Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 20 of 24
Found at i:2617672 original size:13 final size:14
Alignment explanation
Indices: 2617641--2617687 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
2617631 TAAAAATTAC
*
2617641 ATAAAATATAAAAAT
1 ATAAAATAT-AATAT
2617656 ATAAAAT-TAATAT
1 ATAAAATATAATAT
*
2617669 ATAATATATAAT-T
1 ATAAAATATAATAT
2617682 ATAAAA
1 ATAAAA
2617688 AAAGTCAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 16 0.57
14 5 0.18
15 7 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAATATAATAT
Found at i:2617674 original size:26 final size:25
Alignment explanation
Indices: 2617629--2617687 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
2617619 TTTTTTATAT
2617629 AATA-AAAATTACATAAAATATAAA
1 AATATAAAATTACATAAAATATAAA
*
2617653 AATATAAAATTA-ATATATAATATATA
1 AATATAAAATTACATA-A-AATATAAA
*
2617679 ATTATAAAA
1 AATATAAAA
2617688 AAAGTCAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.23
25 8 0.27
26 15 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
AATATAAAATTACATAAAATATAAA
Found at i:2618301 original size:4 final size:4
Alignment explanation
Indices: 2618294--2618318 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2618284 TTAAGAAAGA
2618294 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2618319 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2618688 original size:20 final size:21
Alignment explanation
Indices: 2618650--2618688 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2618640 TCTTTATATT
*
2618650 TTTATTTTTATAATAATTTTA
1 TTTAATTTTATAATAATTTTA
*
2618671 TTTAATTTT-TAATTATTT
1 TTTAATTTTATAATAATTT
2618689 GTAATTGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTAATTTTATAATAATTTTA
Found at i:2619158 original size:16 final size:17
Alignment explanation
Indices: 2619123--2619162 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2619113 TAATATATCA
2619123 ATTATTTTTTGAATTAT
1 ATTATTTTTTGAATTAT
2619140 ATTATTTTTAT-AATT-T
1 ATTATTTTT-TGAATTAT
2619156 ATTATTT
1 ATTATTT
2619163 AAAAACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 13 0.59
18 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTATTTTTTGAATTAT
Found at i:2619619 original size:3 final size:3
Alignment explanation
Indices: 2619613--2619643 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2619603 AAAAAAAGAC
2619613 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2619644 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2622865 original size:237 final size:237
Alignment explanation
Indices: 2622348--2623042 Score: 914
Period size: 237 Copynumber: 3.0 Consensus size: 237
2622338 ACTAGCTGTT
* *
2622348 GGTTCTATTGTCTCTGTTGTTAAAGAGCGACCAGATAATGCATCTCCAATTGTTGTCAAAGGTAA
1 GGTTCTGTTGTCTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCCAATTGTTGTCAAAGGTAA
* * *
2622413 AATTCCTACATCACAATCTGATCAAGGGGGACAAGCCCCCTCGATTAAATCAGA-AGTAGATTCA
66 AATTCCTACATCACAATCTGATCAAGGAGGACAAACCCCCTCGATTAAATCAGAGA-TAGATCCA
*** * * * *
2622477 CTTCCTGATACCACGG-CTCATACTTCACAAT-TG-G----A--AAATGCATCCTTTATGCTGAC
130 CTTCCTGATACTGGGGTC-CATACTTCACAATCGGAGCACTAGGAAATGCTTCCTTTATGATAAC
* * *
2622533 CAAGAA-G-ATATCACTGATTCCCTCTCCATTGCCTGGTATGGAA
194 CAAGAAGGCAT-TCGCTGACTCCCTCTCCATTGCCTGGCATGGAA
* * *
2622576 GGTTCTGTTGTCTCTGTCGTTGAAGAGCAACCAGATAATGCATCTCCAATTGTTGTCAAAGGAAA
1 GGTTCTGTTGTCTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCCAATTGTTGTCAAAGGTAA
* *
2622641 AATTCCTACATCACAATCTGATCAAGGAGGACAAACCCCCTCAATTAAAACAGAGATAGATCCAC
66 AATTCCTACATCACAATCTGATCAAGGAGGACAAACCCCCTCGATTAAATCAGAGATAGATCCAC
** * *
2622706 TTCAAGATACTGGGGTCCATACTTCACAATCGGAGCAACTAGGAAATGCTTCCTCTATGGTAACC
131 TTCCTGATACTGGGGTCCATACTTCACAATCGGAGC-ACTAGGAAATGCTTCCTTTATGATAACC
* *
2622771 AAGAAGGCATTGGC-GACTCCCTCTCCATTGCCTGGCATGGAG
195 AAGAAGGCATTCGCTGACTCCCTCTCCATTGCCTGGCATGGAA
* *
2622813 GGTTCTGTCGTCTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCCAATTGTTGTTAAAGGTAA
1 GGTTCTGTTGTCTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCCAATTGTTGTCAAAGGTAA
* * * * * *
2622878 ACTTCCTACATCACAATTTGATCAAGGAGGACGAACCCCCTTGATTAAATCTGAGATAGATCCGC
66 AATTCCTACATCACAATCTGATCAAGGAGGACAAACCCCCTCGATTAAATCAGAGATAGATCCAC
*
2622943 TTCCTGATACTGGGGTCCGTACTTCACAATCGGAGCGACTAGGAAATGCTTCCTTTATGATAACC
131 TTCCTGATACTGGGGTCCATACTTCACAATCGGAGC-ACTAGGAAATGCTTCCTTTATGATAACC
* *
2623008 CAGAAGACA-TCGCTGACTCCCTCTCCATTGCCTGG
195 AAGAAGGCATTCGCTGACTCCCTCTCCATTGCCTGG
2623043 TAAGGATGGG
Statistics
Matches: 406, Mismatches: 47, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
228 141 0.35
229 3 0.01
230 1 0.00
235 1 0.00
236 3 0.01
237 252 0.62
238 3 0.01
239 2 0.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (237 bp):
GGTTCTGTTGTCTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCCAATTGTTGTCAAAGGTAA
AATTCCTACATCACAATCTGATCAAGGAGGACAAACCCCCTCGATTAAATCAGAGATAGATCCAC
TTCCTGATACTGGGGTCCATACTTCACAATCGGAGCACTAGGAAATGCTTCCTTTATGATAACCA
AGAAGGCATTCGCTGACTCCCTCTCCATTGCCTGGCATGGAA
Found at i:2623980 original size:459 final size:459
Alignment explanation
Indices: 2621670--2625649 Score: 4595
Period size: 459 Copynumber: 8.6 Consensus size: 459
2621660 CTCTGCATTG
* *
2621670 CCTGTAGTACGTGAGAAAGTGTCAGAGGATGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
1 CCTGTAGTACGTGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
* * **
2621735 TAAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCGAACTGCCTCGTGAAAAAGC
66 TGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAAAAGC
* * * * * * *
2621800 AATTGGAACGTTCACATGACGAGAAAATGGCCCACACTGTTTATTTTGGTCAGCACGATCATCCA
131 AATTGAAACGTTCACATGACGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCCA
* * ** ** ** *
2621865 AAGCCACTGAACCTTCCCCTAGCTGTTGGTTCTGTTATCTCTGTTG-TTGA--AGA-ACAACCAG
196 AAGCCACTGAACCTTCCACTAGCTGTTGGTTCTG-T-TGT-TGAAGAGCGACCAGATA-ATGCAT
* *
2621926 AT--AA-CGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCCCCTCA
257 CTCCAATTGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCCCCTCA
* *
2621988 ATTAAATCAGAGAAAGATCCACTTCCTGATAGTGGGGTCCATGCTTCACAATCGGAGCAACTAGG
322 ATTAAATCAGAGAAAGATCCACTTCCTGATACTGGGGTCCATACTTCACAATCGGAGCAACTAGG
* * * ***
2622053 AAATGTTTCCTCTACGATAACCGAGAAGACATTGTTGACTCCCTCTCC-GTTGCCTGGTATGGAA
387 AAATGCTTCCTCTATGATAACCAAGAAGACATCACTGACTCCCTCTCCAG-TGCCTGGTATGGAA
2622117 GGGAGCAGT
451 GGGAGCAGT
* * * **
2622126 CCTGTAGTATGTGAGAAAGTGTCAGAGGACGGGTATAACTGGCATAAATATAAGCAGAAACTTGT
1 CCTGTAGTACGTGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
* *
2622191 TGCAGGAAATGAATTTGTTCGTAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAGAAA-
66 TGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAA-AAAG
* * * * * * *
2622255 CAACTGGAATGTTCATATGATGGGAAAATGGTCGACACTGTTTATTTTGGTCAGCATGATCATCC
130 CAATTGAAACGTTCACATGACGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCC
2622320 AAAGCCACTGAACCTTCCACTAGCTGTTGGTTCTATTGTCTCTGTTGTTAAAGAGCGACCAGATA
195 AAAGCCACTGAACCTTCCACTAGCTGTTGGTTC---TG--T-TGTTG---AAGAGCGACCAGATA
* *
2622385 ATGCATCTCCAATTGTTGTCAAAGGTAAAATTCCTACATCACAATCTGATCAAGGGGGAC-AAGC
251 ATGCATCTCCAATTGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAA-C
* * * *** *
2622449 CCCCTCGATTAAATCAGA-AGTAGATTCACTTCCTGATACCACGG-CTCATACTTCACAAT-TG-
315 CCCCTCAATTAAATCAGAGA-AAGATCCACTTCCTGATACTGGGGTC-CATACTTCACAATCGGA
* * * * * * *
2622510 G-----A--AAATGCATCCTTTATGCTGACCAAGAAGATATCACTGATTCCCTCTCCATTGCCTG
378 GCAACTAGGAAATGCTTCCTCTATGATAACCAAGAAGACATCACTGACTCCCTCTCCAGTGCCTG
** *
2622568 GTATGGAA-GGTTCTGTT
443 GTATGGAAGGGAGCAG-T
* * * ** ** * ** * * * * **
2622585 GTCTCT-GT-CGTTGA-AGAGCAACCAGATAATGCATCTCCAATTGTTGTCAAAGGAAAAAT-TC
1 -CCTGTAGTACG-TGAGAAAG-AGTCAGAGGACGGGTAT--AACTG--G-C---GTAAATATGGG
* * * * * ** ***** ** * * *
2622646 CTACATCACAATCTGATCAAGGAGGACAAACCCCCTC-AA-TTAAAACAGA-G-ATAGATCC--A
55 C-AGA--A-ACT-TGTTGAAGGA-AATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAA
* * ** *** ** * * * * *
2622705 CT-TCAA--GATACTGGGGTCCATAC-TTCACA--ATCGGAGCAACTAG--GAAATGCT-TCCTC
114 CTGCCAAGTGAAAAAGCAATTGAAACGTTCACATGA-CGG-GAAAATGGTCGACA--CTAT--T-
* *** * * **** * ** *
2622761 TATGGTAACCAAGAAGGCATTGGCGACTCCCTCTCCATTG--CCTGGCA-TGGAGGGTTCTG-TC
172 TATGTTGGTC-AGCATG-A-T--C-A-TCCAAAGCCACTGAACCTTCCACT--A--G--CTGTTG
* * *
2622822 GTCTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCCAATTGTTGTTAAAGGTAAACTTCCTAC
224 GT-TCTGTTGTTGAAGAGCGACCAGATAATGCATCTCCAATTGTTGTCAAAGGTAAAATTCCCAC
* ** * * *
2622887 ATCACAATTTGATCAAGGAGGACGAACCCCCTTGATTAAATCTGAGATAGATCCGCTTCCTGATA
288 ATCACAATCTGATCAAGGAGGACGAACCCCCTCAATTAAATCAGAGAAAGATCCACTTCCTGATA
* * * *
2622952 CTGGGGTCCGTACTTCACAATCGGAGCGACTAGGAAATGCTTCCTTTATGATAACCCAGAAGACA
353 CTGGGGTCCATACTTCACAATCGGAGCAACTAGGAAATGCTTCCTCTATGATAACCAAGAAGACA
* * * *
2623017 TCGCTGACTCCCTCTCCATTGCCTGGTAAGGATGGGAGCAGT
418 TCACTGACTCCCTCTCCAGTGCCTGGTATGGAAGGGAGCAGT
*
2623059 CCTGTAGTACATGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
1 CCTGTAGTACGTGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
* * *
2623124 TGAAGGAAATGAATTTATTCGAAGTTATTACAGATGTACACATCCAAACTGCCCAGTGAAAAAGC
66 TGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAAAAGC
* * * * * *
2623189 AATTGAAACGTTCACATGACAGGAAAATGGTTGATACTGTTTATTTTGGTCGGCATGATCATCCA
131 AATTGAAACGTTCACATGACGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCCA
* *
2623254 AAGCCACTGAGCCTTCCACTAGCTGTTGGTTCTGTTGTCTCTGTTGTTGAAGAGCGGCCAGATAA
196 AAGCCACTGAACCTTCCACTAGC---T-G-T-TG--GT-TCTGTTGTTGAAGAGCGACCAGATAA
*
2623319 GGCATCTCCAATTGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCC
252 TGCATCTCCAATTGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCC
* * * *
2623384 CCTTAATTAAATCAGAAAAAGATCCACTTCCTGATACTGGGGTCCATACTTTACAATTGGAGCAA
317 CCTCAATTAAATCAGAGAAAGATCCACTTCCTGATACTGGGGTCCATACTTCACAATCGGAGCAA
*
2623449 CTAGGAAATGCTTCCTCTATGATAACCAAGAAGACATCACTGACTTCCTCTCCAGTGCCTGGTAT
382 CTAGGAAATGCTTCCTCTATGATAACCAAGAAGACATCACTGACTCCCTCTCCAGTGCCTGGTAT
2623514 GGAAGGGAGCAGT
447 GGAAGGGAGCAGT
* * * *
2623527 CCTCTAGTATGTGAGAAAGAGTCAGAAGATGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
1 CCTGTAGTACGTGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
2623592 TGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAAAAGC
66 TGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAAAAGC
*
2623657 AATTGAAACGTTCACATGACGGGAACATGGTCGACACTATTTATGTTGGTCAGCATGATCATCCA
131 AATTGAAACGTTCACATGACGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCCA
* *
2623722 AAGCCACTGAACCTTCCACTAGCTTTTGGTTCTGTTGTTGAAGAGC-AGCCAGATAATGCATCTA
196 AAGCCACTGAACCTTCCACTAGCTGTTGGTTCTGTTGTTGAAGAGCGA-CCAGATAATGCATCTC
* * *
2623786 CAATTGTTGTCGAAGATAAAATT-CCAGCATCACAATCTGATCATGGAGGACGAACCCCCTCAAT
260 CAATTGTTGTCAAAGGTAAAATTCCCA-CATCACAATCTGATCAAGGAGGACGAACCCCCTCAAT
*
2623850 TAAATCAGAGAAAGATCCACTTCCTGATACTGGGGTGCATACTTCACAATCGGAGCAACTAGGAA
324 TAAATCAGAGAAAGATCCACTTCCTGATACTGGGGTCCATACTTCACAATCGGAGCAACTAGGAA
**
2623915 ATGC-TCTCTCTATGATAACCAAGAAGACATCACTGACTCTTTCTCCAGTGCCTGGTATGGAAGG
389 ATGCTTC-CTCTATGATAACCAAGAAGACATCACTGACTCCCTCTCCAGTGCCTGGTATGGAAGG
2623979 GAGCAGT
453 GAGCAGT
* * *
2623986 CCTGTAGT-CTGTGAGAAAGAGTCAGAGGACAGTTATAACTGGCGTAAATATGGCCAGAAACTTG
1 CCTGTAGTAC-GTGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTG
* *
2624050 TTGAAGGAAATGAATTTGTTCGGAGTTATTACAAATGTGCACATCCAAACTGCCAAGTGAAAAAG
65 TTGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAAAAG
*
2624115 CAATTGAAACGTTCACATGATGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCC
130 CAATTGAAACGTTCACATGACGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCC
* *
2624180 AAAGCCACTGAACCTTCCACTAGCTGTTGGTTCTGTTGTTGAAGAGCAACCCGATAATGCATCTC
195 AAAGCCACTGAACCTTCCACTAGCTGTTGGTTCTGTTGTTGAAGAGCGACCAGATAATGCATCTC
*
2624245 CAATTGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCCCCTTAATT
260 CAATTGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCCCCTCAATT
* * * *
2624310 AAATCAGAAAAAGATCCACTTCCTGATACTGGAGTCCATACTTCACAATCAGAGCAACTAGGTAA
325 AAATCAGAGAAAGATCCACTTCCTGATACTGGGGTCCATACTTCACAATCGGAGCAACTAGGAAA
* * *
2624375 TGCTTCCTCTATGATAACCAAAAAGACATCACTGACTCTCTCTCCAGTGCCTGGTATAGAAGGGA
390 TGCTTCCTCTATGATAACCAAGAAGACATCACTGACTCCCTCTCCAGTGCCTGGTATGGAAGGGA
*
2624440 GCAGG
455 GCAGT
* *
2624445 CCTGTAGGACATGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
1 CCTGTAGTACGTGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
** *
2624510 TGAAGGAAATGAATTTGTTCGAAGTTATTACAGGTGTACACATCCAAACTGCCAAGTGAAAAAAC
66 TGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAAAAGC
* * * *
2624575 AATTGAAACGTTCGCATGATGGGAAAATGGTCAACACTATTTATGTTGGTCAGCATGCTCATCCA
131 AATTGAAACGTTCACATGACGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCCA
* *
2624640 AAGCCACTGAAGCTTCCAGTAGCTGTTGGTTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCC
196 AAGCCACTGAACCTTCCACTAGCTGTTGGTTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCC
** *
2624705 AATTGTTGTTGAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCCCTTCAATTA
261 AATTGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCCCCTCAATTA
* * *
2624770 AATCAGAGAAAGATCCACTTCCTGATACTGGAGTCCATACTTCACAATCAGAGCAACTAGGTAAT
326 AATCAGAGAAAGATCCACTTCCTGATACTGGGGTCCATACTTCACAATCGGAGCAACTAGGAAAT
* * *
2624835 GCTTCCTCTATGATAACCAAAAAGACATCACTGACTCTCTCTCCAGTGCCTGGTATAGAAGGGAG
391 GCTTCCTCTATGATAACCAAGAAGACATCACTGACTCCCTCTCCAGTGCCTGGTATGGAAGGGAG
*
2624900 CAGG
456 CAGT
* *
2624904 CCTGTAGGACATGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
1 CCTGTAGTACGTGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
* * * *
2624969 TAAAGGAAATGAATTTGTTCAAAGTTATTACAAGTGTGCACATCCAAACTGCCAAGTGAAAAAGC
66 TGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAAAAGC
* * *
2625034 AATTGAAACGTTCACTTGATGGGAAAATGGTTGACACTATTTATGTTGGTCAGCATGATCATCCA
131 AATTGAAACGTTCACATGACGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCCA
* * * *
2625099 AAGGCACTCAACCTTCCACTAGCTGTTGATTCTGTTGTTGAAGAGCGACCGGATAATGCATCTCC
196 AAGCCACTGAACCTTCCACTAGCTGTTGGTTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCC
* * *
2625164 AATTGTTGTCAAAGGTAAAATTCCCACGTCACAATCTGATCATGGAGGACAAACCCCCTCAATTA
261 AATTGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCCCCTCAATTA
*
2625229 AATCAGAGAAAGATTCACTTCCTGATA-TGGGGGTCCATACTTCACAATCGGAGCAACTAGGAAA
326 AATCAGAGAAAGATCCACTTCCTGATACT-GGGGTCCATACTTCACAATCGGAGCAACTAGGAAA
* * * * **
2625293 TGCTTCCTCTATGATAACCAAGAAGACATCGCTGACTCCCACACCATTGCCTGGTACAGAAGGGA
390 TGCTTCCTCTATGATAACCAAGAAGACATCACTGACTCCCTCTCCAGTGCCTGGTATGGAAGGGA
2625358 GCAGT
455 GCAGT
* * * * *
2625363 CCTGTAGTATGTGTGAAAGAGTTAGGGGATGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
1 CCTGTAGTACGTGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
* * *
2625428 TGAAAGAAATGAATTTGTTCGAAGTTATTACAGATGTACACATCCAAGCTGCCAAGTGAAAAAGC
66 TGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAAAAGC
* * * * *
2625493 AATTGAAATGTTCACATGAGGGGAAAATGGTCGACATTGTTTATTTTGGTCAGCATGATCATCCA
131 AATTGAAACGTTCACATGACGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCCA
* * * *
2625558 AAGCCACTGAGCCTTCCACCAGCTGATGATTTTGTTGTCTCTGTTGTTGAAAAACGACCAGATAA
196 AAGCCACTGAACCTTCCACTAGC---TG---TTG--GT-TCTGTTGTTGAAGAGCGACCAGATAA
** *
2625623 TGTGTCTCCAATTGTTGTTAAAGGTAA
252 TGCATCTCCAATTGTTGTCAAAGGTAA
2625650 GTAAACATTT
Statistics
Matches: 3014, Mismatches: 389, Indels: 230
0.83 0.11 0.06
Matches are distributed among these distances:
456 203 0.07
457 3 0.00
458 14 0.00
459 1754 0.58
460 19 0.01
461 14 0.00
462 37 0.01
463 21 0.01
464 14 0.00
465 144 0.05
466 22 0.01
467 22 0.01
468 573 0.19
469 15 0.00
470 21 0.01
471 31 0.01
472 14 0.00
473 10 0.00
474 75 0.02
475 8 0.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (459 bp):
CCTGTAGTACGTGAGAAAGAGTCAGAGGACGGGTATAACTGGCGTAAATATGGGCAGAAACTTGT
TGAAGGAAATGAATTTGTTCGAAGTTATTACAAATGTACACATCCAAACTGCCAAGTGAAAAAGC
AATTGAAACGTTCACATGACGGGAAAATGGTCGACACTATTTATGTTGGTCAGCATGATCATCCA
AAGCCACTGAACCTTCCACTAGCTGTTGGTTCTGTTGTTGAAGAGCGACCAGATAATGCATCTCC
AATTGTTGTCAAAGGTAAAATTCCCACATCACAATCTGATCAAGGAGGACGAACCCCCTCAATTA
AATCAGAGAAAGATCCACTTCCTGATACTGGGGTCCATACTTCACAATCGGAGCAACTAGGAAAT
GCTTCCTCTATGATAACCAAGAAGACATCACTGACTCCCTCTCCAGTGCCTGGTATGGAAGGGAG
CAGT
Found at i:2630436 original size:80 final size:79
Alignment explanation
Indices: 2630125--2630523 Score: 454
Period size: 79 Copynumber: 5.0 Consensus size: 79
2630115 GATATGAAAT
* * *
2630125 TTTGACATCTTCAAACCTATATCTAGAAATGAAGAAACT-CTTTCCTCATTGAT-GGGATCGATA
1 TTTGACATCTTCGAACCTATATCAAGAAATGAAGAAA-TAC-TTCCTCATTTATGGGGATCGATA
2630188 AAAATGAGAGATGCAA
64 AAAATGAGAGATGCAA
* * * * * *
2630204 TTTGGGCATGTTCAAACCTACATCAAGAAATGAAGAAACACTTTCTCA-TT-TGGAGGAT-GAAT
1 TTT-GACATCTTCGAACCTATATCAAGAAATGAAGAAATACTTCCTCATTTATGG-GGATCG-AT
2630266 AAAAATGAGAGATGCAA
63 AAAAATGAGAGATGCAA
** * * *
2630283 TTTCGACATCTTCGAACCTATATTGAGAAGTGAAGAAACACTTCC-CATTTATGGGGATCAATAA
1 TTT-GACATCTTCGAACCTATATCAAGAAATGAAGAAATACTTCCTCATTTATGGGGATCGATAA
2630347 AAATGAGAGATGCAAA
65 AAATGAGAGATGC-AA
* *
2630363 TTTGACATCTTCGAACTTATATCAAGAAATGAAGAAATGCTTCCTCATTTATGGGGATCGATAAA
1 TTTGACATCTTCGAACCTATATCAAGAAATGAAGAAATACTTCCTCATTTATGGGGATCGATAAA
*
2630428 AATAAGAGATGCAAA
66 AATGAGAGATGC-AA
* * **
2630443 TTTGACATCTTCGAACCTATGTCAAGAAATGAAGAAATGCTTCCTCA-TTAACGGGATC-AGTAA
1 TTTGACATCTTCGAACCTATATCAAGAAATGAAGAAATACTTCCTCATTTATGGGGATCGA-TAA
* *
2630506 AGATGAGAGATGCTA
65 AAATGAGAGATGCAA
2630521 TTT
1 TTT
2630524 CGTTACTTAA
Statistics
Matches: 277, Mismatches: 32, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
77 1 0.00
78 10 0.04
79 149 0.54
80 117 0.42
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (79 bp):
TTTGACATCTTCGAACCTATATCAAGAAATGAAGAAATACTTCCTCATTTATGGGGATCGATAAA
AATGAGAGATGCAA
Found at i:2630436 original size:159 final size:157
Alignment explanation
Indices: 2630125--2630523 Score: 466
Period size: 159 Copynumber: 2.5 Consensus size: 157
2630115 GATATGAAAT
* * * *
2630125 TTTGACATCTTCAAACCTATATCTAGAAATGAAGAAACTCTTTCCTCATTGATGGGATCGATAAA
1 TTTGACATCTTCGAACCTATAT-TAGAAATGAAGAAACAC-TTCCTCATTTATGGGATCAATAAA
* * *
2630190 AATGAGAGATGCAATTTGGGCATGTTCAAACCTACATCAAGAAATGAAGAAACACTTTCTCATTT
64 AATGAGAGATGCAATTTGGACATCTTCAAACCTACATCAAGAAATGAAGAAACACTTCCTCATTT
*
2630255 GGAGGATGAATAAAAATGAGAGATGC-AA
129 GGAGGATGAATAAAAATAAGAGATGCAAA
*
2630283 TTTCGACATCTTCGAACCTATATTGAGAAGTGAAGAAACACTTCC-CATTTATGGGGATCAATAA
1 TTT-GACATCTTCGAACCTATATT-AGAAATGAAGAAACACTTCCTCATTTAT-GGGATCAATAA
* * * **
2630347 AAATGAGAGATGCAAATTT-GACATCTTCGAACTTATATCAAGAAATGAAGAAATGCTTCCTCAT
63 AAATGAGAGATGC-AATTTGGACATCTTCAAACCTACATCAAGAAATGAAGAAACACTTCCTCA-
2630411 TTATGG-GGATCG-ATAAAAATAAGAGATGCAAA
126 TT-TGGAGGAT-GAATAAAAATAAGAGATGCAAA
* * ** * * * *
2630443 TTTGACATCTTCGAACCTATGTCAAGAAATGAAGAAATGCTTCCTCATTAACGGGATCAGTAAAG
1 TTTGACATCTTCGAACCTATAT-TAGAAATGAAGAAACACTTCCTCATTTATGGGATCAATAAAA
*
2630508 ATGAGAGATGCTATTT
65 ATGAGAGATGCAATTT
2630524 CGTTACTTAA
Statistics
Matches: 207, Mismatches: 24, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
157 6 0.03
158 71 0.34
159 116 0.56
160 14 0.07
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (157 bp):
TTTGACATCTTCGAACCTATATTAGAAATGAAGAAACACTTCCTCATTTATGGGATCAATAAAAA
TGAGAGATGCAATTTGGACATCTTCAAACCTACATCAAGAAATGAAGAAACACTTCCTCATTTGG
AGGATGAATAAAAATAAGAGATGCAAA
Found at i:2633535 original size:76 final size:77
Alignment explanation
Indices: 2633423--2633572 Score: 248
Period size: 76 Copynumber: 2.0 Consensus size: 77
2633413 TTTTTAACAC
* * *
2633423 TTTTAAAAGTATATTATTTTTATATTAATTTGATATAGTTATAATTTATTCTTCAAATGTCATCA
1 TTTTAAAAGCATATTACTTTTATATTAATTTGATATAATTATAATTTATTCTTCAAATGTCATCA
2633488 CAAAAAGTTGAA
66 CAAAAAGTTGAA
*
2633500 TTTTAAAAGCATATT-CTTTTATATTAATTTGATATAATTATAATTTATTCTTCAAATTTCATCA
1 TTTTAAAAGCATATTACTTTTATATTAATTTGATATAATTATAATTTATTCTTCAAATGTCATCA
*
2633564 CAAAGAGTT
66 CAAAAAGTT
2633573 AAGTCTTCAT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
76 54 0.79
77 14 0.21
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (77 bp):
TTTTAAAAGCATATTACTTTTATATTAATTTGATATAATTATAATTTATTCTTCAAATGTCATCA
CAAAAAGTTGAA
Found at i:2634453 original size:23 final size:23
Alignment explanation
Indices: 2634427--2634470 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2634417 ACAAATATTT
*
2634427 TATATTATTTTTAAATTAATTAA
1 TATATTATTTATAAATTAATTAA
*
2634450 TATATTATTTATAATTTAATT
1 TATATTATTTATAAATTAATT
2634471 TTTAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTATTTATAAATTAATTAA
Found at i:2634473 original size:35 final size:37
Alignment explanation
Indices: 2634420--2634513 Score: 99
Period size: 35 Copynumber: 2.6 Consensus size: 37
2634410 TGTGTTAACA
* *
2634420 AATATTT-TATAT-TATTTTTAAAT-TAAT-TAATAT
1 AATATTTATATTTATATTTTTAAATATAATATAAAAT
*
2634453 ATTATTTATAATTTA-ATTTTTAAATATAATAATAAAAT
1 AATATTTAT-ATTTATATTTTTAAATATAAT-ATAAAAT
2634491 AATATTTATATTTATTATTTTTA
1 AATATTTATATTTA-TATTTTTA
2634514 CTACATTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
33 6 0.12
34 1 0.02
35 13 0.27
36 4 0.08
37 5 0.10
38 13 0.27
39 7 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (37 bp):
AATATTTATATTTATATTTTTAAATATAATATAAAAT
Found at i:2634480 original size:18 final size:18
Alignment explanation
Indices: 2634433--2634482 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2634423 ATTTTATATT
2634433 ATTTTTAAAT-TAA-TTA
1 ATTTTTAAATATAATTTA
* **
2634449 ATATATTATTTATAATTTA
1 AT-TTTTAAATATAATTTA
2634468 ATTTTTAAATATAAT
1 ATTTTTAAATATAAT
2634483 AATAAAATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
16 2 0.08
17 5 0.20
18 13 0.52
19 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTAAATATAATTTA
Found at i:2636175 original size:2 final size:2
Alignment explanation
Indices: 2636168--2636204 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2636158 TCAAGTTTTC
2636168 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2636205 TATTTAAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2637074 original size:22 final size:22
Alignment explanation
Indices: 2637044--2637087 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2637034 TAACATATTT
*
2637044 TTATTTAAAT-TTAATTATAAAA
1 TTATATAAATATT-ATTATAAAA
2637066 TTATATAAATATTATTATAAAA
1 TTATATAAATATTATTATAAAA
2637088 ATAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTATATAAATATTATTATAAAA
Found at i:2637961 original size:2 final size:2
Alignment explanation
Indices: 2637954--2637984 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2637944 AAGTCCAATA
2637954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2637985 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2637989 original size:2 final size:2
Alignment explanation
Indices: 2637984--2638023 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2637974 ATATATATAT
2637984 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2638024 TTAAAATTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2638904 original size:2 final size:2
Alignment explanation
Indices: 2638897--2638926 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2638887 TTAGCTGAAA
2638897 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2638927 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2649502 original size:15 final size:15
Alignment explanation
Indices: 2649479--2649508 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2649469 GAGCCAATAA
*
2649479 AATTTAATTAAAATT
1 AATTCAATTAAAATT
2649494 AATTCAATTAAAATT
1 AATTCAATTAAAATT
2649509 TTTTATAAAT
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTCAATTAAAATT
Found at i:2649697 original size:20 final size:18
Alignment explanation
Indices: 2649680--2649723 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2649670 GTATTATTAA
2649680 TAAAATATAAAAATTATT
1 TAAAATATAAAAATTATT
*
2649698 TAATATATAAAAA--ATT
1 TAAAATATAAAAATTATT
2649714 TAAAA-ATAAA
1 TAAAATATAAA
2649724 TACAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 7 0.29
18 12 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAATATAAAAATTATT
Found at i:2649973 original size:3 final size:3
Alignment explanation
Indices: 2649965--2650015 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
2649955 AATTTGTGGG
2649965 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
2650010 ATT ATT
1 ATT ATT
2650016 GATGATGTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2650328 original size:20 final size:20
Alignment explanation
Indices: 2650305--2650343 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2650295 ATTTTTTATT
* *
2650305 TTTTTAATTAATTTTTAAAA
1 TTTTTAAATAATATTTAAAA
2650325 TTTTTAAATAATATTTAAA
1 TTTTTAAATAATATTTAAA
2650344 GGGTATTTAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTAAATAATATTTAAAA
Found at i:2650524 original size:2 final size:2
Alignment explanation
Indices: 2650517--2650547 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2650507 TACATTGTTT
2650517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2650548 CAAATGAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2651099 original size:3 final size:3
Alignment explanation
Indices: 2651091--2651116 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2651081 TAAATAAAAA
2651091 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2651117 AATAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2651761 original size:20 final size:20
Alignment explanation
Indices: 2651722--2651761 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2651712 ATATTTTAAT
*
2651722 ATATTATAATTGTATTTAAA
1 ATATTATAATTGTATATAAA
2651742 ATATTATATATT-TATATAAA
1 ATATTATA-ATTGTATATAAA
2651762 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATTATAATTGTATATAAA
Found at i:2653277 original size:14 final size:14
Alignment explanation
Indices: 2653260--2653292 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2653250 ATTTTTATTT
2653260 AAAT-TTAATTATAA
1 AAATATTAA-TATAA
2653274 AAATATTAATATAA
1 AAATATTAATATAA
2653288 AAATA
1 AAATA
2653293 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATATTAATATAA
Found at i:2654370 original size:3 final size:3
Alignment explanation
Indices: 2654362--2654392 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2654352 TTCACAAATC
2654362 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2654393 TGATTGTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2655444 original size:28 final size:29
Alignment explanation
Indices: 2655362--2655445 Score: 113
Period size: 28 Copynumber: 3.0 Consensus size: 29
2655352 TCGCAGATGA
2655362 AATAAAATATTTATTTCAAAAATAAAAAT
1 AATAAAATATTTATTTCAAAAATAAAAAT
* *
2655391 GAT-AAATATTTATTTTAAAAATAAAAAT
1 AATAAAATATTTATTTCAAAAATAAAAAT
2655419 AATAAATATATTTA-TTC--AAATAAAAAT
1 AATAAA-ATATTTATTTCAAAAATAAAAAT
2655446 GTTTACTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.20
28 26 0.53
29 6 0.12
30 7 0.14
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (29 bp):
AATAAAATATTTATTTCAAAAATAAAAAT
Found at i:2655591 original size:20 final size:20
Alignment explanation
Indices: 2655544--2655591 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2655534 AGTTAAGTAT
*
2655544 TAAATTCATATTTATATTAA
1 TAAATTTATATTTATATTAA
** *
2655564 TATTTTTATATTTTTATTAA
1 TAAATTTATATTTATATTAA
2655584 TAAATTTA
1 TAAATTTA
2655592 AATAAAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAATTTATATTTATATTAA
Found at i:2657557 original size:14 final size:15
Alignment explanation
Indices: 2657538--2657566 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2657528 TATCTCTTTT
2657538 TAAAT-AAAAATAAA
1 TAAATAAAAAATAAA
2657552 TAAATAAAAAATAAA
1 TAAATAAAAAATAAA
2657567 AAAAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAATAAAAAATAAA
Found at i:2660758 original size:23 final size:23
Alignment explanation
Indices: 2660720--2660776 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
2660710 TATATCACAT
2660720 ATTTTTG-TATAATTTTTATTCTTA
1 ATTTTTGTTAT-ATTTTTATT-TTA
* *
2660744 ATTTTTGTTATTTTTTTATTTTT
1 ATTTTTGTTATATTTTTATTTTA
*
2660767 ATTTTAGTTA
1 ATTTTTGTTA
2660777 CTTAAGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.38
24 15 0.52
25 3 0.10
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (23 bp):
ATTTTTGTTATATTTTTATTTTA
Found at i:2660760 original size:24 final size:23
Alignment explanation
Indices: 2660732--2660776 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2660722 TTTTGTATAA
*
2660732 TTTTTATTCTTAATTTTTGTTATT
1 TTTTTATT-TTAATTTTAGTTATT
*
2660756 TTTTTATTTTTATTTTAGTTA
1 TTTTTATTTTAATTTTAGTTA
2660777 CTTAAGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTATTTTAATTTTAGTTATT
Found at i:2661528 original size:7 final size:6
Alignment explanation
Indices: 2661494--2661536 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
2661484 TTTTTTTATT
* *
2661494 TAAATT TAAATA TATAT- TAAATA TAAATA TCAAATA TAAATA T
1 TAAATA TAAATA TAAATA TAAATA TAAATA T-AAATA TAAATA T
2661537 TTTATATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.12
6 22 0.69
7 6 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
TAAATA
Found at i:2661528 original size:13 final size:13
Alignment explanation
Indices: 2661507--2661536 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2661497 ATTTAAATAT
*
2661507 ATATTAAATATAA
1 ATATCAAATATAA
2661520 ATATCAAATATAA
1 ATATCAAATATAA
2661533 ATAT
1 ATAT
2661537 TTTATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATCAAATATAA
Found at i:2663856 original size:22 final size:21
Alignment explanation
Indices: 2663824--2663864 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2663814 AAAGTCATTA
2663824 AAATATATGATACATATTTATTG
1 AAATATATGATA-AT-TTTATTG
2663847 AAATA-ATGATAATTTTAT
1 AAATATATGATAATTTTAT
2663865 AACTTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 6 0.33
23 5 0.28
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (21 bp):
AAATATATGATAATTTTATTG
Found at i:2665575 original size:2 final size:2
Alignment explanation
Indices: 2665568--2665609 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2665558 TAATGACATG
* *
2665568 TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2665610 AAACATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2666050 original size:21 final size:20
Alignment explanation
Indices: 2666012--2666055 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
2666002 TAAATAAATT
2666012 AATAAAAATTATATA-TTTA
1 AATAAAAATTATATATTTTA
*
2666031 AATAAAAATTTTATTAATTTTA
1 AATAAAAATTATA-T-ATTTTA
2666053 AAT
1 AAT
2666056 TCATTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 1 0.05
21 1 0.05
22 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAAAAATTATATATTTTA
Found at i:2666053 original size:49 final size:48
Alignment explanation
Indices: 2665995--2666168 Score: 120
Period size: 49 Copynumber: 3.4 Consensus size: 48
2665985 TTTAGTTGAT
2665995 TTAAATTTAAATAAATTAATAAAAATTATATATTTAAATAAAAATTTTA
1 TTAAATTTAAATAAATTAATAAAAATTATATATTT-AATAAAAATTTTA
* * * * ** * * *
2666044 TTAATTTTAAATTCATTTAATATCATGTTAACTCTATTT-TTAAATATTTATTAA
1 TTAAATTTAAA-TAAATTAATA-AAAATT-A-TATATTTAATAAA-AATT-TT-A
*
2666098 TTTAAATTTAAATAAATTAAT-AAAATTATATATTTGAATAAAAAATTGTA
1 -TTAAATTTAAATAAATTAATAAAAATTATATATTT-AAT-AAAAATTTTA
*
2666148 TT-AATTTAAAATAGATTAATA
1 TTAAATTT-AAATAAATTAATA
2666169 TCATGTGGAT
Statistics
Matches: 92, Mismatches: 20, Indels: 25
0.67 0.15 0.18
Matches are distributed among these distances:
48 5 0.05
49 23 0.25
50 15 0.16
51 9 0.10
52 11 0.12
53 11 0.12
54 8 0.09
55 10 0.11
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (48 bp):
TTAAATTTAAATAAATTAATAAAAATTATATATTTAATAAAAATTTTA
Found at i:2666053 original size:55 final size:53
Alignment explanation
Indices: 2665994--2666159 Score: 137
Period size: 50 Copynumber: 3.1 Consensus size: 53
2665984 ATTTAGTTGA
2665994 TTTAAATTTAAATAAATTAATAAAAATTATATATTTAAATAAAAATTTTATTAAT
1 TTTAAATTTAAATAAATTAAT-AAAATTATATATTT-AATAAAAATTTTATTAAT
* * * * ** * * *
2666049 TTTAAA-TTCATTTAA-T-ATCATGTTAACTCTATTT-TTAAATA-TTTATTAA-
1 TTTAAATTTAAATAAATTAATAAAATT-A-TATATTTAATAAAAATTTTATTAAT
*
2666098 TTTAAATTTAAATAAATTAATAAAATTATATATTTGAATAAAAAATTGTATTAAT
1 TTTAAATTTAAATAAATTAATAAAATTATATATTT-AAT-AAAAATTTTATTAAT
*
2666153 TTAAAAT
1 TTTAAAT
2666160 AGATTAATAT
Statistics
Matches: 81, Mismatches: 20, Indels: 20
0.67 0.17 0.17
Matches are distributed among these distances:
49 6 0.07
50 20 0.25
51 10 0.12
52 9 0.11
53 11 0.14
54 13 0.16
55 12 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (53 bp):
TTTAAATTTAAATAAATTAATAAAATTATATATTTAATAAAAATTTTATTAAT
Found at i:2666227 original size:102 final size:104
Alignment explanation
Indices: 2665945--2666239 Score: 393
Period size: 102 Copynumber: 2.9 Consensus size: 104
2665935 TATATCTTCA
* * * * * *
2665945 TTAAAATA-ATTTAATTTTATGT-AGACTTTATTTTTTAATATTTAGTTGATTTAAATTTAAATA
1 TTAAAATACATTTAATATCATGTGA-ACTCTAATTTTAAATATTTA-TTAATTTAAATTTAAATA
*
2666008 AATTAATAAAAATTATATATTTAAAT-AAAAATTTTATTAAT
64 AATTAAT-AAAATTATATATTTAAATAAAAAATTGTATTAAT
* * * *
2666049 TTTAAATTCATTTAATATCATGTTAACTCTATTTTTAAATATTTATTAATTTAAATTTAAATAAA
1 TTAAAATACATTTAATATCATGTGAACTCTAATTTTAAATATTTATTAATTTAAATTTAAATAAA
*
2666114 TTAATAAAATTATATATTTGAATAAAAAATTGTATTAAT
66 TTAATAAAATTATATATTTAAATAAAAAATTGTATTAAT
* *
2666153 TTAAAATAGA-TTAATATCATGTGGA-TCTAATTTTAAATATTTATTAATTTAAATTTAAATAAA
1 TTAAAATACATTTAATATCATGTGAACTCTAATTTTAAATATTTATTAATTTAAATTTAAATAAA
*
2666216 TTAATAAAATTACATATTTAAATA
66 TTAATAAAATTATATATTTAAATA
2666240 TTTAAATAGA
Statistics
Matches: 171, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
102 59 0.35
103 30 0.18
104 51 0.30
105 30 0.18
106 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (104 bp):
TTAAAATACATTTAATATCATGTGAACTCTAATTTTAAATATTTATTAATTTAAATTTAAATAAA
TTAATAAAATTATATATTTAAATAAAAAATTGTATTAAT
Found at i:2666236 original size:48 final size:48
Alignment explanation
Indices: 2666082--2666243 Score: 143
Period size: 48 Copynumber: 3.2 Consensus size: 48
2666072 TAACTCTATT
*
2666082 TTTAAATATTTATTAATTTAAATTTAAATAAATTAATAAAATTATATA
1 TTTAAATATTTATTAATTTAAATTTAAATAAATTAATAAAATTACATA
* ** * **
2666130 TTTGAATA---AAAAATTGTATTAATTTAAAATAGATTAATATCATGTGGATC-TAA
1 TTTAAATATTTATTAATT-TA--AATTT-AAATAAATTAATAAAAT-T--A-CAT-A
2666183 TTTTAAATATTTATTAATTTAAATTTAAATAAATTAATAAAATTACATA
1 -TTTAAATATTTATTAATTTAAATTTAAATAAATTAATAAAATTACATA
2666232 TTTAAATATTTA
1 TTTAAATATTTA
2666244 AATAGAATGC
Statistics
Matches: 87, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
45 5 0.06
46 2 0.02
48 24 0.28
49 16 0.18
50 3 0.03
52 3 0.03
53 15 0.17
54 12 0.14
56 2 0.02
57 5 0.06
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (48 bp):
TTTAAATATTTATTAATTTAAATTTAAATAAATTAATAAAATTACATA
Found at i:2675308 original size:20 final size:21
Alignment explanation
Indices: 2675267--2675308 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
2675257 AACAAAACTC
*
2675267 AATTAAAACAAAAAATATATA
1 AATTAAAACAAAAAATAAATA
2675288 AATT-AAACAAAATAA-AAATA
1 AATTAAAACAAAA-AATAAATA
2675308 A
1 A
2675309 CTCGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (21 bp):
AATTAAAACAAAAAATAAATA
Found at i:2678311 original size:18 final size:19
Alignment explanation
Indices: 2678278--2678340 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 19
2678268 ATATAACATG
2678278 AATATAATAT-AAATTATTA
1 AATA-AATATAAAATTATTA
* *
2678297 AATAAGT-TAAAATTATAA
1 AATAAATATAAAATTATTA
2678315 ACATAAATATAATATATTATTA
1 A-ATAAATATAA-A-ATTATTA
2678337 AATA
1 AATA
2678341 TACATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.03
18 11 0.31
19 9 0.26
20 3 0.09
21 4 0.11
22 7 0.20
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAAATATAAAATTATTA
Found at i:2678349 original size:16 final size:17
Alignment explanation
Indices: 2678318--2678352 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2678308 ATTATAAACA
*
2678318 TAAATATAATATATTAT
1 TAAATATAACATATTAT
2678335 TAAATAT-ACATATTAT
1 TAAATATAACATATTAT
2678351 TA
1 TA
2678353 GTGTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATATAACATATTAT
Found at i:2680687 original size:29 final size:29
Alignment explanation
Indices: 2680648--2680704 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
2680638 AATCATTATC
2680648 TTTAAATTATATAC-AATAAACTTTTAAAA
1 TTTAAATTATAT-CTAATAAACTTTTAAAA
*
2680677 TTTAATTTATATCTTAATAAACTTTTAA
1 TTTAAATTATATC-TAATAAACTTTTAA
2680705 CATACATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 11 0.44
30 13 0.52
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAAATTATATCTAATAAACTTTTAAAA
Found at i:2680803 original size:22 final size:22
Alignment explanation
Indices: 2680778--2680819 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2680768 TTTGATATAA
2680778 TAAAAATATAAAA-AATTTAATT
1 TAAAAA-ATAAAATAATTTAATT
2680800 TAAAAAATAAAATAATTTAA
1 TAAAAAATAAAATAATTTAA
2680820 AGGCCTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAAATAAAATAATTTAATT
Found at i:2681101 original size:17 final size:18
Alignment explanation
Indices: 2681059--2681103 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
2681049 AATATCATGG
2681059 TTTTAA-TTT-ATTTTAT
1 TTTTAATTTTGATTTTAT
**
2681075 TTTTTGTTTTGATTTTA-
1 TTTTAATTTTGATTTTAT
2681092 TTTTAATTTTGA
1 TTTTAATTTTGA
2681104 GTAGTTTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.17
17 13 0.57
18 6 0.26
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (18 bp):
TTTTAATTTTGATTTTAT
Found at i:2686007 original size:16 final size:15
Alignment explanation
Indices: 2685979--2686020 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
2685969 CAATAGATTC
*
2685979 AAATATCTAAATATAT
1 AAATATTTAAATA-AT
2685995 AGAA-ATTTAAATAAT
1 A-AATATTTAAATAAT
2686010 AAATATTTAAA
1 AAATATTTAAA
2686021 AATTAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 2 0.09
15 10 0.43
16 9 0.39
17 2 0.09
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
AAATATTTAAATAAT
Found at i:2686028 original size:21 final size:23
Alignment explanation
Indices: 2685986--2686030 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2685976 TTCAAATATC
*
2685986 TAAATATATAGAAATTTAAATAA
1 TAAATATATAGAAAATTAAATAA
*
2686009 TAAATATTTA-AAAATT-AATAA
1 TAAATATATAGAAAATTAAATAA
2686030 T
1 T
2686031 CGAATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 5 0.25
23 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAATATATAGAAAATTAAATAA
Found at i:2686100 original size:15 final size:15
Alignment explanation
Indices: 2686052--2686104 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
2686042 TGATTAATAA
**
2686052 TTATAATATTCGAAT
1 TTATAATATTTAAAT
2686067 TTA-AATATTATCAAAAT
1 TTATAATATT-T--AAAT
2686084 TTATAATATTTAAAT
1 TTATAATATTTAAAT
2686099 TTATAA
1 TTATAA
2686105 AAAATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 6 0.19
15 13 0.41
17 7 0.22
18 6 0.19
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (15 bp):
TTATAATATTTAAAT
Found at i:2686181 original size:4 final size:4
Alignment explanation
Indices: 2686172--2686196 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2686162 AGATGAGGAC
2686172 CTGG CTGG CTGG CTGG CTGG CTGG C
1 CTGG CTGG CTGG CTGG CTGG CTGG C
2686197 GGTACTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.48, T:0.24
Consensus pattern (4 bp):
CTGG
Found at i:2686471 original size:18 final size:18
Alignment explanation
Indices: 2686445--2686484 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
2686435 AGGTTTCATC
*
2686445 TTATATTTTATTTTTTCTAT
1 TTAT-TTTTATATTTT-TAT
2686465 TTATTTTTATATTTTTAT
1 TTATTTTTATATTTTTAT
2686483 TT
1 TT
2686485 TGAAGAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 10 0.53
20 4 0.21
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TTATTTTTATATTTTTAT
Found at i:2686481 original size:14 final size:14
Alignment explanation
Indices: 2686445--2686485 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
2686435 AGGTTTCATC
2686445 TTATA-TTTTATTT
1 TTATATTTTTATTT
* *
2686458 TT-TCTATTTATTT
1 TTATATTTTTATTT
2686471 TTATATTTTTATTT
1 TTATATTTTTATTT
2686485 T
1 T
2686486 GAAGAGATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
12 1 0.05
13 11 0.50
14 10 0.45
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (14 bp):
TTATATTTTTATTT
Found at i:2693793 original size:2 final size:2
Alignment explanation
Indices: 2693788--2693812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2693778 ATCTTAATAC
2693788 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2693813 AAAGATAATC
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2693902 original size:2 final size:2
Alignment explanation
Indices: 2693895--2693926 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2693885 TGGGTTTCTA
2693895 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
2693927 GTGTGTGTGT
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:2694329 original size:18 final size:18
Alignment explanation
Indices: 2694308--2694342 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2694298 ATAATAACGG
*
2694308 TATTAAATATATTATATT
1 TATTAAATATATGATATT
2694326 TATTAAATATATGATAT
1 TATTAAATATATGATAT
2694343 CATATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TATTAAATATATGATATT
Found at i:2694351 original size:20 final size:18
Alignment explanation
Indices: 2694308--2694348 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2694298 ATAATAACGG
* *
2694308 TATTAAATATATTATATT
1 TATTAAATATATGATATA
2694326 TATTAAATATATGATATCA
1 TATTAAATATATGATAT-A
2694345 TATT
1 TATT
2694349 TAATTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TATTAAATATATGATATA
Found at i:2694578 original size:2 final size:2
Alignment explanation
Indices: 2694571--2694598 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2694561 TTTGAGATAC
2694571 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
2694599 GGAAAACTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2698083 original size:21 final size:21
Alignment explanation
Indices: 2698045--2698089 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2698035 GAATGTGGTA
* * * *
2698045 TAAAATTAATTTTGATAATAT
1 TAAAAATAATTATAATAAAAT
2698066 TAAAAATAATTATAATAAAAT
1 TAAAAATAATTATAATAAAAT
2698087 TAA
1 TAA
2698090 TTAATAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAAAATAATTATAATAAAAT
Found at i:2704150 original size:17 final size:17
Alignment explanation
Indices: 2704110--2704144 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
2704100 AAAAATAAAA
2704110 ATTAAATATAT-TT-AT
1 ATTAAATATATATTCAT
2704125 ATTAAATATATATTCAT
1 ATTAAATATATATTCAT
2704142 ATT
1 ATT
2704145 CGATATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.61
16 2 0.11
17 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAAATATATATTCAT
Found at i:2705420 original size:2 final size:2
Alignment explanation
Indices: 2705413--2705444 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2705403 GTATTGTATC
2705413 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
2705445 TTAATGTTTG
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:2705943 original size:24 final size:25
Alignment explanation
Indices: 2705911--2705977 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 25
2705901 ATTTCAAATG
2705911 AAAAAAATTAATATTTA-TTT-TTTA
1 AAAAAAATTAA-ATTTATTTTATTTA
2705935 AAAAAAATTAAAATTAATATTTTATTTA
1 AAAAAAATT-AAATT--TATTTTATTTA
*
2705963 AAAAATATTAAATTT
1 AAAAAAATTAAATTT
2705978 TTTATCGCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 12 0.32
25 3 0.08
26 2 0.05
27 8 0.22
28 12 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AAAAAAATTAAATTTATTTTATTTA
Found at i:2705948 original size:30 final size:28
Alignment explanation
Indices: 2705914--2705974 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
2705904 TCAAATGAAA
*
2705914 AAAATTAATATTTATTTTTTAAAAAAAATT
1 AAAATTAATA-TT-TTATTTAAAAAAAATT
*
2705944 AAAATTAATATTTTATTTAAAAAATATT
1 AAAATTAATATTTTATTTAAAAAAAATT
2705972 AAA
1 AAA
2705975 TTTTTTATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 17 0.59
29 2 0.07
30 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAATTAATATTTTATTTAAAAAAAATT
Found at i:2706235 original size:28 final size:29
Alignment explanation
Indices: 2706195--2706269 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 29
2706185 TGTATTTAAT
* *
2706195 TTAATAGTATAAATAT-A-AAATTAATAAA
1 TTAAAAGTTTAAATATCATAAATTAA-AAA
* *
2706223 TTAAAAGTTTAAATCTCATTAATTAAAAA
1 TTAAAAGTTTAAATATCATAAATTAAAAA
*
2706252 TTAAAA-TTTAAAAATCAT
1 TTAAAAGTTTAAATATCAT
2706270 GTAAACATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 23 0.59
29 10 0.26
30 6 0.15
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (29 bp):
TTAAAAGTTTAAATATCATAAATTAAAAA
Found at i:2706663 original size:2 final size:2
Alignment explanation
Indices: 2706656--2706686 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2706646 TCACAAATAC
2706656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2706687 AAGATATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2706926 original size:25 final size:25
Alignment explanation
Indices: 2706892--2706948 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
2706882 ATAAAAAATT
*
2706892 AGCTAGATTTTCATACTCGATTTCA
1 AGCTCGATTTTCATACTCGATTTCA
* *
2706917 AGCTCGATTTTCATGCTCGATTTTA
1 AGCTCGATTTTCATACTCGATTTCA
*
2706942 AACTCGA
1 AGCTCGA
2706949 ATATTTTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (25 bp):
AGCTCGATTTTCATACTCGATTTCA
Found at i:2706928 original size:13 final size:13
Alignment explanation
Indices: 2706892--2706940 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
2706882 ATAAAAAATT
*
2706892 AGCTAGATTTTCA
1 AGCTCGATTTTCA
2706905 TA-CTCGA-TTTCA
1 -AGCTCGATTTTCA
2706917 AGCTCGATTTTCA
1 AGCTCGATTTTCA
*
2706930 TGCTCGATTTT
1 AGCTCGATTTT
2706941 AAACTCGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 1 0.03
12 10 0.32
13 19 0.61
14 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.43
Consensus pattern (13 bp):
AGCTCGATTTTCA
Found at i:2711783 original size:30 final size:30
Alignment explanation
Indices: 2711749--2711833 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 30
2711739 ATTTTTAATT
*
2711749 TTTAATTCATGTTTAAATATATTTTTTACA
1 TTTAATTTATGTTTAAATATATTTTTTACA
** **
2711779 TTTAATTTATGCAT-AA-ATATTTTTTATT
1 TTTAATTTATGTTTAAATATATTTTTTACA
* *
2711807 TTTTATTTATATTTAAATA-ATTTTTTA
1 TTTAATTTATGTTTAAATATATTTTTTA
2711834 ATATAAATTA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
28 20 0.45
29 12 0.27
30 12 0.27
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTAATTTATGTTTAAATATATTTTTTACA
Found at i:2712548 original size:22 final size:22
Alignment explanation
Indices: 2712492--2712535 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 22
2712482 ATAAATATTA
2712492 ATAATAAAA-AA-T-TAAAAAT
1 ATAATAAAATAATTATAAAAAT
*
2712511 ATAATAAAATAATTATAAAATT
1 ATAATAAAATAATTATAAAAAT
2712533 ATA
1 ATA
2712536 TTATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 2 0.10
21 1 0.05
22 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATAATAAAATAATTATAAAAAT
Found at i:2712807 original size:15 final size:15
Alignment explanation
Indices: 2712787--2712863 Score: 52
Period size: 16 Copynumber: 4.9 Consensus size: 15
2712777 ATATATTAAT
2712787 AATTTTTATTATATA
1 AATTTTTATTATATA
2712802 AATTTTAATATTATATTA
1 AATTTT--TATTATA-TA
*
2712820 TAATATATTATTATAT-
1 -AAT-TTTTATTATATA
*
2712836 --TTTATATTATATA
1 AATTTTTATTATATA
*
2712849 ATATTTTTATAATAT
1 A-ATTTTTATTATAT
2712864 TCTAAAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
12 9 0.19
13 1 0.02
15 6 0.12
16 10 0.21
17 8 0.17
18 9 0.19
19 3 0.06
20 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTTTTATTATATA
Found at i:2712819 original size:5 final size:5
Alignment explanation
Indices: 2712809--2712899 Score: 59
Period size: 5 Copynumber: 18.8 Consensus size: 5
2712799 ATAAATTTTA
* * *
2712809 ATATT ATATT ATAAT ATATT AT-TAT ATTTT ATATT ATATA ATATT -T-TT
1 ATATT ATATT ATATT ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT
* * *
2712857 ATAAT AT-TCT AAAATT ATTTT ATATT ATA-T A-ATT ATATT ATAT
1 ATATT ATAT-T -ATATT ATATT ATATT ATATT ATATT ATATT ATAT
2712900 CTAAAAATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
3 3 0.05
4 7 0.11
5 52 0.79
6 3 0.05
7 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:2712908 original size:18 final size:18
Alignment explanation
Indices: 2712855--2712910 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
2712845 TATAATATTT
*
2712855 TTATAATAT-TCT-AAAA
1 TTATATTATATCTAAAAA
* *
2712871 TTATTTTATAT-TATATAA
1 TTATATTATATCTA-AAAA
2712889 TTATATTATATCTAAAAA
1 TTATATTATATCTAAAAA
2712907 TTAT
1 TTAT
2712911 CAGCGGTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 8 0.26
17 1 0.03
18 20 0.65
19 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATATTATATCTAAAAA
Found at i:2714145 original size:18 final size:18
Alignment explanation
Indices: 2714109--2714146 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2714099 CATAAATATA
*
2714109 ATAATTATTAAATGTATT
1 ATAATTATTAAATCTATT
2714127 ATAATT-TTAAATCTAATT
1 ATAATTATTAAATCT-ATT
2714145 AT
1 AT
2714147 GATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATAATTATTAAATCTATT
Found at i:2715806 original size:20 final size:20
Alignment explanation
Indices: 2715783--2715847 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
2715773 TTAACTATTA
2715783 AAATATAATATTAAAAAATT
1 AAATATAATATTAAAAAATT
*
2715803 AAAT-TAATATTTAAAATATTT
1 AAATATAATA-TTAAAA-AATT
2715824 AAA-ATAAT-TTAATAAAATAT
1 AAATATAATATTAA-AAAAT-T
2715844 AAAT
1 AAAT
2715848 TTAAACTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 11 0.30
20 16 0.43
21 10 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATAATATTAAAAAATT
Found at i:2715808 original size:26 final size:28
Alignment explanation
Indices: 2715779--2715852 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 28
2715769 ATTTTTAACT
2715779 ATTAAAATATAATA-TTAAAA-AATTAA
1 ATTAAAATATAATATTTAAAATAATTAA
* * *
2715805 ATTAATATTTAAAATATTTAAAATAATTTA
1 ATTAA-A-ATATAATATTTAAAATAATTAA
2715835 A-TAAAATATAA-ATTTAAA
1 ATTAAAATATAATATTTAAA
2715853 CTTAGATCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
26 12 0.31
27 5 0.13
28 7 0.18
29 9 0.23
30 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTAAAATATAATATTTAAAATAATTAA
Found at i:2715891 original size:23 final size:23
Alignment explanation
Indices: 2715859--2715925 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
2715849 TAAACTTAGA
*
2715859 TCCATTTAAACTTAAACTAAAAG
1 TCCATCTAAACTTAAACTAAAAG
* **
2715882 TCCATCTAAAATTAAA-TTCAAG
1 TCCATCTAAACTTAAACTAAAAG
2715904 -CCTATCTAAACTTAAACTAAAA
1 TCC-ATCTAAACTTAAACTAAAA
2715926 TTTCAATTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.06
22 16 0.46
23 17 0.49
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30
Consensus pattern (23 bp):
TCCATCTAAACTTAAACTAAAAG
Found at i:2716834 original size:2 final size:2
Alignment explanation
Indices: 2716827--2716877 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2716817 TGAACTAAAC
2716827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2716869 TA TA TA TA T
1 TA TA TA TA T
2716878 GTTTAAGGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2718354 original size:2 final size:2
Alignment explanation
Indices: 2718347--2718386 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2718337 CTAAAAGAGC
2718347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2718387 GTAAAAGGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2721825 original size:15 final size:16
Alignment explanation
Indices: 2721793--2721827 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2721783 TAAAAAATTT
2721793 TAAAAATAAATATATA
1 TAAAAATAAATATATA
*
2721809 TAAAAATAAA-ATGTA
1 TAAAAATAAATATATA
2721824 TAAA
1 TAAA
2721828 TTTATACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAATAAATATATA
Found at i:2724422 original size:14 final size:13
Alignment explanation
Indices: 2724403--2724452 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
2724393 ATTAAAATCA
2724403 ATAATAAAATATGT
1 ATAATAAAATAT-T
*
2724417 ATAATAAAAAATT
1 ATAATAAAATATT
2724430 AT--TAATAATATT
1 ATAATAA-AATATT
*
2724442 AAAATAAAATA
1 ATAATAAAATA
2724453 GGTATAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
11 3 0.10
12 6 0.20
13 7 0.23
14 14 0.47
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
ATAATAAAATATT
Found at i:2724422 original size:17 final size:17
Alignment explanation
Indices: 2724402--2724447 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
2724392 AATTAAAATC
2724402 AATAATAAAATATGT-AT
1 AATAATAAAATAT-TAAT
2724419 AATAA-AAAATTATTAAT
1 AATAATAAAA-TATTAAT
*
2724436 AATATTAAAATA
1 AATAATAAAATA
2724448 AAATAGGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 5 0.20
17 16 0.64
18 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATAATAAAATATTAAT
Found at i:2724430 original size:39 final size:39
Alignment explanation
Indices: 2724387--2724477 Score: 91
Period size: 39 Copynumber: 2.4 Consensus size: 39
2724377 TTACCATAAT
*
2724387 AATTAAATTAAAATCAATAATAAAATATGTAT-AATAAAA
1 AATTAAATTAAAATCAA-AATAAAATAGGTATAAATAAAA
* * *
2724426 AATTATTAA-TAATATTAAAATAAAATAGGTATAAATAATA
1 AATTA--AATTAAAATCAAAATAAAATAGGTATAAATAAAA
2724466 AATT--ATTAAAAT
1 AATTAAATTAAAAT
2724478 TATTAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
36 1 0.02
37 5 0.12
39 18 0.42
40 17 0.40
41 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (39 bp):
AATTAAATTAAAATCAAAATAAAATAGGTATAAATAAAA
Found at i:2724474 original size:40 final size:39
Alignment explanation
Indices: 2724405--2724486 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 39
2724395 TAAAATCAAT
*
2724405 AATAAAATATGTATAATAAAAAATTATTAATAA-TATTAA
1 AATAAAATAGGTATAATAAAAAATTATTAA-AATTATTAA
*
2724444 AATAAAATAGGTATAAATAATAAATTATTAAAATTATTAA
1 AATAAAATAGGTAT-AATAAAAAATTATTAAAATTATTAA
2724484 AAT
1 AAT
2724487 TATATTTATG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
39 15 0.38
40 24 0.62
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (39 bp):
AATAAAATAGGTATAATAAAAAATTATTAAAATTATTAA
Found at i:2724487 original size:9 final size:9
Alignment explanation
Indices: 2724465--2724489 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2724455 TATAAATAAT
2724465 AAATTATTA
1 AAATTATTA
2724474 AAATTATTA
1 AAATTATTA
2724483 AAATTAT
1 AAATTAT
2724490 ATTTATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAATTATTA
Found at i:2728575 original size:18 final size:19
Alignment explanation
Indices: 2728547--2728586 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2728537 TTTAAAATTT
2728547 TTATAAAATTAAATT-AATA
1 TTATAAAATT-AATTAAATA
2728566 TTAT-AAATTAATTAAATA
1 TTATAAAATTAATTAAATA
2728584 TTA
1 TTA
2728587 ATTTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTATAAAATTAATTAAATA
Found at i:2729376 original size:91 final size:90
Alignment explanation
Indices: 2729281--2729469 Score: 194
Period size: 91 Copynumber: 2.1 Consensus size: 90
2729271 TTTTTAAAGT
* *
2729281 TTATTTTATATGTA-AAT-TATATTTTATTATTTT-TAATGTT-AATA-AAAATTTAAAAATAT-
1 TTATTTTATATGTATAATATAAATTATA-TATTTTAT-AT-TTGAATATAAAA-TTAAAAAT-TC
2729340 AAAGATAAAAATAATTATAATATAAATTTTAA-
61 AAA-AT-AAAATAATT-TAATATAAATTTTAAC
* * * *
2729372 TTATTTTTTATTTATCATATAAATTATATATTTTATATTTGAATATAAAATTAAAACTTCAAAAT
1 TTATTTTATATGTATAATATAAATTATATATTTTATATTTGAATATAAAATTAAAAATTCAAAAT
2729437 AAAATAATTTAATATAAATTTTAAC
66 AAAATAATTTAATATAAATTTTAAC
2729462 TTTATTTT
1 -TTATTTT
2729470 TTTATTGTCA
Statistics
Matches: 84, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
89 15 0.18
90 9 0.11
91 24 0.29
92 24 0.29
93 12 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (90 bp):
TTATTTTATATGTATAATATAAATTATATATTTTATATTTGAATATAAAATTAAAAATTCAAAAT
AAAATAATTTAATATAAATTTTAAC
Found at i:2729411 original size:27 final size:29
Alignment explanation
Indices: 2729354--2729420 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
2729344 ATAAAAATAA
* *
2729354 TTATAATATAAATTTTAATTATTTTTTAT
1 TTATAATATAAATTATAATTATTTTATAT
*
2729383 TTATCATATAAATTAT-A-TATTTTATAT
1 TTATAATATAAATTATAATTATTTTATAT
*
2729410 TT-GAATATAAA
1 TTATAATATAAA
2729421 ATTAAAACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 7 0.21
27 11 0.33
28 1 0.03
29 14 0.42
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (29 bp):
TTATAATATAAATTATAATTATTTTATAT
Found at i:2730392 original size:18 final size:18
Alignment explanation
Indices: 2730344--2730394 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2730334 ATACAAAATT
*
2730344 AATTATAATATTTTAAAAA
1 AATTAT-ATATTATAAAAA
*
2730363 AATTATTTTATTATAAAAA
1 AATTA-TATATTATAAAAA
*
2730382 ATTTATATATTAT
1 AATTATATATTAT
2730395 TTATAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.26
19 19 0.70
20 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTATATATTATAAAAA
Found at i:2730396 original size:11 final size:11
Alignment explanation
Indices: 2730382--2730418 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2730372 ATTATAAAAA
2730382 ATTTATATATT
1 ATTTATATATT
2730393 ATTTATA-ATT
1 ATTTATATATT
*
2730403 -TTAATATATT
1 ATTTATATATT
2730413 ATTTAT
1 ATTTAT
2730419 GATCAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.23
10 6 0.27
11 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTATATATT
Found at i:2730552 original size:27 final size:26
Alignment explanation
Indices: 2730522--2730572 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
2730512 AATTATTTTT
*
2730522 ATAAATATATTTTAAAATTAAAATTAA
1 ATAAAAATATTTTAAAA-TAAAATTAA
*
2730549 ATAAAAATATTTTATAATAAAATT
1 ATAAAAATATTTTAAAATAAAATT
2730573 TATTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAAAAATATTTTAAAATAAAATTAA
Found at i:2730567 original size:16 final size:17
Alignment explanation
Indices: 2730548--2730580 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2730538 ATTAAAATTA
2730548 AATAAAA-ATATTTTAT
1 AATAAAATATATTTTAT
*
2730564 AATAAAATTTATTTTAT
1 AATAAAATATATTTTAT
2730581 TTTAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAAAATATATTTTAT
Found at i:2730842 original size:31 final size:28
Alignment explanation
Indices: 2730788--2730865 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 28
2730778 TAAAGTTTTA
* *
2730788 TAAAAAATACACTTATTTTTTTAACATT
1 TAAAAAATACACTTACTTTTTTAAAATT
2730816 TAAAAAATAACCACTTACCTTTTTTAAAATT
1 TAAAAAAT-A-CACTTA-CTTTTTTAAAATT
* *
2730847 TGCTAAAAATATACTTACT
1 T--AAAAAATACACTTACT
2730866 CCTTAAGCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.20
29 1 0.02
30 8 0.20
31 17 0.41
32 1 0.02
33 6 0.15
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (28 bp):
TAAAAAATACACTTACTTTTTTAAAATT
Found at i:2731356 original size:18 final size:17
Alignment explanation
Indices: 2731318--2731356 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
2731308 AAAAATATTA
2731318 TTTTTTATTTTAATCAAT
1 TTTTTTATTTTAA-CAAT
2731336 TTTTTTATTTTTAA-AAT
1 TTTTTTA-TTTTAACAAT
2731353 TTTT
1 TTTT
2731357 AAAATGATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 7 0.35
19 6 0.30
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTTATTTTAACAAT
Found at i:2731414 original size:25 final size:25
Alignment explanation
Indices: 2731386--2731444 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
2731376 TATTTTAAAA
2731386 TAAAAATAATATA-ATATATT-AATAT
1 TAAAAATAATATATATA-ATTAAAT-T
**
2731411 TAAAGTTAATATATATAATTAAATT
1 TAAAAATAATATATATAATTAAATT
2731436 TAAAAATAA
1 TAAAAATAA
2731445 GTTTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
TAAAAATAATATATATAATTAAATT
Found at i:2732321 original size:17 final size:19
Alignment explanation
Indices: 2732301--2732346 Score: 69
Period size: 17 Copynumber: 2.5 Consensus size: 19
2732291 AATTTTAAAT
2732301 ATAAAAAATTAA-TTTT-G
1 ATAAAAAATTAAGTTTTAG
*
2732318 ATAAAAAAATAAGTTTTAG
1 ATAAAAAATTAAGTTTTAG
2732337 ATAAAAAATT
1 ATAAAAAATT
2732347 TAGATCAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.44
18 4 0.16
19 10 0.40
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (19 bp):
ATAAAAAATTAAGTTTTAG
Found at i:2732345 original size:18 final size:16
Alignment explanation
Indices: 2732301--2732345 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
2732291 AATTTTAAAT
2732301 ATAAAAAATTAATTTTG
1 ATAAAAAA-TAATTTTG
2732318 ATAAAAAAATAAGTTTTAG
1 AT-AAAAAATAA-TTTT-G
2732337 ATAAAAAAT
1 ATAAAAAAT
2732346 TTAGATCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.20
18 17 0.68
19 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAAAAAATAATTTTG
Found at i:2733034 original size:7 final size:8
Alignment explanation
Indices: 2733003--2733073 Score: 51
Period size: 8 Copynumber: 9.0 Consensus size: 8
2732993 TTTAAATTAA
2733003 ATAATTTT
1 ATAATTTT
2733011 ATTAATTTT
1 A-TAATTTT
*
2733020 ATATTTTT
1 ATAATTTT
2733028 A-AATTTTT
1 ATAA-TTTT
*
2733036 ATTATTTT
1 ATAATTTT
*
2733044 A-AA-TAT
1 ATAATTTT
2733050 ATAATTTT
1 ATAATTTT
*
2733058 TTAATATTT
1 ATAAT-TTT
2733067 -TAATTTT
1 ATAATTTT
2733074 TCACATTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
6 3 0.06
7 7 0.14
8 28 0.56
9 12 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
ATAATTTT
Found at i:2733058 original size:24 final size:24
Alignment explanation
Indices: 2733007--2733069 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
2732997 AATTAAATAA
* * *
2733007 TTTTATTAATTTTATATTTTTAAAT
1 TTTTATT-ATTTTAAATATATAAAT
*
2733032 TTTTATTATTTTAAATATATAATT
1 TTTTATTATTTTAAATATATAAAT
*
2733056 TTTTAATATTTTAA
1 TTTTATTATTTTAA
2733070 TTTTTCACAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 26 0.79
25 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTATTATTTTAAATATATAAAT
Found at i:2733059 original size:16 final size:16
Alignment explanation
Indices: 2732991--2733074 Score: 50
Period size: 16 Copynumber: 5.2 Consensus size: 16
2732981 AAAAAATTGA
*
2732991 TTTTTAAATTAAATAAT
1 TTTTTAAA-TATATAAT
* *
2733008 TTTATTAATTTTAT-A-
1 TTT-TTAAATATATAAT
* *
2733023 TTTTTAAAT-TTTTAT
1 TTTTTAAATATATAAT
2733038 TATTTTAAATATATAAT
1 T-TTTTAAATATATAAT
*
2733055 TTTTT-AATATTTTAAT
1 TTTTTAAATA-TATAAT
2733071 TTTT
1 TTTT
2733075 CACATTAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
13 2 0.04
14 6 0.11
15 8 0.15
16 22 0.42
17 11 0.21
18 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTAAATATATAAT
Found at i:2733435 original size:2 final size:2
Alignment explanation
Indices: 2733428--2733459 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2733418 TCTGATCCTC
*
2733428 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2733460 ATGGTACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2733990 original size:21 final size:21
Alignment explanation
Indices: 2733966--2734006 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2733956 TACTTAAAAA
*
2733966 ATTAT-ATTTATTACTAATATT
1 ATTATAATTAATTA-TAATATT
2733987 ATTATAATTAATTATAATAT
1 ATTATAATTAATTATAATAT
2734007 AATAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATAATTAATTATAATATT
Found at i:2739626 original size:17 final size:18
Alignment explanation
Indices: 2739604--2739637 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2739594 TCATATATAA
*
2739604 TTTAAAA-AGAAAAATAT
1 TTTAAAATAAAAAAATAT
2739621 TTTAAAATAAAAAAATA
1 TTTAAAATAAAAAAATA
2739638 CATAATTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TTTAAAATAAAAAAATAT
Found at i:2739886 original size:21 final size:20
Alignment explanation
Indices: 2739825--2739888 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
2739815 TAAAAAGTTA
2739825 TAAAATAATATGTA-TTTTT
1 TAAAATAATATGTATTTTTT
* * **
2739844 TAAGA-AATA-GTAATATAAT
1 TAAAATAATATGT-ATTTTTT
2739863 TAAAATAATATGTATTTTTTT
1 TAAAATAATATGTA-TTTTTT
2739884 TAAAA
1 TAAAA
2739889 AAAACCCATA
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 2 0.06
18 5 0.16
19 10 0.31
20 5 0.16
21 10 0.31
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (20 bp):
TAAAATAATATGTATTTTTT
Found at i:2741882 original size:15 final size:15
Alignment explanation
Indices: 2741862--2741891 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2741852 AATGATTCAG
2741862 GAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAA
2741877 GAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAA
2741892 CTGTGTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAAAAAAA
Found at i:2741883 original size:13 final size:13
Alignment explanation
Indices: 2741865--2741889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2741855 GATTCAGGAA
2741865 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
2741878 AAAAAAAAAAAA
1 AAAAAAAAAAAA
2741890 AACTGTGTAC
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:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:2741883 original size:14 final size:14
Alignment explanation
Indices: 2741864--2741890 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2741854 TGATTCAGGA
2741864 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
2741878 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
2741891 ACTGTGTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:2753844 original size:22 final size:22
Alignment explanation
Indices: 2753819--2753870 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
2753809 ATTATTTTAA
*
2753819 ATAATAATAT-AAATTAACTTTG
1 ATAATAATATAAAAATAA-TTTG
*
2753841 ATAA-AAAATAAAAATAATTTG
1 ATAATAATATAAAAATAATTTG
2753862 AGTAATAAT
1 A-TAATAAT
2753871 TTAACTCGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 9 0.38
22 13 0.54
23 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (22 bp):
ATAATAATATAAAAATAATTTG
Found at i:2753960 original size:21 final size:21
Alignment explanation
Indices: 2753936--2753975 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2753926 ATCTTTATGT
*
2753936 TTGAC-TTAATATTATTTAATC
1 TTGACATTAAT-TTAATTAATC
2753957 TTGACATTAATTTAATTAA
1 TTGACATTAATTTAATTAA
2753976 AATTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
TTGACATTAATTTAATTAATC
Found at i:2754046 original size:22 final size:22
Alignment explanation
Indices: 2753994--2754050 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
2753984 TATATAATAA
* *
2753994 AAATAAAATATTTTTAAAATAT
1 AAATAATATATTTTTAAAAAAT
** * *
2754016 ATTTTATATTTTTTTAAAAAAT
1 AAATAATATATTTTTAAAAAAT
2754038 AAATAATATATTT
1 AAATAATATATTT
2754051 AATAATTTTT
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATAATATATTTTTAAAAAAT
Found at i:2754238 original size:20 final size:20
Alignment explanation
Indices: 2754210--2754247 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2754200 TTAATATTTA
2754210 TATAATTAAAATATTATAAT
1 TATAATTAAAATATTATAAT
*
2754230 TATATTTAAAATATTATA
1 TATAATTAAAATATTATA
2754248 TAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATAATTAAAATATTATAAT
Found at i:2754271 original size:23 final size:22
Alignment explanation
Indices: 2754207--2754266 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
2754197 AATTTAATAT
2754207 TTATATAATTAAAATA-T-TATAA
1 TTATAT-A-TAAAATATTATATAA
*
2754229 TTATATTTAAAATATTATATAA
1 TTATATATAAAATATTATATAA
2754251 TT-TATATAAAAT-TTAT
1 TTATATATAAAATATTAT
2754267 TATATTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 11 0.32
21 10 0.29
22 13 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATATATAAAATATTATATAA
Found at i:2754308 original size:21 final size:20
Alignment explanation
Indices: 2754261--2754308 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
2754251 TTTATATAAA
*
2754261 ATTTATTATATTAATAATTC
1 ATTTATAATATTAATAATTC
*
2754281 ATATTATAATATTAATATATTT
1 AT-TTATAATATTAATA-ATTC
2754303 ATTTAT
1 ATTTAT
2754309 TTTTACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTATAATATTAATAATTC
Found at i:2754947 original size:17 final size:17
Alignment explanation
Indices: 2754912--2754945 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2754902 AATAGTAAAG
2754912 TAATTAAAATACACTTT
1 TAATTAAAATACACTTT
*
2754929 TAATTATAATA-ACTTT
1 TAATTAAAATACACTTT
2754945 T
1 T
2754946 TACATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTAAAATACACTTT
Found at i:2761557 original size:22 final size:21
Alignment explanation
Indices: 2761532--2761573 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2761522 AAAATTAAAA
2761532 ATAT-TTTTA-AATTAATATTT
1 ATATATTTTATAATTAA-ATTT
2761552 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
2761573 A
1 A
2761574 AATAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 10 0.50
22 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:2763119 original size:22 final size:22
Alignment explanation
Indices: 2763091--2763150 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
2763081 TTTAAATTTA
** *
2763091 TTAAATATTATTATTTTATATT
1 TTAAATATTAAAATTTAATATT
2763113 TTAAATATTAAAATTTAATATT
1 TTAAATATTAAAATTTAATATT
2763135 TAATAAATATTAAAAT
1 T--TAAATATTAAAAT
2763151 AATTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 20 0.61
24 13 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATATTAAAATTTAATATT
Found at i:2763163 original size:26 final size:24
Alignment explanation
Indices: 2763114--2763170 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 24
2763104 TTTTATATTT
*
2763114 TAAATATTAAAATTTAATATTTAA
1 TAAATATTAAAATTTAATAATTAA
2763138 TAAATATTAAAATAATTAATAATTAA
1 TAAATATTAAAAT--TTAATAATTAA
2763164 TAAATAT
1 TAAATAT
2763171 ATTTAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 13 0.43
26 17 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAATATTAAAATTTAATAATTAA
Found at i:2763167 original size:19 final size:19
Alignment explanation
Indices: 2763129--2763177 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2763119 ATTAAAATTT
*
2763129 AATATTTAATAAATATTAA
1 AATATTTAATAAATAATAA
* *
2763148 AATAATTAATAATTAATAA
1 AATATTTAATAAATAATAA
2763167 ATATATTTAAT
1 A-ATATTTAAT
2763178 TTAATAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTTAATAAATAATAA
Found at i:2763526 original size:29 final size:30
Alignment explanation
Indices: 2763494--2763559 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
2763484 CTTTTATTAT
2763494 TTTTATTAT-AATTAT-ATTTAAATAATATA
1 TTTTATTATAAATTATAATTT-AATAATATA
* *
2763523 TTTTA-TATAAATTTTAATTTAATTATATA
1 TTTTATTATAAATTATAATTTAATAATATA
2763552 TTTATATT
1 TTT-TATT
2763560 CTCTTCGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 3 0.10
29 21 0.68
30 6 0.19
31 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTTATTATAAATTATAATTTAATAATATA
Found at i:2767116 original size:21 final size:22
Alignment explanation
Indices: 2767086--2767127 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2767076 ATAATATAAA
2767086 ATTTTATTAT-ATTAATATTTAT
1 ATTTTATTATAATTAA-ATTTAT
2767108 ATTTT-TTATAATTAAATTTA
1 ATTTTATTATAATTAAATTTA
2767128 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTATTATAATTAAATTTAT
Done.