Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000893.1 Hibiscus syriacus cultivar Beakdansim tig00001750_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: 734264
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:193283 original size:46 final size:43
Alignment explanation
Indices: 193233--193322 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 43
193223 ACCAAAAGGT
* *
193233 AGAGAAAAACTTG-TCATAAAGGCAGAGAAAAATGTGCCACAAAGAC
1 AGAGAAAAACGTGCT-ATAAAGGCAGAG---AATATGCCACAAAGAC
*
193279 AGAGATAAACGTGCTATAAAGGCAGAGAATATGCCACAAAGAC
1 AGAGAAAAACGTGCTATAAAGGCAGAGAATATGCCACAAAGAC
193322 A
1 A
193323 TAATTATTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
43 16 0.40
46 23 0.57
47 1 0.03
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.13
Consensus pattern (43 bp):
AGAGAAAAACGTGCTATAAAGGCAGAGAATATGCCACAAAGAC
Found at i:211393 original size:28 final size:29
Alignment explanation
Indices: 211335--211408 Score: 132
Period size: 28 Copynumber: 2.6 Consensus size: 29
211325 TGGTTTATGC
211335 TAGTCAACAAATAGTTTTTTTTGAGTAAA
1 TAGTCAACAAATAGTTTTTTTTGAGTAAA
*
211364 TAGTCAACAAATAGTTTTTTTT-AGTTAA
1 TAGTCAACAAATAGTTTTTTTTGAGTAAA
211392 TAGTCAACAAATAGTTT
1 TAGTCAACAAATAGTTT
211409 ATTCTTCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 22 0.50
29 22 0.50
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (29 bp):
TAGTCAACAAATAGTTTTTTTTGAGTAAA
Found at i:211421 original size:28 final size:27
Alignment explanation
Indices: 211335--211421 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 27
211325 TGGTTTATGC
*
211335 TAGTCAACAAATAGTTTTTTTTGAGTAAA
1 TAGTCAACAAATAG-TTTTTTTCAG-AAA
* *
211364 TAGTCAACAAATAGTTTTTTTTAGTTAA
1 TAGTCAACAAATAGTTTTTTTCAG-AAA
211392 TAGTCAACAAATAGTTTATTCTTCA-AAA
1 TAGTCAACAAATAGTTT-TT-TTCAGAAA
211420 TA
1 TA
211422 AGGACCTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
28 33 0.63
29 16 0.31
30 3 0.06
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.41
Consensus pattern (27 bp):
TAGTCAACAAATAGTTTTTTTCAGAAA
Found at i:213793 original size:37 final size:37
Alignment explanation
Indices: 213734--213818 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
213724 ATCCCATTAT
*
213734 TATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 TATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
213770 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 TATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
*
213807 AATTTTTCAAAG
1 TATTTTTCAAAG
213819 TTGGTTGCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 8 0.18
37 36 0.82
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (37 bp):
TATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:218313 original size:37 final size:37
Alignment explanation
Indices: 218255--218373 Score: 172
Period size: 37 Copynumber: 3.3 Consensus size: 37
218245 TCCCATTATC
* * *
218255 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
*
218291 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
*
218327 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
218363 ATTTTTCAAAG
1 ATTTTTCAAAG
218374 TTGGTTGCTA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 28 0.37
36 18 0.24
37 29 0.39
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
Found at i:218339 original size:35 final size:36
Alignment explanation
Indices: 218254--218373 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
218244 ATCCCATTAT
* *
218254 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
218290 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
218326 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
218361 CAATTTTTCAAAG
1 C-ATTTTTCAAAG
218374 TTGGTTGCTA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 34 0.44
36 14 0.18
37 29 0.38
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:230071 original size:17 final size:17
Alignment explanation
Indices: 230049--230081 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
230039 GTTCGAATTG
230049 TTTTTATTATTTAGTTC
1 TTTTTATTATTTAGTTC
*
230066 TTTTTATTTTTTAGTT
1 TTTTTATTATTTAGTT
230082 GTATCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTATTATTTAGTTC
Found at i:232739 original size:19 final size:20
Alignment explanation
Indices: 232715--232762 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
232705 AATGATTTTC
* * *
232715 TTTTGAAAGCTAAAATG-GA
1 TTTTGAAAACCAAAATGAAA
232734 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATGAAA
232754 TTTTGAAAA
1 TTTTGAAAA
232763 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATGAAA
Found at i:233631 original size:14 final size:14
Alignment explanation
Indices: 233583--233631 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
233573 TTTGTTACTC
*
233583 TTTTTTAAATTCAA
1 TTTTTTAAAGTCAA
*
233597 TTTGTTTAAGTGTCAA
1 TTT-TTTAA-AGTCAA
*
233613 GTTTTTAAAGTCAA
1 TTTTTTAAAGTCAA
233627 TTTTT
1 TTTTT
233632 GTTTGGAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 12 0.43
15 10 0.36
16 6 0.21
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (14 bp):
TTTTTTAAAGTCAA
Found at i:234924 original size:13 final size:13
Alignment explanation
Indices: 234905--234980 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
234895 GTCATAACCC
234905 GACCCGACCCGTT
1 GACCCGACCCGTT
*
234918 TACCCGACCCGTT
1 GACCCGACCCGTT
234931 GACCCGACCTGACCTGTT
1 GACCCGA-C---CC-GTT
*
234949 GACCCGACCTGTT
1 GACCCGACCCGTT
*
234962 GACCCGACTCGTT
1 GACCCGACCCGTT
234975 GACCCG
1 GACCCG
234981 TTGACTGTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
13 38 0.72
14 2 0.04
17 3 0.06
18 10 0.19
ACGTcount: A:0.16, C:0.42, G:0.22, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:234935 original size:26 final size:26
Alignment explanation
Indices: 234905--234980 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 26
234895 GTCATAACCC
*
234905 GACCCGACCCGTTTACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGTT
*
234931 GACCCGACCTGACCTGTTGACCCGACCTGTT
1 GACCCGA-C---CC-GTTGACCCGACCCGTT
*
234962 GACCCGACTCGTTGACCCG
1 GACCCGACCCGTTGACCCG
234981 TTGACTGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
26 16 0.38
27 2 0.05
30 3 0.07
31 21 0.50
ACGTcount: A:0.16, C:0.42, G:0.22, T:0.20
Consensus pattern (26 bp):
GACCCGACCCGTTGACCCGACCCGTT
Found at i:234939 original size:31 final size:31
Alignment explanation
Indices: 234901--234969 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
234891 ACCGGTCATA
*
234901 ACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
* * *
234932 ACCCGACCTGACCTGTTGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
234963 ACCCGAC
1 ACCCGAC
234970 TCGTTGACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.17, C:0.45, G:0.20, T:0.17
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:234944 original size:18 final size:18
Alignment explanation
Indices: 234923--234959 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
234913 CCGTTTACCC
234923 GACCCGTTGACCCGACCT
1 GACCCGTTGACCCGACCT
*
234941 GACCTGTTGACCCGACCT
1 GACCCGTTGACCCGACCT
234959 G
1 G
234960 TTGACCCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.41, G:0.24, T:0.19
Consensus pattern (18 bp):
GACCCGTTGACCCGACCT
Found at i:237455 original size:24 final size:24
Alignment explanation
Indices: 237428--237490 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
237418 TGATACGTTA
* * *
237428 TCTGAATTCTGATCTGGATTCTGT
1 TCTGAATTCTGATATGAAATCTGT
237452 TCTG-ATATCTGATATGAAATCTGT
1 TCTGAAT-TCTGATATGAAATCTGT
* *
237476 TTTGATTTCTGATAT
1 TCTGAATTCTGATAT
237491 CTCCGTTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.06
24 29 0.91
25 1 0.03
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGAATTCTGATATGAAATCTGT
Found at i:240185 original size:17 final size:17
Alignment explanation
Indices: 240159--240192 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
240149 TGCGCACTAC
*
240159 CCAAAGCCAACTTGGTA
1 CCAAAACCAACTTGGTA
240176 CCAAAACCAACTTGGTA
1 CCAAAACCAACTTGGTA
240193 GTTCATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.29, G:0.15, T:0.18
Consensus pattern (17 bp):
CCAAAACCAACTTGGTA
Found at i:250188 original size:31 final size:30
Alignment explanation
Indices: 250142--250221 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
250132 TTCGATAATA
*
250142 TAATAATTATTTTATAGTATT-TAGATAAATT
1 TAATAA-TATTTTATAATATTCTA-ATAAATT
* *
250173 TATTAATAATTTTATAATCTTCTAATAAATT
1 TAATAAT-ATTTTATAATATTCTAATAAATT
250204 TAATAAGTATTTTATAAT
1 TAATAA-TATTTTATAAT
250222 TTTTAAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 38 0.90
32 3 0.07
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (30 bp):
TAATAATATTTTATAATATTCTAATAAATT
Found at i:251011 original size:31 final size:32
Alignment explanation
Indices: 250961--251036 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 32
250951 GTTTGAAAAA
*
250961 TTAT-AAATTACTTATTAAATTTAT-TAAA-AGC
1 TTATAAAATTA-TTAATAAATTTATCTAAATA-C
250992 TTATAAAATTATTAATAAATTTATCTAAATAC
1 TTATAAAATTATTAATAAATTTATCTAAATAC
*
251024 -TATAAAATAATTA
1 TTATAAAATTATTA
251037 TTATATTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
31 28 0.70
32 11 0.28
33 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (32 bp):
TTATAAAATTATTAATAAATTTATCTAAATAC
Found at i:254533 original size:16 final size:16
Alignment explanation
Indices: 254508--254540 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
254498 CCCCCTTAGA
254508 AAAATAATTTTTGGCT
1 AAAATAATTTTTGGCT
*
254524 AAAATGATTTTTGGCT
1 AAAATAATTTTTGGCT
254540 A
1 A
254541 GCAAATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (16 bp):
AAAATAATTTTTGGCT
Found at i:256631 original size:20 final size:20
Alignment explanation
Indices: 256606--256661 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
256596 GGCTACTGAA
* *
256606 TTTTTGATCTCGATACCAAT
1 TTTTTGGTCTCGAGACCAAT
*
256626 TTTTTGGTCTCGAGACCGAT
1 TTTTTGGTCTCGAGACCAAT
*
256646 TTTCTGGTCTCGAGAC
1 TTTTTGGTCTCGAGAC
256662 TTACAGCTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTTTGGTCTCGAGACCAAT
Found at i:257628 original size:45 final size:45
Alignment explanation
Indices: 257541--257881 Score: 472
Period size: 45 Copynumber: 7.6 Consensus size: 45
257531 TCTCCATTCA
* * *
257541 TGTTTATAAGGCA-CCATTATGCACTTTAAACTATAGTATACTTTTC
1 TGTTGATAATGCACCCA-TATGCA-TTTCAACTATAGTATACTTTTC
*
257587 TGTTGATAATGCACCCATATGCATTTCAACCATAGTATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTC
*
257632 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATTCTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTC
*
257677 TGTTGATAATGCACCCATATGCATTTCAA-TCATAGTATACTTTTT
1 TGTTGATAATGCACCCATATGCATTTCAACT-ATAGTATACTTTTC
*
257722 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTA
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTC
* *
257767 TGTTGATAATGTACCCATATACATTTCAACTATAGTATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTC
* * * * * *
257812 TGTTGATAATGTACCCATATACATTTCAACTTTGGCAT-CCTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTC
**
257856 ATGCCGATAATGCACCCATATGCATT
1 -TGTTGATAATGCACCCATATGCATT
257882 AGTATTTTCA
Statistics
Matches: 271, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
44 6 0.02
45 244 0.90
46 18 0.07
47 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (45 bp):
TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTC
Found at i:268528 original size:4 final size:4
Alignment explanation
Indices: 268519--268580 Score: 124
Period size: 4 Copynumber: 15.5 Consensus size: 4
268509 ATTCTTATTC
268519 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
268567 TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TT
268581 GTAGTTTTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:270407 original size:853 final size:855
Alignment explanation
Indices: 268751--270466 Score: 2823
Period size: 853 Copynumber: 2.0 Consensus size: 855
268741 AAAGTTCTTC
* *
268751 AAGTCATTTATGATCGTGGTGAACCGATCAGATATCGTCTTAATGTATTCATCAGGCTTCATCTT
1 AAGTCATTTATGATCGTGGTGAACCGATCAGACATCATCTTAATGTATTCATCAGGCTTCATCTT
* *
268816 GAAGTTCTCATAGTTGAGAGTGAGAATGCTAATCTTGGACTTCTTGACTTGGCTTCTTCCTTAAT
66 GAAGTTCTCATAGTTGAGAGTGAGAATGCCAATCTTGGACTTCTTAACTTGGCTTCTTCCTTAAT
*
268881 GAGTGACTTCAAGCTTGTTCCAAATTTCTTTAGCATTAGAGCATGAGGACACTCTACTATACTCA
131 GAGTGACTTCAAGCTTGTTCCAAATTTCTTTAGCATTAGAGCATAAGGACACTCTACTATACTCA
* * * *
268946 TCGGGGCCAAGTGCACAAAAAAGAATGTGCATAGCTTTGGCATTGAGTTGAGCTAGCTTCCTATC
196 TCGGGGACAAGTGCACAAAAAAGAATATGCATAGATTTGGCATTAAGTTGAGCTAGCTTCCTATC
* * * *
269011 TTTGTTGGTCCATTCTGACTTATTTCTTGGAGGAGTAGTGAAGTAATAATGATGACATCCTAAAT
261 TTCGTTGGTCCATTCTAACTTATTTCTTGGAGGAGTAGTGAAGCAATAATGATGACATCCCAAAT
269076 CGAGTAATCGGTATTTTGAACGAACAACATCATCATATTCTTCAAATATGAATAATTTGCACCAT
326 CGAGTAATCGG----TT-AACGAACAACATCATCATATTCTTCAAATATGAATAATTTGCACCAT
* * * *
269141 TGAAGCATTGGGGTCTTGTAATAGAATAAGAATCTTCAATATTGTAGGAGCCGAAAGTTGAAGCC
386 TGAAACATTGGGGTCTTGTAATAGAATAAGAATCTTCAATATTATAAGAGCCAAAAGTTGAAGCC
* *
269206 ATCTTTATCGGTTGATTGAAGAAGTTGATAGAGCTATTTTAGGATCTTCACAATGTTGTTAAACT
451 ATCTTTATCGGTTGATTGAAGAAGTTGATAGAGCTATTTTAGGATCTTCACAAGGTTGTTAAACC
* * *
269271 ATCGATTGTGACCCGCTCTTATACCAATTGTTGAGCTCTTATGAACAATCGAAATGTGCCAAGAT
516 ATCGATTGTGACCCACTCTGATACCAATTGTTGAGCTCTTATGAACAATCCAAATGTGCCAAGAT
269336 AAAAGGTGAATTGGCCTTTTAAAGAATTGTGGTGGATGCAATCAAAAAATTAAAAACTTTATACG
581 AAAAGGTGAATTGGCCTTTTAAAGAATTGTGGTGGATGCAATCAAAAAATTAAAAACTTTATACG
* * *
269401 GTGATTTAGAGTGGTTCAAATTCTAAACCAAGTTTACATCCACTACCTTAGTTATCCACACTAAG
646 CTGATTTAGAGTGGTTCAAATTCTAAACCAAGTTTACATCCACTACATTAGTTATCCACACTAAC
*
269466 GATTTCTCAAATCCACTAGATTTGCAAACCTTTGAGGATAAGGTGTAACCTTACAAAGACACACA
711 AATTTCTCAAATCCACTAGATTTGCAAACCTTTGAGGATAAGGTGTAACCTTACAAAGACACACA
*
269531 AGATTTATACCCTAAAGCCTTGCTTACACACTCTCCCAAAGAGAAATTAAAAATTTAGCAAACAA
776 AGATTTATACCCTAAAACCTTGCTTACACACTCTCCCAAAGAGAAATTAAAAATTTAGCAAACAA
269596 AAGAGAAACCTCACA
841 AAGAGAAACCTCACA
*
269611 AAGTCATTTATGATCGTGGTGAACCGATCATACATCATCTTAATGTATTCATCAGGCTTCATCTT
1 AAGTCATTTATGATCGTGGTGAACCGATCAGACATCATCTTAATGTATTCATCAGGCTTCATCTT
* *
269676 GAAGTTCTCATAGTTGAGAGTGAGAATGCCAATCTTGGACTTCTTAACTTGGTTTCTTCCTTCAT
66 GAAGTTCTCATAGTTGAGAGTGAGAATGCCAATCTTGGACTTCTTAACTTGGCTTCTTCCTTAAT
*
269741 GAGTGACTTCAAGCTTGTTCCAAATTTCTTTAGCATTAGA-CATAAGGACACTCTACTATACTTA
131 GAGTGACTTCAAGCTTGTTCCAAATTTCTTTAGCATTAGAGCATAAGGACACTCTACTATACTCA
* * * *
269805 TCGGGGACAAGTTCACAAAAGAGAAATATTCATGGATTTGGCATTAAGTTGAGCTAGCTTCCTAT
196 TCGGGGACAAGTGCACAAAAAAG-AATATGCATAGATTTGGCATTAAGTTGAGCTAGCTTCCTAT
* *
269870 CTTCGTTGGTCCATTCTAACTTGTTTCTTGGAGGAGTAGGTGAA-CCATCAATGAT-AGCATCCC
260 CTTCGTTGGTCCATTCTAACTTATTTCTTGGAGGAGTA-GTGAAGCAAT-AATGATGA-CATCCC
*
269933 AAATTGAGTAATCGG-T-A-GAACAACATCATCATATTCTTCAAATATGAATAATTTGCACCATT
322 AAATCGAGTAATCGGTTAACGAACAACATCATCATATTCTTCAAATATGAATAATTTGCACCATT
* *
269995 GAAACATTGGGGTCTTGTAATGGAATGAGAATCTTCAATATTATAAGAGCCAAAAGTTGAAGCCA
387 GAAACATTGGGGTCTTGTAATAGAATAAGAATCTTCAATATTATAAGAGCCAAAAGTTGAAGCCA
*
270060 TCTTTATCGGTTGATTGAAGAAGTTGATAGAGCTCTTTTAGGATCTTCACAAGGTTGTTAAACCA
452 TCTTTATCGGTTGATTGAAGAAGTTGATAGAGCTATTTTAGGATCTTCACAAGGTTGTTAAACCA
* * *
270125 TCGATTGTGACCCATTCTGATACCAATTGTTGAGCTCTTATGAATAATCCAAATGTGCCAAGATG
517 TCGATTGTGACCCACTCTGATACCAATTGTTGAGCTCTTATGAACAATCCAAATGTGCCAAGATA
** * * *
270190 AGGGGTGAATTGGCCTTTTAAAGAATTGTGGTGGATGCAATCGAAAAATTAAAAACTTTGTATGC
582 AAAGGTGAATTGGCCTTTTAAAGAATTGTGGTGGATGCAATCAAAAAATTAAAAACTTTATACGC
* * *
270255 TGATTTAGAGTGGTTCGACTTCTAAACCAAGTTTACATCCACTACATTTGTTATCCACACTAACA
647 TGATTTAGAGTGGTTCAAATTCTAAACCAAGTTTACATCCACTACATTAGTTATCCACACTAACA
*
270320 ATTTCTCAAATCCACTAGATTTGCAAACCTTTGAGGATAAGGTGTAACTTTACAAAGACACACAA
712 ATTTCTCAAATCCACTAGATTTGCAAACCTTTGAGGATAAGGTGTAACCTTACAAAGACACACAA
*
270385 GATTTATACCCTAAAACCTTGCTTACACACTCTCCCAAAGAGAAATTACAAATTTAGCAAACAAA
777 GATTTATACCCTAAAACCTTGCTTACACACTCTCCCAAAGAGAAATTAAAAATTTAGCAAACAAA
270450 AGAGAAACCTCACA
842 AGAGAAACCTCACA
270464 AAG
1 AAG
270467 GCAAATGTGT
Statistics
Matches: 798, Mismatches: 54, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
853 487 0.61
854 1 0.00
856 1 0.00
859 42 0.05
860 237 0.30
861 30 0.04
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (855 bp):
AAGTCATTTATGATCGTGGTGAACCGATCAGACATCATCTTAATGTATTCATCAGGCTTCATCTT
GAAGTTCTCATAGTTGAGAGTGAGAATGCCAATCTTGGACTTCTTAACTTGGCTTCTTCCTTAAT
GAGTGACTTCAAGCTTGTTCCAAATTTCTTTAGCATTAGAGCATAAGGACACTCTACTATACTCA
TCGGGGACAAGTGCACAAAAAAGAATATGCATAGATTTGGCATTAAGTTGAGCTAGCTTCCTATC
TTCGTTGGTCCATTCTAACTTATTTCTTGGAGGAGTAGTGAAGCAATAATGATGACATCCCAAAT
CGAGTAATCGGTTAACGAACAACATCATCATATTCTTCAAATATGAATAATTTGCACCATTGAAA
CATTGGGGTCTTGTAATAGAATAAGAATCTTCAATATTATAAGAGCCAAAAGTTGAAGCCATCTT
TATCGGTTGATTGAAGAAGTTGATAGAGCTATTTTAGGATCTTCACAAGGTTGTTAAACCATCGA
TTGTGACCCACTCTGATACCAATTGTTGAGCTCTTATGAACAATCCAAATGTGCCAAGATAAAAG
GTGAATTGGCCTTTTAAAGAATTGTGGTGGATGCAATCAAAAAATTAAAAACTTTATACGCTGAT
TTAGAGTGGTTCAAATTCTAAACCAAGTTTACATCCACTACATTAGTTATCCACACTAACAATTT
CTCAAATCCACTAGATTTGCAAACCTTTGAGGATAAGGTGTAACCTTACAAAGACACACAAGATT
TATACCCTAAAACCTTGCTTACACACTCTCCCAAAGAGAAATTAAAAATTTAGCAAACAAAAGAG
AAACCTCACA
Found at i:271652 original size:31 final size:31
Alignment explanation
Indices: 271587--271652 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
271577 AATAATCATG
* *
271587 TTGTTACAAATCGATAACATTAGTGACCATT
1 TTGTTACAAATCGATAACATTAATGACCAAT
* ** *
271618 TTGTTACAAATTGATAATTTTAATTACCAAT
1 TTGTTACAAATCGATAACATTAATGACCAAT
271649 TTGT
1 TTGT
271653 CATTTTTTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (31 bp):
TTGTTACAAATCGATAACATTAATGACCAAT
Found at i:272362 original size:105 final size:104
Alignment explanation
Indices: 272183--272389 Score: 299
Period size: 105 Copynumber: 2.0 Consensus size: 104
272173 CATCTATTCA
* * * * *
272183 ATACAATTATCAATATAAATTGTGATGAATTTTTTTACACCAAAAATATATTTTGTGACCATCAA
1 ATACAATTATCAATAGAAATTGTGATAAATTTTTTGACAACAAAAATATATTTTGTGACCACCAA
272248 TATTGTCACACTAAGTATTTTTTTAGTGAACAAATGTTTG
66 TATTGTCACACTAAGTA-TTTTTTAGTGAACAAATGTTTG
* **
272288 ATACCATTATCAATAGAAATTGTGATAAATTTATTTGACAATGAAAATATATTTTGTGACCACCA
1 ATACAATTATCAATAGAAATTGTGATAAATTT-TTTGACAACAAAAATATATTTTGTGACCACCA
* *
272353 ATGTT-TCACACTAAGTATTTTTTAGTGACCAAATGTT
65 ATATTGTCACACTAAGTATTTTTTAGTGAACAAATGTT
272390 CGACACTATT
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
104 19 0.21
105 41 0.45
106 31 0.34
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (104 bp):
ATACAATTATCAATAGAAATTGTGATAAATTTTTTGACAACAAAAATATATTTTGTGACCACCAA
TATTGTCACACTAAGTATTTTTTAGTGAACAAATGTTTG
Found at i:272896 original size:3 final size:3
Alignment explanation
Indices: 272883--272917 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
272873 TAATATATAA
272883 TAT TGAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
272918 TAATTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:280697 original size:22 final size:23
Alignment explanation
Indices: 280669--280719 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
280659 CTTCCAGTGT
* *
280669 TATTTTC-AGTTTCTTACCCATG
1 TATTTTCAAATTTCTTACCCATA
280691 TATTTTCATAATTTCTTACCCATA
1 TATTTTCA-AATTTCTTACCCATA
280715 TATTT
1 TATTT
280720 ATGACAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
24 18 0.72
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.53
Consensus pattern (23 bp):
TATTTTCAAATTTCTTACCCATA
Found at i:283365 original size:22 final size:24
Alignment explanation
Indices: 283333--283380 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
283323 ATATCAAGAC
*
283333 TTAAAAA-TTT-TGTACACTTTTT
1 TTAAAAATTTTCTGCACACTTTTT
*
283355 TTAAAACTTTTCTGCACACTTTTT
1 TTAAAAATTTTCTGCACACTTTTT
283379 TT
1 TT
283381 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 3 0.14
24 13 0.59
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (24 bp):
TTAAAAATTTTCTGCACACTTTTT
Found at i:290365 original size:29 final size:26
Alignment explanation
Indices: 290323--290400 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 26
290313 TAAAATTTAC
*
290323 TTTTTTTTAGTATTTGCTATTAGAGACT
1 TTTTTTTTAATATTTG-TATTAGAGA-T
290351 TATTTTTTTAATATTTGTCATTAGAGAT
1 T-TTTTTTTAATATTTGT-ATTAGAGAT
290379 TTTTTTTTAATATTTGTTATTA
1 TTTTTTTTAATATTTG-TATTA
290401 TGAAGTTGCC
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
27 19 0.41
28 5 0.11
29 22 0.48
ACGTcount: A:0.24, C:0.04, G:0.10, T:0.62
Consensus pattern (26 bp):
TTTTTTTTAATATTTGTATTAGAGAT
Found at i:292181 original size:24 final size:24
Alignment explanation
Indices: 292148--292194 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
292138 AATTCGACTT
*
292148 AATTTGAAAAATTAATT-TTTTTTA
1 AATTTAAAAAATT-ATTATTTTTTA
292172 AATTTAAAAAATTATTATTTTTT
1 AATTTAAAAAATTATTATTTTTT
292195 CAACATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
AATTTAAAAAATTATTATTTTTTA
Found at i:292205 original size:24 final size:24
Alignment explanation
Indices: 292152--292206 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
292142 CGACTTAATT
**
292152 TGAAAAATTAATTTTTTTTAAATT
1 TGAAAAATTAATTTTTTTTAAACA
* *
292176 TAAAAAATT-ATTATTTTTTCAACA
1 TGAAAAATTAATT-TTTTTTAAACA
292200 TGAAAAA
1 TGAAAAA
292207 AATTTAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
TGAAAAATTAATTTTTTTTAAACA
Found at i:293281 original size:28 final size:28
Alignment explanation
Indices: 293220--293306 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
293210 AAATAAAACA
293220 AAAACTAAAAATTAGATATG-TTTTTTT
1 AAAACTAAAAATTAGATATGATTTTTTT
* * *
293247 AATACTAAAGATTAGATATGATTTTTTG
1 AAAACTAAAAATTAGATATGATTTTTTT
* *
293275 AAAACTAAATATTATATATGATTTTTTT
1 AAAACTAAAAATTAGATATGATTTTTTT
293303 AAAA
1 AAAA
293307 ATTAAGAGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
27 18 0.35
28 34 0.65
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (28 bp):
AAAACTAAAAATTAGATATGATTTTTTT
Found at i:294383 original size:33 final size:33
Alignment explanation
Indices: 294341--294411 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
294331 GAATAGACTT
*
294341 GGTTTTGAAGAATCAAACCAGTGGCGGGAACTC
1 GGTTTTGAAGAATCAAACCAGTGGCGGGAACAC
*
294374 GGTTTTGAAGAGTCAAACCAGTGGCGGGAACAC
1 GGTTTTGAAGAATCAAACCAGTGGCGGGAACAC
294407 GGTTT
1 GGTTT
294412 CTGATGCTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (33 bp):
GGTTTTGAAGAATCAAACCAGTGGCGGGAACAC
Found at i:298945 original size:52 final size:55
Alignment explanation
Indices: 298847--298966 Score: 183
Period size: 52 Copynumber: 2.2 Consensus size: 55
298837 TGGGAACATA
*
298847 TATGCATTATGCATCTCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCT
1 TATGCATTCTGCA-CTCTACACTTA-TTTTCTTGTCTATCCAGCTTCTTATATGGCT
*
298904 TATGCATTCTGCA-TCTACAC-TA-TTTCTTGTCTATCCTGCTTCTTATATGGCT
1 TATGCATTCTGCACTCTACACTTATTTTCTTGTCTATCCAGCTTCTTATATGGCT
298956 TATGCATTCTG
1 TATGCATTCTG
298967 AGAAGTCATC
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
52 40 0.66
54 2 0.03
55 7 0.11
57 12 0.20
ACGTcount: A:0.18, C:0.23, G:0.12, T:0.47
Consensus pattern (55 bp):
TATGCATTCTGCACTCTACACTTATTTTCTTGTCTATCCAGCTTCTTATATGGCT
Found at i:303597 original size:21 final size:21
Alignment explanation
Indices: 303544--303583 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
303534 CTGTCACATT
303544 ATCAAC-CACGTGGACTACCAC
1 ATCAACAC-CGTGGACTACCAC
303565 ATCAACACCGTGGACTACC
1 ATCAACACCGTGGACTACC
303584 GTGTCAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.38, G:0.15, T:0.15
Consensus pattern (21 bp):
ATCAACACCGTGGACTACCAC
Found at i:306512 original size:48 final size:48
Alignment explanation
Indices: 306441--306540 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
306431 CATACTTTGT
*
306441 GTATGATGGTCATCGATCGATTTTGTTTAATGCATAAGTTGCATTTTC
1 GTATGATGGTCATCGATCAATTTTGTTTAATGCATAAGTTGCATTTTC
* * *
306489 GTATGATGGTTATCGATCAATTTTGTTTAATGCCTATGTTGCATTTTC
1 GTATGATGGTCATCGATCAATTTTGTTTAATGCATAAGTTGCATTTTC
306537 GTAT
1 GTAT
306541 CAGTATTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46
Consensus pattern (48 bp):
GTATGATGGTCATCGATCAATTTTGTTTAATGCATAAGTTGCATTTTC
Found at i:313488 original size:129 final size:130
Alignment explanation
Indices: 313331--313721 Score: 431
Period size: 129 Copynumber: 3.0 Consensus size: 130
313321 AATGGGTTTC
313331 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAAT-GGGTTTTTTC
1 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTC
*
313395 CGTCTTGAAATGGGAAGTGTAGATGAAGATAGTGAAGGAATTAATTGGAGGAGGAGGAGGGAGGA
66 CGTCTTGAAATGGGAAGTGTAGATGAAGATAGTGAAGGAATTAATTGAAGGAGGAGGAGGGAGGA
* * * * *
313460 TCTTGATTTTGAGGAGTTTTTATTAATGAATAAACTGCTCCAGTTAGA-GGAATGGGGGTTTTTC
1 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTC
* * * * * * ** * *
313524 CGTCTTGAAATTGGAAGGAGGAGGTGGAAAATCA-TAGAAAAGGAGGGTTTTTTTAA-TA--A--
66 CGTCTTGAAATGGGAA-GTGTAGAT-GAAGAT-AGT-G--AAGGA--ATTAATTGAAGGAGGAGG
****
313583 ATGGGTTTC
123 A-GGGAGGA
*
313592 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTATGCAATTAGAGGGAATGGGGTTTTTTC
1 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTT-
*
313657 CCGTCTTGAAATGGGAAGTGTAGATGAAGATAGTGAATGAATTAATTGAAGGAGGAGGA-GGAGG
65 CCGTCTTGAAATGGGAAGTGTAGATGAAGATAGTGAAGGAATTAATTGAAGGAGGAGGAGGGAGG
313721 A
130 A
313722 GGAGGAGGAG
Statistics
Matches: 203, Mismatches: 41, Indels: 35
0.73 0.15 0.13
Matches are distributed among these distances:
127 6 0.03
128 6 0.03
129 72 0.35
130 8 0.04
131 9 0.04
132 55 0.27
133 20 0.10
134 21 0.10
135 1 0.00
136 5 0.02
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.34
Consensus pattern (130 bp):
TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTC
CGTCTTGAAATGGGAAGTGTAGATGAAGATAGTGAAGGAATTAATTGAAGGAGGAGGAGGGAGGA
Found at i:313624 original size:132 final size:133
Alignment explanation
Indices: 313149--313674 Score: 612
Period size: 132 Copynumber: 4.0 Consensus size: 133
313139 AACCTTTCAC
*
313149 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTCT--GAAATGGGTTTCTCTTGATTTTGAGG
1 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTTTAAGAAATGGGTTTCTCTTGATTTTGAGG
** *
313212 AGTTTTTATTAATGAATAAACTGCTCCGGTTAGAGGGAATGGGGGATTTTTCCGTCTTGAAATTG
66 AGTTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGG-TTTTTCCGTCTTGAAATGG
313277 GAAG
130 GAAG
*
313281 GAGGAGGTGGAAAATCATAGAAAAGGAGGG-TTTTTTAATAAATGGGTTTCTCTTGATTTTGAGG
1 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTTTAAGAAATGGGTTTCTCTTGATTTTGAGG
* * * *
313345 AGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAAT-GGGTTTTTTCCGTCTTGAAATGGG
66 AGTTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGGTTTTTCCGTCTTGAAATGGG
313409 AA-
131 AAG
* * * * * * ** * ****
313411 GTGTAGAT-GAAGAT-AGT-G--AAGGA--ATTAATTGGAGGAGGAGGA-GGGAGGATCTTGATT
1 GAGGAGGTGGAAAATCA-TAGAAAAGGAGGGTT-TTTTTA--A-GA-AATGGGTTTCTCTTGATT
*
313468 TTGAGGAGTTTTTATTAATGAATAAACTGCTCCAGTTAGA-GGAATGGGGGTTTTTCCGTCTTGA
60 TTGAGGAGTTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGGTTTTTCCGTCTTGA
*
313532 AATTGGAAG
125 AATGGGAAG
*
313541 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTTTAATAAATGGGTTTCTCTTGATTTTGAGG
1 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTTTAAGAAATGGGTTTCTCTTGATTTTGAGG
* ** * *
313606 AGTTTTTTTTAATGAATAAACTTATGCAATTAGAGGGAATGGGGTTTTTTCCCGTCTTGAAATGG
66 AGTTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGGTTTTT-CCGTCTTGAAATGG
313671 GAAG
130 GAAG
313675 TGTAGATGAA
Statistics
Matches: 323, Mismatches: 50, Indels: 40
0.78 0.12 0.10
Matches are distributed among these distances:
125 1 0.00
126 8 0.02
128 8 0.02
129 78 0.24
130 11 0.03
131 33 0.10
132 82 0.25
133 75 0.23
134 22 0.07
135 3 0.01
136 2 0.01
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.34
Consensus pattern (133 bp):
GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTTTAAGAAATGGGTTTCTCTTGATTTTGAGG
AGTTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGGTTTTTCCGTCTTGAAATGGG
AAG
Found at i:313714 original size:3 final size:3
Alignment explanation
Indices: 313706--313747 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
313696 AATTAATTGA
313706 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
313748 TAATTAAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:316652 original size:20 final size:21
Alignment explanation
Indices: 316627--316674 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
316617 CAGATAGTAG
* *
316627 CGATACTGATGTGG-AGGTAT
1 CGATACTGAAGAGGAAGGTAT
*
316647 CGATAC-CAAGAGGAAGGTAT
1 CGATACTGAAGAGGAAGGTAT
316667 CGATACTG
1 CGATACTG
316675 TAATTGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (21 bp):
CGATACTGAAGAGGAAGGTAT
Found at i:317151 original size:47 final size:47
Alignment explanation
Indices: 317076--317168 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
317066 ATACTTTGTG
317076 TATGATGGTCATCGATCGATTTGTTTAATGCATAAGTTGCATTTTCA
1 TATGATGGTCATCGATCGATTTGTTTAATGCATAAGTTGCATTTTCA
* * * *
317123 TATGATGGTTATTGATCGATTT-TGTTAATGCCTATGTTGCATTTTC
1 TATGATGGTCATCGATCGATTTGT-TTAATGCATAAGTTGCATTTTC
317169 GTATCAGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 1 0.02
47 40 0.98
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (47 bp):
TATGATGGTCATCGATCGATTTGTTTAATGCATAAGTTGCATTTTCA
Found at i:324317 original size:20 final size:20
Alignment explanation
Indices: 324294--324429 Score: 114
Period size: 20 Copynumber: 6.7 Consensus size: 20
324284 ACTGGATGAA
*
324294 TGGTATCAATACCAGAGTGT
1 TGGTATCCATACCAGAGTGT
*
324314 TGGTATCCATACCAGA-TGAAC
1 TGGTATCCATACCAGAGTG--T
* * *
324335 TAGTATCCATAACAGTGTGT
1 TGGTATCCATACCAGAGTGT
* *
324355 TGGTATCGATACCGGAGTGT
1 TGGTATCCATACCAGAGTGT
* *
324375 TGGTATCCATACCGGA-TGAAC
1 TGGTATCCATACCAGAGTG--T
***
324396 TGGTATCCATATTGGAGTGT
1 TGGTATCCATACCAGAGTGT
324416 TGGTATCCATACCA
1 TGGTATCCATACCA
324430 AATGAATAAT
Statistics
Matches: 91, Mismatches: 19, Indels: 12
0.75 0.16 0.10
Matches are distributed among these distances:
19 4 0.04
20 56 0.62
21 27 0.30
22 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (20 bp):
TGGTATCCATACCAGAGTGT
Found at i:324355 original size:41 final size:40
Alignment explanation
Indices: 324288--324367 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 40
324278 ATCAATACTG
* *
324288 GATGAATGGTATCAATACCAGAGTGTTGGTATCCATACCA
1 GATGAATAGTATCAATAACAGAGTGTTGGTATCCATACCA
* * *
324328 GATGAACTAGTATCCATAACAGTGTGTTGGTATCGATACC
1 GATGAA-TAGTATCAATAACAGAGTGTTGGTATCCATACC
324368 GGAGTGTTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 6 0.18
41 28 0.82
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (40 bp):
GATGAATAGTATCAATAACAGAGTGTTGGTATCCATACCA
Found at i:324416 original size:61 final size:61
Alignment explanation
Indices: 324294--324429 Score: 191
Period size: 61 Copynumber: 2.2 Consensus size: 61
324284 ACTGGATGAA
*
324294 TGGTATCAATACCAGAGTGTTGGTATCCATACCAGATGAACTAGTATCCATAACAGTGTGT
1 TGGTATCAATACCAGAGTGTTGGTATCCATACCAGATGAACTAGTATCCATAACAGAGTGT
* * * * ***
324355 TGGTATCGATACCGGAGTGTTGGTATCCATACCGGATGAACTGGTATCCATATTGGAGTGT
1 TGGTATCAATACCAGAGTGTTGGTATCCATACCAGATGAACTAGTATCCATAACAGAGTGT
*
324416 TGGTATCCATACCA
1 TGGTATCAATACCA
324430 AATGAATAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (61 bp):
TGGTATCAATACCAGAGTGTTGGTATCCATACCAGATGAACTAGTATCCATAACAGAGTGT
Found at i:325060 original size:32 final size:32
Alignment explanation
Indices: 325023--325172 Score: 124
Period size: 32 Copynumber: 4.7 Consensus size: 32
325013 ATCTGCTACC
* *
325023 CATTATCTAAATGTTATACTGACACTCTTATG
1 CATTATCTGAATGTTATACTGACTCTCTTATG
*** * * * *
325055 CATTATCTGAATACAACATTAACTCTGTTATG
1 CATTATCTGAATGTTATACTGACTCTCTTATG
* *
325087 CATTATTTGAATGTTATACTGACTCTAC-TGTG
1 CATTATCTGAATGTTATACTGACTCT-CTTATG
* *
325119 CATTATATGAATGTTATACTGACTCTAC-TGTG
1 CATTATCTGAATGTTATACTGACTCT-CTTATG
* **
325151 AATTATCTGAATGCAATACTGA
1 CATTATCTGAATGTTATACTGA
325173 AACTATTATA
Statistics
Matches: 94, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
32 94 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (32 bp):
CATTATCTGAATGTTATACTGACTCTCTTATG
Found at i:325900 original size:19 final size:18
Alignment explanation
Indices: 325881--325929 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
325871 GTTGATTTTA
325881 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
325899 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
325918 AAATAAACAAAT
1 AAATAAA-AAAT
325930 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:328366 original size:4 final size:5
Alignment explanation
Indices: 328332--328392 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
328322 TAAGCATCTG
** * *
328332 ATAAA ATAAA ATAAA AT-AA ATGGA ATGAA AT-AA ATAAA ATGAAA ATGAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA
328381 ATGAAA ATAAA A
1 AT-AAA ATAAA A
328393 CGAAATGGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
4 8 0.17
5 31 0.65
6 9 0.19
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:328372 original size:14 final size:14
Alignment explanation
Indices: 328335--328375 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
328325 GCATCTGATA
*
328335 AAATAAAATAAAAT
1 AAATAAAATGAAAT
**
328349 AAATGGAATGAAAT
1 AAATAAAATGAAAT
328363 AAATAAAATGAAA
1 AAATAAAATGAAA
328376 ATGAAATGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (14 bp):
AAATAAAATGAAAT
Found at i:328397 original size:11 final size:11
Alignment explanation
Indices: 328334--328397 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 11
328324 AGCATCTGAT
328334 AAAATAAAAT-
1 AAAATAAAATG
328344 AAAAT-AAATG
1 AAAATAAAATG
* *
328354 -GAATGAAAT-
1 AAAATAAAATG
328363 -AAATAAAATG
1 AAAATAAAATG
*
328373 AAAATGAAATG
1 AAAATAAAATG
*
328384 AAAATAAAACG
1 AAAATAAAATG
328395 AAA
1 AAA
328398 TGGGTTGTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
9 14 0.32
10 9 0.20
11 21 0.48
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:331168 original size:5 final size:5
Alignment explanation
Indices: 331158--331224 Score: 57
Period size: 5 Copynumber: 13.0 Consensus size: 5
331148 ATATATATAT
* *
331158 TAAAA TAAAA TAAAA TAAAA T-AAA GAAAA TAATA TAATAA T-AAA TAATAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA TAA-AA
*
331208 TAGTAA TAAATA TAAAA
1 TA-AAA TAAA-A TAAAA
331225 GGGAAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
4 6 0.12
5 29 0.58
6 15 0.30
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (5 bp):
TAAAA
Found at i:331186 original size:19 final size:20
Alignment explanation
Indices: 331164--331201 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
331154 ATATTAAAAT
331164 AAAATAAAATAA-AATAAAG
1 AAAATAAAATAATAATAAAG
*
331183 AAAATAATATAATAATAAA
1 AAAATAAAATAATAATAAA
331202 TAATAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAATAAAATAATAATAAAG
Found at i:331216 original size:16 final size:15
Alignment explanation
Indices: 331184--331219 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
331174 AAAATAAAGA
331184 AAATAATATAATAAT
1 AAATAATATAATAAT
*
331199 AAATAATAATAGTAAT
1 AAATAAT-ATAATAAT
331215 AAATA
1 AAATA
331220 TAAAAGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAATAATATAATAAT
Found at i:331271 original size:19 final size:19
Alignment explanation
Indices: 331249--331298 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
331239 AGTTGTTTTA
331249 AAATAAAAAAATAAGAATT
1 AAATAAAAAAATAAGAATT
*
331268 AAATAAAAGAAA-AATAATT
1 AAATAAAA-AAATAAGAATT
*
331287 AAATAAATAAAT
1 AAATAAAAAAAT
331299 TAAAGATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
AAATAAAAAAATAAGAATT
Found at i:332579 original size:19 final size:20
Alignment explanation
Indices: 332523--332579 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 20
332513 CTATTTAAAC
**
332523 TAAAATACCTAAAAAATAATA
1 TAAAATA-CTAAAACCTAATA
* * *
332544 TAATATTCTAAATCCTAAT-
1 TAAAATACTAAAACCTAATA
332563 TAAAATACTAAAACCTA
1 TAAAATACTAAAACCTA
332580 TTTCAACTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 14 0.50
20 9 0.32
21 5 0.18
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAATACTAAAACCTAATA
Found at i:337768 original size:32 final size:32
Alignment explanation
Indices: 337732--337840 Score: 89
Period size: 32 Copynumber: 3.4 Consensus size: 32
337722 TCTGCTACGT
337732 ATTATATAAATGCTATACTGACACTCTTGTGC
1 ATTATATAAATGCTATACTGACACTCTTGTGC
* * *
337764 ATTATATGAATGC-A-ACATTA-ACTCTGTCATGC
1 ATTATATAAATGCTATAC-TGACACTCT-T-GTGC
* * * ** *
337796 ATTATCTGAATGTTATACTGACTTTATTGTGC
1 ATTATATAAATGCTATACTGACACTCTTGTGC
337828 ATTATATAAATGC
1 ATTATATAAATGC
337841 AATGTTGAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
30 7 0.12
31 4 0.07
32 39 0.67
33 4 0.07
34 4 0.07
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (32 bp):
ATTATATAAATGCTATACTGACACTCTTGTGC
Found at i:338197 original size:28 final size:28
Alignment explanation
Indices: 338155--338220 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
338145 GAAAAATGTG
*
338155 ATGTTTCTAGATGTTACTGTTATTGTTT
1 ATGTTTCTAGATGTTACTGTTACTGTTT
*
338183 ATGTTTCTAGTTGTTACTGTTACTGTTT
1 ATGTTTCTAGATGTTACTGTTACTGTTT
*
338211 ATATTTCTAG
1 ATGTTTCTAG
338221 CTATTGTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.18, C:0.09, G:0.17, T:0.56
Consensus pattern (28 bp):
ATGTTTCTAGATGTTACTGTTACTGTTT
Found at i:338844 original size:20 final size:21
Alignment explanation
Indices: 338819--338874 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
338809 ATTTGGATAG
* *
338819 GTAGTATCGATACTCTA-GTT
1 GTAGTATCGATACCCTAGGGT
*
338839 GTAGTATCGATGCCCTAGGGT
1 GTAGTATCGATACCCTAGGGT
*
338860 GAAGTATCGATACCC
1 GTAGTATCGATACCC
338875 CTATGAGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
GTAGTATCGATACCCTAGGGT
Found at i:340393 original size:118 final size:117
Alignment explanation
Indices: 340146--340393 Score: 313
Period size: 117 Copynumber: 2.1 Consensus size: 117
340136 CGCTCAGGGC
* *
340146 TAACAATTTTTTTGTATTTATAATTAGGGCCTCTAATTTTCATAAATTAATAAAATTTTAGTTTT
1 TAACCATTTTTTTATATTTATAATTAGGGCCTCTAATTTT-ATAAATTAATAAAATTTTAGTTTT
** * *
340211 TGACCCTCTTTTTTTTATTTTTCTTATTAATTCATCCAATTTTGAATTTAATT
65 TGACCCTCTTTTTTCCATTTCTCTTATTAATTCATCCAATTTTGAATTAAATT
* * *
340264 TAACCATTTTTTTATATTTATAATTGGGGCC-CTTAATATTT-TAAGTTCATAAAATGTTTAGTT
1 TAACCATTTTTTTATATTTATAATTAGGGCCTC-TAAT-TTTATAAATTAATAAAAT-TTTAGTT
* * *
340327 TTTTACCCTC-TTTTTCCATTTCTCTTATTTATTCATTCAATTTTGAATTAAATT
63 TTTGACCCTCTTTTTTCCATTTCTCTTATTAATTCATCCAATTTTGAATTAAATT
* *
340381 TAATCATGTTTTT
1 TAACCATTTTTTT
340394 CTCTTTTTTT
Statistics
Matches: 113, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
117 62 0.55
118 48 0.42
119 3 0.03
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.54
Consensus pattern (117 bp):
TAACCATTTTTTTATATTTATAATTAGGGCCTCTAATTTTATAAATTAATAAAATTTTAGTTTTT
GACCCTCTTTTTTCCATTTCTCTTATTAATTCATCCAATTTTGAATTAAATT
Found at i:348192 original size:15 final size:14
Alignment explanation
Indices: 348172--348210 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
348162 TTTAATTCTA
348172 AATTAATTAAATTG
1 AATTAATTAAATTG
**
348186 AATTTAATTATTTTG
1 AA-TTAATTAAATTG
348201 AATTAATTAA
1 AATTAATTAA
348211 CCATTAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (14 bp):
AATTAATTAAATTG
Found at i:358052 original size:12 final size:12
Alignment explanation
Indices: 358029--358063 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
358019 CCCAAATCGT
358029 AAACTCAACATA
1 AAACTCAACATA
358041 AATACT-AACATA
1 AA-ACTCAACATA
358053 AAACTCAACAT
1 AAACTCAACAT
358064 TTAAGTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (12 bp):
AAACTCAACATA
Found at i:369884 original size:31 final size:30
Alignment explanation
Indices: 369829--369905 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
369819 TAAATTTTAA
* *
369829 AAATATCTTTTATTTTTGTTTTAACTTATT
1 AAATATATTTTATTTTTGTTTTAACTTACT
369859 AAATATATTTTATTTTT-TTACTTAACTTACT
1 AAATATATTTTATTTTTGTT--TTAACTTACT
*
369890 AAATATTTTTTATTTT
1 AAATATATTTTATTTT
369906 AATGTAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.05
30 16 0.38
31 24 0.57
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.62
Consensus pattern (30 bp):
AAATATATTTTATTTTTGTTTTAACTTACT
Found at i:370016 original size:29 final size:29
Alignment explanation
Indices: 369984--370074 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
369974 ATATATTTAA
369984 ATAGTTTATTATTAATTTAATATAAAAAT
1 ATAGTTTATTATTAATTTAATATAAAAAT
* *
370013 ATAGATTTATT-TTTATCTTCACT-TAAAAAT
1 ATAG-TTTATTATTAAT-TT-AATATAAAAAT
* * *
370043 TTATTTTATTATTATTTTAA-ATTAAAAAT
1 ATAGTTTATTATTAATTTAATA-TAAAAAT
370072 ATA
1 ATA
370075 TATTTTATTC
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
28 1 0.02
29 25 0.52
30 20 0.42
31 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (29 bp):
ATAGTTTATTATTAATTTAATATAAAAAT
Found at i:370088 original size:55 final size:57
Alignment explanation
Indices: 369988--370095 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 57
369978 ATTTAAATAG
369988 TTTATTATTAATTTAATATAAAAATATAGATTTATTTTTATCTTCACTTAAAAATTTAT
1 TTTATTATTAATTTAATATAAAAATATA-A-TTATTTTTATCTTCACTTAAAAATTTAT
*
370047 TTTATTATTATTTTAA-ATTAAAAATAT-A-TA-TTTTATTCTTCACTTAAAA
1 TTTATTATTAATTTAATA-TAAAAATATAATTATTTTTA-TCTTCACTTAAAA
370096 GTTAAGATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
54 5 0.11
55 15 0.33
57 1 0.02
58 1 0.02
59 24 0.52
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.53
Consensus pattern (57 bp):
TTTATTATTAATTTAATATAAAAATATAATTATTTTTATCTTCACTTAAAAATTTAT
Found at i:370166 original size:30 final size:30
Alignment explanation
Indices: 370130--370206 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
370120 ATAATGAAAT
370130 AAAAATAAAATATATTTAATAAG-TTAAGAC
1 AAAAATAAAATATATTTAATAAGTTTAA-AC
370160 AAAAATAAAATATATTTAATAAGTTTAAAC
1 AAAAATAAAATATATTTAATAAGTTTAAAC
*
370190 AAAATTAAAATATATTT
1 AAAAATAAAATATATTT
370207 TTAAAATTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 41 0.91
31 4 0.09
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAAATAAAATATATTTAATAAGTTTAAAC
Found at i:371752 original size:3 final size:3
Alignment explanation
Indices: 371736--371780 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
371726 TGACACGATA
371736 ATT A-T ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
371781 TATAATAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:373015 original size:37 final size:37
Alignment explanation
Indices: 372960--373066 Score: 205
Period size: 37 Copynumber: 2.9 Consensus size: 37
372950 CAATTATATT
*
372960 AGTTTATTATTTTGTGAAGATCAAAGATGAGACCTTG
1 AGTTTATTATTTTATGAAGATCAAAGATGAGACCTTG
372997 AGTTTATTATTTTATGAAGATCAAAGATGAGACCTTG
1 AGTTTATTATTTTATGAAGATCAAAGATGAGACCTTG
373034 AGTTTATTATTTTATGAAGATCAAAGATGAGAC
1 AGTTTATTATTTTATGAAGATCAAAGATGAGAC
373067 GGTCAAAATC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (37 bp):
AGTTTATTATTTTATGAAGATCAAAGATGAGACCTTG
Found at i:375845 original size:41 final size:41
Alignment explanation
Indices: 375794--375876 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
375784 TGGTTGAAAC
375794 TAATTACATATTTGGATAAACTTGAGGTTGAAATTGAAATA
1 TAATTACATATTTGGATAAACTTGAGGTTGAAATTGAAATA
375835 TAATTACATATTTGGATAAACTTGAGGTTGAAATTGAAATA
1 TAATTACATATTTGGATAAACTTGAGGTTGAAATTGAAATA
375876 T
1 T
375877 TCAAAAGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (41 bp):
TAATTACATATTTGGATAAACTTGAGGTTGAAATTGAAATA
Found at i:376594 original size:70 final size:70
Alignment explanation
Indices: 376508--376648 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
376498 GACAGCTGGA
376508 AAGAAAAACTAGCAGAAAAGGAAACAATTCTAGAAGGCAACACTCAATCTATCTACTCAAATGAC
1 AAGAAAAACTAGCAGAAAAGGAAACAATTCTAGAAGGCAACACTCAATCTATCTACTCAAATGAC
376573 CTCAC
66 CTCAC
*
376578 AAGATAAACTAGCAGAAAAGGAAACAATTCTAGAAGGCAACACTCAATCTATCTACTCAAATGAC
1 AAGAAAAACTAGCAGAAAAGGAAACAATTCTAGAAGGCAACACTCAATCTATCTACTCAAATGAC
376643 CTCAC
66 CTCAC
376648 A
1 A
376649 CTAGCATCCA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.47, C:0.23, G:0.13, T:0.18
Consensus pattern (70 bp):
AAGAAAAACTAGCAGAAAAGGAAACAATTCTAGAAGGCAACACTCAATCTATCTACTCAAATGAC
CTCAC
Found at i:381677 original size:25 final size:25
Alignment explanation
Indices: 381648--381696 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
381638 GTATAGGGGC
381648 ATAAAATTATTATCTCGCCCAGGGT
1 ATAAAATTATTATCTCGCCCAGGGT
*
381673 ATAAAATTATTATCTCGCCTAGGG
1 ATAAAATTATTATCTCGCCCAGGG
381697 CATTAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (25 bp):
ATAAAATTATTATCTCGCCCAGGGT
Found at i:401325 original size:12 final size:12
Alignment explanation
Indices: 401308--401337 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
401298 AACCAATTTT
401308 TCCTTTCCCTTA
1 TCCTTTCCCTTA
401320 TCCTTTCCCTTA
1 TCCTTTCCCTTA
401332 TCCTTT
1 TCCTTT
401338 TAGCTTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (12 bp):
TCCTTTCCCTTA
Found at i:409114 original size:305 final size:305
Alignment explanation
Indices: 408556--409166 Score: 1190
Period size: 306 Copynumber: 2.0 Consensus size: 305
408546 TCGACGCCGT
408556 TTGAAGAGTATGTCAGAATGTGAGAAACCTCATTCACCCCAATCCCTAAAGGCCTAGGACCCCCT
1 TTGAAGAGTATGTCAGAATGTGAGAAACCTCATTCACCCCAATCCCTAAAGGCCTAGGACCCCCT
408621 ACTGAACCACCAATAGATTTGAATACTACAACCTCACACTATTGCACAAGCGCTCGCGTTGCAAG
66 ACTGAACCACCAATAGATTTGAATACTACAACCTCACACTATTGCACAAGCGCTCGCGTTGCAAG
408686 CCGCACGACATCAATAACACCACCACCATAAATAGCCAAGGTACCTTGCATTGCATTACATAACA
131 CCGCACGACATCAATAACACCACCACCATAAATAGCCAAGGTACCTTGCATTGCATTACATAACA
408751 TGTAGTCTAGTTTTACCTTAGTTTTTATTTAGCATTAAGGATAATGATTCTCTCAAGTTTGGGGG
196 TGTAGTCTAGTTTTACCTTAGTTTTTATTTAGCATTAAGGATAATGATTCTCTCAAGTTTGGGGG
408816 AGGTAGGGTTCCCAAGTCATTGCTTGATAGTATTAGTAGAATGAA
261 AGGTAGGGTTCCCAAGTCATTGCTTGATAGTATTAGTAGAATGAA
408861 TTGAAGAGTATGTCAGAATGTGAGAAACCTCAATTCA-CCCAATCCCTAAAGGCCTTAGGACCCC
1 TTGAAGAGTATGTCAGAATGTGAGAAACCTC-ATTCACCCCAATCCCTAAAGGCC-TAGGACCCC
408925 CTACTGAACCACCAATAGATTTGAATACTACAACCTCACACTATTGCACAAGCGCTCGCGTTGCA
64 CTACTGAACCACCAATAGATTTGAATACTACAACCTCACACTATTGCACAAGCGCTCGCGTTGCA
408990 AGCCGCACGACATCAATAACACCACCACCATAAATAGCCAAGGTACCTTGCATTGCATTACATAA
129 AGCCGCACGACATCAATAACACCACCACCATAAATAGCCAAGGTACCTTGCATTGCATTACATAA
409055 CATGTAGTCTAG-TTTACCTTAGTTTTTATTTAGCATTAAGGATAATGATTCTCTCAAGTTTGGG
194 CATGTAGTCTAGTTTTACCTTAGTTTTTATTTAGCATTAAGGATAATGATTCTCTCAAGTTTGGG
409119 GGAGGTAGGGTTCCCAAGTCATTGCTTGATAGTATTAGTAGAATGAA
259 GGAGGTAGGGTTCCCAAGTCATTGCTTGATAGTATTAGTAGAATGAA
409166 T
1 T
409167 ATGCCATGAC
Statistics
Matches: 304, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
305 148 0.49
306 156 0.51
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (305 bp):
TTGAAGAGTATGTCAGAATGTGAGAAACCTCATTCACCCCAATCCCTAAAGGCCTAGGACCCCCT
ACTGAACCACCAATAGATTTGAATACTACAACCTCACACTATTGCACAAGCGCTCGCGTTGCAAG
CCGCACGACATCAATAACACCACCACCATAAATAGCCAAGGTACCTTGCATTGCATTACATAACA
TGTAGTCTAGTTTTACCTTAGTTTTTATTTAGCATTAAGGATAATGATTCTCTCAAGTTTGGGGG
AGGTAGGGTTCCCAAGTCATTGCTTGATAGTATTAGTAGAATGAA
Found at i:410069 original size:20 final size:20
Alignment explanation
Indices: 410040--410078 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
410030 ATAGCTCATA
*
410040 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
410060 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
410079 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:411537 original size:22 final size:22
Alignment explanation
Indices: 411495--411537 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
411485 TCAATTTACT
* *
411495 TTTTCCAATACATTTCTATTTA
1 TTTTCCAATACATATCCATTTA
411517 TTTTCCACA-ACATATCCATTT
1 TTTTCCA-ATACATATCCATTT
411538 GATGCCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTCCAATACATATCCATTTA
Found at i:414909 original size:2 final size:2
Alignment explanation
Indices: 414904--415044 Score: 112
Period size: 2 Copynumber: 71.0 Consensus size: 2
414894 TGTGTGTGTG
*
414904 TA TA TA TA TA TA TA TA TT TGA -A TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
* * * * *
414945 TA TA TA TA TA TA TA TA TA TA TA -A TA TT TT TGA AA AA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * * * *
414987 TA GT- TT TT TA -A TA TA TA TA TA TA TA TA TG TA TA CA GTG TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
415029 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
415045 GTATGAGTTA
Statistics
Matches: 115, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
1 5 0.04
2 109 0.95
3 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:418556 original size:18 final size:19
Alignment explanation
Indices: 418533--418568 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
418523 CCAGTAATCA
*
418533 TATTCC-CTGGTAATCTTT
1 TATTCCACTGATAATCTTT
418551 TATTCCACTGATAATCTT
1 TATTCCACTGATAATCTT
418569 ACTTTCGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (19 bp):
TATTCCACTGATAATCTTT
Found at i:422438 original size:19 final size:20
Alignment explanation
Indices: 422411--422448 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
422401 GCATTTTCAA
*
422411 TTATGGCATTCGTTCATGCC
1 TTATGGCATCCGTTCATGCC
*
422431 TTAT-GCATCCTTTCATGC
1 TTATGGCATCCGTTCATGC
422449 ATTTTCAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (20 bp):
TTATGGCATCCGTTCATGCC
Found at i:422536 original size:20 final size:20
Alignment explanation
Indices: 422513--422633 Score: 80
Period size: 20 Copynumber: 5.3 Consensus size: 20
422503 TAGGCATCTG
422513 TTCATGCCTTAATGCATCCT
1 TTCATGCCTTAATGCATCCT
* *
422533 TTCATGCATTTTTAATTATGGCATCCA
1 TTCATGC---CTT-A--AT-GCATCCT
422560 TTCATGCCTTAATGCATCCT
1 TTCATGCCTTAATGCATCCT
* *
422580 TTCATGCATTTTCAATTATGACATCCG
1 TTCATGC--CTT--A--ATG-CATCCT
422607 TTCATGCCTTAATGCATCCT
1 TTCATGCCTTAATGCATCCT
422627 TTCATGC
1 TTCATGC
422634 ATTTTCAATT
Statistics
Matches: 79, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
20 32 0.41
21 5 0.06
22 2 0.03
23 4 0.05
24 4 0.05
25 2 0.03
26 5 0.06
27 25 0.32
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (20 bp):
TTCATGCCTTAATGCATCCT
Found at i:422553 original size:91 final size:93
Alignment explanation
Indices: 422398--422646 Score: 391
Period size: 91 Copynumber: 2.7 Consensus size: 93
422388 TTATTTCATG
*
422398 CATGCATTTTCAATTATGGCAT-TCGTTCATGCCTT-ATGCATCCTTTCATGCATTTTCAACTAT
1 CATGCATTTTCAATTATGGCATCT-GTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTAT
*
422461 GGCATCCGTATCATGCCTT-AT-ATCCTTT
65 GGCATCCAT-TCATGCCTTAATCATCCTTT
*
422489 CATGCATTTTCAATTA-GGCATCTGTTCATGCCTTAATGCATCCTTTCATGCATTTTTAATTATG
1 CATGCATTTTCAATTATGGCATCTGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
422553 GCATCCATTCATGCCTTAATGCATCCTTT
66 GCATCCATTCATGCCTTAAT-CATCCTTT
* *
422582 CATGCATTTTCAATTATGACATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
1 CATGCATTTTCAATTATGGCATCTGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
422647 AATTTGATTT
Statistics
Matches: 146, Mismatches: 6, Indels: 9
0.91 0.04 0.06
Matches are distributed among these distances:
90 25 0.17
91 53 0.36
93 23 0.16
94 45 0.31
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (93 bp):
CATGCATTTTCAATTATGGCATCTGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
GCATCCATTCATGCCTTAATCATCCTTT
Found at i:422564 original size:27 final size:27
Alignment explanation
Indices: 422526--422613 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
422516 ATGCCTTAAT
422526 GCATCCTTTCATGCATTTTTAATTATG
1 GCATCCTTTCATGCATTTTTAATTATG
* *
422553 GCATCCATTCATGC---CTT-A--AT-
1 GCATCCTTTCATGCATTTTTAATTATG
*
422573 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTTAATTATG
* *
422600 ACATCCGTTCATGC
1 GCATCCTTTCATGC
422614 CTTAATGCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
20 13 0.28
21 2 0.04
23 2 0.04
24 3 0.06
26 2 0.04
27 25 0.53
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (27 bp):
GCATCCTTTCATGCATTTTTAATTATG
Found at i:422647 original size:47 final size:47
Alignment explanation
Indices: 422398--422646 Score: 400
Period size: 47 Copynumber: 5.4 Consensus size: 47
422388 TTATTTCATG
*
422398 CATGCATTTTCAATTATGGCATTCGTTCATGCCTT-ATGCATCCTTT
1 CATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTT
*
422444 CATGCATTTTCAACTATGGCATCCGTATCATGCCTT-AT--ATCCTTT
1 CATGCATTTTCAATTATGGCATCCGT-TCATGCCTTAATGCATCCTTT
*
422489 CATGCATTTTCAATTA-GGCATCTGTTCATGCCTTAATGCATCCTTT
1 CATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTT
* *
422535 CATGCATTTTTAATTATGGCATCCATTCATGCCTTAATGCATCCTTT
1 CATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTT
*
422582 CATGCATTTTCAATTATGACATCCGTTCATGCCTTAATGCATCCTTT
1 CATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTT
422629 CATGCATTTTCAATTATG
1 CATGCATTTTCAATTATG
422647 AATTTGATTT
Statistics
Matches: 188, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
43 9 0.05
44 10 0.05
45 22 0.12
46 46 0.24
47 101 0.54
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (47 bp):
CATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTT
Found at i:429078 original size:47 final size:47
Alignment explanation
Indices: 428986--429295 Score: 464
Period size: 47 Copynumber: 6.6 Consensus size: 47
428976 CGTATTAACA
*
428986 CATCCATTT-ATGCATTTT-AATATACATGGCATCCTTTCATGCCTTAATG
1 CATCC-TTTCATGCATTTTCAAT-T--ATGGCATCCGTTCATGCCTTAATG
* *
429035 CATCCTTTCATGTATTTTCAATTATGGCATCCGTTCATACCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
*
429082 CATCCTTTCATGCATTTTCAATTATGGCACCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
** *
429129 CATCCTTTCATGCATTTTCAATTATGTTATCCATTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
* *
429176 CATCCTTTCATGCATTTTCAATTTTGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
429223 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAAAT-
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTT-AATG
*
429270 CATCCTTTCTTGCATTTTCAATTATG
1 CATCCTTTCATGCATTTTCAATTATG
429296 AATTTGATTT
Statistics
Matches: 241, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
47 218 0.90
48 6 0.02
49 14 0.06
50 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.43
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
Found at i:429733 original size:22 final size:20
Alignment explanation
Indices: 429683--429736 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
429673 CCAGGCTCCA
* * *
429683 TAGTATCGATAGTTCTATCC
1 TAGTACCGATACTTCTATAC
429703 TAGTACCGATACTTCTATAC
1 TAGTACCGATACTTCTATAC
429723 TATGGTACCGATAC
1 TA--GTACCGATAC
429737 CCCCTTCCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 19 0.66
22 10 0.34
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (20 bp):
TAGTACCGATACTTCTATAC
Found at i:429878 original size:95 final size:95
Alignment explanation
Indices: 429717--429904 Score: 254
Period size: 95 Copynumber: 2.0 Consensus size: 95
429707 ACCGATACTT
* * * * * *
429717 CTATACTATGGTACCGATACCCCCTTCCGGTATCAATACCGAAATTAGCTTCAATGTTTCATGGT
1 CTATACTATGGTACCGATACCCCCTTCCGGAATCAACACCAAAATTAGATCCAATGTTTCAAGGT
* *
429782 ATCGATACCCTTACCAC-AGTATCGATACGA
66 ATCGAAACCCTTACAACGA-TATCGATACGA
* *
429812 CTATACTATGGTACCGATA-CCCCTTCCGGAATCGACACCAAAATTAGATCCAGTGTTTGCAAGG
1 CTATACTATGGTACCGATACCCCCTTCCGGAATCAACACCAAAATTAGATCCAATGTTT-CAAGG
429876 TATCGAAACCCTTACAACGATATCGATAC
65 TATCGAAACCCTTACAACGATATCGATAC
429905 TGTCTCAACG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
94 32 0.40
95 48 0.59
96 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (95 bp):
CTATACTATGGTACCGATACCCCCTTCCGGAATCAACACCAAAATTAGATCCAATGTTTCAAGGT
ATCGAAACCCTTACAACGATATCGATACGA
Found at i:432763 original size:14 final size:14
Alignment explanation
Indices: 432736--432771 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
432726 AAGTCAACAG
* *
432736 GTTGAATCAGGCGA
1 GTTGACTCAAGCGA
432750 GTTGACTCAAGCGA
1 GTTGACTCAAGCGA
432764 GTTGACTC
1 GTTGACTC
432772 GGTTTAGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (14 bp):
GTTGACTCAAGCGA
Found at i:448123 original size:20 final size:22
Alignment explanation
Indices: 448100--448146 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
448090 TTTTTTGAAA
*
448100 TTTTGGCTTTT-TTG-TTTTTT
1 TTTTGCCTTTTCTTGCTTTTTT
448120 TTTTGCCTTTTCTTGCCTTTTTT
1 TTTTGCCTTTTCTTG-CTTTTTT
448143 TTTT
1 TTTT
448147 TGAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 3 0.13
23 10 0.43
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.77
Consensus pattern (22 bp):
TTTTGCCTTTTCTTGCTTTTTT
Found at i:460297 original size:59 final size:59
Alignment explanation
Indices: 460205--460324 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
460195 ACACCCTAAG
* *
460205 ATTGAAATGAGCATAGATGTATAGTTTGTATACGTTACTAAAATATATCTACAGTTAAT
1 ATTGAAATGAGCATAGATGTACAGTTTATATACGTTACTAAAATATATCTACAGTTAAT
*
460264 ATTGAAATGAGCATAGATGTACAGTTTATATACGTTACTAAAATATATCTATAGTTAAT
1 ATTGAAATGAGCATAGATGTACAGTTTATATACGTTACTAAAATATATCTACAGTTAAT
460323 AT
1 AT
460325 ATGTATATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (59 bp):
ATTGAAATGAGCATAGATGTACAGTTTATATACGTTACTAAAATATATCTACAGTTAAT
Found at i:464487 original size:14 final size:15
Alignment explanation
Indices: 464468--464507 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
464458 TAACTATTTT
464468 TCAAAGTCAACGA-G
1 TCAAAGTCAACGATG
*
464482 TCAAAGTCAAC-ATT
1 TCAAAGTCAACGATG
464496 TCAAAGTCAACG
1 TCAAAGTCAACG
464508 GGTTGACTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (15 bp):
TCAAAGTCAACGATG
Found at i:465179 original size:2 final size:2
Alignment explanation
Indices: 465168--465208 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
465158 TTTTAATCTA
465168 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
465209 TAAAAATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:465459 original size:10 final size:10
Alignment explanation
Indices: 465446--465495 Score: 73
Period size: 10 Copynumber: 5.0 Consensus size: 10
465436 AATTTCAATT
*
465446 TTTAATTAAA
1 TTTATTTAAA
*
465456 TTTATTTTAA
1 TTTATTTAAA
*
465466 TTTATTTTAA
1 TTTATTTAAA
465476 TTTATTTAAA
1 TTTATTTAAA
465486 TTTATTTAAA
1 TTTATTTAAA
465496 AGTGGGTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATTTAAA
Found at i:465465 original size:15 final size:15
Alignment explanation
Indices: 465445--465492 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
465435 TAATTTCAAT
465445 TTTTAATTAAATTTA
1 TTTTAATTAAATTTA
* *
465460 TTTTAATTTATTTTA
1 TTTTAATTAAATTTA
* *
465475 ATTTATTTAAATTTA
1 TTTTAATTAAATTTA
465490 TTT
1 TTT
465493 AAAAGTGGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATTAAATTTA
Found at i:466097 original size:232 final size:232
Alignment explanation
Indices: 465691--466150 Score: 776
Period size: 232 Copynumber: 2.0 Consensus size: 232
465681 ATATGCCTAC
** *
465691 TAAAGTTACAATACAATACTCTGACGGAGAATGTTGAAAGTGTTGTTGTGACAGTGCTCTACGAA
1 TAAAGTTACAATACAATACTCTGACGGAGAATACTGAAAGTGTTGTTGTGACAGTGCTCCACGAA
* * *
465756 TGGTCCAGGCTAAAAACCTGCTAACAAAAACATCTGAACGCTGAGCTTATAAAGCTCGGTAGTAT
66 TGGTCCAAGCTAAAAACCTGCTAACAAAAACATCTAAACGCTGAGCTTATAAAGCTCAGTAGTAT
* *
465821 AATCTCCAATCTAGAACAACATTATGAGTTTCATAATCACAAGCATACTAAAGACATGGTACTAA
131 AATCTCCAATATAGAACAACATTATGAGTTTCATAATCACAAGCATACTAAAGACACGGTACTAA
465886 GCAGTAGGTACATGCATGATCTTAATCAAGTGTCAAT
196 GCAGTAGGTACATGCATGATCTTAATCAAGTGTCAAT
* * * *
465923 TAAAGTTACAGTACAATACTCTGATGGAGAATACTGAAAGTGTTGTTGTGATAGTGCTCCATGAA
1 TAAAGTTACAATACAATACTCTGACGGAGAATACTGAAAGTGTTGTTGTGACAGTGCTCCACGAA
* *
465988 TGGTCCAAGCTAAAAACCTGCTAACGAAAACATCTAAACGCTGAGCTTATAAAGCTCAGTGGTAT
66 TGGTCCAAGCTAAAAACCTGCTAACAAAAACATCTAAACGCTGAGCTTATAAAGCTCAGTAGTAT
* *
466053 AATCTCTAATATAGAACAACATTATGAGTTTCATAATCACAAGCATGCTAAAGACACGGTACTAA
131 AATCTCCAATATAGAACAACATTATGAGTTTCATAATCACAAGCATACTAAAGACACGGTACTAA
466118 GCAGTAGGTACATGCATGATCTTAATCAAGTGT
196 GCAGTAGGTACATGCATGATCTTAATCAAGTGT
466151 TGCCTACTTA
Statistics
Matches: 212, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
232 212 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (232 bp):
TAAAGTTACAATACAATACTCTGACGGAGAATACTGAAAGTGTTGTTGTGACAGTGCTCCACGAA
TGGTCCAAGCTAAAAACCTGCTAACAAAAACATCTAAACGCTGAGCTTATAAAGCTCAGTAGTAT
AATCTCCAATATAGAACAACATTATGAGTTTCATAATCACAAGCATACTAAAGACACGGTACTAA
GCAGTAGGTACATGCATGATCTTAATCAAGTGTCAAT
Found at i:472025 original size:20 final size:18
Alignment explanation
Indices: 472002--472051 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
471992 CTTGGCTTGC
472002 TTTCTCTTTTTGAATTTCT
1 TTTCTCTTTTTGAATTT-T
472021 TTT-TCTTTTCTGAATTTT
1 TTTCTCTTTT-TGAATTTT
472039 TTTCTTCTTTTTG
1 TTTC-TCTTTTTG
472052 TCTTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 10 0.36
19 12 0.43
20 6 0.21
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (18 bp):
TTTCTCTTTTTGAATTTT
Found at i:472057 original size:16 final size:14
Alignment explanation
Indices: 472038--472071 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
472028 TTCTGAATTT
472038 TTTTCTTCTTTTTGTC
1 TTTTCTT-TTTTT-TC
472054 TTTTCTTTTTTTTC
1 TTTTCTTTTTTTTC
472068 TTTT
1 TTTT
472072 TGCACTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 5 0.28
16 7 0.39
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:476313 original size:43 final size:43
Alignment explanation
Indices: 476252--476337 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
476242 TAAGTTTTGA
476252 AAAAATAAAAAGTTTATGTACTAAAACAGATCAAAACTGATAT
1 AAAAATAAAAAGTTTATGTACTAAAACAGATCAAAACTGATAT
* * *
476295 AAAAATTAAAAGTTTATGTACTAGAACATATCAAAACTGATAT
1 AAAAATAAAAAGTTTATGTACTAAAACAGATCAAAACTGATAT
476338 TTTAAATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (43 bp):
AAAAATAAAAAGTTTATGTACTAAAACAGATCAAAACTGATAT
Found at i:480115 original size:2 final size:2
Alignment explanation
Indices: 480108--480140 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
480098 CATCCCTAAC
480108 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 T
480141 TCATAATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:480969 original size:22 final size:20
Alignment explanation
Indices: 480936--480977 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
480926 TATTCCTTGT
480936 GTTTTTGTTAGCTCCATCGGAG
1 GTTTTTGTTAGC-CC-TCGGAG
480958 GTTTTT-TATAGCCCTCGGAG
1 GTTTTTGT-TAGCCCTCGGAG
480978 AAAGGAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.32
21 3 0.16
22 10 0.53
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.40
Consensus pattern (20 bp):
GTTTTTGTTAGCCCTCGGAG
Found at i:481447 original size:3 final size:3
Alignment explanation
Indices: 481441--481715 Score: 63
Period size: 3 Copynumber: 92.7 Consensus size: 3
481431 AAATGAAAAT
* *
481441 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATAA ATG GT- ATA TATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -ATA
* * * *
481487 AGT- ATA AGA AT- ATA CT- TTA AT- ATA ATA TATA AAA ATA ATA TATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA
* *
481531 ATA ATA AT- ACA ATA A-C ATA AT- ATA AT- ATA TATA ATA ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA -ATA
* * * * *
481574 ATA CT- ATA AT- ATT ATA AT- CTA TATA A-A AT- ATA CTA CTA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA -ATA
* *
481616 ACGT- ATA ATA TATA ATA TATA TACA AT- CTA TATA AT- ATA ATA ATA
1 A--TA ATA ATA -ATA ATA -ATA -ATA ATA ATA -ATA ATA ATA ATA ATA
* * *
481661 ATA ATA ATA ATG ATA AT- GTA AT- ATA AT- ATA TATA AT- ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
481703 CATA ATA TATA AT
1 -ATA ATA -ATA AT
481716 GTCTCAGATG
Statistics
Matches: 202, Mismatches: 31, Indels: 78
0.65 0.10 0.25
Matches are distributed among these distances:
2 34 0.17
3 121 0.60
4 46 0.23
5 1 0.00
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:481514 original size:5 final size:5
Alignment explanation
Indices: 481504--481699 Score: 83
Period size: 5 Copynumber: 38.4 Consensus size: 5
481494 GAATATACTT
* *
481504 TAATA TAATA T-ATA -AAAA TAATA T-ATAA TAATAA TACA-A TAACA
1 TAATA TAATA TAATA TAATA TAATA TAAT-A TAAT-A TA-ATA TAATA
* *
481548 TAATA TAATA T-ATA TAATA -ATATA TAATA CT-ATAA TATTA TAATC
1 TAATA TAATA TAATA TAATA TA-ATA TAATA -TAAT-A TAATA TAATA
* * * *
481593 TATATA AAATA TACTA CT-ATA TAACGTA TAATATA TAATA TATATA CAATC
1 TA-ATA TAATA TAATA -TAATA TAA--TA T-A-ATA TAATA TA-ATA TAATA
*
481644 T-ATA TAATA T-A-A TAATAA TAATAA TAATGA TAATG TAATA TAATA
1 TAATA TAATA TAATA TAAT-A TAAT-A TAAT-A TAATA TAATA TAATA
481689 T-ATA TAATA TA
1 TAATA TAATA TA
481700 CTACATAATA
Statistics
Matches: 148, Mismatches: 18, Indels: 50
0.69 0.08 0.23
Matches are distributed among these distances:
3 2 0.01
4 23 0.16
5 79 0.53
6 35 0.24
7 7 0.05
8 1 0.01
9 1 0.01
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:481526 original size:13 final size:13
Alignment explanation
Indices: 481508--481539 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
481498 ATACTTTAAT
481508 ATAATATATAAAA
1 ATAATATATAAAA
*
481521 ATAATATATAATA
1 ATAATATATAAAA
481534 ATAATA
1 ATAATA
481540 CAATAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATATATAAAA
Found at i:481597 original size:27 final size:27
Alignment explanation
Indices: 481507--481713 Score: 60
Period size: 26 Copynumber: 7.4 Consensus size: 27
481497 TATACTTTAA
* *
481507 TATAATATATAAAAATAATATATAATA-
1 TATAATATATA-TAATAATATAAAATAC
* *
481534 -ATAATACA-ATAACATAATATAATATA-
1 TATAATATATAT-A-ATAATATAAAATAC
* *
481560 TATAATA-ATAT-ATAATACTATAATAT
1 TATAATATATATAATAATA-TAAAATAC
*
481586 TATAATCTATATAA-AATATACTACTATATAAC
1 TATAATATATATAATAATATA--A--A-AT-AC
*
481618 GTAT-A-ATATATAATATATATACAAT-C
1 -TATAATATATATAATA-ATATAAAATAC
*
481644 TAT-ATA-ATATAATAATAATAATAATAA
1 TATAATATATATAATAAT-ATAA-AATAC
* *
481671 TGATAATGTAATATAATATATATAATATAC
1 T-ATAATAT-ATATAATA-ATATAAAATAC
481701 TACATAATATATA
1 T--ATAATATATA
481714 ATGTCTCAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 51
0.66 0.09 0.25
Matches are distributed among these distances:
24 8 0.06
25 22 0.16
26 32 0.24
27 17 0.13
28 5 0.04
29 3 0.02
30 8 0.06
31 27 0.20
32 5 0.04
33 8 0.06
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (27 bp):
TATAATATATATAATAATATAAAATAC
Found at i:482352 original size:18 final size:18
Alignment explanation
Indices: 482306--482353 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
482296 GGGCACGATA
*
482306 TCCTTCGTCGCGGGTGAC
1 TCCTTCGTCGTGGGTGAC
482324 TCCTTCGTCGTGGGTGAC
1 TCCTTCGTCGTGGGTGAC
*
482342 TCCTTCATCGTG
1 TCCTTCGTCGTG
482354 AAGTTGAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.06, C:0.31, G:0.29, T:0.33
Consensus pattern (18 bp):
TCCTTCGTCGTGGGTGAC
Found at i:482457 original size:49 final size:51
Alignment explanation
Indices: 482342--482462 Score: 135
Period size: 49 Copynumber: 2.4 Consensus size: 51
482332 CGTGGGTGAC
* * *
482342 TCCTTCATCGTGAAGTTG-AGTCCAGATTGAATGTTCTTCTGAGCCGAATA
1 TCCTTCATTGTGAAGTTGAAATCCAGATTAAATGTTCTTCTGAGCCGAATA
* * *
482392 TCATTCGTTGTGAAGTTGAAATCCA-ACTTAAATGTTCTTC-GAGTTC-AA-A
1 TCCTTCATTGTGAAGTTGAAATCCAGA-TTAAATGTTCTTCTGAG-CCGAATA
482441 TCCTTCATTGTGAAGTTGAAAT
1 TCCTTCATTGTGAAGTTGAAAT
482463 TGACTGACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
49 21 0.35
50 21 0.35
51 18 0.30
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (51 bp):
TCCTTCATTGTGAAGTTGAAATCCAGATTAAATGTTCTTCTGAGCCGAATA
Found at i:492588 original size:20 final size:20
Alignment explanation
Indices: 492565--492602 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
492555 CAAATGATAA
492565 AAAATAAAA-AGAAATAAGAC
1 AAAATAAAAGA-AAATAAGAC
*
492585 AAAATGAAAGAAAATAAG
1 AAAATAAAAGAAAATAAG
492603 TTAGTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.11
Consensus pattern (20 bp):
AAAATAAAAGAAAATAAGAC
Found at i:494603 original size:7 final size:7
Alignment explanation
Indices: 494593--494678 Score: 68
Period size: 7 Copynumber: 12.1 Consensus size: 7
494583 CAATATAATC
494593 TATATAA
1 TATATAA
* *
494600 TATACAC
1 TATATAA
494607 TATTATAA
1 TA-TATAA
*
494615 TATATAT
1 TATATAA
494622 TATATAA
1 TATATAA
494629 TA-ATAA
1 TATATAA
*
494635 TACTGTAA
1 TA-TATAA
494643 TATA-ATA
1 TATATA-A
494650 TATATAA
1 TATATAA
*
494657 TATATAC
1 TATATAA
**
494664 TACGTAA
1 TATATAA
494671 TATATAA
1 TATATAA
494678 T
1 T
494679 GTCCCGGACG
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
6 7 0.12
7 42 0.70
8 11 0.18
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:494652 original size:26 final size:27
Alignment explanation
Indices: 494584--494674 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 27
494574 ATATATAAAC
* *
494584 AATATAATCTATATAATATACACTA-T
1 AATATAATATATATAATATATACTAGT
*
494610 TATAATATATATTATATAATAATAATACT-GT
1 AAT-ATA-ATA-TATATAAT-AT-ATACTAGT
494641 AATATAATATATATAATATATACTACGT
1 AATATAATATATATAATATATACTA-GT
494669 AATATA
1 AATATA
494675 TAATGTCCCG
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
26 7 0.13
27 5 0.09
28 18 0.34
29 11 0.21
30 5 0.09
31 7 0.13
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.41
Consensus pattern (27 bp):
AATATAATATATATAATATATACTAGT
Found at i:494656 original size:9 final size:9
Alignment explanation
Indices: 494563--494662 Score: 58
Period size: 8 Copynumber: 12.1 Consensus size: 9
494553 AATAATAAAA
*
494563 ATAATATTT
1 ATAATATAT
494572 A-AATATAT
1 ATAATATAT
*
494580 A-AACA-AT
1 ATAATATAT
*
494587 ATAATCTAT
1 ATAATATAT
494596 AT-A-ATAT
1 ATAATATAT
* *
494603 ACACTAT-T
1 ATAATATAT
494611 ATAATATAT
1 ATAATATAT
*
494620 ATTATATA-
1 ATAATATAT
494628 ATAATA-AT
1 ATAATATAT
*
494636 ACT-GTA-AT
1 A-TAATATAT
494644 ATAATATAT
1 ATAATATAT
494653 ATAATATAT
1 ATAATATAT
494662 A
1 A
494663 CTACGTAATA
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
7 9 0.13
8 32 0.46
9 28 0.41
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (9 bp):
ATAATATAT
Found at i:501066 original size:2 final size:2
Alignment explanation
Indices: 501059--501103 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
501049 ATACGAAATA
501059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
501101 AT A
1 AT A
501104 ATAATAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:501283 original size:4 final size:4
Alignment explanation
Indices: 501274--501318 Score: 63
Period size: 4 Copynumber: 10.8 Consensus size: 4
501264 AAACCGTGAA
*
501274 AAAT AAAT AAAT AAAT AAAT AGAT AAAT AAAT AAAAT AAAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAA
501319 AAGAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 29 0.76
5 9 0.24
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:502415 original size:28 final size:27
Alignment explanation
Indices: 502375--502442 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
502365 GAACCTAAAC
* ** *
502375 AATAA-AAAATAAAATAAAGTAAAGTA
1 AATAATAAAATAAAACAAAACAAAATA
502401 AATGAATAAAATAAAACAAAACAAAATA
1 AAT-AATAAAATAAAACAAAACAAAATA
502429 AATAATAATAATAA
1 AATAATAA-AATAA
502443 TATACTACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 3 0.09
27 7 0.20
28 25 0.71
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (27 bp):
AATAATAAAATAAAACAAAACAAAATA
Found at i:502583 original size:38 final size:37
Alignment explanation
Indices: 502518--502892 Score: 393
Period size: 37 Copynumber: 10.2 Consensus size: 37
502508 TCTATTATAT
* *
502518 TTTTTAAAAA-GTTTTCAAAACTATATATTATAT-AG
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATAAG
502553 TTTTCAAAAATGATTTT-AAAA--A-ATATTATATAAG
1 TTTTCAAAAATG-TTTTAAAAACTATATATTATATAAG
* *
502587 TTTTCAAAAATGTTTTTAAAACTATATATTATATAAT
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATAAG
* *
502624 TTTTCAAAAATGTTTTTAAAACTATATATTATATAAA
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATAAG
** *
502661 TTTTTTAAAACGTTTTAAAAAACTATATATTATATAAG
1 TTTTCAAAAATGTTTT-AAAAACTATATATTATATAAG
*
502699 TTTTTC-AAAATGTTTTAAAAAACTATATATTATATAAT
1 -TTTTCAAAAATGTTTT-AAAAACTATATATTATATAAG
* * *
502737 TTTTAAAAAAATATTTTTAAAACTATATATTATATATA-
1 TTTT-CAAAAATGTTTTAAAAACTATATATTATATA-AG
* *
502775 TTTTC-AAAATGATTTCAAAACTATATATTATATAAG
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATAAG
*
502811 TTTTC-AAAATGTTTTAAAAACCATATATTATAT-A-
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATAAG
*
502845 CTTTC-AAAATGTTTTTTTAAAAAAACTATATATTATATAA-
1 TTTTCAAAAATG---TTTT--AAAAACTATATATTATATAAG
502885 -TTTCAAAA
1 TTTTCAAAA
502893 TCACTTCAAA
Statistics
Matches: 297, Mismatches: 23, Indels: 35
0.84 0.06 0.10
Matches are distributed among these distances:
33 13 0.04
34 29 0.10
35 11 0.04
36 62 0.21
37 72 0.24
38 71 0.24
39 35 0.12
40 4 0.01
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTCAAAAATGTTTTAAAAACTATATATTATATAAG
Found at i:502688 original size:36 final size:36
Alignment explanation
Indices: 502510--502887 Score: 380
Period size: 38 Copynumber: 10.4 Consensus size: 36
502500 TTTACAACTC
*
502510 TATTATAT--TTTTTAAAAA-GTTTTCAAAACTATA
1 TATTATATAATTTTTAAAAATGTTTTAAAAACTATA
* *
502543 TATTATATAGTTTTCAAAAATGATTTT-AAAA--A-A
1 TATTATATAATTTTTAAAAATG-TTTTAAAAACTATA
* *
502576 TATTATATAAGTTTTCAAAAATGTTTTTAAAACTATA
1 TATTATATAA-TTTTTAAAAATGTTTTAAAAACTATA
*
502613 TATTATATAATTTTTCAAAAATGTTTTTAAAACTATA
1 TATTATATAATTTTT-AAAAATGTTTTAAAAACTATA
* *
502650 TATTATATAAATTTTTTAAAACGTTTTAAAAAACTATA
1 TATTATAT-AATTTTTAAAAATGTTTT-AAAAACTATA
*
502688 TATTATATAAGTTTTTCAAAATGTTTTAAAAAACTATA
1 TATTATATAA-TTTTTAAAAATGTTTT-AAAAACTATA
* *
502726 TATTATATAATTTTTAAAAAAATATTTTTAAAACTATA
1 TATTATATAATTTTT--AAAAATGTTTTAAAAACTATA
* * *
502764 TATTATAT-ATATTTTCAAAATGATTTCAAAACTATA
1 TATTATATAAT-TTTTAAAAATGTTTTAAAAACTATA
* * *
502800 TATTATATAAGTTTTCAAAATGTTTTAAAAACCATA
1 TATTATATAATTTTTAAAAATGTTTTAAAAACTATA
* *
502836 TATTATAT-A-CTTTCAAAATGTTTTTTTAAAAAAACTATA
1 TATTATATAATTTTTAAAAATG---TTTT--AAAAACTATA
502875 TATTATATAATTT
1 TATTATATAATTT
502888 CAAAATCACT
Statistics
Matches: 299, Mismatches: 22, Indels: 40
0.83 0.06 0.11
Matches are distributed among these distances:
33 22 0.07
34 27 0.09
35 10 0.03
36 65 0.22
37 67 0.22
38 80 0.27
39 26 0.09
40 1 0.00
41 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
TATTATATAATTTTTAAAAATGTTTTAAAAACTATA
Found at i:504562 original size:41 final size:41
Alignment explanation
Indices: 504488--504884 Score: 308
Period size: 41 Copynumber: 9.7 Consensus size: 41
504478 TAGCGACACT
* * * *
504488 TTTAGCGGCGTTTTT-TGAACAAACGTCGGTAAATACATGTTC
1 TTTAGTGGCGTTTTTAT--ACAAACGCCGCTAAATACATGTAC
* *
504530 TTTAGTGGCGTTTTTATATAAACGCCGCTAAATA-TTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACATGTAC
* * *
504570 TTTAGTGGCATTTTTGTATAAACGCCGCTAAATA-ATGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACATGTAC
* * *
504610 TTTAGTGGCGTTTTAAGCACAAACGACGCTAAA-AGC-TAGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATA-CAT-GTAC
* * * *
504652 TTTAGTGGCGTGTTTGTATAAATGCCGCTAAATA-ATGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACATGTAC
* * ** * *
504692 TTTAGTGGCGTTTTAAGCACAAACGTTGCCAAAGAGTCA--TAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATA--CATGTAC
* * * **
504734 TTTAGTGGTGTTTCTA-AAAAACGCCGCTAAATACCCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACATGTAC
* * * **
504774 TGTAGTGGCGTTTTAAGCACAAACGCCGCTAAATACCCGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATACATGTAC
* * * **
504816 TTTAGTGGCGTTTCTATACAAACGCCGCCAAAGACCCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACATGTAC
*
504857 TTTCGTGGCGTTTTTATACAAACGCCGC
1 TTTAGTGGCGTTTTTATACAAACGCCGC
504885 AATTTATAGT
Statistics
Matches: 286, Mismatches: 54, Indels: 31
0.77 0.15 0.08
Matches are distributed among these distances:
38 1 0.00
40 99 0.35
41 100 0.35
42 84 0.29
43 1 0.00
44 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACATGTAC
Found at i:504584 original size:40 final size:41
Alignment explanation
Indices: 504488--504884 Score: 302
Period size: 40 Copynumber: 9.7 Consensus size: 41
504478 TAGCGACACT
* * * ** *
504488 TTTAGCGGCGTTTTT-TGAACAAACGTCGGTAAATACATGTTC
1 TTTAGTGGCGTTTTTAT--ACAAACGCCGCTAAATACCCGTAC
* **
504530 TTTAGTGGCGTTTTTATATAAACGCCGCTAAATA-TTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTAC
* * * **
504570 TTTAGTGGCATTTTTGTATAAACGCCGCTAAATA-ATGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTAC
* * * **
504610 TTTAGTGGCGTTTTAAGCACAAACGACGCTAAA-AGCTAGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATA-CCCGTAC
* * * * **
504652 TTTAGTGGCGTGTTTGTATAAATGCCGCTAAATA-ATGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTAC
* * ** * * ** *
504692 TTTAGTGGCGTTTTAAGCACAAACGTTGCCAAAGAGTCATAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATACCCGTAC
* * *
504734 TTTAGTGGTGTTTCTA-AAAAACGCCGCTAAATACCCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTAC
* * *
504774 TGTAGTGGCGTTTTAAGCACAAACGCCGCTAAATACCCGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATACCCGTAC
* * *
504816 TTTAGTGGCGTTTCTATACAAACGCCGCCAAAGACCCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTAC
*
504857 TTTCGTGGCGTTTTTATACAAACGCCGC
1 TTTAGTGGCGTTTTTATACAAACGCCGC
504885 AATTTATAGT
Statistics
Matches: 283, Mismatches: 63, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
40 100 0.35
41 98 0.35
42 84 0.30
43 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAATACCCGTAC
Found at i:504673 original size:82 final size:82
Alignment explanation
Indices: 504508--504906 Score: 359
Period size: 82 Copynumber: 4.9 Consensus size: 82
504498 TTTTTTGAAC
* * * * * * *
504508 AAACGTCGGTAAATACATGTTCTTTAGTGGCGTTTTTA-TATAAACGCCGCTAAATATTGTACTT
1 AAACGCCGCTAAATACATGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATATAGTACTT
* *
504572 TAGTGGCATTTTTGTAT
66 TAGTGGCGTGTTTGTAT
*
504589 AAACGCCGCTAAATA-ATGTACTTTAGTGGCGTTTTAAGCACAAACGACGCTAAA-AGCTAGTAC
1 AAACGCCGCTAAATACATGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATA--TAGTAC
504652 TTTAGTGGCGTGTTTGTAT
64 TTTAGTGGCGTGTTTGTAT
* ** * *
504671 AAATGCCGCTAAATA-ATGTACTTTAGTGGCGTTTTAAGCACAAACGTTGCCAAAGAGTCA-TAC
1 AAACGCCGCTAAATACATGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATA-T-AGTAC
* *
504734 TTTAGT-G-GTGTTTCTAAA
64 TTTAGTGGCGTGTTTGT-AT
** * **
504752 AAACGCCGCTAAATACCCGTACTGTAGTGGCGTTTTAAGCACAAACGCCGCTAAATACCCGTACT
1 AAACGCCGCTAAATACATGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATA-TAGTACT
* *
504817 TTAGTGGCGT-TTCTATAC
65 TTAGTGGCGTGTT-TGTAT
* * ** * * * * *
504835 AAACGCCGCCAAAGACCCGTACTTTCGTGGCGTTTTTA-TACAAACGCCGC-AATTTATAGTACA
1 AAACGCCGCTAAATACATGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAA-ATATAGTACT
504898 TTAGTGGCG
65 TTAGTGGCG
504907 CTTTTAAATG
Statistics
Matches: 266, Mismatches: 40, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
80 28 0.11
81 57 0.21
82 138 0.52
83 39 0.15
84 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (82 bp):
AAACGCCGCTAAATACATGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATATAGTACTT
TAGTGGCGTGTTTGTAT
Found at i:504756 original size:122 final size:120
Alignment explanation
Indices: 504506--504849 Score: 311
Period size: 122 Copynumber: 2.8 Consensus size: 120
504496 CGTTTTTTGA
* * * * *
504506 ACAAACGTCGGTAAATA-CATGTTCTTTAGTGGCGTTTTTATATAAACGCCGCTAAATATTGTAC
1 ACAAACGACGCTAAATACCA-GTACTTTAGTGGCG-TTTTGTATAAACGCCGCTAAATAATGTAC
* * * * * * *
504570 TTTAGTGGCATTTTTGTATAAACGCCGCTAAATAATGTACTTTAGTGGCGTTTTAAGC
64 TTTAGTGGCGTTTTAGCACAAACGCCGCCAAAGAATATACTTTAGTGGCGTTTTAA-C
* *
504628 ACAAACGACGCTAAA-AGCTAGTACTTTAGTGGCGTGTTTGTATAAATGCCGCTAAATAATGTAC
1 ACAAACGACGCTAAATA-CCAGTACTTTAGTGGCGT-TTTGTATAAACGCCGCTAAATAATGTAC
** * *
504692 TTTAGTGGCGTTTTAAGCACAAACGTTGCCAAAGAGTCATACTTTAGTGGTGTTTCTAA-
64 TTTAGTGGCGTTTT-AGCACAAACGCCGCCAAAGAAT-ATACTTTAGTGGCGTTT-TAAC
* * * * * **
504751 A-AAACGCCGCTAAATACCCGTACTGTAGTGGCGTTTTAAGCACAAACGCCGCTAAATACCCGTA
1 ACAAACGACGCTAAATACCAGTACTTTAGTGGCGTTTT--GTATAAACGCCGCTAAATA-ATGTA
*
504815 CTTTAGTGGCGTTTCTA-TACAAACGCCGCCAAAGA
63 CTTTAGTGGCGTTT-TAGCACAAACGCCGCCAAAGA
504850 CCCGTACTTT
Statistics
Matches: 181, Mismatches: 30, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
121 5 0.03
122 91 0.50
123 48 0.27
124 33 0.18
125 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (120 bp):
ACAAACGACGCTAAATACCAGTACTTTAGTGGCGTTTTGTATAAACGCCGCTAAATAATGTACTT
TAGTGGCGTTTTAGCACAAACGCCGCCAAAGAATATACTTTAGTGGCGTTTTAAC
Found at i:506238 original size:23 final size:23
Alignment explanation
Indices: 506185--506239 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
506175 TTTTTAAACC
* *
506185 TTTATATAATTTTTTAATAATTA
1 TTTATTTAATATTTTAATAATTA
*
506208 TTTATTTAATATTTTAATATTTA
1 TTTATTTAATATTTTAATAATTA
*
506231 TTTTTTTAA
1 TTTATTTAA
506240 CCTTAATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATTTAATATTTTAATAATTA
Found at i:512760 original size:6 final size:6
Alignment explanation
Indices: 512749--512808 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
512739 CTGTAACCAG
* * * *
512749 AATTAT AATTATT AATTAT AATAAT -ATAAT AATAAT AATAAT AA-TAT
1 AATTAT AATTA-T AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
512796 AATTAT AA-TAT AA
1 AATTAT AATTAT AA
512809 AACGAAACTC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
5 14 0.29
6 29 0.59
7 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTAT
Found at i:512767 original size:13 final size:14
Alignment explanation
Indices: 512749--512798 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
512739 CTGTAACCAG
*
512749 AATTATAATTAT-T
1 AATTATAATAATAT
512762 AATTATAATAATAT
1 AATTATAATAATAT
*
512776 AATAATAATAATAAT
1 AATTATAATAAT-AT
512791 AA-TATAAT
1 AATTATAAT
512799 TATAATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.34
14 17 0.53
15 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTATAATAATAT
Found at i:512772 original size:3 final size:3
Alignment explanation
Indices: 512761--512805 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
512751 TTATAATTAT
* *
512761 TAA TTA TAA TAA T-A TAA TAA TAA TAA TAA TAA T-A TAA TTA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
512806 TAAAACGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:512782 original size:11 final size:11
Alignment explanation
Indices: 512766--512808 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
512756 ATTATTAATT
512766 ATAATAATATA
1 ATAATAATATA
512777 ATAAT-A-ATA
1 ATAATAATATA
512786 ATAATAATATA
1 ATAATAATATA
*
512797 ATTATAATATA
1 ATAATAATATA
512808 A
1 A
512809 AACGAAACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 8 0.28
10 2 0.07
11 19 0.66
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAATAATATA
Found at i:512789 original size:20 final size:20
Alignment explanation
Indices: 512761--512805 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
512751 TTATAATTAT
*
512761 TAATTATAATAATATAATAA
1 TAATAATAATAATATAATAA
*
512781 TAATAATAATAATATAATTA
1 TAATAATAATAATATAATAA
512801 TAATA
1 TAATA
512806 TAAAACGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATAATAATAATATAATAA
Done.