAAAAGCAAACCCTCCAAGGCCAAGGAGCTTACACTAATTTACAGGTCTATTGT
*
12469215 GACATAAAAAACACTATCCCTACATATAAAATGTACAAATCATGATGCATTCAACTCGGGATGAA
131 GACATAAAAAACACTATCCCTACATATAAAATGTACAAATCATGATGCATTCAACTAGGGATGAA
* *
12469280 GACGAGATACATGAATGGTGGCCTTT-TCCTTTGTAAAATGTTTCAAATGC
196 GACGAGATACATGAATGATGGCCTTTCTCC-TTATAAAATGTTTCAAATGC
* **
12469330 CTTTTCCTTTGTAAAATGTTTCAAATGCAACTACCATCCATATCGAAGACAAAAACAACTTCGTG
1 CTTTTCC-TTGTAAAATGTTTCAAATACAACTACCATCCATATCGAAGACAAAAACAACTTCACG
* * *
12469395 CAAAAGAATTACAAAAAGCAAACCCTGCGAGGCCAAGGAGCTTACACTAATTTGCAGGTCTATTG
65 CAAAAGAATTACAAAAAGCAAACCCTCCAAGGCCAAGGAGCTTACACTAATTTACAGGTCTATTG
* *
12469460 TGACATAAAACATACTATCCCTACATATAAAATGTACAAATCATGATGCATTCAACTAGGGATGA
130 TGACATAAAAAACACTATCCCTACATATAAAATGTACAAATCATGATGCATTCAACTAGGGATGA
12469525 AGACGAGATACATGAATGATGGCCTTTCTCCTTATAAAATGTTTCAAATGC
195 AGACGAGATACATGAATGATGGCCTTTCTCCTTATAAAATGTTTCAAATGC
12469576 AACTACCATC
Statistics
Matches: 224, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
245 7 0.03
246 214 0.96
247 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (245 bp):
CTTTTCCTTGTAAAATGTTTCAAATACAACTACCATCCATATCGAAGACAAAAACAACTTCACGC
AAAAGAATTACAAAAAGCAAACCCTCCAAGGCCAAGGAGCTTACACTAATTTACAGGTCTATTGT
GACATAAAAAACACTATCCCTACATATAAAATGTACAAATCATGATGCATTCAACTAGGGATGAA
GACGAGATACATGAATGATGGCCTTTCTCCTTATAAAATGTTTCAAATGC
Found at i:12475663 original size:15 final size:16
Alignment explanation
Indices: 12475635--12475669 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
12475625 TAAATCACTT
*
12475635 AAATAAACAGTAAATC
1 AAATAAACAGTAAAAC
12475651 AAATAAA-AGTAAAAC
1 AAATAAACAGTAAAAC
12475666 AAAT
1 AAAT
12475670 CCAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATAAACAGTAAAAC
Found at i:12475856 original size:3 final size:3
Alignment explanation
Indices: 12475850--12475888 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
12475840 AGACAATGAT
*
12475850 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
12475889 TATTCTGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12484615 original size:22 final size:21
Alignment explanation
Indices: 12484590--12484632 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
12484580 AAAGAACCCT
12484590 AGCCCTAAGGAGCGCCGCAGCA
1 AGCCCTAAGGAGCGCC-CAGCA
* * *
12484612 AGCCTTTAGGTGCGCCCAGCA
1 AGCCCTAAGGAGCGCCCAGCA
12484633 GCCTCGCGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.23, C:0.35, G:0.30, T:0.12
Consensus pattern (21 bp):
AGCCCTAAGGAGCGCCCAGCA
Found at i:12485122 original size:14 final size:13
Alignment explanation
Indices: 12485102--12485133 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
12485092 TAGAGAAACG
12485102 TTTTTTTTATTTT
1 TTTTTTTTATTTT
12485115 TATTTTTTTATTTT
1 T-TTTTTTTATTTT
12485129 TTTTT
1 TTTTT
12485134 CTTTCATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (13 bp):
TTTTTTTTATTTT
Found at i:12485349 original size:15 final size:16
Alignment explanation
Indices: 12485331--12485368 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
12485321 TAAATATTTA
*
12485331 TTATTGTTAT-ATTAT
1 TTATTATTATGATTAT
12485346 TTATTATTATGATTA-
1 TTATTATTATGATTAT
12485361 TTATTATT
1 TTATTATT
12485369 TCTATATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (16 bp):
TTATTATTATGATTAT
Found at i:12485407 original size:16 final size:16
Alignment explanation
Indices: 12485388--12485431 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
12485378 TTATACGTAT
12485388 ATATATATTTTTTTAA
1 ATATATATTTTTTTAA
** *
12485404 ATATATACATTTTTAT
1 ATATATATTTTTTTAA
*
12485420 ATATGTATTTTT
1 ATATATATTTTT
12485432 AAACTTTTTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
ATATATATTTTTTTAA
Found at i:12493422 original size:28 final size:28
Alignment explanation
Indices: 12493380--12493434 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
12493370 GATAAAGATG
12493380 CATCCTGAAGACATGAGAAAGACTACGA
1 CATCCTGAAGACATGAGAAAGACTACGA
*
12493408 CATCCTGAAGGCATGAGAAAGACTACG
1 CATCCTGAAGACATGAGAAAGACTACG
12493435 TTCATTACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.15
Consensus pattern (28 bp):
CATCCTGAAGACATGAGAAAGACTACGA
Found at i:12497170 original size:45 final size:45
Alignment explanation
Indices: 12497102--12497280 Score: 137
Period size: 45 Copynumber: 3.9 Consensus size: 45
12497092 GTTGAAAAGC
* *** *
12497102 AGCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAA-GAA
1 AGCAGATCTTGTCTTCATGTACTGG-CGCGAAGCAGATCAAAGGAA
* * * ** * *
12497147 AGTAAATCTTGTTTTCATGTACTGGCATGAAGTAGATCAAAGGTA
1 AGCAGATCTTGTCTTCATGTACTGGCGCGAAGCAGATCAAAGGAA
* *** *
12497192 A-CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAA
1 AGCAGATCTTGTCTTCATGTACTGG-CGCGAAGCAGATCAAAGG--AA
* *
12497239 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAG
1 AGCAGATCTTGTCTTCATGTACTGGCGCGAAGCAGATCAAAG
12497281 ACATCAGGTC
Statistics
Matches: 98, Mismatches: 31, Indels: 8
0.72 0.23 0.06
Matches are distributed among these distances:
44 28 0.29
45 35 0.36
47 16 0.16
48 19 0.19
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (45 bp):
AGCAGATCTTGTCTTCATGTACTGGCGCGAAGCAGATCAAAGGAA
Found at i:12497213 original size:89 final size:91
Alignment explanation
Indices: 12497104--12497280 Score: 295
Period size: 89 Copynumber: 2.0 Consensus size: 91
12497094 TGAAAAGCAG
* *
12497104 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAA-G-AAAGTAAATCTTGTTTTCATGT
1 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAAGCAAATCTTGTCTTCATGT
12497167 ACTGGCATGAAGTAGATCAAAGGTAA
66 ACTGGCATGAAGTAGATCAAAGGTAA
*
12497193 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAAAGCAGATCTTGTCTTCATG
1 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGG-AAAAGCAAATCTTGTCTTCATG
*
12497258 TACTGGCGTGAAGTAGATCAAAG
65 TACTGGCATGAAGTAGATCAAAG
12497281 ACATCAGGTC
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
89 40 0.49
90 1 0.01
92 40 0.49
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (91 bp):
CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAAGCAAATCTTGTCTTCATGT
ACTGGCATGAAGTAGATCAAAGGTAA
Found at i:12497314 original size:92 final size:89
Alignment explanation
Indices: 12497104--12497315 Score: 255
Period size: 92 Copynumber: 2.3 Consensus size: 89
12497094 TGAAAAGCAG
* * * *
12497104 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGTAAATCTTGTTTTCATGTAC
1 CAGATCCTGCCTTCCCATACTGGTAGCGAAGCAGATCAAAGAAAGCAAATCTTGTCTTCATGTAC
**
12497169 TGGCATGAAGTAGATCAAAGGTAA
66 TGGCATGAAGTAGATCAAAGACAA
* * *
12497193 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAAAGCAGATCTTGTCTTCATG
1 CAGATCCTGCCTTCCCATACTGGTAGCGAAGCAGATCAAA-G--AAAGCAAATCTTGTCTTCATG
* *
12497258 TACTGGCGTGAAGTAGATCAAAGACAT
63 TACTGGCATGAAGTAGATCAAAGACAA
* * *
12497285 CAGGTCCTGTCTTCCTATA-TCGGTAGCGAAG
1 CAGATCCTGCCTTCCCATACT-GGTAGCGAAG
12497316 TGGATCGAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
89 40 0.37
90 1 0.01
91 1 0.01
92 65 0.61
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (89 bp):
CAGATCCTGCCTTCCCATACTGGTAGCGAAGCAGATCAAAGAAAGCAAATCTTGTCTTCATGTAC
TGGCATGAAGTAGATCAAAGACAA
Found at i:12497539 original size:44 final size:45
Alignment explanation
Indices: 12497480--12497592 Score: 138
Period size: 44 Copynumber: 2.5 Consensus size: 45
12497470 ATCTCCCCAT
* * * * **
12497480 ACTGGTGGTGGAGTAGATTGAAGAAAGCAGATCTTGTCTTCACGT
1 ACTGGTCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCACAC
* *
12497525 ACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCAC
1 ACTGGTCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCACAC
*
12497569 ACTGGTGGTGAAGTAGATCGAAGA
1 ACTGGTCGTGAAGTAGATCGAAGA
12497593 TACAAGTCTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 36 0.63
45 21 0.37
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (45 bp):
ACTGGTCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCACAC
Found at i:12499170 original size:15 final size:14
Alignment explanation
Indices: 12499134--12499174 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
12499124 TTTAAAATTT
*
12499134 TTATTATTGTTAGA
1 TTATTATTATTAGA
12499148 TTATTTATTATTATGA
1 TTA-TTATTATTA-GA
12499164 TTATTATTATT
1 TTATTATTATT
12499175 TCTATATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 3 0.12
15 16 0.67
16 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TTATTATTATTAGA
Found at i:12503876 original size:197 final size:198
Alignment explanation
Indices: 12503568--12503934 Score: 458
Period size: 197 Copynumber: 1.9 Consensus size: 198
12503558 TTTTTTTAAA
* * * *
12503568 TTTGAAATTGTAACGTAAAGCATCAAAAAAGTGAAAAAATGGAAATCGAAGCATTCAATTTCTCT
1 TTTGAAATTGTAACGTAAAGCATCAAAAAAGTAAAAAAATGGAAACCGAAGCATTCAAATTCACT
* * * *
12503633 AAAAATGGAAATTTTAAATTACGTAAAACCTTTCAGCCATCATCAAAGATCAACATTGTTGAAAA
66 AAAAATGGAAATATTAAATTACGTAAAACCTTTCAGCCACCATCAAAGATAAACATTGTTAAAAA
* * *
12503698 CTT-AAGTCAACATATTCATAGATCAACAACAAAAACAATAATATTTCGCTATTATTTTTTGAAA
131 ATTGAAGGCAACATACTCATAGATCAACAACAAAAACAATAATATTTCGCTATTATTTTTTGAAA
12503762 AAT
196 AAT
* * **
12503765 TTTGAAATTGTAATGTAAAGCATC-TAAGGGTAAAAAAATTCGG-AACCGAAGCATTCAAATTCA
1 TTTGAAATTGTAACGTAAAGCATCAAAAAAGTAAAAAAA-T-GGAAACCGAAGCATTCAAATTC-
* * * * *
12503828 ACTGAAACT-GAAA-ATTAAATTACGTGACAACCTTCTC-GTCACCATCAAAGATAAATATTGTT
63 ACTAAAAATGGAAATATTAAATTACGT-AAAACCTT-TCAGCCACCATCAAAGATAAACATTGTT
*
12503890 AAAAAATTGAAGGCAACATACTCATGGATCAACAACAAAAACAAT
126 AAAAAATTGAAGGCAACATACTCATAGATCAACAACAAAAACAAT
12503935 CAAACTTCGC
Statistics
Matches: 143, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
196 21 0.15
197 79 0.55
198 43 0.30
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (198 bp):
TTTGAAATTGTAACGTAAAGCATCAAAAAAGTAAAAAAATGGAAACCGAAGCATTCAAATTCACT
AAAAATGGAAATATTAAATTACGTAAAACCTTTCAGCCACCATCAAAGATAAACATTGTTAAAAA
ATTGAAGGCAACATACTCATAGATCAACAACAAAAACAATAATATTTCGCTATTATTTTTTGAAA
AAT
Found at i:12507862 original size:23 final size:24
Alignment explanation
Indices: 12507811--12507855 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
12507801 AAATGTATTT
*
12507811 ATAATATAAAATATTAATATTTTA
1 ATAATATAAAATATGAATATTTTA
12507835 ATAATAT-AAATATGAATATTT
1 ATAATATAAAATATGAATATTT
12507856 ATTTAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAATATAAAATATGAATATTTTA
Found at i:12508495 original size:26 final size:25
Alignment explanation
Indices: 12508456--12508512 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
12508446 AAATTTAATA
*
12508456 AATTAAATTATTTAAAATAAAAAATT
1 AATTTAATTATTT-AAATAAAAAATT
* * *
12508482 AATTTAATTTTTTAGATAAAACATT
1 AATTTAATTATTTAAATAAAAAATT
12508507 AATTTA
1 AATTTA
12508513 TCATAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
AATTTAATTATTTAAATAAAAAATT
Found at i:12512529 original size:20 final size:19
Alignment explanation
Indices: 12512504--12512548 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
12512494 TTAATGACAA
*
12512504 AAATTATTATTTTATAATTT
1 AAATTATTATATTA-AATTT
*
12512524 AAATTATTATATTAATTTT
1 AAATTATTATATTAAATTT
12512543 AAATTA
1 AAATTA
12512549 AATTAGTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTATTATATTAAATTT
Found at i:12513647 original size:19 final size:20
Alignment explanation
Indices: 12513604--12513652 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
12513594 TTATTTAACA
* *
12513604 TATTTATAGTATAACTAATT
1 TATTTATATTATAAATAATT
*
12513624 TATTTATATTATAAATTA-T
1 TATTTATATTATAAATAATT
12513643 TATTTATATT
1 TATTTATATT
12513653 CTTTTAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTATATTATAAATAATT
Found at i:12516689 original size:34 final size:34
Alignment explanation
Indices: 12516648--12516715 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
12516638 TCGAAATTTA
12516648 GGAGGGTTTGAATAAAAACATTAAGTTCGAAAAT
1 GGAGGGTTTGAATAAAAACATTAAGTTCGAAAAT
12516682 GGAGGGTTTGAATAAAAACATTAAGTTCGAAAAT
1 GGAGGGTTTGAATAAAAACATTAAGTTCGAAAAT
12516716 AGACTTGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (34 bp):
GGAGGGTTTGAATAAAAACATTAAGTTCGAAAAT
Found at i:12534958 original size:15 final size:15
Alignment explanation
Indices: 12534934--12534974 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
12534924 TCCTGATCAG
*
12534934 TAAACTTAAATGATT
1 TAAACCTAAATGATT
12534949 TAAACCTAAAATGATT
1 TAAACCT-AAATGATT
*
12534965 TGAACCTAAA
1 TAAACCTAAA
12534975 ATAAGCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (15 bp):
TAAACCTAAATGATT
Found at i:12534962 original size:16 final size:16
Alignment explanation
Indices: 12534941--12534976 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
12534931 CAGTAAACTT
12534941 AAATGATTTAAACCTA
1 AAATGATTTAAACCTA
*
12534957 AAATGATTTGAACCTA
1 AAATGATTTAAACCTA
12534973 AAAT
1 AAAT
12534977 AAGCTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (16 bp):
AAATGATTTAAACCTA
Found at i:12540114 original size:23 final size:23
Alignment explanation
Indices: 12540065--12540107 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12540055 TTTCAATCCC
*
12540065 TTAA-AAATGATGAAACTATAAA
1 TTAACAAATGATAAAACTATAAA
*
12540087 TTAACAAATGATAAAATTATA
1 TTAACAAATGATAAAACTATA
12540108 CTTTAACCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (23 bp):
TTAACAAATGATAAAACTATAAA
Found at i:12542072 original size:8 final size:9
Alignment explanation
Indices: 12542049--12542075 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
12542039 TTACGTGACT
12542049 TTAAAAATA
1 TTAAAAATA
12542058 TTAAAAATA
1 TTAAAAATA
12542067 TTAAAAATA
1 TTAAAAATA
12542076 AATAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAAAATA
Found at i:12543047 original size:13 final size:14
Alignment explanation
Indices: 12543014--12543051 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
12543004 ATACATCTAT
12543014 TATTATTAATTTGTA
1 TATTATT-ATTTGTA
12543029 TA-TATTATTT-TA
1 TATTATTATTTGTA
12543041 TATTATTATTT
1 TATTATTATTT
12543052 AAACATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 12 0.55
14 4 0.18
15 2 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
TATTATTATTTGTA
Found at i:12545223 original size:31 final size:30
Alignment explanation
Indices: 12545155--12545234 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
12545145 CATTTGAACC
* *
12545155 TAAATC-AAGTTTACTATATAAAATTACACA
1 TAAATCAAAATTTA-TATATAAAATTACAAA
* *
12545185 -AAATCAAACTTTATATATCAAATTACAAA
1 TAAATCAAAATTTATATATAAAATTACAAA
*
12545214 TTAAATCAAAATTCATATATA
1 -TAAATCAAAATTTATATATA
12545235 TTTTTTATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
29 19 0.46
30 6 0.15
31 16 0.39
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (30 bp):
TAAATCAAAATTTATATATAAAATTACAAA
Found at i:12546302 original size:15 final size:17
Alignment explanation
Indices: 12546282--12546314 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
12546272 GTTCCTCAAC
12546282 TTTGGT-TTTTA-CCAA
1 TTTGGTCTTTTATCCAA
12546297 TTTGGTCTTTTATCCAA
1 TTTGGTCTTTTATCCAA
12546314 T
1 T
12546315 AAGCACCCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.55
Consensus pattern (17 bp):
TTTGGTCTTTTATCCAA
Found at i:12551346 original size:3 final size:3
Alignment explanation
Indices: 12551338--12551374 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12551328 GTCTGTGTGT
12551338 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12551375 GCTCTAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12558239 original size:20 final size:20
Alignment explanation
Indices: 12558216--12558256 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12558206 TTTTCTACGT
12558216 AATAAAGC-ATAAATGAAAAA
1 AATAAAGCAATAAA-GAAAAA
*
12558236 AATAAATCAATAAAGAAAAA
1 AATAAAGCAATAAAGAAAAA
12558256 A
1 A
12558257 CACTCATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (20 bp):
AATAAAGCAATAAAGAAAAA
Found at i:12559146 original size:13 final size:13
Alignment explanation
Indices: 12559128--12559159 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12559118 TACTTTGACA
12559128 AATTTTGATATTT
1 AATTTTGATATTT
12559141 AATTTTGATATTT
1 AATTTTGATATTT
*
12559154 AGTTTT
1 AATTTT
12559160 TTGTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (13 bp):
AATTTTGATATTT
Found at i:12564897 original size:14 final size:14
Alignment explanation
Indices: 12564878--12564908 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12564868 ATGAGTTCAC
12564878 AAATATAATTACAG
1 AAATATAATTACAG
*
12564892 AAATATATTTACAG
1 AAATATAATTACAG
12564906 AAA
1 AAA
12564909 ATGAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (14 bp):
AAATATAATTACAG
Found at i:12580631 original size:26 final size:25
Alignment explanation
Indices: 12580578--12580643 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
12580568 TGCATTCGAA
*
12580578 TATTTTAATATTTGATTAAAATTATT
1 TATTTTAA-ATTTGATTAAAAGTATT
12580604 TATTTTAAATTTGTATTAAAAAGT-TT
1 TATTTTAAATTTG-ATT-AAAAGTATT
* *
12580630 TAATTTAAACTTGA
1 TATTTTAAATTTGA
12580644 GTTTAATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 6 0.17
26 24 0.69
27 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (25 bp):
TATTTTAAATTTGATTAAAAGTATT
Found at i:12581812 original size:21 final size:21
Alignment explanation
Indices: 12581788--12581833 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12581778 ATAAGTGTTA
*
12581788 AAACCCTAAACTCTAGA-TCAT
1 AAACCCGAAACTCTAGACTC-T
*
12581809 AAACTCGAAACTCTAGACTCT
1 AAACCCGAAACTCTAGACTCT
12581830 AAAC
1 AAAC
12581834 TTTTAAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (21 bp):
AAACCCGAAACTCTAGACTCT
Found at i:12581834 original size:21 final size:21
Alignment explanation
Indices: 12581795--12581834 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12581785 TTAAAACCCT
12581795 AAACTCTAGATCATAAACTCG
1 AAACTCTAGATCATAAACTCG
12581816 AAACTCTAGACTC-TAAACT
1 AAACTCTAGA-TCATAAACT
12581835 TTTAAACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (21 bp):
AAACTCTAGATCATAAACTCG
Found at i:12582111 original size:27 final size:28
Alignment explanation
Indices: 12582063--12582125 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 28
12582053 AACATTGGAA
* * * *
12582063 ATATTTGTATTTTTTTATAATT-TTTAC
1 ATATTTTTATTTTCTAAAAATTATTTAC
*
12582090 ATATTTTTATTTTCTAAAAATTATTTTC
1 ATATTTTTATTTTCTAAAAATTATTTAC
*
12582118 AAATTTTT
1 ATATTTTT
12582126 CAATCAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (28 bp):
ATATTTTTATTTTCTAAAAATTATTTAC
Found at i:12583477 original size:24 final size:24
Alignment explanation
Indices: 12583449--12583501 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
12583439 TTTCTATAAG
* **
12583449 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
12583473 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
12583497 ATTTA
1 ATTTA
12583502 ACTTTGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:12583511 original size:24 final size:24
Alignment explanation
Indices: 12583466--12583511 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
12583456 ATTTATGAGT
*
12583466 ATAATATATTTAGCATTTATTAAC
1 ATAATATATTTAACATTTATTAAC
12583490 ATAATATATTTAAC-TTTGATTA
1 ATAATATATTTAACATTT-ATTA
12583512 GAATTAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (24 bp):
ATAATATATTTAACATTTATTAAC
Found at i:12588688 original size:50 final size:50
Alignment explanation
Indices: 12588613--12588804 Score: 213
Period size: 50 Copynumber: 3.8 Consensus size: 50
12588603 CATTTGGGTA
* *
12588613 AAGAGATCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGAC
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGAT
* * **
12588663 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGAT
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGAT
* * * * * * * *
12588713 GAGAGGTCCCCTATAAGACCATGTTTGGGACATAGCATGGGCACCAACAT
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGAT
* * * *
12588763 GAGAACATCTCATGTAAGACCATGTCTGGGACATGGCTTTGG
1 AAG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGG
12588805 TATGTTATTA
Statistics
Matches: 116, Mismatches: 25, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
50 87 0.75
51 29 0.25
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGAT
Found at i:12589499 original size:51 final size:50
Alignment explanation
Indices: 12589372--12589500 Score: 132
Period size: 50 Copynumber: 2.6 Consensus size: 50
12589362 GGGTAAAGAG
* * * * ** * *
12589372 ATCCTATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAG
1 ATCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCAACATGAGAC
* * * *
12589422 GTCCCCTATAAGACCATGTTTGGGACATAGCATGGGCACCAACATGAGAAC
1 ATCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCAACATGAG-AC
*
12589473 ATCTCATGTAAGACCATGTCTGGGACAT
1 ATCCCATGTAAGACCATGTCTGGGACAT
12589501 GGCTTTGGTA
Statistics
Matches: 61, Mismatches: 17, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
50 37 0.61
51 24 0.39
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (50 bp):
ATCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCAACATGAGAC
Found at i:12596056 original size:16 final size:15
Alignment explanation
Indices: 12596021--12596062 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
12596011 TAATTAATTT
*
12596021 TTTAAAATT-TAAAA
1 TTTAAAATTATTAAA
12596035 TTTAAAATTATTAAA
1 TTTAAAATTATTAAA
*
12596050 TTATAAAAATATT
1 TT-TAAAATTATT
12596063 TTTTTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 9 0.38
15 6 0.25
16 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAAAATTATTAAA
Found at i:12607051 original size:3 final size:3
Alignment explanation
Indices: 12607043--12607068 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12607033 GAAATCTTTA
12607043 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
12607069 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:12626514 original size:79 final size:79
Alignment explanation
Indices: 12626383--12626540 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
12626373 TCACTGTAAA
12626383 AACCCAAATAACCGCAAAGTGATTGGATGTGAAATGAACTTCATGAATTACCTTCTCTCCTGCTA
1 AACCCAAATAACCGCAAAGTGATTGGATGTGAAATGAACTTCATGAATTACCTTCTCTCCTGCTA
12626448 TGTGTTTGGAATCG
66 TGTGTTTGGAATCG
* *
12626462 AACCCAAATAACTGCAAAGTGATTGGATGTGAAATGAATTTCATGAATTACCTTCTCTCCTGCTA
1 AACCCAAATAACCGCAAAGTGATTGGATGTGAAATGAACTTCATGAATTACCTTCTCTCCTGCTA
12626527 TGTGTTTGGAATCG
66 TGTGTTTGGAATCG
12626541 TCTTACTCAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (79 bp):
AACCCAAATAACCGCAAAGTGATTGGATGTGAAATGAACTTCATGAATTACCTTCTCTCCTGCTA
TGTGTTTGGAATCG
Found at i:12642601 original size:232 final size:231
Alignment explanation
Indices: 12642195--12642645 Score: 751
Period size: 232 Copynumber: 1.9 Consensus size: 231
12642185 TTAAATATTA
* *
12642195 GGAGCAAATATATCACAATCTCAACATCAATATACTCAGTAACAAAGCAGGACTACATTCAACCA
1 GGAGCAAATATATCACAATCTCAACATCAATATACTAAGTAACAAAGCAGGACTACATTCAAACA
*
12642260 GTGTCCCACATTTAATATTTGCATACAATCTCTGCTCAGAGAAAAGTGAAACTAAATAAATATTA
66 GTGTACCACATTTAATATTTGCATACAATCTCTGCTCAGAGAAAAGTGAAACTAAATAAATATTA
* * *
12642325 GGAACACAATAAAACCATGCAGCTTCCTCGTGCCCTTCTAATCTCACATGTAAAAGGAGGGCTCT
131 GGAACACAATAAAACCATGCAGCTTCCTCATGCCCTTCTAATCTCACATATAAAAGGAGGACTCT
12642390 TTTATTAACCATTTATGGAAGTCCCAAGTATAGCAAT
196 TTTATTAACCATTTATGGAA-TCCCAAGTATAGCAAT
* * *
12642427 GGAGCAAATATATCATAATCTCAACATCAATATACTAAGTATCAAAGCAGGACTACATTCAAACG
1 GGAGCAAATATATCACAATCTCAACATCAATATACTAAGTAACAAAGCAGGACTACATTCAAACA
* * * *
12642492 GTGTACCATATTTAATATTTGCGTACAATCTCTGCTCGGAGAAAAGTGAAACTAATTAAATATTA
66 GTGTACCACATTTAATATTTGCATACAATCTCTGCTCAGAGAAAAGTGAAACTAAATAAATATTA
*
12642557 GGAACACAATAAAACCATAG-AGCTTCCTCATGTCCTTCTAATCTCACATATAAAAGGAGGACTC
131 GGAACACAATAAAACCAT-GCAGCTTCCTCATGCCCTTCTAATCTCACATATAAAAGGAGGACTC
12642621 TTTTATTAACCATTTATGGAATCCC
195 TTTTATTAACCATTTATGGAATCCC
12642646 TAAGAAATTT
Statistics
Matches: 204, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
231 4 0.02
232 199 0.98
233 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (231 bp):
GGAGCAAATATATCACAATCTCAACATCAATATACTAAGTAACAAAGCAGGACTACATTCAAACA
GTGTACCACATTTAATATTTGCATACAATCTCTGCTCAGAGAAAAGTGAAACTAAATAAATATTA
GGAACACAATAAAACCATGCAGCTTCCTCATGCCCTTCTAATCTCACATATAAAAGGAGGACTCT
TTTATTAACCATTTATGGAATCCCAAGTATAGCAAT
Found at i:12647769 original size:16 final size:16
Alignment explanation
Indices: 12647750--12647783 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12647740 TTCAGAATAT
*
12647750 ATATAATCTAGAAAAA
1 ATATAATCTAAAAAAA
*
12647766 ATATAATTTAAAAAAA
1 ATATAATCTAAAAAAA
12647782 AT
1 AT
12647784 GAAAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
ATATAATCTAAAAAAA
Found at i:12648030 original size:22 final size:21
Alignment explanation
Indices: 12648004--12648060 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
12647994 ATACTATTTT
*
12648004 AATATTTTTAAATTTAT-AAT
1 AATATTTTTAAATTTATAAAA
*
12648024 TATATATTTTAGAATTTTATAAAA
1 AATAT-TTTTA-AA-TTTATAAAA
12648048 AATATTTTTAAAT
1 AATATTTTTAAAT
12648061 ATTTTTAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 4 0.13
23 10 0.33
24 6 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
AATATTTTTAAATTTATAAAA
Found at i:12648062 original size:10 final size:10
Alignment explanation
Indices: 12648047--12648083 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
12648037 ATTTTATAAA
12648047 AAATATTTTT
1 AAATATTTTT
12648057 AAATATTTTT
1 AAATATTTTT
*
12648067 AAACATTTTT
1 AAATATTTTT
*
12648077 ATATATT
1 AAATATT
12648084 ATATATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
AAATATTTTT
Found at i:12650098 original size:6 final size:6
Alignment explanation
Indices: 12650087--12650113 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12650077 TTGTCTCGAT
12650087 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
12650114 AAATAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:12659181 original size:40 final size:40
Alignment explanation
Indices: 12659137--12659271 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 40
12659127 ACCAGTTTGG
*
12659137 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAAATTGA
* * * *
12659177 CACCCAGTGTCTCATCGGTTAAACCGAAG---TAAATTGG
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAAATTGA
** *
12659214 CACCCAGTGCCTCATCAAATTAATCCGAAATAATAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATCCGAAGTAATAAATTGA
*
12659255 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
12659272 ACTCGAAGTC
Statistics
Matches: 77, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 22 0.29
38 8 0.10
40 25 0.32
41 22 0.29
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGGATAATCCGAAGTAATAAATTGA
Found at i:12659259 original size:41 final size:40
Alignment explanation
Indices: 12659137--12659272 Score: 145
Period size: 37 Copynumber: 3.5 Consensus size: 40
12659127 ACCAGTTTGG
* *
12659137 CACCCAGTGCCTCATCGGA-TAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATC-GATTAATCCGAAATAATAAATTGA
* * * * *
12659177 CACCCAGTGTCTCATCGGTTAAACCG--A-AGTAAATTGG
1 CACCCAGTGCCTCATCGATTAATCCGAAATAATAAATTGA
*
12659214 CACCCAGTGCCTCATCAAATTAATCCGAAATAATAAATTGA
1 CACCCAGTGCCTCATC-GATTAATCCGAAATAATAAATTGA
*
12659255 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
12659273 CTCGAAGTCG
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
37 23 0.30
38 7 0.09
39 1 0.01
40 22 0.29
41 23 0.30
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGATTAATCCGAAATAATAAATTGA
Found at i:12659287 original size:41 final size:39
Alignment explanation
Indices: 12659137--12659272 Score: 127
Period size: 41 Copynumber: 3.5 Consensus size: 39
12659127 ACCAGTTTGG
* *
12659137 CACCCAGTGCCTCATCGGA-TAATTCGAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAATTAA-TCGAA-TAATAAATTGA
* * * *
12659177 CACCCAGTGTCTCATCG-GTTAAACCG-A-AGTAAATTGG
1 CACCCAGTGTCTCATCGAATT-AATCGAATAATAAATTGA
* *
12659214 CACCCAGTGCCTCATCAAATTAATCCGAAATAATAAATTGA
1 CACCCAGTGTCTCATCGAATTAAT-CG-AATAATAAATTGA
12659255 CACCCAGTGTCTCATCGA
1 CACCCAGTGTCTCATCGA
12659273 CTCGAAGTCG
Statistics
Matches: 76, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
37 25 0.33
38 4 0.05
39 1 0.01
40 20 0.26
41 26 0.34
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (39 bp):
CACCCAGTGTCTCATCGAATTAATCGAATAATAAATTGA
Found at i:12660277 original size:35 final size:36
Alignment explanation
Indices: 12660231--12660321 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 36
12660221 TTTATCATTA
* *
12660231 TAATATAATAATATATATACT-TA-ACTCTTAAGTTT
1 TAATATTATAATATATATACTATATA-TCTTAACTTT
* *
12660266 TAATATTATAATAT-TATAATATATATTTTAACTTT
1 TAATATTATAATATATATACTATATATCTTAACTTT
*
12660301 AAATAGTTATAATATATATAC
1 TAATA-TTATAATATATATAC
12660322 ACTTATCCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
34 5 0.11
35 27 0.59
36 10 0.22
37 4 0.09
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (36 bp):
TAATATTATAATATATATACTATATATCTTAACTTT
Found at i:12681825 original size:3 final size:3
Alignment explanation
Indices: 12681817--12681871 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
12681807 AAATAGATAT
* * *
12681817 TTA TTA TTA TAA TTA TTA TTA TTG TTA TTA TTA TT- TAA TTGA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
12681861 TTA -TA TTA TTA
1 TTA TTA TTA TTA
12681872 GATCAATGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 4 0.10
3 37 0.88
4 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:12682018 original size:21 final size:21
Alignment explanation
Indices: 12681994--12682036 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12681984 AATAATAATT
*
12681994 AAAATAAAAG-ATAAAACAAAC
1 AAAAT-AAAGCATAAAAAAAAC
12682015 AAAATAAAGCATAAAAAAAAC
1 AAAATAAAGCATAAAAAAAAC
12682036 A
1 A
12682037 GAACCATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.77, C:0.09, G:0.05, T:0.09
Consensus pattern (21 bp):
AAAATAAAGCATAAAAAAAAC
Found at i:12683041 original size:38 final size:39
Alignment explanation
Indices: 12682939--12683047 Score: 105
Period size: 38 Copynumber: 2.8 Consensus size: 39
12682929 GACCTCGAGT
* **
12682939 CGATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA--ACTTTACTTCGGATAGAGC
* * * * *
12682980 CAATGAGATATTGGGTATC-ACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGC
*
12683017 CGATGAGACACTGGGTGTCAACTTTGCTTCG
1 CGATGAGACACTGGGTGTCAACTTTACTTCG
12683048 AACTATCCGA
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
37 15 0.28
38 24 0.44
41 15 0.28
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGC
Found at i:12684233 original size:31 final size:33
Alignment explanation
Indices: 12684198--12684264 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 33
12684188 CAATTTGAAA
* *
12684198 AAACTCCGGTACCA-AAA-TGAATATTGAAGTC
1 AAACTCAGGTACCACAAATTGAATATTGAAATC
*
12684229 AAACTCATGTACCACCAAATTGAATATTGAAATC
1 AAACTCAGGTACCA-CAAATTGAATATTGAAATC
12684263 AA
1 AA
12684265 GTTCAAGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 12 0.40
33 3 0.10
34 15 0.50
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (33 bp):
AAACTCAGGTACCACAAATTGAATATTGAAATC
Found at i:12684275 original size:34 final size:34
Alignment explanation
Indices: 12684208--12684275 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
12684198 AAACTCCGGT
* *
12684208 ACCAAAATGAATATTGAAGTCAAACTCATGTACC
1 ACCAAAATGAATATTGAAATCAAACTCAAGTACC
* **
12684242 ACCAAATTGAATATTGAAATCAAGTTCAAGTACC
1 ACCAAAATGAATATTGAAATCAAACTCAAGTACC
12684276 GAATAGTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (34 bp):
ACCAAAATGAATATTGAAATCAAACTCAAGTACC
Found at i:12686928 original size:27 final size:25
Alignment explanation
Indices: 12686868--12686930 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
12686858 TTACATTTTT
*
12686868 AAATTTAAAAAAAATAGAAGGACTA
1 AAATTTAAAAAAAATAGAAGAACTA
* *
12686893 AATTCTTTAAAATAAAAGTAGATGAACTA
1 AA--ATTTAAAA-AAAA-TAGAAGAACTA
12686922 AAATTTAAA
1 AAATTTAAA
12686931 TGTATGAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
25 2 0.07
27 13 0.43
28 4 0.13
29 11 0.37
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.27
Consensus pattern (25 bp):
AAATTTAAAAAAAATAGAAGAACTA
Found at i:12691714 original size:22 final size:22
Alignment explanation
Indices: 12691684--12691731 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
12691674 TAAAATATAT
* *
12691684 AATTTAAAAAAAAATCTAAAAG
1 AATTCAAAAAAAAATATAAAAG
* *
12691706 AATTCAAAAAAGAATATAAAAT
1 AATTCAAAAAAAAATATAAAAG
12691728 AATT
1 AATT
12691732 TAAGAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (22 bp):
AATTCAAAAAAAAATATAAAAG
Found at i:12695283 original size:175 final size:177
Alignment explanation
Indices: 12694961--12695289 Score: 441
Period size: 175 Copynumber: 1.9 Consensus size: 177
12694951 TTTAATCCCA
* * *
12694961 TTTTTGCATTAAGATCTTGTTTAGCAATGAACATTTGATTTATATGGTTGGTTTTATGTATGATG
1 TTTTTGCATTAAAATCTTGTTTAGCAATGAACATTTGA-GTATAT-GATGG-TTTATGTATGATG
* * * *
12695026 TTTCCTTATCTATATAGCTTTAAAATCAATCAATTTTATCTTATATCTCTTCTTGTATGAATGAA
63 TTTACTTATATATATAGCTTTAAAATCAAGCAATTTTATCTTATATCTCTTCTTATATGAATGAA
*
12695091 CTACTTGCCAACCCCATGGTGTTGGTATCTTTTAATGTTTTAACTTGGTT
128 CTACTTGCCAACCCCATGATGTTGGTATCTTTTAATGTTTTAACTTGGTT
* *
12695141 TTTTTGCATTAAAAATCTTGTTTAGCAATGATCGTTTG-GTATAT-ATGG-TTATGTATGATGTT
1 TTTTTGCATT-AAAATCTTGTTTAGCAATGAACATTTGAGTATATGATGGTTTATGTATGATGTT
* * *
12695203 TACTTGTATATATAGCTTTGAAATCAAGCAATTTTATCTTATAAT-TGTTCTTATATGAATGAAC
65 TACTTATATATATAGCTTTAAAATCAAGCAATTTTATCTTAT-ATCTCTTCTTATATGAATGAAC
* * *
12695267 TGCTTGCTATCCCCATGATGTTG
129 TACTTGCCAACCCCATGATGTTG
12695290 TAATATAATT
Statistics
Matches: 131, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
175 87 0.66
176 2 0.02
177 3 0.02
179 5 0.04
180 10 0.08
181 24 0.18
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.46
Consensus pattern (177 bp):
TTTTTGCATTAAAATCTTGTTTAGCAATGAACATTTGAGTATATGATGGTTTATGTATGATGTTT
ACTTATATATATAGCTTTAAAATCAAGCAATTTTATCTTATATCTCTTCTTATATGAATGAACTA
CTTGCCAACCCCATGATGTTGGTATCTTTTAATGTTTTAACTTGGTT
Found at i:12700389 original size:22 final size:22
Alignment explanation
Indices: 12700363--12700409 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12700353 ATGAGAATTT
*
12700363 TTAAAAATGTTGGAGGGTCTAA
1 TTAAAAATGTTGGAAGGTCTAA
* * *
12700385 TTAAAACTTTTGGAAGGTTTAA
1 TTAAAAATGTTGGAAGGTCTAA
12700407 TTA
1 TTA
12700410 GAATATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (22 bp):
TTAAAAATGTTGGAAGGTCTAA
Found at i:12700413 original size:53 final size:51
Alignment explanation
Indices: 12700315--12700448 Score: 144
Period size: 53 Copynumber: 2.5 Consensus size: 51
12700305 GGATTTAATT
* * * *
12700315 AAAATTTGGACGGTTTAGTTAAAATTTTGAGAGGATTAATGAGAATTTTTA
1 AAAATTTGGAGGGTCTAATTAAAATTTTGAGAGGATTAATGAGAATATTTA
* *
12700366 AAAATGTTGGAGGGTCTAATTAAAACTTTTG-GAAGGTTTAATTAGAATATTTA
1 AAAAT-TTGGAGGGTCTAATTAAAA-TTTTGAG-AGGATTAATGAGAATATTTA
* *
12700419 AAAATTTCGAGGGGAGCTAATTAAAATTTT
1 AAAATTTGGA-GGG-TCTAATTAAAATTTT
12700449 CAAAAATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
51 5 0.07
52 21 0.30
53 34 0.49
54 10 0.14
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (51 bp):
AAAATTTGGAGGGTCTAATTAAAATTTTGAGAGGATTAATGAGAATATTTA
Found at i:12703073 original size:5 final size:5
Alignment explanation
Indices: 12703063--12703090 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12703053 ATAGAGGGAT
12703063 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
12703091 CAATCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:12705434 original size:95 final size:96
Alignment explanation
Indices: 12705267--12705440 Score: 242
Period size: 95 Copynumber: 1.8 Consensus size: 96
12705257 ATTTTCAGCT
* * * * * * *
12705267 TTAGTCGAAAGTAAAAAAAAATGCCGTGTTAGCAATCCGTTAGTGGATTAACGAAATTTTTAACG
1 TTAGTCAAAAGTAAAAAAAAAT-CCATGTCAGCAATCCATTAATAGACTAACGAAATTTTTAACG
*
12705332 ACGGTGACCAATTCGAACAATTATCTTAATTA
65 ACAGTGACCAATTCGAACAATTATCTTAATTA
* *
12705364 TTAGTCAAAAGTAAAAAAATAT-CATGTCAGCAATCCATTAATAGACTAACGAAATTTTTAATGA
1 TTAGTCAAAAGTAAAAAAAAATCCATGTCAGCAATCCATTAATAGACTAACGAAATTTTTAACGA
12705428 CAGTGACCAATTC
66 CAGTGACCAATTC
12705441 AGAGTGACTA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
95 47 0.70
97 20 0.30
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (96 bp):
TTAGTCAAAAGTAAAAAAAAATCCATGTCAGCAATCCATTAATAGACTAACGAAATTTTTAACGA
CAGTGACCAATTCGAACAATTATCTTAATTA
Found at i:12708473 original size:28 final size:27
Alignment explanation
Indices: 12708434--12708488 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
12708424 ACACCTTGAA
12708434 TTGTTCAATTTGACACCTAAATTTTTT
1 TTGTTCAATTTGACACCTAAATTTTTT
* * *
12708461 TTGTCTCAATTTGGCACCTCAGTTTTTT
1 TTGT-TCAATTTGACACCTAAATTTTTT
12708489 CAGTTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.51
Consensus pattern (27 bp):
TTGTTCAATTTGACACCTAAATTTTTT
Found at i:12709452 original size:17 final size:18
Alignment explanation
Indices: 12709430--12709463 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12709420 TTTTATTTTT
12709430 ATATAA-AAATTAAAAAA
1 ATATAATAAATTAAAAAA
*
12709447 ATATAATACATTAAAAA
1 ATATAATAAATTAAAAA
12709464 TATCAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATATAATAAATTAAAAAA
Found at i:12717377 original size:7 final size:7
Alignment explanation
Indices: 12717365--12717401 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
12717355 TCAAAGACAT
12717365 TTAAAAA
1 TTAAAAA
12717372 TTAAAAA
1 TTAAAAA
*
12717379 TTAAATA
1 TTAAAAA
*
12717386 TTAAATA
1 TTAAAAA
12717393 TTAAAAA
1 TTAAAAA
12717400 TT
1 TT
12717402 TCTTTTCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
TTAAAAA
Found at i:12720032 original size:6 final size:6
Alignment explanation
Indices: 12720013--12720050 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
12720003 TCATCACCAA
*
12720013 CATCTT CATTTT CATCTT CATCTT CATCTT CATCTT CA
1 CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CA
12720051 ACATCATCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
CATCTT
Found at i:12720057 original size:18 final size:18
Alignment explanation
Indices: 12720018--12720058 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
12720008 ACCAACATCT
* * *
12720018 TCATTTTCATCTTCATCT
1 TCATCTTCATCTTCAACA
12720036 TCATCTTCATCTTCAACA
1 TCATCTTCATCTTCAACA
12720054 TCATC
1 TCATC
12720059 CTCTCCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (18 bp):
TCATCTTCATCTTCAACA
Found at i:12721353 original size:130 final size:130
Alignment explanation
Indices: 12721136--12721377 Score: 360
Period size: 130 Copynumber: 1.9 Consensus size: 130
12721126 GCTTCACATC
** * * *
12721136 TTTTTCCTTCAATTTCGGGTCACGGCTTCTCACCTACATGGAAACATTGAAATTTCATGACAAAA
1 TTTTTCCTTCAATTTCGGACCACGGCTTCTCACCTACATGAAAACATTGAAATCTCAAGACAAAA
* *
12721201 AAATCACTAATAAATTGACAAAAATTTCAGTTTTCACACCAATTAGCAAAAAAAAAAACAACACT
66 AAATCACTAATAAATTAACAAAAATTTCAATTTTCACA-CAATTAGCAAAAAAAAAAACAACACT
12721266 T
130 T
* * *
12721267 TTTTTCCTTCAATTTCGGACCACTGCTTCTCGCCTAC-TGAAAACATTGAAATCTCAAGATAAAA
1 TTTTTCCTTCAATTTCGGACCACGGCTTCTCACCTACATGAAAACATTGAAATCTCAAGACAAAA
* *
12721331 AGATCACTAATAAATTAACAAAAATTTCAATTTTCACACAGTTAGCA
66 AAATCACTAATAAATTAACAAAAATTTCAATTTTCACACAATTAGCA
12721378 GAACAACAAC
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
129 8 0.08
130 58 0.59
131 33 0.33
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (130 bp):
TTTTTCCTTCAATTTCGGACCACGGCTTCTCACCTACATGAAAACATTGAAATCTCAAGACAAAA
AAATCACTAATAAATTAACAAAAATTTCAATTTTCACACAATTAGCAAAAAAAAAAACAACACTT
Found at i:12721387 original size:3 final size:3
Alignment explanation
Indices: 12721379--12721404 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12721369 CAGTTAGCAG
12721379 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
12721405 TGATCTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:12731560 original size:9 final size:9
Alignment explanation
Indices: 12731546--12731574 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12731536 TCACTAATTT
12731546 AAAATTTTA
1 AAAATTTTA
12731555 AAAATTTTA
1 AAAATTTTA
12731564 AAAATTTTA
1 AAAATTTTA
12731573 AA
1 AA
12731575 GGGCCTAAAT
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):
AAAATTTTA
Found at i:12732250 original size:20 final size:20
Alignment explanation
Indices: 12732227--12732266 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12732217 ACATATTGTT
12732227 ACTGTTCACGACATGACCCC
1 ACTGTTCACGACATGACCCC
* * *
12732247 ACTGTTTATGACTTGACCCC
1 ACTGTTCACGACATGACCCC
12732267 CTTACTCTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.28
Consensus pattern (20 bp):
ACTGTTCACGACATGACCCC
Found at i:12735885 original size:47 final size:47
Alignment explanation
Indices: 12735814--12735908 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
12735804 TTTGTGTGTA
12735814 TCAAATACTAACCCAATAAACACACATTAGTATAAACATAGTAGCTT
1 TCAAATACTAACCCAATAAACACACATTAGTATAAACATAGTAGCTT
* * *
12735861 TCAAATACTAACCCTATAAGCACACATTAGTATGAACATAGTAGCTT
1 TCAAATACTAACCCAATAAACACACATTAGTATAAACATAGTAGCTT
12735908 T
1 T
12735909 TTCTCACTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27
Consensus pattern (47 bp):
TCAAATACTAACCCAATAAACACACATTAGTATAAACATAGTAGCTT
Found at i:12740622 original size:16 final size:16
Alignment explanation
Indices: 12740601--12740631 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12740591 TGCGGGTGAA
*
12740601 AAAGAAAAAGAAAAAG
1 AAAGAAAAACAAAAAG
12740617 AAAGAAAAACAAAAA
1 AAAGAAAAACAAAAA
12740632 TCCAAACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAGAAAAACAAAAAG
Found at i:12741647 original size:32 final size:32
Alignment explanation
Indices: 12741611--12741684 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
12741601 AAAAAATTTT
* *
12741611 AAGTACCGAATTAAGAAAAAAGTGTCAAGTCC
1 AAGTACCAAATTAAGAAAAAAGTATCAAGTCC
* * *
12741643 AAGTATCAAATTAGGAAAAAAGTATCAAGTTC
1 AAGTACCAAATTAAGAAAAAAGTATCAAGTCC
12741675 AAGTACCAAA
1 AAGTACCAAA
12741685 GGTTATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (32 bp):
AAGTACCAAATTAAGAAAAAAGTATCAAGTCC
Found at i:12746506 original size:8 final size:8
Alignment explanation
Indices: 12746493--12746520 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
12746483 TTTAACCCTT
12746493 AAAATAAA
1 AAAATAAA
12746501 AAAATAAA
1 AAAATAAA
12746509 AAAATAAA
1 AAAATAAA
12746517 AAAA
1 AAAA
12746521 AATTTAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:12748865 original size:26 final size:26
Alignment explanation
Indices: 12748829--12748886 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
12748819 GTTTTTTACC
12748829 GAAATAAATTAAAAAAATTAAATACA
1 GAAATAAATTAAAAAAATTAAATACA
*
12748855 GAAATAAATTAAAAAAATTAAATACC
1 GAAATAAATTAAAAAAATTAAATACA
12748881 GAAATA
1 GAAATA
12748887 GGTTGTCAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.22
Consensus pattern (26 bp):
GAAATAAATTAAAAAAATTAAATACA
Found at i:12751565 original size:18 final size:19
Alignment explanation
Indices: 12751524--12751566 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
12751514 ATTTATATTT
* *
12751524 TAAAAATTATTAATTATTA
1 TAAAAATTATCAATTATGA
12751543 T-AAAATTATCAA-TATGA
1 TAAAAATTATCAATTATGA
12751560 TAAAAAT
1 TAAAAAT
12751567 AATTTGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 15 0.71
19 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAAAATTATCAATTATGA
Found at i:12761786 original size:17 final size:18
Alignment explanation
Indices: 12761763--12761813 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
12761753 TTAAAAAATT
12761763 TATTAAAAATTCAAAAAA
1 TATTAAAAATTCAAAAAA
**
12761781 -ATTAAATAAAACAAAAAA
1 TATTAAA-AATTCAAAAAA
12761799 TTATTAAAAATTCAA
1 -TATTAAAAATTCAA
12761814 TCAACTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 6 0.23
18 9 0.35
19 5 0.19
20 6 0.23
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (18 bp):
TATTAAAAATTCAAAAAA
Found at i:12762605 original size:21 final size:23
Alignment explanation
Indices: 12762580--12762623 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12762570 TAAAAAACTA
*
12762580 AAAT-ATTTTTAT-ATTTTTTAT
1 AAATAATTTTAATGATTTTTTAT
12762601 AAATAATTTTAATGATTTTTTAT
1 AAATAATTTTAATGATTTTTTAT
12762624 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
AAATAATTTTAATGATTTTTTAT
Found at i:12762633 original size:29 final size:28
Alignment explanation
Indices: 12762582--12762662 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
12762572 AAAAACTAAA
* *
12762582 ATATTTTTATATTTTTTATAAAT-AATTTT
1 ATATTTTT-TA-TTTTTAAAAATAAATTAT
12762611 AATGATTTTTTATTTTTAAAAATAAATTAT
1 -AT-ATTTTTTATTTTTAAAAATAAATTAT
12762641 ATATTTTTTAATTTTTAAAAAT
1 ATATTTTTT-ATTTTTAAAAAT
12762663 TAAAAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
28 7 0.15
29 24 0.52
30 9 0.20
31 6 0.13
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
ATATTTTTTATTTTTAAAAATAAATTAT
Found at i:12764313 original size:29 final size:29
Alignment explanation
Indices: 12764257--12764313 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
12764247 ATTTTAAAAT
* *
12764257 TTTAATAGTACAATAACTAAATTGATCAA
1 TTTAATAGTACAAGAACTAAATTAATCAA
* * *
12764286 TTTAATAGTAGAGGAACTAATTTAATCA
1 TTTAATAGTACAAGAACTAAATTAATCA
12764314 TGTCTCTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (29 bp):
TTTAATAGTACAAGAACTAAATTAATCAA
Found at i:12765142 original size:36 final size:36
Alignment explanation
Indices: 12765072--12765151 Score: 83
Period size: 36 Copynumber: 2.2 Consensus size: 36
12765062 TAGTAACGAA
* * *
12765072 ATTAACAATAAAATAAATATTATAAAATATTTAAAC
1 ATTAACAACAAAATAAATAATATAAAATAGTTAAAC
*
12765108 ATTAACAACAAAAT-AATAATA-ACATAATAGTTAAAT
1 ATTAACAACAAAATAAATAATATA-A-AATAGTTAAAC
*
12765144 AGTAACAA
1 ATTAACAA
12765152 AAACATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 1 0.03
35 7 0.19
36 29 0.78
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.29
Consensus pattern (36 bp):
ATTAACAACAAAATAAATAATATAAAATAGTTAAAC
Found at i:12768496 original size:21 final size:20
Alignment explanation
Indices: 12768467--12768506 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
12768457 TAAAAAAAAA
12768467 TTTAAAATTTTTAATTTCTT
1 TTTAAAATTTTTAATTTCTT
12768487 TTTAATAATTTTTAATTTCT
1 TTTAA-AATTTTTAATTTCT
12768507 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAAAATTTTTAATTTCTT
Found at i:12772278 original size:29 final size:29
Alignment explanation
Indices: 12772244--12772307 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
12772234 AATTATTGCC
12772244 CTTAATATGTATATATTATTAACTCTAAA
1 CTTAATATGTATATATTATTAACTCTAAA
*
12772273 TTTAATATGTATATATTATTAACTCTAAA
1 CTTAATATGTATATATTATTAACTCTAAA
12772302 CTTAAT
1 CTTAAT
12772308 TATCGAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (29 bp):
CTTAATATGTATATATTATTAACTCTAAA
Found at i:12774703 original size:163 final size:164
Alignment explanation
Indices: 12774389--12774712 Score: 524
Period size: 163 Copynumber: 2.0 Consensus size: 164
12774379 TCAAAATTTC
* ** *
12774389 AACACTAAATCATGCGGGTTTGGATGTAGTATGGTGCAGAGGAAGTAAACCTTGGTTGCTTATTG
1 AACACTAAATCATGCGGGTTTAGATGTAGTATGGTGCAGAGGAAGTAAAAATTGATTGCTTATTG
** *
12774454 CCTGCCAATAAATAACATTTAAATTTTCTATGTTCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
66 CCTGCCAATAAATAACATTTAAATTGGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
*
12774519 TGATTGAGGTCATGGTCATTTTTATCAATATGGT
131 TGATTGAGGTCATGATCATTTTTATCAATATGGT
* * *
12774553 AACACTAAATCATGTGGTTTTAGATTTAGTATGGTGCAGAGGAAGTAAAAATTGATTGCTTATTG
1 AACACTAAATCATGCGGGTTTAGATGTAGTATGGTGCAGAGGAAGTAAAAATTGATTGCTTATTG
* *
12774618 TCTGCCAAT-AATAACATTTTAATTGGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
66 CCTGCCAATAAATAACATTTAAATTGGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
12774682 TGATTGAGGTCATGATCATTTTTATCAATAT
131 TGATTGAGGTCATGATCATTTTTATCAATAT
12774713 AGTTAAATTC
Statistics
Matches: 147, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
163 81 0.55
164 66 0.45
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (164 bp):
AACACTAAATCATGCGGGTTTAGATGTAGTATGGTGCAGAGGAAGTAAAAATTGATTGCTTATTG
CCTGCCAATAAATAACATTTAAATTGGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
TGATTGAGGTCATGATCATTTTTATCAATATGGT
Found at i:12780750 original size:47 final size:46
Alignment explanation
Indices: 12780689--12780796 Score: 137
Period size: 47 Copynumber: 2.3 Consensus size: 46
12780679 TGCAACTGAA
*
12780689 TAATATTTTCTGTAATTACACAAATACACATAACATTA-ACGAAGTTG
1 TAATATTTT-TGTAATTACACAAATACACAAAACATTACA-GAAGTTG
* *
12780736 TAATAGTTTTTGTAATTACATAAATATACAAAACATTACAGAAGTTG
1 TAATA-TTTTTGTAATTACACAAATACACAAAACATTACAGAAGTTG
*
12780783 TCATAATTTTTGTA
1 TAAT-ATTTTTGTA
12780797 GTTAGGTAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
47 48 0.89
48 6 0.11
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (46 bp):
TAATATTTTTGTAATTACACAAATACACAAAACATTACAGAAGTTG
Found at i:12789024 original size:208 final size:208
Alignment explanation
Indices: 12788666--12789088 Score: 819
Period size: 208 Copynumber: 2.0 Consensus size: 208
12788656 GTATTATTGT
* *
12788666 CATCATTGTTCCCTTGATTGTGTGTTTTTTTTTTTCGGTTGTATGGGCAAGCCTTCCCTGTTTTC
1 CATCATTGTTCCCTTGATTGGGTGTTTTTTTTTTTCAGTTGTATGGGCAAGCCTTCCCTGTTTTC
12788731 TACCATTTCTTGTCACATTTTCATTGTTGGTAGTCCTTTACTTAAGCAGTACTGGTTCTTTTGTA
66 TACCATTTCTTGTCACATTTTCATTGTTGGTAGTCCTTTACTTAAGCAGTACTGGTTCTTTTGTA
12788796 CATTTTTTCCCCAAAGAAGTCCCCTATCTAATTGCAGTTAAGTTTCTCGGCCCTCTATGAGTATC
131 CATTTTTTCCCCAAAGAAGTCCCCTATCTAATTGCAGTTAAGTTTCTCGGCCCTCTATGAGTATC
12788861 TGAAACAATTTTG
196 TGAAACAATTTTG
*
12788874 CATCATTGTTCCCTTGATTGGGTGTTTTTTTTTTTCAGTTGTATGGGCAAGCCTTTCCTGTTTTC
1 CATCATTGTTCCCTTGATTGGGTGTTTTTTTTTTTCAGTTGTATGGGCAAGCCTTCCCTGTTTTC
12788939 TACCATTTCTTGTCACATTTTCATTGTTGGTAGTCCTTTACTTAAGCAGTACTGGTTCTTTTGTA
66 TACCATTTCTTGTCACATTTTCATTGTTGGTAGTCCTTTACTTAAGCAGTACTGGTTCTTTTGTA
12789004 CATTTTTTCCCCAAAGAAGTCCCCTATCTAATTGCAGTTAAGTTTCTCGGCCCTCTATGAGTATC
131 CATTTTTTCCCCAAAGAAGTCCCCTATCTAATTGCAGTTAAGTTTCTCGGCCCTCTATGAGTATC
12789069 TGAAACAATTTTG
196 TGAAACAATTTTG
12789082 CATCATT
1 CATCATT
12789089 AGTTTTCATG
Statistics
Matches: 212, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
208 212 1.00
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (208 bp):
CATCATTGTTCCCTTGATTGGGTGTTTTTTTTTTTCAGTTGTATGGGCAAGCCTTCCCTGTTTTC
TACCATTTCTTGTCACATTTTCATTGTTGGTAGTCCTTTACTTAAGCAGTACTGGTTCTTTTGTA
CATTTTTTCCCCAAAGAAGTCCCCTATCTAATTGCAGTTAAGTTTCTCGGCCCTCTATGAGTATC
TGAAACAATTTTG
Found at i:12791998 original size:30 final size:30
Alignment explanation
Indices: 12791957--12792016 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
12791947 ACCCAGGGAG
* *
12791957 CTGGAATTGGAATTGGGATTCAAATTGGAA
1 CTGGAACTGGAACTGGGATTCAAATTGGAA
12791987 CTGGAACTGGAACTGGGATTCAAATTGGAA
1 CTGGAACTGGAACTGGGATTCAAATTGGAA
12792017 TGCGCATCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (30 bp):
CTGGAACTGGAACTGGGATTCAAATTGGAA
Found at i:12793550 original size:22 final size:22
Alignment explanation
Indices: 12793510--12793552 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12793500 ATTAATGTTT
* *
12793510 AATTTGATATTTAATTTTTTTC
1 AATTTGATACTTAAGTTTTTTC
*
12793532 AATTTGATACTTGAGTTTTTT
1 AATTTGATACTTAAGTTTTTT
12793553 TTTATCTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (22 bp):
AATTTGATACTTAAGTTTTTTC
Found at i:12797307 original size:30 final size:31
Alignment explanation
Indices: 12797271--12797334 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
12797261 AATTTTAAAT
12797271 TTTAAAAA-TACAAAAAAATTATAAAAAT-TA
1 TTTAAAAAGTACAAAAAAA-TATAAAAATATA
* *
12797301 TTTAAAAAGTACTAAAATATATAAAAATATA
1 TTTAAAAAGTACAAAAAAATATAAAAATATA
12797332 TTT
1 TTT
12797335 TTTAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (31 bp):
TTTAAAAAGTACAAAAAAATATAAAAATATA
Found at i:12800230 original size:5 final size:6
Alignment explanation
Indices: 12800205--12800229 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12800195 TGCTTATCAA
12800205 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
12800230 AAAAAGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:12807872 original size:36 final size:36
Alignment explanation
Indices: 12807832--12807900 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
12807822 AGCCTAATCA
* * *
12807832 AGCAAGCTCAAGTAGTTCGCTTTTTATCTCAAATTC
1 AGCAAGATCAAGCAGTTCACTTTTTATCTCAAATTC
*
12807868 AGCAAGATCAAGCATTTCACTTTTTATCTCAAA
1 AGCAAGATCAAGCAGTTCACTTTTTATCTCAAA
12807901 ACTTTAGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (36 bp):
AGCAAGATCAAGCAGTTCACTTTTTATCTCAAATTC
Found at i:12809661 original size:20 final size:20
Alignment explanation
Indices: 12809636--12809674 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12809626 TTTTTAGAAA
12809636 CGAAT-ATATTAATATATTTT
1 CGAATAATA-TAATATATTTT
*
12809656 CGAATAATATAATTTATTT
1 CGAATAATATAATATATTT
12809675 CAATTACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
CGAATAATATAATATATTTT
Found at i:12817252 original size:30 final size:31
Alignment explanation
Indices: 12817216--12817278 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
12817206 TATTATACGT
* *
12817216 AAATTTTGATTTT-ATACAATTATATAAATA
1 AAATTTTAATTTTAATACAATTACATAAATA
* *
12817246 AAATTTTAATTTTAATTCAATTACATAATTA
1 AAATTTTAATTTTAATACAATTACATAAATA
12817277 AA
1 AA
12817279 TTAATGATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (31 bp):
AAATTTTAATTTTAATACAATTACATAAATA
Found at i:12817280 original size:30 final size:30
Alignment explanation
Indices: 12817215--12817280 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
12817205 ATATTATACG
* *
12817215 TAAATTTTGATTTTATACAATTATATAAAT
1 TAAATTTTAATTTTATACAATTACATAAAT
* *
12817245 AAAATTTTAATTTTAATTCAATTACAT-AAT
1 TAAATTTTAATTTT-ATACAATTACATAAAT
12817275 TAAATT
1 TAAATT
12817281 AATGATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (30 bp):
TAAATTTTAATTTTATACAATTACATAAAT
Found at i:12822930 original size:59 final size:59
Alignment explanation
Indices: 12822848--12823176 Score: 305
Period size: 59 Copynumber: 5.7 Consensus size: 59
12822838 TATTAGAGAT
* * * * *
12822848 TAACTTGGAC-AAAAAAA-TTCAAACTCTAATGTGGGACCAATTGCCAAGTTCAAGGAC
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTAAGGAC
* * * * * **
12822905 TAAATTGGACAAAAAAAAGTTCAAACCCTAATGTAAGAATAATTGTCAAGTTCGAGGAC
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTAAGGAC
* * * *
12822964 TAACTTGAAC-AAAAAAA-TTTAGGCCCCAATGTGAGAACAATTGCCAAGTTTAGAGG-C
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTA-AGGAC
* * * * ** * *
12823021 TAACTTGGA-TAAAAAATGTTCAAGCCCCAATGTG-GAAAAAATTGTTAAGTTTAGGGAT
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGAG-AACAATTGCCAAGTTTAAGGAC
* * * * *
12823079 TAATTTGAATATAAAAAAGTTCAAGCCCTAATGCGAGAACAATTGCCAAGTTTAAGGAC
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTAAGGAC
*
12823138 TAACTTGGACAAAAAAAAGTTCAA-CCTTCAATGTGAGAA
1 TAACTTGGACAAAAAAAAGTTCAAGCCCT-AATGTGAGAA
12823177 TTGTGGGAAT
Statistics
Matches: 216, Mismatches: 46, Indels: 18
0.77 0.16 0.06
Matches are distributed among these distances:
57 53 0.25
58 55 0.25
59 107 0.50
60 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (59 bp):
TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTAAGGAC
Found at i:12823143 original size:117 final size:115
Alignment explanation
Indices: 12822840--12823161 Score: 348
Period size: 116 Copynumber: 2.8 Consensus size: 115
12822830 AAAGGAAATA
* * * * * * *
12822840 TTAGA-GATTAACTTGGACAAAAAAATTCAAACTCTAATGTGGGACCAATTGCCAAGTTCAAGGA
1 TTAGAGGACTAACTTGAACAAAAAAATTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTAAGGA
* *
12822904 CTAAATTGGACAAAAAAAAGTTCAAACCCTAATGTAAGAATAATTGTCAAG
66 CTAACTTGGA-AAAAAAAAGTTCAAACCCCAATGTAAGAATAATTGTCAAG
* * * *
12822955 TTCGAGGACTAACTTGAACAAAAAAATTTAGGCCCCAATGTGAGAACAATTGCCAAGTTTAGAGG
1 TTAGAGGACTAACTTGAACAAAAAAATTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTA-AGG
* * * *
12823020 -CTAACTTGGATAAAAAATGTTCAAGCCCCAATGTGGAA-AA-AATTGTTAAG
65 ACTAACTTGGAAAAAAAAAGTTCAAACCCCAATGT--AAGAATAATTGTCAAG
* * * *
12823070 TTTAG-GGATTAATTTGAATATAAAAAAGTTCAAGCCCTAATGCGAGAACAATTGCCAAGTTTAA
1 -TTAGAGGACTAACTTGAACA-AAAAAA-TTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTAA
12823134 GGACTAACTTGGACAAAAAAAAGTTCAA
63 GGACTAACTTGGA-AAAAAAAAGTTCAA
12823162 CCTTCAATGT
Statistics
Matches: 171, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
115 45 0.26
116 68 0.40
117 46 0.27
118 12 0.07
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.25
Consensus pattern (115 bp):
TTAGAGGACTAACTTGAACAAAAAAATTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTAAGGA
CTAACTTGGAAAAAAAAAGTTCAAACCCCAATGTAAGAATAATTGTCAAG
Found at i:12837923 original size:42 final size:42
Alignment explanation
Indices: 12837858--12838013 Score: 169
Period size: 42 Copynumber: 3.7 Consensus size: 42
12837848 AAATCGTACA
*
12837858 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
*
12837900 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATC-AATATCG
* * *
12837942 ATGCCGATGTCCCAGACATGGTCTTATACAT-AAATCTCAA-ATCG
1 ATGCCAACGTCCCAGACGTGGTC-T-TACATGAAA--TCAATATCG
12837986 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
12838014 CGATAACATA
Statistics
Matches: 96, Mismatches: 8, Indels: 20
0.77 0.06 0.16
Matches are distributed among these distances:
41 2 0.02
42 51 0.53
43 14 0.15
44 27 0.28
45 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
Found at i:12842934 original size:23 final size:23
Alignment explanation
Indices: 12842908--12842959 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
12842898 ATAAGTGCAA
12842908 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12842931 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12842954 CACTGA
1 CACTGA
12842960 AACGTACACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12843389 original size:17 final size:17
Alignment explanation
Indices: 12843367--12843399 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12843357 AAATTAACAC
12843367 TTCAAACATTCATTATT
1 TTCAAACATTCATTATT
12843384 TTCAAACATTCATTAT
1 TTCAAACATTCATTAT
12843400 CTAACATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (17 bp):
TTCAAACATTCATTATT
Found at i:12848300 original size:41 final size:45
Alignment explanation
Indices: 12848231--12848328 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 45
12848221 ACTGGGACGA
* *
12848231 TGGCATCGATATATGTGATTACGTGTAAGACCATGTCTAGGACAT
1 TGGCATCGATATATGTGATTACGTGTAAGACCATGTCCAGGACAG
* *
12848276 TGGCATCG-TAT-T-TGATT-CGTGTAAGACCCTTTCCAGGACAG
1 TGGCATCGATATATGTGATTACGTGTAAGACCATGTCCAGGACAG
12848317 TGGCATCGATAT
1 TGGCATCGATAT
12848329 GAGATAGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 28 0.58
42 8 0.17
43 1 0.02
44 3 0.06
45 8 0.17
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (45 bp):
TGGCATCGATATATGTGATTACGTGTAAGACCATGTCCAGGACAG
Found at i:12852988 original size:14 final size:14
Alignment explanation
Indices: 12852969--12852998 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12852959 TCGTCAAGAT
*
12852969 ATCTAATGAAATAA
1 ATCTAATAAAATAA
12852983 ATCTAATAAAATAA
1 ATCTAATAAAATAA
12852997 AT
1 AT
12852999 ACTTGTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (14 bp):
ATCTAATAAAATAA
Found at i:12864677 original size:18 final size:19
Alignment explanation
Indices: 12864638--12864690 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
12864628 TATCACTATT
*
12864638 TTTACAAATTAAATACACTA
1 TTTA-AAATTAAATACAATA
12864658 -TTAAAATTGAAATA-AATA
1 TTTAAAATT-AAATACAATA
12864676 TTTAAAATATAAATA
1 TTTAAAAT-TAAATA
12864691 ATGTTACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.28
19 20 0.69
20 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (19 bp):
TTTAAAATTAAATACAATA
Found at i:12865730 original size:182 final size:181
Alignment explanation
Indices: 12865218--12865740 Score: 615
Period size: 180 Copynumber: 2.9 Consensus size: 181
12865208 AAATGTTATT
* ** * *
12865218 TTTTTAGAGAGATAATTATGAAACTTTAAAATATTAGTATTTTATAGACAGTAAAATAAATATTA
1 TTTTTAGAGAGATAATCATGAAACTCAAAAATATTAGT-CTTTATAGACAGTAAAATAAACATTA
* **
12865283 AGGAAACTTTGGTCATAAAAAATATATACA-TTTTTAAACATTTTTTAAATTAAGAATTCTTGAT
65 AGGAAACCTTGGTCATAAAAAA-ATATACATTTTTTAAACATTTTCAAAATTAAGAATTCTTGAT
* * * ** *
12865347 CCAAAATCTGAATTAACAATATTCACGCGTAAAAAATATTACACGAAATATCA
129 CCAAAACCCGAATTAACAATACTCACGTATAAAAAATATGACACGAAATATCA
* * * *
12865400 TTTTTGAGAGGGATAATCATGGACCTCAAAAATATTTA-TCTTTATAGACTGTAAAATAAACATT
1 TTTTT-AGAGAGATAATCATGAAACTCAAAAATA-TTAGTCTTTATAGACAGTAAAATAAACATT
* * * * *
12865464 AAGGAAACCTTGGTCAT-AAAAAATATA-TTTTTTTAAACATTTTCCAAATTAAGGATTTTTAAT
64 AAGGAAACCTTGGTCATAAAAAAATATACATTTTTTAAACATTTTCAAAATTAAGAATTCTTGAT
* * ** *
12865527 CCAAAACCCAAATTAACAATACTCACGTATAAAAGATATGACTGGAAATGTCA
129 CCAAAACCCGAATTAACAATACTCACGTATAAAAAATATGACACGAAATATCA
* * * * * *
12865580 GTTTTTAGAAAGATAATCATGAATCTCAAAAATATTAGTCTTCATTGACCGTAAAATGAACATTA
1 -TTTTTAGAGAGATAATCATGAAACTCAAAAATATTAGTCTTTATAGACAGTAAAATAAACATTA
* * *
12865645 A-GAAACCTTAGTCATAAGAAAAATATACATTTTTTAAACCTTTTCAAAATTAAGAAATCTTGAT
65 AGGAAACCTTGGTCATAA-AAAAATATACATTTTTTAAACATTTTCAAAATTAAGAATTCTTGAT
*
12865709 TCAAAACCCGAATTAACAATACTCACGTATAA
129 CCAAAACCCGAATTAACAATACTCACGTATAA
12865741 GTATAAAAGT
Statistics
Matches: 288, Mismatches: 45, Indels: 16
0.83 0.13 0.05
Matches are distributed among these distances:
179 16 0.06
180 125 0.43
181 19 0.07
182 102 0.35
183 23 0.08
184 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (181 bp):
TTTTTAGAGAGATAATCATGAAACTCAAAAATATTAGTCTTTATAGACAGTAAAATAAACATTAA
GGAAACCTTGGTCATAAAAAAATATACATTTTTTAAACATTTTCAAAATTAAGAATTCTTGATCC
AAAACCCGAATTAACAATACTCACGTATAAAAAATATGACACGAAATATCA
Found at i:12869297 original size:2 final size:2
Alignment explanation
Indices: 12869290--12869317 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12869280 AAAGACGGGC
12869290 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
12869318 TTCTCCTTGT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12872039 original size:21 final size:21
Alignment explanation
Indices: 12871977--12872063 Score: 106
Period size: 21 Copynumber: 4.1 Consensus size: 21
12871967 CATGACCAGT
12871977 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* *
12871997 AAACGACACA-CAAGATGCCTG
1 ATACGACACATAAAG-TGCCTG
*
12872018 ATACGACACATAAAGTGTCTG
1 ATACGACACATAAAGTGCCTG
12872039 ACGTACGACACATAAAGTGCCTG
1 A--TACGACACATAAAGTGCCTG
12872062 AT
1 AT
12872064 CAGCAAAGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
20 12 0.21
21 22 0.39
22 3 0.05
23 20 0.35
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:12872060 original size:44 final size:41
Alignment explanation
Indices: 12871977--12872063 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 41
12871967 CATGACCAGT
*
12871977 ATACGACACATAAGTGCCTGAAACGACACACAAGATGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACAAAAGATGCCTG
* *
12872018 ATACGACACATAAAGTGTCTGACGTACGACACATAAAG-TGCCTG
1 ATACGACACAT-AAGTGCCTGA--AACGACACA-AAAGATGCCTG
12872062 AT
1 AT
12872064 CAGCAAAGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
41 11 0.28
42 9 0.23
44 16 0.41
45 3 0.08
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACAAAAGATGCCTG
Found at i:12873232 original size:14 final size:17
Alignment explanation
Indices: 12873213--12873250 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
12873203 ATTTATTTCT
12873213 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
12873227 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
12873244 TAATATA
1 TAATATA
12873251 CTTATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:12873244 original size:23 final size:24
Alignment explanation
Indices: 12873212--12873275 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
12873202 AATTTATTTC
*
12873212 TTAATATAATATTTATA-ATATAA
1 TTAATTTAATATTTATACATATAA
* *
12873235 TTAATTTAATA-ATATACTTATAA
1 TTAATTTAATATTTATACATATAA
12873258 TTAATTTATATATTTATA
1 TTAATTTA-ATATTTATA
12873276 TAAATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 4 0.12
23 23 0.68
24 3 0.09
25 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAATTTAATATTTATACATATAA
Found at i:12904799 original size:20 final size:21
Alignment explanation
Indices: 12904751--12904799 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
12904741 AACTTAAAAT
*
12904751 TTATTTTTTAATTCTTTTATT
1 TTATTTTTTAATTCTTTTATA
*
12904772 TTCCTTTTTT-A-TCTTTTATA
1 TT-ATTTTTTAATTCTTTTATA
12904792 TTATTTTT
1 TTATTTTT
12904800 CTCTCTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 3 0.12
22 6 0.25
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTTTTTAATTCTTTTATA
Found at i:12904808 original size:26 final size:25
Alignment explanation
Indices: 12904770--12904842 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
12904760 AATTCTTTTA
* *
12904770 TTTTCCTTTTTTATCTTTTATATTAT
1 TTTTCATTCTTTATCTTTTATATT-T
* *
12904796 TTTTC-TCTCTTTATTTTTTGTATTT
1 TTTTCAT-TCTTTATCTTTTATATTT
12904821 TTTTCATTCTTCTA-CTTTTATA
1 TTTTCATTCTT-TATCTTTTATA
12904843 ATGTTTGGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
25 17 0.44
26 22 0.56
ACGTcount: A:0.14, C:0.14, G:0.01, T:0.71
Consensus pattern (25 bp):
TTTTCATTCTTTATCTTTTATATTT
Found at i:12905141 original size:11 final size:11
Alignment explanation
Indices: 12905111--12905152 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
12905101 TTTCTCAAAA
12905111 TTTTA-AATAT
1 TTTTATAATAT
12905121 TTTTATTAATAT
1 TTTTA-TAATAT
12905133 TTTTATAAT-T
1 TTTTATAATAT
12905143 TTTTAATAAT
1 TTTT-ATAAT
12905153 TTATTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
12 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTATAATAT
Found at i:12905145 original size:22 final size:22
Alignment explanation
Indices: 12905111--12905160 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
12905101 TTTCTCAAAA
*
12905111 TTTTAAATATTTTTATTAATAT
1 TTTTAAATATTTTTAATAATAT
12905133 TTTTATAAT-TTTTTAATAAT-T
1 TTTTA-AATATTTTTAATAATAT
12905154 TATTTAA
1 T-TTTAA
12905161 TTGAACTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 19 0.76
23 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTAAATATTTTTAATAATAT
Found at i:12905161 original size:12 final size:11
Alignment explanation
Indices: 12905120--12905161 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
12905110 ATTTTAAATA
*
12905120 TTTTTATTAAT
1 TTTTTAATAAT
12905131 ATTTTT-ATAAT
1 -TTTTTAATAAT
12905142 TTTTTAATAAT
1 TTTTTAATAAT
12905153 TTATTTAAT
1 TT-TTTAAT
12905162 TGAACTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 5 0.19
11 11 0.41
12 11 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:12906181 original size:35 final size:35
Alignment explanation
Indices: 12906140--12906211 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
12906130 TAACCCTTAA
*
12906140 ATAATAAGATAATGCACTTCAACGCACTCAAACCC
1 ATAATAAGATAATGCACGTCAACGCACTCAAACCC
* *
12906175 ATAATAAGATAATGCGCGTCAATGCACTCAAACCC
1 ATAATAAGATAATGCACGTCAACGCACTCAAACCC
12906210 AT
1 AT
12906212 GTTCTCTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (35 bp):
ATAATAAGATAATGCACGTCAACGCACTCAAACCC
Done.