Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 64
Found at i:5746658 original size:46 final size:43
Alignment explanation
Indices: 5746587--5746704 Score: 112
Period size: 46 Copynumber: 2.7 Consensus size: 43
5746577 AGTACCAATC
* * * * *
5746587 TTTTGTTTGATCATTAACAGAAGGAGTTGGATTAGCAT-TATCTTA
1 TTTTGCTTGATTATTCACAGAAGGAGTTGGATAAGCATCGA-C--A
* *
5746632 TTTTGCTTGATTATATCACAGAAGGAGGTAGATAAGCATCGACA
1 TTTTGCTTGATTAT-TCACAGAAGGAGTTGGATAAGCATCGACA
* *
5746676 TTTTGTTTGATTATTCACGGAAGGAGTTG
1 TTTTGCTTGATTATTCACAGAAGGAGTTG
5746705 TATCAACAGT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
43 12 0.20
44 14 0.23
45 12 0.20
46 21 0.35
47 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (43 bp):
TTTTGCTTGATTATTCACAGAAGGAGTTGGATAAGCATCGACA
Found at i:5747700 original size:16 final size:16
Alignment explanation
Indices: 5747655--5747713 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
5747645 TATTAAATAA
*
5747655 ATGCATATTATATAAT
1 ATGCATATTATATAGT
* *
5747671 -TGCATGTTAAATAGT
1 ATGCATATTATATAGT
*
5747686 AAGCATATTATATAG-
1 ATGCATATTATATAGT
5747701 ATTGCATATTATA
1 A-TGCATATTATA
5747714 AATAATAGCC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 13 0.38
16 21 0.62
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (16 bp):
ATGCATATTATATAGT
Found at i:5749138 original size:30 final size:29
Alignment explanation
Indices: 5749103--5749161 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
5749093 ACATTGGATA
5749103 TTAAATA-AATGCATATTATATAATTGCATG
1 TTAAATAGAA-GCATATTATAT-ATTGCATG
*
5749133 TTAAATAGTAAGCATATTATGTATTGCAT
1 TTAAATAG-AAGCATATTATATATTGCAT
5749162 ATTATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 14 0.54
31 10 0.38
32 2 0.08
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (29 bp):
TTAAATAGAAGCATATTATATATTGCATG
Found at i:5750526 original size:15 final size:15
Alignment explanation
Indices: 5750506--5750592 Score: 63
Period size: 15 Copynumber: 5.7 Consensus size: 15
5750496 ACATGTGGTT
5750506 CATATTAAATAATTG
1 CATATTAAATAATTG
* *
5750521 CATATTATA-AATAG
1 CATATTAAATAATTG
5750535 --TATTACATATGACATTG
1 CATATTA-A-AT-A-ATTG
* *
5750552 GATATTAAATAAATG
1 CATATTAAATAATTG
*
5750567 CATATTATATAATTG
1 CATATTAAATAATTG
*
5750582 CATGTTAAATA
1 CATATTAAATA
5750593 GTAAGCATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
12 5 0.09
14 5 0.09
15 32 0.58
16 2 0.04
17 5 0.09
18 1 0.02
19 5 0.09
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (15 bp):
CATATTAAATAATTG
Found at i:5752012 original size:46 final size:46
Alignment explanation
Indices: 5751960--5752074 Score: 221
Period size: 46 Copynumber: 2.5 Consensus size: 46
5751950 CATGTGGTTC
*
5751960 ATATTAAATAATTGCATATTATAAATAGTATTACATATTACATTGG
1 ATATTAAATAAATGCATATTATAAATAGTATTACATATTACATTGG
5752006 ATATTAAATAAATGCATATTATAAATAGTATTACATATTACATTGG
1 ATATTAAATAAATGCATATTATAAATAGTATTACATATTACATTGG
5752052 ATATTAAATAAATGCATATTATA
1 ATATTAAATAAATGCATATTATA
5752075 TAATTGCATG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (46 bp):
ATATTAAATAAATGCATATTATAAATAGTATTACATATTACATTGG
Found at i:5752108 original size:16 final size:16
Alignment explanation
Indices: 5752063--5752121 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
5752053 TATTAAATAA
*
5752063 ATGCATATTATATAAT
1 ATGCATATTATATAGT
* *
5752079 -TGCATGTTAAATAGT
1 ATGCATATTATATAGT
*
5752094 AAGCATATTATATAG-
1 ATGCATATTATATAGT
5752109 ATTGCATATTATA
1 A-TGCATATTATA
5752122 AATAATATCC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 13 0.38
16 21 0.62
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (16 bp):
ATGCATATTATATAGT
Found at i:5752149 original size:14 final size:15
Alignment explanation
Indices: 5752052--5752152 Score: 51
Period size: 15 Copynumber: 6.4 Consensus size: 15
5752042 ATTACATTGG
* *
5752052 ATATTAAATAAATGC
1 ATATTAAATAATTCC
* *
5752067 ATATTATATAATTGC
1 ATATTAAATAATTCC
* * **
5752082 ATGTTAAATAGTAAGC
1 ATATTAAATAAT-TCC
* *
5752098 ATATTATATAGATTGC
1 ATATTAAATA-ATTCC
5752114 ATATTATAAATAATATCCC
1 ATA-T-TAAATAAT-T-CC
5752133 ATATTAAATAATT-C
1 ATATTAAATAATTCC
5752147 ATATTA
1 ATATTA
5752153 GTATGACCTA
Statistics
Matches: 68, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
14 7 0.10
15 22 0.32
16 16 0.24
17 12 0.18
18 7 0.10
19 4 0.06
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.40
Consensus pattern (15 bp):
ATATTAAATAATTCC
Found at i:5757213 original size:28 final size:28
Alignment explanation
Indices: 5757173--5757250 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
5757163 TTTCATTTAT
5757173 ATTATGTCATCAAGTCAGTGCTTGAAAC
1 ATTATGTCATCAAGTCAGTGCTTGAAAC
5757201 ATTATGTCATCAAGTCAGTGCTTGAAAC
1 ATTATGTCATCAAGTCAGTGCTTGAAAC
* *
5757229 ATTATGTCCTCGAGTCAGTGCT
1 ATTATGTCATCAAGTCAGTGCT
5757251 AAAAAGAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (28 bp):
ATTATGTCATCAAGTCAGTGCTTGAAAC
Found at i:5772126 original size:159 final size:160
Alignment explanation
Indices: 5771837--5772155 Score: 631
Period size: 159 Copynumber: 2.0 Consensus size: 160
5771827 CAAAATCGAG
5771837 ATAACCTTGCAGCAGCTCCTTGGGTGGTACATAATAGGTTCGACCTCTTCGATTCCTTTCATTGA
1 ATAACCTTGCAGCAGCTCCTTGGGTGGTACATAATAGGTTCGACCTCTTCGATTCCTTTCATTGA
5771902 AAGGATTGAACGTTTCTTCTGGTGGCCCTTTGGTTTCATCTGAGCATGTGTCAAAGGACGAAGGT
66 AAGGATTGAACGTTTCTTCTGGTGGCCCTTTGGTTTCATCTGAGCATGTGTCAAAGGACGAAGGT
5771967 T-GGGCTGCCCGGATGAGCGACGAGAAAAA
131 TGGGGCTGCCCGGATGAGCGACGAGAAAAA
5771996 ATAACCTTGCAGCAGCTCCTTGGGTGGTACATAATAGGTTCGACCTCTTCGATTCCTTTCATTGA
1 ATAACCTTGCAGCAGCTCCTTGGGTGGTACATAATAGGTTCGACCTCTTCGATTCCTTTCATTGA
5772061 AAGGATTGAACGTTTCTTCTGGTGGCCCTTTGGTTTCATCTGAGCATGTGTCAAAGGACGAAGGT
66 AAGGATTGAACGTTTCTTCTGGTGGCCCTTTGGTTTCATCTGAGCATGTGTCAAAGGACGAAGGT
5772126 TGGGGCTGCCCGGATGAGCGACGAGAAAAA
131 TGGGGCTGCCCGGATGAGCGACGAGAAAAA
5772156 GAAGGCGTGG
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 131 0.82
160 28 0.18
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (160 bp):
ATAACCTTGCAGCAGCTCCTTGGGTGGTACATAATAGGTTCGACCTCTTCGATTCCTTTCATTGA
AAGGATTGAACGTTTCTTCTGGTGGCCCTTTGGTTTCATCTGAGCATGTGTCAAAGGACGAAGGT
TGGGGCTGCCCGGATGAGCGACGAGAAAAA
Found at i:5777362 original size:21 final size:21
Alignment explanation
Indices: 5777296--5777363 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
5777286 ACTTTGGAAT
*
5777296 TTTTCATGGGATGCAACTAGC
1 TTTTCATGGGATGCAACCAGC
* * *
5777317 TTTTCCTAGGATGCAACCAGT
1 TTTTCATGGGATGCAACCAGC
* *
5777338 TTTTCATGGGATGTAACCAAC
1 TTTTCATGGGATGCAACCAGC
5777359 TTTTC
1 TTTTC
5777364 TTGTGAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (21 bp):
TTTTCATGGGATGCAACCAGC
Found at i:5782570 original size:52 final size:52
Alignment explanation
Indices: 5782508--5782611 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
5782498 CTGTACAGAC
5782508 AGATTCCAGAAACCAAAAGTCATTGTCCCTTGGAACTGCATCAAGAATATTT
1 AGATTCCAGAAACCAAAAGTCATTGTCCCTTGGAACTGCATCAAGAATATTT
5782560 AGATTCCAGAAACCAAAAGTCATTGTCCCTTGGAACTGCATCAAGAATATTT
1 AGATTCCAGAAACCAAAAGTCATTGTCCCTTGGAACTGCATCAAGAATATTT
5782612 TGAAAACTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (52 bp):
AGATTCCAGAAACCAAAAGTCATTGTCCCTTGGAACTGCATCAAGAATATTT
Found at i:5785680 original size:80 final size:80
Alignment explanation
Indices: 5785547--5785703 Score: 289
Period size: 80 Copynumber: 2.0 Consensus size: 80
5785537 AATCTTTAAG
*
5785547 AAAATGGATATATCCATATCCACAATGGAATCTAAGTTTGTAGCTTTAGAAAAGTCTACAAAATA
1 AAAATGGATATATCCAGATCCACAATGGAATCTAAGTTTGTAGCTTTAGAAAAGTCTACAAAATA
5785612 AGTTGAATGACTAAA
66 AGTTGAATGACTAAA
5785627 AAAATGGATATAGT-CAGATCCACAATGGAATCTAAGTTTGTAGCTTTAGAAAAGTCTACAAAAT
1 AAAATGGATATA-TCCAGATCCACAATGGAATCTAAGTTTGTAGCTTTAGAAAAGTCTACAAAAT
5785691 AAGTTGAATGACT
65 AAGTTGAATGACT
5785704 TTAGGATTTC
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
80 74 0.99
81 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (80 bp):
AAAATGGATATATCCAGATCCACAATGGAATCTAAGTTTGTAGCTTTAGAAAAGTCTACAAAATA
AGTTGAATGACTAAA
Found at i:5787490 original size:18 final size:18
Alignment explanation
Indices: 5787469--5787504 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5787459 TGCCTTTATT
*
5787469 TATTTAATCTCTTTTTAC
1 TATTTAATCTCATTTTAC
*
5787487 TATTTAATTTCATTTTAC
1 TATTTAATCTCATTTTAC
5787505 CAACCCCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTAATCTCATTTTAC
Found at i:5792629 original size:18 final size:19
Alignment explanation
Indices: 5792606--5792642 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
5792596 CAGCACTTAT
5792606 TTTTCAAAATCAAA-ATAG
1 TTTTCAAAATCAAATATAG
5792624 TTTTCAAAATCAAATATAG
1 TTTTCAAAATCAAATATAG
5792643 ACTTTGGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (19 bp):
TTTTCAAAATCAAATATAG
Found at i:5795148 original size:18 final size:18
Alignment explanation
Indices: 5795125--5795167 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
5795115 AACTCGAATC
5795125 TTAATTTACAATTTGAAG
1 TTAATTTACAATTTGAAG
5795143 TTAATTTACAATTTGAAG
1 TTAATTTACAATTTGAAG
*
5795161 TTTATTT
1 TTAATTT
5795168 GAATTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (18 bp):
TTAATTTACAATTTGAAG
Found at i:5801988 original size:932 final size:916
Alignment explanation
Indices: 5800192--5802049 Score: 3473
Period size: 932 Copynumber: 2.0 Consensus size: 916
5800182 GAACAAAACA
5800192 GTCATGAGCAAAAACATAATTCATCATTCATAAAATAGAAAATAATTGTCTAGGAAAAACAAAGA
1 GTCATG-GCAAAAACATAATTCATCATTCATAAAATAGAAAATAATTGTCTAGGAAAAACAAAGA
*
5800257 TTAACACCAAGTAAGACAATCATGGTATTATAAAAAATTCATCCAATTATCATTGTTTAATACAA
65 TTAAAACCAAGTAAGACAATCATGGTATTATAAAAAATTCATCCAATTATCATTGTTTAATACAA
5800322 CCCCAAATACGTAAAGAAATTAAGAACAAAGGAAGAACGACTCCCAAAATTGGGGGCTCTGTCGT
130 CCCCAAATACGTAAAGAAATTAAGAACAAAGGAAGAACGACTCCCAAAATTGGGGGCTCTGTCGT
5800387 TACAATTCTGACCAGCACCGCGCCTGCCTTGGTGATCAGCCTCTCTCGAGACCTGACCACTGCTC
195 TACAATTCTGACCAGCACCGCGCCTGCCTTGGTGATCAGCCTCTCTCGAGACCTGACCACTGCTC
5800452 TTCTATAGTCTAGCTATGGAGGACACCAAGGAAGATCGGCTGGTAAACGGTGGGGAGCTCACACT
260 TTCTATAGTCTAGCTATGGAGGACACCAAGGAAGATCGGCTGGTAAACGGTGGGGAGCTCACACT
*
5800517 TTAAGTAAGGCTCTCTAACTTCCTCCCCCTTTGGCGGCTACAATTTGATATTTATAGAGGGTAAT
325 TTAAGTAAGGCTCTCTAACTTCCTCCCCCTTTGGCGGCTACAATTTGATATTTATAGAGGGGAAT
*
5800582 CTCCTAGGGTTTTGCATGATTGGAGATCCTTAGACTAAAAAGGAAAGGTGGTTGGCGGCTGTCAA
390 CTCCTAGGGTTTTGCATGATTGGAGATCCTTAGACTAAAAAGGAAAGGTGGTTGGCAGCTGTCAA
5800647 AATTTTAAGGGTTTGCTTGCATGTGAAGAAGTCATCAAGGTGGCTCATAACATAGGCAAATTCGT
455 AATTTTAAGGGTTTGCTTGCATGTGAAGAAGTCATCAAGGTGGCTCATAACATAGGCAAATTCGT
5800712 CATACCCGCTTCAGACTTTCTAGATAAACCTTGCCTTGGCGAGATAAATCTGCTCCTCACGTTCT
520 CATACCCGCTTCAGACTTTCTAGATAAACCTTGCCTTGGCGAGATAAATCTGCTCCTCACGTTCT
5800777 TTAACTTCTCTATTCCATTGGCCCTTACGAATTTTGTTGTCGCGACTGAAATGTTCTTCCTCCGT
585 TTAACTTCTCTATTCCATTGGCCCTTACGAATTTTGTTGTCGCGACTGAAATGTTCTTCCTCCGT
5800842 AAAATTCCTGCACATACACAATCCACAAAAACTCTTTCTCCTCAGCAGCATCAGTTAAACCAAAT
650 AAAATTCCTGCACATACACAATCCACAAAAACTCTTTCTCCTCAGCAGCATCAGTTAAACCAAAT
*
5800907 AAATCTTGCCAAAGCAAAACTTATCCACCACAAGAAAATATAACCTAAATGCAACTAAAATGTTA
715 AAATCTTGCCAAAGCAAAACTTATCCACCACAAGAAAATATAACCTAAATACAACTAAAATGTTA
*
5800972 TGCATACTTTGTTTAGATGAGCAACAACTTAAGTGAAAAGTCTAGAAATTGAGACTTTTTACGGA
780 TGCATACTTTGTTTAGATGAGCAACAACTTAAGTGAAAAGTATAGAAATTGAGACTTTTTACGGA
5801037 GTTTCACACCCGCAAACTTAAGCTATTGCCTGCCCTCAAGCAATTTACAATAGCTAGAAGAAAAT
845 GTTTCACACCCGCAAACTTAAGCTATTGCCTGCCCTCAAGCAATTTACAATAGCTAGAAGAAAAT
5801102 TAAAATT
910 TAAAATT
5801109 GTCATGGCAAAAACATAATTCATCATTCATAAAATAGAAAATAATTGTCTAGGAAAAACAAAGAT
1 GTCATGGCAAAAACATAATTCATCATTCATAAAATAGAAAATAATTGTCTAGGAAAAACAAAGAT
*
5801174 TAAAACCAAGTAAGACAGTCATGGTATTATAAAAAATTCATCCAATTATCATTGTTTAATACAAC
66 TAAAACCAAGTAAGACAATCATGGTATTATAAAAAATTCATCCAATTATCATTGTTTAATACAAC
*
5801239 CCCAAATACGTAAAGAAATTAAGAACAAAGGAAGAACGACTCCGAAAATTGGGGGCTCTGTCGTT
131 CCCAAATACGTAAAGAAATTAAGAACAAAGGAAGAACGACTCCCAAAATTGGGGGCTCTGTCGTT
*
5801304 ACAATTCTGACCAGCATCGCGCCTGCCTTGGTGATCAGCCTCTCTCGAGACCTGACCACTGCTCT
196 ACAATTCTGACCAGCACCGCGCCTGCCTTGGTGATCAGCCTCTCTCGAGACCTGACCACTGCTCT
5801369 TCTATAGTCTAGCTATGGAGGACACCAAGGAAGATCGGCTGGTAAACGGTGGGGAAGCATTGCAG
261 TCTATAGTCTAGCTATGGAGGACACCAAGGAAGATCGGCTGGTAAACGGT--GG--G----G-A-
5801434 TTGCTTGCTCACACTTTAAGTAAGGCTCTCTAACTTCCTCCCCCTTTGGCGGCTACAATTTGATA
316 ------GCTCACACTTTAAGTAAGGCTCTCTAACTTCCTCCCCCTTTGGCGGCTACAATTTGATA
5801499 TTTATAGAGGGGAATCTCCTAGGGTTTTGCATGATTGGAGATCCTTAGACTAAAAAGGAAAGGTG
375 TTTATAGAGGGGAATCTCCTAGGGTTTTGCATGATTGGAGATCCTTAGACTAAAAAGGAAAGGTG
5801564 GTTGGCAGCTGTCAAAATTTTAAGGGTTTGCTTGCATGTGAAGAAGTCATCAAGGTGGCTCATAA
440 GTTGGCAGCTGTCAAAATTTTAAGGGTTTGCTTGCATGTGAAGAAGTCATCAAGGTGGCTCATAA
5801629 CATAGGCAAATTCGTCATACCCGCTTCAGACTTTCTAGATAAACCTTGCCTTGGCGAGATAAATC
505 CATAGGCAAATTCGTCATACCCGCTTCAGACTTTCTAGATAAACCTTGCCTTGGCGAGATAAATC
5801694 TGCTCCTCACGTTCTTTAACTTCTCTATTCCATTGGCCCTTACGAATTTTGTTGTCGCGACTGAA
570 TGCTCCTCACGTTCTTTAACTTCTCTATTCCATTGGCCCTTACGAATTTTGTTGTCGCGACTGAA
5801759 ATGTTCTTCCTCCGTAAAATTCCTGCACATACACAATCCACAAAAACTCTTTCTCCTCAGCAGCA
635 ATGTTCTTCCTCCGTAAAATTCCTGCACATACACAATCCACAAAAACTCTTTCTCCTCAGCAGCA
5801824 TCAGTTAAACCAAATAAATCTTGCCAAAGCAAAACTTATCCACCACAAGAAAATATAACCTAAAT
700 TCAGTTAAACCAAATAAATCTTGCCAAAGCAAAACTTATCCACCACAAGAAAATATAACCTAAAT
5801889 ACAACTAAAATGTTATGCATACTTTGTTTAGATGAGCAACAACTTAAGTGAAAAGTATAGAAATT
765 ACAACTAAAATGTTATGCATACTTTGTTTAGATGAGCAACAACTTAAGTGAAAAGTATAGAAATT
* *
5801954 GAGACTTTTTACGGAGTTTCACACCCGTAAACTTAAGCTATTGTCTGCCCTCAAGCAATTTACAA
830 GAGACTTTTTACGGAGTTTCACACCCGCAAACTTAAGCTATTGCCTGCCCTCAAGCAATTTACAA
5802019 TAGCTAGAAGAAAATTAAAATT
895 TAGCTAGAAGAAAATTAAAATT
5802041 GTCATGGCA
1 GTCATGGCA
5802050 GCAATAGATT
Statistics
Matches: 915, Mismatches: 10, Indels: 17
0.97 0.01 0.02
Matches are distributed among these distances:
916 300 0.33
917 6 0.01
918 2 0.00
920 1 0.00
924 1 0.00
925 1 0.00
932 604 0.66
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (916 bp):
GTCATGGCAAAAACATAATTCATCATTCATAAAATAGAAAATAATTGTCTAGGAAAAACAAAGAT
TAAAACCAAGTAAGACAATCATGGTATTATAAAAAATTCATCCAATTATCATTGTTTAATACAAC
CCCAAATACGTAAAGAAATTAAGAACAAAGGAAGAACGACTCCCAAAATTGGGGGCTCTGTCGTT
ACAATTCTGACCAGCACCGCGCCTGCCTTGGTGATCAGCCTCTCTCGAGACCTGACCACTGCTCT
TCTATAGTCTAGCTATGGAGGACACCAAGGAAGATCGGCTGGTAAACGGTGGGGAGCTCACACTT
TAAGTAAGGCTCTCTAACTTCCTCCCCCTTTGGCGGCTACAATTTGATATTTATAGAGGGGAATC
TCCTAGGGTTTTGCATGATTGGAGATCCTTAGACTAAAAAGGAAAGGTGGTTGGCAGCTGTCAAA
ATTTTAAGGGTTTGCTTGCATGTGAAGAAGTCATCAAGGTGGCTCATAACATAGGCAAATTCGTC
ATACCCGCTTCAGACTTTCTAGATAAACCTTGCCTTGGCGAGATAAATCTGCTCCTCACGTTCTT
TAACTTCTCTATTCCATTGGCCCTTACGAATTTTGTTGTCGCGACTGAAATGTTCTTCCTCCGTA
AAATTCCTGCACATACACAATCCACAAAAACTCTTTCTCCTCAGCAGCATCAGTTAAACCAAATA
AATCTTGCCAAAGCAAAACTTATCCACCACAAGAAAATATAACCTAAATACAACTAAAATGTTAT
GCATACTTTGTTTAGATGAGCAACAACTTAAGTGAAAAGTATAGAAATTGAGACTTTTTACGGAG
TTTCACACCCGCAAACTTAAGCTATTGCCTGCCCTCAAGCAATTTACAATAGCTAGAAGAAAATT
AAAATT
Found at i:5811337 original size:29 final size:29
Alignment explanation
Indices: 5811304--5811421 Score: 87
Period size: 29 Copynumber: 3.9 Consensus size: 29
5811294 AGAGAAAACA
* * *
5811304 AAAGAAAAAGAGATAAGGGAAAAAATAAT
1 AAAGAAAAAGAGAAAAAGAAAAAAATAAT
* *
5811333 AAAGAAAAATAGAAAAAGAAAAAAATAGAAA
1 AAAGAAAAAGAGAAAAAGAAAAAAAT--AAT
*
5811364 AACAGAAAAATAGAAAAAGGAAAAAGAA-AAT
1 AA-AGAAAAAGAGAAAAA-GAAAAA-AATAAT
* *
5811395 ATAGATAAAA-AGAGAGAAGAAAAAAAT
1 AAAGA-AAAAGAGA-AAAAGAAAAAAAT
5811422 TTAAAGGGGG
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
29 24 0.33
30 12 0.16
31 14 0.19
32 15 0.21
33 6 0.08
34 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (29 bp):
AAAGAAAAAGAGAAAAAGAAAAAAATAAT
Found at i:5811339 original size:14 final size:15
Alignment explanation
Indices: 5811322--5811388 Score: 75
Period size: 16 Copynumber: 4.4 Consensus size: 15
5811312 AGAGATAAGG
*
5811322 GAAAAAATA-ATAAA
1 GAAAAAATAGAAAAA
5811336 G-AAAAATAGAAAAA
1 GAAAAAATAGAAAAA
5811350 GAAAAAAATAGAAAAA
1 G-AAAAAATAGAAAAA
*
5811366 CAGAAAAATAGAAAAA
1 GA-AAAAATAGAAAAA
5811382 GGAAAAA
1 -GAAAAA
5811389 GAAAATATAG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
13 7 0.16
14 6 0.13
15 1 0.02
16 30 0.67
17 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.07
Consensus pattern (15 bp):
GAAAAAATAGAAAAA
Found at i:5811348 original size:8 final size:8
Alignment explanation
Indices: 5811335--5811381 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
5811325 AAAATAATAA
5811335 AGAAAAAT
1 AGAAAAAT
*
5811343 AGAAAAAG
1 AGAAAAAT
*
5811351 AAAAAAAT
1 AGAAAAAT
*
5811359 AGAAAAAC
1 AGAAAAAT
5811367 AGAAAAAT
1 AGAAAAAT
5811375 AGAAAAA
1 AGAAAAA
5811382 GGAAAAAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (8 bp):
AGAAAAAT
Found at i:5811358 original size:16 final size:16
Alignment explanation
Indices: 5811337--5811388 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
5811327 AATAATAAAG
5811337 AAAAATAGAAAAAGAA
1 AAAAATAGAAAAAGAA
* *
5811353 AAAAATAGAAAAACAG
1 AAAAATAGAAAAAGAA
5811369 AAAAATAGAAAAAGGAA
1 AAAAATAGAAAAA-GAA
5811386 AAA
1 AAA
5811389 GAAAATATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (16 bp):
AAAAATAGAAAAAGAA
Found at i:5813759 original size:44 final size:44
Alignment explanation
Indices: 5813703--5813786 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
5813693 TACAGATTGG
5813703 ATTCCATCACATAAGGAGGTGGATCAACAT-ACCCTTTTTGTTAT
1 ATTCCATCACATAAGGAGGTGGATCAACATCA-CCTTTTTGTTAT
* *
5813747 ATTCCATTACATAAGGAGTTGGATCAACATCACCTTTTTG
1 ATTCCATCACATAAGGAGGTGGATCAACATCACCTTTTTG
5813787 CTTGATTCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 36 0.97
45 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (44 bp):
ATTCCATCACATAAGGAGGTGGATCAACATCACCTTTTTGTTAT
Found at i:5813885 original size:44 final size:44
Alignment explanation
Indices: 5813837--5813942 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 44
5813827 TTTATTCGAT
* **
5813837 TCCATCATAGAAGGAGGTGGACCAACATTGTCATTTCGCTCAAA
1 TCCATCACAGAAGGAGGTGGACCAACATTACCATTTCGCTCAAA
* * * * * * *
5813881 TCCATTACATAAGGAGTTGGATCAACATTACCATTTTGCTCGAT
1 TCCATCACAGAAGGAGGTGGACCAACATTACCATTTCGCTCAAA
*
5813925 TCTATCACAGAAGGAGGT
1 TCCATCACAGAAGGAGGT
5813943 AGAGTAGCAT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
TCCATCACAGAAGGAGGTGGACCAACATTACCATTTCGCTCAAA
Found at i:5814096 original size:131 final size:132
Alignment explanation
Indices: 5813749--5814262 Score: 444
Period size: 131 Copynumber: 3.9 Consensus size: 132
5813739 TTTGTTATAT
* * * * *
5813749 TCCATTACATAAGGAGTTGGATCAACA-TCACCTTTTTGCTTGATTCTAACACAGAATG-AGTTA
1 TCCATTGCATAAGGAGTTGGAT-AAGATTCACCTTTTTGCTCGATTCTATCACAGAA-GCAGGTA
* * * *
5813812 -AATCAACATCG-ACAT-TTTATTCGATTCCATCATAGAAGGAGGTGGACCAACATTGTCATTTC
64 GAGT-AACATCGAAAATATTT-TT-AATTCCATCACAGAAGGAGGTGGACCAACATTGTCATTTC
5813874 GCTCAAA
126 GCTCAAA
* * * *
5813881 TCCATTACATAAGGAGTTGGATCAACATT-ACCATTTTGCTCGATTCTATCACAGAAGGAGGTAG
1 TCCATTGCATAAGGAGTTGGAT-AAGATTCACCTTTTTGCTCGATTCTATCACAGAAGCAGGTAG
* * * * * * * *
5813945 AGTAGCATCG-ACATTTTTTTTATTCTATCACAGAATGAGGTGGACCAATATTGTTATTTCGCTC
65 AGTAACATCGAAAATATTTTTAATTCCATCACAGAAGGAGGTGGACCAACATTGTCATTTCGCTC
5814009 AAA
130 AAA
* * *
5814012 TCCATTGCATGAGGAGTTGGATTAGTTTCACCCTTTTTGCTCGATTCTATCAC-GAAAGCAGGTA
1 TCCATTGCATAAGGAGTTGGATAAGATTCA-CCTTTTTGCTCGATTCTATCACAG-AAGCAGGTA
** *
5814076 GA-TCAACATC-AAAATATTTTTCAATTCCATCACAGAAGGAAATGGATCAACATTGTCATTTCG
64 GAGT-AACATCGAAAATATTTTT-AATTCCATCACAGAAGGAGGTGGACCAACATTGTCATTTCG
5814139 CTCAAA
127 CTCAAA
* ** *
5814145 TCCATCGCATAAGGAGTTGGACCAGCA-TCA-CTTTTTTCTCGATTCTATCACAGAATG-AGGTA
1 TCCATTGCATAAGGAGTTGGATAAG-ATTCACCTTTTTGCTCGATTCTATCACAGAA-GCAGGTA
* * ** * * * * * *
5814207 TATTAGTATCGACACT-TTGTTCAATTCCATCACAGAAAGAGGTGGATCAACCTTGT
64 GAGTAACATCGAAAATATT-TTTAATTCCATCACAGAAGGAGGTGGACCAACATTGT
5814263 AATTATTTCT
Statistics
Matches: 320, Mismatches: 46, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
130 3 0.01
131 129 0.40
132 119 0.37
133 69 0.22
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (132 bp):
TCCATTGCATAAGGAGTTGGATAAGATTCACCTTTTTGCTCGATTCTATCACAGAAGCAGGTAGA
GTAACATCGAAAATATTTTTAATTCCATCACAGAAGGAGGTGGACCAACATTGTCATTTCGCTCA
AA
Found at i:5814510 original size:9 final size:9
Alignment explanation
Indices: 5814498--5814557 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
5814488 AAATGATTAA
5814498 AAGAAAAAT
1 AAGAAAAAT
5814507 AAG-AAAAT
1 AAGAAAAAT
5814515 AAG-AAAAT
1 AAGAAAAAT
**
5814523 TTGAAAAAAT
1 AAG-AAAAAT
* *
5814533 GAGAAAAAA
1 AAGAAAAAT
*
5814542 AAGAAAAAA
1 AAGAAAAAT
5814551 AAGAAAA
1 AAGAAAA
5814558 TTGAAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
8 14 0.33
9 23 0.53
10 6 0.14
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
AAGAAAAAT
Found at i:5814555 original size:36 final size:36
Alignment explanation
Indices: 5814499--5814588 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 36
5814489 AATGATTAAA
* *
5814499 AGAAAAATAAG-AAAATAAGAAAATTTGAAAAAAT-G
1 AGAAAAAAAAGAAAAAAAAGAAAA-TTGAAAAAATAG
*
5814534 AGAAAAAAAAGAAAAAAAAGAAAATTGAAAAAATAT
1 AGAAAAAAAAGAAAAAAAAGAAAATTGAAAAAATAG
**
5814570 AGTGAAAAAAGAAAAAAAA
1 AGAAAAAAAAGAAAAAAAA
5814589 AGGAGAAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
35 20 0.42
36 28 0.58
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.12
Consensus pattern (36 bp):
AGAAAAAAAAGAAAAAAAAGAAAATTGAAAAAATAG
Found at i:5814557 original size:27 final size:27
Alignment explanation
Indices: 5814527--5814585 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
5814517 GAAAATTTGA
5814527 AAAAATGAGAAAAA-AAAGAAAAAAAAG
1 AAAAATGA-AAAAATAAAGAAAAAAAAG
* * **
5814554 AAAATTGAAAAAATATAGTGAAAAAAG
1 AAAAATGAAAAAATAAAGAAAAAAAAG
5814581 AAAAA
1 AAAAA
5814586 AAAAGGAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (27 bp):
AAAAATGAAAAAATAAAGAAAAAAAAG
Found at i:5815211 original size:136 final size:136
Alignment explanation
Indices: 5814967--5815230 Score: 415
Period size: 136 Copynumber: 1.9 Consensus size: 136
5814957 AAACCCTATC
* * *
5814967 TATAACAACCATCTCTCGTAAACTCATACGTATACGAGTTACAGATGTCACATCACTAATATTAT
1 TATAACAACCATCTCCCGTAAACCCATACGTATACGAGGTACAGATGTCACATCACTAATATTAT
* *
5815032 TGTTCCTAATTCAAAATCCCGTAAAAATTTTGTTTTCATTTTATAAAACCTTTAATTGAATCACC
66 TGTTCCTAATTCAAAATCCCATAAAAATTTTGTTTTCATTTTATAAAACCTTTAATCGAATCACC
5815097 AATAAA
131 AATAAA
* *
5815103 TATAAC-ACTCATCTCCCGTATACCCATTCGTATACGAGGTACAGATGTCACATCACTAATATTA
1 TATAACAAC-CATCTCCCGTAAACCCATACGTATACGAGGTACAGATGTCACATCACTAATATTA
* *
5815167 TTGTTCCTAATTGAAAATCCTATAAAAATATTTG-TTTCATTTTATAAAACCTTTAATCGAATCA
65 TTGTTCCTAATTCAAAATCCCATAAAAAT-TTTGTTTTCATTTTATAAAACCTTTAATCGAATCA
5815231 ATCCTCCTAA
Statistics
Matches: 117, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
135 2 0.02
136 111 0.95
137 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (136 bp):
TATAACAACCATCTCCCGTAAACCCATACGTATACGAGGTACAGATGTCACATCACTAATATTAT
TGTTCCTAATTCAAAATCCCATAAAAATTTTGTTTTCATTTTATAAAACCTTTAATCGAATCACC
AATAAA
Found at i:5827893 original size:3 final size:3
Alignment explanation
Indices: 5827887--5827921 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5827877 ATAATTATTA
*
5827887 TTG TTG TTG TTG TTG TTT TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
5827922 TTTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:5827929 original size:3 final size:3
Alignment explanation
Indices: 5827923--5827948 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5827913 GTTGTTGTTT
5827923 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5827949 TAAAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5829892 original size:216 final size:217
Alignment explanation
Indices: 5829495--5829927 Score: 859
Period size: 216 Copynumber: 2.0 Consensus size: 217
5829485 AGCCCGATAT
5829495 CAGTTTCCCTTAGCGGGTCGTCGCTAAGTGTGTTCACAGAAAGTCGAACTTGCTACCAGCTGATT
1 CAGTTTCCCTTAGCGGGTCGTCGCTAAGTGTGTTCACAGAAAGTCGAACTTGCTACCAGCTGATT
5829560 CTTCCTCCCAACTTTAAACCAGAACAACGTCGACTTTTTGATTTAAAAGTGTTTTGATTTTAAAG
66 CTTCCTCCCAACTTTAAACCAGAACAACGTCGACTTTTTGATTTAAAAGTGTTTTGATTTTAAAG
5829625 GAAAGGTCGATTGCCAATCCTATTTCTCTAGAAAATTGAGAAAATAACCCAAAGGTATTTTAAGT
131 GAAAGGTCGATTGCCAATCCTATTTCTCTAGAAAATTGAGAAAATAACCCAAAGGTATTTTAAGT
5829690 GCTTTTCAATCCTCACAATTGG
196 GCTTTTCAATCCTCACAATTGG
5829712 CAGTTTCCCTTAGCGGGTCGTCGCTAAGTGTGTTCACAGAAAGTCGAACTTGCTACCAGCTGATT
1 CAGTTTCCCTTAGCGGGTCGTCGCTAAGTGTGTTCACAGAAAGTCGAACTTGCTACCAGCTGATT
5829777 CTTCCTCCCAACTTTAAACCAGAAC-ACGTCGACTTTTTGATTTAAAAGTGTTTTGATTTTAAAG
66 CTTCCTCCCAACTTTAAACCAGAACAACGTCGACTTTTTGATTTAAAAGTGTTTTGATTTTAAAG
5829841 GAAAGGTCGATTGCCAATCCTATTTCTCTAGAAAATTGAGAAAATAACCCAAAGGTATTTTAAGT
131 GAAAGGTCGATTGCCAATCCTATTTCTCTAGAAAATTGAGAAAATAACCCAAAGGTATTTTAAGT
5829906 GCTTTTCAATCCTCACAATTGG
196 GCTTTTCAATCCTCACAATTGG
5829928 AATTGAGTCA
Statistics
Matches: 216, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
216 126 0.58
217 90 0.42
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (217 bp):
CAGTTTCCCTTAGCGGGTCGTCGCTAAGTGTGTTCACAGAAAGTCGAACTTGCTACCAGCTGATT
CTTCCTCCCAACTTTAAACCAGAACAACGTCGACTTTTTGATTTAAAAGTGTTTTGATTTTAAAG
GAAAGGTCGATTGCCAATCCTATTTCTCTAGAAAATTGAGAAAATAACCCAAAGGTATTTTAAGT
GCTTTTCAATCCTCACAATTGG
Found at i:5838421 original size:107 final size:107
Alignment explanation
Indices: 5838235--5838448 Score: 428
Period size: 107 Copynumber: 2.0 Consensus size: 107
5838225 CTTCATTCCA
5838235 CATCCTTTGACTTACCTTTATCATGGATTCCCTCACCACTACCCTTGACTTTCAGATTTGCCTTG
1 CATCCTTTGACTTACCTTTATCATGGATTCCCTCACCACTACCCTTGACTTTCAGATTTGCCTTG
5838300 GAAGTCTTGCTCTTCTTGACTCTAAATTCTCTGATGAACTCT
66 GAAGTCTTGCTCTTCTTGACTCTAAATTCTCTGATGAACTCT
5838342 CATCCTTTGACTTACCTTTATCATGGATTCCCTCACCACTACCCTTGACTTTCAGATTTGCCTTG
1 CATCCTTTGACTTACCTTTATCATGGATTCCCTCACCACTACCCTTGACTTTCAGATTTGCCTTG
5838407 GAAGTCTTGCTCTTCTTGACTCTAAATTCTCTGATGAACTCT
66 GAAGTCTTGCTCTTCTTGACTCTAAATTCTCTGATGAACTCT
5838449 ACAGTGATCA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (107 bp):
CATCCTTTGACTTACCTTTATCATGGATTCCCTCACCACTACCCTTGACTTTCAGATTTGCCTTG
GAAGTCTTGCTCTTCTTGACTCTAAATTCTCTGATGAACTCT
Found at i:5841111 original size:45 final size:45
Alignment explanation
Indices: 5841053--5841380 Score: 503
Period size: 45 Copynumber: 7.3 Consensus size: 45
5841043 ATTATTCATT
* * * *
5841053 ATTTCCATGTATGGCAACATTTCATGCCTTTAATGCACTGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
5841099 ATTTCATTTATGGCACCCTTTCATGCCTTTAATGCATCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
5841144 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
5841189 ATTTCATTTATGGCATCATTTCATACCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
5841234 ATTCCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATCC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
5841279 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
5841324 ATTTCATTTATGGCGTCATTTCATGCCTTTAATGCACCGTTGTGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
5841369 ATTTCATTTATG
1 ATTTCATTTATG
5841381 TAATGAAAAC
Statistics
Matches: 258, Mismatches: 24, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
45 254 0.98
46 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:5847956 original size:45 final size:45
Alignment explanation
Indices: 5847891--5848081 Score: 301
Period size: 45 Copynumber: 4.2 Consensus size: 45
5847881 AATTATTCAT
*
5847891 TATTTCCATTTGTGGCATCCTTTCATGCCTTTAATGCACCGTTATG
1 TATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATG
* *
5847937 TATTTCATTTATGGCATCCTTTCATGCTTTTGATGCACCGTTATG
1 TATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATG
* * *
5847982 TATTTCATTTATGGCATCCTTTCATACCTTTAATGTACCGCTATG
1 TATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATG
*
5848027 CATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATG
1 TATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATG
*
5848072 CATTTCATTT
1 TATTTCATTT
5848082 TTGTAATGAA
Statistics
Matches: 133, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 128 0.96
46 5 0.04
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (45 bp):
TATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATG
Found at i:5848622 original size:95 final size:95
Alignment explanation
Indices: 5848451--5848652 Score: 239
Period size: 95 Copynumber: 2.1 Consensus size: 95
5848441 CCCTACCAAG
* *
5848451 GTATCGATACTTCTATACTATGGTACTGATACCCCCTTTCAGTATCGATACCATTTCTACATTTT
1 GTATCGATACTACTATACTATGGTACTGATACCCCCTTTCAGTATCGATACCATTTCTACATTCT
* * **
5848516 GTAGTTGATGGTATCGATACCTTT-CTCTCA
66 GGAATCCATGGTATCGATA-CTTTCCTCTCA
* ** * *
5848546 GTATCGATACTACTATACTATGGTA-TCGATACTCTTTTTCAGTATCGATGCCATTT-TGGCATT
1 GTATCGATACTACTATACTATGGTACT-GATACCCCCTTTCAGTATCGATACCATTTCT-ACATT
* *
5848609 CTGGAATCCATGGTATCGATACTTTCCTTTTA
64 CTGGAATCCATGGTATCGATACTTTCCTCTCA
5848641 GTATCGATACTA
1 GTATCGATACTA
5848653 ATTGTATCAG
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
94 6 0.07
95 85 0.93
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (95 bp):
GTATCGATACTACTATACTATGGTACTGATACCCCCTTTCAGTATCGATACCATTTCTACATTCT
GGAATCCATGGTATCGATACTTTCCTCTCA
Found at i:5854364 original size:43 final size:43
Alignment explanation
Indices: 5854315--5854396 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
5854305 ATAATTATTG
*
5854315 AAAATATTCAAACTAAAATCCTAGAAACAAGAGATAATTCTCT
1 AAAATATTCAAACTAAAATCCTAAAAACAAGAGATAATTCTCT
*
5854358 AAAATATTCAAACTAAAATCCTAAAAATAAGAGATAATT
1 AAAATATTCAAACTAAAATCCTAAAAACAAGAGATAATT
5854397 TCGAATTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (43 bp):
AAAATATTCAAACTAAAATCCTAAAAACAAGAGATAATTCTCT
Found at i:5854928 original size:123 final size:123
Alignment explanation
Indices: 5854709--5854955 Score: 494
Period size: 123 Copynumber: 2.0 Consensus size: 123
5854699 TATGGAGTTT
5854709 TATATGTTTTAGTTAACTATAATCCATTGACATGGCCATGTGATTTATCAGTTAAATTTATTATT
1 TATATGTTTTAGTTAACTATAATCCATTGACATGGCCATGTGATTTATCAGTTAAATTTATTATT
5854774 TGATAGTAAAATTTATTTATCCTATCAACCTATAAATAACTATCATCGCTATACGACA
66 TGATAGTAAAATTTATTTATCCTATCAACCTATAAATAACTATCATCGCTATACGACA
5854832 TATATGTTTTAGTTAACTATAATCCATTGACATGGCCATGTGATTTATCAGTTAAATTTATTATT
1 TATATGTTTTAGTTAACTATAATCCATTGACATGGCCATGTGATTTATCAGTTAAATTTATTATT
5854897 TGATAGTAAAATTTATTTATCCTATCAACCTATAAATAACTATCATCGCTATACGACA
66 TGATAGTAAAATTTATTTATCCTATCAACCTATAAATAACTATCATCGCTATACGACA
5854955 T
1 T
5854956 CGACACAAAT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 124 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (123 bp):
TATATGTTTTAGTTAACTATAATCCATTGACATGGCCATGTGATTTATCAGTTAAATTTATTATT
TGATAGTAAAATTTATTTATCCTATCAACCTATAAATAACTATCATCGCTATACGACA
Found at i:5855939 original size:25 final size:24
Alignment explanation
Indices: 5855884--5855947 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 24
5855874 CTAGGTATTT
*
5855884 ATCTTCAAGATAATTCCAAATTAA
1 ATCTTCAAGATAATTCAAAATTAA
*
5855908 ATATTCAAGATAATTCTAAAATTAA
1 ATCTTCAAGATAATTC-AAAATTAA
*
5855933 ATCTTCAATATAATT
1 ATCTTCAAGATAATT
5855948 TTGGCCCGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
24 15 0.43
25 20 0.57
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (24 bp):
ATCTTCAAGATAATTCAAAATTAA
Found at i:5856280 original size:24 final size:24
Alignment explanation
Indices: 5856248--5856309 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
5856238 TCCACACAAC
*
5856248 ATTATCTTGAAGATTTAATTTTGA
1 ATTATCTTGAAGATTTAATTTGGA
*
5856272 ATTATCTTGAATATTTAATTTGGA
1 ATTATCTTGAAGATTTAATTTGGA
5856296 ATTATCTTGAAGAT
1 ATTATCTTGAAGAT
5856310 GAATACATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (24 bp):
ATTATCTTGAAGATTTAATTTGGA
Found at i:5856423 original size:15 final size:15
Alignment explanation
Indices: 5856403--5856435 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5856393 GTGATAAACC
*
5856403 TTTTAAATTT-ATTA
1 TTTTTAATTTAATTA
5856417 TTTTTAATTTAATTA
1 TTTTTAATTTAATTA
5856432 TTTT
1 TTTT
5856436 GACTTGCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAATTTAATTA
Found at i:5856479 original size:36 final size:36
Alignment explanation
Indices: 5856432--5856512 Score: 162
Period size: 36 Copynumber: 2.2 Consensus size: 36
5856422 AATTTAATTA
5856432 TTTTGACTTGCAAGCCTATGGTAATATTGTGTTATG
1 TTTTGACTTGCAAGCCTATGGTAATATTGTGTTATG
5856468 TTTTGACTTGCAAGCCTATGGTAATATTGTGTTATG
1 TTTTGACTTGCAAGCCTATGGTAATATTGTGTTATG
5856504 TTTTGACTT
1 TTTTGACTT
5856513 TGAGAATTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (36 bp):
TTTTGACTTGCAAGCCTATGGTAATATTGTGTTATG
Found at i:5861205 original size:217 final size:214
Alignment explanation
Indices: 5860823--5861243 Score: 551
Period size: 217 Copynumber: 2.0 Consensus size: 214
5860813 CCTTTAATGC
* * * *
5860823 ATTCTCTCCTTTAAACATAGGTGATGGATTAATGACAAACCATTGGTTTAATATAAATTTGAGTA
1 ATTCTCTCCTTTAAACATAGGTGATGAATTAATGAAAAACCATTGATTTAATATAAATTTGAGCA
* * * * * *
5860888 CAAATTGTGACTTTAGAGGTTAAGAGGTTTGTTGTAATATTTGAAGTTTTGAGTTTGAGCACCGC
66 CAAATAGTGACTTCAGAGATTAAGAGATTTGTTGTAATATTTGAAGTTTCGAGTTCGAGCACCGC
** * * ** * *
5860953 GTATGTAGGGATATGAGCATTCATTGTCGAAGGGTTAAAAGTCTTTAAACATATATTACCTTATA
131 GTATACAGGGATATAACCATTCATCATCAAAGGGTTAAAAGTCTTTAAAAATATATTACCTTATA
*
5861018 TTCACACCAACTAAAATAT
196 TTCAAACCAACTAAAATAT
*
5861037 ATTCTCTCCTTTAAACATAGGTGACT-AATTAATGAAAAACTATTGATTTATATATAAATTTGAG
1 ATTCTCTCCTTTAAACATAGGTGA-TGAATTAATGAAAAACCATTGATTTA-ATATAAATTTGAG
* * *
5861101 CACGAATCAAGTGACTTCA-ATGATTAAGAGATTTGTTGTTATCTTTTGAAGTTTCGAGTTCGAG
64 CACAAAT--AGTGACTTCAGA-GATTAAGAGATTTGTTGTAAT-ATTTGAAGTTTCGAGTTCGAG
*
5861165 CACCG-GTATACAGGGATATAACCATTCATCATCAAAGGGTTAAGAGTCTTTAAAAATATATTAC
125 CACCGCGTATACAGGGATATAACCATTCATCATCAAAGGGTTAAAAGTCTTTAAAAATATATTAC
5861229 CTTATATTCAAACCA
190 CTTATATTCAAACCA
5861244 TATATATATA
Statistics
Matches: 177, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
214 44 0.25
215 19 0.11
216 1 0.01
217 90 0.51
218 23 0.13
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (214 bp):
ATTCTCTCCTTTAAACATAGGTGATGAATTAATGAAAAACCATTGATTTAATATAAATTTGAGCA
CAAATAGTGACTTCAGAGATTAAGAGATTTGTTGTAATATTTGAAGTTTCGAGTTCGAGCACCGC
GTATACAGGGATATAACCATTCATCATCAAAGGGTTAAAAGTCTTTAAAAATATATTACCTTATA
TTCAAACCAACTAAAATAT
Found at i:5861250 original size:2 final size:2
Alignment explanation
Indices: 5861243--5861268 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5861233 TATTCAAACC
5861243 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
5861269 GAGAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5861839 original size:14 final size:11
Alignment explanation
Indices: 5861807--5861832 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5861797 TAATTTATTT
5861807 ATTTAATAATA
1 ATTTAATAATA
5861818 ATTTAATAATA
1 ATTTAATAATA
5861829 ATTT
1 ATTT
5861833 TGTAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:5861954 original size:11 final size:11
Alignment explanation
Indices: 5861938--5861963 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5861928 TAATTAATTT
5861938 ATTTAATAATA
1 ATTTAATAATA
5861949 ATTTAATAATA
1 ATTTAATAATA
5861960 ATTT
1 ATTT
5861964 TCCATAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:5862012 original size:11 final size:11
Alignment explanation
Indices: 5861996--5862035 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
5861986 TTACGTGACT
5861996 GTTCATCATTC
1 GTTCATCATTC
5862007 GTTCATCATTC
1 GTTCATCATTC
5862018 GTTCATCATTC
1 GTTCATCATTC
5862029 GTTCATC
1 GTTCATC
5862036 GTTTGACCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.17, C:0.28, G:0.10, T:0.45
Consensus pattern (11 bp):
GTTCATCATTC
Found at i:5863997 original size:28 final size:28
Alignment explanation
Indices: 5863965--5864019 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5863955 TTTCATAGAA
5863965 GCAGAGGCAAATGAAACAAATAATATAG
1 GCAGAGGCAAATGAAACAAATAATATAG
* *
5863993 GCAGAGGCAAATGAAATACATAATATA
1 GCAGAGGCAAATGAAACAAATAATATA
5864020 ATCATGGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.53, C:0.11, G:0.20, T:0.16
Consensus pattern (28 bp):
GCAGAGGCAAATGAAACAAATAATATAG
Found at i:5865430 original size:40 final size:40
Alignment explanation
Indices: 5865374--5865451 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
5865364 TTATTTATAT
* *
5865374 TTTTATATATTGTTACTTAATTCGAATTGTAATTAAATAG
1 TTTTATATATTATTACTTAATTAGAATTGTAATTAAATAG
* *
5865414 TTTTATATATTATTACTTGATTAGAATTTTAATTAAAT
1 TTTTATATATTATTACTTAATTAGAATTGTAATTAAAT
5865452 TTAAGGTGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (40 bp):
TTTTATATATTATTACTTAATTAGAATTGTAATTAAATAG
Found at i:5865630 original size:43 final size:43
Alignment explanation
Indices: 5865594--5865676 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
5865584 GTGTTTTCAG
*
5865594 AAAAAAAAACTGCTAAATAACAAACCTGTTGTGGTGTTTGTGC
1 AAAAAAAAACCGCTAAATAACAAACCTGTTGTGGTGTTTGTGC
** * * *
5865637 CTAAAAACACCGCTAAATAACAAACCTGTTGCGGCGTTTG
1 AAAAAAAAACCGCTAAATAACAAACCTGTTGTGGTGTTTG
5865677 AAAATACAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (43 bp):
AAAAAAAAACCGCTAAATAACAAACCTGTTGTGGTGTTTGTGC
Found at i:5865692 original size:15 final size:15
Alignment explanation
Indices: 5865672--5865701 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5865662 CTGTTGCGGC
5865672 GTTTGAAAATACAAA
1 GTTTGAAAATACAAA
5865687 GTTTGAAAATACAAA
1 GTTTGAAAATACAAA
5865702 CGCCACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
GTTTGAAAATACAAA
Found at i:5866221 original size:18 final size:19
Alignment explanation
Indices: 5866187--5866227 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
5866177 CAAATGATAG
5866187 ATTTTTTAAATATTAA-TA
1 ATTTTTTAAATATTAATTA
5866205 ATTTTTTAAAT-TGTAATTA
1 ATTTTTTAAATAT-TAATTA
5866224 ATTT
1 ATTT
5866228 GATAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.67
19 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTTTAAATATTAATTA
Found at i:5866345 original size:11 final size:12
Alignment explanation
Indices: 5866327--5866355 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
5866317 AGTATCAAAA
5866327 TATAATATTAAG
1 TATAATATTAAG
5866339 T-TAATATTAAG
1 TATAATATTAAG
5866350 TATAAT
1 TATAAT
5866356 TATTCTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (12 bp):
TATAATATTAAG
Found at i:5867908 original size:2 final size:2
Alignment explanation
Indices: 5867903--5867940 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5867893 AGCCATTCCT
5867903 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5867941 ACTCAGTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5867978 original size:39 final size:39
Alignment explanation
Indices: 5867935--5868013 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
5867925 TCTCTCTCTC
5867935 TCTCTCACTCAGTTCCCATCTTCTCTCTGTATATAAAAA
1 TCTCTCACTCAGTTCCCATCTTCTCTCTGTATATAAAAA
* *
5867974 TCTCTCATTCAGTTCCCATCTTGTCTCTGTATATAAAAA
1 TCTCTCACTCAGTTCCCATCTTCTCTCTGTATATAAAAA
5868013 T
1 T
5868014 GTGCATACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (39 bp):
TCTCTCACTCAGTTCCCATCTTCTCTCTGTATATAAAAA
Found at i:5872969 original size:3 final size:3
Alignment explanation
Indices: 5872961--5872985 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5872951 GAATTGGGTT
5872961 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
5872986 CTAGATATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:5875284 original size:18 final size:17
Alignment explanation
Indices: 5875252--5875285 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5875242 TCAGTCGGTC
5875252 CGGTTTGAACGATTCAA
1 CGGTTTGAACGATTCAA
*
5875269 CGGTTCTGACCGATTCA
1 CGGTT-TGAACGATTCA
5875286 CTAATAGCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (17 bp):
CGGTTTGAACGATTCAA
Found at i:5875687 original size:23 final size:23
Alignment explanation
Indices: 5875652--5875699 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5875642 ATTAAGTATA
*
5875652 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
* *
5875675 ATAATGTAATAGGTATCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
5875698 AT
1 AT
5875700 TAACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:5876652 original size:182 final size:181
Alignment explanation
Indices: 5876339--5876793 Score: 689
Period size: 182 Copynumber: 2.5 Consensus size: 181
5876329 ACTTTTTTAC
* * *
5876339 TACCAGTTTTGTCATTTGTAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTAGGGATCGA
1 TACCTGTTTTGTCATTTG-AGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * * *
5876404 TACATTTTTATAAAGTATCGACACTTTATTGGCGTTATAACTTCTTTTCTTTTAAATTCTAAAAG
65 TACATTTTTATAAAGTATCGACACTTTATTAGCGGTATAACTTCTTCTCTTTTAAATTCCAAAAG
* * * **
5876469 TGTCAATACTTATAATAAAGTATCGACACTTTCAACATTTCTGGTAGCTTTT
130 TGTCAATACTTATAATAAAATATCGACACTATCAACATATCTGGTAGCGCTT
*
5876521 TACC-GATTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCG
1 TACCTG-TTTTGTCATTT-GAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCG
5876585 ATACATTTTTATAAAGTATCGACACTTTATTAGCGGTATAACTTCTTCTCTTTTAAATTCCAAAA
64 ATACATTTTTATAAAGTATCGACACTTTATTAGCGGTATAACTTCTTCTCTTTTAAATTCCAAAA
*
5876650 GTGTCGATACTTATAATAAAATATCGACACTATCAACATATCTGGTAGCGCTT
129 GTGTCAATACTTATAATAAAATATCGACACTATCAACATATCTGGTAGCGCTT
* * * *
5876703 TACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTA-CTGTTATATTGTTATGGATCGA
1 TACCTGTTTTGTCATTT-GAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
*
5876767 AACATTTTTATAAAGTATCGACACTTT
65 TACATTTTTATAAAGTATCGACACTTT
5876794 CAATATATCT
Statistics
Matches: 250, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
181 49 0.20
182 199 0.80
183 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (181 bp):
TACCTGTTTTGTCATTTGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTAGCGGTATAACTTCTTCTCTTTTAAATTCCAAAAGT
GTCAATACTTATAATAAAATATCGACACTATCAACATATCTGGTAGCGCTT
Found at i:5876902 original size:112 final size:112
Alignment explanation
Indices: 5876665--5877126 Score: 759
Period size: 112 Copynumber: 4.1 Consensus size: 112
5876655 GATACTTATA
* * * * *
5876665 ATAAAATATCGACACTATCAACATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
5876730 TTTGTCATTTTTTTA-CTGTTATATTGTTATGGATCGAAACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGAAACATTTTT
* *
5876776 ATAAAGTATCGACACTTTCAATATATCTGGTAACGCTTTACCTATTTTTTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
5876841 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGAAACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGAAACATTTTT
*
5876888 ATAAAGTATCGACACTTTCAATATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
5876953 TTTGTCATTTTTTTACCTGTTATATTGTTATGAATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGAAACATTTTT
* * *
5877000 ATAAAATATCGACACTTTCAATATAT-TCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGG
1 ATAAAGTATCGACACTTTCAATATATCT-GGTAACGCTTTACCTGTTTTGTCATTTATAGACCGG
*
5877064 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATC-AATATATTTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGAA-ACATTTTT
5877112 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
5877127 AAACCGACAA
Statistics
Matches: 328, Mismatches: 20, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
111 74 0.23
112 254 0.77
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCTGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGAAACATTTTT
Found at i:5877807 original size:31 final size:32
Alignment explanation
Indices: 5877769--5877863 Score: 128
Period size: 30 Copynumber: 3.1 Consensus size: 32
5877759 AAATGATACG
5877769 CTCTCAACCCGAAAACATTCACAC-ATCAATC
1 CTCTCAACCCGAAAACATTCACACAATCAATC
5877800 CTCTCAACCCGAAAACATT-ACACAAT-AATC
1 CTCTCAACCCGAAAACATTCACACAATCAATC
* * *
5877830 CTCTCAACCCGTAAACA-TCACCCGA-CAATC
1 CTCTCAACCCGAAAACATTCACACAATCAATC
5877860 CTCT
1 CTCT
5877864 TATCTTTGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
29 1 0.02
30 36 0.62
31 21 0.36
ACGTcount: A:0.37, C:0.39, G:0.04, T:0.20
Consensus pattern (32 bp):
CTCTCAACCCGAAAACATTCACACAATCAATC
Found at i:5879573 original size:23 final size:20
Alignment explanation
Indices: 5879543--5879600 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
5879533 AGGGTTTCAA
5879543 AGTGCATCCATGCACC-TGCCACT
1 AGTGCATCCATGCACCATG----T
*
5879566 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGT
5879586 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
5879601 TCCATTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 15 0.47
23 15 0.47
24 2 0.06
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGT
Found at i:5880971 original size:19 final size:20
Alignment explanation
Indices: 5880947--5880994 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
5880937 AACGATTTTC
5880947 TTTTGAAAACAAAAAT-AAA
1 TTTTGAAAACAAAAATGAAA
* *
5880966 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
5880986 TTTTGAAAA
1 TTTTGAAAA
5880995 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:5881792 original size:20 final size:20
Alignment explanation
Indices: 5881769--5881806 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5881759 ATATGTACTT
*
5881769 AATTTTAACAATTGGTATCA
1 AATTTAAACAATTGGTATCA
5881789 AATTTAAACAATTGGTAT
1 AATTTAAACAATTGGTAT
5881807 TGCATAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (20 bp):
AATTTAAACAATTGGTATCA
Found at i:5882156 original size:21 final size:21
Alignment explanation
Indices: 5882132--5882171 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5882122 AAACAATTGG
5882132 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
5882153 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
5882172 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:5882419 original size:21 final size:21
Alignment explanation
Indices: 5882393--5882490 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
5882383 AGGGTGTCAA
5882393 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
5882414 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
5882435 AGTGCATCCATACACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
5882456 AGTGCATCGATGCA-CCATGC
1 AGTGCATCCATGCACCCCTGC
*
5882476 AGTGTATCCATGCAC
1 AGTGCATCCATGCAC
5882491 TCCATTTCGA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
20 17 0.24
21 53 0.76
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:5882535 original size:20 final size:20
Alignment explanation
Indices: 5882510--5882562 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
5882500 AATGCACTTA
*
5882510 GTGCATCGATGCATTCTGCT
1 GTGCATCGATGCATCCTGCT
*
5882530 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGCT
*
5882550 GTGCATCCATGCA
1 GTGCATCGATGCA
5882563 CGAAGGCTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:5884767 original size:3 final size:3
Alignment explanation
Indices: 5884755--5884792 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
5884745 ACCATCATCA
* *
5884755 TCG TCA TCG TCG TCG TCG TCG TCG TCG TCG TTG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
5884793 ATAGTCATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.32, G:0.29, T:0.37
Consensus pattern (3 bp):
TCG
Found at i:5886676 original size:16 final size:15
Alignment explanation
Indices: 5886640--5886686 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
5886630 GGTCGCTCTC
*
5886640 ATAAAAATATTAATA
1 ATAAAAATAATAATA
5886655 ATTAAAAATAATAAT-
1 A-TAAAAATAATAATA
*
5886670 ATATAAACTAATAATA
1 ATA-AAAATAATAATA
5886686 A
1 A
5886687 AAAGTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 2 0.07
15 12 0.44
16 13 0.48
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAAATAATAATA
Found at i:5886697 original size:27 final size:28
Alignment explanation
Indices: 5886650--5886703 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
5886640 ATAAAAATAT
*
5886650 TAATAATTAAAAATAATAATATATAAAC
1 TAATAATTAAAAATAATAATAAATAAAC
*
5886678 TAATAA-TAAAAAGTTA-AATAAATAAA
1 TAATAATTAAAAA-TAATAATAAATAAA
5886704 TTATTACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
TAATAATTAAAAATAATAATAAATAAAC
Found at i:5886864 original size:19 final size:20
Alignment explanation
Indices: 5886821--5886864 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
5886811 ATAACTGCAA
5886821 AAAATATAAAATAATTAAAT
1 AAAATATAAAATAATTAAAT
5886841 AAAATACTAAAA-AA-TAAAT
1 AAAATA-TAAAATAATTAAAT
*
5886860 TAAAT
1 AAAAT
5886865 GGAATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 8 0.36
21 5 0.23
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATATAAAATAATTAAAT
Found at i:5887025 original size:22 final size:21
Alignment explanation
Indices: 5886979--5887018 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5886969 TTATAGGATG
5886979 GGATGGGAAGTGTGAATGGAC
1 GGATGGGAAGTGTGAATGGAC
*
5887000 GGATGGGGAGTGTGAATGG
1 GGATGGGAAGTGTGAATGG
5887019 TCCGGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.53, T:0.20
Consensus pattern (21 bp):
GGATGGGAAGTGTGAATGGAC
Found at i:5888707 original size:4 final size:4
Alignment explanation
Indices: 5888698--5888748 Score: 61
Period size: 4 Copynumber: 12.8 Consensus size: 4
5888688 TATAGCTTAT
*
5888698 TATG TATG TATG TATG TATG TATA TA-G CTTAT- TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG --TATG TATG TATG TATG TATG
5888746 TAT
1 TAT
5888749 ATTTTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 3 0.07
4 36 0.88
5 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:5888725 original size:32 final size:32
Alignment explanation
Indices: 5888688--5888748 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
5888678 GTTATCATTG
5888688 TATAGCTTATTATGTATGTATGTATGTATGTA
1 TATAGCTTATTATGTATGTATGTATGTATGTA
5888720 TATAGCTTATTATGTATGTATGTATGTAT
1 TATAGCTTATTATGTATGTATGTATGTAT
5888749 ATTTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (32 bp):
TATAGCTTATTATGTATGTATGTATGTATGTA
Found at i:5893113 original size:24 final size:24
Alignment explanation
Indices: 5893086--5893131 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5893076 AAAGTGAGAT
*
5893086 TTTAAAAACCACAT-TAATTTTTAA
1 TTTAAAAA-CAAATGTAATTTTTAA
5893110 TTTAAAAACAAATGTAATTTTT
1 TTTAAAAACAAATGTAATTTTT
5893132 TTAAAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (24 bp):
TTTAAAAACAAATGTAATTTTTAA
Found at i:5893130 original size:23 final size:22
Alignment explanation
Indices: 5893085--5893139 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
5893075 AAAAGTGAGA
*
5893085 TTTTAAAAACCACATTAATTTT
1 TTTTAAAAACCAAATTAATTTT
5893107 TAATTTAAAAA-CAAATGTAATTTT
1 T--TTTAAAAACCAAAT-TAATTTT
*
5893131 TTTAAAAAA
1 TTTTAAAAA
5893140 ACTATCGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 8 0.29
23 4 0.14
24 16 0.57
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTTAAAAACCAAATTAATTTT
Found at i:5895752 original size:53 final size:53
Alignment explanation
Indices: 5895672--5895823 Score: 216
Period size: 53 Copynumber: 2.9 Consensus size: 53
5895662 CGACCAGCGG
* * * *
5895672 GTTCGTTCCTTCTTGCTTCAAGGAGTAGAACTCGAATAATTTTCTGCCTAC-A
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATTTTCTGCCTACGA
*
5895724 TGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATTTTCTGTCTACGA
1 -GTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATTTTCTGCCTACGA
* * *
5895778 GTTTGCTCCCTCTTGCTTCAGGGAGTAGAACTTGAACAATCTTCTG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATTTTCTG
5895824 GTGTGATTAT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 89 0.99
54 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (53 bp):
GTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATTTTCTGCCTACGA
Found at i:5896335 original size:42 final size:42
Alignment explanation
Indices: 5896242--5896663 Score: 244
Period size: 42 Copynumber: 9.6 Consensus size: 42
5896232 ACATCCTACC
* * * *
5896242 CGAAGGACTTA-TGGATGACCCGAAGGATTT-ATCATCTTGCC
1 CGAAAGACTTACT-GATGGCCCGAAGGATTTAATCATCATGCT
*
5896283 CGAAAAACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
* *
5896325 CGAAAGACTTACTGATGGCCTGAAGGATTTCATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
* * **
5896367 CGAAAGACTTATTGATGGCACTTACTGATGGATTTGCTTCA-CTACT-CTT
1 CGAAAGACTTACTGATGGC-C---C-GAAGGATTT-AATCATC-A-TGC-T
* * ** ** *
5896416 CCGTGAAGGCTTACAAATTACCTGAAGGATTTAATCATCATGCT
1 -CG-AAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
* * * * *
5896460 CGAAAAACTTACTGATGGCCCGAAGGACTTCATTATCATTCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
* * **
5896502 CGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCA-CTACT-CTT
1 CGAAAGACTTACTGATGGC-C---C-GAAGGATTT-AATCATC-A-TGC-T
* * ** ** * *
5896551 CGGTGAAGGCTTACAAATTACCCAAAGAATTTAATCATCATGCT
1 C-G-AAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
* *
5896595 CGAAAGACTTACTGATGGCCTGAAGGATTTAAACATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
* *
5896637 CGAAAGACTTATTGATGACCCGAAGGA
1 CGAAAGACTTACTGATGGCCCGAAGGA
5896664 CTTACTAAGT
Statistics
Matches: 287, Mismatches: 66, Indels: 55
0.70 0.16 0.13
Matches are distributed among these distances:
41 25 0.09
42 167 0.58
43 5 0.02
44 5 0.02
45 10 0.03
46 16 0.06
47 17 0.06
48 11 0.04
49 5 0.02
50 5 0.02
51 21 0.07
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (42 bp):
CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
Found at i:5896448 original size:135 final size:135
Alignment explanation
Indices: 5896301--5896653 Score: 589
Period size: 135 Copynumber: 2.6 Consensus size: 135
5896291 TTACTGATGG
5896301 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGATTTCATCATCATGC
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGATTTCATCATCATGC
5896366 TCGAAAGACTTATTGATGGCACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACA
66 TCGAAAGACTTATTGATGGCACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACA
5896431 AATTA
131 AATTA
* * * * * *
5896436 CCTGAAGGATTTAATCATCATGCTCGAAAAACTTACTGATGGCCCGAAGGACTTCATTATCATTC
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGATTTCATCATCATGC
* * *
5896501 TCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCACTACTCTTCGGTGAAGGCTTACA
66 TCGAAAGACTTATTGATGGCACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACA
5896566 AATTA
131 AATTA
* * * *
5896571 CCCAAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGATTTAAACATCATGC
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGATTTCATCATCATGC
5896636 TCGAAAGACTTATTGATG
66 TCGAAAGACTTATTGATG
5896654 ACCCGAAGGA
Statistics
Matches: 198, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 198 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (135 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGATTTCATCATCATGC
TCGAAAGACTTATTGATGGCACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACA
AATTA
Found at i:5896526 original size:13 final size:13
Alignment explanation
Indices: 5896508--5896532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5896498 TTCTCGAAAG
5896508 ACTTACTGATGGC
1 ACTTACTGATGGC
5896521 ACTTACTGATGG
1 ACTTACTGATGG
5896533 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:5903564 original size:49 final size:47
Alignment explanation
Indices: 5903511--5903616 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 47
5903501 TATCTACCCC
5903511 CATGCTTTATTATTCAAAAATAAATCCTAACCGCATGATATCTAATTCG
1 CATGCTTTATT-TTCAAAAATAAA-CCTAACCGCATGATATCTAATTCG
* * *
5903560 CATGC-TT-GTTTGAAAAATAAACCTAACCGCATGATATCTAGTTCG
1 CATGCTTTATTTTCAAAAATAAACCTAACCGCATGATATCTAATTCG
5903605 CATGCATTTATT
1 CATGC-TTTATT
5903617 CGAAAAACGA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
45 28 0.56
46 11 0.22
47 3 0.06
48 3 0.06
49 5 0.10
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (47 bp):
CATGCTTTATTTTCAAAAATAAACCTAACCGCATGATATCTAATTCG
Found at i:5911385 original size:2 final size:2
Alignment explanation
Indices: 5911318--5911370 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
5911308 GTTTAACCCA
5911318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
5911359 AT AT AT AT AT AT
1 AT AT AT AT AT AT
5911371 GAAACAAGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5912617 original size:30 final size:29
Alignment explanation
Indices: 5912499--5912631 Score: 128
Period size: 30 Copynumber: 4.6 Consensus size: 29
5912489 TTATTTTTAG
* * * *
5912499 TTTATTTTTGTTTTAACTTATAAATCTA-
1 TTTATTCTTATTTTAACTTAAAAATATAT
5912527 TTTA-TCTTATTTTAA-TATAAAAATATATGT
1 TTTATTCTTATTTTAACT-TAAAAATATA--T
* * * *
5912557 TTTAATCTTATCTTCACTTAAAAGTATAT
1 TTTATTCTTATTTTAACTTAAAAATATAT
5912586 TTTATTCTTATTTTAACTTAAAAAATATAT
1 TTTATTCTTATTTTAACTT-AAAAATATAT
*
5912616 TTTATTCTTATCTTAA
1 TTTATTCTTATTTTAA
5912632 ATTTTTAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.01
27 17 0.20
28 4 0.05
29 17 0.20
30 28 0.33
31 18 0.21
32 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTATTCTTATTTTAACTTAAAAATATAT
Found at i:5912798 original size:2 final size:2
Alignment explanation
Indices: 5912791--5912826 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5912781 ATTGAAGATA
5912791 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
5912827 TTGTTGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5912911 original size:33 final size:30
Alignment explanation
Indices: 5912874--5913006 Score: 110
Period size: 32 Copynumber: 4.3 Consensus size: 30
5912864 AAGATATTTA
5912874 AAAATATATATTTTTAAAAATTAAGATAAGAAT
1 AAAATATATATTTTT--AAATTAAGATAA-AAT
* *
5912907 -AAA-ATATATTTTTAAGTGAAGATAAAGAT
1 AAAATATATATTTTTAAATTAAGATAAA-AT
* *
5912936 AAAATATATATATTTTACATTAAAATAAAAGT
1 AAAATATATAT-TTTTAAATTAAGATAAAA-T
** * *
5912968 AAAATATAT-TTAATAAGTTAAGAAAAAAT
1 AAAATATATATTTTTAAATTAAGATAAAAT
5912997 AAGAATATAT
1 AA-AATATAT
5913007 TTAATAAGTT
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
28 1 0.01
29 15 0.18
30 22 0.27
31 18 0.22
32 26 0.32
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.35
Consensus pattern (30 bp):
AAAATATATATTTTTAAATTAAGATAAAAT
Found at i:5912941 original size:62 final size:61
Alignment explanation
Indices: 5912874--5913006 Score: 155
Period size: 61 Copynumber: 2.1 Consensus size: 61
5912864 AAGATATTTA
* * *
5912874 AAAATATATAT-TTTTAAAAATTAAGATAAGAA-TAAAATATATTT-TTAAGTGAAGATAAAGAT
1 AAAATATATATATTTT--AAATTAAAATAA-AAGTAAAATATATTTAATAAGTGAAGA-AAAAAT
* *
5912936 AAAATATATATATTTTACATTAAAATAAAAGTAAAATATATTTAATAAGTTAAGAAAAAAT
1 AAAATATATATATTTTAAATTAAAATAAAAGTAAAATATATTTAATAAGTGAAGAAAAAAT
5912997 AAGAATATAT
1 AA-AATATAT
5913007 TTAATAAGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
60 2 0.03
61 29 0.47
62 27 0.44
63 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.35
Consensus pattern (61 bp):
AAAATATATATATTTTAAATTAAAATAAAAGTAAAATATATTTAATAAGTGAAGAAAAAAT
Found at i:5913004 original size:30 final size:31
Alignment explanation
Indices: 5912962--5913035 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 31
5912952 ACATTAAAAT
*
5912962 AAAAGTAA-AATATATTTAATAAGTTAAGA-
1 AAAAATAAGAATATATTTAATAAGTTAAGAC
*
5912991 AAAAATAAGAATATATTTAATAAGTTAATAC
1 AAAAATAAGAATATATTTAATAAGTTAAGAC
5913022 AAAAATAAG-ATATA
1 AAAAATAAGAATATA
5913036 AGATATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.17
30 25 0.61
31 9 0.22
ACGTcount: A:0.61, C:0.01, G:0.08, T:0.30
Consensus pattern (31 bp):
AAAAATAAGAATATATTTAATAAGTTAAGAC
Found at i:5924346 original size:18 final size:18
Alignment explanation
Indices: 5924323--5924365 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5924313 CTTTATATTA
*
5924323 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
* *
5924341 TTTATTTGATTCTTATCT
1 TTTATTTAATTATTATCT
5924359 TTTATTT
1 TTTATTT
5924366 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:5924516 original size:21 final size:23
Alignment explanation
Indices: 5924412--5924516 Score: 56
Period size: 24 Copynumber: 4.4 Consensus size: 23
5924402 ACTACTATTA
* **
5924412 TTTATTATTTTATTATATTTCCCT
1 TTTATT-TTTTTTTATATTTCTAT
5924436 TTTATTTATTATTATTATTATTT-TAT
1 TTTATTT-TT-TT-TTA-TATTTCTAT
* *
5924462 TTTGTTTTGTTTTTAT-TTTCTCT
1 TTTATTTT-TTTTTATATTTCTAT
**
5924485 TTTAACATTTTTTTATATTT-T-T
1 TTT-ATTTTTTTTTATATTTCTAT
5924507 TTTATTTTTT
1 TTTATTTTTT
5924517 CTTTTCTGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
21 5 0.08
22 7 0.11
23 15 0.24
24 16 0.25
25 4 0.06
26 11 0.17
27 5 0.08
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTATTTTTTTTTATATTTCTAT
Found at i:5932937 original size:39 final size:40
Alignment explanation
Indices: 5932883--5932997 Score: 150
Period size: 39 Copynumber: 2.9 Consensus size: 40
5932873 TTAAGGGGGA
5932883 AATTTAAGAGTCTCTTAGGAGTTAGAGAT-TTTTATTGTG
1 AATTTAAGAGTCTCTTAGGAGTTAGAGATCTTTTATTGTG
*
5932922 AATTTAAGAGTCTCTTGAGG-GTTAGAG-TGTTTTATTGTG
1 AATTTAAGAGTCTCTT-AGGAGTTAGAGATCTTTTATTGTG
*
5932961 AATTTGAGAGT-TCTT-GGAAGTTAGAGAGTCTTTTATT
1 AATTTAAGAGTCTCTTAGG-AGTTAGAGA-TCTTTTATT
5932998 TTTTAGTATA
Statistics
Matches: 68, Mismatches: 2, Indels: 11
0.84 0.02 0.14
Matches are distributed among these distances:
36 2 0.03
38 12 0.18
39 43 0.63
40 11 0.16
ACGTcount: A:0.26, C:0.05, G:0.25, T:0.43
Consensus pattern (40 bp):
AATTTAAGAGTCTCTTAGGAGTTAGAGATCTTTTATTGTG
Found at i:5940948 original size:39 final size:40
Alignment explanation
Indices: 5940894--5940999 Score: 155
Period size: 39 Copynumber: 2.7 Consensus size: 40
5940884 ACTTAAGGGG
5940894 GAATTTAAGAGTCTCTTGGGAGTTAGAGAT-TTTTATTAT
1 GAATTTAAGAGTCTCTTGGGAGTTAGAGATGTTTTATTAT
* *
5940933 GAATTTAAGAGTCTCTTGGGAGTTAGA-TTGTTTTATTGT
1 GAATTTAAGAGTCTCTTGGGAGTTAGAGATGTTTTATTAT
* *
5940972 GAATTTAAGAGT-TCTTGGAAGTTTGAGA
1 GAATTTAAGAGTCTCTTGGGAGTTAGAGA
5941000 GTATTTGTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 13 0.22
39 47 0.78
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.42
Consensus pattern (40 bp):
GAATTTAAGAGTCTCTTGGGAGTTAGAGATGTTTTATTAT
Found at i:5942775 original size:45 final size:45
Alignment explanation
Indices: 5942711--5942802 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
5942701 AGCATGATAA
5942711 TCTCTAGGGAAATAAAGGTACAAAATTAATTGATTTTTTAGTCAT
1 TCTCTAGGGAAATAAAGGTACAAAATTAATTGATTTTTTAGTCAT
5942756 TCTCTAGGGAAATAAAGGTACAAAATTAATTGATTTTTTAGTCAT
1 TCTCTAGGGAAATAAAGGTACAAAATTAATTGATTTTTTAGTCAT
5942801 TC
1 TC
5942803 CTACGATTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (45 bp):
TCTCTAGGGAAATAAAGGTACAAAATTAATTGATTTTTTAGTCAT
Found at i:5945219 original size:14 final size:14
Alignment explanation
Indices: 5945200--5945247 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
5945190 TGTTTGACAC
5945200 AAAAAAAAATGAAA
1 AAAAAAAAATGAAA
*
5945214 AAAAAATAATGGAAAA
1 AAAAAAAAAT-G-AAA
5945230 AAACAAAAAAT-AAA
1 AAA-AAAAAATGAAA
5945244 AAAA
1 AAAA
5945248 TGAATTGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 1 0.03
14 15 0.52
15 1 0.03
16 6 0.21
17 6 0.21
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.08
Consensus pattern (14 bp):
AAAAAAAAATGAAA
Found at i:5945228 original size:15 final size:13
Alignment explanation
Indices: 5945200--5945251 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 13
5945190 TGTTTGACAC
5945200 AAAAAAAAATGAA
1 AAAAAAAAATGAA
5945213 AAAAAAATAATGGAA
1 AAAAAAA-AAT-GAA
*
5945228 AAAAACAAA--AA
1 AAAAAAAAATGAA
*
5945239 ATAAAAAAATGAA
1 AAAAAAAAATGAA
5945252 TTGGAGTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
11 9 0.28
13 9 0.28
14 5 0.16
15 9 0.28
ACGTcount: A:0.81, C:0.02, G:0.08, T:0.10
Consensus pattern (13 bp):
AAAAAAAAATGAA
Found at i:5947311 original size:7 final size:7
Alignment explanation
Indices: 5947301--5947335 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
5947291 CATTAAATCA
5947301 TAAAATT
1 TAAAATT
5947308 TAAAATT
1 TAAAATT
5947315 TAAAATT
1 TAAAATT
5947322 TAAAATT
1 TAAAATT
5947329 TAAAATT
1 TAAAATT
5947336 AATCTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAAAATT
Found at i:5947318 original size:21 final size:21
Alignment explanation
Indices: 5947295--5947335 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5947285 AAATTACATT
5947295 AAATCATAAAATTTAAAATTTA
1 AAAT-ATAAAATTTAAAATTTA
*
5947317 AAATTTAAAATTTAAAATT
1 AAATATAAAATTTAAAATT
5947336 AATCTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATATAAAATTTAAAATTTA
Found at i:5949267 original size:65 final size:64
Alignment explanation
Indices: 5949198--5949339 Score: 189
Period size: 65 Copynumber: 2.2 Consensus size: 64
5949188 AATTAAATTG
* *
5949198 AACATCGAATGCATTTCATGCATCGATGCACTTA-CCATGCATCGATGCACTAAGGAT-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCAC-CAGCCATGCATCAATGCACTAAGGATATTT-TG
5949261 AA
64 -A
* ** *
5949263 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCAATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACCAGCCATGCATCAATGCACTAAGGATATTTTGA
5949327 AACATCGAATGCA
1 AACATCGAATGCA
5949340 CTTGATATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
64 15 0.22
65 51 0.74
66 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACCAGCCATGCATCAATGCACTAAGGATATTTTGA
Found at i:5955197 original size:42 final size:44
Alignment explanation
Indices: 5955150--5955244 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
5955140 TTGTGCTTCA
*
5955150 TGCATCGATACACC-T-AACAGTGCATCGATACAT-CCTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATACATGCCTTGAATG
* * *
5955192 TGCATCGATGCACCATGAAGGTGCACCGATGCATGCCTTGAATG
1 TGCATCGATACACCATGAAAGTGCACCGATACATGCCTTGAATG
5955236 TGCATCGAT
1 TGCATCGAT
5955245 GCACAGGGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 13 0.28
43 13 0.28
44 20 0.43
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATACATGCCTTGAATG
Found at i:5955238 original size:23 final size:22
Alignment explanation
Indices: 5955169--5955247 Score: 106
Period size: 21 Copynumber: 3.6 Consensus size: 22
5955159 ACACCTAACA
*
5955169 GTGCATCGATACATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
* *
5955191 GTGCATCGATGCA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
5955212 GTGCACCGATGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
5955235 GTGCATCGATGCA
1 GTGCATCGATGCA
5955248 CAGGGTCACA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.38
22 12 0.25
23 18 0.38
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:5956841 original size:21 final size:21
Alignment explanation
Indices: 5956799--5956842 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5956789 ACCCCGGGAG
* *
5956799 CTAGCTCTTCACGAGCTTCTC
1 CTAGATCTTCACGAGCTCCTC
* *
5956820 CTAGATCTTCTCGTGCTCCTC
1 CTAGATCTTCACGAGCTCCTC
5956841 CT
1 CT
5956843 CCAGCACTAG
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:0.11, C:0.39, G:0.14, T:0.36
Consensus pattern (21 bp):
CTAGATCTTCACGAGCTCCTC
Found at i:5958038 original size:65 final size:64
Alignment explanation
Indices: 5957935--5958094 Score: 186
Period size: 65 Copynumber: 2.5 Consensus size: 64
5957925 AATTAAATTG
* *
5957935 AACATCGAATGCATTTCATGCATCGATGCACTTACCATGCA-CAGATGCACTAAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCATC-GATGCACTAAGGATATTT-TG
5957998 AA
64 -A
** *
5958000 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-CCATGCATCGATGCACTAAGGATATTTTGA
* *
5958064 AACATCAAATGCACTTG--GCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
5958095 TTAGTGTACA
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
62 12 0.14
63 1 0.01
64 17 0.20
65 50 0.60
66 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCATCGATGCACTAAGGATATTTTGA
Found at i:5960025 original size:2 final size:2
Alignment explanation
Indices: 5960018--5960048 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5960008 TACGTACGTG
5960018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5960049 TGATGTCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5960691 original size:21 final size:21
Alignment explanation
Indices: 5960667--5960816 Score: 150
Period size: 21 Copynumber: 7.2 Consensus size: 21
5960657 TTGAAAATCG
*
5960667 CGTTGTGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
5960688 CGTTGCGAT--TTTTCA-TTT
1 CGTTGCGATAGTCTACAGTGT
5960706 CACGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
5960729 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
*
5960750 CGTTGCGATAGTCTATAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
5960771 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
5960789 AGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
5960812 CGTTG
1 CGTTG
5960817 TGATTTTCCA
Statistics
Matches: 104, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
18 4 0.04
19 7 0.07
20 18 0.17
21 63 0.61
22 8 0.08
23 4 0.04
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:5960718 original size:41 final size:40
Alignment explanation
Indices: 5960667--5960843 Score: 221
Period size: 41 Copynumber: 4.3 Consensus size: 40
5960657 TTGAAAATCG
* *
5960667 CGTTGTGATAGTCTACAGTGTCGTTGCGATTTTTCATTTCA
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTT-A
* * *
5960708 CGTTGCGATAGTCTACAGTGTCGTTGCGATAGTCTACAGTGT-
1 CGTTGCGATAGTCTACAGTGTCGTTGCGAT--TTTCCA-TTTA
*
5960750 CGTTGCGATAGTCTATAGTGTCGTTGCGATTTTCCATTTA
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTA
* *
5960790 GCGTTGCGATAGTCTACAGTGTCGTTGTGATTTTCCATTTCG
1 -CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTT-A
5960832 CGTTGCGATAGT
1 CGTTGCGATAGT
5960844 TTTAAAAATG
Statistics
Matches: 119, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.02
40 4 0.03
41 78 0.66
42 29 0.24
43 4 0.03
44 2 0.02
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.40
Consensus pattern (40 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTA
Found at i:5961709 original size:6 final size:6
Alignment explanation
Indices: 5961683--5961718 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5961673 TCTCGTCTCG
5961683 GGTC-T GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
5961719 AATACGTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 14 0.48
6 15 0.52
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:5961715 original size:12 final size:12
Alignment explanation
Indices: 5961683--5961718 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
5961673 TCTCGTCTCG
5961683 GGTC-TGGTCG-
1 GGTCGTGGTCGT
5961693 GGTCG-GGTCGT
1 GGTCGTGGTCGT
5961704 GGTCGTGGTCGT
1 GGTCGTGGTCGT
5961716 GGT
1 GGT
5961719 AATACGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.39
11 5 0.22
12 9 0.39
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (12 bp):
GGTCGTGGTCGT
Found at i:5961829 original size:20 final size:20
Alignment explanation
Indices: 5961804--5961958 Score: 91
Period size: 20 Copynumber: 7.6 Consensus size: 20
5961794 TTTTAAAACT
5961804 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
5961824 ATCGCAACGAC-ACTATAGACT
1 ATCGCAACG-CGA-AATGGAAA
**
5961845 ATCGCAACATGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
5961865 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
5961886 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
5961906 ACCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
5961927 ATCGCAACACGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
5961947 ATCGCAACGCGA
1 ATCGCAACGCGA
5961959 TTTTCAACTA
Statistics
Matches: 95, Mismatches: 31, Indels: 18
0.66 0.22 0.12
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 48 0.51
21 36 0.38
22 3 0.03
23 3 0.03
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:5961850 original size:21 final size:21
Alignment explanation
Indices: 5961824--5961894 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
5961814 GAAATGGAAA
5961824 ATCGCAACGACACTATAGACT
1 ATCGCAACGACACTATAGACT
* **
5961845 ATCGCAACATGA-A--ATGGAAA
1 ATCGCAAC--GACACTATAGACT
*
5961865 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTATAGACT
5961886 ATCGCAACG
1 ATCGCAACG
5961895 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
20 12 0.32
21 20 0.53
22 1 0.03
23 2 0.05
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.17
Consensus pattern (21 bp):
ATCGCAACGACACTATAGACT
Found at i:5961934 original size:21 final size:21
Alignment explanation
Indices: 5961908--5961977 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
5961898 AATGGAAAAC
5961908 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
* ** ** *
5961929 CGCAACACGAAATGGAA-AAT
1 CGCAACGCGATTTTCAACTAT
5961949 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
5961970 CGCAACGC
1 CGCAACGC
5961978 AAAATGCAGC
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
CGCAACGCGATTTTCAACTAT
Found at i:5961941 original size:82 final size:82
Alignment explanation
Indices: 5961801--5961955 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 82
5961791 CATTTTTAAA
* *
5961801 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTATAGACTATCGCAACATGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAACCGCAACGACACTATAGACTATCGCAACACGAAATGGAAAA
5961866 TCGCAACGACACTGTAG
66 TCGCAACGACACTGTAG
* *
5961883 ACTATCGCAACGCGAAATGGAAAACCGCAACG-CGATTTTCA-ACTATCGCAACACGAAATGGAA
1 ACTATCGCAACGCGAAATGGAAAACCGCAACGAC-ACTAT-AGACTATCGCAACACGAAATGGAA
5961946 AATCGCAACG
64 AATCGCAACG
5961956 CGATTTTCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
81 1 0.01
82 65 0.97
83 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (82 bp):
ACTATCGCAACGCGAAATGGAAAACCGCAACGACACTATAGACTATCGCAACACGAAATGGAAAA
TCGCAACGACACTGTAG
Found at i:5961983 original size:41 final size:40
Alignment explanation
Indices: 5961800--5961983 Score: 219
Period size: 41 Copynumber: 4.5 Consensus size: 40
5961790 CCATTTTTAA
*
5961800 AACTATCGCAACGCGAAATGGAAAATCGCAACGACACTAT
1 AACTATCGCAACGCGAAATGGAAAATCGCAACGACACTTT
** *
5961840 AGACTATCGCAACATGAAATGGAAAATCGCAACGACACTGT
1 A-ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTTT
* *
5961881 AGACTATCGCAACGCGAAATGGAAAACCGCAACG-CGATTTT
1 A-ACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTTT
* *
5961922 CAACTATCGCAACACGAAATGGAAAATCGCAACG-CGATTTT
1 -AACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTTT
*
5961963 CAACTATCGCAACGCAAAATG
1 -AACTATCGCAACGCGAAATG
5961984 CAGCGGGAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
40 2 0.02
41 126 0.98
42 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.17
Consensus pattern (40 bp):
AACTATCGCAACGCGAAATGGAAAATCGCAACGACACTTT
Found at i:5975779 original size:2 final size:2
Alignment explanation
Indices: 5975768--5975798 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5975758 AAGAACTAAT
5975768 TA TA -A 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
5975799 ACCCAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5976841 original size:18 final size:17
Alignment explanation
Indices: 5976818--5976857 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5976808 TTAGAATATC
5976818 AAAATAAATTATTAATTA
1 AAAATAAA-TATTAATTA
* *
5976836 AAAATATATATTAATTT
1 AAAATAAATATTAATTA
5976853 AAAAT
1 AAAAT
5976858 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATAAATATTAATTA
Found at i:5976945 original size:41 final size:41
Alignment explanation
Indices: 5976887--5976969 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
5976877 CCACTCGCCC
5976887 TTCAATCCATCCATGACCCATATGCCATAGCCTAGCACAGG
1 TTCAATCCATCCATGACCCATATGCCATAGCCTAGCACAGG
*
5976928 TTCAATCCATCCCTGACCCATATGCCATAGCCTAGCACAGG
1 TTCAATCCATCCATGACCCATATGCCATAGCCTAGCACAGG
5976969 T
1 T
5976970 AAACAACTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.23
Consensus pattern (41 bp):
TTCAATCCATCCATGACCCATATGCCATAGCCTAGCACAGG
Found at i:5977222 original size:13 final size:14
Alignment explanation
Indices: 5977199--5977236 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
5977189 ACACTTAGAG
5977199 ATTTTTAAAATAAT
1 ATTTTTAAAATAAT
5977213 ATTTTT-AAATAAT
1 ATTTTTAAAATAAT
5977226 ATTTTTTAAAA
1 A-TTTTTAAAA
5977237 AATTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 11 0.50
15 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTTAAAATAAT
Found at i:5982847 original size:41 final size:39
Alignment explanation
Indices: 5982789--5982963 Score: 127
Period size: 41 Copynumber: 4.3 Consensus size: 39
5982779 TAACATTAAC
** *
5982789 GGCGTTTTTCAACAAACGCTGCTAAAACTCGTACTTTAGT
1 GGCGTTTTTTGACAAACGCCGCTAAAA-TCGTACTTTAGT
* *
5982829 GGCGTTTATTTGACAAACGCCGCCATAGAATCGTTCTTTAGT
1 GGCGTTT-TTTGACAAACGCCG-C-TAAAATCGTACTTTAGT
** * ** * ** *
5982871 GGCGTTTTTAAACAAATGCAAC-AATAGGGTACATATATCGT
1 GGCGTTTTTTGACAAACGCCGCTAAAATCGTAC-T-T-TAGT
5982912 GGCGTTTTTTGACAAACGCCGCTAAATACTCGTACTTTAGT
1 GGCGTTTTTTGACAAACGCCGCTAAA-A-TCGTACTTTAGT
*
5982953 GACGTTTTTTG
1 GGCGTTTTTTG
5982964 TTCTCAAACG
Statistics
Matches: 100, Mismatches: 26, Indels: 17
0.70 0.18 0.12
Matches are distributed among these distances:
38 5 0.05
39 1 0.01
40 9 0.09
41 53 0.53
42 22 0.22
43 6 0.06
44 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (39 bp):
GGCGTTTTTTGACAAACGCCGCTAAAATCGTACTTTAGT
Found at i:5989791 original size:14 final size:14
Alignment explanation
Indices: 5989772--5989804 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5989762 CCATCTCGCA
5989772 TTTTGCATTCT-TAT
1 TTTTGCA-TCTATAT
5989786 TTTTGCATCTATAT
1 TTTTGCATCTATAT
5989800 TTTTG
1 TTTTG
5989805 TATTTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.64
Consensus pattern (14 bp):
TTTTGCATCTATAT
Found at i:5993226 original size:41 final size:42
Alignment explanation
Indices: 5993169--5993250 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 42
5993159 TTTGAAGATG
*
5993169 AGAAAAGAAAAAAAAAA-GGAACAAAGGAGAAA-GAAAAAAAT
1 AGAAAAGAAAAAAAAAAGGGAA-AAAGGAAAAATGAAAAAAAT
*
5993210 AGAAAA-AAAAAGAAAAAGGGAAAAATGAAAAATGAAAAAAA
1 AGAAAAGAAAAA-AAAAAGGGAAAAAGGAAAAATGAAAAAAA
5993251 ATAACAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
40 5 0.14
41 19 0.53
42 12 0.33
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (42 bp):
AGAAAAGAAAAAAAAAAGGGAAAAAGGAAAAATGAAAAAAAT
Found at i:5993228 original size:33 final size:33
Alignment explanation
Indices: 5993177--5993251 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 33
5993167 TGAGAAAAGA
5993177 AAAAAAAAAGGAACAAAGGAGAAAGAA-AAAAATAG
1 AAAAAAAAAGGAACAAAGG-GAAA-AAGAAAAAT-G
5993212 AAAAAAAAA-GAA-AAAGGGAAAAATGAAAAATG
1 AAAAAAAAAGGAACAAAGGGAAAAA-GAAAAATG
5993244 AAAAAAAA
1 AAAAAAAA
5993252 TAACAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
31 2 0.05
32 13 0.34
33 11 0.29
34 3 0.08
35 9 0.24
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.04
Consensus pattern (33 bp):
AAAAAAAAAGGAACAAAGGGAAAAAGAAAAATG
Found at i:5993241 original size:34 final size:33
Alignment explanation
Indices: 5993177--5993251 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 33
5993167 TGAGAAAAGA
*
5993177 AAAAAAAAAGGAACAAAGGAGAAAGAAAAAAATAG
1 AAAAAAAAAGGAACAAAGGAAAAAG-AAAAAAT-G
5993212 AAAAAAAAA-GAA-AAAGGGAAAAATG-AAAAATG
1 AAAAAAAAAGGAACAAA-GGAAAAA-GAAAAAATG
5993244 AAAAAAAA
1 AAAAAAAA
5993252 TAACAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
32 9 0.24
33 9 0.24
34 9 0.24
35 10 0.27
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.04
Consensus pattern (33 bp):
AAAAAAAAAGGAACAAAGGAAAAAGAAAAAATG
Found at i:5993293 original size:13 final size:13
Alignment explanation
Indices: 5993275--5993300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5993265 AAAAATAGGA
5993275 AATAATAAAAAAG
1 AATAATAAAAAAG
5993288 AATAATAAAAAAG
1 AATAATAAAAAAG
5993301 GGAAGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AATAATAAAAAAG
Found at i:5995396 original size:91 final size:91
Alignment explanation
Indices: 5995292--5995562 Score: 364
Period size: 91 Copynumber: 3.0 Consensus size: 91
5995282 ACCAATTAAT
* * * * *
5995292 ATTTCCAATGGAGAGTTCATAATAAGAAAAACTCATCCAACGAGGGAGAAGAAGTTCATAACGAT
1 ATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAG
*
5995357 AAGGACTTGTTCAACCTT-GCATCAAC
66 AAGAACTTGTTCAACCTTGGC-TCAAC
* * * * *
5995383 ATTTCCAGTGGAGATTTCATAATGAGAATAACTCATCCGATAAGGGAGAAAAAGTTCATAATGAG
1 ATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAG
* * *
5995448 AACAACTTGTTCAACATTGGCTCAAT
66 AAGAACTTGTTCAACCTTGGCTCAAC
* * *
5995474 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATACGATGAGGGACAAGAAGTTCATAATGAG
1 ATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAG
*
5995539 AAGAACTTGTTCAACCTTAGCTCA
66 AAGAACTTGTTCAACCTTGGCTCA
5995563 TTTCCATCAC
Statistics
Matches: 155, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
91 153 0.99
92 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (91 bp):
ATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTGGCTCAAC
Done.