Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_pilon, whole genome shotgun sequence
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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 31
Found at i:1394840 original size:42 final size:42
Alignment explanation
Indices: 1394786--1394901 Score: 196
Period size: 42 Copynumber: 2.8 Consensus size: 42
1394776 ATTACATTCT
* * *
1394786 GGAAAACCAATTACGTTAAACAAACATGGGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
1394828 GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
*
1394870 GAAAAACGAATTACGTGAAACAAACACGGGAA
1 GGAAAACGAATTACGTGAAACAAACACGGGAA
1394902 TTCGAGGAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (42 bp):
GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
Found at i:1396117 original size:17 final size:17
Alignment explanation
Indices: 1396097--1396144 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1396087 GTTTTTTTCT
1396097 TTATTTTATTTTTAATA
1 TTATTTTATTTTTAATA
*
1396114 TTATTTCT-TTTTTCATA
1 TTATTT-TATTTTTAATA
*
1396131 TTAGATTTATTTTT
1 TTA-TTTTATTTTT
1396145 TAGGTTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTTATTTTTAATA
Found at i:1397510 original size:20 final size:20
Alignment explanation
Indices: 1397473--1397511 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1397463 TCCATACTAA
* * *
1397473 TTTGTTTTTTTTCTTTTGCT
1 TTTGTTTCTTATCATTTGCT
1397493 TTTGTTTCTTATCATTTGC
1 TTTGTTTCTTATCATTTGC
1397512 ATCATTACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.13, G:0.10, T:0.72
Consensus pattern (20 bp):
TTTGTTTCTTATCATTTGCT
Found at i:1398525 original size:65 final size:64
Alignment explanation
Indices: 1398395--1398536 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 64
1398385 AAATAAATTG
* *
1398395 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATTGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCGATGCACTCAGGATTTTATG-A
* * * *
1398460 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGC-CTTCTGGCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCATCGATGCAC-TCAGGAT-TTTAT
1398522 GA
63 GA
1398524 AACATCGAATGCA
1 AACATCGAATGCA
1398537 CTGTATCGGT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
64 15 0.22
65 48 0.71
66 5 0.07
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCGATGCACTCAGGATTTTATGA
Found at i:1404226 original size:20 final size:20
Alignment explanation
Indices: 1404201--1404273 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
1404191 TGCTTAATGT
1404201 ATCGATACACCTAACAGTGC
1 ATCGATACACCTAACAGTGC
*
1404221 ATCGATACACCTAACAGTAC
1 ATCGATACACCTAACAGTGC
* *
1404241 ATCGATGCATCCTTGAA-TGTGC
1 ATCGATACA-CC-T-AACAGTGC
1404263 ATCGATACACC
1 ATCGATACACC
1404274 ATGAAGGTGC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 27 0.60
21 4 0.09
22 12 0.27
23 2 0.04
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (20 bp):
ATCGATACACCTAACAGTGC
Found at i:1404264 original size:42 final size:44
Alignment explanation
Indices: 1404217--1404312 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
1404207 ACACCTAACA
* *
1404217 GTGCATCGATACACC-T-AACAGTACATCGATGCA-TCCTTGAAT
1 GTGCATCGATACACCATGAA-AGTACACCGATGCACGCCTTGAAT
* *
1404259 GTGCATCGATACACCATGAAGGTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATACACCATGAAAGTACACCGATGCACGCCTTGAAT
1404303 GTGCATCGAT
1 GTGCATCGAT
1404313 GCACAAGGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 15 0.32
43 12 0.26
44 20 0.43
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (44 bp):
GTGCATCGATACACCATGAAAGTACACCGATGCACGCCTTGAAT
Found at i:1404306 original size:23 final size:23
Alignment explanation
Indices: 1404240--1404317 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
1404230 CCTAACAGTA
*
1404240 CATCGATGCA-TCCTTGAATGTG
1 CATCGATGCACACCTTGAATGTG
* *
1404262 CATCGAT--ACACCATGAAGGTG
1 CATCGATGCACACCTTGAATGTG
* *
1404283 CACCGATGCACGCCTTGAATGTG
1 CATCGATGCACACCTTGAATGTG
1404306 CATCGATGCACA
1 CATCGATGCACA
1404318 AGGCCATGCA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.34
22 7 0.16
23 21 0.48
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
CATCGATGCACACCTTGAATGTG
Found at i:1404333 original size:43 final size:42
Alignment explanation
Indices: 1404240--1404335 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 42
1404230 CCTAACAGTA
* * *
1404240 CATCGATGCATCCTTGAATGTGCATCGATACACCATGAAGGTG
1 CATCGATGCAGCCTTGAATGTGCATCGATACACAAGGAA-GTG
* * *
1404283 CACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGCCA-TG
1 CATCGATGCA-GCCTTGAATGTGCATCGATACACAAGG-AAGTG
1404326 CATCGATGCA
1 CATCGATGCA
1404336 TCCGTCGGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
43 20 0.45
44 23 0.52
45 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (42 bp):
CATCGATGCAGCCTTGAATGTGCATCGATACACAAGGAAGTG
Found at i:1405887 original size:21 final size:21
Alignment explanation
Indices: 1405845--1405888 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1405835 ACTCCGGGAG
* *
1405845 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
1405866 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
1405887 CT
1 CT
1405889 CCGGCACCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:1407014 original size:65 final size:63
Alignment explanation
Indices: 1406895--1407104 Score: 210
Period size: 65 Copynumber: 3.3 Consensus size: 63
1406885 TTTATCAAAG
* * * **
1406895 TGATGCACCGATGCACCAATTCATGCATCGATGCAC-CATGAAATAAATTG-AACATTGAATGCA
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-G-GATATTTTGAAACATTGAATGCA
1406958 TT
62 TT
* *
1406960 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATTGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATTGAATGCAT
1407024 T
63 T
* * * * * *
1407025 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATACACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATTGAATGCATT
1407089 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1407105 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 46 0.37
65 66 0.54
66 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATTGAATGCATT
Found at i:1407284 original size:16 final size:16
Alignment explanation
Indices: 1407263--1407293 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1407253 CCACTAAGCA
1407263 TCCCCAACGTTCAGAG
1 TCCCCAACGTTCAGAG
1407279 TCCCCAACGTTCAGA
1 TCCCCAACGTTCAGA
1407294 ATCATTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.19
Consensus pattern (16 bp):
TCCCCAACGTTCAGAG
Found at i:1410933 original size:244 final size:244
Alignment explanation
Indices: 1410477--1410935 Score: 532
Period size: 244 Copynumber: 1.9 Consensus size: 244
1410467 AGTAAAACTC
** * * * * * *
1410477 AACTCAACGGCGAGGAGTTATTTTCAAATCAATGTCTTCAAGTTAAATTGTAGCTTCACGACGAA
1 AACTCAACAACGAGGAGCTATTTTCAAACCAAGGTCTTCAAGTCAAATTGCAACTTCACGACGAA
* ** * * * *
1410542 GGATATTAGACTAGAAAAATACCCAAAATCAGTTGTGATTTAGCTTAACTTAACAACGATGAGCT
66 GGATATTAGACTAGAAAAAGACCCAAAATCAACTGCGATTTAGCTTAACTCAACAACAAGGAGCT
* * * * * *
1410607 ACATCCCAGTCCATATTTTGAGCTAGATTTCTACATCATGATGAAGAATATCATGCTCAAGTCAT
131 ACATCCCAGTCCAAATTTCGAGCTAGATTTCAACATCACGACGAAGAATATCATGATCAAGTCAT
*
1410672 TCGAGATCGACTCAACTTCATGGTGAATGATTAATCCACAATTTAGCTT
196 TCGAGATCAACTCAACTTCATGGTGAATGATTAATCCACAATTTAGCTT
*
1410721 AACTCAACAACGAGGAGCTATTTTTC-AACCAAGGTCTTCAAGTCAAATAT-CAACTTCACGACT
1 AACTCAACAACGAGGAGCTA-TTTTCAAACCAAGGTCTTCAAGTCAAAT-TGCAACTTCACGACG
* * * *
1410784 AAGGATATTATACTA-AAAGAAGACCCAAAATCAACTGCGGTTTAGCTTAACTCAATAATAAGGA
64 AAGGATATTAGACTAGAAA-AAGACCCAAAATCAACTGCGATTTAGCTTAACTCAACAACAAGGA
* ** * *
1410848 GTTATTTCCCAGTCCAAATTTCGAGCTAGATTTCAACTTCACGACGAATG-ATATCATGATTAAG
128 GCTACATCCCAGTCCAAATTTCGAGCTAGATTTCAACATCACGACGAA-GAATATCATGATCAAG
* *
1410912 TCTTTC-ACGATCAATTCAACTTCA
192 TCATTCGA-GATCAACTCAACTTCA
1410936 CGACGAATGA
Statistics
Matches: 176, Mismatches: 34, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
243 4 0.02
244 165 0.94
245 7 0.04
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (244 bp):
AACTCAACAACGAGGAGCTATTTTCAAACCAAGGTCTTCAAGTCAAATTGCAACTTCACGACGAA
GGATATTAGACTAGAAAAAGACCCAAAATCAACTGCGATTTAGCTTAACTCAACAACAAGGAGCT
ACATCCCAGTCCAAATTTCGAGCTAGATTTCAACATCACGACGAAGAATATCATGATCAAGTCAT
TCGAGATCAACTCAACTTCATGGTGAATGATTAATCCACAATTTAGCTT
Found at i:1410948 original size:47 final size:47
Alignment explanation
Indices: 1410879--1410992 Score: 210
Period size: 47 Copynumber: 2.4 Consensus size: 47
1410869 CGAGCTAGAT
*
1410879 TTCAACTTCACGACGAATGATATCATGATTAAGTCTTTCACGATCAA
1 TTCAACTTCACGACGAATGATATCATGATTAAGTCTTCCACGATCAA
1410926 TTCAACTTCACGACGAATGATATCATGATTAAGTCTTCCACGATCAA
1 TTCAACTTCACGACGAATGATATCATGATTAAGTCTTCCACGATCAA
*
1410973 TTCAACTTCACGATGAATGA
1 TTCAACTTCACGACGAATGA
1410993 GTCATCCATA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (47 bp):
TTCAACTTCACGACGAATGATATCATGATTAAGTCTTCCACGATCAA
Found at i:1411164 original size:133 final size:133
Alignment explanation
Indices: 1410926--1411300 Score: 482
Period size: 133 Copynumber: 2.8 Consensus size: 133
1410916 TCACGATCAA
* * * *
1410926 TTCAACTTCACGACGAATGATATCATGATTAAGTCTTCCACGATCAATTCAACTTCACGATGAAT
1 TTCAACTTCACGACGAATGATATCATGATCAAGTCATCCAAGATCAACTCAACTTCACGATGAAT
* * *
1410991 GAGTCATCCATAATTTAGATTAACTCAATAATAAGGAGCTATTTCCCAATCCAGATTTCGAGCTA
66 GAGTCAACCATAATTTAGATTAACTCAAAAATGAGGAGCTATTTCCCAATCCAGATTTCGAGCTA
1411056 GAT
131 GAT
** * * * *
1411059 TTCAACTTCACGGTGAATAATATCATGCTCAAGTCATCCAAGATCGAA-TCAAGTTCACGATAAA
1 TTCAACTTCACGACGAATGATATCATGATCAAGTCATCCAAGATC-AACTCAACTTCACGATGAA
* * *
1411123 GGAGTCAACCATAATTTAGATTAACTCAAAAATGAGGAGCTATTTCCCAGTCCAGATTTTGAGCT
65 TGAGTCAACCATAATTTAGATTAACTCAAAAATGAGGAGCTATTTCCCAATCCAGATTTCGAGCT
1411188 AGAT
130 AGAT
* * * * * * *
1411192 TTAAACTTCATGACAAATGATATCATGTTCAAGTCATCCAAGATTAACTTAACTTCACGACGAAT
1 TTCAACTTCACGACGAATGATATCATGATCAAGTCATCCAAGATCAACTCAACTTCACGATGAAT
* * * * *
1411257 GAGTCAACCACAATTTAGCTTAACTCAACAGTGAGGAGTTATTT
66 GAGTCAACCATAATTTAGATTAACTCAAAAATGAGGAGCTATTT
1411301 TCATCCAACT
Statistics
Matches: 207, Mismatches: 33, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
132 2 0.01
133 203 0.98
134 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (133 bp):
TTCAACTTCACGACGAATGATATCATGATCAAGTCATCCAAGATCAACTCAACTTCACGATGAAT
GAGTCAACCATAATTTAGATTAACTCAAAAATGAGGAGCTATTTCCCAATCCAGATTTCGAGCTA
GAT
Found at i:1412577 original size:14 final size:13
Alignment explanation
Indices: 1412551--1412585 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1412541 GTAAACTGAC
*
1412551 ATTTTTCTTTTAT
1 ATTTTTTTTTTAT
1412564 ATTTATTTTTTTAT
1 ATTT-TTTTTTTAT
1412578 ATTTTTTT
1 ATTTTTTT
1412586 GACTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTTTAT
Found at i:1412773 original size:3 final size:3
Alignment explanation
Indices: 1412756--1412792 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1412746 CTGGTCTAAT
*
1412756 TTA TCA TTA -TA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1412793 ATAATATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1414544 original size:14 final size:14
Alignment explanation
Indices: 1414484--1414548 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
1414474 CATTATGTTC
*
1414484 TATATATTATATTA
1 TATATATTTTATTA
* * *
1414498 AATAAATATTATTA
1 TATATATTTTATTA
*** *
1414512 TCCCTATTTT-TTG
1 TATATATTTTATTA
1414525 TATATATTTTATTA
1 TATATATTTTATTA
1414539 TATATATTTT
1 TATATATTTT
1414549 TAAAATAGCT
Statistics
Matches: 35, Mismatches: 15, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
13 9 0.26
14 26 0.74
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (14 bp):
TATATATTTTATTA
Found at i:1418256 original size:17 final size:16
Alignment explanation
Indices: 1418218--1418264 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1418208 GAAAGAAAAT
1418218 GCAAAGAAAAAAGAGA
1 GCAAAGAAAAAAGAGA
*
1418234 GAAAAGAAAAACA-ATGA
1 GCAAAGAAAAA-AGA-GA
*
1418251 GCAAAGATAAAAGA
1 GCAAAGAAAAAAGA
1418265 TAAAAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.68, C:0.06, G:0.21, T:0.04
Consensus pattern (16 bp):
GCAAAGAAAAAAGAGA
Found at i:1418263 original size:33 final size:33
Alignment explanation
Indices: 1418203--1418283 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
1418193 AAAGCAAAAG
1418203 GAAAAGAAAGAAAAT--GCAAAGAAAAAAGAGA
1 GAAAAGAAAGAAAATGAGCAAAGAAAAAAGAGA
* *
1418234 GAAAAGAAA-AACAATGAGCAAAGATAAAAGATA
1 GAAAAGAAAGAA-AATGAGCAAAGAAAAAAGAGA
*
1418267 AAAAAGAAAGAAAATGA
1 GAAAAGAAAGAAAATGA
1418284 ATCAAGTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 2 0.05
31 12 0.28
33 27 0.63
34 2 0.05
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.06
Consensus pattern (33 bp):
GAAAAGAAAGAAAATGAGCAAAGAAAAAAGAGA
Found at i:1422318 original size:61 final size:61
Alignment explanation
Indices: 1422255--1422525 Score: 319
Period size: 61 Copynumber: 4.4 Consensus size: 61
1422245 ATCTTCAGAC
* * * * * *
1422255 AATTAGAATTTCTCAGCAAGAATGAACAACATTATCTTCAGATTTACTATCCTTCAATAAC
1 AATTAGAATTCCTCAGCAAGAAGGAACAACATTGTCTTCAGATTCACTATCCTTCAAGAAA
*
1422316 AATTA-AACTTCCTCAGCAAGAAGGAACAACATTGTCATCAGATTCACTATCCTTCAAGAAA
1 AATTAGAA-TTCCTCAGCAAGAAGGAACAACATTGTCTTCAGATTCACTATCCTTCAAGAAA
* * *
1422377 AATTAGACTTCCCCAGCAAGTAGGAACAACATTGTCTTCAGATTCACTATCCTTCAAGAAA
1 AATTAGAATTCCTCAGCAAGAAGGAACAACATTGTCTTCAGATTCACTATCCTTCAAGAAA
* * * * * * * *
1422438 AAATATACTTCCGCAGCAAAAAGGAACAACATTGTCTTCAGATTCACCATCCTACAAGAAC
1 AATTAGAATTCCTCAGCAAGAAGGAACAACATTGTCTTCAGATTCACTATCCTTCAAGAAA
* * ** *
1422499 GACTAGTTTTCCTCACCAAGAAGGAAC
1 AATTAGAATTCCTCAGCAAGAAGGAAC
1422526 CATGTCGAAT
Statistics
Matches: 181, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
60 2 0.01
61 178 0.98
62 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.26
Consensus pattern (61 bp):
AATTAGAATTCCTCAGCAAGAAGGAACAACATTGTCTTCAGATTCACTATCCTTCAAGAAA
Found at i:1423292 original size:17 final size:17
Alignment explanation
Indices: 1423267--1423300 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1423257 GGGTTCTAAT
1423267 TTATCATTATATTATTA
1 TTATCATTATATTATTA
* *
1423284 TTATTATTATTTTATTA
1 TTATCATTATATTATTA
1423301 ATAATATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATCATTATATTATTA
Found at i:1425874 original size:26 final size:24
Alignment explanation
Indices: 1425843--1425890 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
1425833 TTTTCTTTTA
1425843 AATTTTAATTTGATCATCTTTTTACT
1 AATTTTAATTTGAT--TCTTTTTACT
**
1425869 AATTTTCCTTTGATTCTTTTTA
1 AATTTTAATTTGATTCTTTTTA
1425891 AATAGACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
26 12 0.60
ACGTcount: A:0.23, C:0.12, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTTAATTTGATTCTTTTTACT
Found at i:1427551 original size:21 final size:19
Alignment explanation
Indices: 1427525--1427572 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1427515 CATTAAATTC
1427525 ATAAAAAATATCAATACTA
1 ATAAAAAATATCAATACTA
1427544 ATAAAAAATATCAATACTA
1 ATAAAAAATATCAATACTA
*
1427563 ATATAAAATA
1 ATAAAAAATA
1427573 AAATTTGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAAAATATCAATACTA
Found at i:1427865 original size:21 final size:21
Alignment explanation
Indices: 1427841--1427882 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1427831 GCATGTGATA
1427841 TATTATAGAGCTCCAAAATTT
1 TATTATAGAGCTCCAAAATTT
*
1427862 TATTATAGAGTTCCAAAATTT
1 TATTATAGAGCTCCAAAATTT
1427883 AGTGCGTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
TATTATAGAGCTCCAAAATTT
Found at i:1429367 original size:14 final size:14
Alignment explanation
Indices: 1429350--1429385 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1429340 TAAAAATAGT
*
1429350 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
1429364 AAATTAAAGGACTG
1 AAATTAAAGGAATG
1429378 AAATTAAA
1 AAATTAAA
1429386 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:1429652 original size:21 final size:20
Alignment explanation
Indices: 1429623--1429664 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1429613 AAGTTATAGG
*
1429623 TTAGTGGTTAGCAGTAAGAAA
1 TTAGCGGTTAG-AGTAAGAAA
*
1429644 TTAGCGGTTAGAGTTAGAAA
1 TTAGCGGTTAGAGTAAGAAA
1429664 T
1 T
1429665 GTTAGTAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.31
Consensus pattern (20 bp):
TTAGCGGTTAGAGTAAGAAA
Found at i:1429879 original size:105 final size:105
Alignment explanation
Indices: 1429670--1429881 Score: 268
Period size: 105 Copynumber: 2.0 Consensus size: 105
1429660 GAAATGTTAG
* *
1429670 TAGAGTTCGGGCCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGGTCGTATAATAA
1 TAGAGTCCGGACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGGTCGTATAATAA
* * * * *
1429735 TTCAAACAAATTAATAAGAAAAATTAATAGTAGGAAATAA
66 TTCAAACAAACTAATAACAAAAATAAATAATAGAAAATAA
* * * *
1429775 TAGAGTCCGGACCATAATAATGTGGATCGTACCCCGGATTGGGTCACCACAAGGTCGTATAATGA
1 TAGAGTCCGGACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGGTCGTATAATAA
*
1429840 TTC-GA-AAACTAATAACAATAAATAAATAAATA-AATAATAA
66 TTCAAACAAACTAATAACAA-AAATAAAT-AATAGAA-AATAA
1429880 TA
1 TA
1429882 TATCATATTC
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
103 11 0.12
104 9 0.10
105 72 0.78
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (105 bp):
TAGAGTCCGGACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGGTCGTATAATAA
TTCAAACAAACTAATAACAAAAATAAATAATAGAAAATAA
Found at i:1431078 original size:23 final size:23
Alignment explanation
Indices: 1431048--1431093 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1431038 ACAAGTTCTC
1431048 ATTATGAACTTCTTTCGAAAATG
1 ATTATGAACTTCTTTCGAAAATG
1431071 ATTATGAACTTCTTTCGAAAATG
1 ATTATGAACTTCTTTCGAAAATG
1431094 TTGACAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTATGAACTTCTTTCGAAAATG
Found at i:1431845 original size:245 final size:244
Alignment explanation
Indices: 1431397--1431912 Score: 761
Period size: 245 Copynumber: 2.1 Consensus size: 244
1431387 CAAATGACAA
** *
1431397 ACTGATAGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTATTTTTTTTTATA
1 ACTGATAGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTA----TCTTTATA
* *
1431462 AAAAAAAATCAATTTTCAGAAAAGATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTTT
62 AAAAAAAATCAATTTTCAAAAAAAATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTTT
* * * *
1431527 AAAAAAAATGTGAAAAGATCCTGCCCGAAAGTCTTATGGATGGCCCGAGGGACTTATTATCTTGC
127 AAAAAAAATGTGAAAACATCCTGCCCGAAAGTCTTATGAATGGCCCGAAGGACTTATCATCTTGC
*
1431592 TTGAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTT
192 TCGAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTT
* *
1431645 ACTGATAGCCTGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTA-CTTT-TCAAAA
1 ACTGATAGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTATCTTTATAAAAA
1431708 AAAATCAATTTTCATAAAAAAAAAATTAAATGAGAAACTTTGAAAATCGCTTTCTCA-TTTTTTT
66 AAAATCAATTTTC----AAAAAAAATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTTT
* ** *
1431772 GAAAATCATGTGAAAACATCCTGCCC-AAAGGTCTTATGAATGGCCCGAAGGACTTATCATCTTT
127 AAAAAAAATGTGAAAACATCCTGCCCGAAA-GTCTTATGAATGGCCCGAAGGACTTATCATCTTG
1431836 CTCGAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTT
191 CTCGAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTT
*
1431890 ACTGATGGCCCGAAGGGACTTAC
1 ACTGATAGCCCGAA-GGACTTAC
1431913 CCATCAAGAA
Statistics
Matches: 244, Mismatches: 18, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
242 18 0.07
243 3 0.01
244 3 0.01
245 124 0.51
246 46 0.19
248 50 0.20
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (244 bp):
ACTGATAGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTATCTTTATAAAAA
AAAATCAATTTTCAAAAAAAATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTTTAAAA
AAAATGTGAAAACATCCTGCCCGAAAGTCTTATGAATGGCCCGAAGGACTTATCATCTTGCTCGA
AAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTT
Found at i:1432097 original size:52 final size:51
Alignment explanation
Indices: 1431973--1432345 Score: 250
Period size: 52 Copynumber: 7.1 Consensus size: 51
1431963 TATAGTTATC
* * * * ****
1431973 ATCAAGAAACCCTTAAAATTTAGGCTCAGCTTCTTTAAAAAATCATTGGATGCC
1 ATCAAGAAACCC-TAAAA-ATAGGCTTAGCTCCTTT-AAAAATCATTTGAAAAT
* * * **
1432027 ATCAAGTACCCCTTAAAATCAGGCTTAGCTCCTTTAAAGTTCATTTGAAAAT
1 ATCAAGAAACCCTAAAAAT-AGGCTTAGCTCCTTTAAAAATCATTTGAAAAT
* * *
1432079 ATCAAGAAACCCAAAAAATAGGCTTATCTTCTTTTAAAAATCATTTGAAAACT
1 ATCAAGAAACCCTAAAAATAGGCTTAGC-TCCTTTAAAAATCATTTGAAAA-T
* ** * * * *** *
1432132 -TCAAGAAACCCCTAAAATTAGGCTTAATTTCTTAAAAAATTATGCAAAAAC
1 ATCAAGAAA-CCCTAAAAATAGGCTTAGCTCCTTTAAAAATCATTTGAAAAT
* * *
1432183 ATCAAGAAACCCCTAAAAAT-GGCTTAGCTTC-TTAAAAATAATTTGAAAAC
1 ATCAAGAAA-CCCTAAAAATAGGCTTAGCTCCTTTAAAAATCATTTGAAAAT
* * *
1432233 ATCATGAAACCACTAAAAATTAGGCTTAGCTTCTTAAAAAATCATTTGAAGAAAT
1 ATCAAGAAACC-CTAAAAA-TAGGCTTAGCTCCTTTAAAAATCATTTG-A-AAAT
* ** *
1432288 CATCGAGAAACTTCC-AAAAACCGGACTTAGCTCTTTTAAAAATCATTTGAAAAT
1 -ATCAAGAAAC--CCTAAAAATAGG-CTTAGCTCCTTTAAAAATCATTTGAAAAT
1432342 ATCA
1 ATCA
1432346 TATCAAGAAA
Statistics
Matches: 251, Mismatches: 53, Indels: 31
0.75 0.16 0.09
Matches are distributed among these distances:
49 2 0.01
50 29 0.12
51 18 0.07
52 97 0.39
53 48 0.19
54 15 0.06
55 6 0.02
56 34 0.14
57 1 0.00
58 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (51 bp):
ATCAAGAAACCCTAAAAATAGGCTTAGCTCCTTTAAAAATCATTTGAAAAT
Found at i:1432136 original size:104 final size:105
Alignment explanation
Indices: 1431973--1432345 Score: 321
Period size: 104 Copynumber: 3.5 Consensus size: 105
1431963 TATAGTTATC
** * * * *** *
1431973 ATCAAGAAACCCTTAAAATTTAGGCTCAGCTTCTTTAAAAAATCATTGGATGCCATCAAG-TACC
1 ATCAAGAAACCC--AAAAAATAGGCTTAGCTTCTTTTAAAAATCATTTGAAAACATCAAGAAACC
* * * *
1432037 CCTTAAAATCAGGCTTAGCTCCTTTAAAGTTCATTTGAAAAT
64 CCTTAAAATTAGGCTTAGCTTCTTAAAAATTCATTTGAAAAT
* *
1432079 ATCAAGAAACCCAAAAAATAGGCTTATCTTCTTTTAAAAATCATTTGAAAACTTCAAGAAACCCC
1 ATCAAGAAACCCAAAAAATAGGCTTAGCTTCTTTTAAAAATCATTTGAAAACATCAAGAAACCCC
** *** *
1432144 -TAAAATTAGGCTTAATTTCTTAAAAAATT-ATGCAAAAAC
66 TTAAAATTAGGCTTAGCTTCTT-AAAAATTCATTTGAAAAT
* * * *
1432183 ATCAAGAAACCCCTAAAAAT-GGCTTAGCTTC--TTAAAAATAATTTGAAAACATCATGAAACCA
1 ATCAAGAAA-CCCAAAAAATAGGCTTAGCTTCTTTTAAAAATCATTTGAAAACATCAAGAAACCC
* *
1432245 CTAAAAATTAGGCTTAGCTTCTTAAAAAATCATTTGAAGAAAT
65 CTTAAAATTAGGCTTAGCTTCTTAAAAATTCATTTG-A-AAAT
* ** *
1432288 CATCGAGAAACTTCC-AAAAACCGGACTTAGC-TCTTTTAAAAATCATTTGAAAATATCA
1 -ATCAAGAAAC--CCAAAAAATAGG-CTTAGCTTCTTTTAAAAATCATTTGAAAACATCA
1432346 TATCAAGAAA
Statistics
Matches: 214, Mismatches: 39, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
102 34 0.16
103 20 0.09
104 79 0.37
105 23 0.11
106 25 0.12
107 6 0.03
108 6 0.03
109 21 0.10
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (105 bp):
ATCAAGAAACCCAAAAAATAGGCTTAGCTTCTTTTAAAAATCATTTGAAAACATCAAGAAACCCC
TTAAAATTAGGCTTAGCTTCTTAAAAATTCATTTGAAAAT
Found at i:1432290 original size:53 final size:53
Alignment explanation
Indices: 1431972--1432282 Score: 303
Period size: 52 Copynumber: 6.0 Consensus size: 53
1431962 TTATAGTTAT
* * * * ***
1431972 CATCAAGAAACCCTTAAAATTTAGGCTCAGCTTCTTTAAAAAATCATTGGATGC
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC-TTAAAAAATCATTTGAAAA
* * * * * **
1432026 CATCAAG-TACCCCTTAAAATCAGGCTTAGCTCCTTTAAAGTTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTAAAAAATCATTTGAAAA
* * * *
1432078 TATCAAGAAA-CCC-AAAAAATAGGCTTATCTTCTTTTAAAAATCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC-TTAAAAAATCATTTGAAAA
* ** * ***
1432130 CTTCAAGAAACCCCT-AAAATTAGGCTTAATTTCTTAAAAAATTATGCAAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTAAAAAATCATTTGAAAA
*
1432182 CATCAAGAAACCCCTAAAAA-T-GGCTTAGCTTCTT-AAAAATAATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTAAAAAATCATTTGAAAA
* *
1432232 CATCATGAAACCACTAAAAATTAGGCTTAGCTTCTTAAAAAATCATTTGAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTAAAAAATCATTTGAA
1432283 GAAATCATCG
Statistics
Matches: 206, Mismatches: 43, Indels: 17
0.77 0.16 0.06
Matches are distributed among these distances:
50 30 0.15
51 26 0.13
52 88 0.43
53 55 0.27
54 7 0.03
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTAAAAAATCATTTGAAAA
Found at i:1432411 original size:59 final size:58
Alignment explanation
Indices: 1432322--1432448 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 58
1432312 ACTTAGCTCT
* * * * * *
1432322 TTTAAAAATCATTTGAAAATATCATATCAAGAAACC-TCTGAAAATCAGACCTAGTTTC
1 TTTAAAATTCTTTTAAAAACATCATATCAAGAAACCTTC-AAAAATCAAACCTAGTTTC
* *
1432380 TTTAAAGATTCTTTTAAAAACATCATGTCAAGAAACCTTCAAAAATCAAACGTAGTTTC
1 TTTAAA-ATTCTTTTAAAAACATCATATCAAGAAACCTTCAAAAATCAAACCTAGTTTC
1432439 TTTAAAATTC
1 TTTAAAATTC
1432449 ATATCGATTG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 10 0.17
59 47 0.80
60 2 0.03
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.33
Consensus pattern (58 bp):
TTTAAAATTCTTTTAAAAACATCATATCAAGAAACCTTCAAAAATCAAACCTAGTTTC
Found at i:1434039 original size:2 final size:2
Alignment explanation
Indices: 1434032--1434082 Score: 93
Period size: 2 Copynumber: 25.0 Consensus size: 2
1434022 TTATTGTATG
1434032 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
1434074 TA TA CTA TA
1 TA TA -TA TA
1434083 ATCGCCTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1449441 original size:14 final size:14
Alignment explanation
Indices: 1449424--1449474 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1449414 TAAAAATAGT
1449424 AAATTAAAGTAATG
1 AAATTAAAGTAATG
* *
1449438 AAATTAAAGGATTG
1 AAATTAAAGTAATG
1449452 AAATTAAA-TAAATG
1 AAATTAAAGT-AATG
1449466 AAAATTAAA
1 -AAATTAAA
1449475 TAACAGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 23 0.74
15 8 0.26
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (14 bp):
AAATTAAAGTAATG
Found at i:1449472 original size:15 final size:15
Alignment explanation
Indices: 1449452--1449515 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
1449442 TAAAGGATTG
1449452 AAATTAAATAA-ATGA
1 AAATTAAATAACA-GA
1449467 AAATTAAATAACAGA
1 AAATTAAATAACAGA
* ** *
1449482 AATTTAAATGTGCATA
1 AAATTAAAT-AACAGA
1449498 AAATTAAATAACA-A
1 AAATTAAATAACAGA
1449512 AAAT
1 AAAT
1449516 AAAGGAGCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
14 5 0.12
15 23 0.57
16 12 0.30
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (15 bp):
AAATTAAATAACAGA
Found at i:1449484 original size:14 final size:14
Alignment explanation
Indices: 1449424--1449490 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
1449414 TAAAAATAGT
1449424 AAATTAAAGT-AATG
1 AAATTAAA-TAAATG
** *
1449438 AAATTAAAGGATTG
1 AAATTAAATAAATG
1449452 AAATTAAATAAATG
1 AAATTAAATAAATG
1449466 AAAATTAAATAACA-G
1 -AAATTAAATAA-ATG
1449481 AAATTTAAAT
1 AAA-TTAAAT
1449491 GTGCATAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
14 25 0.57
15 18 0.41
16 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.28
Consensus pattern (14 bp):
AAATTAAATAAATG
Found at i:1449532 original size:31 final size:31
Alignment explanation
Indices: 1449466--1449535 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1449456 TAAATAAATG
* * *
1449466 AAAATTAAATAACAGAAATTTAAATGTGCAT
1 AAAATTAAATAACAGAAATATAAAGGAGCAT
1449497 AAAATTAAATAACA-AAA-ATAAAGGAGCAAT
1 AAAATTAAATAACAGAAATATAAAGGAGC-AT
*
1449527 AAAAATAAA
1 AAAATTAAA
1449536 ATGTTAGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.21
30 13 0.38
31 14 0.41
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (31 bp):
AAAATTAAATAACAGAAATATAAAGGAGCAT
Found at i:1449714 original size:16 final size:15
Alignment explanation
Indices: 1449680--1449743 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 15
1449670 TAATTAACGA
1449680 TTAGAAAAGTTAG-ATG
1 TTAG-AAAGTTAGCA-G
1449696 TTAGAAAAGTTAGCAG
1 TTAG-AAAGTTAGCAG
** *
1449712 TTAG-TGGTTAACAG
1 TTAGAAAGTTAGCAG
1449726 TTAGAAA-TTAGCAG
1 TTAGAAAGTTAGCAG
1449740 TTAG
1 TTAG
1449744 TGTTAGAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 21 0.52
16 18 0.45
17 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (15 bp):
TTAGAAAGTTAGCAG
Found at i:1450516 original size:33 final size:33
Alignment explanation
Indices: 1450479--1450541 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1450469 CCCACACATC
1450479 CGAGAGGCT-TAAAGCCAACCCCAACGCCAGCGT
1 CGAGA-GCTATAAAGCCAACCCCAACGCCAGCGT
*
1450512 CGAGAGCTATAAAGCCAACCTCAACGCCAG
1 CGAGAGCTATAAAGCCAACCCCAACGCCAG
1450542 TAACGACCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.33, C:0.35, G:0.22, T:0.10
Consensus pattern (33 bp):
CGAGAGCTATAAAGCCAACCCCAACGCCAGCGT
Found at i:1451319 original size:55 final size:56
Alignment explanation
Indices: 1451235--1451348 Score: 221
Period size: 55 Copynumber: 2.1 Consensus size: 56
1451225 TACTATAATT
1451235 TTATTACTTGCAGACAACATGAGATTGTTGAT-AAATTGATCCTCAAGCATATTCA
1 TTATTACTTGCAGACAACATGAGATTGTTGATGAAATTGATCCTCAAGCATATTCA
1451290 TTATTACTTGCAGACAACATGAGATTGTTGATGAAATTGATCCTCAAGCATATTCA
1 TTATTACTTGCAGACAACATGAGATTGTTGATGAAATTGATCCTCAAGCATATTCA
1451346 TTA
1 TTA
1451349 GTCAATCACA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 32 0.55
56 26 0.45
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (56 bp):
TTATTACTTGCAGACAACATGAGATTGTTGATGAAATTGATCCTCAAGCATATTCA
Found at i:1452154 original size:60 final size:60
Alignment explanation
Indices: 1452034--1452168 Score: 159
Period size: 60 Copynumber: 2.2 Consensus size: 60
1452024 TTGGTTAATG
* * * ** *
1452034 AATTTTTAAATATTTTAATTTCATTCCTAAACTATGACTATCATTTTAAATTTGTTCTCA
1 AATTTTTAAACATTTCAATTTCATTCCTAAACTATGACTATCATTCTAAATCGGTCCTCA
*
1452094 AATTTTTGAACATTTCAATTTCA-TCTCTAAACTATGATCT-TCATTCTAAATCGGTCCTCA
1 AATTTTTAAACATTTCAATTTCATTC-CTAAACTATGA-CTATCATTCTAAATCGGTCCTCA
1452154 AACTTTTTAAA-ATTT
1 AA-TTTTTAAACATTT
1452169 TGAATTTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 2 0.03
60 53 0.83
61 9 0.14
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (60 bp):
AATTTTTAAACATTTCAATTTCATTCCTAAACTATGACTATCATTCTAAATCGGTCCTCA
Found at i:1456345 original size:2 final size:2
Alignment explanation
Indices: 1456338--1456381 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1456328 GGAAACCCTA
1456338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1456380 AT
1 AT
1456382 CCAGCAAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1460492 original size:37 final size:37
Alignment explanation
Indices: 1460449--1460528 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 37
1460439 ATTTTTTAAC
*
1460449 ATTTTTTATT-CC-ACCAAAAATGTTACGAAGAAGTCAAT
1 ATTTTTAATTGCCGACCAAAAATGTTA--AA-AAGTCAAT
* *
1460487 ATTTTTAATTGCCGACCGAAAATGTTAAAAAGTTAAT
1 ATTTTTAATTGCCGACCAAAAATGTTAAAAAGTCAAT
1460524 ATTTT
1 ATTTT
1460529 AGGTTAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 12 0.32
38 11 0.30
39 2 0.05
40 12 0.32
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (37 bp):
ATTTTTAATTGCCGACCAAAAATGTTAAAAAGTCAAT
Found at i:1460536 original size:21 final size:21
Alignment explanation
Indices: 1460510--1460554 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1460500 GACCGAAAAT
1460510 GTTAAAAAGTTAATATTTTAG
1 GTTAAAAAGTTAATATTTTAG
*
1460531 GTTAAAAAGTTAATATTTTTG
1 GTTAAAAAGTTAATATTTTAG
1460552 GTT
1 GTT
1460555 CTGCCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (21 bp):
GTTAAAAAGTTAATATTTTAG
Found at i:1477055 original size:6 final size:6
Alignment explanation
Indices: 1477041--1477144 Score: 52
Period size: 6 Copynumber: 16.7 Consensus size: 6
1477031 AGACACACAA
* * * *
1477041 AAAAAG AAAATG AAAAGG AAAAA- AATAAAT AAATAA- AATAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAA-AAG AAAAAG AAAAAG
* * * *
1477089 -AAAAG AAAAAATG AAAAAA AAGAGAAG GAAAAG AAGAAG AAGAAG AAGAAAG
1 AAAAAG -AAAAA-G AAAAAG AA-A-AAG AAAAAG AAAAAG AAAAAG AA-AAAG
1477141 AAAA
1 AAAA
1477145 TGGATCAAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
5 9 0.12
6 44 0.57
7 20 0.26
8 4 0.05
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:1477086 original size:30 final size:28
Alignment explanation
Indices: 1477041--1477123 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 28
1477031 AGACACACAA
1477041 AAAAAGAAAATGAAAAGGAAAA-AAATAAAT
1 AAAAA-AAAA-GAAAAGGAAAAGAAA-AAAT
*
1477071 AAATAAAATAAGAAAAAGAAAAGAAAAAAT
1 AAA-AAAA-AAGAAAAGGAAAAGAAAAAAT
* *
1477101 GAAAAAAAAGAGAAGGAAAAGAA
1 AAAAAAAAAGAAAAGGAAAAGAA
1477124 GAAGAAGAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 14 0.30
29 4 0.09
30 21 0.46
31 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (28 bp):
AAAAAAAAAGAAAAGGAAAAGAAAAAAT
Found at i:1477108 original size:22 final size:21
Alignment explanation
Indices: 1477075--1477120 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1477065 ATAAATAAAT
*
1477075 AAAATAAGAAAAAGAAAAGAA
1 AAAATAAAAAAAAGAAAAGAA
* *
1477096 AAAATGAAAAAAAAGAGAAGGA
1 AAAAT-AAAAAAAAGAAAAGAA
1477118 AAA
1 AAA
1477121 GAAGAAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (21 bp):
AAAATAAAAAAAAGAAAAGAA
Found at i:1479018 original size:54 final size:54
Alignment explanation
Indices: 1478954--1479404 Score: 606
Period size: 54 Copynumber: 8.4 Consensus size: 54
1478944 TGCATTGTTA
* *
1478954 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* *
1479008 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTGATGAATGA-CG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * *
1479061 TATAGGCACTAAGTGTGCAACTCA-TAGAATTCATCATATGTTGATGAACAACCA
1 TATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
* * * * * *
1479115 TATAGGCATTAAGTGTGCAAACCACGGAATTCATTATATGCTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
*
1479169 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACTG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* *
1479223 TATAGACACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
*
1479277 TATAGGCACTAAGTGTGCAACCCAC-ATAATTCATCATATTTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
* * * * * * *
1479331 TATAAGTACTAA-TAGTGTAACCCATGAATTTCATCATATGTTGATGAACTATCG
1 TATAGGCACTAAGT-GTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
1479385 TACT-GGCACTAAGTGTGCAA
1 TA-TAGGCACTAAGTGTGCAA
1479405 AATTCATAAT
Statistics
Matches: 347, Mismatches: 42, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
52 1 0.00
53 48 0.14
54 295 0.85
55 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
Found at i:1481997 original size:2 final size:2
Alignment explanation
Indices: 1481990--1482060 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1481980 TTAATTAGTT
1481990 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
1482032 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 T
1482061 GAATGCCAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1485500 original size:19 final size:18
Alignment explanation
Indices: 1485448--1485532 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 18
1485438 GACACACACA
* *
1485448 AAAAAGAAAAGGAAAAGG
1 AAAAAGAAAAGAAAAAAG
* *
1485466 AAAAAAAGAAATAAAATAAG
1 AAAAAGA-AAAGAAAA-AAG
1485486 AAAAAGAAAAGAAAAAATG
1 AAAAAGAAAAGAAAAAA-G
*
1485505 AAAAAAAAAAGAAGGAAAAG
1 AAAAAGAAAAGAA--AAAAG
*
1485525 AAGAAGAA
1 AAAAAGAA
1485533 GAGAGAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
18 8 0.15
19 26 0.49
20 15 0.28
21 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAAG
Found at i:1485526 original size:39 final size:39
Alignment explanation
Indices: 1485448--1485542 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 39
1485438 GACACACACA
* *
1485448 AAAAAGAAAAG-GAAAAGGAAAAAAAGAAATAAAATAAG
1 AAAAAGAAAAGAGAAAATGAAAAAAAGAAAGAAAATAAG
*
1485486 AAAAAGAAAAGAAAAAATGAAAAAAA-AAAGAAGGAA-AAG
1 AAAAAGAAAAGAGAAAATGAAAAAAAGAAAGAA--AATAAG
* *
1485525 AAGAAGAAGAGAGAAAAT
1 AAAAAGAAAAGAGAAAAT
1485543 AGATCAAGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
38 16 0.33
39 30 0.62
40 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (39 bp):
AAAAAGAAAAGAGAAAATGAAAAAAAGAAAGAAAATAAG
Found at i:1485541 original size:33 final size:33
Alignment explanation
Indices: 1485447--1485532 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
1485437 AGACACACAC
* * *
1485447 AAAA-AAGAAAAGGAAAAGGAAAAAA--AGAAAT
1 AAAAGAAGAAAAAGAAAA-GAAAAAATGAAAAAA
*
1485478 AAAATAAGAAAAAGAAAAGAAAAAATGAAAAAA
1 AAAAGAAGAAAAAGAAAAGAAAAAATGAAAAAA
*
1485511 AAAAGAAGGAAAAGAAGAAGAA
1 AAAAGAAGAAAAAGAA-AAGAA
1485533 GAGAGAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
31 11 0.24
32 12 0.26
33 18 0.39
34 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (33 bp):
AAAAGAAGAAAAAGAAAAGAAAAAATGAAAAAA
Found at i:1487584 original size:54 final size:54
Alignment explanation
Indices: 1487521--1487972 Score: 611
Period size: 54 Copynumber: 8.4 Consensus size: 54
1487511 TGCATTGTTA
1487521 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
* * *
1487575 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTGATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
* * * *
1487629 TATAGGCACTAAGTGTGCAACTCATAGAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
* * * *
1487683 TATAGGCATTAAGTGTGCAACCCACGAAATTCATTATATGTTGATGAACGACCC
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
* *
1487737 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACTG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
* * * * * *
1487791 AATAGACACTAAGTGTGCAACCCACAGAATTCATCATATATTGATGAACAACCA
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
* * *
1487845 TATAGGCATTAAGTGTGCAACCCACAGAATTCATCATATTTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
* * * * * * *
1487899 TATAAGTACTAA-TAGTGTAACCCACGAAATTCATTATATGTTGATGAACTATCG
1 TATAGGCACTAAGT-GTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
1487953 TACT-GGCACTAAGTGTGCAA
1 TA-TAGGCACTAAGTGTGCAA
1487973 AATTCATAAT
Statistics
Matches: 346, Mismatches: 49, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 343 0.99
55 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
Found at i:1490134 original size:21 final size:20
Alignment explanation
Indices: 1490089--1490145 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1490079 GGATTATATA
1490089 AGGTCCTTCGGGACATGTACT
1 AGGTCCTTCGGGACA-GTACT
1490110 AGGTCCTTCGGGACA-TACAT
1 AGGTCCTTCGGGACAGTAC-T
*
1490130 GAGGTCATTCGGGACA
1 -AGGTCCTTCGGGACA
1490146 AATTTCACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 3 0.09
20 1 0.03
21 29 0.88
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (20 bp):
AGGTCCTTCGGGACAGTACT
Found at i:1502369 original size:21 final size:21
Alignment explanation
Indices: 1502345--1502442 Score: 97
Period size: 23 Copynumber: 4.5 Consensus size: 21
1502335 CAGAAGAAAT
1502345 CGATACCCCTTGAAGGGGAAC
1 CGATACCCCTTGAAGGGGAAC
* *
1502366 CGATTCCCCCTTTTAAGGGGAAC
1 CGA-TACCCC-TTGAAGGGGAAC
* *
1502389 CGATTCCCCCTTTTAAGGGGAAC
1 CGA-TACCCC-TTGAAGGGGAAC
* * *
1502412 CGATTCCCCTTGTAGGGGAAT
1 CGATACCCCTTGAAGGGGAAC
1502433 CGATACCCCT
1 CGATACCCCT
1502443 CTGGGGTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
21 21 0.31
22 10 0.15
23 37 0.54
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.23
Consensus pattern (21 bp):
CGATACCCCTTGAAGGGGAAC
Found at i:1502387 original size:23 final size:23
Alignment explanation
Indices: 1502357--1502441 Score: 129
Period size: 23 Copynumber: 3.8 Consensus size: 23
1502347 ATACCCCTTG
1502357 AAGGGGAACCGATTCCCCCTTTT
1 AAGGGGAACCGATTCCCCCTTTT
1502380 AAGGGGAACCGATTCCCCCTTTT
1 AAGGGGAACCGATTCCCCCTTTT
*
1502403 AAGGGGAACCGATT-CCCCTTGT
1 AAGGGGAACCGATTCCCCCTTTT
* *
1502425 -AGGGGAATCGATACCCC
1 AAGGGGAACCGATTCCCC
1502442 TCTGGGGTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.19
22 10 0.17
23 37 0.64
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (23 bp):
AAGGGGAACCGATTCCCCCTTTT
Found at i:1504357 original size:17 final size:16
Alignment explanation
Indices: 1504328--1504393 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
1504318 CATTTTGGAT
*
1504328 ATTTTGGAATGTTTGA
1 ATTTTGGATTGTTTGA
1504344 ATTTGTGGATTGTTTG-
1 ATTT-TGGATTGTTTGA
* *
1504360 ACTTTGAATTTGTTTGA
1 ATTTTGGA-TTGTTTGA
1504377 ATTTATGGA-TGTTTGA
1 ATTT-TGGATTGTTTGA
1504393 A
1 A
1504394 CTTATATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.07
16 22 0.54
17 13 0.32
18 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (16 bp):
ATTTTGGATTGTTTGA
Found at i:1506481 original size:21 final size:21
Alignment explanation
Indices: 1506452--1506514 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1506442 GTTGAGGGAT
*
1506452 TATATGAGGTCCTTTAGGACA
1 TATATGAGGTCCTTCAGGACA
* *
1506473 TATACGAGGTCCTTCGGGACA
1 TATATGAGGTCCTTCAGGACA
*
1506494 TATATGAGGTCCTTCGGGACA
1 TATATGAGGTCCTTCAGGACA
1506515 AAATTCACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (21 bp):
TATATGAGGTCCTTCAGGACA
Found at i:1507019 original size:31 final size:31
Alignment explanation
Indices: 1506983--1507043 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1506973 AACTTAAAAG
*
1506983 AGTTTTGA-AATACTGAGATTTAAATAATTTT
1 AGTTTT-ACAATACTGAAATTTAAATAATTTT
1507014 AGTTTTACAATACTGAAATTTAAATAATTT
1 AGTTTTACAATACTGAAATTTAAATAATTT
1507044 ATACAACTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1507553 original size:17 final size:16
Alignment explanation
Indices: 1507493--1507553 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
1507483 ATATTATATT
1507493 TAAAATTAAATCAAA-A
1 TAAAATTAAAT-AAATA
1507509 T--AATTAAAATAAATA
1 TAAAATT-AAATAAATA
*
1507524 TAAAATTTTAATAATATA
1 TAAAA-TTAAATAA-ATA
1507542 TAAAATTAAATA
1 TAAAATTAAATA
1507554 TCTATAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
14 7 0.19
15 6 0.16
16 1 0.03
17 13 0.35
18 10 0.27
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATTAAATAAATA
Found at i:1507611 original size:64 final size:65
Alignment explanation
Indices: 1507535--1507693 Score: 274
Period size: 63 Copynumber: 2.5 Consensus size: 65
1507525 AAAATTTTAA
1507535 TAATATATAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AAAAA
1 TAATAT-TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAA
1507599 T
65 T
1507600 TAATATTAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAT
1 TAATATTAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAT
1507664 TAATATTAAAATTAAA-ATC-A-AATATAATAT
1 TAATATTAAAATTAAATATCTATAATATAATAT
1507694 AATATAAAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
62 10 0.11
63 45 0.49
64 29 0.32
65 8 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (65 bp):
TAATATTAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAT
Found at i:1507650 original size:26 final size:26
Alignment explanation
Indices: 1507597--1507678 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 26
1507587 TTTATTTAAA
1507597 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-TAT
1507622 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
* *
1507648 AATTTAT-TTAAAAAATTAATATTAA
1 AATTAATATTAAAAAATTAATATTAT
1507673 AATTAA
1 AATTAA
1507679 AATCAAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
24 16 0.32
25 11 0.22
26 11 0.22
27 1 0.02
28 11 0.22
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:1513439 original size:54 final size:54
Alignment explanation
Indices: 1513375--1513922 Score: 703
Period size: 54 Copynumber: 10.2 Consensus size: 54
1513365 TGCATTGTTA
* * * *
1513375 TATAGGCACTAAGTGTACAACCCACGGAATACATCATATGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
1513429 TATAGTCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* **
1513483 TATAGGCACTAAGTGAGCAACCCA-AGGAATTCATCATATGTTGATGAATAACCG
1 TATAGGCACTAAGTGTGCAACCCACA-GAATTCATCATATGTTGATGAACGACCG
*
1513537 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGATCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * *
1513591 TATAGGCACTAAGTGTGGAACCCATAAAATTCATCATATGTTGATGAACGATCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
1513645 TATAGGCACTAAGTGTGCAACCCAC-GAAATTCATCATACGTTGATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCG
** * * * *
1513699 TATAGAAACTAAGTGTACAACCCACAGAATTCAACTTATGTTGATGAACGATCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
1513753 TATAGGCACTAAGTGTGCAACCCTCAGAATTCATCATATGTTGATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * * *
1513807 TGTA---ACTAATTGTGCAACCTA-AGGAATTCATCATATGTTGATGAACAACCA
1 TATAGGCACTAAGTGTGCAACCCACA-GAATTCATCATATGTTGATGAACGACCG
* * * * * *
1513858 TATAAGCACTAAGTGTACAAACCACAGAATTCATAATATGTTTATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
*
1513912 TATTGGCACTA
1 TATAGGCACTA
1513923 CTTGTGCATC
Statistics
Matches: 428, Mismatches: 57, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
50 1 0.00
51 42 0.10
53 1 0.00
54 381 0.89
55 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
Found at i:1515495 original size:45 final size:45
Alignment explanation
Indices: 1515439--1516001 Score: 497
Period size: 45 Copynumber: 12.5 Consensus size: 45
1515429 TAAAGAGAAA
* * **
1515439 TCAATCTTTTAGTGTTTTCATTCTTGACTTTCTTGTGAAGATTAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
* ** *
1515484 TCAATCGTTTAGTGAGGTTATTCTTGACTTTCTCGTGAAGAGGAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
* * * **
1515529 TCAATCTTGTAATGTTGTCATTATTGACTTTCTAATGAAGAGGAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
* * * * * *
1515574 TCAATATTTTGGTGATGTTATTCTTGACTTTCTCATGAAGATGAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
* *
1515619 TCAATATTTTAGTGTTGTCATTCTTGACTTTCGT-TTGAAG-GTGAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTC-TCGTGAAGAG-GAG
* * ** * * *
1515664 TCAACCTTTAAGTAATGTCATTCTTGATTTTCTCGCGAAGAAGAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
* * * * *
1515709 TCAATCTTTCAGTGATGTGATTCTTGACTTCCTCGCGAAGAGGAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
* * * *
1515754 TCAACCTTTTAGTGATGTCCTTCTTGACTTTCTCACT-AAGAGGAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTC-GTGAAGAGGAG
* * * * * *
1515799 TCAACCTTTTAGTGATGTCCTTTTTTACTTTCTCGCGAAGAGGAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
* * * *
1515844 AT-AACCTTTTAGTGATGTCATTCTTGACTTTCTTGTGAAGAGGAT
1 -TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
* * * **
1515889 TTAACCTTTTAGTGTTGTCTTTCTTGACTTTCGAGCTG-AGAGGAG
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCG-TGAAGAGGAG
* * ** ** *
1515934 TCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCAAAGAATAA
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
* *
1515979 TCAACCTTTTAGTGATGTCATTC
1 TCAATCTTTTAGTGTTGTCATTC
1516002 ACAACTTGAC
Statistics
Matches: 429, Mismatches: 79, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
44 2 0.00
45 423 0.99
46 4 0.01
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (45 bp):
TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAG
Found at i:1515576 original size:90 final size:90
Alignment explanation
Indices: 1515439--1516001 Score: 569
Period size: 90 Copynumber: 6.3 Consensus size: 90
1515429 TAAAGAGAAA
* * ** * * * *
1515439 TCAATCTTTTAGTGTTTTCATTCTTGACTTTCTTGTGAAGATTAGTCAATCGTTTAGTGAGGTTA
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTAGTGAAGAGGAGTCAACCTTTTAGTGATGTCA
1515504 TTCTTGACTTTCTCGTGAAGAGGAG
66 TTCTTGACTTTCTCGTGAAGAGGAG
* * * * ** * *
1515529 TCAATCTTGTAATGTTGTCATTATTGACTTTCTAATGAAGAGGAGTCAATATTTTGGTGATGTTA
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTAGTGAAGAGGAGTCAACCTTTTAGTGATGTCA
* *
1515594 TTCTTGACTTTCTCATGAAGATGAG
66 TTCTTGACTTTCTCGTGAAGAGGAG
* * * *
1515619 TCAATATTTTAGTGTTGTCATTCTTGACTTTCGT-TTGAAG-GTGAGTCAACCTTTAAGTAATGT
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTC-TAGTGAAGAG-GAGTCAACCTTTTAGTGATGT
* * *
1515682 CATTCTTGATTTTCTCGCGAAGAAGAG
64 CATTCTTGACTTTCTCGTGAAGAGGAG
* * * * * * *
1515709 TCAATCTTTCAGTGATGTGATTCTTGACTTCCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCC
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTAGTGAAGAGGAGTCAACCTTTTAGTGATGTCA
*
1515774 TTCTTGACTTTCTCACT-AAGAGGAG
66 TTCTTGACTTTCTC-GTGAAGAGGAG
* * * * * * *
1515799 TCAACCTTTTAGTGATGTCCTTTTTTACTTTCTCGCGAAGAGGAGAT-AACCTTTTAGTGATGTC
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTAGTGAAGAGGAG-TCAACCTTTTAGTGATGTC
* *
1515863 ATTCTTGACTTTCTTGTGAAGAGGAT
65 ATTCTTGACTTTCTCGTGAAGAGGAG
* * * *
1515889 TTAACCTTTTAGTGTTGTCTTTCTTGACTTTCGAGCTG-AGAGGAGTCAACCTTTTAGTGATGTC
1 TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTAG-TGAAGAGGAGTCAACCTTTTAGTGATGTC
** ** *
1515953 ATTCTTGACTTTCTCGCAAAGAATAA
65 ATTCTTGACTTTCTCGTGAAGAGGAG
* *
1515979 TCAACCTTTTAGTGATGTCATTC
1 TCAATCTTTTAGTGTTGTCATTC
1516002 ACAACTTGAC
Statistics
Matches: 393, Mismatches: 71, Indels: 18
0.82 0.15 0.04
Matches are distributed among these distances:
89 4 0.01
90 385 0.98
91 4 0.01
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (90 bp):
TCAATCTTTTAGTGTTGTCATTCTTGACTTTCTAGTGAAGAGGAGTCAACCTTTTAGTGATGTCA
TTCTTGACTTTCTCGTGAAGAGGAG
Found at i:1517295 original size:131 final size:131
Alignment explanation
Indices: 1517085--1517416 Score: 513
Period size: 131 Copynumber: 2.5 Consensus size: 131
1517075 ATAGAAATTA
* * * * *
1517085 ATCTTCCCTGAAGAGTAGTGAAGCAAATCAATCTCGACTCAATCCTCCTTGAAGAGTAGTGAAGT
1 ATCTTCTCTGAAGAGTAGTGAAGCAAATCAACCTCGATTCAATCTTCCTTGAAGAGCAGTGAAGT
* * * * *
1517150 GAATCAAAGTTTCCACATCTGATCTGGCCC-GAAGAGCAGCGGAGTAGATCCCTTTTTTCATATT
66 GAATCAAAGTTTCCAAATCTGATCT-ACCCTGAAGAGCAGCGGAGCAGATCCCTTTCTTCAGATT
1517214 TG
130 TG
* *
1517216 ATCTTCTCTGAAGAGCAGTGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGT
1 ATCTTCTCTGAAGAGTAGTGAAGCAAATCAACCTCGATTCAATCTTCCTTGAAGAGCAGTGAAGT
1517281 GAATCAAAGTTTCCAAATCTGATCTACCCTGAAGAGCAGCGGAGCAGATCCCTTTCTTCAGATTT
66 GAATCAAAGTTTCCAAATCTGATCTACCCTGAAGAGCAGCGGAGCAGATCCCTTTCTTCAGATTT
1517346 G
131 G
* * *
1517347 ATCTTCTCTAAAAAGTAGTGAAGCAAATCAACCTCGATTCAATCTTCCTTGGAGAGCAGTGAAGT
1 ATCTTCTCTGAAGAGTAGTGAAGCAAATCAACCTCGATTCAATCTTCCTTGAAGAGCAGTGAAGT
1517412 GAATC
66 GAATC
1517417 CACGTTTCTT
Statistics
Matches: 183, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
130 3 0.02
131 180 0.98
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (131 bp):
ATCTTCTCTGAAGAGTAGTGAAGCAAATCAACCTCGATTCAATCTTCCTTGAAGAGCAGTGAAGT
GAATCAAAGTTTCCAAATCTGATCTACCCTGAAGAGCAGCGGAGCAGATCCCTTTCTTCAGATTT
G
Found at i:1519239 original size:2 final size:2
Alignment explanation
Indices: 1519232--1519260 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1519222 TAGTTATGTA
1519232 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 A
1519261 GCTTATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1523387 original size:11 final size:10
Alignment explanation
Indices: 1523373--1523463 Score: 61
Period size: 10 Copynumber: 9.5 Consensus size: 10
1523363 AAACACACAC
*
1523373 AAAAAGATAG
1 AAAAAGAAAG
1523383 AAAAAGAAA-
1 AAAAAGAAAG
*
1523392 AGAAA-AAAG
1 AAAAAGAAAG
1523401 -AAAA-AAAG
1 AAAAAGAAAG
*
1523409 AAAAAAAAAGG
1 AAAAAGAAA-G
1523420 AAAAAGGAAA-
1 AAAAA-GAAAG
1523430 AAAAGAGAAAG
1 AAAA-AGAAAG
*
1523441 AAAGAG-AAG
1 AAAAAGAAAG
*
1523450 AAGAAGAAA-
1 AAAAAGAAAG
1523459 AAAAA
1 AAAAA
1523464 CATATTAAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
8 10 0.15
9 19 0.29
10 23 0.35
11 10 0.15
12 3 0.05
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:1523394 original size:15 final size:14
Alignment explanation
Indices: 1523374--1523459 Score: 74
Period size: 15 Copynumber: 6.3 Consensus size: 14
1523364 AACACACACA
1523374 AAAAGATAGAAAAAG
1 AAAAGA-AGAAAAAG
1523389 AAAAG-A-AAAAAG
1 AAAAGAAGAAAAAG
*
1523401 AAAAAAAGAAAAA-
1 AAAAGAAGAAAAAG
1523414 AAAAG--GAAAAAGG
1 AAAAGAAGAAAAA-G
* *
1523427 AAAAAAAGAGAAAG
1 AAAAGAAGAAAAAG
*
1523441 AAAGAGAAGAAGAAG
1 AAA-AGAAGAAAAAG
1523456 AAAA
1 AAAA
1523460 AAAACATATT
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
11 6 0.11
12 10 0.18
13 10 0.18
14 10 0.18
15 21 0.37
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (14 bp):
AAAAGAAGAAAAAG
Found at i:1523422 original size:26 final size:26
Alignment explanation
Indices: 1523381--1523462 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 26
1523371 ACAAAAAGAT
1523381 AGAAAAAGAAAA-GAAAAAAGAAAAAA
1 AGAAAAA-AAAAGGAAAAAAGAAAAAA
*
1523407 AGAAAAAAAAAGGAAAAAGGAAAAAA
1 AGAAAAAAAAAGGAAAAAAGAAAAAA
* *
1523433 AGAGAAAGAAAGAGAAGAAGAAGAAAAAA
1 AGAAAAAAAAAG-GAA-AA-AAGAAAAAA
1523462 A
1 A
1523463 ACATATTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 4 0.08
26 30 0.62
27 3 0.06
28 2 0.04
29 9 0.19
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (26 bp):
AGAAAAAAAAAGGAAAAAAGAAAAAA
Found at i:1525254 original size:2 final size:2
Alignment explanation
Indices: 1525249--1525297 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1525239 TATAAATGTG
1525249 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
1525291 TA TA TA T
1 TA TA TA T
1525298 TTTATTCTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1525316 original size:24 final size:23
Alignment explanation
Indices: 1525289--1525334 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1525279 TATATATATA
*
1525289 TATATATATTTTATTCTATTTTAT
1 TATATATAGTTTATT-TATTTTAT
*
1525313 TATATCTAGTTTATTTATTTTA
1 TATATATAGTTTATTTATTTTA
1525335 ATTTGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (23 bp):
TATATATAGTTTATTTATTTTAT
Found at i:1532477 original size:98 final size:99
Alignment explanation
Indices: 1532354--1532585 Score: 279
Period size: 99 Copynumber: 2.4 Consensus size: 99
1532344 CCTAAAGCGA
* * * **
1532354 TCAGATCTCTTCAATACGGATGAGCAGTGTCGTTTCCAAGATTGACC-GATGTCC-TCAGAGAGA
1 TCAGATCTCTTCAATGCGGATGAGCAGTGTCGTTTCCAAGATTAACCTAACATCCTTC-GAGAGA
* * *
1532417 ATGAAAAATGTCATCTTTAATTTAATCGAAAGTGG
65 ATGAAAAATGTCATCTTTAATTCAACCAAAAGTGG
* ** *
1532452 TCAGATCTTTTCAATGCATATGAGCAGTGTCGTTTCCAAGATTAACCTAACATCCTTCGAGAGAC
1 TCAGATCTCTTCAATGCGGATGAGCAGTGTCGTTTCCAAGATTAACCTAACATCCTTCGAGAGAA
* * *
1532517 TTAACAATGTCATCTTTAATTCACCCAAAAGTGG
66 TGAAAAATGTCATCTTTAATTCAACCAAAAGTGG
* * *
1532551 TCAAATCTCTTCAATGTGGATGAGCAATGTCGTTT
1 TCAGATCTCTTCAATGCGGATGAGCAGTGTCGTTT
1532586 TGAACATCAA
Statistics
Matches: 111, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
98 42 0.38
99 67 0.60
100 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (99 bp):
TCAGATCTCTTCAATGCGGATGAGCAGTGTCGTTTCCAAGATTAACCTAACATCCTTCGAGAGAA
TGAAAAATGTCATCTTTAATTCAACCAAAAGTGG
Found at i:1533366 original size:22 final size:22
Alignment explanation
Indices: 1533338--1533380 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1533328 ATCCAAGTTG
1533338 TTTTTATTATTATTATCATTTA
1 TTTTTATTATTATTATCATTTA
* *
1533360 TTTTTATTTTTATTATTATTT
1 TTTTTATTATTATTATCATTT
1533381 TATTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTATTATTATTATCATTTA
Found at i:1533372 original size:19 final size:18
Alignment explanation
Indices: 1533344--1533385 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1533334 GTTGTTTTTA
1533344 TTATTATTATCATTTATTT
1 TTATTATTATCA-TTATTT
* *
1533363 TTATTTTTATTATTA-TT
1 TTATTATTATCATTATTT
1533380 TTATTA
1 TTATTA
1533386 ATAATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 7 0.35
18 3 0.15
19 10 0.50
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTATTATCATTATTT
Found at i:1533373 original size:12 final size:12
Alignment explanation
Indices: 1533344--1533385 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1533334 GTTGTTTTTA
*
1533344 TTATTATTATCAT
1 TTATTATTAT-TT
*
1533357 TTATTTTTATTT
1 TTATTATTATTT
1533369 TTATTATTA-TT
1 TTATTATTATTT
1533380 TTATTA
1 TTATTA
1533386 ATAATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 8 0.31
12 9 0.35
13 9 0.35
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:1536995 original size:32 final size:31
Alignment explanation
Indices: 1536954--1537013 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
1536944 AGCAGACCTC
1536954 TAATAATAAATATTAGAAAAAAATTAAACTCT
1 TAATAATAAATATTA-AAAAAAATTAAACTCT
*
1536986 TAATAATAAATATTAAAAATAATTAAAC
1 TAATAATAAATATTAAAAAAAATTAAAC
1537014 CCTATAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (31 bp):
TAATAATAAATATTAAAAAAAATTAAACTCT
Found at i:1537217 original size:18 final size:20
Alignment explanation
Indices: 1537194--1537232 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1537184 GGTTAATTTT
1537194 TAAAA-TTAAA-ATAAAATA
1 TAAAATTTAAAGATAAAATA
*
1537212 TAAAATTTAAAGATTAAATA
1 TAAAATTTAAAGATAAAATA
1537232 T
1 T
1537233 TTACTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAAATTTAAAGATAAAATA
Found at i:1539318 original size:48 final size:47
Alignment explanation
Indices: 1539240--1539337 Score: 178
Period size: 48 Copynumber: 2.1 Consensus size: 47
1539230 GCTTCCCGAG
1539240 TTCTTTAATCTCTTTTTTTTGTGTTTGTATGTTTTATCATAATCAAT
1 TTCTTTAATCTCTTTTTTTTGTGTTTGTATGTTTTATCATAATCAAT
*
1539287 TTCTTTGATCTCTTTTTTTTTGTGTTTGTATGTTTTATCATAATCAAT
1 TTCTTTAATCTC-TTTTTTTTGTGTTTGTATGTTTTATCATAATCAAT
1539335 TTC
1 TTC
1539338 CTGCTACAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 11 0.22
48 38 0.78
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.62
Consensus pattern (47 bp):
TTCTTTAATCTCTTTTTTTTGTGTTTGTATGTTTTATCATAATCAAT
Found at i:1547829 original size:22 final size:21
Alignment explanation
Indices: 1547804--1547845 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1547794 GCTAAAGAAG
1547804 AGATTGAGACTTAAATATTTTT
1 AGATTGAGACTTAAAT-TTTTT
* *
1547826 AGATTTAGGCTTAAATTTTT
1 AGATTGAGACTTAAATTTTT
1547846 AATTAATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (21 bp):
AGATTGAGACTTAAATTTTTT
Found at i:1550710 original size:61 final size:60
Alignment explanation
Indices: 1550625--1550761 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 60
1550615 TATTTTTTTG
* * * *
1550625 AATTAAAAAATTAAAGACGGTATATTTATATATCGCCTACGCTATTCACTATTTCTTTCA
1 AATTAAAAAATTAAAGACGCTATATTTACAAATCGCCTACACTATTCACTATTTCTTTCA
* * **
1550685 AATTAAAAAAATTAAAGACGCTATATTTACAAATCGTCTATACTATTCACTATTTCTTTTG
1 AATT-AAAAAATTAAAGACGCTATATTTACAAATCGCCTACACTATTCACTATTTCTTTCA
*
1550746 AA-TAAAAATTTAAAGA
1 AATTAAAAAATTAAAGA
1550762 TGGTGTTCCT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 12 0.18
60 5 0.07
61 50 0.75
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (60 bp):
AATTAAAAAATTAAAGACGCTATATTTACAAATCGCCTACACTATTCACTATTTCTTTCA
Found at i:1554535 original size:24 final size:24
Alignment explanation
Indices: 1554508--1554560 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1554498 AGTGTAAACA
1554508 GTTCAAATATCAAACTAATAGAAT
1 GTTCAAATATCAAACTAATAGAAT
* *
1554532 GTTCAAATATCAAACTATTAGATT
1 GTTCAAATATCAAACTAATAGAAT
1554556 GTTCA
1 GTTCA
1554561 TTCAAATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (24 bp):
GTTCAAATATCAAACTAATAGAAT
Found at i:1563702 original size:14 final size:14
Alignment explanation
Indices: 1563683--1563711 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1563673 TTAGGCCAAC
1563683 TAGGACTACTAGCT
1 TAGGACTACTAGCT
1563697 TAGGACTACTAGCT
1 TAGGACTACTAGCT
1563711 T
1 T
1563712 GGGTGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (14 bp):
TAGGACTACTAGCT
Found at i:1566410 original size:20 final size:20
Alignment explanation
Indices: 1566385--1566465 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 20
1566375 TTTTGGTGCA
1566385 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCCAT
* * *
1566405 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATACCCCC-AT
*
1566426 GAAGGGAATCGATTCCCCCCA-
1 G-AGGGAATCGA-TACCCCCAT
*
1566447 CAGGGGAATCGATACCCCC
1 GA-GGGAATCGATACCCCC
1566466 CTGGGGTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 23 0.47
21 11 0.22
22 9 0.18
23 6 0.12
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCAT
Found at i:1566438 original size:22 final size:20
Alignment explanation
Indices: 1566385--1566444 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
1566375 TTTTGGTGCA
*
1566385 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATTCCCCCAT
* *
1566405 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCC-AT
1566426 GAAGGGAATCGATTCCCCC
1 G-AGGGAATCGATTCCCCC
1566445 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 16 0.47
21 2 0.06
22 16 0.47
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (20 bp):
GAGGGAATCGATTCCCCCAT
Found at i:1568114 original size:12 final size:12
Alignment explanation
Indices: 1568097--1568121 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1568087 GAGCCTGAAT
1568097 AGCCCGAGGAGC
1 AGCCCGAGGAGC
1568109 AGCCCGAGGAGC
1 AGCCCGAGGAGC
1568121 A
1 A
1568122 AGCACAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.40, T:0.00
Consensus pattern (12 bp):
AGCCCGAGGAGC
Found at i:1570293 original size:13 final size:14
Alignment explanation
Indices: 1570275--1570304 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1570265 TCACCAAATT
1570275 TTCTTCCTCTTT-C
1 TTCTTCCTCTTTAC
1570288 TTCTTCCTCTTTAC
1 TTCTTCCTCTTTAC
1570302 TTC
1 TTC
1570305 AATGTTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (14 bp):
TTCTTCCTCTTTAC
Found at i:1571355 original size:8 final size:8
Alignment explanation
Indices: 1571342--1571366 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1571332 TATCAAATCA
1571342 TATCACCC
1 TATCACCC
1571350 TATCACCC
1 TATCACCC
1571358 TATCACCC
1 TATCACCC
1571366 T
1 T
1571367 TCATTCCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (8 bp):
TATCACCC
Found at i:1574712 original size:95 final size:95
Alignment explanation
Indices: 1574549--1574720 Score: 292
Period size: 95 Copynumber: 1.8 Consensus size: 95
1574539 ATTATGTATA
1574549 TACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAGAT
1 TACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAGAT
1574614 TCAGCTAGCCTGATAAAGGTGATTATAATG
66 TCAGCTAGCCTGATAAAGGTGATTATAATG
** * *
1574644 TACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCCG-CTTTATGGATAATA
1 TACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACG-CCCCGACTTTATGGATAAGA
1574708 TTCAGCTAGCCTG
65 TTCAGCTAGCCTG
1574721 CAACAAATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
95 67 0.93
96 5 0.07
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (95 bp):
TACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAGAT
TCAGCTAGCCTGATAAAGGTGATTATAATG
Found at i:1575520 original size:21 final size:21
Alignment explanation
Indices: 1575495--1575544 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1575485 TGAGACAGTT
1575495 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
1575516 TCTCTTGAAACAAATTTTTTC
1 TCTCTTGAAACAAATTTTGTC
1575537 TCTCTTGA
1 TCTCTTGA
1575545 GACAGTTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.46
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:1575683 original size:36 final size:35
Alignment explanation
Indices: 1575580--1575774 Score: 230
Period size: 36 Copynumber: 5.4 Consensus size: 35
1575570 TTGAATATGT
* *
1575580 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
1575615 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTC-CTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
1575652 TTTCCATAT-AAACAAATTTTGTCTCTTTTGAGACAG
1 TTTCC-T-TGAAACAAATTTTGTCTCTCTTGAGACAG
*
1575688 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAG
1 TTTC-CTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
1575724 TTTTCCTTGAACCAAAGTTTTGTCTCTCTTGAGACAT
1 -TTTCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
1575761 TTTCTCTTGAAACA
1 TTTC-CTTGAAACA
1575775 CCAACCTTTG
Statistics
Matches: 136, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
35 5 0.04
36 71 0.52
37 59 0.43
38 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (35 bp):
TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1575729 original size:73 final size:71
Alignment explanation
Indices: 1575580--1575774 Score: 257
Period size: 73 Copynumber: 2.7 Consensus size: 71
1575570 TTGAATATGT
* * * * *
1575580 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTT
1 TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTCTCTT
1575645 GAGACAG
65 GAGACAG
*
1575652 TTTCCATAT-AAACAAATTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
1 TTTCC-T-TGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
*
1575716 TGAGATAG
64 TGAGACAG
* *
1575724 TTTTCCTTGAACCAAAGTTTTGTCTCTCTTGAGACATTTTCTCTTGAAACA
1 -TTTCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1575775 CCAACCTTTG
Statistics
Matches: 108, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
71 1 0.01
72 33 0.31
73 73 0.68
74 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (71 bp):
TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTG
AGACAG
Found at i:1575870 original size:33 final size:33
Alignment explanation
Indices: 1575828--1575911 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
1575818 CTGGAGACAA
*
1575828 TTTCTCTTGAAACACAAAAAACCTTTG-AAATCG
1 TTTCTCTTGAAACACAAAAAACATTTGAAAAT-G
1575861 TTTCTCTTGAAACACAAAAAACATTTGAAAATG
1 TTTCTCTTGAAACACAAAAAACATTTGAAAATG
1575894 TTTCTCTTGAAACACAAA
1 TTTCTCTTGAAACACAAA
1575912 GACCTTCGAG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 45 0.92
34 4 0.08
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (33 bp):
TTTCTCTTGAAACACAAAAAACATTTGAAAATG
Found at i:1576041 original size:80 final size:80
Alignment explanation
Indices: 1575908--1576103 Score: 225
Period size: 80 Copynumber: 2.4 Consensus size: 80
1575898 TCTTGAAACA
* * *
1575908 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCAAGGGCCATCATTTGCAGCATAACTCAAGTCT
1 CAAAGACCTTAGAGTTCAACTACACTCAGCTTCAAGGGCCATCATTTGCAGCATAACTCAAGTCG
*
1575973 AGAAGGGTTATCTGC
66 AGAAGGGCTATCTGC
* * * *
1575988 CAAAGACCTTAGAGTTCAATTCCATTCAGC-TCTAA-GGCGCATCATTTGCAGCATAACTTAAGT
1 CAAAGACCTTAGAGTTCAACTACACTCAGCTTC-AAGGGC-CATCATTTGCAGCATAACTCAAGT
1576051 CGAGAAGGGCTATCTGCCAAC
64 CGAGAAGGGCTATCTG----C
* * *
1576072 CAAAAACCTTCGAGTTCGACTACACTCAGCTT
1 CAAAGACCTTAGAGTTCAACTACACTCAGCTT
1576104 AGAGGTAAAT
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
79 5 0.05
80 64 0.67
84 25 0.26
85 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (80 bp):
CAAAGACCTTAGAGTTCAACTACACTCAGCTTCAAGGGCCATCATTTGCAGCATAACTCAAGTCG
AGAAGGGCTATCTGC
Found at i:1578173 original size:11 final size:11
Alignment explanation
Indices: 1578156--1578215 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
1578146 TCACTGTTAA
1578156 TATTTTTATTT
1 TATTTTTATTT
*
1578167 CATTTTTTATTT
1 TA-TTTTTATTT
1578179 T-TATTTTATTT
1 TAT-TTTTATTT
*
1578190 TATTTTTGTTT
1 TATTTTTATTT
1578201 TA-TTTTATTAT
1 TATTTTTATT-T
1578212 TATT
1 TATT
1578216 ATTACTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 7 0.17
11 22 0.55
12 11 0.28
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:1578179 original size:5 final size:5
Alignment explanation
Indices: 1578159--1578215 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
1578149 CTGTTAATAT
* * *
1578159 TTTTA TTTCA TTTT- TTAT- TTTTA TTTTA TTTTA TTTTTG TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
1578208 TTATTA TT
1 TT-TTA TT
1578216 ATTACTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
4 6 0.14
5 28 0.65
6 9 0.21
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:1578179 original size:6 final size:6
Alignment explanation
Indices: 1578156--1578225 Score: 51
Period size: 5 Copynumber: 12.2 Consensus size: 6
1578146 TCACTGTTAA
* *
1578156 TATTTT TA-TTT CATTTTT TATTTT TA-TTT TA-TTT TATTTT T-GTTT
1 TATTTT TATTTT TA-TTTT TATTTT TATTTT TATTTT TATTTT TATTTT
* *
1578201 TA-TTT TATTAT TATTAT TACTTTT T
1 TATTTT TATTTT TATTTT TA-TTTT T
1578226 TCCTCTCTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
5 23 0.43
6 22 0.42
7 8 0.15
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:1578264 original size:13 final size:13
Alignment explanation
Indices: 1578248--1578298 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
1578238 TTATGCTTTT
*
1578248 TATTTATTATTAA
1 TATTTTTTATTAA
*
1578261 TATTTTTTGTTAA
1 TATTTTTTATTAA
1578274 T-TTATTTTATTAA
1 TATT-TTTTATTAA
1578287 TATTTTTTATTA
1 TATTTTTTATTA
1578299 TTTGCTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 2 0.06
13 29 0.88
14 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TATTTTTTATTAA
Found at i:1580059 original size:37 final size:38
Alignment explanation
Indices: 1580012--1580094 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
1580002 TTTTGTTCGG
*
1580012 GTCGGTTCGGG-TTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
*
1580049 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
1580087 GTTCGGGT
1 G-TCGGGT
1580095 TTAGGGTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 10 0.24
38 26 0.62
39 6 0.14
ACGTcount: A:0.11, C:0.11, G:0.39, T:0.40
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:1580297 original size:249 final size:244
Alignment explanation
Indices: 1579830--1580333 Score: 798
Period size: 247 Copynumber: 2.0 Consensus size: 244
1579820 TATATTCGGG
*
1579830 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACTGACCCGAAAATATATATAATTCAGGT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGT
*
1579895 CGGATCGGATTAAGTCATTGTTTTTATTAAATAATTTTTTTTTATTTCGGGTCGGGTCAGGTTGG
66 CGGATCGGATTAAGTCATTGGTTTTATTAAATAATTTTTTTTTATTTCGGGTCGGGTCAGGTTGG
* *
1579960 ATTTCTAATTCATATATTCGGGTCGGGTCGGATAAAACTTTATTTTGTTCGGGTCGGTTCGGGTT
131 ATTTCTAATTCATATATT---GTCGGGTCGGATAAAACTTTATTTTGTTCGGGTCGGGTCGGATT
1580025 TTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATAT
193 TTTTAAGTGTGATATTCGGGTCGAGTC-GGTCGGGTTTTTTTAAGTGTGATAT
*
1580078 TCGGGTCGGGTTCGGGTTTAGGGTG-AAAAAACCGGACCGACCCGAAAATATATATAATTCGGGT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGT
* *
1580142 CGGGTCGGATTAAGTCATTGGTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTTCGGGTT
66 CGGATCGGATTAAGTCATTGGTTTTATTAAAT---AAT--TTTTTT-TTATTTCGGG-TCGGGTC
* * *
1580207 GGGTTGGATTTCTAATTCATATA-T-TCGGGTCGGATGAAATTTTATTTTGTTCGGGTCGGGTCG
124 AGGTTGGATTTCTAATTCATATATTGTCGGGTCGGATAAAACTTTATTTTGTTCGGGTCGGGTCG
1580270 GATTTTTTAAGTGTGATATTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATAT
189 GATTTTTTAAGTGTGATATTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATAT
1580326 TCGGGTCG
1 TCGGGTCG
1580334 AGTCGGTCGG
Statistics
Matches: 239, Mismatches: 10, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
247 67 0.28
248 58 0.24
249 66 0.28
250 3 0.01
252 6 0.03
253 11 0.05
254 28 0.12
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (244 bp):
TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGT
CGGATCGGATTAAGTCATTGGTTTTATTAAATAATTTTTTTTTATTTCGGGTCGGGTCAGGTTGG
ATTTCTAATTCATATATTGTCGGGTCGGATAAAACTTTATTTTGTTCGGGTCGGGTCGGATTTTT
TAAGTGTGATATTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:1580302 original size:32 final size:34
Alignment explanation
Indices: 1580256--1580381 Score: 157
Period size: 37 Copynumber: 3.6 Consensus size: 34
1580246 TTTTATTTTG
*
1580256 TTCGGGTCG-GGTC-GGATTTTTTAAGTGTGATA
1 TTCGGGTCGAGGTCGGGTTTTTTTAAGTGTGATA
1580288 TTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGA---GGTCGGGTTTTTTTAAGTGTGATA
1580325 TTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGA---GGTCGGGTTTTTTTAAGTGTGATA
* *
1580362 TTCGGGTCGAGTTAGGGTTT
1 TTCGGGTCGAGGTCGGGTTT
1580382 AAGGTGAAAA
Statistics
Matches: 86, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
32 9 0.10
34 8 0.09
36 4 0.05
37 65 0.76
ACGTcount: A:0.13, C:0.10, G:0.36, T:0.40
Consensus pattern (34 bp):
TTCGGGTCGAGGTCGGGTTTTTTTAAGTGTGATA
Found at i:1580313 original size:37 final size:37
Alignment explanation
Indices: 1580272--1580373 Score: 204
Period size: 37 Copynumber: 2.8 Consensus size: 37
1580262 TCGGGTCGGA
1580272 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGTCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGTCGGGT
1580309 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGTCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGTCGGGT
1580346 TTTTTTAAGTGTGATATTCGGGTCGAGT
1 TTTTTTAAGTGTGATATTCGGGTCGAGT
1580374 TAGGGTTTAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.15, C:0.10, G:0.33, T:0.42
Consensus pattern (37 bp):
TTTTTTAAGTGTGATATTCGGGTCGAGTCGGTCGGGT
Found at i:1580344 original size:285 final size:288
Alignment explanation
Indices: 1580012--1580638 Score: 1014
Period size: 286 Copynumber: 2.2 Consensus size: 288
1580002 TTTTGTTCGG
1580012 GTCGGTTCGGG-TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGAT
1 GTCGG-TCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGAT
* * *
1580076 ATTCGGGTCGGGTTCGGGTTTAGGGTG-AAAAAACCGGACCGACCCGAAAATATATATAATTCGG
65 ATTCGGGTCGAGTTAGGGTTTAAGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGG
* *
1580140 GTCGGGTCGGATTAAGTCATTGGTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTTCGGG
130 GTCGAGTCGGATTAAGTCACTGGTTTTATTAAATAAAAATAATTTTTTATTATTTCGGG-TCGGG
* * *
1580205 TTGGGTTGGATTTCTAATTCATATA-T-TCGGGTCGGATGAAATTTTATTTTGTTCGGGTCGGGT
194 TCGGGTCGGATTTCTAATTCATATATTGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGT
1580268 CGGATTTTTTAAGTGTGATATTCGGGTCGA
259 CGGATTTTTTAAGTGTGATATTCGGGTCGA
1580298 GTCGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTC-GGTCGGGTTTTTTTAAGTGTGATA
1 GTCGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATA
*
1580362 TTCGGGTCGAGTTAGGGTTTAAGGTGAAAAAAATCGGACCGACCCGAAAATATATATAATTCGGG
66 TTCGGGTCGAGTTAGGGTTTAAGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGG
* * *
1580427 TCGAGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTTTGGGTCGGGTC
131 TCGAGTCGGATTAAGTCACTGGTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC
*
1580492 GGGTCGGATTTCTAATTCATTTATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGG
196 GGGTCGGATTTCTAATTCATATATT---GTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGG
*
1580557 TCGGGTTTTTTAAGTGTGATATTCGGGTCGA
258 TCGGATTTTTTAAGTGTGATATTCGGGTCGA
*
1580588 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTC-AGGTCGGGTCGGGTT
1 GTC-GGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA-GTCGGGTCGGGTT
1580639 CGGGTTTAGG
Statistics
Matches: 316, Mismatches: 15, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
285 79 0.25
286 125 0.40
290 69 0.22
291 34 0.11
292 9 0.03
ACGTcount: A:0.21, C:0.11, G:0.30, T:0.38
Consensus pattern (288 bp):
GTCGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATA
TTCGGGTCGAGTTAGGGTTTAAGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGG
TCGAGTCGGATTAAGTCACTGGTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC
GGGTCGGATTTCTAATTCATATATTGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCG
GATTTTTTAAGTGTGATATTCGGGTCGA
Found at i:1580613 original size:38 final size:38
Alignment explanation
Indices: 1580550--1580638 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
1580540 ATTTTGTTCG
*
1580550 GGTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTC-
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
1580586 GAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
1 G-GTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
1580625 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
1580639 CGGGTTTAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
36 1 0.02
37 11 0.22
38 36 0.73
39 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.39, T:0.37
Consensus pattern (38 bp):
GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
Found at i:1581233 original size:16 final size:17
Alignment explanation
Indices: 1581212--1581257 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
1581202 TATGGAATTG
1581212 GATTCCAATTCCT-ACA
1 GATTCCAATTCCTCACA
*
1581228 GATTCCAATTCATTCACA
1 GATTCCAATTC-CTCACA
*
1581246 GATTTCAATTCC
1 GATTCCAATTCC
1581258 CTCATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:1593150 original size:11 final size:11
Alignment explanation
Indices: 1593134--1593158 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1593124 CAAAACCCTT
1593134 AAAAATCTTAA
1 AAAAATCTTAA
1593145 AAAAATCTTAA
1 AAAAATCTTAA
1593156 AAA
1 AAA
1593159 CTTTTTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATCTTAA
Found at i:1593541 original size:29 final size:27
Alignment explanation
Indices: 1593508--1593576 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 27
1593498 ATTAGATAAA
1593508 AAAATAAATAAATATTTAATAAATCAAA-G
1 AAAATAAATAAATA---AATAAATCAAAGG
1593537 AAAATAAATAAATAAATAAATCAAAGG
1 AAAATAAATAAATAAATAAATCAAAGG
*
1593564 AAAAAAAGATAAA
1 AAAATAA-ATAAA
1593577 AATAAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
26 11 0.30
27 7 0.19
28 5 0.14
29 14 0.38
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (27 bp):
AAAATAAATAAATAAATAAATCAAAGG
Found at i:1593579 original size:26 final size:26
Alignment explanation
Indices: 1593507--1593628 Score: 82
Period size: 26 Copynumber: 4.8 Consensus size: 26
1593497 TATTAGATAA
1593507 AAAAATAAATAAATATTTAATAAATCAAAG
1 AAAAA-AAATAAATA---AATAAATCAAAG
*
1593537 AAAATAAATAAATAAATAAATCAAAG
1 AAAAAAAATAAATAAATAAATCAAAG
* *
1593563 -GAAAAAA-AGAT-AA-AAAT-AAA-
1 AAAAAAAATAAATAAATAAATCAAAG
*
1593583 AATAAAAAAT-ATTAAATAAATCAAAGG
1 AA-AAAAAATAAATAAATAAATCAAA-G
1593610 AAAAAATAA-AAA-AAATAAA
1 AAAAAA-AATAAATAAATAAA
1593629 AAAATGTTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
21 3 0.04
22 11 0.15
23 4 0.05
24 7 0.09
25 8 0.11
26 23 0.31
27 5 0.07
29 9 0.12
30 4 0.05
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (26 bp):
AAAAAAAATAAATAAATAAATCAAAG
Found at i:1593599 original size:46 final size:44
Alignment explanation
Indices: 1593537--1593630 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 44
1593527 TAAATCAAAG
* *
1593537 AAAATAAATAAATAAATAAATCAAAGGAAAAAA-AGATAAAAATA
1 AAAATAAAAAAATAAATAAATCAAAGGAAAAAATA-AAAAAAATA
1593581 AAAATAAAAAATATTAAATAAATCAAAGGAAAAAATAAAAAAAATA
1 AAAATAAAAAA-A-TAAATAAATCAAAGGAAAAAATAAAAAAAATA
1593627 AAAA
1 AAAA
1593631 AATGTTAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 10 0.22
45 1 0.02
46 33 0.73
47 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (44 bp):
AAAATAAAAAAATAAATAAATCAAAGGAAAAAATAAAAAAAATA
Found at i:1593717 original size:40 final size:41
Alignment explanation
Indices: 1593675--1593750 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
1593665 ATAAGAAGTA
*
1593675 AAAAATAAAA-CAAACAAATAAATAAAT-AAATAAAATACT
1 AAAAATAAAAGCAAAAAAATAAATAAATAAAATAAAATACT
* * *
1593714 AAAATTAAAAGGAAAAAAATAAATAATTAAAATAAAA
1 AAAAATAAAAGCAAAAAAATAAATAAATAAAATAAAA
1593751 AATGCTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 9 0.29
40 14 0.45
41 8 0.26
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.18
Consensus pattern (41 bp):
AAAAATAAAAGCAAAAAAATAAATAAATAAAATAAAATACT
Found at i:1593730 original size:21 final size:21
Alignment explanation
Indices: 1593706--1593766 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1593696 ATAAATAAAT
1593706 AAAATACTAAAATTAAAAGGAA
1 AAAATACTAAAATTAAAA-GAA
*
1593728 AAAA-A-TAAATAATTAAAATAA
1 AAAATACT-AA-AATTAAAAGAA
*
1593749 AAAATGCTAAAATTAAAA
1 AAAATACTAAAATTAAAA
1593767 AAGGGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 1 0.03
21 17 0.52
22 14 0.42
23 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAATACTAAAATTAAAAGAA
Found at i:1593769 original size:45 final size:41
Alignment explanation
Indices: 1593690--1593790 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 41
1593680 TAAAACAAAC
1593690 AAATAAATAAAT-AAATAAAATACTAAAATTAAAAGGAAAA
1 AAATAAATAAATAAAATAAAATACTAAAATTAAAAGGAAAA
* * *
1593730 AAATAAATAATTAAAATAAAAAATGCTAAAATTAAAAAAGGGAAA
1 AAATAAATAAATAAAAT--AAAATACTAAAATT--AAAAGGAAAA
* *
1593775 AAATGAATAACTAAAA
1 AAATAAATAAATAAAA
1593791 ATTTAAAGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 11 0.22
41 4 0.08
43 13 0.25
45 23 0.45
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (41 bp):
AAATAAATAAATAAAATAAAATACTAAAATTAAAAGGAAAA
Found at i:1595035 original size:9 final size:9
Alignment explanation
Indices: 1595014--1595094 Score: 55
Period size: 9 Copynumber: 8.9 Consensus size: 9
1595004 TGGACCGAAT
1595014 TAAAATAAAA
1 TAAAAT-AAA
1595024 TAAAATAAA
1 TAAAATAAA
1595033 TAAAAT-AA
1 TAAAATAAA
*
1595041 -AACATATAA
1 TAAAATA-AA
1595050 T-AAATAAA
1 TAAAATAAA
*
1595058 -AAGTATAAA
1 TAA-AATAAA
1595067 TAAAGATAAA
1 TAAA-ATAAA
1595077 TAATAAT-AA
1 TAA-AATAAA
1595086 TAATAATAA
1 TAA-AATAA
1595095 TATAGTATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
7 4 0.07
8 5 0.09
9 29 0.50
10 19 0.33
11 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (9 bp):
TAAAATAAA
Found at i:1595053 original size:21 final size:19
Alignment explanation
Indices: 1595014--1595096 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 19
1595004 TGGACCGAAT
1595014 TAAAATAAAATAAAATAAA
1 TAAAATAAAATAAAATAAA
*
1595033 TAAAATAAAACATATAATAAA
1 TAAAAT-AAA-ATAAAATAAA
1595054 TAAAAAGTATAAATAAAGATAAA
1 T-AAAA-TA-AAATAAA-ATAAA
1595077 TAATAATAATAATAATAATA
1 TAA-AATAA-AATAA-AATA
1595097 TAGTATATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
19 6 0.11
20 3 0.06
21 11 0.21
22 21 0.40
23 12 0.23
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.25
Consensus pattern (19 bp):
TAAAATAAAATAAAATAAA
Found at i:1595064 original size:16 final size:17
Alignment explanation
Indices: 1595028--1595070 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
1595018 ATAAAATAAA
1595028 ATAAATAAAATAAAACAT
1 ATAAAT-AAATAAAACAT
1595046 AT-AATAAATAAAA-AGT
1 ATAAATAAATAAAACA-T
1595062 ATAAATAAA
1 ATAAATAAA
1595071 GATAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 11 0.48
17 9 0.39
18 2 0.09
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
ATAAATAAATAAAACAT
Found at i:1595177 original size:35 final size:36
Alignment explanation
Indices: 1595094--1595309 Score: 249
Period size: 36 Copynumber: 5.9 Consensus size: 36
1595084 AATAATAATA
* * *
1595094 ATATAGTATATATATTTTCAAAAATATTTCCCAAAACT
1 ATATATTATATATGTTTTCAAAAATATTT-TC-AAACT
* *
1595132 ATATAATATAT-TTTTTTCAAAAATATTTTCAAACT
1 ATATATTATATATGTTTTCAAAAATATTTTCAAACT
* ** *
1595167 ATATATTATATATATTTTTGAAAATGTTTTCAAAACT
1 ATATATTATATATGTTTTCAAAAATATTTTC-AAACT
*
1595204 ATATATTATATA-GTTTTCAAAAATATTTTAAAACT
1 ATATATTATATATGTTTTCAAAAATATTTTCAAACT
*
1595239 ATATATTATATAAGTTTTCAAAAATATTTTCAAAAACT
1 ATATATTATATATGTTTTCAAAAATATTTTC--AAACT
* *
1595277 ATATATTATATATATTTTC-AAAATGTTTTCAAA
1 ATATATTATATATGTTTTCAAAAATATTTTCAAA
1595310 AAATATACAT
Statistics
Matches: 156, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
35 35 0.22
36 46 0.29
37 43 0.28
38 32 0.21
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATATTATATATGTTTTCAAAAATATTTTCAAACT
Found at i:1595307 original size:37 final size:37
Alignment explanation
Indices: 1595094--1595466 Score: 323
Period size: 37 Copynumber: 9.6 Consensus size: 37
1595084 AATAATAATA
* * * *
1595094 ATATAGTATATATATTTTCAAAAATATTTCCCAAAACT
1 ATATATTATATATATTTTC-AAAATGTTTTCAAAAACT
* * *
1595132 ATATAATATAT-TTTTTTCAAAAATATTTTC--AAACT
1 ATATATTATATATATTTTC-AAAATGTTTTCAAAAACT
*
1595167 ATATATTATATATATTTTTGAAAATGTTTTC-AAAACT
1 ATATATTATATATA-TTTTCAAAATGTTTTCAAAAACT
* *
1595204 ATATATTATATA-GTTTTCAAAAATATTTT--AAAACT
1 ATATATTATATATATTTTC-AAAATGTTTTCAAAAACT
*
1595239 ATATATTATATA-AGTTTTCAAAAATATTTTCAAAAACT
1 ATATATTATATATA-TTTTC-AAAATGTTTTCAAAAACT
*
1595277 ATATATTATATATATTTTCAAAATGTTTTCAAAAAAT
1 ATATATTATATATATTTTCAAAATGTTTTCAAAAACT
* *
1595314 ATACATTAAATATATATTTTTAAAATGTTTTTCAAAAAACTATATTAT
1 ATATATT--ATATATATTTTCAAAATG-TTTTC-AAAAAC-------T
1595362 ATATATATATATATATATATTCAAAATGTTTT-AAAAACTATT
1 ATATAT-TATATATAT-T-TTCAAAATGTTTTCAAAAAC---T
1595404 ATATATATATATATATATATTCAAAATGTTTTCAAAAACT
1 ATATAT-TATATATAT-T-TTCAAAATGTTTTCAAAAACT
1595444 ATATATTATATATATTTTCAAAA
1 ATATATTATATATATTTTCAAAA
1595467 ACCGATTTTT
Statistics
Matches: 292, Mismatches: 20, Indels: 47
0.81 0.06 0.13
Matches are distributed among these distances:
35 37 0.13
36 36 0.12
37 67 0.23
38 34 0.12
39 27 0.09
40 12 0.04
41 5 0.02
42 34 0.12
43 6 0.02
46 6 0.02
47 8 0.03
48 11 0.04
49 9 0.03
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (37 bp):
ATATATTATATATATTTTCAAAATGTTTTCAAAAACT
Found at i:1595364 original size:35 final size:33
Alignment explanation
Indices: 1595132--1595365 Score: 146
Period size: 36 Copynumber: 6.4 Consensus size: 33
1595122 TCCCAAAACT
* * * **
1595132 ATATAATATATTTTTTTCAAAAATATTTTCAAACT
1 ATATATTATATATTTTT--AAAATGTTTTCAAAAA
*
1595167 ATATATTATATATATTTTTGAAAATGTTTTCAAAACT
1 ATATA-T-TATATATTTTT-AAAATGTTTTCAAAA-A
* * *
1595204 ATATATTATATAGTTTTCAAAAATATTTT-AAAACT
1 ATATATTATATA-TTTT-TAAAATGTTTTCAAAA-A
* *
1595239 ATATATTATATAAGTTTTCAAAAATATTTTCAAAAA
1 ATATATTATAT-A-TTTT-TAAAATGTTTTCAAAAA
1595275 CTATATATTATATATATTTTCAAAATGTTTTCAAAAA
1 --ATATATTATATAT-TTTT-AAAATGTTTTCAAAAA
1595312 ATATACATTAAATATATATTTTTAAAATGTTTTTCAAAAA
1 ATAT--A-T---TATATATTTTTAAAATG-TTTTCAAAAA
1595352 ACTATATTATATAT
1 A-TATATTATATAT
1595366 ATATATATAT
Statistics
Matches: 170, Mismatches: 10, Indels: 38
0.78 0.05 0.17
Matches are distributed among these distances:
35 39 0.23
36 46 0.27
37 40 0.24
38 13 0.08
39 7 0.04
40 15 0.09
41 10 0.06
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (33 bp):
ATATATTATATATTTTTAAAATGTTTTCAAAAA
Found at i:1595446 original size:89 final size:86
Alignment explanation
Indices: 1595276--1595458 Score: 239
Period size: 88 Copynumber: 2.1 Consensus size: 86
1595266 TTTCAAAAAC
* * *
1595276 TATATAT-TATATATATTTTCAAAATGTTTTCAAAAAATATACATTAAATATATATTTTTAAAAT
1 TATATATATATATATATATTCAAAATGTTTTCAAAAAATATACATTAAATATATATATTCAAAAT
1595340 GTTTTTCAAAAAACTATATTAT
66 GTTTTTCAAAAAACTATA-TAT
* *
1595362 ATATATATATATATATATATTCAAAATGTTTT-AAAAACTATTATATATATATATATATATATTC
1 -TATATATATATATATATATTCAAAATGTTTTCAAAAA--A-TATACAT-TAAATATATATATTC
1595426 AAAATG-TTTTC-AAAAACTATATAT
61 AAAATGTTTTTCAAAAAACTATATAT
1595450 TATATATAT
1 TATATATAT
1595459 TTTCAAAAAC
Statistics
Matches: 86, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
87 21 0.24
88 25 0.29
89 11 0.13
90 11 0.13
91 18 0.21
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (86 bp):
TATATATATATATATATATTCAAAATGTTTTCAAAAAATATACATTAAATATATATATTCAAAAT
GTTTTTCAAAAAACTATATAT
Done.