Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012297.1 Kokia drynarioides strain JFW-HI SEQ_127298, 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: 427781
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 212 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:299170 original size:78 final size:78
Alignment explanation
Indices: 299075--299228 Score: 281
Period size: 78 Copynumber: 2.0 Consensus size: 78
299065 AAAAAGAGAG
* *
299075 TATCGCAATATCGAAGCATGAAAGTTGTGATACTCTTGACAATGTTGAAAAAAAGGAAGATTGAG
1 TATCGCAATATCGAAGCATGAAAGTTGTGATACTCTTGACAAGGTTGAAAAAAAAGAAGATTGAG
299140 CCACCAACAATGA
66 CCACCAACAATGA
*
299153 TATCGCAATATCGAAGCATGGAAGTTGTGATACTCTTGACAAGGTTGAAAAAAAAGAAGATTGAG
1 TATCGCAATATCGAAGCATGAAAGTTGTGATACTCTTGACAAGGTTGAAAAAAAAGAAGATTGAG
299218 CCACCAACAAT
66 CCACCAACAAT
299229 TGTATTTTGA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.23
Consensus pattern (78 bp):
TATCGCAATATCGAAGCATGAAAGTTGTGATACTCTTGACAAGGTTGAAAAAAAAGAAGATTGAG
CCACCAACAATGA
Found at i:301340 original size:2 final size:2
Alignment explanation
Indices: 301329--301365 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
301319 GGCGTACTCC
301329 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
301366 AGTGAAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:304856 original size:19 final size:18
Alignment explanation
Indices: 304817--304858 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
304807 TATATTTTTT
*
304817 AAAATATTAATTATTATA
1 AAAATATTAATTATAATA
*
304835 AAAATTATTAA-TATAATG
1 AAAA-TATTAATTATAATA
304853 AAAATA
1 AAAATA
304859 ATTTTTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 13 0.62
19 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATATTAATTATAATA
Found at i:315862 original size:26 final size:24
Alignment explanation
Indices: 315831--315878 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
315821 ACAAAGACCC
*
315831 AAGTGATACAAAAAGAATTAAAATAG
1 AAGTGAGACAAAAA-AA-TAAAATAG
*
315857 AAGTGAGCCAAAAAAATAAAAT
1 AAGTGAGACAAAAAAATAAAAT
315879 TTGGATGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 2 0.10
26 12 0.60
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.17
Consensus pattern (24 bp):
AAGTGAGACAAAAAAATAAAATAG
Found at i:318960 original size:2 final size:2
Alignment explanation
Indices: 318953--319005 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
318943 GTAAATTATT
318953 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
318995 GA GA GA GA GA G
1 GA GA GA GA GA G
319006 TACCATGGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:319711 original size:16 final size:15
Alignment explanation
Indices: 319690--319721 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
319680 TTGAATTTAG
319690 TATTTTTTTTTGTAAA
1 TATTTTTTTTT-TAAA
319706 TATTTTTTTTTTAAA
1 TATTTTTTTTTTAAA
319721 T
1 T
319722 TAAATATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TATTTTTTTTTTAAA
Found at i:319722 original size:55 final size:54
Alignment explanation
Indices: 319662--319769 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 54
319652 TAATTTATTA
* *
319662 TAAATTAAATATGATTGATTGAATTTAGTATTTTTTTTTG-TAAATATTTTTTTTT
1 TAAATTAAATATGATTGATTGAATTTA--ATATTTTTATGATAAATATTTTTTTTT
319717 TAAATTAAATATGATTGATTGAATTTAATATTTTTATGATAAATATTTTTTTT
1 TAAATTAAATATGATTGATTGAATTTAATATTTTTATGATAAATATTTTTTTT
319770 AAATGATTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
53 9 0.18
54 14 0.28
55 27 0.54
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.57
Consensus pattern (54 bp):
TAAATTAAATATGATTGATTGAATTTAATATTTTTATGATAAATATTTTTTTTT
Found at i:326053 original size:52 final size:52
Alignment explanation
Indices: 325975--326107 Score: 203
Period size: 52 Copynumber: 2.6 Consensus size: 52
325965 CTCATTTAAT
* *
325975 ACTCACGATAACACATAGTTATCGGACCTCATAATCCGAAAAAGATTCATAC
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGAAAAAGATTCATAC
* * *
326027 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGAAAAAGATTCATAC
* *
326079 ACTCACGATGACATATAGTCATCAGACCT
1 ACTCACGATGACACATAGTCATCGGACCT
326108 TTTGCATTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.24
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCGGACCTCATAATCCGAAAAAGATTCATAC
Found at i:327043 original size:30 final size:30
Alignment explanation
Indices: 326996--327510 Score: 283
Period size: 30 Copynumber: 17.3 Consensus size: 30
326986 AGTTTTGAGG
*
326996 AGTTTA-GGGTTAAAATGTAATTTTAGAAA
1 AGTTTAGGGGTCAAAATGTAATTTTAGAAA
* * * *
327025 AGTTTAGGGGTAAAAATGTAACTTTGGGAA
1 AGTTTAGGGGTCAAAATGTAATTTTAGAAA
* * *
327055 AGTTT-GGGGTCAAAATATAATTTTTGAGA
1 AGTTTAGGGGTCAAAATGTAATTTTAGAAA
* * * *
327084 AGTTTTGGAGTCAAAATGTGA-TTTCGAGAA
1 AGTTTAGGGGTCAAAATGTAATTTTAGA-AA
* * * * * *
327114 GGTTT-GGTAGTTAAAATGTGATTTTGGAGA
1 AGTTTAGG-GGTCAAAATGTAATTTTAGAAA
* * *
327144 AG-TTCGAGGGTCAAAATGTGATTTTAGATA
1 AGTTTAG-GGGTCAAAATGTAATTTTAGAAA
* *
327174 AGTTTACGGGTCAACACATG--ATTTTAGAGA
1 AGTTTAGGGGTCAA-A-ATGTAATTTTAGAAA
* * *
327204 AGTTTCGAGGTCAAAATGAAATTTT-GAAAA
1 AGTTTAGGGGTCAAAATGTAATTTTAG-AAA
* *
327234 AGTTTTA-GAGTCCAAATGTAATTTTAGAAA
1 AG-TTTAGGGGTCAAAATGTAATTTTAGAAA
** * *
327264 AGTTT-GAGGGTCAAAACATGATTTTAGAGA
1 AGTTTAG-GGGTCAAAATGTAATTTTAGAAA
* * *
327294 AGTTTCGAGGTCAAAATGTAAGTTTAGAAA
1 AGTTTAGGGGTCAAAATGTAATTTTAGAAA
* * *
327324 AGTTTTA--TGTCCAAACGTAATTTTAGAAA
1 AG-TTTAGGGGTCAAAATGTAATTTTAGAAA
** * *
327353 AGTTT-GAGGGTCAAAACATGATTTTAAAAA
1 AGTTTAG-GGGTCAAAATGTAATTTTAGAAA
* * * * *
327383 ATTTTCA-AGGTTAAAATGCAGTTTT-GAAAA
1 AGTTT-AGGGGTCAAAATGTAATTTTAG-AAA
* * *
327413 AGTTTAAGGGTGAAAATGTAATTTTTG-AA
1 AGTTTAGGGGTCAAAATGTAATTTTAGAAA
* *
327442 AGTTTAATGGGTTAAAATGTAATTTTAG-AA
1 AGTTT-AGGGGTCAAAATGTAATTTTAGAAA
* * *
327472 AGTTTAAGGGTTAAAATGTAATTTCT-GATA
1 AGTTTAGGGGTCAAAATGTAATTT-TAGAAA
327502 AGTTTAGGG
1 AGTTTAGGG
327511 ACCTATTGGA
Statistics
Matches: 378, Mismatches: 78, Indels: 59
0.73 0.15 0.11
Matches are distributed among these distances:
28 6 0.02
29 90 0.24
30 261 0.69
31 18 0.05
32 3 0.01
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (30 bp):
AGTTTAGGGGTCAAAATGTAATTTTAGAAA
Found at i:329174 original size:39 final size:39
Alignment explanation
Indices: 329134--329662 Score: 280
Period size: 39 Copynumber: 13.6 Consensus size: 39
329124 GATTATAATT
* *
329134 TGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTGATT
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * * * * * * ** *
329173 TGCCCCAAGCACGGGGTAAAAAATCGGATG-TTGCAATA
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * * * * *
329211 TGTCCTAGGTTCGAGGTAAGAGATTTGTTCATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * *
329250 TGCCCCAGGCTCGGGGTAAAAGA-TCG--AATGGCTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGG-TG--ATC
* * * * * *
329289 TGCCCTAGACTCGAGGTAAGAGATTGGCTAATGGTGGTC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * * * * * ** * * **
329328 TACCTCATGATCAGGGTAAAAGATTGAATGGTTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* *
329367 TGCCTCAGGCTGGGGGTAAGAGATTGGTTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * * **
329406 TGCCTCAGGCTCGAGGTAAAAGATTGACTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * * * * * * * **
329445 TGGCCCAAGCTCGAGGTAAAAGATCGGATGGTTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* *
329484 TGCCCCAAGCTCGGCGTAAGAGATTGGTTGATGGTGA-C
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * ** ****
329522 TTGCCCCAAGCTCGGGGTAA-AGATCGAATGATTACAATC
1 -TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * **
329561 TGCCCCAAGCTCGGGGTAAGAGATTGGCTGATAATGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * *
329600 TGCCCCAGGCTCGGGGTAAAAGATCGATTGACT-GTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGA-TGGTGATC
* * *
329639 TGTCCCATGATCGGGGTAAGAGAT
1 TGCCCCAGGCTCGGGGTAAGAGAT
329663 CGGAATCTTC
Statistics
Matches: 361, Mismatches: 118, Indels: 22
0.72 0.24 0.04
Matches are distributed among these distances:
36 4 0.01
37 2 0.01
38 54 0.15
39 291 0.81
40 3 0.01
41 2 0.01
42 5 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (39 bp):
TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
Found at i:329431 original size:78 final size:78
Alignment explanation
Indices: 329032--329432 Score: 312
Period size: 78 Copynumber: 5.2 Consensus size: 78
329022 TTTTTTTTTT
* * ** * * * * * * *
329032 GTAAGAGATTGGATGGTTGCAATCTGCCTTTGTCACAGGGTAAGAGAATGGCTGACGGTGATTTG
1 GTAAAAGATTGAATGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTG
* *
329097 CCTCATGATC-AGG
66 CCTCAGGCTCGA-G
* ** * *
329110 GTAAAAGATT-AAGTGATTATAATTTGCC-CTAGGCTCGGGGTAAGAGATTGGTTGATGGTGATT
1 GTAAAAGATTGAA-TGGTTGCAATCTGCCTC-AGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
* * * *
329173 TGCCCCAAGCACGGG
64 TGCCTCAGGCTCGAG
* * * * * * * *
329188 GTAAAAAATCGGAT-GTTGCAATATGTCCT-AGGTTCGAGGTAAGAGATTTGTTCATGGTGATCT
1 GTAAAAGATTGAATGGTTGCAATCTG-CCTCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCT
* *
329251 GCCCCAGGCTCGGG
65 GCCTCAGGCTCGAG
* * * * * * *
329265 GTAAAAGATCGAATGGCTGCAATCTGCC-CTAGACTCGAGGTAAGAGATTGGCTAATGGTGGTCT
1 GTAAAAGATTGAATGGTTGCAATCTGCCTC-AGGCTCGGGGTAAGAGATTGGTTGATGGTGATCT
* * *
329329 ACCTCATGATC-AGG
65 GCCTCAGGCTCGA-G
*
329343 GTAAAAGATTGAATGGTTGCAATCTGCCTCAGGCTGGGGGTAAGAGATTGGTTGATGGTGATCTG
1 GTAAAAGATTGAATGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTG
329408 CCTCAGGCTCGAG
66 CCTCAGGCTCGAG
329421 GTAAAAGATTGA
1 GTAAAAGATTGA
329433 CTGATGGTGA
Statistics
Matches: 252, Mismatches: 59, Indels: 24
0.75 0.18 0.07
Matches are distributed among these distances:
77 63 0.25
78 186 0.74
79 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (78 bp):
GTAAAAGATTGAATGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTG
CCTCAGGCTCGAG
Found at i:329446 original size:78 final size:78
Alignment explanation
Indices: 329069--329640 Score: 245
Period size: 78 Copynumber: 7.4 Consensus size: 78
329059 CTTTGTCACA
* * * * * * * * ** *
329069 GGGTAAGAGAATGGCTGACGGTGATTTGCCTCATGATC-AGGGTAAAAGATTAAGTGATTATAAT
1 GGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTCGA-GGTAAAAGATTGACTGATGGTGAT
*
329133 TTGCCCTAGGCTCG
65 CTGCCCTAGGCTCG
* * * * * * * *
329147 GGGTAAGAGATTGGTTGATGGTGATTTGCCCCAAGCACGGGGTAAAA-AAT--CGGATGTTGCAA
1 GGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGATTGACTGATGGTG--A
* * *
329209 TATGTCCTAGGTTCG
64 TCTGCCCTAGGCTCG
* * * * * *
329224 AGGTAAGAGATTTGTTCATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGA---ATGGCTGCA
1 GGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGATTGACTGATGG-TG--
*
329286 ATCTGCCCTAGACTCG
63 ATCTGCCCTAGGCTCG
* * * * * * * * * * **
329302 AGGTAAGAGATTGGCTAATGGTGGTCTACCTCATGATC-AGGGTAAAAGATTGAATGGTTGCAAT
1 GGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTCGA-GGTAAAAGATTGACTGATGGTGAT
*
329366 CTG-CCTCAGGCTGG
65 CTGCCCT-AGGCTCG
329380 GGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGATTGACTGATGGTGATC
1 GGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGATTGACTGATGGTGATC
*
329445 TGGCCC-AAGCTCG
66 T-GCCCTAGGCTCG
* * * * * * ** * * * **
329458 AGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGCTCG-GCGTAAGAGATTGGTTGATGGTGA-
1 GGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTCGAG-GTAAAAGATTGACTGATGGTGAT
* *
329521 CTTGCCCCAAGCTCG
65 C-TGCCCTAGGCTCG
* ** **** * * * * * **
329536 GGGTAA-AGATCGAATGATTACAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATAATGATC
1 GGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGATTGACTGATGGTGATC
*
329600 TGCCCCAGGCTCG
66 TGCCCTAGGCTCG
* * *
329613 GGGTAAAAGATCGATTGACT-GTGATCTG
1 GGGTAAGAGATTGGTTGA-TGGTGATCTG
329641 TCCCATGATC
Statistics
Matches: 387, Mismatches: 85, Indels: 44
0.75 0.16 0.09
Matches are distributed among these distances:
75 4 0.01
77 134 0.35
78 242 0.63
79 3 0.01
80 2 0.01
81 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (78 bp):
GGGTAAGAGATTGGTTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGATTGACTGATGGTGATC
TGCCCTAGGCTCG
Found at i:329934 original size:48 final size:48
Alignment explanation
Indices: 329868--329960 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
329858 CCTTCAAATA
* * * *
329868 TTCATGGTACTGAGTTCACTGTTGCAGCCTCAA-CCTTTCTCATCATAT
1 TTCATGGTACCGAATTCACCGTTACAGCCTCAATCC-TTCTCATCATAT
329916 TTCATGGTACCGAATTCACCGTTACAGCCTCAATCCTTCTCATCA
1 TTCATGGTACCGAATTCACCGTTACAGCCTCAATCCTTCTCATCA
329961 CATCTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.95
49 2 0.05
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (48 bp):
TTCATGGTACCGAATTCACCGTTACAGCCTCAATCCTTCTCATCATAT
Found at i:330085 original size:49 final size:49
Alignment explanation
Indices: 329984--330086 Score: 143
Period size: 49 Copynumber: 2.1 Consensus size: 49
329974 GTCGGGTTCA
* ** *
329984 CCATTGAGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTTG
1 CCATTGAGGCCTCAACCTTTCCATTCAAATCTTCATGGTACCAAATTCG
* * *
330033 CCATTGCGGCCTCAACCTTTGCATTTAAATCTTCATGGTACCAAATTCG
1 CCATTGAGGCCTCAACCTTTCCATTCAAATCTTCATGGTACCAAATTCG
330082 CCATT
1 CCATT
330087 ATTTGGTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (49 bp):
CCATTGAGGCCTCAACCTTTCCATTCAAATCTTCATGGTACCAAATTCG
Found at i:330736 original size:112 final size:112
Alignment explanation
Indices: 330482--330792 Score: 277
Period size: 112 Copynumber: 2.8 Consensus size: 112
330472 ACTAACCGTC
* * * * *
330482 ATTTCAATGTAAAAATGCTTT-AACAGGGTTGTAAGGTAGATAAAATTAAATTTTATTGGAGGT-
1 ATTTCAATGCAAAAATGCTTTGAACA-GGTTGCAAGGTGGATAAAAGTAAATTGTATTGGAGGTC
* * * ***
330545 AGAGCTC--ACG-A-G-AATGA--AAAGAATTATTAGTCCA-CTAATTGTT
65 A-AACTCGAACGAATGAAAAGATTAAA-AATTATTGGTCCACCT-ACCATT
** * * *
330588 ATTTCAATGCAAATGTGCTTTGAATAGGTTGTAAGGTGGATAAAAGTGAATTGTATTGGAGG-CA
1 ATTTCAATGCAAAAATGCTTTGAACAGGTTGCAAGGTGGATAAAAGTAAATTGTATTGGAGGTCA
* * *
330652 AAGGTGGAATGAATGAAAAGATTAAAAATTATTGGTCCACCTACCATT
66 AA-CTCGAACGAATGAAAAGATTAAAAATTATTGGTCCACCTACCATT
* * *
330700 ATTTCAATGCAAAAATGC-TTGAGCAGGTTAGCAAGGTGGATAAAATTAAATTTTATTGGAGGTC
1 ATTTCAATGCAAAAATGCTTTGAACAGGTT-GCAAGGTGGATAAAAGTAAATTGTATTGGAGGTC
*
330764 AAACTCGCACGAATGAAAAGATTAAAAAT
65 AAACTCGAACGAATGAAAAGATTAAAAAT
330793 AACCCACATT
Statistics
Matches: 163, Mismatches: 29, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
105 1 0.01
106 52 0.32
107 3 0.02
108 2 0.01
109 1 0.01
110 1 0.01
111 13 0.08
112 81 0.50
113 9 0.06
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (112 bp):
ATTTCAATGCAAAAATGCTTTGAACAGGTTGCAAGGTGGATAAAAGTAAATTGTATTGGAGGTCA
AACTCGAACGAATGAAAAGATTAAAAATTATTGGTCCACCTACCATT
Found at i:338861 original size:59 final size:60
Alignment explanation
Indices: 338726--338870 Score: 138
Period size: 59 Copynumber: 2.5 Consensus size: 60
338716 TTAAAACATA
* * * * *
338726 ATTTTGAAAAAAGGTTAGG-GTAAAAATGTAACTTTGGGAAAGTTTGGGGTCAAAATATG
1 ATTTTGAAGAAAGTTTGGGAGTCAAAATGTAACTTTGGGAAAGTTTGGAGTCAAAATATG
* * * *
338785 ATTTTGAAGAAA-TTTTGGAGTCAAAATGTGA-TTTCGGGAAGGTTTGGTAGTCAAAATGTG
1 ATTTTGAAGAAAGTTTGGGAGTCAAAATGTAACTTT-GGGAAAGTTTGG-AGTCAAAATATG
*
338845 ATTTT--AGAAAAGTTTGGGGGTCAAAA
1 ATTTTGAAG-AAAGTTTGGGAGTCAAAA
338871 CATGATTTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
58 9 0.13
59 35 0.49
60 27 0.38
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (60 bp):
ATTTTGAAGAAAGTTTGGGAGTCAAAATGTAACTTTGGGAAAGTTTGGAGTCAAAATATG
Found at i:338880 original size:30 final size:30
Alignment explanation
Indices: 338764--339188 Score: 250
Period size: 30 Copynumber: 14.2 Consensus size: 30
338754 TAACTTTGGG
338764 AAAG-TTTGGGGTCAAAATATGATTTT-GA
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
* * * * *
338792 AGAAATTTTGGAGTCAAAATGTGA-TTTCGG
1 A-AAGTTTTGGGGTCAAAATATGATTTTAGA
* * * *
338822 GAAGGTTTGGTAGTCAAAATGTGATTTTAGA
1 AAAGTTTTGG-GGTCAAAATATGATTTTAGA
* *
338853 AAAGTTTGGGGGTCAAAACATGATTTTAGA
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
* *** *** *
338883 GAAGTTTCAAGGTCAAAATGCAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
* * * *
338913 AAAGTTTTGAGATCTAAATGT-AGTTTTAGA
1 AAAGTTTTGGGGTCAAAATATGA-TTTTAGA
* * *
338943 AAAGTTTAGGGGTTAAAATATGATTTTAAA
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
* * * *
338973 AAAGTTTTGAGGTTAAAATGTAATTTTAGA
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
* ** * * *
339003 AAAGTTTTAGGGTTTAAATGTAATTTTAAA
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
*
339033 AAAG-TTTGGGAGTCAAAACATGATTTTAGA
1 AAAGTTTTGGG-GTCAAAATATGATTTTAGA
* * * * * * *
339063 AAAGTTTCGAGGTTAAAATGTAATTTCAAA
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
* * * * *
339093 AAAGTTTTAGGGTGAAAATGTAATTTTAGG
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
* ** *
339123 AAAGCTTAAGGGTCAAAATATAATTTTAG-
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
* * * *
339152 AAACTTTAGAGGTCAAAATATGATTTTTGA
1 AAAGTTTTGGGGTCAAAATATGATTTTAGA
*
339182 CAAGTTT
1 AAAGTTT
339189 AGGGACCTAT
Statistics
Matches: 306, Mismatches: 81, Indels: 18
0.76 0.20 0.04
Matches are distributed among these distances:
28 1 0.00
29 41 0.13
30 248 0.81
31 16 0.05
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.35
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATATGATTTTAGA
Found at i:338900 original size:90 final size:88
Alignment explanation
Indices: 338764--339170 Score: 333
Period size: 90 Copynumber: 4.6 Consensus size: 88
338754 TAACTTTGGG
* * * * * *
338764 AAAGTTT-GGGGTCAAAATATGATTTT-GAAGAAATTTTG-GAGTCAAAATGTGATTTCGGGAAG
1 AAAGTTTGGGGGTCAAAACATGATTTTAGAA-AAGTTTCGAG-GTCAAAATGTAATTTCGGAAAA
*
338826 GTTTGGTAGTCAAAATGTGATTTTAGA
64 GTTT-GTAGTCTAAATGT-ATTTTAGA
* * * *
338853 AAAGTTTGGGGGTCAAAACATGATTTTAGAGAAGTTTCAAGGTCAAAATGCAATTTTGGAAAAGT
1 AAAGTTTGGGGGTCAAAACATGATTTTAGAAAAGTTTCGAGGTCAAAATGTAATTTCGGAAAAGT
338918 TT-TGAGATCTAAATGTAGTTTTAGA
66 TTGT-AG-TCTAAATGTA-TTTTAGA
* * * * * * **
338943 AAAGTTTAGGGGTTAAAATATGATTTTAAAAAAGTTTTGAGGTTAAAATGTAATTTTAGAAAAGT
1 AAAGTTTGGGGGTCAAAACATGATTTTAGAAAAGTTTCGAGGTCAAAATGTAATTTCGGAAAAGT
* *
339008 TT-TAGGGTTTAAATGTAATTTTAAA
66 TTGTA--GTCTAAATGT-ATTTTAGA
* * **
339033 AAAGTTTGGGAGTCAAAACATGATTTTAGAAAAGTTTCGAGGTTAAAATGTAATTTCAAAAAAGT
1 AAAGTTTGGGGGTCAAAACATGATTTTAGAAAAGTTTCGAGGTCAAAATGTAATTTCGGAAAAGT
** *
339098 TT-TAGGGTGAAAATGTAATTTTAGG
66 TTGTA--GTCTAAATGT-ATTTTAGA
* ** * * * *
339123 AAAGCTTAAGGGTCAAAATATAATTTTAG-AAACTTTAGAGGTCAAAAT
1 AAAGTTTGGGGGTCAAAACATGATTTTAGAAAAGTTTCGAGGTCAAAAT
339171 ATGATTTTTG
Statistics
Matches: 265, Mismatches: 44, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
88 1 0.00
89 27 0.10
90 232 0.88
91 5 0.02
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (88 bp):
AAAGTTTGGGGGTCAAAACATGATTTTAGAAAAGTTTCGAGGTCAAAATGTAATTTCGGAAAAGT
TTGTAGTCTAAATGTATTTTAGA
Found at i:340051 original size:2 final size:2
Alignment explanation
Indices: 340044--340071 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
340034 ATAAATGATA
340044 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
340072 TAAAACGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:341205 original size:18 final size:16
Alignment explanation
Indices: 341174--341209 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
341164 CCTCAATACC
341174 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
341190 ATTTCATTCCTCAATTTA
1 ATTTCATT--TCAATTTA
341208 AT
1 AT
341210 ATTACTAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:344639 original size:16 final size:16
Alignment explanation
Indices: 344615--344647 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
344605 TCCTTACAAA
*
344615 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
344631 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
344647 T
1 T
344648 AAAATCATCA
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:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:346209 original size:26 final size:24
Alignment explanation
Indices: 346180--346227 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
346170 AACCAAACCA
*
346180 AATTATATTTTTATTTAATATAAATT
1 AATTATAATTTT-TTT-ATATAAATT
*
346206 AATTTTAATTTTTTTATATAAA
1 AATTATAATTTTTTTATATAAA
346228 AATAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 3 0.15
26 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTATAATTTTTTTATATAAATT
Found at i:346248 original size:21 final size:23
Alignment explanation
Indices: 346215--346259 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
346205 TAATTTTAAT
*
346215 TTTTTTATATAAAA-A-TAAAAA
1 TTTTATATATAAAATAGTAAAAA
*
346236 TTTTATATTTAAAATAGTAAAAA
1 TTTTATATATAAAATAGTAAAAA
346259 T
1 T
346260 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTTTATATATAAAATAGTAAAAA
Found at i:349916 original size:36 final size:35
Alignment explanation
Indices: 349869--349961 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 35
349859 ATGCTTATTC
349869 CCTGTTGACCCAAAGGTCATGATGCTCATTTCACTT
1 CCTGTTGACCCAAAGGTCATGATGCTCATTTCAC-T
* *
349905 CCTGTTGACCCAAAGGTAATGATGCTCATTTTACT
1 CCTGTTGACCCAAAGGTCATGATGCTCATTTCACT
*
349940 CCTTATTGACCCAAAGGTCATG
1 CC-TGTTGACCCAAAGGTCATG
349962 CCTGTTACTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 3 0.06
36 49 0.94
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (35 bp):
CCTGTTGACCCAAAGGTCATGATGCTCATTTCACT
Found at i:350327 original size:25 final size:25
Alignment explanation
Indices: 350278--350328 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
350268 AGAAAGATAG
350278 TTATAAGCAGTTATTAATAAGAATT
1 TTATAAGCAGTTATTAATAAGAATT
350303 TTATAAGCAGTTATTAATAAGAATT
1 TTATAAGCAGTTATTAATAAGAATT
350328 T
1 T
350329 AACATTACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (25 bp):
TTATAAGCAGTTATTAATAAGAATT
Found at i:357977 original size:24 final size:24
Alignment explanation
Indices: 357938--358012 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
357928 AATTTGACTT
* *
357938 AAACAACTAAACAGAGATTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* * *
357962 AAATAAATAAATAGAGTTTAATTT
1 AAACAAATAAACAGAGTTTAATTG
357986 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
358010 AAA
1 AAA
358013 GATTATTTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.27
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:359085 original size:31 final size:31
Alignment explanation
Indices: 359026--359087 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
359016 CAACACAGTT
* *
359026 CGCATGTATGAGTCTGTCGTATCTATGAATC
1 CGCATGTATGAGTATGTCATATCTATGAATC
*
359057 CGCATGTATGAGTATGTTATAT-TCATGAATC
1 CGCATGTATGAGTATGTCATATCT-ATGAATC
359088 TTCTTCTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (31 bp):
CGCATGTATGAGTATGTCATATCTATGAATC
Found at i:359111 original size:45 final size:44
Alignment explanation
Indices: 359047--359136 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
359037 GTCTGTCGTA
* *
359047 TCTATGAATCCGCATGTATGAGTATGTTATAT-TCATGAATCTTCT
1 TCTATGAATACGCATGTATGAGTATG-CATATCT-ATGAATCTTCT
*
359092 TCTATGAATACGCATGTATGAGTCTGCATATCTATGAATCTTCT
1 TCTATGAATACGCATGTATGAGTATGCATATCTATGAATCTTCT
359136 T
1 T
359137 TTAGGAGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (44 bp):
TCTATGAATACGCATGTATGAGTATGCATATCTATGAATCTTCT
Found at i:359605 original size:24 final size:24
Alignment explanation
Indices: 359577--359659 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
359567 CTAATAAGAA
*
359577 TTTAACTCAAACAAATAAATAGAG
1 TTTAACTGAAACAAATAAATAGAG
*
359601 TTTAACTGAAACAATTAAATAGAG
1 TTTAACTGAAACAAATAAATAGAG
* * *
359625 TTTAATTGAAACAAATAAACAAAG
1 TTTAACTGAAACAAATAAATAGAG
359649 TTTAACTGAAA
1 TTTAACTGAAA
359660 GATTATTTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (24 bp):
TTTAACTGAAACAAATAAATAGAG
Found at i:368450 original size:21 final size:20
Alignment explanation
Indices: 368426--368469 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
368416 TTATAGAAAA
*
368426 TAAAGATGATTAATTAAAGAT
1 TAAAGATAATTAATTAAAG-T
*
368447 TAAAGTTAATTAATTAAAGT
1 TAAAGATAATTAATTAAAGT
368467 TAA
1 TAA
368470 TTAAACCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.36
Consensus pattern (20 bp):
TAAAGATAATTAATTAAAGT
Found at i:368462 original size:14 final size:14
Alignment explanation
Indices: 368445--368473 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
368435 TTAATTAAAG
368445 ATTAAAGTTAATTA
1 ATTAAAGTTAATTA
368459 ATTAAAGTTAATTA
1 ATTAAAGTTAATTA
368473 A
1 A
368474 ACCTTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
ATTAAAGTTAATTA
Found at i:369774 original size:49 final size:49
Alignment explanation
Indices: 369654--369774 Score: 129
Period size: 49 Copynumber: 2.5 Consensus size: 49
369644 GGGCCATCCG
* * *
369654 AGATGGTAGATTATCGAAATAATGGAAACCATCATTGTTAGATCATTCA
1 AGATGGTAGAATATCGAAATAGTGGAAACCATCATTGTCAGATCATTCA
** * *
369703 AGATGGTAGAATATATAGATAGT-GAAAGCCATCATTGTCGGATCA-TCTA
1 AGATGGTAGAATATCGAAATAGTGGAAA-CCATCATTGTCAGATCATTC-A
* *
369752 GGATGATAGAATATCGAAATAGT
1 AGATGGTAGAATATCGAAATAGT
369775 TTGAACCATC
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
48 6 0.10
49 52 0.90
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (49 bp):
AGATGGTAGAATATCGAAATAGTGGAAACCATCATTGTCAGATCATTCA
Found at i:371002 original size:28 final size:28
Alignment explanation
Indices: 370971--371052 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
370961 ATGCTATTAT
* *
370971 AGAATAGAGAGCACACAAAGTGCTAATC
1 AGAATAAAGAGAACACAAAGTGCTAATC
*
370999 AGAATATAGAGAACACAAAGTGCTAATC
1 AGAATAAAGAGAACACAAAGTGCTAATC
* * **
371027 AAAACAAAGATTACACAAAGTGCTAA
1 AGAATAAAGAGAACACAAAGTGCTAA
371053 ATACACGTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.51, C:0.16, G:0.17, T:0.16
Consensus pattern (28 bp):
AGAATAAAGAGAACACAAAGTGCTAATC
Found at i:373274 original size:2 final size:2
Alignment explanation
Indices: 373267--373298 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
373257 TGTCACTTGA
373267 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
373299 GGTATTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:374061 original size:16 final size:17
Alignment explanation
Indices: 374042--374074 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
374032 ATTATATAAA
374042 AATAT-TTTTAAAATAT
1 AATATGTTTTAAAATAT
*
374058 AATATGTTTTAATATAT
1 AATATGTTTTAAAATAT
374075 TTCATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
AATATGTTTTAAAATAT
Found at i:388044 original size:10 final size:10
Alignment explanation
Indices: 388012--388045 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
388002 TTTTATTTTT
*
388012 AAATATATAA
1 AAATATAAAA
388022 AAATAATAAAA
1 AAAT-ATAAAA
388033 AAATATAAAA
1 AAATATAAAA
388043 AAA
1 AAA
388046 CACGTGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATATAAAA
Found at i:388349 original size:2 final size:2
Alignment explanation
Indices: 388342--388366 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
388332 AACTCGTGTT
388342 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 T
388367 TAGAAGTTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:396918 original size:21 final size:22
Alignment explanation
Indices: 396894--396936 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
396884 AAATAATTTT
*
396894 AATAATTTT-ATATTTTTAAAA
1 AATAATTTTAATAATTTTAAAA
396915 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
396937 TCATTTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:397276 original size:36 final size:36
Alignment explanation
Indices: 397236--397402 Score: 142
Period size: 36 Copynumber: 5.0 Consensus size: 36
397226 TAATGGATCT
397236 TCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAA
1 TCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAA
* * **
397272 TCCCATGCTGTTGAACGAGATATTGAGTC-T-T--A
1 TCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAA
* * *
397304 --CCAAGCTCCTAAACAAGATATCAAGTCTTCTCAA
1 TCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAA
** *
397338 TCCCAATATCTTGAACGAGATATCAAG---ACT---
1 TCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAA
**
397368 TCCCAAGCTCTTGAACGAGATATTGAGTCTTCTCA
1 TCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCA
397403 GGTTCTTGAA
Statistics
Matches: 98, Mismatches: 22, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
30 43 0.44
31 1 0.01
32 2 0.02
33 4 0.04
34 2 0.02
35 1 0.01
36 45 0.46
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (36 bp):
TCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAA
Found at i:397352 original size:66 final size:66
Alignment explanation
Indices: 397233--397402 Score: 225
Period size: 66 Copynumber: 2.6 Consensus size: 66
397223 AAATAATGGA
* * **
397233 TCTTCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAATCCCATGCTGTTGAACGAGATATTGA
1 TCTTCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAATCCCATGATCTTGAACGAGATATCAA
397298 G
66 G
* * * *
397299 TCTTACCAAGCTCCTAAACAAGATATCAAGTCTTCTCAATCCCAAT-ATCTTGAACGAGATATCA
1 TCTTCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAATCCC-ATGATCTTGAACGAGATATCA
397363 AG
65 AG
* **
397365 ACTTCCCAAGCTCTTGAACGAGATATTGAGTCTTCTCA
1 TCTTCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCA
397403 GGTTCTTGAA
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 86 0.98
67 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (66 bp):
TCTTCCCAAGCTCTTGAACGAGATATCAAGTCTTCTCAATCCCATGATCTTGAACGAGATATCAA
G
Found at i:402362 original size:9 final size:9
Alignment explanation
Indices: 402344--402396 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
402334 GTCAGCAAAT
402344 AATT-TTAA
1 AATTATTAA
402352 AATTATTAA
1 AATTATTAA
402361 AATTATT--
1 AATTATTAA
402368 --TT-TTAA
1 AATTATTAA
402374 AA-TA-TAA
1 AATTATTAA
402381 AATTATTAA
1 AATTATTAA
402390 AATTATT
1 AATTATT
402397 TTTTTGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 6 0.16
8 6 0.16
9 21 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTATTAA
Found at i:402368 original size:20 final size:20
Alignment explanation
Indices: 402340--402396 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
402330 CCACGTCAGC
*
402340 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
402360 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
402380 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
402397 TTTTTGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:402391 original size:29 final size:31
Alignment explanation
Indices: 402349--402421 Score: 114
Period size: 29 Copynumber: 2.4 Consensus size: 31
402339 CAAATAATTT
402349 TAAAATTATTAAAATTA-TTTTTTAAAATA-
1 TAAAATTATTAAAATTATTTTTTTAAAATAG
*
402378 TAAAATTATTAAAATTATTTTTTTGAAATAG
1 TAAAATTATTAAAATTATTTTTTTAAAATAG
*
402409 TAAAATTAATAAA
1 TAAAATTATTAAA
402422 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 17 0.43
30 11 0.28
31 12 0.30
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTTAAAATAG
Found at i:402428 original size:30 final size:29
Alignment explanation
Indices: 402349--402428 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
402339 CAAATAATTT
*
402349 TAAAATTATTAAA-ATTATTTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTTAAAATA
* *
402378 TAAAATTATTAAAATTATTTTTTTGAAATA
1 TAAAATTATT-AAATAATTTTTTTAAAATA
*
402408 GTAAAATTAATAAATAATTTT
1 -TAAAATTATTAAATAATTTT
402429 AATTTTCAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 10 0.23
30 23 0.53
31 10 0.23
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
TAAAATTATTAAATAATTTTTTTAAAATA
Found at i:403588 original size:30 final size:27
Alignment explanation
Indices: 403554--403623 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 27
403544 ATTAAAATTA
403554 TTTAATAATTTTATTATTTCAAATTTTCTT
1 TTTAATAATTTTA-TATTT-AAATTTT-TT
*
403584 TTTAATAAATTTATATTTAAATTTTTT
1 TTTAATAATTTTATATTTAAATTTTTT
403611 TTTAATAATTTTA
1 TTTAATAATTTTA
403624 AAATCATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 14 0.37
28 7 0.18
29 5 0.13
30 12 0.32
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTAATAATTTTATATTTAAATTTTTT
Found at i:405623 original size:33 final size:38
Alignment explanation
Indices: 405586--405661 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 38
405576 TAATCTGACC
*
405586 TAATTAGTAGCAGTAAATT-TGT-T-CAG-T-TAAATT
1 TAATTACTAGCAGTAAATTATGTGTACAGTTATAAATT
* *
405619 TAATTACTAGTAGTATATTATGTGTACAGTTATAAATT
1 TAATTACTAGCAGTAAATTATGTGTACAGTTATAAATT
405657 TAATT
1 TAATT
405662 CATATTCTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 16 0.46
34 3 0.09
35 1 0.03
36 3 0.09
37 1 0.03
38 11 0.31
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (38 bp):
TAATTACTAGCAGTAAATTATGTGTACAGTTATAAATT
Found at i:407511 original size:15 final size:14
Alignment explanation
Indices: 407492--407518 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
407482 TTCGATTTTT
407492 TTTTTTAAATATTA
1 TTTTTTAAATATTA
407506 TTTTTTAAATATT
1 TTTTTTAAATATT
407519 TCGTAAATTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTAAATATTA
Found at i:410111 original size:16 final size:16
Alignment explanation
Indices: 410090--410139 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
410080 AGGGTTTTCA
410090 TATTTATTTACAAGTT
1 TATTTATTTACAAGTT
410106 TATTTA-TT-C-A-TT
1 TATTTATTTACAAGTT
* *
410118 TGTTTATCTACAAGTT
1 TATTTATTTACAAGTT
410134 TATTTA
1 TATTTA
410140 GGTTTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 2 0.07
15 3 0.11
16 13 0.48
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (16 bp):
TATTTATTTACAAGTT
Found at i:411684 original size:11 final size:9
Alignment explanation
Indices: 411641--411675 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
411631 GTTAATGGAT
411641 TTGAGAGAG
1 TTGAGAGAG
*
411650 TTTGAGAAAG
1 -TTGAGAGAG
411660 TTGAGAGAG
1 TTGAGAGAG
411669 TTGAGAG
1 TTGAGAG
411676 GGAGTTGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.40, T:0.26
Consensus pattern (9 bp):
TTGAGAGAG
Found at i:413519 original size:26 final size:26
Alignment explanation
Indices: 413452--413516 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
413442 GACTCATTCT
413452 AGAATTAATAAAAATAATTTTTTATA
1 AGAATTAATAAAAATAATTTTTTATA
413478 AGAATTAATAAAAATAATTTTTTATA
1 AGAATTAATAAAAATAATTTTTTATA
413504 AGAATT-ATAAAAA
1 AGAATTAATAAAAA
413517 ATATAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
25 7 0.18
26 32 0.82
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (26 bp):
AGAATTAATAAAAATAATTTTTTATA
Found at i:417310 original size:3 final size:3
Alignment explanation
Indices: 417302--417326 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
417292 GTGACTAGGC
417302 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
417327 TGCAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:419670 original size:15 final size:14
Alignment explanation
Indices: 419652--419698 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
419642 TTCAAAAAAC
419652 AATAAATGATATTTA
1 AATAAAT-ATATTTA
419667 AATAAATATATTT-
1 AATAAATATATTTA
*
419680 -ATAGATCATATTTA
1 AATAAAT-ATATTTA
419694 AATAA
1 AATAA
419699 TTAAATACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.19
13 6 0.22
14 6 0.22
15 10 0.37
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (14 bp):
AATAAATATATTTA
Found at i:419970 original size:22 final size:21
Alignment explanation
Indices: 419940--419992 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
419930 TTCAAAATTT
*
419940 AAATTTAAAAATATATAAAAA
1 AAATTTAAAAATAGATAAAAA
419961 AAATTCTAAAAATAGATATAAAA
1 AAATT-TAAAAATAGATA-AAAA
* *
419984 GAGTTTAAA
1 AAATTTAAA
419993 TTTTGATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 15 0.56
23 7 0.26
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTTAAAAATAGATAAAAA
Found at i:423418 original size:58 final size:58
Alignment explanation
Indices: 423328--423494 Score: 280
Period size: 58 Copynumber: 2.9 Consensus size: 58
423318 ACAAAGAATC
*
423328 TGTGTTCAAGTATCGGTTGACACCGGCCATGGGTTCAATCCTTAGACAACCCCGAAAT
1 TGTGTTCAAGTCTCGGTTGACACCGGCCATGGGTTCAATCCTTAGACAACCCCGAAAT
*
423386 TGTGTTCAAGTCTCGGTTGACACTGGCCATGGGTTCAATCCTTAGACAACCCCGAAAT
1 TGTGTTCAAGTCTCGGTTGACACCGGCCATGGGTTCAATCCTTAGACAACCCCGAAAT
* * * *
423444 TATGTTCAAGTCTCGGTTGACACCAGTCATGGGTTCAATCGTTAGACAACC
1 TGTGTTCAAGTCTCGGTTGACACCGGCCATGGGTTCAATCCTTAGACAACC
423495 GCTATGCCTA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 102 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (58 bp):
TGTGTTCAAGTCTCGGTTGACACCGGCCATGGGTTCAATCCTTAGACAACCCCGAAAT
Found at i:425001 original size:4 final size:4
Alignment explanation
Indices: 424992--425058 Score: 82
Period size: 4 Copynumber: 16.5 Consensus size: 4
424982 CAAATAAACG
* *
424992 AGAA AGAA AGAA AGAAA AGAA ATAA AGAA AGAA AGAA AGAGA GGAA AGAA
1 AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGA-A AGAA AGAA
*
425042 AGAA A-AA GGAA AGAA AG
1 AGAA AGAA AGAA AGAA AG
425059 GTAATAAGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
3 2 0.04
4 45 0.83
5 7 0.13
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (4 bp):
AGAA
Found at i:425018 original size:17 final size:16
Alignment explanation
Indices: 424992--425058 Score: 82
Period size: 17 Copynumber: 4.1 Consensus size: 16
424982 CAAATAAACG
424992 AGAAAGAAAGAAAGAAA
1 AGAAAGAAAGAAAG-AA
*
425009 AGAAATAAAGAAAGAA
1 AGAAAGAAAGAAAGAA
*
425025 AGAAAGAGAGGAAAGAA
1 AGAAAGA-AAGAAAGAA
*
425042 AGAAA-AAGGAAAGAA
1 AGAAAGAAAGAAAGAA
425057 AG
1 AG
425059 GTAATAAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
15 11 0.24
16 9 0.20
17 26 0.57
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (16 bp):
AGAAAGAAAGAAAGAA
Found at i:425019 original size:21 final size:21
Alignment explanation
Indices: 424993--425058 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
424983 AAATAAACGA
424993 GAAAGAAAGAAAGAAA-AGAAA
1 GAAAGAAAGAAAGAAAGAG-AA
* *
425014 TAAAGAAAGAAAGAAAGAGAG
1 GAAAGAAAGAAAGAAAGAGAA
*
425035 GAAAGAAAGAAA-AAGGA-AA
1 GAAAGAAAGAAAGAAAGAGAA
425054 GAAAG
1 GAAAG
425059 GTAATAAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 6 0.15
20 4 0.10
21 27 0.69
22 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAAGAGAA
Found at i:425143 original size:19 final size:19
Alignment explanation
Indices: 425098--425143 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
425088 GTATGATATC
*
425098 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
**
425117 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCGTATTTAA
425137 TTTTTAA
1 TTTTTAA
425144 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Done.