Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold260
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: 1006324
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 7
Found at i:185351 original size:17 final size:18
Alignment explanation
Indices: 185329--185362 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
185319 TAAGCTTTCA
185329 AAATATTTA-CCTAAATT
1 AAATATTTATCCTAAATT
185346 AAATATTTATCCTAAAT
1 AAATATTTATCCTAAAT
185363 GAATAATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATTTATCCTAAATT
Found at i:191603 original size:6 final size:6
Alignment explanation
Indices: 191594--191620 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
191584 TAAAAATTAA
191594 AAATTC AAATTC AAATTC AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAA
191621 AAATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTC
Found at i:191758 original size:26 final size:26
Alignment explanation
Indices: 191729--191857 Score: 231
Period size: 26 Copynumber: 5.0 Consensus size: 26
191719 ACATGAACAA
*
191729 CATGGGAAAGGAAATAGAAAATGCAG
1 CATGGGAAAGGAAATAAAAAATGCAG
*
191755 CATGGGAAAGGAAATAGAAAATGCAG
1 CATGGGAAAGGAAATAAAAAATGCAG
191781 CATGGGAAAGGAAATAAAAAATGCAG
1 CATGGGAAAGGAAATAAAAAATGCAG
191807 CATGGGAAAGGAAATAAAAAATGCAG
1 CATGGGAAAGGAAATAAAAAATGCAG
*
191833 CATGGGAAAGGAAATAAAAATTGCA
1 CATGGGAAAGGAAATAAAAAATGCA
191858 ATTGGAGACA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 101 1.00
ACGTcount: A:0.52, C:0.08, G:0.28, T:0.12
Consensus pattern (26 bp):
CATGGGAAAGGAAATAAAAAATGCAG
Found at i:192240 original size:44 final size:43
Alignment explanation
Indices: 192177--192273 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 43
192167 AAAGCAGCTC
* * * *
192177 CAACAGCAGCACCAGCTCCAGCGGCAACTGACAGCTCTAGCATG
1 CAACAGCAGCACCAACTCCAGCAGCAACTG-CAGCTCCAGCACG
** * *
192221 CAACAGCAGCAGTAACTCCAGCAGCGACTGGAGCTCCAGCACG
1 CAACAGCAGCACCAACTCCAGCAGCAACTGCAGCTCCAGCACG
*
192264 CGACAGCAGC
1 CAACAGCAGC
192274 TCCAGTGAGA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 19 0.43
44 25 0.57
ACGTcount: A:0.30, C:0.36, G:0.25, T:0.09
Consensus pattern (43 bp):
CAACAGCAGCACCAACTCCAGCAGCAACTGCAGCTCCAGCACG
Found at i:192257 original size:18 final size:19
Alignment explanation
Indices: 192236--192278 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
192226 GCAGCAGTAA
* *
192236 CTCCAGCA-GCGACTGGAG
1 CTCCAGCACGCGACAGCAG
192254 CTCCAGCACGCGACAGCAG
1 CTCCAGCACGCGACAGCAG
192273 CTCCAG
1 CTCCAG
192279 TGAGAGCAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.09
Consensus pattern (19 bp):
CTCCAGCACGCGACAGCAG
Found at i:193308 original size:51 final size:52
Alignment explanation
Indices: 193220--193319 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 52
193210 CAATTGCTCA
* * *
193220 TAATCGGGGATACTCCAAGCCCGGTTTTATTTTC-AAAACACCAATTTCCTT
1 TAATCAGGGATACTCCAAGCCCGATTTTATTTCCAAAAACACCAATTTCCTT
* *
193271 TAATCAGGGATACTCCAA-CTTCGATTTTGTTTCCAAAAAACACCAATTT
1 TAATCAGGGATACTCCAAGC-CCGATTTTATTTCC-AAAAACACCAATTT
193320 TTCACAATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 1 0.02
51 27 0.66
53 13 0.32
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (52 bp):
TAATCAGGGATACTCCAAGCCCGATTTTATTTCCAAAAACACCAATTTCCTT
Found at i:193354 original size:31 final size:28
Alignment explanation
Indices: 193326--193402 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
193316 ATTTTTCACA
*
193326 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
193354 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
193382 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
193403 GCTTCCAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:193505 original size:51 final size:51
Alignment explanation
Indices: 193419--193914 Score: 365
Period size: 51 Copynumber: 9.5 Consensus size: 51
193409 AAAATATTGA
* * * *
193419 TTTCTCATAATGGGGGATACTCCAACCCTGATTTTATTTCTAAAACACTAAT
1 TTTC-CATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
* * * *
193471 TTTCCATAATCAGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAA
1 TTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAAT
*
193523 TTTCCTTTAATCGGGGATACTCCAACCCCGGTTTTATTT-TAAAAACACCAAT
1 TTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAAT
* * * * * ***** * *
193575 CTTT-CACAATCGAGGATATTCCAACCTCGTTATTTCATCGGGGATACTCCAA-
1 -TTTCCATAATCGGGGATACTCCAACCCCGGT-TTT-ATTTCTAAAACACCAAT
** * * * * ***
193627 -CCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-
1 TTTCCA-TA-AT-C--GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
* * *
193681 TTTCTCATAATTGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTAAT
1 TTTC-CATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
* * * *
193733 TTTTCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAA
1 TTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAAT
* *
193785 TTTCCTTTAATCGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAA-
1 TTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
* * ** * *
193836 TTTCCTTTAATCGGAGATACTCCAACTTCGATTTTATTTCCAAAAACACCAAT
1 TTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTATTT-CTAAAACACCAAT
* * *
193889 TTTTCACAATCGAGGATACTCCAACC
1 TTTCCATAATCGGGGATACTCCAACC
193915 TCGTTATTTC
Statistics
Matches: 348, Mismatches: 77, Indels: 38
0.75 0.17 0.08
Matches are distributed among these distances:
51 152 0.44
52 86 0.25
53 80 0.23
54 7 0.02
55 6 0.02
56 17 0.05
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
TTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
Found at i:193546 original size:104 final size:101
Alignment explanation
Indices: 193426--193914 Score: 378
Period size: 104 Copynumber: 4.7 Consensus size: 101
193416 TGATTTCTCA
* * * *
193426 TAATGGGGGATACTCCAACCCTGATTTTATTTCTAAAACACTAATTTTCCATAATCAGGGATACT
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCCATAATC-GGGATACT
*
193491 CTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTT
65 CCAACCCCGGTTTTATTTTT-AAAACACC-AATTTCCTT
*
193530 TAATCGGGGATACTCCAACCCCGGTTTTATTT-TAAAAACACCAATCTTT-CACAATCGAGGATA
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAAT-TTTCCATAATCG-GGATA
* * * ***** * * ** *
193593 TTCCAACCTCGTTATTTCATCGGGGATACTCCAA-CCCCAT
63 CTCCAACCCCGGT-TTT-ATTTTTAAAACACCAATTTCCTT
* * * * *** *
193633 TACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTCTCATAATTGGGG
1 TA-AT-C--GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTC-CATAA-TCGGG
* * *
193697 ATACTCCAACCCTGGTTTTATTTCTAAAACACTAATTT--TT
60 ATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTCCTT
* * * *
193737 CATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGGA
1 --TAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAATTTTCC-ATAATC-GGGA
193802 TACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTCCTT
61 TACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTCCTT
* ** * * * *
193843 TAATCGGAGATACTCCAACTTCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATAC
1 TAATCGGGGATACTCCAACCCCGGTTTTATTT-CTAAAACACCAATTTTCCATAATCG-GGATAC
193908 TCCAACC
64 TCCAACC
193915 TCGTTATTTC
Statistics
Matches: 293, Mismatches: 68, Indels: 49
0.71 0.17 0.12
Matches are distributed among these distances:
102 26 0.09
103 32 0.11
104 150 0.51
105 24 0.08
106 9 0.03
107 50 0.17
108 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (101 bp):
TAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCCATAATCGGGATACTC
CAACCCCGGTTTTATTTTTAAAACACCAATTTCCTT
Found at i:193768 original size:262 final size:257
Alignment explanation
Indices: 193217--193836 Score: 1019
Period size: 262 Copynumber: 2.4 Consensus size: 257
193207 TCTCAATTGC
* * *
193217 TCATAATCGGGGATACTCCAAGCCCGGTTTTA-TTTTCAAAACACC-AATTTCCTTTAATCAGGG
1 TCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGG
** * * * *
193280 ATACTCCAACTTCGATTTTGTTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCT
66 ATACTCCAACCCCGGTTTTATTT--TAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCT
*
193345 CGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTCCA
129 CGTTATTTCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTCCA
193410 AAATATTGATTTCTCATAATGGGGGATACTCCAACCCTGATTTTATTTCTAAAACACTAATTTT
194 AAATATTGATTTCTCATAATGGGGGATACTCCAACCCTGATTTTATTTCTAAAACACTAATTTT
* *
193474 CCATAATCAGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGG
1 TCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGG
*
193539 ATACTCCAACCCCGGTTTTATTTTAAAAACACCAATCTTTCACAATCGAGGATATTCCAACCTCG
66 ATACTCCAACCCCGGTTTTATTTTAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCTCG
193604 TTATTTCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTT
131 TTATTTCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGC-----TT
* *
193669 CCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTAATT
191 CCAAAATATTGATTTCTCATAATGGGGGATACTCCAACCCTGATTTTATTTCTAAAACACTAATT
193734 TT
256 TT
193736 TCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGG
1 TCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGG
*
193801 ATACTCCAACCCCGGTTTTATTTTTAAAACACCAAT
66 ATACTCCAACCCCGGTTTTATTTTAAAAACACCAAT
193837 TTCCTTTAAT
Statistics
Matches: 338, Mismatches: 18, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
257 124 0.37
258 13 0.04
259 36 0.11
262 165 0.49
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (257 bp):
TCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGG
ATACTCCAACCCCGGTTTTATTTTAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCTCG
TTATTTCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTCCAAA
ATATTGATTTCTCATAATGGGGGATACTCCAACCCTGATTTTATTTCTAAAACACTAATTTT
Found at i:193811 original size:211 final size:211
Alignment explanation
Indices: 193431--193811 Score: 493
Period size: 211 Copynumber: 1.8 Consensus size: 211
193421 TCTCATAATG
* * * *
193431 GGGGATACTCCAACCCTGATTTTATTTCTAAAACACTAATTTTCCATAATCAGGGATACTCTAAC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTTCCATAATCAGGGATACTCCAAC
* *
193496 CCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGGATACTCCAACCCCGGTTTTATT
66 CCCGGTTTTATTTCTCAAAACACCAAATTTCCTATAATCGGGGATACTCCAACCCCGGTTTTATT
* *
193561 TTAAAAACACCAATCTTTCACAATCGAGGATATTCCAACCTCGTTATTTCATCGGGGATACTCCA
131 TTAAAAACACCAATATTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCA
193626 ACCCCATTACCTCCGA
196 ACCCCATTACCTCCGA
* * * * **
193642 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTTC-CATAATCAGGGATACTCCAA
* * * * *
193706 CCCTGGTTTTATTTCT-AAAACACTAATTTTTC-ATAATCGGGGATACTCTAACCCCGGTTTTAT
65 CCCCGGTTTTATTTCTCAAAACACCAAATTTCCTATAATCGGGGATACTCCAACCCCGGTTTTA-
* *
193769 TTTTCAAAACACCAA-ATTTC-CTTTAATCGGGGATACTCCAACC
129 TTTTAAAAACACCAATATTTCAC---AATCGAGGATACTCCAACC
193812 CCGGTTTTAT
Statistics
Matches: 144, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
208 1 0.01
209 32 0.22
210 31 0.22
211 80 0.56
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (211 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTTCCATAATCAGGGATACTCCAAC
CCCGGTTTTATTTCTCAAAACACCAAATTTCCTATAATCGGGGATACTCCAACCCCGGTTTTATT
TTAAAAACACCAATATTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCA
ACCCCATTACCTCCGA
Found at i:193934 original size:28 final size:28
Alignment explanation
Indices: 193902--193973 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
193892 TCACAATCGA
* ** *
193902 GGATACTCCAACCTCGTTATTTCATCA-G
1 GGATACTCCAACCCCGTTACCTC-TAAGG
193930 GGATACTCCAACCCCGTTACCTCTAAGG
1 GGATACTCCAACCCCGTTACCTCTAAGG
193958 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
193974 GCTTTATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 2 0.05
28 37 0.95
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACCTCTAAGG
Found at i:193935 original size:314 final size:313
Alignment explanation
Indices: 193418--194022 Score: 953
Period size: 314 Copynumber: 1.9 Consensus size: 313
193408 CAAAATATTG
* * * *
193418 ATTTCTCATAATGGGGGATACTCCAACCCTGATTTTATTTCTAAAACACTAATTTTCCATAATCA
1 ATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAAATTTCCATAATCA
* *
193483 GGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGGATACTCCAA
66 GGGATACTCCAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGAGATACTCCAA
* * *
193548 CCCCGGTTTTATTTTAAAAACACCAATCTTTCACAATCGAGGATATTCCAACCTCGTTATTTCAT
131 CCCCGATTTTATTTCAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCTCGTTATTTCAT
* *
193613 CGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATAT
196 CAGGGATACTCCAACCCCATTACCTCCAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATAT
*
193678 TGATTTCTCATAATTGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTA
261 CGATTTCTCATAATTGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTA
* * * * *
193731 ATTTTTCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAAT
1 ATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAAATTTCC-ATAAT
*
193796 CGGGGATACTCCAACCCCGGTTTTATTTTT-AAAACACC-AATTTCCTTTAATCGGAGATACTCC
64 CAGGGATACTCCAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGAGATACTCC
** *
193859 AACTTCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTT
129 AACCCCGATTTTATTT-CAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCTCGTTATTT
* * *
193924 CATCAGGGATACTCCAACCCCGTTACCTCTAAGGGGATACTCCAACCCCGGCTTTATTTCCAGAA
193 CATCAGGGATACTCCAACCCCATTACCTCCAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAA
193989 TATCGATTTCTCATAATTGGGGATACTCCAACCC
258 TATCGATTTCTCATAATTGGGGATACTCCAACCC
194023 CGTTATTTCC
Statistics
Matches: 265, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
313 73 0.28
314 160 0.60
315 32 0.12
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (313 bp):
ATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAAATTTCCATAATCA
GGGATACTCCAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGAGATACTCCAA
CCCCGATTTTATTTCAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCTCGTTATTTCAT
CAGGGATACTCCAACCCCATTACCTCCAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATAT
CGATTTCTCATAATTGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTA
Found at i:194019 original size:79 final size:78
Alignment explanation
Indices: 193929--194131 Score: 219
Period size: 79 Copynumber: 2.6 Consensus size: 78
193919 TATTTCATCA
* * *
193929 GGGATACTCCAACCCCGTTACCTCTAAGGGGATACTCCAACCCCGGCTTTATTTCCAGAAT-ATC
1 GGGATACTCCAACCCCGTTA-TTCTAAGGGGATACTCCAACCCCGACTTTATTTCC-CAATCATC
* **
193993 GATTTCTCATAATTG
64 GATTTCTCACAACCG
** * * * *
194008 GGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCTAATCCCGATTTTATTTCCCAATCATCG
1 GGGATACTCCAACCCCGTTA-TTCTAAGGGGATACTCCAACCCCGACTTTATTTCCCAATCATCG
*
194073 ATTTTTCACAACCG
65 ATTTCTCACAACCG
* * *
194087 GGGATACTCCAACCCCATTATTTTCAAGGAGATACTCCAACCCCG
1 GGGATACTCCAACCCCGTTATTCT-AAGGGGATACTCCAACCCCG
194132 TTATTATCTC
Statistics
Matches: 100, Mismatches: 22, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
78 5 0.05
79 95 0.95
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATTCTAAGGGGATACTCCAACCCCGACTTTATTTCCCAATCATCGA
TTTCTCACAACCG
Found at i:205454 original size:12 final size:11
Alignment explanation
Indices: 205435--205488 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
205425 CTTCTCTTAA
205435 AAAAAAAAATC
1 AAAAAAAAATC
*
205446 AACAAAAAATTC
1 AA-AAAAAAATC
*
205458 AAAAAAAAAAAC
1 -AAAAAAAAATC
*
205470 GAAAAAAAA-C
1 AAAAAAAAATC
205480 AAAAAAAAA
1 AAAAAAAAA
205489 ACGAACCTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 9 0.25
11 10 0.28
12 15 0.42
13 2 0.06
ACGTcount: A:0.83, C:0.09, G:0.02, T:0.06
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:205461 original size:25 final size:22
Alignment explanation
Indices: 205433--205493 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 22
205423 ACCTTCTCTT
205433 AAAAAAAAAAATC-AACAAAAAATTC
1 AAAAAAAAAAA-CGAA-AAAAAA--C
205458 AAAAAAAAAAACGAAAAAAAAC
1 AAAAAAAAAAACGAAAAAAAAC
205480 -AAAAAAAAAACGAA
1 AAAAAAAAAAACGAA
205494 CCTGCTTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 14 0.40
22 1 0.03
24 7 0.20
25 13 0.37
ACGTcount: A:0.82, C:0.10, G:0.03, T:0.05
Consensus pattern (22 bp):
AAAAAAAAAAACGAAAAAAAAC
Found at i:206622 original size:95 final size:95
Alignment explanation
Indices: 206455--206657 Score: 336
Period size: 95 Copynumber: 2.1 Consensus size: 95
206445 ACTTTCCTAG
206455 TCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTTAGTCCCCAAAGAGCAGGACGCCTTTCA
1 TCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTTAGTCCCCAAAGAGCAGGACGCCTTTCA
*
206520 AAGCCCACACAAGTTGGTGGCACTTTTC-AA
66 AAACCCACACAAGTTGGTGGCA-TTTTCTAA
* * *
206550 TCCTCAAAAAGCAGGACGCTCTCTCCTTTCACCCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTA
1 TCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTTAGTCCCCAAAGAGCAGGACGCCTTTCA
* *
206615 AAACCCACACGAGTTGGTGGCATTTTCTAG
66 AAACCCACACAAGTTGGTGGCATTTTCTAA
206645 TCCTCAAAGAGCA
1 TCCTCAAAGAGCA
206658 ACACCTTTTC
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 5 0.05
95 95 0.95
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (95 bp):
TCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTTAGTCCCCAAAGAGCAGGACGCCTTTCA
AAACCCACACAAGTTGGTGGCATTTTCTAA
Found at i:206726 original size:26 final size:26
Alignment explanation
Indices: 206696--206783 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
206686 GTTGGTGGCA
206696 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
* * * ** *
206722 CCTTTCAAAGCCCACACAAGTTGGTGG-CA
1 CCTTTC--AGTCCTCA-AAG-AGCAGGACG
206751 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
206777 CCTTTCA
1 CCTTTCA
206784 AAGCCCACAT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
25 3 0.07
26 17 0.38
27 6 0.13
28 6 0.13
29 10 0.22
30 3 0.07
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAGAGCAGGACG
Found at i:206843 original size:56 final size:55
Alignment explanation
Indices: 206584--207114 Score: 641
Period size: 55 Copynumber: 9.4 Consensus size: 55
206574 CCTTTCACCC
* *
206584 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAACCCACACGAGTTGGTGGCATT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATT
* ** * * **
206639 TTCTAGTCCTCAAAGAGCAACACCTTTTCCTTTTAGAGCCCACACAAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGA-C---GCCTTTTAAAGCCCACACAAGTTGGTGGCATT
* * **
206698 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATT
* * *
206753 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCAATT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGC-ATT
206809 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATT
*
206864 TTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACATACA-TTGGTGGCAATT
1 TTT-TAGTCCTCAAAGAGCAGGACGCC---T--TTT-AAAGCCCACACA-AGTTGGTGGC-ATT
* * * * *
206927 TTCTAGTCCTCAAAGAGCATGATGCCTTTCAAAGCCCACATAAGTTGGTGGCAATT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGC-ATT
* **
206983 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATT
* * * * * *
207038 TTTCAGTTCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATT
207093 TTTTAGTCCTCAAAGAGCAGGA
1 TTTTAGTCCTCAAAGAGCAGGA
207115 TACACTTTAT
Statistics
Matches: 418, Mismatches: 43, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
55 176 0.42
56 144 0.34
57 2 0.00
58 1 0.00
59 46 0.11
61 3 0.01
62 40 0.10
63 6 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (55 bp):
TTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATT
Found at i:206962 original size:174 final size:167
Alignment explanation
Indices: 206587--207114 Score: 726
Period size: 174 Copynumber: 3.1 Consensus size: 167
206577 TTCACCCTTT
* * ** *
206587 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAACCCACACGAGTTGGTGGC-ATTTTCTAGTCCTCA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCAATTTTTTAGTCCTCA
** * *
206651 AAGAGCAACACCTTTTCCTTTTAGAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC
66 AAGAGCAGGA-C---GCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC
*
206716 AGGACGCCTTTCAAAGCCCAC-ACAAGTTGGTGGCACCTTTC
127 AGGACGCCTTTCAAAGCCCACAAC-AGTTGGTGGCACTTTTC
206757 -AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCAATTTTTTAGTCCTCA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCAATTTTTTAGTCCTCA
**
206821 AAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCTAGTCCTCAAAGAGCAGG
66 AAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGG
*
206886 ACGCCTTTTCCTTTCAAAGCCCACATACA-TTGGTGGCAATTTTC
130 ACG------CCTTTCAAAGCCCACA-ACAGTTGGTGGCACTTTTC
* *
206930 TAGTCCTCAAAGAGCATGATGCCTTTCAAAGCCCACATAAGTTGGTGGCAATTTTTTAGTCCTCA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCAATTTTTTAGTCCTCA
* * *
206995 AAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTCAGTTCTCAAAGAGCAAGA
66 AAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
207060 CGCCTTTCAAAGCCCAC-ACGAGTTGGTGGCACTTTT-
131 CGCCTTTCAAAGCCCACAAC-AGTTGGTGGCACTTTTC
207096 TAGTCCTCAAAGAGCAGGA
1 TAGTCCTCAAAGAGCAGGA
207115 TACACTTTAT
Statistics
Matches: 323, Mismatches: 22, Indels: 30
0.86 0.06 0.08
Matches are distributed among these distances:
165 2 0.01
166 51 0.16
167 48 0.15
169 45 0.14
170 22 0.07
173 46 0.14
174 107 0.33
175 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (167 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCAATTTTTTAGTCCTCA
AAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
CGCCTTTCAAAGCCCACAACAGTTGGTGGCACTTTTC
Found at i:207746 original size:6 final size:6
Alignment explanation
Indices: 207737--207769 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
207727 TAAAAATTAA
207737 AAATTC AAATTC AAATTC AAATTC AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAA
207770 AAATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTC
Found at i:207928 original size:26 final size:26
Alignment explanation
Indices: 207875--207924 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
207865 AAAACATGAA
207875 CAGCATGGGAAAGGAAATAGAAAATG
1 CAGCATGGGAAAGGAAATAGAAAATG
207901 CAGCATGGGAAAGGAAATA-AAAAT
1 CAGCATGGGAAAGGAAATAGAAAAT
207925 TGCAATTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.52, C:0.08, G:0.28, T:0.12
Consensus pattern (26 bp):
CAGCATGGGAAAGGAAATAGAAAATG
Found at i:208266 original size:18 final size:18
Alignment explanation
Indices: 208241--208382 Score: 101
Period size: 18 Copynumber: 7.8 Consensus size: 18
208231 AACACGCAAA
208241 AGCAGCTCCAGCAGCAGC
1 AGCAGCTCCAGCAGCAGC
* *
208259 ACCAGCTCCAGCGGCAGC
1 AGCAGCTCCAGCAGCAGC
* * *
208277 -GACAACTCTAGCACGCAAC
1 AG-CAGCTCCAGCA-GCAGC
* *
208296 AGCAGCTCCAACAGTAGC
1 AGCAGCTCCAGCAGCAGC
* *
208314 AGCAACTCCAGCAG-TGAC
1 AGCAGCTCCAGCAGCAG-C
* * *
208332 TGCAGCTCTAGCACGCAAC
1 AGCAGCTCCAGCA-GCAGC
208351 AGCAGCTCCAGCGAG-AGC
1 AGCAGCTCCAGC-AGCAGC
*
208369 AGCAACTCCAGCAG
1 AGCAGCTCCAGCAG
208383 GTAGCAATCT
Statistics
Matches: 93, Mismatches: 24, Indels: 15
0.70 0.18 0.11
Matches are distributed among these distances:
17 3 0.03
18 63 0.68
19 25 0.27
20 2 0.02
ACGTcount: A:0.30, C:0.37, G:0.24, T:0.09
Consensus pattern (18 bp):
AGCAGCTCCAGCAGCAGC
Found at i:208300 original size:55 final size:54
Alignment explanation
Indices: 208233--208382 Score: 180
Period size: 55 Copynumber: 2.7 Consensus size: 54
208223 ACGACTCCAA
* * *
208233 CACGCAAAAGCAGCTCCAGCAGCAGCACCAGCTCCAGC-G-GCAGC-GACAACTCTAG
1 CACGCAACAGCAGCTCCAGCAG-AGCAGCAACTCCAGCAGTG-A-CTG-CAACTCTAG
* *
208288 CACGCAACAGCAGCTCCAACAGTAGCAGCAACTCCAGCAGTGACTGCAGCTCTAG
1 CACGCAACAGCAGCTCCAGCAG-AGCAGCAACTCCAGCAGTGACTGCAACTCTAG
208343 CACGCAACAGCAGCTCCAGCGAGAGCAGCAACTCCAGCAG
1 CACGCAACAGCAGCTCCAGC-AGAGCAGCAACTCCAGCAG
208383 GTAGCAATCT
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
55 78 0.93
56 5 0.06
57 1 0.01
ACGTcount: A:0.31, C:0.37, G:0.23, T:0.09
Consensus pattern (54 bp):
CACGCAACAGCAGCTCCAGCAGAGCAGCAACTCCAGCAGTGACTGCAACTCTAG
Found at i:208623 original size:8 final size:10
Alignment explanation
Indices: 208603--208636 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
208593 TTCGATATAC
208603 TTTTTTGATA
1 TTTTTTGATA
208613 TTTTTT-A-A
1 TTTTTTGATA
208621 TTTTTTGATA
1 TTTTTTGATA
208631 TTTTTT
1 TTTTTT
208637 CCTCGAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 7 0.32
9 2 0.09
10 13 0.59
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (10 bp):
TTTTTTGATA
Found at i:209343 original size:51 final size:52
Alignment explanation
Indices: 209255--209354 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 52
209245 CAATTGCTCA
* * *
209255 TAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTCCTT
1 TAATCAGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCCTT
* * *
209306 TAATCAGGGATACTCCAACTCTGATTTTGTTTCCAAAAAACACCAATTT
1 TAATCAGGGATACTCCAACCCCGATTTTATTTCC-AAAAACACCAATTT
209355 TTCACAATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 28 0.68
53 13 0.32
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (52 bp):
TAATCAGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCCTT
Found at i:209526 original size:51 final size:51
Alignment explanation
Indices: 209454--209949 Score: 367
Period size: 51 Copynumber: 9.5 Consensus size: 51
209444 AAAATATTGA
* *
209454 TTTCTCATAAT-GGGAGATACTCCAACCCCGATTTTATTTCTAAAACACTAAT
1 TTTC-CATAATCGGG-GATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
* * *
209506 TTTCCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAA
1 TTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAAT
* * *
209558 TTTCCTTTAATCAGGGATACTTCAACCCCGGTTTTATTT-TAAAAACACCAAT
1 TTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAAT
* * * * * ***** * *
209610 CTTT-CACAATCGAGGATATTCCAACCTCGTTATTTCATCGGGGATACTCCAA-
1 -TTTCCATAATCGGGGATACTCCAACCCCGGT-TTT-ATTTCTAAAACACCAAT
** * * * * ***
209662 -CCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCAAAAATATTGA-
1 TTTCCA-TA-AT-C--GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
* * *
209716 TTTCTCATAATTGGGGATACTCCAACCCCGGTTTTATTTCTAAAATACTAAT
1 TTTC-CATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
* * * * *
209768 TTTTCATAATCGGGGATACTCTAACCCCAGTTTTATTTTTCAAAACACCAAA
1 TTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAAT
* *
209820 TTTCCTTTAATCGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAA-
1 TTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
* * * *
209871 TTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
1 TTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTATTT-CTAAAACACCAAT
* * *
209924 TTTTCACAATCGAGGATACTCCAACC
1 TTTCCATAATCGGGGATACTCCAACC
209950 TCGTTATTTC
Statistics
Matches: 350, Mismatches: 74, Indels: 40
0.75 0.16 0.09
Matches are distributed among these distances:
51 153 0.44
52 89 0.25
53 78 0.22
54 7 0.02
55 6 0.02
56 17 0.05
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
TTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
Found at i:209593 original size:104 final size:102
Alignment explanation
Indices: 209469--209949 Score: 389
Period size: 104 Copynumber: 4.6 Consensus size: 102
209459 CATAATGGGA
* * *
209469 GATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCATAATCGGGGATACTCTAACCCC
1 GATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCCATAATCGGGGATACTCCAACCCC
209534 GGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCAGG
66 GGTTTTATTTTT-AAAACACC-AATTTCCTTTAATCAGG
* * * *
209573 GATACTTCAACCCCGGTTTTATTT-TAAAAACACCAATCTTT-CACAATCGAGGATATTCCAACC
1 GATACTCCAACCCCGGTTTTATTTCT-AAAACACCAAT-TTTCCATAATCGGGGATACTCCAACC
* * ***** * * ** * *
209636 TCGTTATTTCATCGGGGATACTCCAA-CCCCATTACCTCCGAGGG
64 CCGGT-TTT-ATTTTTAAAACACCAATTTCCTTTA-AT-C-A-GG
* * * *** *
209680 GATACTCCAACCCCGGCTTTATTTCAAAAATATTGA-TTTCTCATAATTGGGGATACTCCAACCC
1 GATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTC-CATAATCGGGGATACTCCAACCC
* * * *
209744 CGGTTTTATTTCTAAAATACTAATTT--TTCATAATCGGG
65 CGGTTTTATTTTTAAAACACCAATTTCCTT--TAATCAGG
* * * * *
209782 GATACTCTAACCCCAGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGGATACTCCAACC
1 GATACTCCAACCCCGGTTTTATTTCT-AAAACACCAATTTTCC-ATAATCGGGGATACTCCAACC
*
209847 CCGGTTTTATTTTTAAAACACCAATTTCCTTTAATCGGG
64 CCGGTTTTATTTTTAAAACACCAATTTCCTTTAATCAGG
* * * * * *
209886 GATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACC
1 GATACTCCAACCCCGGTTTTATTT-CTAAAACACCAATTTTCCATAATCGGGGATACTCCAACC
209950 TCGTTATTTC
Statistics
Matches: 285, Mismatches: 72, Indels: 41
0.72 0.18 0.10
Matches are distributed among these distances:
102 23 0.08
103 31 0.11
104 147 0.52
105 23 0.08
106 10 0.04
107 51 0.18
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (102 bp):
GATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCCATAATCGGGGATACTCCAACCCC
GGTTTTATTTTTAAAACACCAATTTCCTTTAATCAGG
Found at i:209805 original size:262 final size:257
Alignment explanation
Indices: 209252--209871 Score: 985
Period size: 262 Copynumber: 2.4 Consensus size: 257
209242 TCTCAATTGC
*
209252 TCATAATCGGGGATACTCCAACCCCGGTTTTA-TTTTCAAAACACC-AATTTCCTTTAATCAGGG
1 TCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCAGGG
* * * * * *
209315 ATACTCCAACTCTGATTTTGTTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCT
66 ATACTCCAACCCCGGTTTTATTT--TAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCT
* * *
209380 CGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCTGGCTTCCA
129 CGTTATTTCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTCAA
209445 AAATATTGATTTCTCATAATGGGAGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT
194 AAATATTGATTTCTCATAATGGGAGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT
*
209509 CCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCAGGG
1 TCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCAGGG
* *
209574 ATACTTCAACCCCGGTTTTATTTTAAAAACACCAATCTTTCACAATCGAGGATATTCCAACCTCG
66 ATACTCCAACCCCGGTTTTATTTTAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCTCG
209639 TTATTTCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTT
131 TTATTTCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGC-----TT
* *
209704 CAAAAATATTGATTTCTCATAATTGGG-GATACTCCAACCCCGGTTTTATTTCTAAAATACTAAT
191 CAAAAATATTGATTTCTCATAA-TGGGAGATACTCCAACCCCGATTTTATTTCTAAAACACTAAT
209768 TTT
255 TTT
* *
209771 TCATAATCGGGGATACTCTAACCCCAGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCGGGG
1 TCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCAGGG
*
209836 ATACTCCAACCCCGGTTTTATTTTTAAAACACCAAT
66 ATACTCCAACCCCGGTTTTATTTTAAAAACACCAAT
209872 TTCCTTTAAT
Statistics
Matches: 335, Mismatches: 20, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
257 125 0.37
258 13 0.04
259 36 0.11
262 157 0.47
263 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (257 bp):
TCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCAGGG
ATACTCCAACCCCGGTTTTATTTTAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCTCG
TTATTTCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTCAAAA
ATATTGATTTCTCATAATGGGAGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT
Found at i:209961 original size:314 final size:313
Alignment explanation
Indices: 209444--210059 Score: 972
Period size: 314 Copynumber: 2.0 Consensus size: 313
209434 CCTGGCTTCC
* * * *
209444 AAAATATTGATTTCTCATAATGGGAGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT
1 AAAATACTAATTTCTCATAATGGGAGATACTCCAACCCCGATTTTATTTCTAAAACACCAAATTT
*
209509 CCATAATCGGGGATACTCTAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCAGGG
66 CCATAATCGGGGATACTCCAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCAGGG
* * * *
209574 ATACTTCAACCCCGGTTTTATTTTAAAAACACCAATCTTTCACAATCGAGGATATTCCAACCTCG
131 ATACTCCAACCCCGATTTTATTTCAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCTCG
*
209639 TTATTTCATCGGGGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTA-TT
196 TTATTTCATCGGGGATACTCCAACCCCATTACCTCCAAGGGGATACTCCAACCCCGGCTTTATTT
209703 TCAAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCGGTTTTATTTCT
261 TC-AAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCGGTTTTATTTCT
* * *
209757 AAAATACTAATTTTTCATAATCGGG-GATACTCTAACCCC-AGTTTTATTTTTCAAAACACCAAA
1 AAAATACTAATTTCTCATAAT-GGGAGATACTCCAACCCCGA-TTTTATTTCT-AAAACACCAAA
*
209820 TTTCCTTTAATCGGGGATACTCCAACCCCGGTTTTATTTTT-AAAACACC-AATTTCCTTTAATC
63 TTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATC
* * *
209883 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAA
127 AGGGATACTCCAACCCCGATTTTATTT-CAAAAACACCAATCTTTCACAATCGAGGATACTCCAA
*
209948 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGGCTT
191 CCTCGTTATTTCATCGGGGATACTCCAACCCCATTACCTCCAAGGGGATACTCCAACCCCGGCTT
*
210013 TATTTTCAGAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
256 TATTTTCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
210060 TTATTTCCGA
Statistics
Matches: 278, Mismatches: 19, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
312 1 0.00
313 77 0.28
314 163 0.59
315 37 0.13
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (313 bp):
AAAATACTAATTTCTCATAATGGGAGATACTCCAACCCCGATTTTATTTCTAAAACACCAAATTT
CCATAATCGGGGATACTCCAACCCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATCAGGG
ATACTCCAACCCCGATTTTATTTCAAAAACACCAATCTTTCACAATCGAGGATACTCCAACCTCG
TTATTTCATCGGGGATACTCCAACCCCATTACCTCCAAGGGGATACTCCAACCCCGGCTTTATTT
TCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCGGTTTTATTTCT
Found at i:209968 original size:28 final size:29
Alignment explanation
Indices: 209932--210008 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
209922 ATTTTTCACA
* * * *
209932 ATCGAGGATACTCCAACCTCGTTA-TTTC
1 ATCGGGGATACTCCAACCCCGTTACCTCC
209960 ATCGGGGATACTCCAACCCCGTTACCTCC
1 ATCGGGGATACTCCAACCCCGTTACCTCC
*
209989 A-AGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
210009 GCTTTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 40 0.93
29 3 0.07
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTACCTCC
Found at i:210094 original size:79 final size:79
Alignment explanation
Indices: 209962--210166 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 79
209952 GTTATTTCAT
** *
209962 CGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGGCTTTATTT-TCAGAAT-
1 CGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGACTTTATTTCTC--AATC
* * *
210025 ATTGATTTCTCATAAT
64 ATCGATTTCTCACAAC
* * * * *
210041 TGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCTAATCCCGATTTTATTTCTCAATCAT
1 CGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGACTTTATTTCTCAATCAT
*
210106 CGATTTTTCACAAC
66 CGATTTCTCACAAC
* * *
210120 CGGGGATACTCCAACCCCATTATTTTCAAGAGGATACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCG
210167 TTATTATCTC
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
78 3 0.03
79 100 0.95
80 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGACTTTATTTCTCAATCAT
CGATTTCTCACAAC
Found at i:210853 original size:33 final size:33
Alignment explanation
Indices: 210811--210875 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
210801 TCAACGATTT
210811 GTATCGATACATAAAGTGTTGTATCGATACAAC
1 GTATCGATACATAAAGTGTTGTATCGATACAAC
*** *
210844 GTATCGATACATATTTTTTTGTATCGATACAA
1 GTATCGATACATAAAGTGTTGTATCGATACAA
210876 TTTAAGCTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (33 bp):
GTATCGATACATAAAGTGTTGTATCGATACAAC
Found at i:211006 original size:52 final size:52
Alignment explanation
Indices: 210950--211078 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
210940 CACTGATCTT
* *
210950 TGTATCGATACATGCAGGCAAATTTGCCCATATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
211002 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
211054 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
211079 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:214811 original size:2 final size:2
Alignment explanation
Indices: 214804--214860 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
214794 GTACGCTACC
214804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
214846 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
214861 GAGAATGCTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:215116 original size:2 final size:2
Alignment explanation
Indices: 215111--215136 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
215101 TTTTCCAAGT
215111 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
215137 ATGTATTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:215541 original size:17 final size:17
Alignment explanation
Indices: 215507--215555 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
215497 AAATAAATTA
215507 AAATA-TTTTTATATTTT
1 AAATATTTTTTA-ATTTT
*
215524 -AATTTTATTTTAATTTT
1 AAATATT-TTTTAATTTT
215541 AAATATTTTTTAATT
1 AAATATTTTTTAATT
215556 AAATAAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 3 0.11
17 14 0.52
18 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AAATATTTTTTAATTTT
Found at i:215780 original size:14 final size:14
Alignment explanation
Indices: 215732--215781 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
215722 AACAGTTTTT
215732 TTATATTTTAAAAA
1 TTATATTTTAAAAA
*
215746 TTATACTTTT--TAA
1 TTATA-TTTTAAAAA
*
215759 TAATATTTTAAAAA
1 TTATATTTTAAAAA
215773 TTATATTTT
1 TTATATTTT
215782 TTTATAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 15 0.52
15 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATATTTTAAAAA
Found at i:215798 original size:28 final size:27
Alignment explanation
Indices: 215734--215794 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
215724 CAGTTTTTTT
215734 ATATTTTAAAAATTATACTTTTTAATA
1 ATATTTTAAAAATTATACTTTTTAATA
* *
215761 ATATTTTAAAAATTATATTTTTTTATA
1 ATATTTTAAAAATTATACTTTTTAATA
*
215788 GTATTTT
1 ATATTTT
215795 TAAATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
ATATTTTAAAAATTATACTTTTTAATA
Found at i:215804 original size:19 final size:19
Alignment explanation
Indices: 215780--215817 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
215770 AAATTATATT
*
215780 TTTTTATAGTATTTTTAAA
1 TTTTTATAGTAATTTTAAA
*
215799 TTTTTATATTAATTTTAAA
1 TTTTTATAGTAATTTTAAA
215818 ATAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTTATAGTAATTTTAAA
Found at i:215829 original size:25 final size:26
Alignment explanation
Indices: 215796--215844 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
215786 TAGTATTTTT
* *
215796 AAATTTTTATATTA-ATTTTAAAATA
1 AAATATTTATATTATATTATAAAATA
*
215821 AAATATTTATTTTATATTATAAAA
1 AAATATTTATATTATATTATAAAA
215845 ATTAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATATTTATATTATATTATAAAATA
Found at i:218346 original size:7 final size:7
Alignment explanation
Indices: 218334--218363 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
218324 CTGGTGTGCT
218334 AATATTA
1 AATATTA
218341 AATATTA
1 AATATTA
218348 AATATTA
1 AATATTA
218355 AATATTA
1 AATATTA
218362 AA
1 AA
218364 CTAATAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATATTA
Found at i:219733 original size:18 final size:18
Alignment explanation
Indices: 219706--219747 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
219696 GTGCATATAC
219706 AAAG-AAAGAGAAAAAAG
1 AAAGAAAAGAGAAAAAAG
*
219723 AAAGAAAAGAGGAAAAAG
1 AAAGAAAAGAGAAAAAAG
219741 AAA-AAAA
1 AAAGAAAA
219748 ATTATATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGAGAAAAAAG
Found at i:219819 original size:25 final size:26
Alignment explanation
Indices: 219785--219835 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
219775 TATTTAAAGT
219785 ATTAT-AAAAATTTTATTTATATAAA
1 ATTATAAAAAATTTTATTTATATAAA
219810 ATTATAAAAAATTTTATTTATATAAA
1 ATTATAAAAAATTTTATTTATATAAA
219836 TTTTTAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTATAAAAAATTTTATTTATATAAA
Found at i:219838 original size:15 final size:15
Alignment explanation
Indices: 219786--219839 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
219776 ATTTAAAGTA
219786 TTATAAAAATTTTAT
1 TTATAAAAATTTTAT
219801 TTATATAAAA--TTA-
1 TTATA-AAAATTTTAT
219814 -TA-AAAAATTTTAT
1 TTATAAAAATTTTAT
*
219827 TTATATAAATTTT
1 TTATAAAAATTTT
219840 TAAGTGGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
10 4 0.12
11 1 0.03
12 5 0.16
14 5 0.16
15 13 0.41
16 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATAAAAATTTTAT
Found at i:220473 original size:2 final size:2
Alignment explanation
Indices: 220468--220499 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
220458 GTTAAAAAAT
220468 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
220500 CACACATTTA
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):
TA
Found at i:220713 original size:35 final size:35
Alignment explanation
Indices: 220673--220744 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
220663 TTATCTACAC
*
220673 ATTATTTTTTACTTGAAGGAAGGGAGATTTTAAAT
1 ATTATTTTTTACTTGAAGGAACGGAGATTTTAAAT
*
220708 ATTATTTTTTACTTGAAGGAACGGTGATTTTAAAT
1 ATTATTTTTTACTTGAAGGAACGGAGATTTTAAAT
220743 AT
1 AT
220745 GAAGGGAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.44
Consensus pattern (35 bp):
ATTATTTTTTACTTGAAGGAACGGAGATTTTAAAT
Found at i:220755 original size:54 final size:54
Alignment explanation
Indices: 220691--220801 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
220681 TTACTTGAAG
220691 GAAGGGAGATTTTAAATATTATTTTTTACTTGAAGGAACGGTGATTTTAAATAT
1 GAAGGGAGATTTTAAATATTATTTTTTACTTGAAGGAACGGTGATTTTAAATAT
*
220745 GAAGGGAGATTTTAAATATTATTTTTTACTTGAAGGAAGGGTGATTTTAAATAT
1 GAAGGGAGATTTTAAATATTATTTTTTACTTGAAGGAACGGTGATTTTAAATAT
220799 GAA
1 GAA
220802 ATGAAAGGTC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.40
Consensus pattern (54 bp):
GAAGGGAGATTTTAAATATTATTTTTTACTTGAAGGAACGGTGATTTTAAATAT
Found at i:220895 original size:19 final size:20
Alignment explanation
Indices: 220871--220919 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
220861 TTTGTTACAC
220871 AAAAATAATTTA-GTCAATA
1 AAAAATAATTTATGTCAATA
*
220890 AAAAATGATTTATTGGTCAATA
1 AAAAATAATTTA-T-GTCAATA
220912 AAAAATAA
1 AAAAATAA
220920 GGCATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
22 14 0.56
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (20 bp):
AAAAATAATTTATGTCAATA
Found at i:221072 original size:14 final size:16
Alignment explanation
Indices: 221048--221079 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
221038 TTATCAATAA
221048 AATTATTTAAAAT-TT
1 AATTATTTAAAATATT
221063 AATT-TTTAAAATATT
1 AATTATTTAAAATATT
221078 AA
1 AA
221080 AATATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTATTTAAAATATT
Found at i:221201 original size:29 final size:32
Alignment explanation
Indices: 221169--221231 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
221159 TTTAATAATA
*
221169 TAATATAA-T-TTATTTTAATAATAA-ATTAT
1 TAATATAATTATTATTTTAATAAAAATATTAT
*
221198 TAATCTAATTAATTATTTTAATAAAAATATTAT
1 TAATATAATT-ATTATTTTAATAAAAATATTAT
221231 T
1 T
221232 TAAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 7 0.25
30 1 0.04
32 14 0.50
33 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
TAATATAATTATTATTTTAATAAAAATATTAT
Found at i:221231 original size:17 final size:17
Alignment explanation
Indices: 221209--221249 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
221199 AATCTAATTA
*
221209 ATTATTTTAATAAA-AAT
1 ATTA-TTTAAAAAATAAT
221226 ATTATTTAAAAAATAAT
1 ATTATTTAAAAAATAAT
221243 ATT-TTTA
1 ATTATTTA
221250 TTCAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATTTAAAAAATAAT
Found at i:221504 original size:28 final size:26
Alignment explanation
Indices: 221479--221534 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
221469 AGTGTTTATA
*
221479 ATAAATAGTATTATTTTAAGTATTTAAT
1 ATAAATA-TAATATTTT-AGTATTTAAT
* *
221507 ATTAATATAATATTTTAGTATTAAAT
1 ATAAATATAATATTTTAGTATTTAAT
221533 AT
1 AT
221535 TATTAAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 8 0.32
28 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (26 bp):
ATAAATATAATATTTTAGTATTTAAT
Found at i:221677 original size:19 final size:20
Alignment explanation
Indices: 221643--221687 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
221633 AAATAATATT
221643 TAATAATAATTATCTTAG-A
1 TAATAATAATTATCTTAGAA
* * *
221662 TAATAATATTTTTCTTTGAA
1 TAATAATAATTATCTTAGAA
221682 TAATAA
1 TAATAA
221688 ATTATAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
TAATAATAATTATCTTAGAA
Found at i:221809 original size:15 final size:15
Alignment explanation
Indices: 221791--221841 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
221781 TATAATTTGT
221791 AAATATTTAATAATA
1 AAATATTTAATAATA
*
221806 AAATTTTTAAT-ATAA
1 AAATATTTAATAAT-A
*
221821 ATAATACTTTAATAGTA
1 A-AATA-TTTAATAATA
221838 AAAT
1 AAAT
221842 CCATAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.07
15 12 0.41
16 6 0.21
17 8 0.28
18 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
AAATATTTAATAATA
Found at i:221944 original size:423 final size:436
Alignment explanation
Indices: 221274--222101 Score: 1351
Period size: 423 Copynumber: 1.9 Consensus size: 436
221264 TATAACATTA
* *
221274 TTAAATTTTAAATATTATTTTTAATATTTTATTGATAATTTTTTTATATTAATTTTTAAAATAAA
1 TTAAAATTTAAATATTATTTTTAATATTTTATTGATAATTTGTTTATATTAATTTTTAAAATAAA
* *
221339 TTTATATAAACTTTAACTTATAAATATTAAATAAAAAATTCTTAATATGAAAATATTAATATTTT
66 TTTATATAAACTATAACTTATAAATATTAAATAAAAAATTCTTAATAT--AAATATTAATACTTT
*
221404 AATAGTATGAATATCCATAGAAATAATATTTTAATAATTATTATTTTTTAAATATTTATATAATT
129 AATAGTA-GAATATCCATAGAAATAATATTTTAATAATTATTATATTTTAAATATTTATATAATT
221469 AGTGTTTATAATAAATAGTATTATTTTAAGTATTTAATATTAATATAATATTTTAGTATTAAATA
193 AGTGTTTATAATAAATAGTATTATTTTAAGTATTTAATATTAATATAATATTTTAGTATTAAATA
*
221534 TTATTAAAGGAGTACTATTTTAATATT-AAAA-ATATAGTTTAATGATGAATAGTTATT-ATATT
258 TTATTAAAGGAGTACTATTTTAATATTAAAAATATATAGTTTAATGATGAATAATTATTAATATT
* *
221596 TTAATATCTTTGTCAATATTACTATTTAAAAATTGTAAAATAATATTTAATAATAATTATCTTAG
323 TTAATATCTTTGCCAATATTACTATTGAAAAATTGTAAAATAATATTTAATAATAATTATCTTAG
221661 -ATAA-TAATATTTTTCTTTGAATAATAAATTATAACATCATTAATATT
388 TATAAGTAATATTTTTCTTTGAATAATAAATTATAACATCATTAATATT
221708 TTAAAATTTAAATATTA-TTTTAATATTTTA-TGAT-ATTTGTTTATATTAATTTTTAAAATAAA
1 TTAAAATTTAAATATTATTTTTAATATTTTATTGATAATTTGTTTATATTAATTTTTAAAATAAA
* * * *
221770 TTTATATAAACTATAATTTGTAAATATTTAATAATAAAATTTTTAATAT-AA-A-TAATACTTTA
66 TTTATATAAACTATAACTTATAAATATTAAATAA-AAAATTCTTAATATAAATATTAATACTTTA
*
221832 ATAGTA-AA-ATCCATAGAAATAATATTTTAATAATTCTTATATTTTAAATATTTATATAATTAG
130 ATAGTAGAATATCCATAGAAATAATATTTTAATAATTATTATATTTTAAATATTTATATAATTAG
*
221895 T-TTTATGATAAATAGTATTATTTTAAGTATTTAATATTAATATAATATTTTAGTATTAAATATT
195 TGTTTATAATAAATAGTATTATTTTAAGTATTTAATATTAATATAATATTTTAGTATTAAATATT
* * * *
221959 ATTAAAGTATTATTATTTTAATATTAAAAATATATAGTTTAATGATGAATAATTTTTAATATTTT
260 ATTAAAGGAGTACTATTTTAATATTAAAAATATATAGTTTAATGATGAATAATTATTAATATTTT
*
222024 AATATCTTTGCCAATATTACTATTGGAAAATTGTAAAATAATATTTAATAATAATTATCTTAGTA
325 AATATCTTTGCCAATATTACTATTGAAAAATTGTAAAATAATATTTAATAATAATTATCTTAGTA
222089 TAAGTAATATTTT
390 TAAGTAATATTTT
222102 AATAATAAAT
Statistics
Matches: 369, Mismatches: 19, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
423 84 0.23
424 58 0.16
425 26 0.07
426 67 0.18
427 19 0.05
428 10 0.03
429 2 0.01
431 57 0.15
432 17 0.05
433 13 0.04
434 16 0.04
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (436 bp):
TTAAAATTTAAATATTATTTTTAATATTTTATTGATAATTTGTTTATATTAATTTTTAAAATAAA
TTTATATAAACTATAACTTATAAATATTAAATAAAAAATTCTTAATATAAATATTAATACTTTAA
TAGTAGAATATCCATAGAAATAATATTTTAATAATTATTATATTTTAAATATTTATATAATTAGT
GTTTATAATAAATAGTATTATTTTAAGTATTTAATATTAATATAATATTTTAGTATTAAATATTA
TTAAAGGAGTACTATTTTAATATTAAAAATATATAGTTTAATGATGAATAATTATTAATATTTTA
ATATCTTTGCCAATATTACTATTGAAAAATTGTAAAATAATATTTAATAATAATTATCTTAGTAT
AAGTAATATTTTTCTTTGAATAATAAATTATAACATCATTAATATT
Found at i:229866 original size:79 final size:79
Alignment explanation
Indices: 229703--229907 Score: 227
Period size: 79 Copynumber: 2.6 Consensus size: 79
229693 AACCTCCTTT
* * * *** *
229703 TTATTTCCAAAATATTAATTTTTTTCATCTTAGGGATACTCCAAACCC-ATTATTTTTTAGGGGA
1 TTATTTCCAAAATATTAA-ATTTTTCATCTTAGGGATACTCC-AACCCTATCAATTCCGAGGAGA
* *
229767 TACTTCAACCCCGTTT
64 TACTTCAACCCCGCTC
* *
229783 TTATTTTCAAAATATTAAATTTTTCATCTTAAGGATACTCCAACCCTATCAATTCCGAGGAGATA
1 TTATTTCCAAAATATTAAATTTTTCATCTTAGGGATACTCCAACCCTATCAATTCCGAGGAGATA
*
229848 -TTCCAATCCCGCTC
66 CTT-CAACCCCGCTC
** *
229862 TTATTTCCAAAATGCTAAATTTTTCATCTT-GGGATACTCTAACCCT
1 TTATTTCCAAAATATTAAATTTTTCATCTTAGGGATACTCCAACCCT
229908 GTTTCTTTTT
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
78 21 0.20
79 68 0.64
80 17 0.16
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (79 bp):
TTATTTCCAAAATATTAAATTTTTCATCTTAGGGATACTCCAACCCTATCAATTCCGAGGAGATA
CTTCAACCCCGCTC
Found at i:232380 original size:16 final size:16
Alignment explanation
Indices: 232319--232380 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
232309 CTCGAATCCC
*
232319 AAATGACCCAAAACTCA
1 AAATGACCC-AAACTCG
* * *
232336 AAATAACTCAAACCCG
1 AAATGACCCAAACTCG
* * *
232352 AAATTATCTAAACTCG
1 AAATGACCCAAACTCG
232368 AAATGACCCAAAC
1 AAATGACCCAAAC
232381 AATTAACCCG
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
16 26 0.79
17 7 0.21
ACGTcount: A:0.50, C:0.27, G:0.06, T:0.16
Consensus pattern (16 bp):
AAATGACCCAAACTCG
Found at i:235006 original size:67 final size:67
Alignment explanation
Indices: 234898--235041 Score: 216
Period size: 67 Copynumber: 2.1 Consensus size: 67
234888 TGGCATTATA
* *
234898 CTTAGTTGCTCTCATTTCTATTGATTTTGCCATGCAAAGTAGTGGTGTAGCAACTCCAAGTACTA
1 CTTAGCTGCTCTCATCTCTATTGATTTTGCCATGCAAAGTAGTGGTGTAGCAACTCCAAGTACTA
234963 TG
66 TG
* * ** * *
234965 CTTAGCTGCTCTTATCTCTATTGGTTTTGCCATGCAAAGTAGTGGTGTAGCAACTTTAAGTATTG
1 CTTAGCTGCTCTCATCTCTATTGATTTTGCCATGCAAAGTAGTGGTGTAGCAACTCCAAGTACTA
235030 TG
66 TG
235032 CTTAGCTGCT
1 CTTAGCTGCT
235042 TGTCGCCATT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (67 bp):
CTTAGCTGCTCTCATCTCTATTGATTTTGCCATGCAAAGTAGTGGTGTAGCAACTCCAAGTACTA
TG
Found at i:235721 original size:36 final size:37
Alignment explanation
Indices: 235672--235746 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 37
235662 TTTGGACATA
*
235672 TAATTTTAGTTATTTAT-GA-TATATA-ACATTTTATT
1 TAATTCTAGTTATTTATCGATTATATATACATTTT-TT
*
235707 TAATTCTAGCTTATTTATCTATTATATATACATTTTTT
1 TAATTCTAG-TTATTTATCGATTATATATACATTTTTT
235745 TA
1 TA
235747 TTAATTATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 8 0.24
36 8 0.24
37 1 0.03
38 10 0.29
39 7 0.21
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (37 bp):
TAATTCTAGTTATTTATCGATTATATATACATTTTTT
Found at i:236987 original size:19 final size:19
Alignment explanation
Indices: 236963--237001 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
236953 TTAATTAAGT
236963 TTGGATTTCAAAAGATAAA
1 TTGGATTTCAAAAGATAAA
236982 TTGGATTTCAAAAGATAAA
1 TTGGATTTCAAAAGATAAA
237001 T
1 T
237002 GATTAATAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (19 bp):
TTGGATTTCAAAAGATAAA
Found at i:237927 original size:12 final size:12
Alignment explanation
Indices: 237910--237955 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
237900 TGCCGCCAAT
237910 TTTGAAATTCAA
1 TTTGAAATTCAA
*
237922 TTTGAAATAGTAAA
1 TTTGAAAT--TCAA
237936 TGTTGAAATTCAA
1 T-TTGAAATTCAA
237949 TTTGAAA
1 TTTGAAA
237956 CAGTGAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (12 bp):
TTTGAAATTCAA
Found at i:237967 original size:27 final size:27
Alignment explanation
Indices: 237911--237967 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
237901 GCCGCCAATT
*
237911 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAATG
237938 TTGAAATTCAATTTGAAACAGTGAAA-G
1 TTGAAATTCAATTTGAAACAGT-AAATG
237965 TTG
1 TTG
237968 CACAGTACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAATG
Found at i:242641 original size:12 final size:12
Alignment explanation
Indices: 242624--242655 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
242614 GAAAACAAAG
242624 GCTGCCAACTGT
1 GCTGCCAACTGT
242636 GCTGCCAACTGT
1 GCTGCCAACTGT
*
242648 GCCGCCAA
1 GCTGCCAA
242656 TTTTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:242672 original size:12 final size:12
Alignment explanation
Indices: 242657--242702 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
242647 TGCCGCCAAT
242657 TTTGAAATTCAA
1 TTTGAAATTCAA
*
242669 TTTGAAATAGTAAA
1 TTTGAAAT--TCAA
242683 TGTTGAAATTCAA
1 T-TTGAAATTCAA
242696 TTTGAAA
1 TTTGAAA
242703 CAGTGAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (12 bp):
TTTGAAATTCAA
Found at i:242714 original size:27 final size:27
Alignment explanation
Indices: 242658--242714 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
242648 GCCGCCAATT
* *
242658 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
242685 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
242712 TTG
1 TTG
242715 CACAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:246452 original size:21 final size:20
Alignment explanation
Indices: 246428--246471 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
246418 AAAAAAAAAT
* *
246428 TTATATTAATTTTAACTATTA
1 TTATATTAAATTTAA-TAGTA
246449 TTATATTAAATTTAATAGTA
1 TTATATTAAATTTAATAGTA
246469 TTA
1 TTA
246472 AAGATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATATTAAATTTAATAGTA
Found at i:251534 original size:34 final size:34
Alignment explanation
Indices: 251467--251683 Score: 267
Period size: 34 Copynumber: 6.4 Consensus size: 34
251457 ATGTAAAGAA
* *
251467 TGTTGATTAAAT-GGTGATTTGATAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * * *
251500 TATTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
251534 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* **
251568 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
251602 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
251636 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
251670 TGTTGATTAAATGG
1 TGTTGATTAAATGG
251684 TGGTTTTTAC
Statistics
Matches: 157, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
33 14 0.09
34 142 0.90
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:251659 original size:102 final size:101
Alignment explanation
Indices: 251467--251683 Score: 344
Period size: 102 Copynumber: 2.1 Consensus size: 101
251457 ATGTAAAGAA
** * * *
251467 TGTTGATTAAATGGTGATTTGATAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
251532 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
*
251568 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
* * *
251633 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
251670 TGTTGATTAAATGG
1 TGTTGATTAAATGG
251684 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 14 0.13
102 92 0.87
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:256148 original size:34 final size:34
Alignment explanation
Indices: 256091--256307 Score: 276
Period size: 34 Copynumber: 6.4 Consensus size: 34
256081 AAGTGGGAGA
*
256091 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
256124 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
256158 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
256192 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
256226 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
256260 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
*
256294 ATTGTTGATCAAAT
1 ATTGTTGATTAAAT
256308 AGTGGTTTTT
Statistics
Matches: 160, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
33 17 0.11
34 143 0.89
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:256234 original size:102 final size:101
Alignment explanation
Indices: 256091--256307 Score: 335
Period size: 102 Copynumber: 2.1 Consensus size: 101
256081 AAGTGGGAGA
** * * * *
256091 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
256156 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
256192 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
256257 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
256294 ATTGTTGATCAAAT
1 ATTGTTGATTAAAT
256308 AGTGGTTTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:265224 original size:28 final size:28
Alignment explanation
Indices: 265171--265225 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
265161 ACTCAAATCA
* **
265171 TTAGGTAAGTAACTTACCAATTTTTTTG
1 TTAGGTAAGTAACTTAACAAGATTTTTG
*
265199 TTAGGTAAGTAACTTAACTAGATTTTT
1 TTAGGTAAGTAACTTAACAAGATTTTT
265226 TAGCTCAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (28 bp):
TTAGGTAAGTAACTTAACAAGATTTTTG
Found at i:267964 original size:2 final size:2
Alignment explanation
Indices: 267949--267982 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
267939 TTATTAATGT
* *
267949 TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
267983 AGCTAAATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:268058 original size:2 final size:2
Alignment explanation
Indices: 268051--268077 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
268041 ATTGAGAAGT
268051 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 T
268078 GCTAAATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:268074 original size:94 final size:93
Alignment explanation
Indices: 267959--268130 Score: 299
Period size: 94 Copynumber: 1.8 Consensus size: 93
267949 TATATATGTG
267959 TATATATATATATATATATATATAAGCTAAATGCTAAAGTGCATTATTGTATAATATCTTAAAAA
1 TATATATATATATATATATATATAAGCTAAATGCTAAAGTGCATTATTGTATAATATCTTAAAAA
268024 GTTATTTATTTATTCTAATTGAGAAGTTA
66 GTTATTT-TTTATTCTAATTGAGAAGTTA
* * * *
268053 TATATATATATATATATATATATATGCTAAATGCTCAAGTTCATTATTTTATAATATCTTAAAAA
1 TATATATATATATATATATATATAAGCTAAATGCTAAAGTGCATTATTGTATAATATCTTAAAAA
268118 GTTATTTTTTATT
66 GTTATTTTTTATT
268131 TTTATGATAA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 6 0.08
94 68 0.92
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (93 bp):
TATATATATATATATATATATATAAGCTAAATGCTAAAGTGCATTATTGTATAATATCTTAAAAA
GTTATTTTTTATTCTAATTGAGAAGTTA
Found at i:269173 original size:51 final size:51
Alignment explanation
Indices: 269117--269219 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
269107 TTGAATTTAA
* *
269117 TAATATATTCGCACGAATTATGTATAACTCCTTAAGGTGTTTGTTTGGATC
1 TAATATATTCACACGAATTATGTATAACTCCTTAAGGTGTTTGTTTAGATC
*
269168 TAATATATTCACACGAATTATGTATAACTCCTTGAGGTGTTTGTTTAGATC
1 TAATATATTCACACGAATTATGTATAACTCCTTAAGGTGTTTGTTTAGATC
269219 T
1 T
269220 TCACTAGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (51 bp):
TAATATATTCACACGAATTATGTATAACTCCTTAAGGTGTTTGTTTAGATC
Found at i:274487 original size:13 final size:13
Alignment explanation
Indices: 274463--274494 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
274453 CTATTTTGAG
274463 TTAAGC-TTTATC
1 TTAAGCTTTTATC
274475 TTAAGCTTTTATC
1 TTAAGCTTTTATC
274488 TTAAGCT
1 TTAAGCT
274495 CCTATGAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (13 bp):
TTAAGCTTTTATC
Found at i:274591 original size:2 final size:2
Alignment explanation
Indices: 274584--274609 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
274574 TGCATTCTTG
274584 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
274610 GCATACTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:277003 original size:3 final size:3
Alignment explanation
Indices: 276995--277045 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
276985 TGAATTTTTA
276995 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
277043 TAT
1 TAT
277046 AAATAATACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:285773 original size:2 final size:2
Alignment explanation
Indices: 285766--285792 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
285756 TTGGTACTAG
285766 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 T
285793 TACTACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:288337 original size:23 final size:23
Alignment explanation
Indices: 288302--288346 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
288292 TTTAATAATT
*
288302 TATATATTCGTATTATATTTATA
1 TATATATTCGTATTATAATTATA
288325 TATATTATT-GTATTATAATTAT
1 TATA-TATTCGTATTATAATTAT
288347 GTTTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
TATATATTCGTATTATAATTATA
Found at i:289547 original size:28 final size:27
Alignment explanation
Indices: 289488--289556 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
289478 CACCAATTTG
* * *
289488 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGATTATTTTATA
289515 TTTGTCAAAAATGGTGATT-TCCTTTATA
1 TTTGTCAAAAATGGTGATTAT--TTTATA
*
289543 TTTGTCAAATATGG
1 TTTGTCAAAAATGG
289557 AGGCTTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.50
28 17 0.47
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGATTATTTTATA
Found at i:289665 original size:20 final size:20
Alignment explanation
Indices: 289640--289678 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
289630 GGCTCTCTCC
289640 TCCCTCTCAAGTATCCCTCA
1 TCCCTCTCAAGTATCCCTCA
**
289660 TCCCTCTCTTGTATCCCTC
1 TCCCTCTCAAGTATCCCTC
289679 TTCAATTCTT
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:0.13, C:0.46, G:0.05, T:0.36
Consensus pattern (20 bp):
TCCCTCTCAAGTATCCCTCA
Found at i:294232 original size:20 final size:20
Alignment explanation
Indices: 294207--294252 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
294197 AAATAGAGGC
*
294207 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
294227 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
294247 TCCCTC
1 TCCCTC
294253 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:295476 original size:18 final size:18
Alignment explanation
Indices: 295449--295510 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
295439 ATATTTTAAA
295449 ATTTAAATATTAAAAATT
1 ATTTAAATATTAAAAATT
* *
295467 ATTTATATATTAAAATTT
1 ATTTAAATATTAAAAATT
*
295485 ATATAAATA-T-AAAATT
1 ATTTAAATATTAAAAATT
*
295501 TTTTAAATAT
1 ATTTAAATAT
295511 AATTATAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
16 12 0.33
17 1 0.03
18 23 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTAAATATTAAAAATT
Found at i:295489 original size:16 final size:16
Alignment explanation
Indices: 295439--295501 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
295429 AGATAAATAA
*
295439 ATATTTTAAAATTTA-
1 ATATATTAAAATTTAT
*
295454 A-ATATTAAAAATTATTT
1 ATATATT-AAAATT-TAT
295471 ATATATTAAAATTTAT
1 ATATATTAAAATTTAT
*
295487 ATAAATATAAAATTT
1 ATATAT-TAAAATTT
295502 TTTAAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 4 0.10
15 7 0.18
16 8 0.21
17 15 0.38
18 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATTAAAATTTAT
Found at i:299929 original size:6 final size:6
Alignment explanation
Indices: 299910--299942 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
299900 GGTTTAAGTG
*
299910 ATGGTA ATGTTA ATGGTA ATGGTA ATGGTA ATG
1 ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA ATG
299943 ATGATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (6 bp):
ATGGTA
Found at i:301184 original size:2 final size:2
Alignment explanation
Indices: 301179--301206 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
301169 TTCTAATCCT
301179 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
301207 GTTGTTGTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:303945 original size:25 final size:25
Alignment explanation
Indices: 303913--303968 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
303903 AAATTAAAAA
303913 TATT-TAGTAAATAATATTATTTAT
1 TATTATAGTAAATAATATTATTTAT
303937 TATTATAGTAAATAATATTATTTAT
1 TATTATAGTAAATAATATTATTTAT
303962 TATTATA
1 TATTATA
303969 ATCAAATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
TATTATAGTAAATAATATTATTTAT
Found at i:304439 original size:2 final size:2
Alignment explanation
Indices: 304432--304469 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
304422 TTAATCTATC
304432 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
304470 TCAATGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:305795 original size:2 final size:2
Alignment explanation
Indices: 305788--305816 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
305778 TCTTTTGTAT
305788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
305817 GTTTTGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:305863 original size:22 final size:22
Alignment explanation
Indices: 305838--305881 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
305828 TTAATTCATA
305838 ATATTTTAATTAT-TTTTCTATT
1 ATATTTTAATTATATTTT-TATT
305860 ATATTTTAATTATATTTTTATT
1 ATATTTTAATTATATTTTTATT
305882 TTACATAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
ATATTTTAATTATATTTTTATT
Found at i:305871 original size:11 final size:11
Alignment explanation
Indices: 305838--305877 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
305828 TTAATTCATA
305838 ATATTTTAATT
1 ATATTTTAATT
*
305849 AT-TTTTCTATT
1 ATATTTT-AATT
305860 ATATTTTAATT
1 ATATTTTAATT
305871 ATATTTT
1 ATATTTT
305878 TATTTTACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATATTTTAATT
Found at i:307678 original size:14 final size:14
Alignment explanation
Indices: 307661--307706 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 14
307651 AATAAAAATC
307661 TTAAAATTTATATA
1 TTAAAATTTATATA
307675 TTAAAAATTATTTATATA
1 TT--AAA--ATTTATATA
307693 TTAAAATTTATATA
1 TTAAAATTTATATA
307707 AATATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.39
16 6 0.21
18 11 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAAATTTATATA
Found at i:307689 original size:18 final size:18
Alignment explanation
Indices: 307666--307703 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
307656 AAATCTTAAA
307666 ATTTATATATTAAAAATT
1 ATTTATATATTAAAAATT
*
307684 ATTTATATATTAAAATTT
1 ATTTATATATTAAAAATT
307702 AT
1 AT
307704 ATAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATATATTAAAAATT
Found at i:307711 original size:18 final size:18
Alignment explanation
Indices: 307672--307716 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
307662 TAAAATTTAT
* * *
307672 ATATTAAAAATTATTTAT
1 ATATTAAAATTTATATAA
307690 ATATTAAAATTTATATAA
1 ATATTAAAATTTATATAA
307708 ATA-TAAAAT
1 ATATTAAAAT
307717 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTAAAATTTATATAA
Found at i:307711 original size:20 final size:18
Alignment explanation
Indices: 307670--307727 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
307660 CTTAAAATTT
*
307670 ATATATTAAAAATTATTT
1 ATATATTAAAAATTATTA
*
307688 ATATATTAAAATTTATATA
1 ATATATTAAAAATTAT-TA
307707 A-ATA-TAAAATATT-TTA
1 ATATATTAAAA-ATTATTA
307723 A-ATAT
1 ATATAT
307728 AATTATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 6 0.18
17 6 0.18
18 20 0.59
19 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATATTAAAAATTATTA
Found at i:307718 original size:27 final size:28
Alignment explanation
Indices: 307688--307748 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
307678 AAAATTATTT
*
307688 ATATATTAAAAT-TTA-TATAAATATAAA
1 ATATATTAAAATATAATTAT-AATATAAA
*
307715 ATAT-TTTAAATATAATTATAATATAAA
1 ATATATTAAAATATAATTATAATATAAA
307742 A-ATATTA
1 ATATATTA
307749 TATAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 8 0.29
27 17 0.61
28 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATATTAAAATATAATTATAATATAAA
Found at i:307746 original size:19 final size:19
Alignment explanation
Indices: 307722--307759 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
307712 AAAATATTTT
307722 AAATATAAT-TATAATATAA
1 AAATATAATATA-AATATAA
*
307741 AAATATTATATAAATATAA
1 AAATATAATATAAATATAA
307760 TATGAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATAATATAAATATAA
Found at i:313918 original size:31 final size:31
Alignment explanation
Indices: 313882--313953 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
313872 TTTATATATT
313882 TTTATTATTCATGTGG-TAAGCTTTTAATTAA
1 TTTATTATTCATGTGGCT-AGCTTTTAATTAA
* * * *
313913 TTTATTTTTTATGTGGCTAGCTTTTATTTAT
1 TTTATTATTCATGTGGCTAGCTTTTAATTAA
313944 TATTATTATT
1 T-TTATTATT
313954 AATTTTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 26 0.76
32 8 0.24
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.60
Consensus pattern (31 bp):
TTTATTATTCATGTGGCTAGCTTTTAATTAA
Found at i:315515 original size:16 final size:18
Alignment explanation
Indices: 315491--315573 Score: 65
Period size: 16 Copynumber: 4.9 Consensus size: 18
315481 TTTATTATGT
315491 TATTATTATATTTA-A-AA
1 TATT-TTATATTTATATAA
315508 TATTTTATATTTATATAA
1 TATTTTATATTTATATAA
*
315526 TTTTTTATATATTAT-TAA
1 TATTTTATAT-TTATATAA
*
315544 T-TTATA-ATATTATAT-A
1 TATTTTATAT-TTATATAA
315560 -ATTTTATA-TTATAT
1 TATTTTATATTTATAT
315574 TTTTTATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
15 6 0.11
16 21 0.37
17 11 0.19
18 15 0.26
19 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTATATTTATATAA
Found at i:315533 original size:18 final size:18
Alignment explanation
Indices: 315496--315564 Score: 74
Period size: 18 Copynumber: 4.0 Consensus size: 18
315486 TATGTTATTA
*
315496 TTATATTTA-A-AATATT
1 TTATATTTATATAATTTT
315512 TTATATTTATATAATTTT
1 TTATATTTATATAATTTT
*
315530 TTATATATTAT-TAATTTA
1 TTATAT-TTATATAATTTT
*
315548 TAATA-TTATATAATTTT
1 TTATATTTATATAATTTT
315565 ATATTATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
16 13 0.29
17 7 0.16
18 21 0.47
19 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTTATATAATTTT
Found at i:315535 original size:25 final size:24
Alignment explanation
Indices: 315507--315573 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 24
315497 TATATTTAAA
*
315507 ATATTTTATATTTATATAATTTTTTAT
1 ATATTTTATA-TTATATAA--TATTAT
315534 ATATTATTA-ATT-TATAATATTAT
1 ATATT-TTATATTATATAATATTAT
315557 ATAATTTTATATTATAT
1 AT-ATTTTATATTATAT
315574 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
23 10 0.29
24 6 0.17
25 8 0.23
26 2 0.06
27 6 0.17
28 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATATTTTATATTATATAATATTAT
Found at i:315565 original size:18 final size:18
Alignment explanation
Indices: 315509--315567 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 18
315499 TATTTAAAAT
315509 ATTTTAT-AT-TTATATA
1 ATTTTATAATATTATATA
*
315525 ATTTTTTATATATTAT-TA
1 ATTTTATA-ATATTATATA
315543 A-TTTATAATATTATATA
1 ATTTTATAATATTATATA
315560 ATTTTATA
1 ATTTTATA
315568 TTATATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 13 0.36
17 8 0.22
18 11 0.31
19 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTATAATATTATATA
Found at i:317793 original size:20 final size:20
Alignment explanation
Indices: 317768--317839 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
317758 TACCCAGATC
*
317768 TATCGATATATTTTTCAATG
1 TATCGATACATTTTTCAATG
* * *
317788 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATG
*
317808 TATCGATACATTCTTCAATG
1 TATCGATACATTTTTCAATG
317828 TATCGATACATT
1 TATCGATACATT
317840 CTGTCTTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:326356 original size:27 final size:27
Alignment explanation
Indices: 326274--326685 Score: 353
Period size: 27 Copynumber: 15.0 Consensus size: 27
326264 TTTTTTTTCA
* *
326274 AAGTCCATAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
326301 AAAGTCCACCACTCCGCGG--TGCCTTTTT
1 -AAGTCCACAACTCCGTGGCAT-CC-TTTT
* * *
326329 AAGTTCACAACTCTGTGGCATCCGTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
326356 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * **
326383 AAGTCCATAAATTTGTGGCATCCGTTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* * * **
326411 AAGCCCACAACTCCATGGCGTTTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
326438 AAAGTCTACAACTCCGTGGTACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* *
326466 AAGTCCACAACTCCATGGCATCCATTTC
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* * *
326494 AAGTCTACAACTCCGTGGCGTTCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
326521 AAAGTCCACAACTCCGTGGTACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* *
326549 AAGTCTACAACTTCGTGGCA-CTCTTTT
1 AAGTCCACAACTCCGTGGCATC-CTTTT
326576 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
326603 AAGTCCATAACTTCGTGACATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* * * * **
326631 AAGCCCACAAGTCGGTGGCACCCTTCCA
1 AAGTCCACAACTCCGTGGCATCCTT-TT
* *
326659 AAGTCCACAACTTCGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
326686 TAAGCCCATA
Statistics
Matches: 297, Mismatches: 75, Indels: 25
0.75 0.19 0.06
Matches are distributed among these distances:
26 1 0.00
27 153 0.52
28 142 0.48
29 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:326438 original size:55 final size:55
Alignment explanation
Indices: 326274--326689 Score: 267
Period size: 55 Copynumber: 7.6 Consensus size: 55
326264 TTTTTTTTCA
* * * * ** **
326274 AAGTCCATAACTCCGTGGCA-CCCTTTTAAAGTCCACCACTCCGCGGTGCCTTTTT
1 AAGTCCACAACTCTGTGGCATCCGTTTT-AAGTCCACAACTCCATGGCACCTTTTT
* * *
326329 AAGTTCACAACTCTGTGGCATCCG-TTTAAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGCATCCGTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * * * ***
326383 AAGTCCATAAATTTGTGGCATCCGTTTTAAGCCCACAACTCCATGGCGTTTTTTT
1 AAGTCCACAACTCTGTGGCATCCGTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * * * * *
326438 AAAGTCTACAACTCCGTGGTA-CCCTTTTAAGTCCACAACTCCATGGCATCCATTTC
1 -AAGTCCACAACTCTGTGGCATCCGTTTTAAGTCCACAACTCCATGGCA-CCTTTTT
* * * * * * *
326494 AAGTCTACAACTCCGTGGCGTTC-TTTTAAAGTCCACAACTCCGTGGTACCCTTTT
1 AAGTCCACAACTCTGTGGCATCCGTTTT-AAGTCCACAACTCCATGGCACCTTTTT
* *
326549 AAGTCTACAACT-TCGTGGCA-CTC-TTTTAAGTCCACAACTCCGTGGCATCC-TTTT
1 AAGTCCACAACTCT-GTGGCATC-CGTTTTAAGTCCACAACTCCATGGCA-CCTTTTT
* * * * * ** ***
326603 AAGTCCATAACT-TCGTGACATCCTTTTTAAGCCCACAAGTCGGTGGCACCCTTCCA
1 AAGTCCACAACTCT-GTGGCATCCGTTTTAAGTCCACAACTCCATGGCA-CCTTTTT
**
326659 AAGTCCACAACT-TCGTGGCATCTTTTTTAAG
1 AAGTCCACAACTCT-GTGGCATCCGTTTTAAG
326690 CCCATAAGTC
Statistics
Matches: 293, Mismatches: 56, Indels: 23
0.79 0.15 0.06
Matches are distributed among these distances:
54 83 0.28
55 143 0.49
56 67 0.23
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (55 bp):
AAGTCCACAACTCTGTGGCATCCGTTTTAAGTCCACAACTCCATGGCACCTTTTT
Found at i:326466 original size:83 final size:82
Alignment explanation
Indices: 326268--326677 Score: 364
Period size: 83 Copynumber: 5.0 Consensus size: 82
326258 GTGCCATTTT
* * * * *
326268 TTTTCAAAGTCCATAACTCCGTGGCACCCTTTTAAAGTCCACCACTCCGCGG--TGCCTTTTTAA
1 TTTT-AAAGTCCACAACTCCGTGGTACCCTTTT-AAGTCCACAACTTCGTGGCAT-CC-TTTTAA
* * * *
326331 GTTCACAACTCTGTGGCATCC
62 GTCCACAACTCCGTGGCGTTC
* * * * * *
326352 GTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAAATTTGTGGCATCCGTTTTAAGCC
1 TTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTTCGTGGCATCC-TTTTAAGTC
* *
326416 CACAACTCCATGGCGTTT
65 CACAACTCCGTGGCGTTC
* * * *
326434 TTTTAAAGTCTACAACTCCGTGGTACCCTTTTAAGTCCACAACTCCATGGCATCCATTTCAAGTC
1 TTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTTCGTGGCATCC-TTTTAAGTC
*
326499 TACAACTCCGTGGCGTTC
65 CACAACTCCGTGGCGTTC
*
326517 TTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGTCTACAACTTCGTGGCA-CTCTTTTAAGTC
1 TTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTTCGTGGCATC-CTTTTAAGTC
* *
326581 CACAACTCCGTGGCATCC
65 CACAACTCCGTGGCGTTC
* * ** * * * * **
326599 TTTT-AAGTCCATAACTTCGTGACATCCTTTTTAAGCCCACAA-GTCGGTGGCACCCTTCCAAAG
1 TTTTAAAGTCCACAACTCCGTGGTA-CCCTTTTAAGTCCACAACTTC-GTGGCATCCTT-TTAAG
*
326662 TCCACAACTTCGTGGC
63 TCCACAACTCCGTGGC
326678 ATCTTTTTTA
Statistics
Matches: 269, Mismatches: 49, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
81 30 0.11
82 102 0.38
83 134 0.50
84 3 0.01
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (82 bp):
TTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGTCC
ACAACTCCGTGGCGTTC
Found at i:326688 original size:56 final size:55
Alignment explanation
Indices: 326549--327133 Score: 244
Period size: 56 Copynumber: 10.2 Consensus size: 55
326539 GTACCCTTTT
* * * * * * **
326549 AAGTCTACAACTTCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCATCCTT-TT
1 AAGTCCACAACTTCGTGGCACTTTTTTAAGCCCACAAGTCAGTGGCACCCTTCCA
* * * *
326603 AAGTCCATAACTTCGTGACATCCTTTTTAAGCCCACAAGTCGGTGGCACCCTTCCA
1 AAGTCCACAACTTCGTGGCA-CTTTTTTAAGCCCACAAGTCAGTGGCACCCTTCCA
*
326659 AAGTCCACAACTTCGTGGCATCTTTTTTAAGCCCATAAGTCAGTGGCACCCTTCCA
1 AAGTCCACAACTTCGTGGCA-CTTTTTTAAGCCCACAAGTCAGTGGCACCCTTCCA
* * * * *** *
326715 AAGCCCATAAGTTAGTGGCACTCTTTTTAAGCCCACAAGTCAGTGGCATTATTTCA
1 AAGTCCACAACTTCGTGGCACT-TTTTTAAGCCCACAAGTCAGTGGCACCCTTCCA
* ** ** * **
326771 AAGCCCACACAAGTCGGTGGCAACTCATTTGAAAGCCCATACAAGTCGGTGGCAACCCATTTTA
1 AAGTCCACA-ACTTC-GTGGC-ACT--TTTTTAAGCCC--ACAAGTCAGTGGC-ACCC-TTCCA
* ** * * ** *
326835 AAGCCCACACAAGTCGATGGTAACCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCA
1 AAGTCCACA-ACTTCG-TGG---CACTTTTTTAAGCCCACAAGTCAGTGGCACCCTTC-CA
* ** ** ** *
326896 AAGCCCACACAAATCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACTTTTTTCA
1 AAGTCCACA-ACTTC-GTGGCA-CTTTTTTAAGCCCACAAGTCAGTGGCAC-CCTTCCA
* * * * ** * *
326955 AAGCCCACAA-GTCAGTGACATCCTTTCAAAGCCCGCAAGGT-AGTGGCACCCTTTCA
1 AAGTCCACAACTTC-GTGGCA-CTTTTTTAAGCCCACAA-GTCAGTGGCACCCTTCCA
* * * ** * * *
327011 AAGCCCACAAGC-TAGTGGCACCCTTTCAAAGCCCACAAGTCAGTAGCACCATTTCA
1 AAGTCCACAA-CTTCGTGGCA-CTTTTTTAAGCCCACAAGTCAGTGGCACCCTTCCA
* * * * * * *
327067 AAGCCCACAA-GTCAGTGGCACTCTTTTTAAAGCACATAAGTTAGTGGCATCCTTTCA
1 AAGTCCACAACTTC-GTGGCACT-TTTTT-AAGCCCACAAGTCAGTGGCACCCTTCCA
*
327124 AAGCCCACAA
1 AAGTCCACAA
327134 GTCAGTGGCA
Statistics
Matches: 431, Mismatches: 73, Indels: 51
0.78 0.13 0.09
Matches are distributed among these distances:
54 17 0.04
55 32 0.07
56 171 0.40
57 67 0.16
58 9 0.02
59 40 0.09
60 13 0.03
61 21 0.05
62 25 0.06
63 2 0.00
64 32 0.07
66 1 0.00
67 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (55 bp):
AAGTCCACAACTTCGTGGCACTTTTTTAAGCCCACAAGTCAGTGGCACCCTTCCA
Found at i:326704 original size:28 final size:28
Alignment explanation
Indices: 326631--327235 Score: 443
Period size: 28 Copynumber: 20.7 Consensus size: 28
326621 CATCCTTTTT
* * * *
326631 AAGCCCACAAGTCGGTGGCACCCTTCCA
1 AAGCCCACAAGTCAGTGGCATCTTTTCA
* * **
326659 AAGTCCACAACTTC-GTGGCATCTTTTTT
1 AAGCCCACAA-GTCAGTGGCATCTTTTCA
* * * *
326687 AAGCCCATAAGTCAGTGGCACCCTTCCA
1 AAGCCCACAAGTCAGTGGCATCTTTTCA
* * *
326715 AAGCCCATAAGTTAGTGGCACTCTTTT-T
1 AAGCCCACAAGTCAGTGGCA-TCTTTTCA
326743 AAGCCCACAAGTCAGTGGCAT-TATTTCA
1 AAGCCCACAAGTCAGTGGCATCT-TTTCA
* * *
326771 AAGCCCACACAAGTCGGTGGCAACTCATTTGA
1 AAG-CC-CACAAGTCAGTGGC-A-TCTTTTCA
* *
326803 AAGCCCATACAAGTCGGTGGCAACCCATTTT-A
1 AAGCCC--ACAAGTCAGTGGC-A-TC-TTTTCA
* * *
326835 AAGCCCACACAAGTC-GATGGTAACCCATTTCA
1 AAG-CC-CACAAGTCAG-TGG-CA-TCTTTTCA
*
326867 AAGCCCACAAGTCAGTGGCATCCTTCTCA
1 AAGCCCACAAGTCAGTGGCAT-CTTTTCA
*
326896 AAGCCCACACAAATCAGTGGCATCTTTTCA
1 AAG-CC-CACAAGTCAGTGGCATCTTTTCA
*
326926 AAGCCCACAAGTCAGTGGCACTTTTTTCA
1 AAGCCCACAAGTCAGTGGCA-TCTTTTCA
* *
326955 AAGCCCACAAGTCAGTGACATCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCTTTTCA
* * *
326983 AAGCCCGCAAGGT-AGTGGCACCCTTTCA
1 AAGCCCACAA-GTCAGTGGCATCTTTTCA
* *
327011 AAGCCCACAAG-CTAGTGGCACCCTTTCA
1 AAGCCCACAAGTC-AGTGGCATCTTTTCA
* * *
327039 AAGCCCACAAGTCAGTAGCACCATTTCA
1 AAGCCCACAAGTCAGTGGCATCTTTTCA
*
327067 AAGCCCACAAGTCAGTGGCACTCTTTTTA
1 AAGCCCACAAGTCAGTGGCA-TCTTTTCA
* * * *
327096 AAGCACATAAGTTAGTGGCATCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCTTTTCA
* *
327124 AAGCCCACAAGTCAGTGGCACCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCTTTTCA
*
327152 AAGCCCACAAG-CTAGTGGTAACTCTTTTCA
1 AAGCCCACAAGTC-AGTGG-CA-TCTTTTCA
*
327182 AAGCCCACACGAGTCGGTGGCAACTCTTTTCA
1 AAGCCCACA--AGTCAGTGGC-A-TCTTTTCA
*
327214 AAGCCTACACAAGTTAGTGGCA
1 AAGCC--CACAAGTCAGTGGCA
327236 CATTTTTAAA
Statistics
Matches: 473, Mismatches: 67, Indels: 71
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.00
27 8 0.02
28 230 0.49
29 70 0.15
30 51 0.11
31 26 0.05
32 76 0.16
33 6 0.01
34 5 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCATCTTTTCA
Found at i:327119 original size:141 final size:141
Alignment explanation
Indices: 326673--327245 Score: 553
Period size: 141 Copynumber: 3.9 Consensus size: 141
326663 CCACAACTTC
* ** * * * * *
326673 GTGGCATCTTTTTTAAGCCCATAAGTCAGTGGCACCCTTCCAAAGCCCATAAGTTAGTGGCACTC
1 GTGGCATCCTTTCAAAGCCCACAAGT-AGTGGCACCCTTTCAAAGCCCACAAGCTAGTGGCACCC
** ** * * *
326738 TTTTTAAGCCCACAAGTCAGTGGCATTATTTCAAAGCCCACACAAGTCGGTGGCAACTCATTTGA
65 TTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAG-CCACACAAGTCAGTGGC-ACTCTTTTTA
*
326803 AAGCCCATACAAGTCG
128 AAGCCCAT--AAGTCA
* * * *
326819 GTGGCAACCCATTTTAAAGCCCACACAAGTCGATGGTAACCCATTTCAAAGCCCACAAG-TCAGT
1 GTGGC-ATCC-TTTCAAAG-CC-CACAAGTAG-TGG-CACCC-TTTCAAAGCCCACAAGCT-AGT
* * * *
326883 GGCATCCTTCTCAAAGCCCACACAAATCAGTGGCATCTTTTCAAAGCC-CACAAGTCAGTGGCAC
58 GGCACCCTT-TCAAAG-CC-CACAAGTCAGTGGCACCATTTCAAAGCCACACAAGTCAGTGGCAC
*
326947 T-TTTTTCAAAGCCCACAAGTCA
120 TCTTTTT-AAAGCCCATAAGTCA
* *
326969 GTGACATCCTTTCAAAGCCCGCAAGGTAGTGGCACCCTTTCAAAGCCCACAAGCTAGTGGCACCC
1 GTGGCATCCTTTCAAAGCCCACAA-GTAGTGGCACCCTTTCAAAGCCCACAAGCTAGTGGCACCC
*
327034 TTTCAAAGCCCACAAGTCAGTAGCACCATTTCAAAGCC-CACAAGTCAGTGGCACTCTTTTTAAA
65 TTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCCACACAAGTCAGTGGCACTCTTTTTAAA
* *
327098 GCACATAAGTTA
130 GCCCATAAGTCA
*
327110 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGCTAGTGGTAACT
1 GTGGCATCCTTTCAAAGCCCACAAGT-AGTGGCACCCTTTCAAAGCCCACAAGCTAGTGG-CAC-
* * * * *
327175 CTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCTACACAAGTTAGTGGCAC-AT
63 CCTTTCAAAGCCCACA--AGTCAGTGGC-AC-CATTTCAAAGCC-ACACAAGTCAGTGGCACTCT
327239 TTTTAAA
123 TTTTAAA
327246 AGAAAAGGCC
Statistics
Matches: 360, Mismatches: 43, Indels: 46
0.80 0.10 0.10
Matches are distributed among these distances:
140 2 0.01
141 108 0.30
142 9 0.03
143 21 0.06
144 27 0.08
145 13 0.04
146 14 0.04
147 18 0.05
148 22 0.06
149 21 0.06
150 18 0.05
151 8 0.02
152 35 0.10
153 17 0.05
154 4 0.01
155 23 0.06
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.24
Consensus pattern (141 bp):
GTGGCATCCTTTCAAAGCCCACAAGTAGTGGCACCCTTTCAAAGCCCACAAGCTAGTGGCACCCT
TTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCCACACAAGTCAGTGGCACTCTTTTTAAAG
CCCATAAGTCA
Found at i:328149 original size:20 final size:20
Alignment explanation
Indices: 328126--328200 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
328116 AAGTACCCAG
*
328126 ATGTATCGATATATTTTTAA
1 ATGTATCGATACATTTTTAA
* * * *
328146 ATGTATTGATACATGTATGA
1 ATGTATCGATACATTTTTAA
* *
328166 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTAA
*
328186 ATGTATCAATACATT
1 ATGTATCGATACATT
328201 CTATCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTAA
Found at i:330394 original size:27 final size:27
Alignment explanation
Indices: 330363--330432 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
330353 TTTATTCATC
330363 GGGGATACTCCAACCCTATTCTTCTGA
1 GGGGATACTCCAACCCTATTCTTCTGA
*
330390 GGGGATACTCCAACCCTATTTTTCTGA
1 GGGGATACTCCAACCCTATTCTTCTGA
330417 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
330433 CGCTTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (27 bp):
GGGGATACTCCAACCCTATTCTTCTGA
Found at i:335172 original size:19 final size:19
Alignment explanation
Indices: 335148--335197 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
335138 AAACCGTAAC
335148 TGTATCGATACATAAATGT
1 TGTATCGATACATAAATGT
* *
335167 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAATGT
335186 TGTATCGATACA
1 TGTATCGATACA
335198 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAATGT
Found at i:341828 original size:13 final size:13
Alignment explanation
Indices: 341810--341836 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
341800 TACATTATGT
341810 TTGTATCGATACA
1 TTGTATCGATACA
341823 TTGTATCGATACA
1 TTGTATCGATACA
341836 T
1 T
341837 GAAACTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:341901 original size:13 final size:13
Alignment explanation
Indices: 341883--341912 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
341873 GATACATGGC
341883 ACATTGTATCGAT
1 ACATTGTATCGAT
341896 ACATTGTATCGAT
1 ACATTGTATCGAT
341909 ACAT
1 ACAT
341913 GATGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:341903 original size:33 final size:32
Alignment explanation
Indices: 341866--341933 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
341856 TTACCACTAT
341866 TTGTATCGATACATG-GCACATTGTATCGATACA
1 TTGTATCGATACATGAG-A-ATTGTATCGATACA
341899 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGA-GAATTGTATCGATACA
341932 TT
1 TT
341934 ACTTCAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACATGAGAATTGTATCGATACA
Found at i:343380 original size:18 final size:18
Alignment explanation
Indices: 343357--343394 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
343347 CTTCCAAAAT
343357 CATGGGACAAGCTTGCAA
1 CATGGGACAAGCTTGCAA
*
343375 CATGGGATAAGCTTGCAA
1 CATGGGACAAGCTTGCAA
343393 CA
1 CA
343395 ACACACGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (18 bp):
CATGGGACAAGCTTGCAA
Found at i:343563 original size:239 final size:239
Alignment explanation
Indices: 343137--343602 Score: 824
Period size: 239 Copynumber: 1.9 Consensus size: 239
343127 CCAAGCAAAT
* *
343137 ATGGGACAAGCTTGCAACGACACACGAGGGTACAAACTAAGTCAAAGAGTCCAAAATCAGCATGC
1 ATGGGACAAGCTTGCAACAACACACGAGGGTACAAACCAAGTCAAAGAGTCCAAAATCAGCATGC
* * *
343202 TCACCCTTGATTATGAGCTTTTCCAAATGAAAATCGATGAAAATATAAGGAAATATCCGATCGGT
66 TCACCCTTGATTATGAGCTTTTCCAAATGAAAATCAATGAAAATATAAGAAAATATCCGATCAGT
* * *
343267 TTACCGACATCGTTAACGGGCTTAAAACACTCGAGAAGACTTATCCCAACAAAGAGATAGTGAAG
131 TTACCGACATCATTAACAGGCTTAAAACACTCGAGAAGACTTATCCCAACAAAGAGATAGTGAAA
343332 AAGCTTCTCAATAGTCTTCCAAAATCATGGGACAAGCTTGCAAC
196 AAGCTTCTCAATAGTCTTCCAAAATCATGGGACAAGCTTGCAAC
*
343376 ATGGGATAAGCTTGCAACAACACACGAGGGTACAAACCAAGTCAAAGAGTCCAAAATCAGCATGC
1 ATGGGACAAGCTTGCAACAACACACGAGGGTACAAACCAAGTCAAAGAGTCCAAAATCAGCATGC
*
343441 TCACCCTTGATTATGAGCTTTTCCAAATGAAAATCAATGAAAATATAAGAAAATGTCCGATCAGT
66 TCACCCTTGATTATGAGCTTTTCCAAATGAAAATCAATGAAAATATAAGAAAATATCCGATCAGT
* *
343506 TTACCGACATCATTAACAGGCTTAAAACACTCGGGAAGACTTATCCCAACAAAGAGATGGTGAAA
131 TTACCGACATCATTAACAGGCTTAAAACACTCGAGAAGACTTATCCCAACAAAGAGATAGTGAAA
343571 AAGCTTCTCAATAGTCTTCCAAAATCATGGGA
196 AAGCTTCTCAATAGTCTTCCAAAATCATGGGA
343603 AGCTAAAGTC
Statistics
Matches: 215, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
239 215 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (239 bp):
ATGGGACAAGCTTGCAACAACACACGAGGGTACAAACCAAGTCAAAGAGTCCAAAATCAGCATGC
TCACCCTTGATTATGAGCTTTTCCAAATGAAAATCAATGAAAATATAAGAAAATATCCGATCAGT
TTACCGACATCATTAACAGGCTTAAAACACTCGAGAAGACTTATCCCAACAAAGAGATAGTGAAA
AAGCTTCTCAATAGTCTTCCAAAATCATGGGACAAGCTTGCAAC
Found at i:348507 original size:20 final size:21
Alignment explanation
Indices: 348469--348508 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
348459 TTTCAAATTT
* *
348469 CTTCATTTTTACTTGAAAATA
1 CTTCATTTTTACATCAAAATA
348490 CTTCATTTTT-CATCAAAAT
1 CTTCATTTTTACATCAAAAT
348509 TATCAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (21 bp):
CTTCATTTTTACATCAAAATA
Done.