Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold365
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: 1826335
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 11
Found at i:293161 original size:167 final size:166
Alignment explanation
Indices: 292640--293166 Score: 373
Period size: 167 Copynumber: 3.2 Consensus size: 166
292630 TCCCGAGGAG
* ** * *
292640 ATTTTTCTTAATTTTTAATTTTTAAAATTCATAAAATATTATTATTTACTTTACAT-T-AAATTA
1 ATTTTTCTTAGTTTAAAATTTTTAAAATCCATAAAATATTATTATTTA-TTT-CATATGAAATCA
* * ** * * ** * *
292703 GTTTTCAAAAATTCCTTCATTTTCATTA-TTTTTTTATTTTTT-CTCTAAAATT-TTCTATTTTT
64 GTTTTAAAAAATTCATTCATCATCATGAGTTGTTAAATTTTTTCCT-TGAAATTCTCCTA-TTTT
* * * * *** *
292765 GAAATACGGAGTTTTCTACT-TCGTATATTTTTTTGG-GAGG
127 GAAAGACAGAATTTTCTACTCTC-TAAATTTTCCAGGAGA-A
* * * * *
292805 ATTTTTCTTGGTTGT-TAATTTTTAAAATCCATAAAATATTATTATTTATTTTATATTAAATTAG
1 ATTTTTCTTAGTT-TAAAATTTTTAAAATCCATAAAATATTATTATTTATTTCATATGAAATCAG
* ** * *
292869 TTTTCAAAAATTCATTCATTTTCATGAGTTGTTAAATTTTTTCCTTGAATTTTTCCTATTTTGAA
65 TTTTAAAAAATTCATTCATCATCATGAGTTGTTAAATTTTTTCCTTGAAATTCTCCTATTTTGAA
* ***
292934 AGTACAGAGTTTTCTACTCTCTAAATTTTTTTGGAGAA
130 AG-ACAGAATTTTCTACTCTCTAAATTTTCCAGGAGAA
** * *
292972 ATTTTTCTTAGTTTTTAATTTTTAAAATCCATCAAATATTATTATTTATTTCATATGAAATCATT
1 ATTTTTCTTAGTTTAAAATTTTTAAAATCCATAAAATATTATTATTTATTTCATATGAAATCAGT
** *
293037 TTTAAAAAATTTCATTCATCATCATGAGTT-TTTGATTTTTTTCTTGAAATTCTCCT-TTTGCTG
66 TTTAAAAAA-TTCATTCATCATCATGAGTTGTTAAATTTTTTCCTTGAAATTCTCCTATTT--TG
* *
293100 AGAA-ACCA-AATTTTCTATTC-CATAAATATTTCCAGG-GAG
128 A-AAGA-CAGAATTTTCTACTCTC-TAAAT-TTTCCAGGAGAA
* *
293139 A-TTTTCTTTGGTTTAAAATTTTTTAAAT
1 ATTTTTC-TTAGTTTAAAATTTTTAAAAT
293167 GTACCTAATA
Statistics
Matches: 304, Mismatches: 40, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
163 2 0.01
164 4 0.01
165 75 0.25
166 35 0.12
167 154 0.51
168 32 0.11
169 2 0.01
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (166 bp):
ATTTTTCTTAGTTTAAAATTTTTAAAATCCATAAAATATTATTATTTATTTCATATGAAATCAGT
TTTAAAAAATTCATTCATCATCATGAGTTGTTAAATTTTTTCCTTGAAATTCTCCTATTTTGAAA
GACAGAATTTTCTACTCTCTAAATTTTCCAGGAGAA
Found at i:295359 original size:154 final size:154
Alignment explanation
Indices: 295079--295766 Score: 748
Period size: 154 Copynumber: 4.5 Consensus size: 154
295069 CTATAATTCC
* * *
295079 TTTTTAAGTCTTTTAGGGATATC-GAGCACTTTTACGTCGAAGGTATCCCCT-AGAGGCATTCT-
1 TTTTTAAGTCTTTTAGGGGTATCAG-GTACTTTTACGTCGAAGGTATCCCCTAAG-GGCATTTTC
* * * * *
295141 GCTAATTTTTTAAAACCAAGTTCTAGGTTATCATTGGATCTGCTTTTATACCGAAGGTAGATATT
64 G-TAATTTTTTAAAACCAAG-TCTAGGTTGTCACTGGGTCTGCTTTTATGCCGAAGATAGATATT
*
295206 TAGGATAGGTTCAT-CCATTTAAAATCT
127 TAGGATAGGTTCATCCCATTCAAAATCT
* * * * *
295233 TTTTTAAGTCCTTTAGGGGTATTAAGTACTTTTACGTCGAAGGCATCCCCTAAGGGCATTTTTGT
1 TTTTTAAGTCTTTTAGGGGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAAGGGCATTTTCGT
* *
295298 AATTTTTTAAAACCAAGTACTAGGTTGTCACTGGGTCTGCTTTTATGCCAAAAATAGATATTTAG
66 AATTTTTTAAAACCAAGT-CTAGGTTGTCACTGGGTCTGCTTTTATGCCGAAGATAGATATTTAG
**
295363 GATAGGTTCATCCCATTCATGATCT
130 GATAGGTTCATCCCATTCAAAATCT
* * * **** * * * *
295388 TTTTTAAATCTTTTAGGGGTATCAGGTACTTCTACGTCAAAAACGTCCCCTAGGGGTATTCTGGT
1 TTTTTAAGTCTTTTAGGGGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAAGGGCATTTTCGT
* *
295453 AA-TTTTTAAGAATCGAGTCTTAGGTTGTCACT-GGTCTGCTTTTATGCCGAAGATAGATATTT-
66 AATTTTTTAA-AACCAAGTC-TAGGTTGTCACTGGGTCTGCTTTTATGCCGAAGATAGATATTTA
* * * *
295515 GGAATAGGTTCATCTCTTTTAAAATCC
129 GG-ATAGGTTCATCCCATTCAAAATCT
* * ** *
295542 TTTTTAAGTCTTTTAGGGGTATGAGGTACTTTTACATCGAAGGTATCGTCTAGGGGCATTTTCGT
1 TTTTTAAGTCTTTTAGGGGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAAGGGCATTTTCGT
* * ** *
295607 AATTTTTTAAAA-TAAGTCCTAGGTTGTCACTCGGTCCACTTTTATGCCGAAGGTAGATATTTAG
66 AATTTTTTAAAACCAAGT-CTAGGTTGTCACTGGGTCTGCTTTTATGCCGAAGATAGATATTTAG
** *
295671 GATAGGTTCATCCCATTCATGATCA
130 GATAGGTTCATCCCATTCAAAATCT
* * * *
295696 TTTTTAAGTCTTTTAGGGGTATCGGGTACTTCTATGTCGAAGGTATCCCC--AGAGGCATTTTCA
1 TTTTTAAGTCTTTTAGGGGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAAG-GGCATTTTCG
295759 TAATTTTT
65 TAATTTTT
295767 CTTCAACTTA
Statistics
Matches: 447, Mismatches: 74, Indels: 27
0.82 0.14 0.05
Matches are distributed among these distances:
152 1 0.00
153 35 0.08
154 317 0.71
155 94 0.21
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (154 bp):
TTTTTAAGTCTTTTAGGGGTATCAGGTACTTTTACGTCGAAGGTATCCCCTAAGGGCATTTTCGT
AATTTTTTAAAACCAAGTCTAGGTTGTCACTGGGTCTGCTTTTATGCCGAAGATAGATATTTAGG
ATAGGTTCATCCCATTCAAAATCT
Found at i:295702 original size:308 final size:309
Alignment explanation
Indices: 295124--295729 Score: 862
Period size: 308 Copynumber: 2.0 Consensus size: 309
295114 GTCGAAGGTA
*
295124 TCCCCTAGAGGCATTCTGCTAATTTTTTAAAACCAAGTTCTAGGTTATCATTGGATCTGCTTTTA
1 TCCCCTAGAGGCATTCTGCTAATTTTTTAAAACCAAGTTCTAGGTTATCACTGGATCTGCTTTTA
* *
295189 TACCGAAGGTAGATATTTAGGATAGGTTCATCCATTTAAAATCTTTTTTAAGTCCTTTAGGGGTA
66 TACCGAAGATAGATATTTAGGATAGGTTCATCCATTTAAAATCCTTTTTAAGTCCTTTAGGGGTA
* * *
295254 TTAAGTACTTTTACGTCGAAGGCATCCCCTAAGGGCATTTTTGTAATTTTTTAAAACCAAGTACT
131 TGAAGTACTTTTACATCGAAGGCATCCCCTAAGGGCATTTTCGTAATTTTTTAAAACCAAGTACT
* **
295319 AGGTTGTCACTGGGTCTGCTTTTATGCCAAAAATAGATATTTAGGATAGGTTCATCCCATTCATG
196 AGGTTGTCACTCGGTCCACTTTTATGCCAAAAATAGATATTTAGGATAGGTTCATCCCATTCATG
*
295384 ATCTTTTTTAAATCTTTTAGGGGTATCAGGTACTTCTACGTCAAAAACG
261 ATCATTTTTAAATCTTTTAGGGGTATCAGGTACTTCTACGTCAAAAACG
* * * * * *
295433 TCCCCTAGGGGTATTCTGGTAA-TTTTTAAGAATCGAG-TCTTAGGTTGTCACTGG-TCTGCTTT
1 TCCCCTAGAGGCATTCTGCTAATTTTTTAA-AACCAAGTTC-TAGGTTATCACTGGATCTGCTTT
* * *
295495 TATGCCGAAGATAGATATTT-GGAATAGGTTCATCTCTTTTAAAATCCTTTTTAAGTCTTTTAGG
64 TATACCGAAGATAGATATTTAGG-ATAGGTTCATC-CATTTAAAATCCTTTTTAAGTCCTTTAGG
* * ** * *
295559 GGTATGAGGTACTTTTACATCGAAGGTATCGTCTAGGGGCATTTTCGTAATTTTTTAAAA-TAAG
127 GGTATGAAGTACTTTTACATCGAAGGCATCCCCTAAGGGCATTTTCGTAATTTTTTAAAACCAAG
* * **
295623 TCCTAGGTTGTCACTCGGTCCACTTTTATGCCGAAGGTAGATATTTAGGATAGGTTCATCCCATT
192 TACTAGGTTGTCACTCGGTCCACTTTTATGCCAAAAATAGATATTTAGGATAGGTTCATCCCATT
* *
295688 CATGATCATTTTTAAGTCTTTTAGGGGTATCGGGTACTTCTA
257 CATGATCATTTTTAAATCTTTTAGGGGTATCAGGTACTTCTA
295730 TGTCGAAGGT
Statistics
Matches: 262, Mismatches: 31, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
307 2 0.01
308 146 0.56
309 114 0.44
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (309 bp):
TCCCCTAGAGGCATTCTGCTAATTTTTTAAAACCAAGTTCTAGGTTATCACTGGATCTGCTTTTA
TACCGAAGATAGATATTTAGGATAGGTTCATCCATTTAAAATCCTTTTTAAGTCCTTTAGGGGTA
TGAAGTACTTTTACATCGAAGGCATCCCCTAAGGGCATTTTCGTAATTTTTTAAAACCAAGTACT
AGGTTGTCACTCGGTCCACTTTTATGCCAAAAATAGATATTTAGGATAGGTTCATCCCATTCATG
ATCATTTTTAAATCTTTTAGGGGTATCAGGTACTTCTACGTCAAAAACG
Found at i:297935 original size:17 final size:17
Alignment explanation
Indices: 297910--297957 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
297900 ACACAACATT
*
297910 CCTAAGTTTAACTTATC
1 CCTAGGTTTAACTTATC
*
297927 CCTAGGTTTAAC-CATC
1 CCTAGGTTTAACTTATC
* *
297943 CTTAGGTTTGACTTA
1 CCTAGGTTTAACTTA
297958 AAAAAAAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (17 bp):
CCTAGGTTTAACTTATC
Found at i:298958 original size:57 final size:60
Alignment explanation
Indices: 298829--299067 Score: 209
Period size: 60 Copynumber: 4.1 Consensus size: 60
298819 TACAAGGTAA
* * * *
298829 ACTTAGGCAAAACCCTAAGTCTGAAAATAAAAATTTCATAGGCGAAACTAGTATGGGGTG
1 ACTTGGGCAAAACCCTAAGTCTAAAAATAAAAATATCATAGGCGAAACTAGTATGGAGTG
* *
298889 ACTTGGGCAAAACCCT-AGTCTAAAAATAAAAATATC-TAGGTGAAGCTAGTAT-GAGTG
1 ACTTGGGCAAAACCCTAAGTCTAAAAATAAAAATATCATAGGCGAAACTAGTATGGAGTG
* * * ** *** * * **
298946 ACTTGGGCAAAACCTTAAGTTTAAAAATAAAAAGATTTTAAATGAAACCAATATAAAGTG
1 ACTTGGGCAAAACCCTAAGTCTAAAAATAAAAATATCATAGGCGAAACTAGTATGGAGTG
* ** * * * * *
299006 ACTTAGGTGAAACCCTAAGTCTAAAAATAAAAGTA-CATTGACAAAACTAGTAT-AAGTG
1 ACTTGGGCAAAACCCTAAGTCTAAAAATAAAAATATCATAGGCGAAACTAGTATGGAGTG
299064 ACTT
1 ACTT
299068 AGGAAAAATC
Statistics
Matches: 145, Mismatches: 31, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
57 19 0.13
58 40 0.28
59 39 0.27
60 47 0.32
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (60 bp):
ACTTGGGCAAAACCCTAAGTCTAAAAATAAAAATATCATAGGCGAAACTAGTATGGAGTG
Found at i:298975 original size:58 final size:58
Alignment explanation
Indices: 298695--298978 Score: 225
Period size: 58 Copynumber: 4.8 Consensus size: 58
298685 GAACTTGGGT
* ** * * *
298695 GAAACTAGTACGAGGTGACTTGGGTGAAACCTTAAGTTTGAAAATAAAAAAAGCCTAGGC
1 GAAACTAGTATGA-GTGACTTGGGCAAAACCTTAAGTTTAAAAATAAAAATA-TCTAGGC
* * * ** * * *
298755 CAAATTAATATGAGTGACTTGGGTGAAACCTTAAATCTT-AAAATAAAAA-GT-TGGGC
1 GAAACTAGTATGAGTGACTTGGGCAAAACCTTAAGT-TTAAAAATAAAAATATCTAGGC
* ** * * * * * *
298811 AAAACTAGTACAAGGTAAACTTAGGCAAAACCCTAAGTCTGAAAATAAAAATTTCATAGGC
1 GAAACTAGTATGA-GT-GACTTGGGCAAAACCTTAAGTTTAAAAATAAAAATATC-TAGGC
* * * *
298872 GAAACTAGTATGGGGTGACTTGGGCAAAACCCT-AGTCTAAAAATAAAAATATCTAGGT
1 GAAACTAGTAT-GAGTGACTTGGGCAAAACCTTAAGTTTAAAAATAAAAATATCTAGGC
*
298930 GAAGCTAGTATGAGTGACTTGGGCAAAACCTTAAGTTTAAAAATAAAAA
1 GAAACTAGTATGAGTGACTTGGGCAAAACCTTAAGTTTAAAAATAAAAA
298979 GATTTTAAAT
Statistics
Matches: 180, Mismatches: 35, Indels: 20
0.77 0.15 0.09
Matches are distributed among these distances:
56 12 0.07
57 22 0.12
58 54 0.30
59 51 0.28
60 26 0.14
61 15 0.08
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (58 bp):
GAAACTAGTATGAGTGACTTGGGCAAAACCTTAAGTTTAAAAATAAAAATATCTAGGC
Found at i:299268 original size:46 final size:43
Alignment explanation
Indices: 299196--299290 Score: 102
Period size: 46 Copynumber: 2.1 Consensus size: 43
299186 CTGCATTGCA
*
299196 AACTGACCTACCAAATTCATTGGGCTTTAACTCTTAGTATAGATGCC
1 AACT-ACCTACCAAATTCATTAGGCTTT-ACTCTTAGTAT-G-TGCC
* * *
299243 AACTACCTACCAGTATT-ATTAGGCTTTTCTCTTGGTATGTGCC
1 AACTACCTACCA-AATTCATTAGGCTTTACTCTTAGTATGTGCC
299286 AACTA
1 AACTA
299291 GGTAGATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
43 9 0.21
44 1 0.02
45 9 0.21
46 17 0.40
47 7 0.16
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (43 bp):
AACTACCTACCAAATTCATTAGGCTTTACTCTTAGTATGTGCC
Found at i:308660 original size:15 final size:15
Alignment explanation
Indices: 308636--308665 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
308626 AAAGAGGAAG
*
308636 TCTTTTGGAGGTGTT
1 TCTTTGGGAGGTGTT
308651 TCTTTGGGAGGTGTT
1 TCTTTGGGAGGTGTT
308666 GAAGAGCTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.37, T:0.50
Consensus pattern (15 bp):
TCTTTGGGAGGTGTT
Found at i:309456 original size:21 final size:20
Alignment explanation
Indices: 309407--309462 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
309397 TACAATAAGC
*
309407 CTTA-GTATCGATACATTCA
1 CTTATGTATCGATACATTAA
309426 CTTATGTATCGATACATTAA
1 CTTATGTATCGATACATTAA
*
309446 CTTATTGTATCTATACA
1 CTTA-TGTATCGATACA
309463 AATTATAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.12
20 18 0.55
21 11 0.33
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (20 bp):
CTTATGTATCGATACATTAA
Found at i:312470 original size:682 final size:683
Alignment explanation
Indices: 311164--312524 Score: 2697
Period size: 682 Copynumber: 2.0 Consensus size: 683
311154 ACTTGAGTAC
311164 TAATCAAACCCACTCTAAGACATCCAAATGCCTTAGGAAGGTAAACACCAGATGACTCCTAATTT
1 TAATCAAACCCACTCTAAGACATCCAAATGCCTTAGGAAGGTAAACACCAGATGACTCCTAATTT
311229 GGTTAAAAATAAAAATAAGGGACAACATTGCACTGTTAGGATTCTTGATTTTATTACGGGTTCAT
66 GGTTAAAAATAAAAATAAGGGACAACATTGCACTGTTAGGATTCTTGATTTTATTACGGGTTCAT
311294 TCAAAGTCAATACAAGAAAAAAAAAAGATACCTTTGATAAGGTAGCTTTACAATGTTTAATTTGA
131 TCAAAGTCAATACAAGAAAAAAAAAAGATACCTTTGATAAGGTAGCTTTACAATGTTTAATTTGA
311359 AAGTATTAAGAAAATCTCAAAAATTGCATTCTAAAAGAAAATATTTTTTGAATTTGCACTTGGCT
196 AAGTATTAAGAAAATCTCAAAAATTGCATTCTAAAAGAAAATATTTTTTGAATTTGCACTTGGCT
311424 TAGCATTAACAGCAAGTGTAGAGAAGTAGATACAACAAAATTCAAAAAATGGCCCAAGGCTTATT
261 TAGCATTAACAGCAAGTGTAGAGAAGTAGATACAACAAAATTCAAAAAATGGCCCAAGGCTTATT
311489 CAAATTCAGAATGTTGCAAATGGTATATCACTAGAAACAAAATTTCATTTAGTTTTAAGGAAAAT
326 CAAATTCAGAATGTTGCAAATGGTATATCACTAGAAACAAAATTTCATTTAGTTTTAAGGAAAAT
311554 ATCAAAAAAATGAAAAAATCATTTAGGGGTCAAAAATGGCTTATATTAAGTAATAGTCATTGTGC
391 ATCAAAAAAATGAAAAAATCATTTAGGGGTCAAAAATGGCTTATATTAAGTAATAGTCATTGTGC
311619 TGAGAGGTTCTAAATAACACGTAATTGAAAATTTGATTTAGTTCTTTAGGAGGAACAAAAAGCTC
456 TGAGAGGTTCTAAATAACACGTAATTGAAAATTTGATTTAGTTCTTTAGGAGGAACAAAAAGCTC
311684 ATTTGAAAGCTAACTTGATTTTTTTAAAGAAAAATTAGAAAATTTTGTATAAATCATTTGGGTCT
521 ATTTGAAAGCTAACTTGATTTTTTTAAAGAAAAATTAGAAAATTTTGTATAAATCATTTGGGTCT
311749 CGAACTGCTGATAAGCAAGCAAAAGAACACCCATTAGCCATGCCATTAGCAACAACCAACACAAG
586 CGAACTGCTGATAAGCAAGCAAAAGAACACCCATTAGCCATGCCATTAGCAACAACCAACACAAG
311814 GCTCATGTCAAGGCATGTAATCAACTAGGAAGG
651 GCTCATGTCAAGGCATGTAATCAACTAGGAAGG
311847 TAATCAAACCCACTCTAAGACATCCAAATGCCTTAGGAAGGTAAACACCAGATGACTCCTAATTT
1 TAATCAAACCCACTCTAAGACATCCAAATGCCTTAGGAAGGTAAACACCAGATGACTCCTAATTT
311912 GGTTAAAAATAAAAATAA-GGACAACATTGCACTGTTAGGATTCTTGATTTTATTACGGGTTCAT
66 GGTTAAAAATAAAAATAAGGGACAACATTGCACTGTTAGGATTCTTGATTTTATTACGGGTTCAT
311976 TCAAAGTCAATACAAGAAAAAAAAAAGATACCTTTGATAAGGTAGCTTTACAATGTTTAATTTGA
131 TCAAAGTCAATACAAGAAAAAAAAAAGATACCTTTGATAAGGTAGCTTTACAATGTTTAATTTGA
312041 AAGTATTAAGAAAATCTCAAAAATTGCATTCTAAAAGAAAATATTTTTTGAATTTGCACTTGGCT
196 AAGTATTAAGAAAATCTCAAAAATTGCATTCTAAAAGAAAATATTTTTTGAATTTGCACTTGGCT
312106 TAGCATTAACAGCAAGTGTAGAGAAGTAGATACAACAAAATTCAAAAAATGGCCCAAGGCTTATT
261 TAGCATTAACAGCAAGTGTAGAGAAGTAGATACAACAAAATTCAAAAAATGGCCCAAGGCTTATT
312171 CAAATTCAGAATGTTGCAAATGGTATATCACTAGAAACAAAATTTCATTTAGTTTTAAGGAAAAT
326 CAAATTCAGAATGTTGCAAATGGTATATCACTAGAAACAAAATTTCATTTAGTTTTAAGGAAAAT
312236 ATCAAAAAAATGAAAAAATCATTTAGGGGTCAAAAATGGCTTATATTAAGTAATAGTCATTGTGC
391 ATCAAAAAAATGAAAAAATCATTTAGGGGTCAAAAATGGCTTATATTAAGTAATAGTCATTGTGC
* *
312301 TGAGAGGTTCTAAATAACACGTAATTGAAAATTTGATTTAGTTTTTTAGGATGAACAAAAAGCTC
456 TGAGAGGTTCTAAATAACACGTAATTGAAAATTTGATTTAGTTCTTTAGGAGGAACAAAAAGCTC
312366 ATTTGAAAGCTAACTTGATTTTTTTAAAGAAAAATTAGAAAATTTTGTATAAATCATTTGGGTCT
521 ATTTGAAAGCTAACTTGATTTTTTTAAAGAAAAATTAGAAAATTTTGTATAAATCATTTGGGTCT
312431 CGAACTGCTGATAAGCAAGCAAAAGAACACCCATTAGCCATGCCATTAGCAACAACCAACACAAG
586 CGAACTGCTGATAAGCAAGCAAAAGAACACCCATTAGCCATGCCATTAGCAACAACCAACACAAG
312496 GCTCATGTCAAGGCATGTAATCAACTAGG
651 GCTCATGTCAAGGCATGTAATCAACTAGG
312525 TTAAAATCTA
Statistics
Matches: 676, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
682 593 0.88
683 83 0.12
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (683 bp):
TAATCAAACCCACTCTAAGACATCCAAATGCCTTAGGAAGGTAAACACCAGATGACTCCTAATTT
GGTTAAAAATAAAAATAAGGGACAACATTGCACTGTTAGGATTCTTGATTTTATTACGGGTTCAT
TCAAAGTCAATACAAGAAAAAAAAAAGATACCTTTGATAAGGTAGCTTTACAATGTTTAATTTGA
AAGTATTAAGAAAATCTCAAAAATTGCATTCTAAAAGAAAATATTTTTTGAATTTGCACTTGGCT
TAGCATTAACAGCAAGTGTAGAGAAGTAGATACAACAAAATTCAAAAAATGGCCCAAGGCTTATT
CAAATTCAGAATGTTGCAAATGGTATATCACTAGAAACAAAATTTCATTTAGTTTTAAGGAAAAT
ATCAAAAAAATGAAAAAATCATTTAGGGGTCAAAAATGGCTTATATTAAGTAATAGTCATTGTGC
TGAGAGGTTCTAAATAACACGTAATTGAAAATTTGATTTAGTTCTTTAGGAGGAACAAAAAGCTC
ATTTGAAAGCTAACTTGATTTTTTTAAAGAAAAATTAGAAAATTTTGTATAAATCATTTGGGTCT
CGAACTGCTGATAAGCAAGCAAAAGAACACCCATTAGCCATGCCATTAGCAACAACCAACACAAG
GCTCATGTCAAGGCATGTAATCAACTAGGAAGG
Found at i:314357 original size:20 final size:20
Alignment explanation
Indices: 314326--314380 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
314316 CTGCCAGTTT
*
314326 CATGTATTGATACAATTCAA
1 CATGTATCGATACAATTCAA
* *
314346 -AGTGTATCGATACTA-TGAA
1 CA-TGTATCGATACAATTCAA
314365 CATGTATCGATACAAT
1 CATGTATCGATACAAT
314381 GTATCGATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTCAA
Found at i:314384 original size:13 final size:13
Alignment explanation
Indices: 314366--314390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
314356 TACTATGAAC
314366 ATGTATCGATACA
1 ATGTATCGATACA
314379 ATGTATCGATAC
1 ATGTATCGATAC
314391 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:314389 original size:32 final size:33
Alignment explanation
Indices: 314348--314411 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
314338 CAATTCAAAG
*
314348 TGTATCGATACTATG-AACATGTATCGATACAA
1 TGTATCGATACTAAGCAACATGTATCGATACAA
*
314380 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
314412 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:320286 original size:52 final size:52
Alignment explanation
Indices: 320138--320266 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
320128 CAAAATATGA
*
320138 AAATTTGCTTGCATGTATCGATACATTTCATAATGTATCGATACATCTAGGC
1 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
320190 AAATTTGCTTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
320242 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCTTGCATGTATCGATACA
320267 AAGATCAGTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:320374 original size:17 final size:16
Alignment explanation
Indices: 320352--320414 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 16
320342 ATTTGTACAT
320352 TGTATCGATACAAAACA
1 TGTATCGATACAAAA-A
*
320369 TGTATCGATAC---AT
1 TGTATCGATACAAAAA
320382 TGTATCGATACAACAATTA
1 TGTATCGATACAA-AA--A
320401 TGTATCGATACAAA
1 TGTATCGATACAAA
320415 TCGTTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
17 12 0.32
18 1 0.03
19 13 0.34
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (16 bp):
TGTATCGATACAAAAA
Found at i:320381 original size:30 final size:32
Alignment explanation
Indices: 320347--320412 Score: 109
Period size: 30 Copynumber: 2.1 Consensus size: 32
320337 TTCGTATTTG
320347 TACATTGTATCGATACAA-AA-CATGTATCGA
1 TACATTGTATCGATACAACAATCATGTATCGA
*
320377 TACATTGTATCGATACAACAATTATGTATCGA
1 TACATTGTATCGATACAACAATCATGTATCGA
320409 TACA
1 TACA
320413 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 18 0.55
31 2 0.06
32 13 0.39
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (32 bp):
TACATTGTATCGATACAACAATCATGTATCGA
Found at i:320387 original size:13 final size:13
Alignment explanation
Indices: 320369--320393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
320359 ATACAAAACA
320369 TGTATCGATACAT
1 TGTATCGATACAT
320382 TGTATCGATACA
1 TGTATCGATACA
320394 ACAATTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:321172 original size:53 final size:53
Alignment explanation
Indices: 321033--321179 Score: 174
Period size: 52 Copynumber: 2.8 Consensus size: 53
321023 ACCAATACGT
* *
321033 TGATTCACA-GCCAACGATATTGGGTTTAAAGATGAGAAAGAATGCCAATGTGC
1 TGATTCA-AGGCCAACGACATTGGGTTTAAAGATGAGAAAGAATGCCAATGTGA
* * * * *
321086 TGATTCACGGTCAGCGACATT-AGTCTTGAAGATGAG-AAGAATGCCAATGTGA
1 TGATTCAAGGCCAACGACATTGGGT-TTAAAGATGAGAAAGAATGCCAATGTGA
*
321138 TGATTCAAGGCCAACGACATTGGGTTTCAAAGATGACAAAGA
1 TGATTCAAGGCCAACGACATTGGGTTT-AAAGATGAGAAAGA
321180 CGCCAATATG
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
52 37 0.49
53 35 0.46
54 4 0.05
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (53 bp):
TGATTCAAGGCCAACGACATTGGGTTTAAAGATGAGAAAGAATGCCAATGTGA
Found at i:321223 original size:105 final size:105
Alignment explanation
Indices: 321033--321225 Score: 228
Period size: 105 Copynumber: 1.8 Consensus size: 105
321023 ACCAATACGT
* * * * * * *
321033 TGATTCACAGCCAACGATATTGGGTTTAAAGATGAGAAAGAATGCCAATGTGCTGATTCACGGTC
1 TGATTCACAGCCAACGACATTGGGTTTAAAGATGACAAAGAACGCCAATATGCGGATTCAAGGCC
* * *
321098 AGCGACATTAGTCTTGAAGATGAGAAGAATGCCAATGTGA
66 AGCAACATTAGACTTAAAGATGAGAAGAATGCCAATGTGA
*
321138 TGATTCA-AGGCCAACGACATTGGGTTTCAAAGATGACAAAG-ACGCCAATATGCGGATTTAAGG
1 TGATTCACA-GCCAACGACATTGGGTTT-AAAGATGACAAAGAACGCCAATATGCGGATTCAAGG
* * *
321201 CCTGCAATATTGGACTTAAAGATGA
64 CCAGCAACATTAGACTTAAAGATGA
321226 TAAGGGCGCC
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
104 1 0.01
105 59 0.82
106 12 0.17
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (105 bp):
TGATTCACAGCCAACGACATTGGGTTTAAAGATGACAAAGAACGCCAATATGCGGATTCAAGGCC
AGCAACATTAGACTTAAAGATGAGAAGAATGCCAATGTGA
Found at i:321239 original size:52 final size:52
Alignment explanation
Indices: 321166--321272 Score: 133
Period size: 52 Copynumber: 2.1 Consensus size: 52
321156 ATTGGGTTTC
* * * *
321166 AAAGATGACAAAGACGCCAATATGCGGATTTAAGGCCTGCAATATTGGACTT
1 AAAGATGACAAAGACGCCAATATGCGAATTCAAGACCAGCAATATTGGACTT
* * * * *
321218 AAAGATGATAAGGGCGCCAATATGCTAATTCAAGACCAGCGATATTGGACTT
1 AAAGATGACAAAGACGCCAATATGCGAATTCAAGACCAGCAATATTGGACTT
321270 AAA
1 AAA
321273 ATGGAGGTGC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (52 bp):
AAAGATGACAAAGACGCCAATATGCGAATTCAAGACCAGCAATATTGGACTT
Found at i:321643 original size:49 final size:46
Alignment explanation
Indices: 321571--321743 Score: 172
Period size: 43 Copynumber: 3.7 Consensus size: 46
321561 ATTGGGCTTA
* * *
321571 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGATGCCGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTTTTAAAGAT---GG
* * **
321620 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTT-AA-A-GG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTTTTAAAGATGG
*
321663 TGTCAATATGCTGATTCAAGGCCAGCGATATTAGGTTTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATT-GGTTTTAAAGAT---GG
* *
321713 TGCCAATATGCTTATTCAAGGCCAACGATAT
1 TGCCAATATGCTGATTCAAGGCCAGCGATAT
321744 CGGACTTAAA
Statistics
Matches: 102, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
43 31 0.30
44 4 0.04
45 2 0.02
46 1 0.01
47 1 0.01
48 2 0.02
49 31 0.30
50 30 0.29
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (46 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTTTTAAAGATGG
Found at i:321693 original size:22 final size:22
Alignment explanation
Indices: 321625--321693 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
321615 GCCGGTGCCA
*
321625 ATATGCTGATTCAAGGCCAACG
1 ATATGCTGATTCAAGGCCAGCG
* * * *
321647 ATAT-CGGACTTAAAGG--TGTCA
1 ATATGCTGA-TTCAAGGCCAG-CG
321668 ATATGCTGATTCAAGGCCAGCG
1 ATATGCTGATTCAAGGCCAGCG
321690 ATAT
1 ATAT
321694 TAGGTTTTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
21 14 0.42
22 18 0.55
23 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (22 bp):
ATATGCTGATTCAAGGCCAGCG
Found at i:321716 original size:93 final size:89
Alignment explanation
Indices: 321437--321751 Score: 341
Period size: 87 Copynumber: 3.5 Consensus size: 89
321427 TGAGAAAAGT
* * * *
321437 GATAAAGATGCCAATATGCTGATTCACGGCCAACGATATTGGACTT-GTGCCAATGTGCTAATTC
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAGTGCCAATGTGCTGATTC
** * **
321501 AAGGTTAGCGGCATTGGACTTAAA
66 AAGGCCAGCGACATTGGTTTTAAA
* * * * * * *
321525 GA-CAAGGTGCCAATACG-TCAATTCAAAGCCAGCGATATTGGGCTTA-TGCCAATGTGCTGATT
1 GATAAAGGTGCCAATATGCT-GATTCAAGGCCAACGATATCGGACTTAGTGCCAATGTGCTGATT
*
321587 CAAGGCCAGCAACATTGGTTTTAAA
65 CAAGGCCAGCGACATTGGTTTTAAA
*** * *
321612 GATGCCGGTGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGGTGTCAATATGCTGA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATCGGACTT--A-GTGCCAATGTGCTGA
*
321677 TTCAAGGCCAGCGATATTAGGTTTTAAA
63 TTCAAGGCCAGCGACATT-GGTTTTAAA
*
321705 GATAAAGGTGCCAATATGCTTATTCAAGGCCAACGATATCGGACTTA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTA
321752 AAGGAAGATG
Statistics
Matches: 186, Mismatches: 32, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
86 1 0.01
87 69 0.37
88 34 0.18
89 1 0.01
90 1 0.01
91 1 0.01
92 28 0.15
93 51 0.27
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (89 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAGTGCCAATGTGCTGATTC
AAGGCCAGCGACATTGGTTTTAAA
Found at i:321845 original size:28 final size:27
Alignment explanation
Indices: 321773--321845 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
321763 CACCAACTTG
321773 TGTGGGCTTTTGAAAGGGTTGCATCAACT
1 TGTGGGC-TTTGAAA-GGTTGCATCAACT
* **
321802 TGTGTGCTTGTG-AAGGTTGCCATTGACT
1 TGTGGGCTT-TGAAAGGTTG-CATCAACT
321830 TGTGGGCTTTGAAAGG
1 TGTGGGCTTTGAAAGG
321846 AGTGCCACCG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 7 0.19
28 22 0.59
29 8 0.22
ACGTcount: A:0.18, C:0.12, G:0.34, T:0.36
Consensus pattern (27 bp):
TGTGGGCTTTGAAAGGTTGCATCAACT
Found at i:321941 original size:35 final size:34
Alignment explanation
Indices: 321874--322231 Score: 403
Period size: 34 Copynumber: 10.6 Consensus size: 34
321864 GCTTAAAATG
* *
321874 GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGA
*
321908 GTGCCGCGGAGTTGTGGGCTTAAAAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGGCTT-AAAAGGAAAAAGA
321943 GTGCCACGGAGTTGTGGGCTTAAAAGG-AAAA-A
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGA
*
321975 ----CGCGGAGTTGTGGGCTTAAAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGA
**
322005 GTGCCATAGAGTTGTGGGCTTAAAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGA
* *
322039 GTGTCACGGAGTTGTGGGCTTAAAAAAGAAAAA-A
1 GTGCCACGGAGTTGTGGGCTT-AAAAGGAAAAAGA
* * * *
322073 GGTGCCACGGACTCGTGGACTTAGAAGGAAAAAG-
1 -GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGA
** * * *
322107 GCACCACGGACTTGTGGACTTAGAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGA
322141 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAAAGA
1 GTGCCACGGAGTTGTGGGCTTAAAAGG--AAAAAGA
* *
322177 GTG-CACAGAGTTGTGGGCTTTAAAAAGAAAAACG-
1 GTGCCACGGAGTTGTGGGC-TTAAAAGGAAAAA-GA
*
322211 GTGCCACAGAGTTGTGGGCTT
1 GTGCCACGGAGTTGTGGGCTT
322232 CGGAAAAAGG
Statistics
Matches: 280, Mismatches: 28, Indels: 32
0.82 0.08 0.09
Matches are distributed among these distances:
28 22 0.08
29 4 0.01
30 1 0.00
32 1 0.00
33 34 0.12
34 111 0.40
35 90 0.32
36 17 0.06
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (34 bp):
GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGA
Found at i:321967 original size:28 final size:29
Alignment explanation
Indices: 321829--322067 Score: 106
Period size: 34 Copynumber: 7.6 Consensus size: 29
321819 TGCCATTGAC
** * * *
321829 TTGTGGGCTTTGAAAGGAGTGCCACCGAT
1 TTGTGGGCTTAAAAAAGAGTGCCACGGAG
* *
321858 TTGTGGGCTT-AAAATG-GTGCCACAGAG
1 TTGTGGGCTTAAAAAAGAGTGCCACGGAG
* *
321885 TTGTGGACTTAAAAGGAAAAAGAGTGCCGCGGAG
1 TTGTGGGCTT---A--AAAAAGAGTGCCACGGAG
321919 TTGTGGGCTTAAAAAGGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTT----A--AAAAAGAGTGCCACGGAG
* **** *
321954 TTGTGGGCTT-AAAAGGAAAAACGCGGAG
1 TTGTGGGCTTAAAAAAGAGTGCCACGGAG
**
321982 TTGTGGGCTTAAAAGGAAAAAGAGTGCCATAGAG
1 TTGTGGGCTT---A--AAAAAGAGTGCCACGGAG
*
322016 TTGTGGGCTTAAAAGGAAAAAGAGTGTCACGGAG
1 TTGTGGGCTT---A--AAAAAGAGTGCCACGGAG
322050 TTGTGGGCTTAAAAAAGA
1 TTGTGGGCTTAAAAAAGA
322068 AAAAAGGTGC
Statistics
Matches: 169, Mismatches: 27, Indels: 28
0.75 0.12 0.12
Matches are distributed among these distances:
27 18 0.11
28 26 0.15
29 17 0.10
31 1 0.01
33 5 0.03
34 69 0.41
35 33 0.20
ACGTcount: A:0.33, C:0.11, G:0.34, T:0.21
Consensus pattern (29 bp):
TTGTGGGCTTAAAAAAGAGTGCCACGGAG
Found at i:322049 original size:131 final size:132
Alignment explanation
Indices: 321874--322231 Score: 456
Period size: 131 Copynumber: 2.7 Consensus size: 132
321864 GCTTAAAATG
* *
321874 GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCGCGGAGTTGTGGGCTTAAAAAGGAAA
1 GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAGTG-CACGGAGTTGTGGGCTTAAAAA-GAAA
* * *
321939 AAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AAAA-A-CGCGGAGTTGTGGGCTTAAAAGGAAA
64 AAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGACCACGGACTTGTGGACTTAAAAGGAAA
322001 AAGA
129 AAGA
*
322005 GTGCCATAGAGTTGTGGGCTTAAAAGGAAAAAGAGTGTCACGGAGTTGTGGGCTTAAAAAAGAAA
1 GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAGTG-CACGGAGTTGTGGGCTT-AAAAAGAAA
* * * * *
322070 AA-AGGTGCCACGGACTCGTGGACTTAGAAGGAAAAAGGCACCACGGACTTGTGGACTTAGAAGG
64 AAGA-GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAA-G-ACCACGGACTTGTGGACTTAAAAGG
322134 AAAAAGA
126 AAAAAGA
* *
322141 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAAAGAGTGCACAGAGTTGTGGGCTTTAAAAAGAA
1 GTGCCACAGAGTTGTGGGCTTAAAAGG--AAAAAGAGTGCACGGAGTTGTGGGC-TTAAAAAGAA
*
322206 AAACG-GTGCCACAGAGTTGTGGGCTT
63 AAA-GAGTGCCACGGAGTTGTGGGCTT
322232 CGGAAAAAGG
Statistics
Matches: 196, Mismatches: 19, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
130 1 0.01
131 80 0.41
132 9 0.05
135 1 0.01
136 51 0.26
137 42 0.21
138 12 0.06
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (132 bp):
GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCACGGAGTTGTGGGCTTAAAAAGAAAAA
GAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGACCACGGACTTGTGGACTTAAAAGGAAAAA
GA
Found at i:322256 original size:30 final size:31
Alignment explanation
Indices: 322203--322261 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
322193 GCTTTAAAAA
* *
322203 GAAAAACGGTGCCACAGAGTTGTGGGCTTCG
1 GAAAAACGGCGCCACAGACTTGTGGGCTTCG
*
322234 GAAAAA-GGCGCCACTGACTTGTGGGCTT
1 GAAAAACGGCGCCACAGACTTGTGGGCTT
322262 TTGACAGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.20
Consensus pattern (31 bp):
GAAAAACGGCGCCACAGACTTGTGGGCTTCG
Found at i:323611 original size:1 final size:1
Alignment explanation
Indices: 323605--323687 Score: 85
Period size: 1 Copynumber: 83.0 Consensus size: 1
323595 ATCCGGACCC
* * * * * * *
323605 TTTTTTTTGTTTTTTTTTTGTTTTTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
323670 GTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTT
323688 GTGGAGGACA
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:323619 original size:7 final size:7
Alignment explanation
Indices: 323607--323687 Score: 128
Period size: 7 Copynumber: 11.6 Consensus size: 7
323597 CCGGACCCTT
323607 TTTTTTG
1 TTTTTTG
*
323614 TTTTTTT
1 TTTTTTG
*
323621 TTTGTTTT
1 TTT-TTTG
323629 TTTTTTG
1 TTTTTTG
323636 TTTTTTG
1 TTTTTTG
323643 TTTTTTG
1 TTTTTTG
323650 TTTTTTG
1 TTTTTTG
323657 TTTTTTG
1 TTTTTTG
323664 TTTTTTG
1 TTTTTTG
323671 TTTTTTG
1 TTTTTTG
323678 TTTTTT-
1 TTTTTTG
323684 TTTT
1 TTTT
323688 GTGGAGGACA
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
6 4 0.06
7 60 0.85
8 7 0.10
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (7 bp):
TTTTTTG
Found at i:337671 original size:52 final size:52
Alignment explanation
Indices: 337523--337651 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
337513 CGAAATATGA
337523 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
337575 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
337627 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
337652 AAGATTAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:337678 original size:13 final size:13
Alignment explanation
Indices: 337660--337684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
337650 CAAAGATTAG
337660 TGTATCGATACAA
1 TGTATCGATACAA
337673 TGTATCGATACA
1 TGTATCGATACA
337685 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:337765 original size:19 final size:18
Alignment explanation
Indices: 337737--337801 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
337727 AACTGTACAT
*
337737 TGTATTGATACAAAACTTA
1 TGTATCGATACAAAA-TTA
337756 TGTATCGATAC---A-T-
1 TGTATCGATACAAAATTA
337769 TGTATCGATACAACAATTA
1 TGTATCGATACAA-AATTA
337788 TGTATCGATACAAA
1 TGTATCGATACAAA
337802 TCGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
18 2 0.05
19 23 0.59
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAAATTA
Found at i:337773 original size:32 final size:32
Alignment explanation
Indices: 337732--337799 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
337722 TTCGTAACTG
*
337732 TACATTGTATTGATACAA-AACTTATGTATCGA
1 TACATTGTATCGATACAACAA-TTATGTATCGA
337764 TACATTGTATCGATACAACAATTATGTATCGA
1 TACATTGTATCGATACAACAATTATGTATCGA
337796 TACA
1 TACA
337800 AATCGTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACAATTATGTATCGA
Found at i:337774 original size:13 final size:13
Alignment explanation
Indices: 337756--337780 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
337746 ACAAAACTTA
337756 TGTATCGATACAT
1 TGTATCGATACAT
337769 TGTATCGATACA
1 TGTATCGATACA
337781 ACAATTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:338601 original size:13 final size:13
Alignment explanation
Indices: 338583--338607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
338573 ACAATTCACT
338583 ATGTATCGATACA
1 ATGTATCGATACA
338596 ATGTATCGATAC
1 ATGTATCGATAC
338608 TGAGTGAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:347757 original size:20 final size:20
Alignment explanation
Indices: 347720--347758 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
347710 ACATTGGTCT
*
347720 AATGTATCGATATATTAGGC
1 AATGTATCGATACATTAGGC
*
347740 AATGTATCGATACCTTAGG
1 AATGTATCGATACATTAGG
347759 GCCCAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTAGGC
Found at i:348494 original size:65 final size:65
Alignment explanation
Indices: 348346--348483 Score: 165
Period size: 65 Copynumber: 2.1 Consensus size: 65
348336 TTTAGGCTTA
* * ** *
348346 ACCTATTTCTAG--ATACATAGGTTTGACTTAAAAAGAAAATTACTAGAATTTGTTCTTAGCTCG
1 ACCTATTTCTAGAAAGAAATAGGTTTGACTTAAAAAGAAAAAGACTAGAATTTGTTCTAAGCTCG
* *
348409 ACCTATTTCTAGAAAGAAATAGGTTTGACTTAAAAAGAAAAAGATTTA-AAGTTCTTTTCTAAGC
1 ACCTATTTCTAGAAAGAAATAGGTTTGACTTAAAAAGAAAAAGA-CTAGAA-TT-TGTTCTAAGC
348473 TCG
63 TCG
348476 ACCTATTT
1 ACCTATTT
348484 TTAAGAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 12 0.19
65 28 0.44
66 4 0.06
67 19 0.30
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (65 bp):
ACCTATTTCTAGAAAGAAATAGGTTTGACTTAAAAAGAAAAAGACTAGAATTTGTTCTAAGCTCG
Found at i:350373 original size:79 final size:78
Alignment explanation
Indices: 350283--350762 Score: 510
Period size: 79 Copynumber: 6.2 Consensus size: 78
350273 AACAACGGGG
* * * * *
350283 TTGGAGTATCCCCTCAAAAATAACGGGATTGGAATATCCTCGATTATGAAAAATCGATGATTTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCC-CGATTATGAAAAATTGATGTTTTAG
350348 AAATAAAATCAGGA
65 AAATAAAATCAGGA
* * *
350362 TTGGAGTATCCCCTCGGAAATAAGGGGGTTGGAGTATCCCTGACTATGAAAAATTGATGTTTTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC-GATTATGAAAAATTGATGTTTTAG
*
350427 AAATAAAA-CCGGA
65 AAATAAAATCAGGA
* * * * *
350440 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATTAATATTTTA
1 -TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT-CCCGATTATGAAAAATTGATGTTTTA
** *
350505 GAAATAAAGCCAGGG
64 GAAATAAAATCAGGA
* * *
350520 TTGGGGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCG---ATGAAAAATTAATGTTTTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT-CCCGATTATGAAAAATTGATGTTTTAG
* * *
350582 AAATAAAACCGGGG
65 AAATAAAATCAGGA
* *
350596 TTGG-GTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCCA--ATGAAAAATTGATGTTTTAGA
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCGATTATGAAAAATTGATGTTTTAGA
* * *
350658 GATAAAATCGGGG
66 AATAAAATCAGGA
* * * * * *
350671 TTGGAGTGTCCCCTCGAAAATAACGGGGTTAGAGTATCCCTGATTGTG-AAAAGTCAGTGTTTTG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC-GATTATGAAAAATTGA-TGTTTTA
*
350735 GAAATAAAATCA-AA
64 GAAATAAAATCAGGA
350749 GTTGGAGTATCCCC
1 -TTGGAGTATCCCC
350763 GATTATGGAA
Statistics
Matches: 345, Mismatches: 45, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
74 3 0.01
75 65 0.19
76 66 0.19
77 1 0.00
78 11 0.03
79 193 0.56
80 6 0.02
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.27
Consensus pattern (78 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCGATTATGAAAAATTGATGTTTTAGA
AATAAAATCAGGA
Found at i:350551 original size:158 final size:157
Alignment explanation
Indices: 350257--350762 Score: 589
Period size: 158 Copynumber: 3.2 Consensus size: 157
350247 GACGAGAAAT
* * * * *
350257 TTAATATTTTAGAGAA-AACAA-CGGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAATAT
1 TTAATGTTTTAGA-AATAA-AACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
* * * *
350320 CCTCGATTATGAAAAATCGATGA-TTTAGAAATAAAATCAGGATTGGAGTATCCCCTCGGAAATA
64 CC-CCATTATGAAAAATTGAT-ATTTTAGAAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATA
*
350384 AGGGGGTTGGAGTATCCCTGACTATGAAAAA
127 ACGGGGTTGGAGTATCCCTGACTATGAAAAA
* *
350415 TTGATGTTTTAGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCC
1 TTAATGTTTTAGAAATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCC
* * ** * *
350480 CCAATTATGAGAAATTAATATTTTAGAAATAAAGCCAGGGTTGGGGTATCCCCTCGAAAATAATG
66 CC-ATTATGAAAAATTGATATTTTAGAAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACG
*
350545 GGGTTGGAGTATCCC---CGATGAAAAA
130 GGGTTGGAGTATCCCTGACTATGAAAAA
* *
350570 TTAATGTTTTAGAAATAAAACCGGGGTTGG-GTATCCTCTCGAAAATAACGGGGTTGGAGTATCC
1 TTAATGTTTTAGAAATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCC
* * * *
350634 CCA--ATGAAAAATTGATGTTTTAGAGATAAAATCGGGGTTGGAGTGTCCCCTCGAAAATAACGG
66 CCATTATGAAAAATTGATATTTTAGAAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACGG
* * * *
350697 GGTTAGAGTATCCCTGATTGTGAAAAG
131 GGTTGGAGTATCCCTGACTATGAAAAA
* * * * **
350724 TCAGTGTTTTGGAAATAAAATCAAAGTTGGAGTATCCCC
1 TTAATGTTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
350763 GATTATGGAA
Statistics
Matches: 295, Mismatches: 45, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
151 63 0.21
153 1 0.00
154 63 0.21
155 44 0.15
157 6 0.02
158 118 0.40
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (157 bp):
TTAATGTTTTAGAAATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCC
CCATTATGAAAAATTGATATTTTAGAAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACGG
GGTTGGAGTATCCCTGACTATGAAAAA
Found at i:350757 original size:51 final size:51
Alignment explanation
Indices: 350702--350818 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
350692 AACGGGGTTA
* * *
350702 GAGTATCCCTGATTGT-GAAAAGTCAGTGTTTTGGAAATAAAATCAAAGTTG
1 GAGTATCCCCGATTATGGAAAA-TCAGTGTTTTAGAAATAAAATCAAAGTTG
** **
350753 GAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGGAAAATCAGTGTTTTAGAAATAAAATCAAAGTTG
350804 GAGTATCCCCGATTA
1 GAGTATCCCCGATTA
350819 AGAAAAATTG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 53 0.91
52 5 0.09
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTATGGAAAATCAGTGTTTTAGAAATAAAATCAAAGTTG
Found at i:350826 original size:51 final size:51
Alignment explanation
Indices: 350727--350866 Score: 174
Period size: 51 Copynumber: 2.7 Consensus size: 51
350717 TGAAAAGTCA
** * *
350727 GTGTTTTGGAAATAAAATCAAAGTTGGAGTATCCCCGATTATGGAAAATGG
1 GTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATGG
* *
350778 GTGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATTG
1 GTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATGG
* * * *
350829 ATGTTTTGGAAATGAAACCGG-GATTGAAGTATCCCCGA
1 GTGTTTTGGAAATAAAATCGGAG-TTGGAGTATCCCCGA
350867 GATGAAAAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
50 1 0.01
51 76 0.99
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (51 bp):
GTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATGG
Found at i:353228 original size:13 final size:13
Alignment explanation
Indices: 353210--353238 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
353200 ACAATGAGCC
353210 ATGTATCGATACA
1 ATGTATCGATACA
353223 ATGTATCGATACA
1 ATGTATCGATACA
353236 ATG
1 ATG
353239 AGTAATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:353231 original size:33 final size:33
Alignment explanation
Indices: 353189--353256 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
353179 TACATTGTAA
*
353189 AATGTATCGATACAATGAGCCATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
*
353222 AATGTATCGATACAATGAGTAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
353255 AA
1 AA
353257 ATTGTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:353247 original size:20 final size:18
Alignment explanation
Indices: 353169--353256 Score: 69
Period size: 20 Copynumber: 4.8 Consensus size: 18
353159 AAAATGCCTG
*
353169 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG--A
353189 AATGTATCGATACAATGA
1 AATGTATCGATACAATGA
*
353207 GCCATGTATCGATAC-----
1 --AATGTATCGATACAATGA
353222 AATGTATCGATACAATGA
1 AATGTATCGATACAATGA
353240 GTAATGTATCGATACAA
1 --AATGTATCGATACAA
353257 ATTGTGAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
13 12 0.21
18 1 0.02
20 43 0.77
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (18 bp):
AATGTATCGATACAATGA
Found at i:355118 original size:3 final size:3
Alignment explanation
Indices: 355110--355135 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
355100 CAATGTTGAA
355110 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
355136 AGTTGACTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:355615 original size:21 final size:20
Alignment explanation
Indices: 355589--355637 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
355579 GATGTGCTTA
355589 AAAAGAAAGAAGAAGAATTAG
1 AAAAGAAAGAAG-AGAATTAG
* *
355610 AAAAGAAAATAAGTGAATTAG
1 AAAAG-AAAGAAGAGAATTAG
355631 AAAAGAA
1 AAAAGAA
355638 GATAATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.68
22 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.12
Consensus pattern (20 bp):
AAAAGAAAGAAGAGAATTAG
Found at i:355642 original size:21 final size:21
Alignment explanation
Indices: 355603--355649 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
355593 GAAAGAAGAA
355603 GAATTAGAAAAGAAAATAAGT
1 GAATTAGAAAAGAAAATAAGT
* *
355624 GAATTAGAAAAGAAGATAATT
1 GAATTAGAAAAGAAAATAAGT
355645 GAATT
1 GAATT
355650 GCAAGTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.23
Consensus pattern (21 bp):
GAATTAGAAAAGAAAATAAGT
Found at i:363057 original size:13 final size:13
Alignment explanation
Indices: 363039--363064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
363029 ACAAAGATCC
363039 ATGTATCGATACA
1 ATGTATCGATACA
363052 ATGTATCGATACA
1 ATGTATCGATACA
363065 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:363060 original size:33 final size:33
Alignment explanation
Indices: 363018--363084 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
363008 AAAATTTCCA
***
363018 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
363051 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
363084 A
1 A
363085 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:363128 original size:19 final size:18
Alignment explanation
Indices: 363104--363171 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
363094 CAGTAGCTAA
363104 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
363123 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
363138 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
363155 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
363172 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:363144 original size:13 final size:13
Alignment explanation
Indices: 363126--363150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
363116 ACAATACTTA
363126 TGTATCGATACAT
1 TGTATCGATACAT
363139 TGTATCGATACA
1 TGTATCGATACA
363151 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:363148 original size:32 final size:32
Alignment explanation
Indices: 363107--363169 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
363097 TAGCTAATTA
*
363107 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
363139 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
363170 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:363644 original size:31 final size:31
Alignment explanation
Indices: 363609--363687 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
363599 GGTATTCATT
363609 ATCAAATTTCATCAATT-CTTTTTCGA-ATTTC
1 ATCAAATTTCATCAATTAC-TTTTC-ATATTTC
*
363640 ATCAAATTTACATC-ATTACTTTTCATTTTTC
1 ATCAAATTT-CATCAATTACTTTTCATATTTC
363671 ATCAAAATATTCATCAA
1 ATC-AAAT-TTCATCAA
363688 AAACGGTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
30 1 0.02
31 24 0.59
32 13 0.32
33 3 0.07
ACGTcount: A:0.34, C:0.19, G:0.01, T:0.46
Consensus pattern (31 bp):
ATCAAATTTCATCAATTACTTTTCATATTTC
Found at i:365964 original size:21 final size:20
Alignment explanation
Indices: 365924--365962 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
365914 TTAAGTATAA
365924 ATATTTTTCAAGCATTAAATC
1 ATATTTTTCAAG-ATTAAATC
365945 ATATGTTTTCAAG-TTAAA
1 ATAT-TTTTCAAGATTAAA
365963 ATGATACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 4 0.24
22 8 0.47
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (20 bp):
ATATTTTTCAAGATTAAATC
Found at i:372296 original size:45 final size:46
Alignment explanation
Indices: 372232--372325 Score: 163
Period size: 45 Copynumber: 2.0 Consensus size: 46
372222 TGGTTGGCAT
372232 TAAAATTTCATCTCAAAATCATG-CATATCTATGTGGAAGTTCATG
1 TAAAATTTCATCTCAAAATCATGACATATCTATGTGGAAGTTCATG
*
372277 TAAAATTTCATCTCAAAATCATGTATATATCTATGTGGAAGTTCATG
1 TAAAATTTCATCTCAAAATCATG-ACATATCTATGTGGAAGTTCATG
372324 TA
1 TA
372326 TCCACGAGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 23 0.50
47 23 0.50
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (46 bp):
TAAAATTTCATCTCAAAATCATGACATATCTATGTGGAAGTTCATG
Found at i:373205 original size:30 final size:30
Alignment explanation
Indices: 373171--373227 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
373161 ATTTTATAAA
373171 AATAA-AATAAAATTAAAATTAAATAATTTT
1 AATAATAATAAAATT-AAATTAAATAATTTT
** *
373201 AATAATAATTTAATTTAATTAAATAAT
1 AATAATAATAAAATTAAATTAAATAAT
373228 ATAATATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 16 0.70
31 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AATAATAATAAAATTAAATTAAATAATTTT
Found at i:374391 original size:21 final size:20
Alignment explanation
Indices: 374365--374415 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
374355 TGAATACGAT
*
374365 ATAAAAAATAATTAAAATATA
1 ATAAAAAATAA-TAAAAAATA
*
374386 ATAAAAATATGATAAAAAATA
1 ATAAAAA-ATAATAAAAAATA
374407 A-AAAAAATA
1 ATAAAAAATA
374416 CAAATACGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 5 0.19
21 16 0.62
22 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
ATAAAAAATAATAAAAAATA
Found at i:374405 original size:12 final size:11
Alignment explanation
Indices: 374365--374415 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
374355 TGAATACGAT
374365 ATAAAAA-ATA
1 ATAAAAATATA
*
374375 ATTAAAATATA
1 ATAAAAATATA
*
374386 ATAAAAATATG
1 ATAAAAATATA
374397 ATAAAAA-ATA
1 ATAAAAATATA
*
374407 AAAAAAATA
1 ATAAAAATA
374416 CAAATACGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 14 0.41
11 20 0.59
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:374477 original size:25 final size:26
Alignment explanation
Indices: 374449--374513 Score: 89
Period size: 25 Copynumber: 2.5 Consensus size: 26
374439 TATTTTTAAA
374449 TATATAAATATAAATTA-TTAAAATT
1 TATATAAATATAAATTACTTAAAATT
*
374474 TATATAAATATAAATTACTTTAAATT
1 TATATAAATATAAATTACTTAAAATT
374500 T-TATTATAATATAA
1 TATA-TA-AATATAA
374514 TAAAATATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 19 0.53
26 10 0.28
27 7 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TATATAAATATAAATTACTTAAAATT
Found at i:375161 original size:2 final size:2
Alignment explanation
Indices: 375154--375185 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
375144 TTAGATTATG
375154 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
375186 GGGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:376314 original size:3 final size:3
Alignment explanation
Indices: 376303--376369 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
376293 ATAATTATAA
*
376303 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT AAT T-T TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
* * *
376349 TTT TAT AAT TAA TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
376370 TATTTTGATT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 8 0.16
3 41 0.80
4 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:377183 original size:24 final size:23
Alignment explanation
Indices: 377154--377198 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
377144 AATATTTTAA
*
377154 TATTATTTATAAAATTAAAAATTT
1 TATTATTAATAAAA-TAAAAATTT
*
377178 TATTATTAATATAATAAAAAT
1 TATTATTAATAAAATAAAAAT
377199 GAAATGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATTAATAAAATAAAAATTT
Found at i:379784 original size:2 final size:2
Alignment explanation
Indices: 379777--379801 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
379767 AATAACAAAA
379777 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
379802 GAGTACCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:385017 original size:90 final size:91
Alignment explanation
Indices: 384856--385028 Score: 244
Period size: 90 Copynumber: 1.9 Consensus size: 91
384846 TAGCACACAA
**
384856 TTAGAAGCTTACTTCAATATTACTGACTTTTCAAGACTAAAAGAAAACAATAATACATCCACTGC
1 TTAGAAGCTTACTTCAATATTACCAACTTTTCAAGAC-AAAAGAAAACAATAATACATCCACTGC
384921 AAGAGAATGAATAATGAACACATGCTG
65 AAGAGAATGAATAATGAACACATGCTG
* * *
384948 TTAGAAGCTTACTTCAATCTTACCAATTTTTGAAGAC-AAAGAAAACAATAATACATCCA-T-CA
1 TTAGAAGCTTACTTCAATATTACCAACTTTTCAAGACAAAAGAAAACAATAATACATCCACTGCA
*
385010 CATGAGAATGAATGATGAA
66 -A-GAGAATGAATAATGAA
385029 TGCCTAACTT
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
88 2 0.03
89 2 0.03
90 37 0.51
92 32 0.44
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.27
Consensus pattern (91 bp):
TTAGAAGCTTACTTCAATATTACCAACTTTTCAAGACAAAAGAAAACAATAATACATCCACTGCA
AGAGAATGAATAATGAACACATGCTG
Found at i:388437 original size:3 final size:3
Alignment explanation
Indices: 388429--388455 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
388419 AACAGAAGCG
388429 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
388456 ACCGGCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:388675 original size:17 final size:17
Alignment explanation
Indices: 388653--388686 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
388643 ACCAATTGGA
388653 CATTTTAATATAATTAT
1 CATTTTAATATAATTAT
*
388670 CATTTTAATATGATTAT
1 CATTTTAATATAATTAT
388687 TAAATTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (17 bp):
CATTTTAATATAATTAT
Found at i:389827 original size:173 final size:173
Alignment explanation
Indices: 389519--389865 Score: 498
Period size: 173 Copynumber: 2.0 Consensus size: 173
389509 TTATGTATAC
*
389519 TAAAATTATATCTATGAATAAATTATAATACATCTTTTTACAAAATTAAGTTAAAAATTTTTAGT
1 TAAAATTATATCTATGAATAAATTATAATACATCTGTTTACAAAATTAAGTTAAAAATTTTTAGT
* * *
389584 AAAATAGTAGAGTAGAGTAATATAAAATAATCATAAATATAACCGACATTTATGAAAATAAATAT
66 AAAAAAGTAGAGTAGAATAATATAAAATAATCATAAATATAACCGACATTTATAAAAATAAATAT
* *
389649 TTTCAACGTCTATACAAAAGTAGAGTAGAGAT-GAATAAAGTAA
131 TTTCAACATCTATACAAAAATAGAGTAGAGATAG-ATAAAGTAA
* * *
389692 TAAAATTATGTTTATGAATAAATTATAATACATCTGTTTACAAAATTAAGTTACAAATTTTTAGT
1 TAAAATTATATCTATGAATAAATTATAATACATCTGTTTACAAAATTAAGTTAAAAATTTTTAGT
* * * * * ** * *
389757 AAAAAAGTGGAGTGGAATAATATAAAATAATTATAAATTTAATCGATTTTTATAAAAATGAATGT
66 AAAAAAGTAGAGTAGAATAATATAAAATAATCATAAATATAACCGACATTTATAAAAATAAATAT
* *
389822 TTTCAACATCTATATAAAAATAGAGTGGAGATAGATAAAGTAA
131 TTTCAACATCTATACAAAAATAGAGTAGAGATAGATAAAGTAA
389865 T
1 T
389866 TTACAATTCT
Statistics
Matches: 153, Mismatches: 20, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
173 152 0.99
174 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (173 bp):
TAAAATTATATCTATGAATAAATTATAATACATCTGTTTACAAAATTAAGTTAAAAATTTTTAGT
AAAAAAGTAGAGTAGAATAATATAAAATAATCATAAATATAACCGACATTTATAAAAATAAATAT
TTTCAACATCTATACAAAAATAGAGTAGAGATAGATAAAGTAA
Found at i:390601 original size:2 final size:2
Alignment explanation
Indices: 390555--390584 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
390545 ACACACACAC
390555 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
390585 TGCAAATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:395624 original size:20 final size:21
Alignment explanation
Indices: 395599--395694 Score: 110
Period size: 20 Copynumber: 4.7 Consensus size: 21
395589 AAAGGACAGA
* *
395599 ATGTATCGATACATT-CATAC
1 ATGTATCGATACATTGGATAG
*
395619 ATGTATCGATACATT-GAAAG
1 ATGTATCGATACATTGGATAG
* *
395639 ATGTATTGATACATCTGGGTA-
1 ATGTATCGATACAT-TGGATAG
395660 ATGTATCGATACATTGGA-AG
1 ATGTATCGATACATTGGATAG
395680 ATGTATCGATACATT
1 ATGTATCGATACATT
395695 TGGGTAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 48 0.74
21 14 0.22
22 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (21 bp):
ATGTATCGATACATTGGATAG
Found at i:395672 original size:41 final size:41
Alignment explanation
Indices: 395619--395701 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
395609 ACATTCATAC
*
395619 ATGTATCGATACATTGAAAGATGTATTGATACATCTGGGTA
1 ATGTATCGATACATTGAAAGATGTATCGATACATCTGGGTA
* *
395660 ATGTATCGATACATTGGAAGATGTATCGATACATTTGGGTA
1 ATGTATCGATACATTGAAAGATGTATCGATACATCTGGGTA
395701 A
1 A
395702 AAATGTGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.34
Consensus pattern (41 bp):
ATGTATCGATACATTGAAAGATGTATCGATACATCTGGGTA
Found at i:396099 original size:12 final size:11
Alignment explanation
Indices: 396078--396105 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
396068 TGCACCACCC
396078 TTTTTCTTTTT
1 TTTTTCTTTTT
396089 TTTTTCTTTTT
1 TTTTTCTTTTT
396100 TTTTTC
1 TTTTTC
396106 AAATAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:396725 original size:17 final size:17
Alignment explanation
Indices: 396703--396737 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
396693 AGTGCTTTAG
396703 AGAATTCAACCTTATCA
1 AGAATTCAACCTTATCA
*
396720 AGAATTCAGCCTTATCA
1 AGAATTCAACCTTATCA
396737 A
1 A
396738 TTCTCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.29
Consensus pattern (17 bp):
AGAATTCAACCTTATCA
Found at i:398836 original size:25 final size:23
Alignment explanation
Indices: 398786--398828 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
398776 AGTTAAGTAT
398786 AAATGTTTTTCAAGTAATAAATC
1 AAATGTTTTTCAAGTAATAAATC
398809 AAATG-TTTTCAAGTAA-AAAT
1 AAATGTTTTTCAAGTAATAAAT
398829 AATTCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (23 bp):
AAATGTTTTTCAAGTAATAAATC
Found at i:398953 original size:20 final size:19
Alignment explanation
Indices: 398930--398977 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
398920 ACCCAGACGC
* *
398930 ATCGATACATATTGCTTTGT
1 ATCGATACATATT-CATAGT
*
398950 ATCGATACATGTTCATAGT
1 ATCGATACATATTCATAGT
398969 ATCGATACA
1 ATCGATACA
398978 CCTTGAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (19 bp):
ATCGATACATATTCATAGT
Found at i:411023 original size:2 final size:2
Alignment explanation
Indices: 411018--411045 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
411008 AATGTAATGC
411018 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
411046 AAATATTGTA
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):
TA
Found at i:413675 original size:38 final size:38
Alignment explanation
Indices: 413583--413681 Score: 100
Period size: 37 Copynumber: 2.7 Consensus size: 38
413573 TAAGTTATTT
*
413583 ATTTTTAATTTATT-T-TAACATAAATATAATTTTAATA
1 ATTTTT-ATTTATTATATAATATAAATATAATTTTAATA
* *
413620 ATTTTTAATTATCATATAATATAAAT-TAATTTTAAT-
1 ATTTTTATTTATTATATAATATAAATATAATTTTAATA
*
413656 TTTTAATTATTTATTATAT-ATATAAA
1 ATTT--TTATTTATTATATAATATAAA
413682 CATTTAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
36 8 0.15
37 24 0.46
38 20 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (38 bp):
ATTTTTATTTATTATATAATATAAATATAATTTTAATA
Found at i:413688 original size:34 final size:34
Alignment explanation
Indices: 413618--413691 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
413608 ATAATTTTAA
* *
413618 TAATTTTTAATTATCATATAATATAAATTAATTT
1 TAATTTTTAATTATCATATAATATAAATAAAATT
* * *
413652 TAATTTTTAATTAT-TTATTATATATATAAACATT
1 TAATTTTTAATTATCATATAATATAAATAAA-ATT
413686 TAATTT
1 TAATTT
413692 AATATCTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 12 0.35
34 22 0.65
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (34 bp):
TAATTTTTAATTATCATATAATATAAATAAAATT
Found at i:416201 original size:13 final size:13
Alignment explanation
Indices: 416183--416207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
416173 ATGTTGCACA
416183 GTATCGATACATT
1 GTATCGATACATT
416196 GTATCGATACAT
1 GTATCGATACAT
416208 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:416220 original size:20 final size:21
Alignment explanation
Indices: 416195--416245 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
416185 ATCGATACAT
**
416195 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
416215 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
416236 TGTATCGATA
1 TGTATCGATA
416246 TAGGTCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:416304 original size:19 final size:20
Alignment explanation
Indices: 416280--416330 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
416270 TAGCCAAACT
**
416280 TGTATCGATACA-CATAGTA
1 TGTATCGATACACCATAAAA
416299 TGTATCGATACACCATAAAA
1 TGTATCGATACACCATAAAA
416319 TGTATCGATACA
1 TGTATCGATACA
416331 ATGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (20 bp):
TGTATCGATACACCATAAAA
Found at i:417903 original size:9 final size:9
Alignment explanation
Indices: 417889--417919 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
417879 CATCAAGGAC
417889 GATGAAGAT
1 GATGAAGAT
417898 GATGAAGAT
1 GATGAAGAT
*
417907 GATGATGAT
1 GATGAAGAT
417916 GATG
1 GATG
417920 GTGACTCAGA
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:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (9 bp):
GATGAAGAT
Found at i:420536 original size:26 final size:26
Alignment explanation
Indices: 420500--420552 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
420490 CTAGATCATC
420500 CCTTAGAAATACTTGCGATTATGTAG
1 CCTTAGAAATACTTGCGATTATGTAG
420526 CCTTAGAAATACTTGCGATTATGTAG
1 CCTTAGAAATACTTGCGATTATGTAG
420552 C
1 C
420553 TTTTCTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (26 bp):
CCTTAGAAATACTTGCGATTATGTAG
Found at i:422272 original size:8 final size:8
Alignment explanation
Indices: 422259--422284 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
422249 ATTTGATTAA
422259 ATTTTGTG
1 ATTTTGTG
422267 ATTTTGTG
1 ATTTTGTG
422275 ATTTTGTG
1 ATTTTGTG
422283 AT
1 AT
422285 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:422507 original size:13 final size:13
Alignment explanation
Indices: 422489--422524 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
422479 GCATTCTCTG
*
422489 TATCGATACATTA
1 TATCGATACACTA
*
422502 TATCGATACACTG
1 TATCGATACACTA
422515 TATCGATACA
1 TATCGATACA
422525 AGGGGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (13 bp):
TATCGATACACTA
Found at i:422699 original size:22 final size:21
Alignment explanation
Indices: 422656--422696 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
422646 CAAATTTCTT
422656 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
422678 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
422697 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:424951 original size:13 final size:13
Alignment explanation
Indices: 424933--424957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
424923 ATGTTGCACA
424933 GTATCGATACATT
1 GTATCGATACATT
424946 GTATCGATACAT
1 GTATCGATACAT
424958 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:424970 original size:20 final size:21
Alignment explanation
Indices: 424945--424995 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
424935 ATCGATACAT
**
424945 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
424965 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
424986 TGTATCGATA
1 TGTATCGATA
424996 TAGGTCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:427027 original size:19 final size:19
Alignment explanation
Indices: 426973--427032 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
426963 GGTATTTTTG
*
426973 ATAAAAAGGTAAAATTTGAA
1 ATAAAAAGGCAAAATTT-AA
* *
426993 ATTAAAA-TCAATAATTTAA
1 ATAAAAAGGCAA-AATTTAA
*
427012 ATAAAAAGGCAAAATTAAA
1 ATAAAAAGGCAAAATTTAA
427031 AT
1 AT
427033 TTTTGAGAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (19 bp):
ATAAAAAGGCAAAATTTAA
Found at i:434534 original size:20 final size:19
Alignment explanation
Indices: 434505--434579 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
434495 AAAAAGACAT
434505 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
434524 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
434545 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
434565 AATGTATCGATACAT
1 AATGTATCGATACAT
434580 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:434562 original size:40 final size:39
Alignment explanation
Indices: 434502--434579 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
434492 GGTAAAAAGA
*
434502 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
434541 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
434580 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:440400 original size:24 final size:25
Alignment explanation
Indices: 440365--440411 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
440355 ATAAAAAGTC
* *
440365 AAAAGCAAAAGCACAAAATAAAATT
1 AAAAGCAAAAGCAAAAAAAAAAATT
440390 AAAAG-AAAAGCAAAAAAAAAAA
1 AAAAGCAAAAGCAAAAAAAAAAA
440412 AAAACAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (25 bp):
AAAAGCAAAAGCAAAAAAAAAAATT
Found at i:442416 original size:36 final size:36
Alignment explanation
Indices: 442337--442914 Score: 346
Period size: 36 Copynumber: 16.2 Consensus size: 36
442327 AAAAATCTTT
* * * * *
442337 AAAG-CTTGTCTTGAGGAAATTTTAGC-AAAACCTCT
1 AAAGCCTT-TCTTGAGGATATTTCATCAAAAACTTCC
* * * *
442372 AAAACCTCTCTTAAGGATATTTCATCAAAAATTTCC
1 AAAGCCTTTCTTGAGGATATTTCATCAAAAACTTCC
442408 AAAGCCTCTT-TTGAGGATATTTCATCAAGAATACTTCC
1 AAAGCCT-TTCTTGAGGATATTTCATCAA-AA-ACTTCC
* * *
442446 AAAGCCTTTCTTAAGGATATTTTAGC-AAAA-TGTCC
1 AAAGCCTTTCTTGAGGATATTTCATCAAAAACT-TCC
* * * *
442481 AACA-CTTTTCTT-TGGATACTTCATAAAAAACTTCC
1 AA-AGCCTTTCTTGAGGATATTTCATCAAAAACTTCC
* * * * *
442516 AAAGCCTCAT-TTGAGGACATCTCATAAAAAACTTTC
1 AAAGCCT-TTCTTGAGGATATTTCATCAAAAACTTCC
* * * *
442552 AAAGCCTCTCTTAAGGACATTTTCATCAAAGACTT-C
1 AAAGCCTTTCTTGAGGATA-TTTCATCAAAAACTTCC
** * * *
442588 AAAATCTTTCTTGAGGATACTTCATCAAAAGCTTCT
1 AAAGCCTTTCTTGAGGATATTTCATCAAAAACTTCC
* * * *
442624 AAAGCCTTTCTTGAGGATGTTTCATTAAGAACTTCT
1 AAAGCCTTTCTTGAGGATATTTCATCAAAAACTTCC
* * *
442660 AAAGCCTTTTTTGAGGACATTTCATTAAAAAAACTAT-C
1 AAAGCCTTTCTTGAGGATATTTCA-T-CAAAAACT-TCC
* * **
442698 AAAGCCTTTCTTGAAGACATTTTTTCAAAAA-TCTCC
1 AAAGCCTTTCTTGAGGATATTTCATCAAAAACT-TCC
* ** *
442734 AAAGCCTTTCTTAACAATATTTCGTCAAAAACTTCC
1 AAAGCCTTTCTTGAGGATATTTCATCAAAAACTTCC
* * * * *
442770 AAAG-TTTCTCTTGAGGATGTCTCATTAAAAACTTTC
1 AAAGCCTT-TCTTGAGGATATTTCATCAAAAACTTCC
* *
442806 AGAGCCTTTCTTGAGGATATTTCA--AAAACCTTCC
1 AAAGCCTTTCTTGAGGATATTTCATCAAAAACTTCC
* * * * *
442840 -AAGCCTCTCTCGAGGATACTT-ATCAAATA-TTTC
1 AAAGCCTTTCTTGAGGATATTTCATCAAAAACTTCC
* * * * *
442873 AAAACCTCTT-TTGAGGATGTTTTATTAAAGACTTCC
1 AAAGCCT-TTCTTGAGGATATTTCATCAAAAACTTCC
442909 AAAGCC
1 AAAGCC
442915 AAGATGAGAA
Statistics
Matches: 415, Mismatches: 99, Indels: 57
0.73 0.17 0.10
Matches are distributed among these distances:
32 1 0.00
33 20 0.05
34 35 0.08
35 67 0.16
36 217 0.52
37 23 0.06
38 51 0.12
39 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (36 bp):
AAAGCCTTTCTTGAGGATATTTCATCAAAAACTTCC
Found at i:442762 original size:146 final size:144
Alignment explanation
Indices: 442500--442849 Score: 354
Period size: 146 Copynumber: 2.4 Consensus size: 144
442490 CTTTGGATAC
* * ** * *
442500 TTCATAAAAAACTTCCAAAGCCTCATTTGAGGACATCTCATAAAAAACTTTCAAAGCCTCTCTTA
1 TTCATTAAAAACTTCTAAAGCCTTTTTTGAGGACATTTCATAAAAAACTATCAAAGCCTCTCTTA
* * * * ** * *
442565 AGGACATTTTCATCAAAGACTTCAAAATCTTTCTTGAGGATACTTCATCAAAAGCTTCTAAAGCC
66 AGGACATTTTCATCAAAAACTCCAAAACCTTTCTTAACAATACTTCATCAAAAACTTCCAAAG-C
442630 TT-TCTTGAGGATGT
130 TTCTCTTGAGGATGT
* *
442644 TTCATTAAGAACTTCTAAAGCCTTTTTTGAGGACATTTCATTAAAAAAACTATCAAAGCCTTTCT
1 TTCATTAAAAACTTCTAAAGCCTTTTTTGAGGACATTTCA-T-AAAAAACTATCAAAGCCTCTCT
* * * *
442709 TGAA-GACATTTT-TTCAAAAATCTCCAAAGCCTTTCTTAACAATATTTCGTCAAAAACTTCCAA
64 T-AAGGACATTTTCATCAAAAA-CTCCAAAACCTTTCTTAACAATACTTCATCAAAAACTTCCAA
*
442772 AGTTTCTCTTGAGGATGT
127 AGCTTCTCTTGAGGATGT
* * * * * *
442790 CTCATTAAAAACTT-TCAGAGCCTTTCTTGAGGATATTTC--AAAAACCT-TCCAAGCCTCTCT
1 TTCATTAAAAACTTCT-AAAGCCTTTTTTGAGGACATTTCATAAAAAACTATCAAAGCCTCTCT
442850 CGAGGATACT
Statistics
Matches: 171, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
141 11 0.06
142 7 0.04
144 34 0.20
145 10 0.06
146 107 0.63
147 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (144 bp):
TTCATTAAAAACTTCTAAAGCCTTTTTTGAGGACATTTCATAAAAAACTATCAAAGCCTCTCTTA
AGGACATTTTCATCAAAAACTCCAAAACCTTTCTTAACAATACTTCATCAAAAACTTCCAAAGCT
TCTCTTGAGGATGT
Found at i:443445 original size:50 final size:50
Alignment explanation
Indices: 443379--443477 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
443369 GTCATGCTAG
* * * *
443379 CTGGCACTTGATAGGAAGGTCAAGTCCTACAGAGTCAAAGTCCATATTAC
1 CTGGCACCTAATAGGAAGGTCAAATCCTACAAAGTCAAAGTCCATATTAC
* *
443429 CTGGCACCTAATAGGAAGGTCAAATCCTATAAAGTCCAAGTCCATATTA
1 CTGGCACCTAATAGGAAGGTCAAATCCTACAAAGTCAAAGTCCATATTA
443478 GGTAGCACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (50 bp):
CTGGCACCTAATAGGAAGGTCAAATCCTACAAAGTCAAAGTCCATATTAC
Found at i:443728 original size:51 final size:51
Alignment explanation
Indices: 443584--443846 Score: 257
Period size: 51 Copynumber: 5.2 Consensus size: 51
443574 CAAGTATGGA
* * *
443584 GAGGTCAAGCCCTATAGAGTCATAGTCCACACTAGTTGGCAAC-CGTATAGG
1 GAGGTCAAGCCCTATAGAGTCATAGTCCACACTAGTTAGC-ACTTGTATAAG
* * * * * * *
443635 GAGGTCCAGCCCTA-AAAAT-ATAAGTCCACAAGTGGTTGGCACTTATATAAG
1 GAGGTCAAGCCCTATAGAGTCAT-AGTCCAC-ACTAGTTAGCACTTGTATAAG
* * *
443686 GAGGTTAAGCCCTATAGAGTCATAATCCACACTAGTTAGCACTCGTATAAG
1 GAGGTCAAGCCCTATAGAGTCATAGTCCACACTAGTTAGCACTTGTATAAG
* * * *
443737 GAGGTGAAACCCTATAGAGTCGA-AGTCCACACTAGCTAGCACTTGTATAGG
1 GAGGTCAAGCCCTATAGAGTC-ATAGTCCACACTAGTTAGCACTTGTATAAG
* * *
443788 GAGGTCAATCCCTATAGAGTCCA-AGTCCACATTAGTTAGCAATTGTATAAG
1 GAGGTCAAGCCCTATAGAGT-CATAGTCCACACTAGTTAGCACTTGTATAAG
*
443839 GAGATCAA
1 GAGGTCAA
443847 ACCTTATAAA
Statistics
Matches: 174, Mismatches: 31, Indels: 14
0.79 0.14 0.06
Matches are distributed among these distances:
49 2 0.01
50 12 0.07
51 147 0.84
52 11 0.06
53 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (51 bp):
GAGGTCAAGCCCTATAGAGTCATAGTCCACACTAGTTAGCACTTGTATAAG
Found at i:443779 original size:102 final size:102
Alignment explanation
Indices: 443584--443858 Score: 286
Period size: 102 Copynumber: 2.7 Consensus size: 102
443574 CAAGTATGGA
* * * *
443584 GAGGTCAAGCCCTATAGAGTCATAGTCCACACTAGTTGGCAAC-CGTATAGGGAGGTCCAGCCCT
1 GAGGTCAAGCCCTATAGAGTCATAGTCCACACTAGTTAGC-ACTCGTATAAGGAGGTCAAACCCT
* * * * *
443648 AAAAATATAAGTCCACAAGTGGTTGGCACTTATATAAG
65 AAAAATAGAAGTCCACAACTAGCTAGCACTTATATAAG
* * *
443686 GAGGTTAAGCCCTATAGAGTCATAATCCACACTAGTTAGCACTCGTATAAGGAGGTGAAACCCTA
1 GAGGTCAAGCCCTATAGAGTCATAGTCCACACTAGTTAGCACTCGTATAAGGAGGTCAAACCCTA
* * * * *
443751 TAGAGTCGAAGTCCAC-ACTAGCTAGCACTTGTATAGG
66 -AAAATAGAAGTCCACAACTAGCTAGCACTTATATAAG
* * * * * *
443788 GAGGTCAATCCCTATAGAGTCCA-AGTCCACATTAGTTAGCAATTGTATAAGGAGATCAAACCTT
1 GAGGTCAAGCCCTATAGAGT-CATAGTCCACACTAGTTAGCACTCGTATAAGGAGGTCAAACCCT
443852 ATAAAAT
65 A-AAAAT
443859 CCAGGTCCAT
Statistics
Matches: 142, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
101 2 0.01
102 127 0.89
103 13 0.09
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (102 bp):
GAGGTCAAGCCCTATAGAGTCATAGTCCACACTAGTTAGCACTCGTATAAGGAGGTCAAACCCTA
AAAATAGAAGTCCACAACTAGCTAGCACTTATATAAG
Found at i:443867 original size:51 final size:51
Alignment explanation
Indices: 443584--443897 Score: 235
Period size: 51 Copynumber: 6.2 Consensus size: 51
443574 CAAGTATGGA
* * * *
443584 GAGGTCAAGCCCTATAGAGT-CATAGTCCACACTAGTTGGCAAC-CGTATAGG
1 GAGGTCAAACCCTATAGAGTCCA-AGTCCACACTAGTTAGC-ACTTGTATAAG
* * * * ** * * * *
443635 GAGGTCCAGCCCTA-AAAATATAAGTCCACAAGTGGTTGGCACTTATATAAG
1 GAGGTCAAACCCTATAGAGTCCAAGTCCAC-ACTAGTTAGCACTTGTATAAG
* * * *
443686 GAGGTTAAGCCCTATAGAGT-CATAATCCACACTAGTTAGCACTCGTATAAG
1 GAGGTCAAACCCTATAGAGTCCA-AGTCCACACTAGTTAGCACTTGTATAAG
* * * *
443737 GAGGTGAAACCCTATAGAGTCGAAGTCCACACTAGCTAGCACTTGTATAGG
1 GAGGTCAAACCCTATAGAGTCCAAGTCCACACTAGTTAGCACTTGTATAAG
* * *
443788 GAGGTCAATCCCTATAGAGTCCAAGTCCACATTAGTTAGCAATTGTATAAG
1 GAGGTCAAACCCTATAGAGTCCAAGTCCACACTAGTTAGCACTTGTATAAG
* * * * * * * * *
443839 GAGATCAAACCTTATAAAATCCAGGTCCATACAAGTTGGCAC--CTAGTAAG
1 GAGGTCAAACCCTATAGAGTCCAAGTCCACACTAGTTAGCACTTGTA-TAAG
443889 GAGGTCAAA
1 GAGGTCAAA
443898 ACTTGTAAGG
Statistics
Matches: 209, Mismatches: 47, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
49 2 0.01
50 24 0.11
51 173 0.83
52 10 0.05
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (51 bp):
GAGGTCAAACCCTATAGAGTCCAAGTCCACACTAGTTAGCACTTGTATAAG
Found at i:444357 original size:114 final size:115
Alignment explanation
Indices: 444091--444473 Score: 402
Period size: 115 Copynumber: 3.3 Consensus size: 115
444081 GGCCAAAGAG
*
444091 TATTTAA-TAATTTATTTAAGCTTATTTTATTTAATTATATT-GA-GCCATAAATTATTTAATTT
1 TATTTAATTAATTTATTTAGGCTTATTTTATTTAATTATATTGGATG--ATAAATTATTTAATTT
* * *
444153 AAGGCCAAGTCTTATAAAAAATATATATTAGATAAAATAGGTATCACATGCT
64 AAGGCCAAGTCTTATAAAAAATATATATTAAATAAAATAGGCACCACATGCT
* * * ** *
444205 AATTTAATTAATTTATTTAGACTTATTTTATCTAATTATATTGGATGATTTACTATTTAATTTAA
1 TATTTAATTAATTTATTTAGGCTTATTTTATTTAATTATATTGGATGATAAATTATTTAATTTAA
* * * * *
444270 GGCCAAGT-TT-TACAAAAATATATATTAAATAAACTATGCCCCACGTGTT
66 GGCCAAGTCTTATA-AAAAATATATATTAAATAAAATAGGCACCACATGCT
* * * *
444319 TATTTAATTAATTTATATAGGCTTATTTTATTTTATTATATTGGATCATCAATTATTTAATTTAA
1 TATTTAATTAATTTATTTAGGCTTATTTTATTTAATTATATTGGATGATAAATTATTTAATTTAA
** ** * ** *
444384 GGTTAAACCTTATAAAAAATATATATTAAACAAAATAGGGC-GTA-AGTGCA
66 GGCCAAGTCTTATAAAAAATATATATTAAATAAAATA-GGCACCACA-TGCT
* *
444434 CATTTAATTAATTTATTTAGAGCCTATTTTATTTAATTAT
1 TATTTAATTAATTTATTTAG-GCTTATTTTATTTAATTAT
444474 GTTCGACCAA
Statistics
Matches: 220, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
113 2 0.01
114 96 0.44
115 98 0.45
116 23 0.10
117 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.44
Consensus pattern (115 bp):
TATTTAATTAATTTATTTAGGCTTATTTTATTTAATTATATTGGATGATAAATTATTTAATTTAA
GGCCAAGTCTTATAAAAAATATATATTAAATAAAATAGGCACCACATGCT
Found at i:454570 original size:165 final size:165
Alignment explanation
Indices: 454298--454631 Score: 641
Period size: 165 Copynumber: 2.0 Consensus size: 165
454288 AATGAAAAGT
454298 TAGGAACATCAGGGTTTAGCAACGAGATTCATTTATGTCCACCAAGCTTTCTTTTGAACAACTAG
1 TAGGAACATCAGGGTTTAGCAACGAGATTCATTTATGTCCACCAAGCTTTCTTTTGAACAACTAG
*
454363 GCAGTGATAGAAATTCCCATATTTTTTTAATCTATTTCAAATTAATATTAGTAACTAACCTTAAT
66 GCAGTGATAGAAATTCCCATATTTTTTTAATCTATTTCAAATTAATATTAGTAACTAACCCTAAT
454428 TGCTTTTGCCATAAAGCTAGTAGGGATATTTTGTA
131 TGCTTTTGCCATAAAGCTAGTAGGGATATTTTGTA
*
454463 TAGGAACATCGGGGTTTAGCAACGAGATTCATTTATGTCCACCAAGCTTTCTTTTGAACAACTAG
1 TAGGAACATCAGGGTTTAGCAACGAGATTCATTTATGTCCACCAAGCTTTCTTTTGAACAACTAG
*
454528 GCAGTGATAGAAATTCCTATATTTTTTTAATCTATTTCAAATTAATATTAGTAACTAACCCTAAT
66 GCAGTGATAGAAATTCCCATATTTTTTTAATCTATTTCAAATTAATATTAGTAACTAACCCTAAT
454593 TGCTTTTGCCATAAAGCTAGTAGGGATATTTTGTA
131 TGCTTTTGCCATAAAGCTAGTAGGGATATTTTGTA
454628 TAGG
1 TAGG
454632 CTTTCTTTGA
Statistics
Matches: 166, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 166 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (165 bp):
TAGGAACATCAGGGTTTAGCAACGAGATTCATTTATGTCCACCAAGCTTTCTTTTGAACAACTAG
GCAGTGATAGAAATTCCCATATTTTTTTAATCTATTTCAAATTAATATTAGTAACTAACCCTAAT
TGCTTTTGCCATAAAGCTAGTAGGGATATTTTGTA
Found at i:455280 original size:13 final size:13
Alignment explanation
Indices: 455262--455286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
455252 GTCCCCAATT
455262 AGTAACCAATATA
1 AGTAACCAATATA
455275 AGTAACCAATAT
1 AGTAACCAATAT
455287 TAATCTTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (13 bp):
AGTAACCAATATA
Found at i:457105 original size:166 final size:165
Alignment explanation
Indices: 456822--457369 Score: 539
Period size: 166 Copynumber: 3.3 Consensus size: 165
456812 TTTTAATACC
* * * * * * * *
456822 AAAATTCCTTAAATATTGTCATTTAA-TCACTATAAAATCAGTTTTGAAAAATTCATTCATTTTT
1 AAAATTCATCAAATATTATTATTTAATTCA-TATTAAATCAGTTTTCAAAAATTTATTCATTTTC
* * * * * **
456886 ATAAATTTTCCATTTTCCCTT-AAAATTCTCTTGTTTTTCGAAATACGGAGTTTTCTACTCTGTA
65 ATGAGTTTTCAATTTTTCCTTGAAAATTCTCTT-TTTTT-GAAATACAGAGTTTTCTACTCCATA
*
456950 AATATTTTCGGGAGGATTTTTCTTAGTTTATAATTTTT
128 AATGTTTTCGGGAGGATTTTTCTTAGTTTATAATTTTT
*
456988 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCATTTTTCAAAAATTTATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATTTATTCATTTTCA
* * * * * * *
457053 TGAGTTTTTAATTTGTTCCTTGAAATTTTTCTTTTTTTTAAATACAGAGTTTTCAACTCCATCAC
66 TGAGTTTTCAATTT-TTCCTTGAAAATTCTCTTTTTTTGAAATACAGAGTTTTCTACTCCATAAA
** *
457118 TGTTTTCTAG-GGATTTTTCTTAGTTTTTAATTTTT
130 TGTTTTCGGGAGGATTTTTCTTAGTTTATAATTTTT
* * * *
457153 AAAATTTATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCTAAAATTTATTTATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATTTATTCATTTTCA
* * ** * * ** * ** *
457218 TGAGTTTTGAGTTTCTTTTTTGAAACTTCCCAATTTTTGAAAAATTGAGTTTTCTATTCCATAAA
66 TGAGTTTTCAATTT-TTCCTTGAAAATTCTCTTTTTTTGAAATACAGAGTTTTCTACTCCATAAA
* *
457283 TGTTTTCTTGGGA--ATTTTTCTTGGTTTAAAATTTTT
130 TGTTTTC--GGGAGGATTTTTCTTAGTTTATAATTTTT
* * * * * *
457319 AAAATTCATCTAATATTATTATTAAATTTACATTAAATTAGTTTTGAAAAA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAA
457370 CTCAAATTAT
Statistics
Matches: 312, Mismatches: 64, Indels: 12
0.80 0.16 0.03
Matches are distributed among these distances:
165 138 0.44
166 151 0.48
167 14 0.04
168 9 0.03
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (165 bp):
AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATTTATTCATTTTCA
TGAGTTTTCAATTTTTCCTTGAAAATTCTCTTTTTTTGAAATACAGAGTTTTCTACTCCATAAAT
GTTTTCGGGAGGATTTTTCTTAGTTTATAATTTTT
Found at i:457385 original size:166 final size:163
Alignment explanation
Indices: 456963--457397 Score: 467
Period size: 165 Copynumber: 2.6 Consensus size: 163
456953 ATTTTCGGGA
*
456963 GGATTTTTCTTAGTTTATAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATCA
1 GGATTTTTCTTAGTTTATAATTTTTAAAATTCATCAAATATTATTA-TTAATTTATATTAAATCA
* * * * * ** ** *
457028 TTTTTCAAAAATTTATTCATTTTCATGAGTTTTTAATTTGTTCCTTGAAATTTTTCTTTTTTTTA
65 GTTTTCAAAAATTAATT-ATTTTCATGAGTTTTGAATTTCTTCCTTGAAACTTCCCAATTTTTGA
* * *
457093 AATACAGAGTTTTCAACTCCATCACTGTTTTCTAG
129 AAAACAGAGTTTTCAACTCCATAAATGTTTTCTAG
* * *
457128 GGATTTTTCTTAGTTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTCATATTAAATCA
1 GGATTTTTCTTAGTTTATAATTTTTAAAATTCATCAAATATTATTATTAATTT-ATATTAAATCA
* * * **
457193 GTTTTCTAAAATTTATTTATTTTCATGAGTTTTGAGTTTCTTTTTTGAAACTTCCCAATTTTTGA
65 GTTTTC-AAAAATTAATTATTTTCATGAGTTTTGAATTTCTTCCTTGAAACTTCCCAATTTTTGA
** * * *
457258 AAAATTGAGTTTTCTATTCCATAAATGTTTTCTTG
129 AAAACAGAGTTTTCAACTCCATAAATGTTTTCTAG
* * * * *
457293 GGAATTTTTCTTGGTTTAAAATTTTTAAAATTCATCTAATATTATTATTAAATTTACATTAAATT
1 GG-ATTTTTCTTAGTTTATAATTTTTAAAATTCATCAAATATTATTATT-AATTTATATTAAATC
* * * *
457358 AGTTTTGAAAAACTCAAATTA-TTTCATGAATTCTGAATTT
64 AGTTTTCAAAAA-T-TAATTATTTTCATGAGTTTTGAATTT
457398 TTTGTATATA
Statistics
Matches: 222, Mismatches: 42, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
164 5 0.02
165 129 0.58
166 80 0.36
167 8 0.04
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.52
Consensus pattern (163 bp):
GGATTTTTCTTAGTTTATAATTTTTAAAATTCATCAAATATTATTATTAATTTATATTAAATCAG
TTTTCAAAAATTAATTATTTTCATGAGTTTTGAATTTCTTCCTTGAAACTTCCCAATTTTTGAAA
AACAGAGTTTTCAACTCCATAAATGTTTTCTAG
Found at i:457532 original size:16 final size:17
Alignment explanation
Indices: 457501--457570 Score: 74
Period size: 16 Copynumber: 4.2 Consensus size: 17
457491 CATTGCTAAG
*
457501 AATTGATTTTAA-TTTT
1 AATTTATTTTAATTTTT
457517 AATTT-TTTTAATTTTT
1 AATTTATTTTAATTTTT
* *
457533 AATTTATTTTTATTAATT
1 AATTTATTTTAATT-TTT
*
457551 AATTTATTTT-ATATTT
1 AATTTATTTTAATTTTT
457567 AATT
1 AATT
457571 GGCTAAGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
15 6 0.13
16 19 0.41
17 9 0.20
18 12 0.26
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (17 bp):
AATTTATTTTAATTTTT
Found at i:457533 original size:22 final size:21
Alignment explanation
Indices: 457507--457570 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 21
457497 TAAGAATTGA
457507 TTTTAATTTTAATTTTT-TTAAT
1 TTTTAA-TTT-ATTTTTATTAAT
457529 TTTTAATTTATTTTTATTAA-
1 TTTTAATTTATTTTTATTAAT
457549 --TTAATTTATTTTATATTTAAT
1 TTTTAATTTATTTT-TA-TTAAT
457570 T
1 T
457571 GGCTAAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
18 12 0.32
19 2 0.05
20 10 0.27
21 7 0.19
22 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTAATTTATTTTTATTAAT
Found at i:457538 original size:21 final size:22
Alignment explanation
Indices: 457507--457567 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
457497 TAAGAATTGA
457507 TTTTAATTTTAATTTTT-TTAAT
1 TTTTAATTTT-ATTTTTATTAAT
457529 TTTTAA-TTTATTTTTATTAAT
1 TTTTAATTTTATTTTTATTAAT
*
457550 TAATTT-ATTTTATATTTA
1 T--TTTAATTTTATTTTTA
457568 ATTGGCTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 6 0.18
21 9 0.26
22 7 0.21
23 12 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTAATTTTATTTTTATTAAT
Found at i:461975 original size:18 final size:18
Alignment explanation
Indices: 461952--461991 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
461942 AATGTTTGGT
461952 AGCCTTGGAAGCCATGGC
1 AGCCTTGGAAGCCATGGC
461970 AGCCTTGGAAGCCATGGC
1 AGCCTTGGAAGCCATGGC
461988 AGCC
1 AGCC
461992 AATGAGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.30, G:0.33, T:0.15
Consensus pattern (18 bp):
AGCCTTGGAAGCCATGGC
Found at i:463037 original size:39 final size:39
Alignment explanation
Indices: 462983--463128 Score: 148
Period size: 39 Copynumber: 3.5 Consensus size: 39
462973 AGACAAGGTG
462983 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATA
* ** * *
463022 CCAATGTGCTGATTCAAGGCCAGCGACGTTGGTCTTAAAGACAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-------A--TA
*
463070 CCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTATA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATA
*
463109 CCAATGTGCTGATTCAAGGC
1 CCAATATGCTGATTCAAGGC
463129 TAGTGACGTT
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
39 52 0.60
41 1 0.01
46 1 0.01
48 32 0.37
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (39 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATA
Found at i:463081 original size:87 final size:87
Alignment explanation
Indices: 462934--463193 Score: 430
Period size: 87 Copynumber: 3.0 Consensus size: 87
462924 GTAAAGAATG
* * * *
462934 CCAATGTTCTGATTCAAGGCCAATGACATTGGGTTTTAAAGACAAGGTGCCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGTGACGTT-GGTCTTAAAGACAAGGTGCCAATATGCTGATTCA
462999 AGGCCAGCGATATTGGGCTTATA
65 AGGCCAGCGATATTGGGCTTATA
*
463022 CCAATGTGCTGATTCAAGGCCAGCGACGTTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGTGACGTTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
463087 GGCTAGCGATATTGGGCTTATA
66 GGCCAGCGATATTGGGCTTATA
* *
463109 CCAATGTGCTGATTCAAGGCTAGTGACGTTGGTCTTAAAGACAAAGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGTGACGTTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
463174 GGCCAACGATATTGGGCTTA
66 GGCCAGCGATATTGGGCTTA
463194 GAAGAAGATG
Statistics
Matches: 161, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 135 0.84
88 26 0.16
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (87 bp):
CCAATGTGCTGATTCAAGGCCAGTGACGTTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGGCTTATA
Found at i:463095 original size:48 final size:47
Alignment explanation
Indices: 463022--463176 Score: 164
Period size: 48 Copynumber: 3.4 Consensus size: 47
463012 TGGGCTTATA
* *
463022 CCAATGTGCTGATTCAAGGCCAGCGACGTTGGTCTTAAAGACAAGGTG
1 CCAATATGCTGATTCAAGGCTAGCGACGTTGGTCTTAAAGACAA-GTG
** * *
463070 CCAATATGCTGATTCAAGGCTAGCGATATTGGGCTT-------A-TA
1 CCAATATGCTGATTCAAGGCTAGCGACGTTGGTCTTAAAGACAAGTG
* *
463109 CCAATGTGCTGATTCAAGGCTAGTGACGTTGGTCTTAAAGACAAAGTG
1 CCAATATGCTGATTCAAGGCTAGCGACGTTGGTCTTAAAGAC-AAGTG
463157 CCAATATGCTGATTCAAGGC
1 CCAATATGCTGATTCAAGGC
463177 CAACGATATT
Statistics
Matches: 85, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
39 32 0.38
41 1 0.01
47 1 0.01
48 51 0.60
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (47 bp):
CCAATATGCTGATTCAAGGCTAGCGACGTTGGTCTTAAAGACAAGTG
Found at i:463274 original size:28 final size:28
Alignment explanation
Indices: 463202--463703 Score: 479
Period size: 28 Copynumber: 17.8 Consensus size: 28
463192 TAGAAGAAGA
*
463202 TGCCACCAACTTGTATGGGCTTTTGAAAGGGT
1 TGCCACTAACTTG--TGGGCTTTTG-AA-GGT
* *
463234 TG-CACCAACTTGTGTGCTTTTGAAGGT
1 TGCCACTAACTTGTGGGCTTTTGAAGGT
*
463261 TGCCACTACCTTGTGGG-TTTTGAAAAGG-
1 TGCCACTAACTTGTGGGCTTTTG--AAGGT
* *
463289 TGCCACTAACTTGTGGGCTTTTGAAAAGA
1 TGCCACTAACTTGTGGGCTTTTG-AAGGT
* * * * ***
463318 TACCATTGACTTATGGGCTTTTGAAAAAA
1 TGCCACTAACTTGTGGGCTTTTG-AAGGT
463347 TGCCACTAACTTGTGGGCTTTTGAAGGT
1 TGCCACTAACTTGTGGGCTTTTGAAGGT
* *
463375 TGCCACTACCTTGTGGGC-TTTGAAGAGG
1 TGCCACTAACTTGTGGGCTTTTGAAG-GT
463403 TGCCACTAACTTGTGGGC-TTTGAAGGT
1 TGCCACTAACTTGTGGGCTTTTGAAGGT
**
463430 TGCCACTAACTTGTGGGC-TTTGAAAAT
1 TGCCACTAACTTGTGGGCTTTTGAAGGT
* *
463457 GTGCCACTAACTTGTGGGCTTTTGAAAAGA
1 -TGCCACTAACTTGTGGGCTTTTG-AAGGT
* *
463487 TGCCATTGACTTGTGGGCTTTTGAAGGT
1 TGCCACTAACTTGTGGGCTTTTGAAGGT
* *
463515 TGCCATTGACTTGTGGGC-TTTGAAAAGG-
1 TGCCACTAACTTGTGGGCTTTTG--AAGGT
* * ***
463543 TCCCACTAACTTGTGGGCTTTTAAAAAAA
1 TGCCACTAACTTGTGGGCTTTT-GAAGGT
* * *
463572 TGCCACTGACTTATGGGCTTTTGAAGAGG
1 TGCCACTAACTTGTGGGCTTTTGAAG-GT
463601 TGCCACTAACTTGTGGGC-TTTGAAGGT
1 TGCCACTAACTTGTGGGCTTTTGAAGGT
*
463628 TGCCACTAACTTGTGGGC-ATTGAAAAGG-
1 TGCCACTAACTTGTGGGCTTTTG--AAGGT
463656 TGCCACTAACTTGTGGGC-TTTGAAGGT
1 TGCCACTAACTTGTGGGCTTTTGAAGGT
463683 TGCCACTAACTTGTGGGCTTT
1 TGCCACTAACTTGTGGGCTTT
463704 GAAAAGGTAA
Statistics
Matches: 403, Mismatches: 48, Indels: 42
0.82 0.10 0.09
Matches are distributed among these distances:
26 4 0.01
27 87 0.22
28 165 0.41
29 132 0.33
30 3 0.01
31 10 0.02
32 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (28 bp):
TGCCACTAACTTGTGGGCTTTTGAAGGT
Found at i:463578 original size:169 final size:169
Alignment explanation
Indices: 463240--463711 Score: 623
Period size: 169 Copynumber: 2.8 Consensus size: 169
463230 GGGTTGCACC
* * * *
463240 AACTTGTGTGCTTTTGAAGGTTGCCACTACCTTGTGGGTTTTGAAAAGGTGCCACTAACTTGTGG
1 AACTTGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGAAAATGTGCCACTAACTTGTGG
* * ***
463305 GCTTTTGAAAAGATACCATTGACTTATGGGCTTTTGAAAAAATGCCACTAACTTGTGGGCTTTTG
66 GCTTTTGAAAAGATGCCATTGACTTGTGGGCTTTTG-AAGGTTGCCACTAACTTGTGGGC-TTTG
* * * * **
463370 --AAGGTTGCCACTACCTTGTGGGCTTTGAAGAGGTGCCACT
129 AAAAGG-TCCCACTAACTTGTGGGCTTTAAAAAAATGCCACT
463410 AACTTGTGGGC-TTTGAAGGTTGCCACTAACTTGTGGGCTTTGAAAATGTGCCACTAACTTGTGG
1 AACTTGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGAAAATGTGCCACTAACTTGTGG
* *
463474 GCTTTTGAAAAGATGCCATTGACTTGTGGGCTTTTGAAGGTTGCCATTGACTTGTGGGCTTTGAA
66 GCTTTTGAAAAGATGCCATTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGAA
463539 AAGGTCCCACTAACTTGTGGGCTTTTAAAAAAATGCCACT
131 AAGGTCCCACTAACTTGTGGGC-TTTAAAAAAATGCCACT
* * * **
463579 GACTTATGGGCTTTTGAAGAGGTGCCACTAACTTGTGGGCTTTGAAGGT-TGCCACTAACTTGTG
1 AACTTGTGGGCTTTTGAAG-GTTGCCACTAACTTGTGGGCTTTGAAAATGTGCCACTAACTTGTG
* * * *
463643 GGC-ATTGAAAAGGTGCCACTAACTTGTGGGC-TTTGAAGGTTGCCACTAACTTGTGGGCTTTGA
65 GGCTTTTGAAAAGATGCCATTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGA
463706 AAAGGT
130 AAAGGT
463712 AAGGGATGTC
Statistics
Matches: 269, Mismatches: 28, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
167 4 0.01
168 70 0.26
169 134 0.50
170 35 0.13
171 26 0.10
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (169 bp):
AACTTGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGAAAATGTGCCACTAACTTGTGG
GCTTTTGAAAAGATGCCATTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGAA
AAGGTCCCACTAACTTGTGGGCTTTAAAAAAATGCCACT
Found at i:464112 original size:37 final size:37
Alignment explanation
Indices: 464070--464154 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
464060 AAAGATGAAG
*
464070 CATAAATGCATTATGCAAAATGAAATGTTATGAATGT
1 CATAAATGCATCATGCAAAATGAAATGTTATGAATGT
464107 CATAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CATAAATGCATCATGCAAAATGAAATGTTATGAATGT
*
464144 CACAAATGCAT
1 CATAAATGCAT
464155 GATTGTGGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (37 bp):
CATAAATGCATCATGCAAAATGAAATGTTATGAATGT
Found at i:464926 original size:17 final size:19
Alignment explanation
Indices: 464892--464926 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
464882 GTATACTTTT
464892 TGACAAACAAGTGATTAAG
1 TGACAAACAAGTGATTAAG
464911 TGACAAA-AAG-GATTAA
1 TGACAAACAAGTGATTAA
464927 TTTTGGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (19 bp):
TGACAAACAAGTGATTAAG
Found at i:465192 original size:1 final size:1
Alignment explanation
Indices: 465188--465249 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
465178 CTTTTTGTTG
* * * ** * * *
465188 TTTTTTTTCTTTTTGTTTTTTGTTTTTTTTTGGTTGTTTTTTTTTTGTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
465250 GCGGAGGATG
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (1 bp):
T
Found at i:465201 original size:18 final size:17
Alignment explanation
Indices: 465179--465249 Score: 92
Period size: 17 Copynumber: 4.1 Consensus size: 17
465169 ATCCGGACCC
465179 TTTTTGTTGTTTTTTTT
1 TTTTTGTTGTTTTTTTT
465196 CTTTTTGTT-TTTTGTTTT
1 -TTTTTGTTGTTTT-TTTT
465214 TTTTTGGTTGTTTTTTTT
1 TTTTT-GTTGTTTTTTTT
465232 TTGTTT-TTGTTTTTTTT
1 TT-TTTGTTGTTTTTTTT
465249 T
1 T
465250 GCGGAGGATG
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
17 21 0.43
18 21 0.43
19 7 0.14
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.86
Consensus pattern (17 bp):
TTTTTGTTGTTTTTTTT
Found at i:465206 original size:11 final size:10
Alignment explanation
Indices: 465179--465250 Score: 74
Period size: 10 Copynumber: 6.9 Consensus size: 10
465169 ATCCGGACCC
*
465179 TTTTTGTTGT
1 TTTTTTTTGT
*
465189 TTTTTTTCTTT
1 TTTTTTT-TGT
465200 TTGTTTTTTGT
1 TT-TTTTTTGT
465211 TTTTTTTTGGT
1 TTTTTTTT-GT
465222 TGTTTTTTT-T
1 T-TTTTTTTGT
*
465232 TTGTTTTTGT
1 TTTTTTTTGT
465242 TTTTTTTTG
1 TTTTTTTTG
465251 CGGAGGATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
9 6 0.12
10 23 0.44
11 11 0.21
12 12 0.23
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:465208 original size:14 final size:13
Alignment explanation
Indices: 465179--465250 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
465169 ATCCGGACCC
*
465179 TTTTTG-TTGTTT
1 TTTTTGTTTTTTT
* *
465191 TTTTTCTTTTTGT
1 TTTTTGTTTTTTT
465204 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
*
465217 TTGGTTGTTTTTTT
1 TT-TTTGTTTTTTT
465231 TTTGTT-TTTGTTTT
1 TTT-TTGTTT-TTTT
465245 TTTTTG
1 TTTTTG
465251 CGGAGGATGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
12 5 0.10
13 22 0.46
14 21 0.44
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:465215 original size:32 final size:31
Alignment explanation
Indices: 465179--465246 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 31
465169 ATCCGGACCC
*
465179 TTTTTGTT-GTTTTTTTTCTTTTTGTTTTTTGT
1 TTTTTGTTGGTTGTTTTT-TTTTTG-TTTTTGT
*
465211 TTTTTTTTGGTTGTTTTTTTTTTGTTTTTGT
1 TTTTTGTTGGTTGTTTTTTTTTTGTTTTTGT
465242 TTTTT
1 TTTTT
465247 TTTGCGGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 12 0.36
32 13 0.39
33 8 0.24
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.85
Consensus pattern (31 bp):
TTTTTGTTGGTTGTTTTTTTTTTGTTTTTGT
Found at i:479251 original size:13 final size:13
Alignment explanation
Indices: 479229--479286 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
479219 GGCAATAGCT
*
479229 TTGTAGCGATACA
1 TTGTATCGATACA
479242 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
479258 CTTATGTATCGATACA
1 --T-TGTATCGATACA
479274 TTGTATCGATACA
1 TTGTATCGATACA
479287 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Done.