Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold323
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: 764456
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.32
Warning! 36661 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:409007 original size:11 final size:11
Alignment explanation
Indices: 408991--409015 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
408981 TTAAATTTTA
408991 AAAAATTAATT
1 AAAAATTAATT
409002 AAAAATTAATT
1 AAAAATTAATT
409013 AAA
1 AAA
409016 TGATGATGCA
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:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAATTAATT
Found at i:414101 original size:27 final size:27
Alignment explanation
Indices: 414060--414112 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
414050 TTTTGGTGTA
* *
414060 TTTCGGATGGATTAGCTCTTATGAGCG
1 TTTCAGATGGATTAGCTCGTATGAGCG
*
414087 TTTCAGATGGTTTAGCTCGTATGAGC
1 TTTCAGATGGATTAGCTCGTATGAGC
414113 ATTAGTGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (27 bp):
TTTCAGATGGATTAGCTCGTATGAGCG
Found at i:414139 original size:35 final size:36
Alignment explanation
Indices: 414086--414160 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 36
414076 TCTTATGAGC
* * *
414086 GTTTCAGATGGTTTAGCTCGTATGAGCA-TTAGTGT
1 GTTTCAGAGGGATAAGCTCGTATGAGCATTTAGTGT
* * *
414121 GTTTCAGAGGGATAAGCTCTTATGAGTATTTGGTGT
1 GTTTCAGAGGGATAAGCTCGTATGAGCATTTAGTGT
414157 GTTT
1 GTTT
414161 TGGTTGGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.20, C:0.09, G:0.29, T:0.41
Consensus pattern (36 bp):
GTTTCAGAGGGATAAGCTCGTATGAGCATTTAGTGT
Found at i:415729 original size:81 final size:81
Alignment explanation
Indices: 415589--415757 Score: 311
Period size: 81 Copynumber: 2.1 Consensus size: 81
415579 TTATTTGTGT
* *
415589 TATTCTTATTCAATCAAGATTCTCCTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTATTA
1 TATTGTTATTCAATCAAGATTCTCCTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTAGTA
415654 ATAGACAAGTTTCATA
66 ATAGACAAGTTTCATA
*
415670 TATTGTTATTCAATCAAGATTCTCTTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTAGTA
1 TATTGTTATTCAATCAAGATTCTCCTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTAGTA
415735 ATAGACAAGTTTCATA
66 ATAGACAAGTTTCATA
415751 TATTGTT
1 TATTGTT
415758 TTCTGCCAGA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (81 bp):
TATTGTTATTCAATCAAGATTCTCCTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTAGTA
ATAGACAAGTTTCATA
Found at i:415807 original size:20 final size:19
Alignment explanation
Indices: 415778--415815 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
415768 AAGTAGTGAG
415778 AATTTATTTTCTAAGAATA
1 AATTTATTTTCTAAGAATA
*
415797 AATTCTATTTTCTGAGAAT
1 AATT-TATTTTCTAAGAAT
415816 TACAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:423277 original size:215 final size:216
Alignment explanation
Indices: 422895--423325 Score: 855
Period size: 215 Copynumber: 2.0 Consensus size: 216
422885 TTTAAAGGAA
422895 TTAAATATAATATAATATATTTATTTATTATTTATTATTTTTAAAGGATTAATTTTTTTTTTAAT
1 TTAAATATAATATAATATATTTATTTATTATTTATTATTTTTAAAGGATTAATTTTTTTTTTAAT
422960 TTTAGAGGTTAAAATAAAGTTTTATCATAAAATAATTTTTAATTTTATTATTTTATAAGAGATTT
66 TTTAGAGGTTAAAATAAAGTTTTATCATAAAATAATTTTTAATTTTATTATTTTATAAGAGATTT
423025 AAATCTTATTTTTAGAGTGCCAAGACTCTCGTCTTCCTCTCATATTAGCCCACATGCGTGGGACA
131 AAATCTTATTTTTAGAGTGCCAAGACTCTCGTCTTCCTCTCATATTAGCCCACATGCGTGGGACA
423090 TATTTCGTATCTTTAAAATAG
196 TATTTCGTATCTTTAAAATAG
423111 TTAAATATAA-ATAATATATTTATTTATTATTTATTATTTTTAAAGGATTAATTTTTTTTTTAAT
1 TTAAATATAATATAATATATTTATTTATTATTTATTATTTTTAAAGGATTAATTTTTTTTTTAAT
423175 TTTAGAGGTTAAAATAAAGTTTTATCATAAAATAATTTTTAATTTTATTATTTTATAAGAGATTT
66 TTTAGAGGTTAAAATAAAGTTTTATCATAAAATAATTTTTAATTTTATTATTTTATAAGAGATTT
423240 AAATCTTATTTTTAGAGTGCCAAGACTCTCGTCTTCCTCTCATATTAGCCCACATGCGTGGGACA
131 AAATCTTATTTTTAGAGTGCCAAGACTCTCGTCTTCCTCTCATATTAGCCCACATGCGTGGGACA
423305 TATTTCGTATCTTTAAAATAG
196 TATTTCGTATCTTTAAAATAG
423326 ATCGAATCTT
Statistics
Matches: 215, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
215 205 0.95
216 10 0.05
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (216 bp):
TTAAATATAATATAATATATTTATTTATTATTTATTATTTTTAAAGGATTAATTTTTTTTTTAAT
TTTAGAGGTTAAAATAAAGTTTTATCATAAAATAATTTTTAATTTTATTATTTTATAAGAGATTT
AAATCTTATTTTTAGAGTGCCAAGACTCTCGTCTTCCTCTCATATTAGCCCACATGCGTGGGACA
TATTTCGTATCTTTAAAATAG
Found at i:424480 original size:25 final size:24
Alignment explanation
Indices: 424447--424494 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
424437 ATATGTTTTG
* *
424447 TTTATTTATTTATCTATTTATTAT
1 TTTATTTATTTATATATATATTAT
424471 TTTATATTATTTATATATATATTA
1 TTTAT-TTATTTATATATATATTA
424495 AAAATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTATTTATTTATATATATATTAT
Found at i:430296 original size:2 final size:2
Alignment explanation
Indices: 430289--430323 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
430279 TTTATTTGGT
430289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
430324 TTCAGTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:430426 original size:51 final size:51
Alignment explanation
Indices: 430327--430428 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
430317 TATATATTTC
* *
430327 AGTGAATTCTGGGGGTTTAAATTTTTGGGTATTTTTCTTTTTTTCTAAGTT
1 AGTGAATTCTGGGGGTTTAAATTGTTGGGTATTTTTCTTTTTTGCTAAGTT
430378 AGTGAATTCTGGGGGTTTAAATTGTTGGGT-TTTTT-TTTGTTCTGCTAAGTT
1 AGTGAATTCTGGGGGTTTAAATTGTTGGGTATTTTTCTTT-TT-TGCTAAGTT
430429 TTTCATGTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
49 3 0.06
50 7 0.15
51 37 0.79
ACGTcount: A:0.17, C:0.06, G:0.25, T:0.53
Consensus pattern (51 bp):
AGTGAATTCTGGGGGTTTAAATTGTTGGGTATTTTTCTTTTTTGCTAAGTT
Found at i:434381 original size:21 final size:20
Alignment explanation
Indices: 434351--434390 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
434341 GCGCAAAACA
434351 AAAACCATGAAAAATGTGGAG
1 AAAACCATG-AAAATGTGGAG
* *
434372 AAAACTATGATAATGTGGA
1 AAAACCATGAAAATGTGGA
434391 CTGAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (20 bp):
AAAACCATGAAAATGTGGAG
Found at i:435038 original size:2 final size:2
Alignment explanation
Indices: 434994--435027 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
434984 GTCATCTCTT
434994 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
435028 ATTTTATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:440027 original size:126 final size:127
Alignment explanation
Indices: 439876--440130 Score: 487
Period size: 126 Copynumber: 2.0 Consensus size: 127
439866 AAAGCATGTG
439876 ATTTAAGAAGTAGGTTTCGACAAAAAAAAAAAGGCAAATTTAAAATGTGGATCGGGTTTGGGCTT
1 ATTTAAGAAGTAGGTTTCGACAAAAAAAAAAAGGCAAATTTAAAATGTGGATCGGGTTTGGGCTT
439941 CAACATTGAAGGCCCGAGCTTGA-CCCATTTTATACTTTTGTAATATATTTTTATTTTATTTT
66 CAACATTGAAGGCCCGAGCTTGACCCCA-TTTATACTTTTGTAATATATTTTTATTTTATTTT
440003 ATTTAAGAAG-AGGTTTCGACAAAAAAAAAAAGGCAAATTTAAAATGTGGATCGGGTTTGGGCTT
1 ATTTAAGAAGTAGGTTTCGACAAAAAAAAAAAGGCAAATTTAAAATGTGGATCGGGTTTGGGCTT
440067 CAACATTGAAGGCCCGAGCTTGACCCCATTTATACTTTTGTAATATATTTTTATTTTATTTT
66 CAACATTGAAGGCCCGAGCTTGACCCCATTTATACTTTTGTAATATATTTTTATTTTATTTT
440129 AT
1 AT
440131 ATATTATATA
Statistics
Matches: 127, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
126 113 0.89
127 14 0.11
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (127 bp):
ATTTAAGAAGTAGGTTTCGACAAAAAAAAAAAGGCAAATTTAAAATGTGGATCGGGTTTGGGCTT
CAACATTGAAGGCCCGAGCTTGACCCCATTTATACTTTTGTAATATATTTTTATTTTATTTT
Found at i:452331 original size:17 final size:16
Alignment explanation
Indices: 452304--452335 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
452294 AAACTGTTTG
452304 TTTTCTTTATTTTTAT
1 TTTTCTTTATTTTTAT
452320 TTTTCTTTTATTTTTA
1 TTTTC-TTTATTTTTA
452336 AAATATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTATTTTTAT
Found at i:452979 original size:3 final size:3
Alignment explanation
Indices: 452973--453010 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
452963 TTATTTAACC
452973 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT
453011 TCCTCTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:462700 original size:26 final size:27
Alignment explanation
Indices: 462671--462728 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
462661 TTAATAATTG
462671 TAATTAATTTTTATTTT-TAAATTATC
1 TAATTAATTTTTATTTTGTAAATTATC
* *
462697 TAA-TATTTTTTATTTTGTATATTATC
1 TAATTAATTTTTATTTTGTAAATTATC
*
462723 TTATTA
1 TAATTA
462729 TTAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.44
26 13 0.48
27 2 0.07
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (27 bp):
TAATTAATTTTTATTTTGTAAATTATC
Found at i:462727 original size:24 final size:24
Alignment explanation
Indices: 462678--462727 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
462668 TTGTAATTAA
462678 TTTTTATTTTTAAATTATCTAATAT
1 TTTTTATTTTTAAATTATCT-ATAT
*
462703 TTTTTATTTTGTATATTATCT-TAT
1 TTTTTATTTT-TAAATTATCTATAT
462727 T
1 T
462728 ATTAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 10 0.43
26 9 0.39
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTTATTTTTAAATTATCTATAT
Found at i:468310 original size:15 final size:15
Alignment explanation
Indices: 468266--468316 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
468256 AGAAAACCCG
*
468266 AATATCTCAAACTCAA
1 AATAT-TCAAACTTAA
*
468282 AATAATTTAAACTTAA
1 AAT-ATTCAAACTTAA
*
468298 AATATTCAAACTTGA
1 AATATTCAAACTTAA
468313 AATA
1 AATA
468317 ATCCTAACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 14 0.47
16 14 0.47
17 2 0.07
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (15 bp):
AATATTCAAACTTAA
Found at i:475092 original size:21 final size:22
Alignment explanation
Indices: 475066--475127 Score: 56
Period size: 27 Copynumber: 2.6 Consensus size: 22
475056 TTAATAGATC
475066 CTTCAATTTTTTTTTCTTTCA-
1 CTTCAATTTTTTTTTCTTTCAT
475087 CTTCAACCTTTCATTTCATTTCTTTCAT
1 CTTCAA--TTT--TTT--TTTCTTTCAT
475115 CTT-AATTTTTTTT
1 CTTCAATTTTTTTT
475128 CTCAAAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
21 8 0.24
23 6 0.18
25 6 0.18
27 11 0.32
28 3 0.09
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (22 bp):
CTTCAATTTTTTTTTCTTTCAT
Found at i:477788 original size:38 final size:38
Alignment explanation
Indices: 477732--477804 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
477722 AGCATGCTTA
* *
477732 ACCAAAAATAAGTCGAATTCCTTGTCGTCCACCACTGT
1 ACCAAAAATAAGTCGAATTCCTTATCCTCCACCACTGT
*
477770 ACCAAAAATAAGTGGAATTCCTTATCCTCCACCAC
1 ACCAAAAATAAGTCGAATTCCTTATCCTCCACCAC
477805 CGTTTGACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (38 bp):
ACCAAAAATAAGTCGAATTCCTTATCCTCCACCACTGT
Found at i:478106 original size:21 final size:21
Alignment explanation
Indices: 478084--478136 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
478074 ATATATTTTA
478084 AAAT-TATAGAAAA-TAGAAAT
1 AAATATATA-AAAAGTAGAAAT
478104 AAATATATAAAAAGTAGAAA-
1 AAATATATAAAAAGTAGAAAT
*
478124 ATATATTATAAAA
1 AAATA-TATAAAA
478137 TATAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (21 bp):
AAATATATAAAAAGTAGAAAT
Found at i:479152 original size:558 final size:559
Alignment explanation
Indices: 478083--479204 Score: 2230
Period size: 558 Copynumber: 2.0 Consensus size: 559
478073 AATATATTTT
478083 AAAA-TTATAGAAAATAGAAATAAATATATAAAAAGTAGAAAATATATTATAAAATATAATATTA
1 AAAAGTTATAGAAAATAGAAATAAATATATAAAAAGTAGAAAATATATTATAAAATATAATATTA
478147 AAATAGAAAATTTTCAAAATTATAAAAATAAAAATTCATTAATTTCATTAAATAGTTAAATGTTT
66 AAATAGAAAATTTTCAAAATTATAAAAATAAAAATTCATTAATTTCATTAAATAGTTAAATGTTT
478212 TTAACCTTAAAAATTAAACAATATATAGGTAATTTGTGTTCGTGTTCTTCCAAAATTATTTTTTT
131 TTAACCTTAAAAATTAAACAATATATAGGTAATTTGTGTTCGTGTTCTTCCAAAATTATTTTTTT
478277 TCTATTTGTTCTTCATCTACAAATTTAAAACCAATATGCTAAAATTTATAAAATTTGCCTAAAGT
196 TCTATTTGTTCTTCATCTACAAATTTAAAACCAATATGCTAAAATTTATAAAATTTGCCTAAAGT
478342 CTAATTAGAAAAAACTCAATGTAAACAAAGACAGCCCAAAATTGTTTATAGTAATCTAAGAGTTC
261 CTAATTAGAAAAAACTCAATGTAAACAAAGACAGCCCAAAATTGTTTATAGTAATCTAAGAGTTC
478407 TTTTGTACAAAGTCAAAAATTTTCTAGAAAATATATCAGTGTGATAGACCCAAATAAATTTAAAC
326 TTTTGTACAAAGTCAAAAATTTTCTAGAAAATATATCAGTGTGATAGACCCAAATAAATTTAAAC
478472 TAAATTAAGGGTGAGTTTGGATAGGCGGTGCATTTACCTGCGGTTAGTGTAAAAACAGTGGTGGC
391 TAAATTAAGGGTGAGTTTGGATAGGCGGTGCATTTACCTGCGGTTAGTGTAAAAACAGTGGTGGC
478537 GTGAGATTAGACACTGTAACGATACTATAGCGTGAAACAAAAAGTAAGCTAAACGCACCGCACCG
456 GTGAGATTAGACACTGTAACGATACTATAGCGTGAAACAAAAAGTAAGCTAAACGCACCGCACCG
478602 CACCTAACCCACCCTAAGTAACATAGTGAAAGAGCTGCA
521 CACCTAACCCACCCTAAGTAACATAGTGAAAGAGCTGCA
478641 AAAAGTTATAGAAAA-AGAAATAAATATATAAAAAGTAGAAAATATATTATAAAATATAATATTA
1 AAAAGTTATAGAAAATAGAAATAAATATATAAAAAGTAGAAAATATATTATAAAATATAATATTA
478705 AAATAGAAAATTTTCAAAATTATAAAAATAAAAATTCATTAATTTCATTAAATAGTTAAATGTTT
66 AAATAGAAAATTTTCAAAATTATAAAAATAAAAATTCATTAATTTCATTAAATAGTTAAATGTTT
478770 TTAACCTTAAAAATTAAACAATATATAGGTAATTTGTGTTCGTGTTCTTCCAAAATTATTTTTTT
131 TTAACCTTAAAAATTAAACAATATATAGGTAATTTGTGTTCGTGTTCTTCCAAAATTATTTTTTT
478835 TCTATTTGTTCTTCATCTACAAATTTAAAACCAATATGCTAAAATTTATAAAATTTGCCTAAAGT
196 TCTATTTGTTCTTCATCTACAAATTTAAAACCAATATGCTAAAATTTATAAAATTTGCCTAAAGT
478900 CTAATTAGAAAAAACTCAATGTAAACAAAGACAGCCCAAAATTGTTTATAGTAATCTAAGAGTTC
261 CTAATTAGAAAAAACTCAATGTAAACAAAGACAGCCCAAAATTGTTTATAGTAATCTAAGAGTTC
478965 TTTTGTACAAAGTCAAAAATTTTCTAGAAAATATATCAGTGTGATAGACCCAAATAAATTTAAAC
326 TTTTGTACAAAGTCAAAAATTTTCTAGAAAATATATCAGTGTGATAGACCCAAATAAATTTAAAC
479030 TAAATTAAGGGTGAGTTTGGATAGGCGGTGCATTTACCTGCGGTTAGTGTAAAAACAGTGGTGGC
391 TAAATTAAGGGTGAGTTTGGATAGGCGGTGCATTTACCTGCGGTTAGTGTAAAAACAGTGGTGGC
479095 GTGAGATTAGACACTGTAACGATACTATAGCGTGAAACAAAAAGTAAGCTAAACGCACCGCACCG
456 GTGAGATTAGACACTGTAACGATACTATAGCGTGAAACAAAAAGTAAGCTAAACGCACCGCACCG
479160 CACCTAACCCACCCTAAGTAACATAGTGAAAGAGCTGCA
521 CACCTAACCCACCCTAAGTAACATAGTGAAAGAGCTGCA
479199 AAAAGT
1 AAAAGT
479205 GGAGACCCCT
Statistics
Matches: 563, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
558 553 0.98
559 10 0.02
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (559 bp):
AAAAGTTATAGAAAATAGAAATAAATATATAAAAAGTAGAAAATATATTATAAAATATAATATTA
AAATAGAAAATTTTCAAAATTATAAAAATAAAAATTCATTAATTTCATTAAATAGTTAAATGTTT
TTAACCTTAAAAATTAAACAATATATAGGTAATTTGTGTTCGTGTTCTTCCAAAATTATTTTTTT
TCTATTTGTTCTTCATCTACAAATTTAAAACCAATATGCTAAAATTTATAAAATTTGCCTAAAGT
CTAATTAGAAAAAACTCAATGTAAACAAAGACAGCCCAAAATTGTTTATAGTAATCTAAGAGTTC
TTTTGTACAAAGTCAAAAATTTTCTAGAAAATATATCAGTGTGATAGACCCAAATAAATTTAAAC
TAAATTAAGGGTGAGTTTGGATAGGCGGTGCATTTACCTGCGGTTAGTGTAAAAACAGTGGTGGC
GTGAGATTAGACACTGTAACGATACTATAGCGTGAAACAAAAAGTAAGCTAAACGCACCGCACCG
CACCTAACCCACCCTAAGTAACATAGTGAAAGAGCTGCA
Found at i:479947 original size:67 final size:68
Alignment explanation
Indices: 479871--480008 Score: 197
Period size: 67 Copynumber: 2.0 Consensus size: 68
479861 TAAATTTATA
* * * *
479871 AATAAATTAATAAGATAAAAAGATACATATTTTTAGATATAATATAATAAATT-AAAAAGTTAAT
1 AATAAATTAATAAGATAAAAAGATACATACTTTTAAATATAATATAAGAAATTAAAAAAATTAAT
479935 TTT
66 TTT
* * * *
479938 AATAAATTAATAGGATAAAAAGATAGATACTTTTAAATTTAATTTAAGAAATTAAAAAAATTAAT
1 AATAAATTAATAAGATAAAAAGATACATACTTTTAAATATAATATAAGAAATTAAAAAAATTAAT
480003 TTT
66 TTT
480006 AAT
1 AAT
480009 TTTACATTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
67 46 0.74
68 16 0.26
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (68 bp):
AATAAATTAATAAGATAAAAAGATACATACTTTTAAATATAATATAAGAAATTAAAAAAATTAAT
TTT
Found at i:492214 original size:17 final size:17
Alignment explanation
Indices: 492192--492225 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
492182 CGGATCATTT
*
492192 CAAGTTCAAGTTAGTTC
1 CAAGTTCAAGTCAGTTC
*
492209 CAAGTTCCAGTCAGTTC
1 CAAGTTCAAGTCAGTTC
492226 GGATTTGTAT
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:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (17 bp):
CAAGTTCAAGTCAGTTC
Found at i:495824 original size:14 final size:14
Alignment explanation
Indices: 495805--495839 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
495795 TTGACATTTT
*
495805 TTCTAATGATACTA
1 TTCTAACGATACTA
495819 TTCTAACGATACTA
1 TTCTAACGATACTA
495833 TTCTAAC
1 TTCTAAC
495840 ATGTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:497127 original size:62 final size:62
Alignment explanation
Indices: 497043--497206 Score: 292
Period size: 62 Copynumber: 2.6 Consensus size: 62
497033 ATTACAACAT
497043 TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAC
1 TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAC
* * *
497105 TACAACATTAAAATTTGAAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAT
1 TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAC
*
497167 TACAACATTAAAACTTGGAACAAACTTTGTAATAGAAATT
1 TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
497207 AGGTACATTG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 96 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (62 bp):
TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAC
Found at i:498538 original size:20 final size:21
Alignment explanation
Indices: 498512--498558 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
498502 AAATAAAAAC
498512 TTAAACTTAAACTAGCAACAA
1 TTAAACTTAAACTAGCAACAA
*
498533 -TAAACTTAAGCTAGCAACAA
1 TTAAACTTAAACTAGCAACAA
498553 TTAAAC
1 TTAAAC
498559 CAATAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.23
Consensus pattern (21 bp):
TTAAACTTAAACTAGCAACAA
Found at i:503123 original size:18 final size:18
Alignment explanation
Indices: 503100--503135 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
503090 AATAATACAT
503100 TTTCTTTCTTCTCTTTTC
1 TTTCTTTCTTCTCTTTTC
*
503118 TTTCTTTCTTCTGTTTTC
1 TTTCTTTCTTCTCTTTTC
503136 CCTCTCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTCTTTCTTCTCTTTTC
Found at i:506249 original size:34 final size:34
Alignment explanation
Indices: 506205--506277 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
506195 GTATCTTAAA
*
506205 AGAATTAGGGATTATATACTTGTGTAATCTAGGC
1 AGAACTAGGGATTATATACTTGTGTAATCTAGGC
*
506239 AGAACTAGGGATTATATGCTTGTGTAATCTAGGC
1 AGAACTAGGGATTATATACTTGTGTAATCTAGGC
506273 AGAAC
1 AGAAC
506278 CTTACTCCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (34 bp):
AGAACTAGGGATTATATACTTGTGTAATCTAGGC
Found at i:519330 original size:15 final size:14
Alignment explanation
Indices: 519302--519328 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
519292 CACATACCTT
519302 TTTTTTAATATTTA
1 TTTTTTAATATTTA
519316 TTTTTTAATATTT
1 TTTTTTAATATTT
519329 TACTATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:520056 original size:32 final size:29
Alignment explanation
Indices: 520020--520088 Score: 70
Period size: 32 Copynumber: 2.3 Consensus size: 29
520010 ATCGGTGTAG
520020 TAATAAATTATACAAAACTTAA-TATTATATA
1 TAATAAATTATA-AAAAC--AAGTATTATATA
* *
520051 TTAATAATTTTTAAAAACAAGTATTATATA
1 -TAATAAATTATAAAAACAAGTATTATATA
520081 TAA-AAATT
1 TAATAAATT
520089 TTAATTCCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 4 0.12
29 5 0.15
30 9 0.27
31 5 0.15
32 10 0.30
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (29 bp):
TAATAAATTATAAAAACAAGTATTATATA
Found at i:520419 original size:28 final size:28
Alignment explanation
Indices: 520368--521034 Score: 946
Period size: 28 Copynumber: 23.4 Consensus size: 28
520358 TATTTACCGG
*
520368 ATTAATTTAAAACCCTAACCCTAACCTAA
1 ATTAATTAAAAACCCTAA-CCTAACCTAA
* *
520397 ATTAATTAAAAAACCTAATCTAACCTAA
1 ATTAATTAAAAACCCTAACCTAACCTAA
*
520425 ATTAACTAAAAACCCTAACCTAACCTAA
1 ATTAATTAAAAACCCTAACCTAACCTAA
520453 ATTAATTAAAAACCCTAAACCTAACCTAA
1 ATTAATTAAAAACCCT-AACCTAACCTAA
* *
520482 ATTAATTTAAAACCCTAATCTAACCTTAA
1 ATTAATTAAAAACCCTAACCTAACC-TAA
520511 ATTAATT-AAAACCCTAAACCTAACCTAA
1 ATTAATTAAAAACCCT-AACCTAACCTAA
520539 ATTAATTAAAAACCCTAAACCTAACCTAA
1 ATTAATTAAAAACCCT-AACCTAACCTAA
*
520568 ATTAATTTAAAACCCTAAACCTAACCTAA
1 ATTAATTAAAAACCCT-AACCTAACCTAA
* **
520597 AATAA-CCAAAACCCTAACCTAACCTAA
1 ATTAATTAAAAACCCTAACCTAACCTAA
520624 ATTAATTAAAAACCCTAAACCTAACCTAA
1 ATTAATTAAAAACCCT-AACCTAACCTAA
* *
520653 ATTAATTTAAAACCCTAATCTAACCTAA
1 ATTAATTAAAAACCCTAACCTAACCTAA
*
520681 ATTAACTAAAAACCCTAACCTAACCTAA
1 ATTAATTAAAAACCCTAACCTAACCTAA
520709 ATTAATTAAAAACCCTAAACCTAACCTAA
1 ATTAATTAAAAACCCT-AACCTAACCTAA
* *
520738 ATTAATTTAAAACCCTAATCTAACCTAA
1 ATTAATTAAAAACCCTAACCTAACCTAA
*
520766 ATTAACTAAAAACCCTAACCTAACCTAA
1 ATTAATTAAAAACCCTAACCTAACCTAA
520794 ATTAATTAAAAACCCTAAACCTAACCTAAA
1 ATTAATTAAAAACCCT-AACCTAACCT-AA
520824 ATTAATTAAAAACCCTAAACCTAACCCTAA
1 ATTAATTAAAAACCCT-AACCTAA-CCTAA
520854 ATTAATT-AAAACCCTAACCCTAACCTAA
1 ATTAATTAAAAACCCTAA-CCTAACCTAA
* *
520882 ATTAATTAAAAAACCTAATCTAACCTAA
1 ATTAATTAAAAACCCTAACCTAACCTAA
*
520910 ATTAACTAAAATA-CCTAACCTAACCTAA
1 ATTAATTAAAA-ACCCTAACCTAACCTAA
*
520938 AATAATTAAAAACCCTAAACCTAACCTAA
1 ATTAATTAAAAACCCT-AACCTAACCTAA
*
520967 ATTAATTTAAAACCCTAACCCTAACCTAA
1 ATTAATTAAAAACCCTAA-CCTAACCTAA
* *
520996 ATTAATTAAAAAACCTAATCTAACCTAA
1 ATTAATTAAAAACCCTAACCTAACCTAA
*
521024 ATTAACTAAAA
1 ATTAATTAAAA
521035 NNNNNNNNNN
Statistics
Matches: 581, Mismatches: 41, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
27 17 0.03
28 273 0.47
29 253 0.44
30 35 0.06
31 3 0.01
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.25
Consensus pattern (28 bp):
ATTAATTAAAAACCCTAACCTAACCTAA
Found at i:520522 original size:85 final size:84
Alignment explanation
Indices: 520368--521034 Score: 987
Period size: 85 Copynumber: 7.8 Consensus size: 84
520358 TATTTACCGG
* * * * *
520368 ATTAATTTAAAACCCTAACCCTAACCTAAATTAATTAAAAAACCTAATCTAACCTAAATTAACTA
1 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAA-TT
520433 AAAACCCTAACCTAACCTAA
65 AAAACCCTAACCTAACCTAA
520453 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAATCTAACCTTAAATTAATT
1 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAATCTAACC-TAAATTAATT
520518 AAAACCCTAAACCTAACCTAA
65 AAAACCCT-AACCTAACCTAA
* * **
520539 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAAACCTAACCTAAAATAACC
1 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCT-AATCTAACCTAAATTAATT
520604 AAAACCCTAACCTAACCTAA
65 AAAACCCTAACCTAACCTAA
*
520624 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAACTA
1 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAA-TT
520689 AAAACCCTAACCTAACCTAA
65 AAAACCCTAACCTAACCTAA
*
520709 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAACTA
1 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAA-TT
520774 AAAACCCTAACCTAACCTAA
65 AAAACCCTAACCTAACCTAA
* *
520794 ATTAATTAAAAACCCTAAACCTAACCTAAAATTAATTAAAAACCCTAAACCTAACCCTAAATTAA
1 ATTAATTAAAAACCCTAAACCTAACCT-AAATTAATTTAAAACCCT-AATCTAA-CCTAAATTAA
520859 TTAAAACCCTAACCCTAACCTAA
63 TTAAAACCCTAA-CCTAACCTAA
* * * * * *
520882 ATTAATTAAAAAACCT-AATCTAACCTAAATTAA-CTAAAATACCTAACCTAACCTAAAATAATT
1 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAA-CCCTAATCTAACCTAAATTAATT
520945 AAAAACCCTAAACCTAACCTAA
65 -AAAACCCT-AACCTAACCTAA
* * * * *
520967 ATTAATTTAAAACCCTAACCCTAACCTAAATTAATTAAAAAACCTAATCTAACCTAAATTAACTA
1 ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAATTA
521032 AAA
66 AAA
521035 NNNNNNNNNN
Statistics
Matches: 538, Mismatches: 31, Indels: 26
0.90 0.05 0.04
Matches are distributed among these distances:
84 26 0.05
85 295 0.55
86 144 0.27
87 38 0.07
88 35 0.07
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.25
Consensus pattern (84 bp):
ATTAATTAAAAACCCTAAACCTAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAATTA
AAACCCTAACCTAACCTAA
Found at i:520927 original size:18 final size:19
Alignment explanation
Indices: 520904--520941 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
520894 ACCTAATCTA
*
520904 ACCTAAATTAA-CTAAAAT
1 ACCTAAACTAACCTAAAAT
*
520922 ACCTAACCTAACCTAAAAT
1 ACCTAAACTAACCTAAAAT
520941 A
1 A
520942 ATTAAAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (19 bp):
ACCTAAACTAACCTAAAAT
Found at i:521018 original size:23 final size:24
Alignment explanation
Indices: 520387--521018 Score: 122
Period size: 29 Copynumber: 22.4 Consensus size: 24
520377 AAACCCTAAC
520387 CCTAACCTAAATTAA-TTAAAAAA
1 CCTAACCTAAATTAATTTAAAAAA
* *
520410 CCTAATCTAACCTAAATTAACTAAAAACCCTAA
1 -C----CTAACCTAAATTAATTTAAAA----AA
*
520443 CCTAACCTAAATTAATTAAAAACCCTAAA
1 CCTAACCTAAATTAATT-TAAA----AAA
520472 CCTAACCTAAATTAATTTAAAACCCTAA
1 CCTAACCTAAATTAATTTAAAA----AA
* *
520500 TCTAACCTTAAATTAATTAAAACCCTAAA
1 CCTAACC-TAAATTAATTTAAA----AAA
*
520529 CCTAACCTAAATTAATTAAAAACCCTAAA
1 CCTAACCTAAATTAATT-TAAA----AAA
520558 CCTAACCTAAATTAATTTAAAACCCTAAA
1 CCTAACCTAAATTAATTT-AAA----AAA
* **
520587 CCTAACCTAAAATAA-CCAAAACCCTAA
1 CCTAACCTAAATTAATTTAAAA----AA
*
520614 CCTAACCTAAATTAATTAAAAACCCTAAA
1 CCTAACCTAAATTAATT-TAAA----AAA
520643 CCTAACCTAAATTAATTTAAAACCCTAA
1 CCTAACCTAAATTAATTTAAAA----AA
* * *
520671 TCTAACCTAAATTAACTAAAAACCCTAA
1 CCTAACCTAAATTAATTTAAAA----AA
*
520699 CCTAACCTAAATTAATTAAAAACCCTAAA
1 CCTAACCTAAATTAATT-TAAA----AAA
520728 CCTAACCTAAATTAATTTAAAACCCTAA
1 CCTAACCTAAATTAATTTAAAA----AA
* * *
520756 TCTAACCTAAATTAACTAAAAACCCTAA
1 CCTAACCTAAATTAATTTAAAA----AA
*
520784 CCTAACCTAAATTAATTAAAAACCCTAAA
1 CCTAACCTAAATTAATT-TAAA----AAA
*
520813 CCTAACCTAAAATTAATTAAAAACCCTAAA
1 CCTAACCT-AAATTAATT-TAAA----AAA
520843 CCTAACCCTAAATTAA-TTAAAACCCTAA
1 CCTAA-CCTAAATTAATTTAAAA----AA
520871 CCCTAACCTAAATTAA-TTAAAAAA
1 -CCTAACCTAAATTAATTTAAAAAA
* *
520895 CCTAATCTAACCTAAATTAACTAAAATACCTAA
1 -C----CTAACCTAAATTAATTTAAA-A---AA
* *
520928 CCTAACCTAAAATAATTAAAAACCCTAAA
1 CCTAACCTAAATTAATT-TAAA----AAA
520957 CCTAACCTAAATTAATTTAAAACCCTAA
1 CCTAACCTAAATTAATTTAAAA----AA
520985 CCCTAACCTAAATTAA-TTAAAAAA
1 -CCTAACCTAAATTAATTTAAAAAA
*
521009 CCTAATCTAA
1 CCTAACCTAA
521019 CCTAAATTAA
Statistics
Matches: 498, Mismatches: 32, Indels: 157
0.72 0.05 0.23
Matches are distributed among these distances:
23 10 0.02
24 12 0.02
27 19 0.04
28 200 0.40
29 207 0.42
30 34 0.07
31 3 0.01
32 4 0.01
33 9 0.02
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (24 bp):
CCTAACCTAAATTAATTTAAAAAA
Found at i:524465 original size:9 final size:9
Alignment explanation
Indices: 524439--524523 Score: 107
Period size: 9 Copynumber: 9.2 Consensus size: 9
524429 TTTGGTTAAA
524439 AATTACCCG
1 AATTACCCG
* *
524448 ACTTGCCCG
1 AATTACCCG
524457 AATTACCCG
1 AATTACCCG
*
524466 ACTTACCCG
1 AATTACCCG
524475 AATTACCCG
1 AATTACCCG
*
524484 AATTACCGG
1 AATTACCCG
*
524493 AAAATTACCCA
1 --AATTACCCG
524504 AATTACCCG
1 AATTACCCG
524513 AATTACCCG
1 AATTACCCG
524522 AA
1 AA
524524 AATTACCCAN
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
9 57 0.89
11 7 0.11
ACGTcount: A:0.34, C:0.33, G:0.12, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:534171 original size:2 final size:2
Alignment explanation
Indices: 534164--534188 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
534154 ATTGTAGGGG
534164 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
534189 ATAAAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:537486 original size:2 final size:2
Alignment explanation
Indices: 537479--537508 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
537469 CTAACTCAGG
537479 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
537509 ATCCTACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:541179 original size:14 final size:14
Alignment explanation
Indices: 541160--541193 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
541150 TTGGTATCAA
541160 ATTGGTTGAATTGG
1 ATTGGTTGAATTGG
**
541174 ATTGGTTGGTTTGG
1 ATTGGTTGAATTGG
541188 ATTGGT
1 ATTGGT
541194 CTCGGTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (14 bp):
ATTGGTTGAATTGG
Found at i:543771 original size:14 final size:14
Alignment explanation
Indices: 543752--543785 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
543742 TAAGACTGAG
543752 ACCAATCCAAACCA
1 ACCAATCCAAACCA
**
543766 ACCAATCCAATTCA
1 ACCAATCCAAACCA
543780 ACCAAT
1 ACCAAT
543786 TTGATACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (14 bp):
ACCAATCCAAACCA
Found at i:544338 original size:33 final size:33
Alignment explanation
Indices: 544290--544352 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
544280 TTGTCACTTG
* *
544290 TCACTTGTCATTGATCAGATAAGTGTAGCTAAA
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAA
544323 TCACTTATCACTGATCAGATAAGTGTAGCT
1 TCACTTATCACTGATCAGATAAGTGTAGCT
544353 GAAGCTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (33 bp):
TCACTTATCACTGATCAGATAAGTGTAGCTAAA
Found at i:549886 original size:15 final size:15
Alignment explanation
Indices: 549866--549894 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
549856 TCGCAGCGGC
549866 AGCAGCCTTCTTCTG
1 AGCAGCCTTCTTCTG
549881 AGCAGCCTTCTTCT
1 AGCAGCCTTCTTCT
549895 TGCTCGCGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.17, T:0.34
Consensus pattern (15 bp):
AGCAGCCTTCTTCTG
Found at i:551836 original size:25 final size:26
Alignment explanation
Indices: 551806--551874 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
551796 ATTTTGAACT
551806 TATATTATTTATTTTAAATTGTTCTA
1 TATATTATTTATTTTAAATTGTTCTA
* * * *
551832 T-TATTATTTACTTTAAGTTTTTTTA
1 TATATTATTTATTTTAAATTGTTCTA
**
551857 TATATTATGCATTTTAAA
1 TATATTATTTATTTTAAA
551875 CTATATTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
25 21 0.62
26 13 0.38
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (26 bp):
TATATTATTTATTTTAAATTGTTCTA
Found at i:558032 original size:15 final size:15
Alignment explanation
Indices: 558012--558040 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
558002 TTGCAGCCGC
558012 AGCAGCCTTCTTCTG
1 AGCAGCCTTCTTCTG
558027 AGCAGCCTTCTTCT
1 AGCAGCCTTCTTCT
558041 TGCTTGCGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.17, T:0.34
Consensus pattern (15 bp):
AGCAGCCTTCTTCTG
Found at i:558929 original size:34 final size:33
Alignment explanation
Indices: 558857--558926 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
558847 ATATGTATAC
* * *
558857 TAAATAACACTAAAATAAATACAACTTAACAAG
1 TAAATATCTCTAAAATAAATACAAATTAACAAG
558890 TAAATATCTCTAAAAT-AATAACAAAATTAACAA-
1 TAAATATCTCTAAAATAAAT-AC-AAATTAACAAG
558923 TAAA
1 TAAA
558927 ATAAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 3 0.09
33 20 0.62
34 9 0.28
ACGTcount: A:0.61, C:0.13, G:0.01, T:0.24
Consensus pattern (33 bp):
TAAATATCTCTAAAATAAATACAAATTAACAAG
Found at i:559398 original size:17 final size:16
Alignment explanation
Indices: 559369--559422 Score: 99
Period size: 16 Copynumber: 3.3 Consensus size: 16
559359 GCTCATTTCA
559369 GTGTATTGGATTAGAG
1 GTGTATTGGATTAGAG
559385 GTGTATTGGGATTAGAG
1 GTGTATT-GGATTAGAG
559402 GTGTATTGGATTAGAG
1 GTGTATTGGATTAGAG
559418 GTGTA
1 GTGTA
559423 ATAGCTAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (16 bp):
GTGTATTGGATTAGAG
Found at i:559487 original size:44 final size:45
Alignment explanation
Indices: 559403--559493 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
559393 GGATTAGAGG
* * *
559403 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
559448 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
559492 TG
1 TG
559494 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:561515 original size:18 final size:18
Alignment explanation
Indices: 561492--561533 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
561482 AAAAGGGCTT
561492 TTATTGGTAAATTGCCCG
1 TTATTGGTAAATTGCCCG
561510 TTATTGGTAAATTGCCCG
1 TTATTGGTAAATTGCCCG
561528 TTATTG
1 TTATTG
561534 AAAAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (18 bp):
TTATTGGTAAATTGCCCG
Found at i:565773 original size:32 final size:32
Alignment explanation
Indices: 565737--565801 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
565727 GAGCTTATTG
565737 AGATGCTTACATGTAATTCTTGCTTTCTCTTT
1 AGATGCTTACATGTAATTCTTGCTTTCTCTTT
565769 AGATGCTTACATGTAATTCTTGCTTTCTCTTT
1 AGATGCTTACATGTAATTCTTGCTTTCTCTTT
565801 A
1 A
565802 CTTCGTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.49
Consensus pattern (32 bp):
AGATGCTTACATGTAATTCTTGCTTTCTCTTT
Found at i:571178 original size:16 final size:15
Alignment explanation
Indices: 571151--571189 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
571141 TAATTCCATA
571151 TTAAAACATATAAAT
1 TTAAAACATATAAAT
*
571166 TTAAAATCATATATAT
1 TTAAAA-CATATAAAT
571182 TTGAAAAC
1 TT-AAAAC
571190 TTTTTCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (15 bp):
TTAAAACATATAAAT
Found at i:573992 original size:18 final size:18
Alignment explanation
Indices: 573955--573993 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
573945 ACACTCAGAT
*
573955 TAGTTTATTAAATGAGAA
1 TAGTTTATTAAATGAAAA
*
573973 TAGTTTATTAAATTAAAA
1 TAGTTTATTAAATGAAAA
573991 TAG
1 TAG
573994 AGTTATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (18 bp):
TAGTTTATTAAATGAAAA
Found at i:574581 original size:27 final size:27
Alignment explanation
Indices: 574549--574600 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
574539 CATTTTAGTC
574549 CTTTGGCACCATT-GGTGCCGCCAATCT
1 CTTTGGCACC-TTAGGTGCCGCCAATCT
574576 CTTTGGCACCTTAGGTGCCGCCAAT
1 CTTTGGCACCTTAGGTGCCGCCAAT
574601 GTGATTGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.15, C:0.33, G:0.23, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCTTAGGTGCCGCCAATCT
Found at i:574608 original size:27 final size:27
Alignment explanation
Indices: 574551--574609 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
574541 TTTTAGTCCT
*
574551 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* *
574578 TTGGCACC-TTAGGTGCCGCCAATGTGA
1 TTGGCACCATT-GGTGCCGCCAATCTCA
574605 TTGGC
1 TTGGC
574610 CTGATTAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.29
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:574713 original size:26 final size:27
Alignment explanation
Indices: 574662--574728 Score: 127
Period size: 26 Copynumber: 2.5 Consensus size: 27
574652 TTTTTTTGCT
574662 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
574689 ATATTTTGGTAAAT-AAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
574715 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
574729 TTTCTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 26 0.65
27 14 0.35
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:577538 original size:78 final size:79
Alignment explanation
Indices: 577448--577605 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 79
577438 ATTGGTTGAA
577448 ATTTCTTTTTTAATACCTCAATGTTTCAAGTTTCAACCTTGGTATTACAATATTTTTTTAAAAAA
1 ATTTCTTTTTTAATACCTCAATGTTTCAAGTTTCAACCTTGGTATTACAATATTTTTTTAAAAAA
577513 ATAT-TAAATTATT
66 ATATATAAATTATT
577526 ATTTCTTTTTTAATACCTCAATGTTTCAAGTTTCAACCTTGGTATTACAATATTTTTTTAAAAAA
1 ATTTCTTTTTTAATACCTCAATGTTTCAAGTTTCAACCTTGGTATTACAATATTTTTTTAAAAAA
577591 ATATATAAATTATT
66 ATATATAAATTATT
577605 A
1 A
577606 AAAGACACAA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 69 0.87
79 10 0.13
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.48
Consensus pattern (79 bp):
ATTTCTTTTTTAATACCTCAATGTTTCAAGTTTCAACCTTGGTATTACAATATTTTTTTAAAAAA
ATATATAAATTATT
Found at i:596063 original size:42 final size:42
Alignment explanation
Indices: 596017--596229 Score: 273
Period size: 42 Copynumber: 4.9 Consensus size: 42
596007 ATTTAACCAA
*
596017 TATGGGTTTCTGTTCAGCTTTTACGAGCTTCTGTTCAACCCT
1 TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
*
596059 TATGGGTTTCTGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACTCT
1 TA--------TGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
*
596109 TATGGGTTTCCGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
1 TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
*
596151 TATGGGTTTCCGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
1 TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
* * * * *
596193 TATAGGTTTCTATTTAGCTCTCATGAGCTTCTGTTCA
1 TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCA
596230 GCTTTCGAGC
Statistics
Matches: 153, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
42 113 0.74
50 40 0.26
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (42 bp):
TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
Found at i:596069 original size:21 final size:21
Alignment explanation
Indices: 596017--596070 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
596007 ATTTAACCAA
* **
596017 TATGGGTTTCTGTTCAGCTTT
1 TATGGGTTTCTGTTCAACCCT
* * *
596038 TACGAGCTTCTGTTCAACCCT
1 TATGGGTTTCTGTTCAACCCT
596059 TATGGGTTTCTG
1 TATGGGTTTCTG
596071 GGTTTCTGTT
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.44
Consensus pattern (21 bp):
TATGGGTTTCTGTTCAACCCT
Found at i:596100 original size:21 final size:21
Alignment explanation
Indices: 596074--596246 Score: 145
Period size: 21 Copynumber: 8.3 Consensus size: 21
596064 GTTTCTGGGT
596074 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * *
596095 TTCTGTTCAACTCTTATGGGT
1 TTCTGTTCAGCTCTTACGAGC
*
596116 TTCCGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * * *
596137 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTCAGCTCTTACGAGC
*
596158 TTCCGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * *
596179 TTCTGTTCAACCCTTA-TAGGT
1 TTCTGTTCAGCTCTTACGA-GC
* * * *
596200 TTCTATTTAGCTCTCATGAGC
1 TTCTGTTCAGCTCTTACGAGC
596221 TTCTGTTCAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTACGAGC
596240 TTCTGTT
1 TTCTGTT
596247 AACGATGTAC
Statistics
Matches: 113, Mismatches: 37, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
19 11 0.10
20 2 0.02
21 99 0.88
22 1 0.01
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.42
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:598643 original size:30 final size:31
Alignment explanation
Indices: 598578--598635 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
598568 TACCAAGTGT
598578 TATTAATTTGATAATAATAATTATTAAATTA
1 TATTAATTTGATAATAATAATTATTAAATTA
*
598609 -ATTAATTT-A-AATAATATTTA-TAAATTA
1 TATTAATTTGATAATAATAATTATTAAATTA
598636 CATATTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 7 0.27
28 10 0.38
29 1 0.04
30 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
TATTAATTTGATAATAATAATTATTAAATTA
Found at i:604332 original size:642 final size:642
Alignment explanation
Indices: 603109--604383 Score: 2469
Period size: 642 Copynumber: 2.0 Consensus size: 642
603099 TACATTCCAC
603109 AGGTCAAGCATGATAAGCTTGACAAAAAGGCAGAAGCTGGCATTTTTGTTGGGTATAGCACTGTA
1 AGGTCAAGCATGATAAGCTTGACAAAAAGGCAGAAGCTGGCATTTTTGTTGGGTATAGCACTGTA
603174 TCTAAAGCTTACAGAGTCTTTCAACCACACACTGGACGTGTTATTGTGAGCAGAGATGTTTATTT
66 TCTAAAGCTTACAGAGTCTTTCAACCACACACTGGACGTGTTATTGTGAGCAGAGATGTTTATTT
603239 TGTTGAAAATGAGCAATGGAATTGGGAAGACTCGATCAAGACGAACCAAAGGTCTAGTACACCAA
131 TGTTGAAAATGAGCAATGGAATTGGGAAGACTCGATCAAGACGAACCAAAGGTCTAGTACACCAA
*
603304 ATCGTTCTACAATTGGCAGCACGTTAGAAGAGCTTGAAGATGAAGGGCAAGATGTTTTGGCTGAT
196 ATCGTTCTACAATTGGCAGCACGTTAGAAGAGCTTAAAGATGAAGGGCAAGATGTTTTGGCTGAT
603369 GATGCGCCTGTCAGAGGTACAAGGCTGCTCTCCGACATTTACCAAAGATGTAACATGGCTATTTG
261 GATGCGCCTGTCAGAGGTACAAGGCTGCTCTCCGACATTTACCAAAGATGTAACATGGCTATTTG
*
603434 TGAGCCTGCAGGGTATTATGATGTAAAAAACAGTCAACATTGGATGGCTGCAATGAATGAGGAGA
326 TGAGCCTGCAGGGTATTATGATGCAAAAAACAGTCAACATTGGATGGCTGCAATGAATGAGGAGA
* * *
603499 TTTCAATGATCGAGAAAAACAAAACTTGGGAATTGGTTGATCGACTTCTAGACAGAAAGATAATT
391 TTTCAATGACCGAGAAAAACAAAACTTGGGAATTGGTTAATCGACCTCTAGACAGAAAGATAATT
603564 GGAGTAAGATGGGTGTTCAGAACGGAACTAAATCCCGATGGTTCAGTTAACAAATTCAAAGCAAG
456 GGAGTAAGATGGGTGTTCAGAACGGAACTAAATCCCGATGGTTCAGTTAACAAATTCAAAGCAAG
603629 ACTTGTTGTGAAGGGATATGCACAAGTCTTTGGAGCCGATTATTTAGAAACATTTGCACCTGTTG
521 ACTTGTTGTGAAGGGATATGCACAAGTCTTTGGAGCCGATTATTTAGAAACATTTGCACCTGTTG
*
603694 CCAGGCTTGACATTGTAAGGTTGCTGTTTGCTCTTGCTGCACAAAAGAACTGTCTAG
586 CCAGGCTTGACATTGTAAGGTTACTGTTTGCTCTTGCTGCACAAAAGAACTGTCTAG
603751 AGGTCAAGCATGATAAGCTTGACAAAAAGGCAGAAGCTGGCATTTTTGTTGGGTATAGCACTGTA
1 AGGTCAAGCATGATAAGCTTGACAAAAAGGCAGAAGCTGGCATTTTTGTTGGGTATAGCACTGTA
603816 TCTAAAGCTTACAGAGTCTTTCAACCACACACTGGACGTGTTATTGTGAGCAGAGATGTTTATTT
66 TCTAAAGCTTACAGAGTCTTTCAACCACACACTGGACGTGTTATTGTGAGCAGAGATGTTTATTT
603881 TGTTGAAAATGAGCAATGGAATTGGGAAGACTCGATCAAGACGAACCAAAGGTCTAGTACACCAA
131 TGTTGAAAATGAGCAATGGAATTGGGAAGACTCGATCAAGACGAACCAAAGGTCTAGTACACCAA
603946 ATCGTTCTACAATTGGCAGCACGTTAGAAGAGCTTAAAGATGAAGGGCAAGATGTTTTGGCTGAT
196 ATCGTTCTACAATTGGCAGCACGTTAGAAGAGCTTAAAGATGAAGGGCAAGATGTTTTGGCTGAT
*
604011 GATGCGCCTGTCAGAGGTACAAGGGTGCTCTCCGACATTTACCAAAGATGTAACATGGCTATTTG
261 GATGCGCCTGTCAGAGGTACAAGGCTGCTCTCCGACATTTACCAAAGATGTAACATGGCTATTTG
604076 TGAGCCTGCAGGGTATTATGATGCAAAAAACAGTCAACATTGGATGGCTGCAATGAATGAGGAGA
326 TGAGCCTGCAGGGTATTATGATGCAAAAAACAGTCAACATTGGATGGCTGCAATGAATGAGGAGA
*
604141 TTTCGATGACCGAGAAAAACAAAACTTGGGAATTGGTTAATCGACCTCTAGACAGAAAGATAATT
391 TTTCAATGACCGAGAAAAACAAAACTTGGGAATTGGTTAATCGACCTCTAGACAGAAAGATAATT
604206 GGAGTAAGATGGGTGTTCAGAACGGAACTAAATCCCGATGGTTCAGTTAACAAATTCAAAGCAAG
456 GGAGTAAGATGGGTGTTCAGAACGGAACTAAATCCCGATGGTTCAGTTAACAAATTCAAAGCAAG
*
604271 ACTTGTTGTGAAGGGATATGCACAAGTCTTTGGAGTCGATTATTTAGAAACATTTGCACCTGTTG
521 ACTTGTTGTGAAGGGATATGCACAAGTCTTTGGAGCCGATTATTTAGAAACATTTGCACCTGTTG
604336 CCAGGCTTGACATTGTAAGGTTACTGTTTGCTCTTGCTGCACAAAAGA
586 CCAGGCTTGACATTGTAAGGTTACTGTTTGCTCTTGCTGCACAAAAGA
604384 TCTGGAAAGT
Statistics
Matches: 624, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
642 624 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (642 bp):
AGGTCAAGCATGATAAGCTTGACAAAAAGGCAGAAGCTGGCATTTTTGTTGGGTATAGCACTGTA
TCTAAAGCTTACAGAGTCTTTCAACCACACACTGGACGTGTTATTGTGAGCAGAGATGTTTATTT
TGTTGAAAATGAGCAATGGAATTGGGAAGACTCGATCAAGACGAACCAAAGGTCTAGTACACCAA
ATCGTTCTACAATTGGCAGCACGTTAGAAGAGCTTAAAGATGAAGGGCAAGATGTTTTGGCTGAT
GATGCGCCTGTCAGAGGTACAAGGCTGCTCTCCGACATTTACCAAAGATGTAACATGGCTATTTG
TGAGCCTGCAGGGTATTATGATGCAAAAAACAGTCAACATTGGATGGCTGCAATGAATGAGGAGA
TTTCAATGACCGAGAAAAACAAAACTTGGGAATTGGTTAATCGACCTCTAGACAGAAAGATAATT
GGAGTAAGATGGGTGTTCAGAACGGAACTAAATCCCGATGGTTCAGTTAACAAATTCAAAGCAAG
ACTTGTTGTGAAGGGATATGCACAAGTCTTTGGAGCCGATTATTTAGAAACATTTGCACCTGTTG
CCAGGCTTGACATTGTAAGGTTACTGTTTGCTCTTGCTGCACAAAAGAACTGTCTAG
Found at i:609227 original size:34 final size:34
Alignment explanation
Indices: 609188--609254 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
609178 GGTAAAAAGT
609188 TATATTTATATATTTATTTTAACATAAATAATTA
1 TATATTTATATATTTATTTTAACATAAATAATTA
* * * *
609222 TATATTTATTTGTTTATTTTAATATAACTAATT
1 TATATTTATATATTTATTTTAACATAAATAATT
609255 TTATTCATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (34 bp):
TATATTTATATATTTATTTTAACATAAATAATTA
Found at i:614447 original size:18 final size:17
Alignment explanation
Indices: 614426--614471 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
614416 TTACTTTTGT
614426 TTTCTTTAAATATTTTA
1 TTTCTTTAAATATTTTA
*
614443 GTTTCTTTAATATGTTTTA
1 -TTTCTTTAA-ATATTTTA
614462 TTTCTTTAAA
1 TTTCTTTAAA
614472 AATATTGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 18 0.69
19 7 0.27
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTCTTTAAATATTTTA
Found at i:617018 original size:6 final size:7
Alignment explanation
Indices: 616996--617025 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
616986 GGATCTTGAC
616996 TTTAAAA
1 TTTAAAA
617003 TTTAAAA
1 TTTAAAA
*
617010 TTTAAAT
1 TTTAAAA
617017 TTTAAAA
1 TTTAAAA
617024 TT
1 TT
617026 ATTAGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
TTTAAAA
Found at i:630320 original size:34 final size:34
Alignment explanation
Indices: 630281--630345 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
630271 AAAATTTATA
630281 TTTAATACAAT-AAA-ATGCTTATTATATTTATTTT
1 TTTAATACAATGAAACATGC--ATTATATTTATTTT
630315 TTTAATACAATGAAACATGCATTATATTTAT
1 TTTAATACAATGAAACATGCATTATATTTAT
630346 AGTGTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 22 0.76
35 3 0.10
36 4 0.14
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.48
Consensus pattern (34 bp):
TTTAATACAATGAAACATGCATTATATTTATTTT
Found at i:630447 original size:17 final size:17
Alignment explanation
Indices: 630427--630462 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
630417 ATATTTTTAA
*
630427 AAAAATTAATTTAAAAT
1 AAAAATTAATCTAAAAT
630444 AAAAATTAATCTAAAAT
1 AAAAATTAATCTAAAAT
630461 AA
1 AA
630463 GCACATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTAATCTAAAAT
Found at i:633079 original size:2 final size:2
Alignment explanation
Indices: 633072--633096 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
633062 GGCTAGTTTC
633072 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
633097 GGCATCACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:633403 original size:1 final size:1
Alignment explanation
Indices: 633397--633427 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
633387 ATGCCAGGGA
*
633397 TTTTTTTTATTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
633428 GGGTTTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:639074 original size:2 final size:2
Alignment explanation
Indices: 639067--639104 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
639057 CTAGTTGCAC
639067 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
639105 TTCAACAGCA
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):
CT
Found at i:657417 original size:7 final size:7
Alignment explanation
Indices: 657396--657430 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
657386 ATTTTTTTAA
657396 TTTAA-T
1 TTTAATT
657402 TTT-ATT
1 TTTAATT
657408 TTTAATT
1 TTTAATT
657415 TTTAATT
1 TTTAATT
657422 TTTAATT
1 TTTAATT
657429 TT
1 TT
657431 AAAATTCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 1 0.04
6 7 0.26
7 19 0.70
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTAATT
Found at i:657432 original size:6 final size:6
Alignment explanation
Indices: 657390--657432 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
657380 TTCACTATTT
*
657390 TTTTAA -TTTAA TTTTAT TTTTAA TTTTTAA TTTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA -TTTTAA TTTTAA
657433 AATTCATGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 15 0.45
7 13 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:659388 original size:3 final size:3
Alignment explanation
Indices: 659380--659416 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
659370 GATTCGCATC
659380 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
659417 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:663873 original size:11 final size:11
Alignment explanation
Indices: 663857--663881 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
663847 TTTTTTTTAA
663857 TTTTAAAATAT
1 TTTTAAAATAT
663868 TTTTAAAATAT
1 TTTTAAAATAT
663879 TTT
1 TTT
663882 NNNNNNNNNN
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:664131 original size:11 final size:11
Alignment explanation
Indices: 664117--664153 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
664107 TTTTTTTTAA
664117 TTTTAAAATAT
1 TTTTAAAATAT
664128 TTTTAAAATAT
1 TTTTAAAATAT
664139 TTTTAAAAT-T
1 TTTTAAAATAT
664149 TTTTA
1 TTTTA
664154 TTTTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:664149 original size:40 final size:39
Alignment explanation
Indices: 664067--664164 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 39
664057 AAATATATTT
* * **
664067 ATTTTTTAAATTTTAAAATATTTTTTACTTACTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTAA
*
664107 TTTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
* *
664145 AATTTTTTATTTTTAAAATA
1 ATTTTTTTAATTTTAAAATA
664165 AATTTTTGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
38 24 0.48
40 26 0.52
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
Found at i:664803 original size:21 final size:20
Alignment explanation
Indices: 664763--664804 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
664753 TTTAATAATT
*
664763 TTTAAACCTAAATCTTAAAC
1 TTTAAACCTAAATATTAAAC
*
664783 TTTAAATCCTGAATATTAAAC
1 TTTAAA-CCTAAATATTAAAC
664804 T
1 T
664805 CTGAACCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAAACCTAAATATTAAAC
Found at i:665910 original size:22 final size:21
Alignment explanation
Indices: 665882--665932 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
665872 TTTTAATTTT
665882 TAATTTTAAAATATTTTTAAAA
1 TAATTTT-AAATATTTTTAAAA
***
665904 TAATTTTTTTTATTTTTAAAA
1 TAATTTTAAATATTTTTAAAA
665925 TAAATTTT
1 T-AATTTT
665933 TTGTGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTTAAATATTTTTAAAA
Found at i:665933 original size:22 final size:21
Alignment explanation
Indices: 665893--665934 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
665883 AATTTTAAAA
665893 TATTTTTAAAATAATTTTTTT
1 TATTTTTAAAATAATTTTTTT
*
665914 TATTTTTAAAATAAATTTTTT
1 TATTTTTAAAATAATTTTTTT
665935 GTGTTTATTA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTTAAAATAATTTTTTT
Found at i:671716 original size:19 final size:20
Alignment explanation
Indices: 671692--671743 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
671682 AGGGTCGTAG
671692 AAAATAAACAA-AAAATAAA
1 AAAATAAACAATAAAATAAA
671711 AAAAT--ACAATAAAATAAA
1 AAAATAAACAATAAAATAAA
*
671729 AAAAAAACACAATAA
1 AAAATAA-ACAATAA
671744 CAAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 4 0.14
18 12 0.43
19 5 0.18
21 7 0.25
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAATAAACAATAAAATAAA
Found at i:671746 original size:27 final size:22
Alignment explanation
Indices: 671701--671760 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 22
671691 GAAAATAAAC
*
671701 AAAAAATAAAAAAATACAATAAA
1 AAAAAAAAAAAAAATACAA-AAA
*
671724 ATAAAAAAAAAACACAATAACAAAGA
1 A-AAAAAAAAAA-A-AAT-ACAAAAA
671750 AAAAAAAAAAA
1 AAAAAAAAAAA
671761 GAAGCACTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 1 0.03
24 9 0.29
25 11 0.35
26 6 0.19
27 4 0.13
ACGTcount: A:0.83, C:0.07, G:0.02, T:0.08
Consensus pattern (22 bp):
AAAAAAAAAAAAAATACAAAAA
Found at i:671753 original size:24 final size:23
Alignment explanation
Indices: 671698--671759 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
671688 GTAGAAAATA
* *
671698 AACAAAAAATAAAAAAATACAAT
1 AACAAAAAAAAAAAAAACACAAT
*
671721 -A-AAATAAAAAAAAAACACAAT
1 AACAAAAAAAAAAAAAACACAAT
671742 AACAAAGAAAAAAAAAAA
1 AACAAA-AAAAAAAAAAA
671760 AGAAGCACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 17 0.53
22 2 0.06
23 3 0.09
24 10 0.31
ACGTcount: A:0.82, C:0.08, G:0.02, T:0.08
Consensus pattern (23 bp):
AACAAAAAAAAAAAAAACACAAT
Found at i:672348 original size:16 final size:16
Alignment explanation
Indices: 672308--672348 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
672298 TAACAATTTA
* *
672308 AACCCTAAAATAATAT
1 AACCCTAAACTAAAAT
672324 AA-CCT-AACTAAAAT
1 AACCCTAAACTAAAAT
672338 AACCCTAAACT
1 AACCCTAAACT
672349 TTAAAACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 9 0.43
15 6 0.29
16 6 0.29
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (16 bp):
AACCCTAAACTAAAAT
Found at i:673141 original size:60 final size:60
Alignment explanation
Indices: 673077--673258 Score: 156
Period size: 60 Copynumber: 3.2 Consensus size: 60
673067 TAAATTTAAA
673077 TTAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTT
1 TTAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTT
* * * *** *** *
673137 TTAATTTTTAAATAA--TA-TATAAATT-TAAAATT----A-T-ATAA-GA-AAAAACTA
1 TTAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTT
* *
673185 TAATTTT-CAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTT
1 TTAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTT
*
673244 TTAATTTTTAAATAA
1 TTAATTTTCAAATAA
673259 TATATAAATT
Statistics
Matches: 84, Mismatches: 25, Indels: 26
0.62 0.19 0.19
Matches are distributed among these distances:
47 6 0.07
48 9 0.11
49 4 0.05
50 10 0.12
51 5 0.06
52 1 0.01
55 1 0.01
56 5 0.06
57 10 0.12
58 4 0.05
59 9 0.11
60 20 0.24
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (60 bp):
TTAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTT
Found at i:673264 original size:107 final size:108
Alignment explanation
Indices: 673078--673297 Score: 424
Period size: 107 Copynumber: 2.0 Consensus size: 108
673068 AAATTTAAAT
673078 TAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTTTTAATT
1 TAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTTTTAATT
673143 TTTAAATAATATATAAATTTAAAATTATATAAGAAA-AAACTA
66 TTTAAATAATATATAAATTTAAAATTATATAAGAAAGAAACTA
673185 TAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTTTTAATT
1 TAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTTTTAATT
673250 TTTAAATAATATATAAATTTAAAATTATATAAGAAAGTAAACTA
66 TTTAAATAATATATAAATTTAAAATTATATAAGAAAG-AAACTA
673294 TAAT
1 TAAT
673298 GTTACTTTGG
Statistics
Matches: 111, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
107 101 0.91
109 10 0.09
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (108 bp):
TAATTTTCAAATAACGTATTTTTAATTGTTGTATTACCCATTGATAATGATAATTTCTTTTAATT
TTTAAATAATATATAAATTTAAAATTATATAAGAAAGAAACTA
Found at i:679965 original size:16 final size:17
Alignment explanation
Indices: 679933--679965 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
679923 ATCTCTTTTT
*
679933 CCGTAAGTTTGATTGAA
1 CCGTAAGATTGATTGAA
679950 CCGTAAGATT-ATTGAA
1 CCGTAAGATTGATTGAA
679966 TTGAGTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (17 bp):
CCGTAAGATTGATTGAA
Found at i:692022 original size:14 final size:14
Alignment explanation
Indices: 691986--692042 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
691976 TATATAGTCT
691986 ATTATAAAAATATA
1 ATTATAAAAATATA
*
692000 GACTATAAAAATATA
1 -ATTATAAAAATATA
* *
692015 ATTTTAAAAAAATA
1 ATTATAAAAATATA
*
692029 ATCATAAAAATATA
1 ATTATAAAAATATA
692043 TAATTTAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
14 22 0.63
15 13 0.37
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (14 bp):
ATTATAAAAATATA
Found at i:693719 original size:6 final size:6
Alignment explanation
Indices: 693696--693754 Score: 64
Period size: 6 Copynumber: 9.5 Consensus size: 6
693686 TTAGTTCATC
** * *
693696 TTTATT TTTCCT TTTATT TCTATT TGTAGTGT TTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTA-T-T TTTATT TTTATT TTTATT
693746 TTTATT TTT
1 TTTATT TTT
693755 TTAATTTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 38 0.86
7 2 0.05
8 4 0.09
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:695257 original size:7 final size:7
Alignment explanation
Indices: 695245--695274 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
695235 GATGCATGCA
695245 TGCATGT
1 TGCATGT
695252 TGCATGT
1 TGCATGT
695259 TGCATGT
1 TGCATGT
695266 TGCATGT
1 TGCATGT
695273 TG
1 TG
695275 AGGGGATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.43
Consensus pattern (7 bp):
TGCATGT
Found at i:695837 original size:12 final size:12
Alignment explanation
Indices: 695817--695859 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
695807 TTAACTCCCT
695817 TTTTTAAAATAA
1 TTTTTAAAATAA
* *
695829 TTTTAAAAATAT
1 TTTTTAAAATAA
*
695841 TTTTTAAAAT-T
1 TTTTTAAAATAA
695852 TTTTTAAA
1 TTTTTAAA
695860 CCGTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTTAAAATAA
Found at i:696985 original size:7 final size:7
Alignment explanation
Indices: 696973--696997 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
696963 AGTCGATTGA
696973 TATTTAG
1 TATTTAG
696980 TATTTAG
1 TATTTAG
696987 TATTTAG
1 TATTTAG
696994 TATT
1 TATT
696998 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:698198 original size:23 final size:23
Alignment explanation
Indices: 698168--698718 Score: 256
Period size: 23 Copynumber: 22.2 Consensus size: 23
698158 AATACCCTTA
698168 AATTAAAAACCCTAACCTAATTT
1 AATTAAAAACCCTAACCTAATTT
*
698191 AATTAAAAACCTTAAACCCTAA---
1 AATTAAAAACCCT-AA-CCTAATTT
* ***
698213 ACTTAAAAACCCTAACC-CCCTT
1 AATTAAAAACCCTAACCTAATTT
*
698235 AACTTAGAAACCCTAACCTAATTT
1 AA-TTAAAAACCCTAACCTAATTT
*
698259 AATTAAAAACCCTAACCTAATTA
1 AATTAAAAACCCTAACCTAATTT
698282 AATTAAAAACCCTAACCTAATTT
1 AATTAAAAACCCTAACCTAATTT
* **
698305 AATAAAAAAACTTTAAACCCTAA---
1 AAT-TAAAAACCCT-AA-CCTAATTT
*
698328 ACTTAAAAACCCTAACCTAATTT
1 AATTAAAAACCCTAACCTAATTT
698351 AATTAAAAACCCTAAACCCTAA---
1 AATTAAAAACCCT-AA-CCTAATTT
*
698373 ACTTAAAAACCCTAACCTAATTT
1 AATTAAAAACCCTAACCTAATTT
**
698396 AATTAAAAACAGTAAACCCTAAACTTAAAAAT
1 AATTAAAAACCCT-AA-CCT-AA-TT-----T
*
698428 AATTAAAAACCCTAAACCCTTAACTT
1 AATTAAAAACCCT-AA-CC-TAATTT
*
698454 AA--AAACCCTAACCTTAACCTAATTT
1 AATTAAA----AACCCTAACCTAATTT
*
698479 AATTAAAAACCCTAAACCCTTAACTT
1 AATTAAAAACCCT-AA-CC-TAATTT
*
698505 AA--AAACCCTAACCTTAACCTAATTT
1 AATTAAA----AACCCTAACCTAATTT
*
698530 AATTAAAAACCCTAAACCCTTAACTT
1 AATTAAAAACCCT-AA-CC-TAATTT
*
698556 AA--AAACCCTAACCTTAACCTAATTT
1 AATTAAA----AACCCTAACCTAATTT
*
698581 AATTAAAAACCCTAAACCCTTAACTT
1 AATTAAAAACCCT-AA-CC-TAATTT
698607 AA--AAACCCTAACCCTAACCTAATTT
1 AATTAAA----AACCCTAACCTAATTT
698632 AATTAAAAACCCTAAACCATAACCTAATT
1 AATTAAAAACCCT-AACC-TAA--T--TT
698661 AAATTAAAAACCCTAACCCTAATTT
1 -AATTAAAAACCCTAA-CCTAATTT
698686 AATTTTATTAAAAACCCTAACCCTAATTT
1 -A----ATTAAAAACCCTAA-CCTAATTT
698715 AATT
1 AATT
698719 TAATTAAAAA
Statistics
Matches: 414, Mismatches: 41, Indels: 145
0.69 0.07 0.24
Matches are distributed among these distances:
20 12 0.03
21 6 0.01
22 31 0.07
23 115 0.28
24 42 0.10
25 56 0.14
26 39 0.09
27 24 0.06
28 22 0.05
29 30 0.07
30 15 0.04
31 1 0.00
32 20 0.05
33 1 0.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (23 bp):
AATTAAAAACCCTAACCTAATTT
Found at i:698210 original size:45 final size:45
Alignment explanation
Indices: 698161--698649 Score: 237
Period size: 51 Copynumber: 10.1 Consensus size: 45
698151 AACCATTAAT
*
698161 ACCCTTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCTTAA
1 ACCCTTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
*** *
698206 ACCC-TAAACTTAAAAACCCTAACC-CCCTTAACTTAGAAACCCT-A
1 ACCCTTAAA-TTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAA
* * *
698250 ACCTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT-A
1 ACC--CTTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
* * * ** *
698296 ACCTAATTTAATAAAAAAACTTTAAACCCTAA---ACTTAAAAACCCT-A
1 ACC--CTTAAAT-TAAAAACCCT-AA-CCTAATTTAATTAAAAACCCTAA
* * *
698342 ACCTAATTTAATTAAAAACCCTAAACCCTAA---ACTTAAAAACCCT-A
1 ACC--CTTAAATTAAAAACCCT-AA-CCTAATTTAATTAAAAACCCTAA
* * **
698387 ACCTAATTTAATTAAAAACAGTAAACCCTAAACTTAAAAATAATTAAAAACCCTAA
1 ACC--CTTAAATTAAAAACCCT-AA-CCT-AA-TT-----TAATTAAAAACCCTAA
*
698443 ACCCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
1 ACCCTTAAATTAAAAA--C---CC-TAACCTAATTTAATTAAAAACCCTAA
*
698494 ACCCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
1 ACCCTTAAATTAAAAA--C---CC-TAACCTAATTTAATTAAAAACCCTAA
*
698545 ACCCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
1 ACCCTTAAATTAAAAA--C---CC-TAACCTAATTTAATTAAAAACCCTAA
*
698596 ACCCTTAACTTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA
1 ACCCTTAAATT--AAA----AACCCTAACCTAATTTAATTAAAAACCCTAA
698647 ACC
1 ACC
698650 ATAACCTAAT
Statistics
Matches: 385, Mismatches: 27, Indels: 58
0.82 0.06 0.12
Matches are distributed among these distances:
44 12 0.03
45 85 0.22
46 65 0.17
47 13 0.03
48 2 0.01
49 5 0.01
51 158 0.41
52 2 0.01
53 3 0.01
54 10 0.03
55 13 0.03
56 7 0.02
57 4 0.01
58 3 0.01
59 2 0.01
60 1 0.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (45 bp):
ACCCTTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
Found at i:698274 original size:46 final size:45
Alignment explanation
Indices: 698215--698426 Score: 284
Period size: 45 Copynumber: 4.6 Consensus size: 45
698205 AACCCTAAAC
* * *
698215 TTAAAAACCCTAACCCCCTTAACTTAGAAACCCTAACCTAATTTAA
1 TTAAAAACCCTAA-ACCCTAAACTTAAAAACCCTAACCTAATTTAA
*
698261 TTAAAAACCCT-AA-CCTAATTAAATTAAAAACCCTAACCTAATTTAA
1 TTAAAAACCCTAAACCCT-A--AACTTAAAAACCCTAACCTAATTTAA
* **
698307 TAAAAAAACTTTAAACCCTAAACTTAAAAACCCTAACCTAATTTAA
1 T-TAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTTAA
698353 TTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTTAA
1 TTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTTAA
**
698398 TTAAAAACAGTAAACCCTAAACTTAAAAA
1 TTAAAAACCCTAAACCCTAAACTTAAAAA
698427 TAATTAAAAA
Statistics
Matches: 147, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
43 3 0.02
45 69 0.47
46 62 0.42
47 7 0.05
48 3 0.02
49 3 0.02
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.25
Consensus pattern (45 bp):
TTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTTAA
Found at i:698435 original size:32 final size:32
Alignment explanation
Indices: 698395--698458 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
698385 TAACCTAATT
*
698395 TAATTAAAAACAGTAAACCCTAAACTTAAAAA
1 TAATTAAAAACACTAAACCCTAAACTTAAAAA
* *
698427 TAATTAAAAACCCTAAACCCTTAACTTAAAAA
1 TAATTAAAAACACTAAACCCTAAACTTAAAAA
698459 CCCTAACCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.23
Consensus pattern (32 bp):
TAATTAAAAACACTAAACCCTAAACTTAAAAA
Found at i:698458 original size:22 final size:20
Alignment explanation
Indices: 698430--698573 Score: 72
Period size: 22 Copynumber: 6.0 Consensus size: 20
698420 TTAAAAATAA
698430 TTAAAAACCCTAAACCCTTAAC
1 TTAAAAACCCT-AA-CCTTAAC
698452 TTAAAAACCCTAACCTTAACC
1 TTAAAAACCCTAACCTTAA-C
698473 TAATTTAATTAAAAACCCTAAACCCTTAAC
1 --------TTAAAAACCCT-AA-CCTTAAC
698503 TTAAAAACCCTAACCTTAACC
1 TTAAAAACCCTAACCTTAA-C
698524 TAATTTAATTAAAAACCCTAAACCCTTAAC
1 --------TTAAAAACCCT-AA-CCTTAAC
698554 TTAAAAACCCTAACCTTAAC
1 TTAAAAACCCTAACCTTAAC
698574 CTAATTTAAT
Statistics
Matches: 100, Mismatches: 0, Indels: 46
0.68 0.00 0.32
Matches are distributed among these distances:
20 19 0.19
21 8 0.08
22 33 0.33
29 22 0.22
30 6 0.06
31 12 0.12
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAAAAACCCTAACCTTAAC
Found at i:698490 original size:29 final size:29
Alignment explanation
Indices: 698447--698852 Score: 326
Period size: 29 Copynumber: 14.6 Consensus size: 29
698437 CCCTAAACCC
*
698447 TTAACTTAAAAACCCTAACCTTAACCTAAT
1 TTAA-TTAAAAACCCTAACCCTAACCTAAT
698477 TTAATTAAAAACCCTAAACCCT----T-A-
1 TTAATTAAAAACCCT-AACCCTAACCTAAT
* *
698501 --ACTTAAAAACCCTAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
698528 TTAATTAAAAACCCTAAACCCT----T-A-
1 TTAATTAAAAACCCT-AACCCTAACCTAAT
* *
698552 --ACTTAAAAACCCTAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
698579 TTAATTAAAAACCCTAAACCCT----T-A-
1 TTAATTAAAAACCCT-AACCCTAACCTAAT
*
698603 --ACTTAAAAACCCTAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
*
698630 TTAATTAAAAACCCTAAACCATAACCTAAT
1 TTAATTAAAAACCCT-AACCCTAACCTAAT
* **
698660 TAAATTAAAAACCCTAACCCTAATTTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
* **
698689 TTTATTAAAAACCCTAACCCTAATTTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
698718 TTAATTAAAAACCCTAAACCCTAACCTAAT
1 TTAATTAAAAACCCT-AACCCTAACCTAAT
* * **
698748 TAAATTAAAAAACCTAACCCTAATTTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
* * *
698777 TTTATTAAAAACCCTAACCCAAAACCCTAAC
1 TTAATTAAAAACCCTAACCC-TAA-CCTAAT
* *
698808 CTAATTAAATTAA---AAACCCTAACCTAAT
1 TTAATTAAA--AACCCTAACCCTAACCTAAT
*
698836 TTTATTAAAAACCCTAA
1 TTAATTAAAAACCCTAA
698853 ACTAAATTAA
Statistics
Matches: 300, Mismatches: 40, Indels: 73
0.73 0.10 0.18
Matches are distributed among these distances:
21 16 0.05
22 36 0.12
25 6 0.02
26 8 0.03
28 12 0.04
29 132 0.44
30 78 0.26
31 10 0.03
33 2 0.01
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (29 bp):
TTAATTAAAAACCCTAACCCTAACCTAAT
Found at i:698491 original size:51 final size:51
Alignment explanation
Indices: 698427--698649 Score: 437
Period size: 51 Copynumber: 4.4 Consensus size: 51
698417 AACTTAAAAA
698427 TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATT
1 TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATT
698478 TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATT
1 TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATT
698529 TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATT
1 TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATT
*
698580 TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAACCTAATT
1 TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATT
698631 TAATTAAAAACCCTAAACC
1 TAATTAAAAACCCTAAACC
698650 ATAACCTAAT
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 171 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (51 bp):
TAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATT
Found at i:698608 original size:22 final size:20
Alignment explanation
Indices: 698579--698621 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
698569 TTAACCTAAT
698579 TTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCT-AACCC
698600 TTAACTTAAAAACCCTAACCC
1 TTAA-TTAAAAACCCTAACCC
698621 T
1 T
698622 AACCTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAATTAAAAACCCTAACCC
Found at i:698674 original size:59 final size:58
Alignment explanation
Indices: 698600--698844 Score: 276
Period size: 59 Copynumber: 4.1 Consensus size: 58
698590 CCCTAAACCC
* * **
698600 TTAACTTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCATAACCTAA
1 TTAAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAATTTAA
** *
698659 TTAAATTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACCCTAACCCTAATTTAA
1 TTAAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAA
* * *
698717 TTTAATTAAAAACCCTAAACCCTAACCTAATTAAATTAAAAAACCTAACCCTAATTTAA
1 TTAAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAA
** * *
698776 TTTTATTAAAAACCCTAACCCAAAACCCTAACCTAATTAAATTAAAAACCCTAA-CCTAATTTTA
1 TTAAATTAAAAACCCT-------AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAA
698840 TTAAA
1 TTAAA
698845 AACCCTAAAC
Statistics
Matches: 161, Mismatches: 18, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
58 25 0.16
59 93 0.58
64 12 0.07
65 31 0.19
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (58 bp):
TTAAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAA
Found at i:698711 original size:88 final size:88
Alignment explanation
Indices: 698605--698796 Score: 348
Period size: 88 Copynumber: 2.2 Consensus size: 88
698595 AACCCTTAAC
698605 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCATAACCTAATTAAATTAAAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCATAACCTAATTAAATTAAAA
*
698670 ACCCTAACCCTAATTTAATTTTA
66 AACCTAACCCTAATTTAATTTTA
** *
698693 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAATTAAAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCATAACCTAATTAAATTAAAA
698758 AACCTAACCCTAATTTAATTTTA
66 AACCTAACCCTAATTTAATTTTA
698781 TTAAAAACCCTAACCC
1 TTAAAAACCCTAACCC
698797 AAAACCCTAA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 100 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (88 bp):
TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCATAACCTAATTAAATTAAAA
AACCTAACCCTAATTTAATTTTA
Found at i:698802 original size:13 final size:13
Alignment explanation
Indices: 698784--698808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
698774 AATTTTATTA
698784 AAAACCCTAACCC
1 AAAACCCTAACCC
698797 AAAACCCTAACC
1 AAAACCCTAACC
698809 TAATTAAATT
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:0.48, C:0.44, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAACCCTAACCC
Found at i:698825 original size:88 final size:85
Alignment explanation
Indices: 698605--698852 Score: 291
Period size: 88 Copynumber: 2.8 Consensus size: 85
698595 AACCCTTAAC
* ** *
698605 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCATAACCTAATTAAATTAAAA
1 TTAAAAACCCTAACCCAAACCTAACCTAATTAAAAA--C-AAACCCTAACCTAATTAAATTAAAA
698670 ACCCTAACCCTAATTTAATTTTA
63 ACCCTAACCCTAATTTAATTTTA
* ** **
698693 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTAAATTAAAA
1 TTAAAAACCCTAACCCAAACCTAACCTAATTAAAAA--C-AAACCCTAACCTAATTAAATTAAAA
*
698758 AACCTAACCCTAATTTAATTTTA
63 ACCCTAACCCTAATTTAATTTTA
**
698781 TTAAAAACCCTAACCCAAAACCCTAACCTAATTAAATTAA-AAACCCTAACCTAATTTTATTAAA
1 TTAAAAACCCTAACCC-AAA-CCTAACCTAATTAAA--AACAAACCCTAACCTAATTAAATTAAA
698845 AACCCTAA
62 AACCCTAA
698853 ACTAAATTAA
Statistics
Matches: 144, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
88 129 0.90
89 2 0.01
90 11 0.08
92 2 0.01
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (85 bp):
TTAAAAACCCTAACCCAAACCTAACCTAATTAAAAACAAACCCTAACCTAATTAAATTAAAAACC
CTAACCCTAATTTAATTTTA
Found at i:698826 original size:23 final size:23
Alignment explanation
Indices: 698797--698862 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
698787 ACCCTAACCC
698797 AAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATTA
**
698820 AAAACCCTAACCTAATTTTATTA
1 AAAACCCTAACCTAATTAAATTA
*
698843 AAAACCCTAAACTAAATTAA
1 AAAACCCTAACCT-AATTAA
698863 TAATTTTACT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 33 0.89
24 4 0.11
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAACCCTAACCTAATTAAATTA
Found at i:698845 original size:59 final size:61
Alignment explanation
Indices: 698727--698852 Score: 184
Period size: 65 Copynumber: 2.0 Consensus size: 61
698717 TTTAATTAAA
*
698727 AACCCTAAACCCTAACCTAATTAAATTAAAAAACCTAACCCTAATTTAATTTTATTAAAAACCCT
1 AACCCAAAACCCTAACCTAATTAAATTAAAAAACCTAACCC----TTAATTTTATTAAAAACCCT
*
698792 AACCCAAAACCCTAACCTAATTAAATTAAAAACCCTAA-CC-TAATTTTATTAAAAACCCT
1 AACCCAAAACCCTAACCTAATTAAATTAAAAAACCTAACCCTTAATTTTATTAAAAACCCT
698851 AA
1 AA
698853 ACTAAATTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
59 21 0.36
64 2 0.03
65 36 0.61
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (61 bp):
AACCCAAAACCCTAACCTAATTAAATTAAAAAACCTAACCCTTAATTTTATTAAAAACCCT
Found at i:699813 original size:137 final size:137
Alignment explanation
Indices: 699547--699806 Score: 394
Period size: 137 Copynumber: 1.9 Consensus size: 137
699537 ACACCTTGGT
* *
699547 GCGGTCTGTCAAACTCTGTCACGCGAAACCATAAATTGTCTCGATCGTGACACACTATGTGCATG
1 GCGGTCTGTCAAACTCTGTCACGCGAAACCATAAATTGTCTCGATCATGACACACTATGTGCATA
** *
699612 GTGTTTGCCCTCGCCTTGGCCTTGTTAATTTCTTGAACTACCTTACTGCACCATACATGTCCTCC
66 GTGTTCACCCGCGCCTTGGCCTTGTTAATTTCTTGAACTACCTTACTGCACCATACATGTCCTCC
699677 TTACAGC
131 TTACAGC
* * * *
699684 GCGGTCTGTCAAACTTTGTCACGCTAAACCATAAGTTGTCTCGATCATGACACACTGTGTGCATA
1 GCGGTCTGTCAAACTCTGTCACGCGAAACCATAAATTGTCTCGATCATGACACACTATGTGCATA
* * * * *
699749 GTGTTCACTCGCGCCTTGGCCTTTTTAATTTCTTGCACTACTTTACTGCACTATACAT
66 GTGTTCACCCGCGCCTTGGCCTTGTTAATTTCTTGAACTACCTTACTGCACCATACAT
699807 AGCCTCCCTG
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
137 109 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.33
Consensus pattern (137 bp):
GCGGTCTGTCAAACTCTGTCACGCGAAACCATAAATTGTCTCGATCATGACACACTATGTGCATA
GTGTTCACCCGCGCCTTGGCCTTGTTAATTTCTTGAACTACCTTACTGCACCATACATGTCCTCC
TTACAGC
Found at i:702413 original size:124 final size:125
Alignment explanation
Indices: 702191--702563 Score: 563
Period size: 124 Copynumber: 3.0 Consensus size: 125
702181 CAAACATGCT
* *
702191 ACTGTAGCAAAAGCGCGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGC-AATTTCACAAATTCTTCTCAAATAGCATCCTGCT
*
702256 ATAAGCGAA-TTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACCG
65 AGAAGC-AATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACCG
*
702317 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTT-ACAAATTCTTCTCAAATAGTATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
*
702381 GAAGCAATTTTATACTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTTCCATGACCT
66 GAAGCAATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACCG
* * *
702440 ACTGTAGCAAAAGCACGTCCACAAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
** * **** *
702505 GAAGTGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACC
66 GAAGCAATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACC
702564 TAAAAACCCT
Statistics
Matches: 227, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
123 59 0.26
124 115 0.51
125 24 0.11
126 29 0.13
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (125 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
GAAGCAATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACCG
Found at i:716347 original size:12 final size:12
Alignment explanation
Indices: 716302--716348 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
716292 TAAGAAAATT
716302 ATTATTAAATATA
1 ATTATT-AATATA
*
716315 A-T-TTAATAAA
1 ATTATTAATATA
*
716325 ATTCTTAATATA
1 ATTATTAATATA
716337 ATTATTAATATA
1 ATTATTAATATA
716349 TGAATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 6 0.21
11 3 0.10
12 19 0.66
13 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTATTAATATA
Found at i:719143 original size:14 final size:15
Alignment explanation
Indices: 719116--719153 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
719106 TTAATAGGAC
719116 TAAAT-TTAAGAAAA
1 TAAATATTAAGAAAA
*
719130 TAAATATTAAAAAAA
1 TAAATATTAAGAAAA
719145 T-AATATTAA
1 TAAATATTAA
719154 TTTCATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
TAAATATTAAGAAAA
Found at i:719971 original size:10 final size:9
Alignment explanation
Indices: 719958--720017 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
719948 TTTATATTTG
719958 AAATTATTGA
1 AAATTATT-A
719968 AAATTAATTA
1 AAATT-ATTA
*
719978 AAATTATAA
1 AAATTATTA
719987 AAATTCA-TA
1 AAATT-ATTA
* *
719996 CAATATATAA
1 AAAT-TATTA
720006 AAATTATTA
1 AAATTATTA
720015 AAA
1 AAA
720018 ACATTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
9 20 0.50
10 17 0.43
11 3 0.08
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (9 bp):
AAATTATTA
Found at i:719991 original size:9 final size:9
Alignment explanation
Indices: 719967--720038 Score: 56
Period size: 9 Copynumber: 7.4 Consensus size: 9
719957 GAAATTATTG
*
719967 AAAATTAATT
1 AAAATT-ATA
719977 AAAATTATA
1 AAAATTATA
719986 AAAATTCAT-
1 AAAATT-ATA
*
719995 ACAATATATA
1 AAAAT-TATA
720005 AAAATTATTAA
1 AAAATTA-T-A
*
720016 AAACATTTTA
1 AAA-ATTATA
720026 AAAATTATA
1 AAAATTATA
720035 AAAA
1 AAAA
720039 AATAGAAGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
9 25 0.49
10 18 0.35
11 5 0.10
12 3 0.06
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:719991 original size:19 final size:19
Alignment explanation
Indices: 719967--720017 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
719957 GAAATTATTG
719967 AAAATTAATTAAAAT-TATA
1 AAAATT-ATTAAAATATATA
*
719986 AAAATTCA-TACAATATATA
1 AAAATT-ATTAAAATATATA
720005 AAAATTATTAAAA
1 AAAATTATTAAAA
720018 ACATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTATTAAAATATATA
Found at i:720018 original size:10 final size:10
Alignment explanation
Indices: 719958--720038 Score: 50
Period size: 10 Copynumber: 8.3 Consensus size: 10
719948 TTTATATTTG
*
719958 AAATTATTGA
1 AAATTATTAA
719968 AAATTAATT-A
1 AAATT-ATTAA
719978 AAATTA-TAA
1 AAATTATTAA
719987 AAATTCA-T-A
1 AAATT-ATTAA
*
719996 CAA-TATATAA
1 AAATTAT-TAA
720006 AAATTATTAAA
1 AAATTATT-AA
720017 AACATT-TTAA
1 AA-ATTATTAA
720027 AAATTA-TAA
1 AAATTATTAA
720036 AAA
1 AAA
720039 AATAGAAGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.02
8 2 0.03
9 20 0.34
10 21 0.36
11 12 0.20
12 3 0.05
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (10 bp):
AAATTATTAA
Found at i:720511 original size:16 final size:15
Alignment explanation
Indices: 720446--720523 Score: 57
Period size: 16 Copynumber: 4.5 Consensus size: 15
720436 AAATTTATTT
720446 AAAATGATAAAATATAA
1 AAAAT-ATAAAATAT-A
*
720463 AAAATGGAGAAAAGTATTA
1 AAAAT--ATAAAA-TA-TA
720482 AAAATTATTAAAATGATA
1 AAAA-TA-TAAAAT-ATA
720500 AAAATATAAAATATAA
1 AAAATATAAAATAT-A
720516 AAAATATA
1 AAAATATA
720524 TGAAAAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
15 2 0.04
16 15 0.29
17 7 0.13
18 14 0.27
19 12 0.23
20 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (15 bp):
AAAATATAAAATATA
Found at i:720542 original size:18 final size:20
Alignment explanation
Indices: 720507--720568 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
720497 ATAAAAATAT
*
720507 AAAATA-TAAAAAATATATGA
1 AAAATATTAAAATATATA-GA
*
720527 AAAATGTTAAAA-ATATAGA
1 AAAATATTAAAATATATAGA
*
720546 AAATTATTAAAATATATAGA
1 AAAATATTAAAATATATAGA
720566 AAA
1 AAA
720569 TTGCAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 12 0.32
20 20 0.54
21 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAATATTAAAATATATAGA
Found at i:720549 original size:54 final size:53
Alignment explanation
Indices: 720446--720561 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 53
720436 AAATTTATTT
* * *
720446 AAAATGATAAAATATAAAAAATGGAGAAAAGTATTAAAAATTATTAAAATGATA
1 AAAAT-ATAAAATATAAAAAATAGAGAAAAATATTAAAAATTATGAAAATGATA
* * * *
720500 AAAATATAAAATATAAAAAATATATGAAAAATGTTAAAAA-TATAGAAAATTATT
1 AAAATATAAAATATAAAAAATAGA-GAAAAATATTAAAAATTAT-GAAAATGATA
720554 AAAATATA
1 AAAATATA
720562 TAGAAAATTG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 20 0.38
54 33 0.62
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.28
Consensus pattern (53 bp):
AAAATATAAAATATAAAAAATAGAGAAAAATATTAAAAATTATGAAAATGATA
Found at i:720569 original size:20 final size:20
Alignment explanation
Indices: 720516--720570 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
720506 TAAAATATAA
* *
720516 AAAATATAT-GAAAAATGTT
1 AAAATATATAGAAAATTATT
720535 AAAA-ATATAGAAAATTATT
1 AAAATATATAGAAAATTATT
720554 AAAATATATAGAAAATT
1 AAAATATATAGAAAATT
720571 GCAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 4 0.12
19 16 0.50
20 12 0.38
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAATATATAGAAAATTATT
Found at i:720577 original size:20 final size:20
Alignment explanation
Indices: 720515--720577 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
720505 ATAAAATATA
*
720515 AAAAATATAT-GAAAAATGT
1 AAAAATATATAGAAAATTGT
* *
720534 TAAAA-ATATAGAAAATTAT
1 AAAAATATATAGAAAATTGT
* *
720553 TAAAATATATAGAAAATTGC
1 AAAAATATATAGAAAATTGT
720573 AAAAA
1 AAAAA
720578 AAAGTATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 4 0.11
19 16 0.44
20 16 0.44
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (20 bp):
AAAAATATATAGAAAATTGT
Found at i:720699 original size:18 final size:18
Alignment explanation
Indices: 720678--720715 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
720668 ATGAAATTGC
*
720678 AATAAAATATTAGAATAT
1 AATAAAATATTAAAATAT
*
720696 AATAAAGTATTAAAATAT
1 AATAAAATATTAAAATAT
720714 AA
1 AA
720716 AACATGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AATAAAATATTAAAATAT
Found at i:721123 original size:19 final size:19
Alignment explanation
Indices: 721099--721144 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
721089 ACAAGTTATG
721099 TATTTTTT-AAATTTTAAT
1 TATTTTTTCAAATTTTAAT
*
721117 ATATTTTTTGCAATTTTTAAT
1 -TATTTTTT-CAAATTTTAAT
721138 TATTTTT
1 TATTTTT
721145 AAGAACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 7 0.29
21 9 0.38
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTTCAAATTTTAAT
Found at i:721131 original size:20 final size:19
Alignment explanation
Indices: 721099--721144 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
721089 ACAAGTTATG
721099 TATTTTTTAAA-TTTTAAT
1 TATTTTTTAAATTTTTAAT
*
721117 ATATTTTTTGCAATTTTTAAT
1 -TATTTTTT-AAATTTTTAAT
721138 TATTTTT
1 TATTTTT
721145 AAGAACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 9 0.38
21 7 0.29
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTTAAATTTTTAAT
Found at i:724990 original size:11 final size:11
Alignment explanation
Indices: 724938--725010 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
724928 CACTATTATA
*
724938 TTATTATTATT
1 TTATTATTGTT
724949 TTATTATTGTTGT
1 TTATTATTG-T-T
* *
724962 TTAGGTATTGTA
1 TTA-TTATTGTT
*
724974 TAATTATTGTT
1 TTATTATTGTT
724985 TTATTATTAGTT
1 TTATTATT-GTT
* *
724997 TTACTATTATT
1 TTATTATTGTT
725008 TTA
1 TTA
725011 GAAACTTTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
11 26 0.53
12 13 0.27
13 5 0.10
14 5 0.10
ACGTcount: A:0.25, C:0.01, G:0.10, T:0.64
Consensus pattern (11 bp):
TTATTATTGTT
Found at i:725087 original size:11 final size:12
Alignment explanation
Indices: 725058--725090 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
725048 TATTTAAATA
725058 TAAATATTATTTT
1 TAAAT-TTATTTT
725071 TAAATTTATTTT
1 TAAATTTATTTT
725083 T-AATTTAT
1 TAAATTTAT
725091 CGGGAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 8 0.40
13 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TAAATTTATTTT
Done.