Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold308
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: 505154
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 4 of 4
Found at i:437069 original size:39 final size:39
Alignment explanation
Indices: 437015--437090 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
437005 AAGAAGGATG
437015 CCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTT
1 CCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTT
437054 CCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCAC
437091 CTTTTTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (39 bp):
CCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTT
Found at i:437100 original size:32 final size:32
Alignment explanation
Indices: 437062--437127 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
437052 TTCCTTTTTC
437062 TTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 TTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * *
437094 TTTTTAAAGCCTACATAAGTTGGTGTCACCTT
1 TTTTTAAAGCCCACACAAGTTGGTGGCACCTT
437126 TT
1 TT
437128 AGCCTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (32 bp):
TTTTTAAAGCCCACACAAGTTGGTGGCACCTT
Found at i:437185 original size:67 final size:68
Alignment explanation
Indices: 437094--437264 Score: 238
Period size: 67 Copynumber: 2.5 Consensus size: 68
437084 GTGGCACCTT
* * *
437094 TTTTTAAAGCCTACATAAGTTGGTGTCACCTTTTAG-CCTTCAAAAAGCAGGATGCCTTTCC-TT
1 TTTTTAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCCTT-AAAAAGCAGGACGCCTTTCCTTT
437157 TTTC
65 TTTC
* * * *
437161 TTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTTAAAGAGCAGGACGTCTTTCCTTTT
1 TTTTTAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCCTTAAAAAGCAGGACGCCTTTCC-TTT
437226 TTTC
65 TTTC
437230 TTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTT
1 TTTTT-AAAGCCCACATAAGTTGGTGGCACCTTTT
437265 TCTTTTTAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
67 49 0.54
68 4 0.04
69 11 0.12
70 27 0.30
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (68 bp):
TTTTTAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCCTTAAAAAGCAGGACGCCTTTCCTTTT
TTC
Found at i:441946 original size:31 final size:32
Alignment explanation
Indices: 441911--441978 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
441901 AATTTTTCAT
*
441911 TGTATCAACACATT-TGGGGTTTTAG-CCTAAA
1 TGTATCAACACATTCT-GGGTTTTAGACCCAAA
* * *
441942 TGTATCGATACATTCTGGGTTTTTGACCCAAA
1 TGTATCAACACATTCTGGGTTTTAGACCCAAA
441974 TGTAT
1 TGTAT
441979 TGATATATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 20 0.65
32 11 0.35
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (32 bp):
TGTATCAACACATTCTGGGTTTTAGACCCAAA
Found at i:444177 original size:19 final size:19
Alignment explanation
Indices: 444133--444188 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
444123 CTGCCAATCT
*
444133 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
444153 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
444172 CATGTATCGATACAATG
1 CATGTATCGATACAATG
444189 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:444191 original size:13 final size:13
Alignment explanation
Indices: 444173--444199 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
444163 TACAATGAGC
444173 ATGTATCGATACA
1 ATGTATCGATACA
444186 ATGTATCGATACA
1 ATGTATCGATACA
444199 A
1 A
444200 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:444880 original size:58 final size:59
Alignment explanation
Indices: 444790--444906 Score: 200
Period size: 58 Copynumber: 2.0 Consensus size: 59
444780 ATTTCAAAAA
* *
444790 AAAATTCTCCCCCTTAATCAAATCATTTCTCCCCTTTTGTCAAATAAT-AAAAATTTAT
1 AAAATTCTCCCCCTTAATCAAAGCATTTCTCCCCGTTTGTCAAATAATAAAAAATTTAT
*
444848 AAAATTCTCCCCCTTAATGAAAGCATTTCTCCCCGTTTGTCAAATAATAAAAAATTTAT
1 AAAATTCTCCCCCTTAATCAAAGCATTTCTCCCCGTTTGTCAAATAATAAAAAATTTAT
444907 TTATTTTCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 45 0.82
59 10 0.18
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAATTCTCCCCCTTAATCAAAGCATTTCTCCCCGTTTGTCAAATAATAAAAAATTTAT
Found at i:446348 original size:19 final size:20
Alignment explanation
Indices: 446315--446354 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
446305 GGTTGTGACT
446315 TGGGAGTACCGATCGCGACC
1 TGGGAGTACCGATCGCGACC
446335 TGGGAGTA-CGATCGCGACC
1 TGGGAGTACCGATCGCGACC
446354 T
1 T
446355 AGGATAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (20 bp):
TGGGAGTACCGATCGCGACC
Found at i:446983 original size:19 final size:19
Alignment explanation
Indices: 446948--446988 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
446938 CTATAGACCC
446948 TAATTCATATCAAGCAAACA
1 TAATTCATATCAAGC-AACA
*
446968 TAATTCA-ATCATGCAACA
1 TAATTCATATCAAGCAACA
446986 TAA
1 TAA
446989 CAAACATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.27
Consensus pattern (19 bp):
TAATTCATATCAAGCAACA
Found at i:453124 original size:13 final size:13
Alignment explanation
Indices: 453106--453131 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
453096 ACAAAGATCC
453106 ATGTATCGATACA
1 ATGTATCGATACA
453119 ATGTATCGATACA
1 ATGTATCGATACA
453132 TTTCGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:453143 original size:20 final size:20
Alignment explanation
Indices: 453118--453155 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
453108 GTATCGATAC
453118 AATGTATCGATACATTTCGT
1 AATGTATCGATACATTTCGT
453138 AATGTATCGATACATTTC
1 AATGTATCGATACATTTC
453156 CTTGGCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTCGT
Found at i:453191 original size:13 final size:13
Alignment explanation
Indices: 453169--453226 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
453159 GGCAGTAGCT
*
453169 TTGTAGCGATACA
1 TTGTATCGATACA
453182 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
453198 CTTATGTATCGATACA
1 --T-TGTATCGATACA
453214 TTGTATCGATACA
1 TTGTATCGATACA
453227 AATTGTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:454988 original size:3 final size:3
Alignment explanation
Indices: 454980--455004 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
454970 TCCGAGTCAC
454980 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
455005 TTCCTCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:456703 original size:19 final size:19
Alignment explanation
Indices: 456659--456714 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
456649 CTGCCAATCT
*
456659 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
456679 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
456698 CATGTATCGATACAATG
1 CATGTATCGATACAATG
456715 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:456717 original size:13 final size:13
Alignment explanation
Indices: 456699--456725 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
456689 TACAATGAGC
456699 ATGTATCGATACA
1 ATGTATCGATACA
456712 ATGTATCGATACA
1 ATGTATCGATACA
456725 A
1 A
456726 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:458302 original size:80 final size:80
Alignment explanation
Indices: 458139--458294 Score: 183
Period size: 79 Copynumber: 2.0 Consensus size: 80
458129 TTCATTCCCG
* * ***
458139 TTTTTACTTCCAAAATACCAAAATTTTAACCATCGAGGATACTCCAACCCCATTATTTTTTAGGG
1 TTTTTACTTCCAAAATACCAAAATTTTAACCATCGAGGATACTCCAACCCCATCATCTCCGAGGG
458204 GATACTCCAACCCCA
66 GATACTCCAACCCCA
** * *
458219 TTTTTACTTCCAAAATATTAAAATTTTCACC-TC-AGGGATACTCCAACCTC-TCCATCTCCGAG
1 TTTTTACTTCCAAAATACCAAAATTTTAACCATCGA-GGATACTCCAACCCCAT-CATCTCCGAG
*
458281 GGGATACTCTAACC
64 GGGATACTCCAACC
458295 TCGATTTTCA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
78 2 0.03
79 34 0.53
80 28 0.44
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (80 bp):
TTTTTACTTCCAAAATACCAAAATTTTAACCATCGAGGATACTCCAACCCCATCATCTCCGAGGG
GATACTCCAACCCCA
Found at i:463150 original size:20 final size:21
Alignment explanation
Indices: 463104--463157 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
463094 AGGTTAAGTA
*
463104 AAAAAAATTAAAAGGTCAAAC
1 AAAAAAATTAAAAGATCAAAC
* *
463125 TAAAAAGTT-AAAGATCAAAC
1 AAAAAAATTAAAAGATCAAAC
*
463145 AAAAAAATCAAAA
1 AAAAAAATTAAAA
463158 TTAAAGTAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.69, C:0.09, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAAAAATTAAAAGATCAAAC
Found at i:464200 original size:19 final size:19
Alignment explanation
Indices: 464176--464334 Score: 118
Period size: 19 Copynumber: 9.7 Consensus size: 19
464166 CAAACAATAA
*
464176 TTGTATCGATGCATAAGTG
1 TTGTATCGATACATAAGTG
464195 TTGTATCG----ATAA-TG
1 TTGTATCGATACATAAGTG
464209 ---TATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
464225 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
464239 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
464257 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
464271 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
464289 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
464303 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
464321 TTGTATCGACTACA
1 TTGTATCGA-TACA
464335 ATGTATCGCT
Statistics
Matches: 113, Mismatches: 0, Indels: 53
0.68 0.00 0.32
Matches are distributed among these distances:
11 5 0.04
13 33 0.29
14 2 0.02
15 14 0.12
16 2 0.02
17 6 0.05
19 47 0.42
20 4 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:464244 original size:13 final size:13
Alignment explanation
Indices: 464226--464314 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
464216 ACATAAGTGT
464226 TGTATCGATACAA
1 TGTATCGATACAA
464239 TGTATCGATACATAA
1 TGTATCGATAC--AA
464254 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
464271 TGTATCGATACATAA
1 TGTATCGATAC--AA
464286 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
464303 TGTATCGATACA
1 TGTATCGATACA
464315 TAAGTGTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:464246 original size:32 final size:32
Alignment explanation
Indices: 464177--464347 Score: 301
Period size: 32 Copynumber: 5.4 Consensus size: 32
464167 AAACAATAAT
*
464177 TGTATCGATGCATAAGTGTTGTATCGAT--AA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
464207 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
464239 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
464271 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
464303 TGTATCGATACATAAGTGTTGTATCGACTACAA
1 TGTATCGATACATAAGTGTTGTATCGA-TACAA
*
464336 TGTATCGCTACA
1 TGTATCGATACA
464348 AAGCTACTGC
Statistics
Matches: 136, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
30 27 0.20
32 93 0.68
33 16 0.12
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:464390 original size:96 final size:96
Alignment explanation
Indices: 464177--464430 Score: 259
Period size: 96 Copynumber: 2.7 Consensus size: 96
464167 AAACAATAAT
* ***
464177 TGTATCGATGCATAAGTGTTGTATCGAT--AATGTATCGATACATAAGTGTTGTATCGATACAAT
1 TGTATCGATACATAACCCTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAAT
** * * *
464240 GTATCGATACATAAGTGTTGTATCGATACAA
66 GTATCGATACATAAGTACTGCATAGAGACAA
***
464271 TGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGACTACAA
1 TGTATCGATACATAACCCTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGA-TACAA
*
464336 TGTATCGCTACA-AAGCTACTGCCA-AG-GA-AA
65 TGTATCGATACATAAG-TACTG-CATAGAGACAA
* * * * *
464366 TGTATCGATACATTACCCTATGTATCGATACATTGTATCGATACATCGATTTTTGTATCGATACA
1 TGTATCGATACATAACCCT-TGTATCGATACAATGTATCGATACAT-AAGTGTTGTATCGATACA
464431 TTTGGGAATT
Statistics
Matches: 138, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
94 27 0.20
95 17 0.12
96 62 0.45
97 31 0.22
98 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (96 bp):
TGTATCGATACATAACCCTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAAT
GTATCGATACATAAGTACTGCATAGAGACAA
Found at i:464404 original size:13 final size:13
Alignment explanation
Indices: 464386--464411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
464376 CATTACCCTA
464386 TGTATCGATACAT
1 TGTATCGATACAT
464399 TGTATCGATACAT
1 TGTATCGATACAT
464412 CGATTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:473468 original size:52 final size:51
Alignment explanation
Indices: 473383--473506 Score: 203
Period size: 52 Copynumber: 2.4 Consensus size: 51
473373 ATATGAAAAG
* *
473383 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
**
473434 TTTGCCTGCATGTATCGATACATTTTCTAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
473486 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
473507 AAGATCAGTG
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
51 21 0.31
52 47 0.69
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:473519 original size:51 final size:51
Alignment explanation
Indices: 473383--473526 Score: 184
Period size: 52 Copynumber: 2.8 Consensus size: 51
473373 ATATGAAAAG
* *
473383 TTGCTTGCATGTATCGATACATTTAAT-AGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATCAGTGTATCGATACATCTGGGCAAAT
*** *
473435 TTGCCTGCATGTATCGATACATTTTCTAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACAAAATC-AGTGTATCGATACATCTGGGCAAAT
473486 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-ATCAGTGTATCGATACA
473527 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
50 2 0.02
51 34 0.42
52 45 0.56
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACAAAATCAGTGTATCGATACATCTGGGCAAAT
Found at i:473533 original size:13 final size:13
Alignment explanation
Indices: 473515--473573 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
473505 CAAAGATCAG
473515 TGTATCGATACAA
1 TGTATCGATACAA
473528 TGTATCGATAC-A
1 TGTATCGATACAA
473540 T-T-T-GAGT--AA
1 TGTATCGA-TACAA
473549 TGTATCGATACAA
1 TGTATCGATACAA
473562 TGTATCGATACA
1 TGTATCGATACA
473574 TTTGAGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 4 0.10
13 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:473558 original size:34 final size:34
Alignment explanation
Indices: 473515--473594 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
473505 CAAAGATCAG
473515 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
473549 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
473583 TGTATCGATACA
1 TGTATCGATACA
473595 TTTTTTGGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATTTGAGTAA
Found at i:473651 original size:33 final size:33
Alignment explanation
Indices: 473614--473680 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
473604 AGTAGCTTAA
473614 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
473647 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
473680 A
1 A
473681 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:473654 original size:13 final size:13
Alignment explanation
Indices: 473636--473660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
473626 CAAAAAAATA
473636 TGTATCGATACAT
1 TGTATCGATACAT
473649 TGTATCGATACA
1 TGTATCGATACA
473661 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:474684 original size:52 final size:52
Alignment explanation
Indices: 474550--474761 Score: 203
Period size: 52 Copynumber: 4.2 Consensus size: 52
474540 GAAAAGTGAT
* * * *
474550 AAAGATGCCAATATGTTGATTCACGGCCAACGCT--ATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCC-A-GCTACATTGGACTTAAAGATG-G-A
* * *
474604 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
474657 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
474700 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
474752 AAAGGTGCCA
1 AAAGGTGCCA
474762 CCGATTTGTG
Statistics
Matches: 131, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
43 37 0.28
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 42 0.32
53 9 0.07
54 6 0.05
55 33 0.25
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:474718 original size:43 final size:43
Alignment explanation
Indices: 474657--474746 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
474647 TAAAGATGGA
*
474657 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
474700 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
474743 AAAG
1 AAAG
474747 ATGGAAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:474934 original size:58 final size:59
Alignment explanation
Indices: 474752--475221 Score: 351
Period size: 57 Copynumber: 8.0 Consensus size: 59
474742 TAAAGATGGA
* * ** *
474752 AAAGG-TGCCACCGATTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
*
474809 -AAGGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
** * *
474865 AAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-
1 AAAGGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
***
474924 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * * * * * **
474983 AAAAGGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT-GACTTGTGGGCTT----TTG
* * * * ** * **
475044 AAAAAGAG-TGCCACGGAGTTGTGGACTTTGGAAAA-GACGCCACCGACTTGTGGGCTTCGG
1 --AAAG-GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * * *
475104 AAAAGGGTGCCACTGATTTGTGGGC-TTT--AAAGGTTGCCACTGACTTGTGGGCTTTCG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
*** *** *
475161 AAAAAAATGCCACTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTTG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
475220 AA
1 AA
475222 GGGTGATGAA
Statistics
Matches: 330, Mismatches: 60, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
55 22 0.07
56 12 0.04
57 86 0.26
58 74 0.22
59 48 0.15
60 48 0.15
61 1 0.00
62 19 0.06
63 1 0.00
64 14 0.04
65 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (59 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
Found at i:474937 original size:88 final size:87
Alignment explanation
Indices: 474752--475008 Score: 385
Period size: 88 Copynumber: 3.0 Consensus size: 87
474742 TAAAGATGGA
* * ** *** * *
474752 AAAGG-TGCCACCGATTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGT
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGG
*
474814 TGCCACTGACTTGTGGGCTTTT
66 TGCCACTAACTTGTGGGCTTTT
474836 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGG
474901 GTGCCACTAACTTGTGGGCTTTT
65 GTGCCACTAACTTGTGGGCTTTT
474924 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGG
474989 GTGCCACTAACTTGTGGGCT
65 GTGCCACTAACTTGTGGGCT
475009 GAAAAGAGTG
Statistics
Matches: 158, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
84 5 0.03
85 40 0.25
86 4 0.03
87 1 0.01
88 106 0.67
89 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.32
Consensus pattern (87 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGG
TGCCACTAACTTGTGGGCTTTT
Found at i:475220 original size:30 final size:30
Alignment explanation
Indices: 474750--475221 Score: 386
Period size: 30 Copynumber: 16.1 Consensus size: 30
474740 CTTAAAGATG
* * **
474750 GAAAAGG-TGCCACCGATTTGTGGGCTTCG
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
474779 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
*
474808 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
*
474836 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
474864 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* * *
474894 GAACAGGGTGCCACTAACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
*
474924 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
474952 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
474982 GAAAAGGGTGCCACTAACTTGTGGGC---T
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* * * **
475009 GAAAA-GAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 GAAAAGGA-TGCCACT-GACTTGTGGGCTT----TT
* * * * *
475043 GAAAAAGAGTGCCACGGAGTTGTGGACTTTG
1 GAAAAGGA-TGCCACTGACTTGTGGGCTTTT
* * **
475074 GAAAA-GACGCCACCGACTTGTGGGCTTCG
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
475103 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
475132 --AAAGGTTGCCACTGACTTGTGGGCTTTC
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
475160 GAAAAAAATGCCACTGACTTGTGGGC-TTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
** *
475189 GAAAAAAATGCCACTGACTTGTGGACTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
475219 GAA
1 GAA
475222 GGGTGATGAA
Statistics
Matches: 366, Mismatches: 54, Indels: 45
0.79 0.12 0.10
Matches are distributed among these distances:
26 2 0.01
27 61 0.17
28 57 0.16
29 59 0.16
30 159 0.43
31 5 0.01
34 5 0.01
35 18 0.05
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (30 bp):
GAAAAGGATGCCACTGACTTGTGGGCTTTT
Found at i:476689 original size:21 final size:19
Alignment explanation
Indices: 476659--476771 Score: 111
Period size: 21 Copynumber: 5.7 Consensus size: 19
476649 CCGGACCCCC
*
476659 TTTTTTGTTTTTGTTTGTT
1 TTTTTTTTTTTTGTTTGTT
476678 TTTTTATTGTTTTTGTTT-TT
1 TTTTT-TT-TTTTTGTTTGTT
*
476698 TTTTTTTTCCTTTTGTTTTTT
1 TTTTTTTT--TTTTGTTTGTT
*
476719 TTTTTTTTTTTTTTTTGGTT
1 TTTTTTTTTTTTGTTT-GTT
* * *
476739 TTTCATTTTTTTCGTTCGTT
1 TTT-TTTTTTTTTGTTTGTT
476759 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
476772 GAGGACGCCG
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.01
19 22 0.28
20 27 0.35
21 28 0.36
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTTTTGTTTGTT
Found at i:476690 original size:20 final size:20
Alignment explanation
Indices: 476666--476771 Score: 103
Period size: 20 Copynumber: 5.3 Consensus size: 20
476656 CCCTTTTTTG
476666 TTTTTGTTTGTTTTTTTATT
1 TTTTTGTTTGTTTTTTTATT
476686 GTTTTTGTTT-TTTTTTT-TT
1 -TTTTTGTTTGTTTTTTTATT
*
476705 TCCTTTTGTTT-TTTTTTTTTT
1 T--TTTTGTTTGTTTTTTTATT
* * *
476726 TTTTTTTTTGGTTTTTCATT
1 TTTTTGTTTGTTTTTTTATT
*
476746 TTTTTCGTTCGTTTTTTT-TT
1 TTTTT-GTTTGTTTTTTTATT
476766 TTTTTG
1 TTTTTG
476772 GAGGACGCCG
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
18 1 0.01
19 10 0.14
20 41 0.57
21 20 0.28
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (20 bp):
TTTTTGTTTGTTTTTTTATT
Found at i:476741 original size:36 final size:36
Alignment explanation
Indices: 476672--476772 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 36
476662 TTTGTTTTTG
*
476672 TTTGTTTTTTTATTGTTTTTGTTTTTTTT--TTTTTCCT
1 TTTGTTTTTTT-TT-TTTTT-TTTTTTTTGGTTTTTCAT
476709 TTTGTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCAT
1 TTTGTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCAT
* **
476745 TTT-TTTCGTTCGTTTTTTTTTTTTTTGG
1 TTTGTTT-TTTTTTTTTTTTTTTTTTTGG
476773 AGGACGCCGT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
34 8 0.14
35 8 0.14
36 30 0.53
37 11 0.19
ACGTcount: A:0.02, C:0.05, G:0.10, T:0.83
Consensus pattern (36 bp):
TTTGTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCAT
Found at i:476750 original size:1 final size:1
Alignment explanation
Indices: 476659--476734 Score: 71
Period size: 1 Copynumber: 76.0 Consensus size: 1
476649 CCGGACCCCC
* * * * * * ** *
476659 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTTTTCCTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
476724 TTTTTTTTTTT
1 TTTTTTTTTTT
476735 GGTTTTTCAT
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.01, C:0.03, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:486476 original size:10 final size:10
Alignment explanation
Indices: 486461--486487 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
486451 ATGTATCAAG
486461 CAAAAACAAA
1 CAAAAACAAA
486471 CAAAAACAAA
1 CAAAAACAAA
486481 CAAAAAC
1 CAAAAAC
486488 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:500782 original size:1 final size:1
Alignment explanation
Indices: 500776--500895 Score: 159
Period size: 1 Copynumber: 120.0 Consensus size: 1
500766 GGCGTCCTCC
** * *
500776 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAAAAAAAAAAACAAAAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
500841 AAAAAAAAAAAAAAAAAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
500896 GGGGGTCCGG
Statistics
Matches: 102, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 102 1.00
ACGTcount: A:0.93, C:0.05, G:0.01, T:0.02
Consensus pattern (1 bp):
A
Found at i:500844 original size:44 final size:44
Alignment explanation
Indices: 500777--500895 Score: 184
Period size: 44 Copynumber: 2.7 Consensus size: 44
500767 GCGTCCTCCA
*
500777 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA--AAAAAAAAAAAC
500823 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAC
* * *
500867 AAAAACAATAAAAAAACAAACAAAAAAAA
1 AAAAAAAAAAAAAAAACAAAAAAAAAAAA
500896 GGGGGTCCGG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 38 0.55
46 31 0.45
ACGTcount: A:0.92, C:0.05, G:0.01, T:0.02
Consensus pattern (44 bp):
AAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAC
Found at i:500880 original size:65 final size:64
Alignment explanation
Indices: 500775--500895 Score: 208
Period size: 64 Copynumber: 1.9 Consensus size: 64
500765 CGGCGTCCTC
500775 CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAAAAAAAAAAACAAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAAAAAAAAAAACAAAAAAAAAAAAAAAA
*
500839 CAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAACAAT-AAAAAAACAAACAAAAAAAA
1 CAAAAAAAAAAAAAAAAAAAAAAAAAA-AAAAA-AATGAAAAAAAAAAACAAAAAAAA
500896 GGGGGTCCGG
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
64 27 0.50
65 24 0.44
66 3 0.06
ACGTcount: A:0.92, C:0.06, G:0.01, T:0.02
Consensus pattern (64 bp):
CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAAAAAAAAAAACAAAAAAAAAAAAAAAA
Found at i:502394 original size:30 final size:28
Alignment explanation
Indices: 502332--502795 Score: 355
Period size: 29 Copynumber: 16.0 Consensus size: 28
502322 TCACCCTTCA
* *
502332 AAAGTCCACAAGTCAGTGGCATTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
*
502360 AAAGCCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTC
* *
502389 GAAAGCCCACAAGTCAGTGGCAAC-CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTC
*
502417 AAAGCCCACAA-TCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTT-C
* *
502446 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTT-C
* * *
502475 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TC-TTTTC
* * * *
502505 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCA-TCTTTTC
* *
502539 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTC
*
502566 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCAT-CTTTTC
* * *
502596 AAAAGCCCACAAGTCAGTGGCAACCTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTC
* * **
502625 AAAGCCCACAAGTTAGTGGCACCCGTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
*
502653 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCAT-CTTTTC
* **
502683 AAAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTC
* *
502712 AAAGCCCACAAGTCAGTGGCAAC-CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
* *
502739 AAAGCCCACAAATCAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTC
* * * *
502768 GAAGCCCACAAATCGGTGGCACCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
502796 CATCGTTAAG
Statistics
Matches: 360, Mismatches: 52, Indels: 48
0.78 0.11 0.10
Matches are distributed among these distances:
26 10 0.03
27 53 0.15
28 59 0.16
29 130 0.36
30 81 0.22
31 4 0.01
34 5 0.01
35 18 0.05
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTC
Found at i:502867 original size:43 final size:43
Alignment explanation
Indices: 502801--502888 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
502791 TTTTCCATCG
*
502801 TTAAGTCCAATGTAGCCGACCTTGAATCAGCACATTGGCACCT
1 TTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCACCT
* * *
502844 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
1 TTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCACCT
502887 TT
1 TT
502889 TCCATCTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (43 bp):
TTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCACCT
Found at i:502920 original size:52 final size:53
Alignment explanation
Indices: 502842--502978 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 53
502832 ACATTGGCAC
* *
502842 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
* * *
502894 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC-TTTTC-CAT
* * * *
502949 CTTTAAG-CCCATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
502979 ACATATTGGC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
52 38 0.54
53 2 0.03
54 22 0.31
55 9 0.13
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
Found at i:503833 original size:13 final size:13
Alignment explanation
Indices: 503815--503839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
503805 CATAAAGTGG
503815 TGTATCGATACAA
1 TGTATCGATACAA
503828 TGTATCGATACA
1 TGTATCGATACA
503840 TGTTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:503918 original size:12 final size:12
Alignment explanation
Indices: 503901--503925 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
503891 CATCACTTAA
503901 ATGTATCGATAC
1 ATGTATCGATAC
503913 ATGTATCGATAC
1 ATGTATCGATAC
503925 A
1 A
503926 CTGATCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:503977 original size:52 final size:51
Alignment explanation
Indices: 503913--504114 Score: 300
Period size: 52 Copynumber: 3.9 Consensus size: 51
503903 GTATCGATAC
***
503913 ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACT-ATAAATGTATCGATACATGCAGGCAAATTTGCCCAG
503965 ATGTATCGATACACTATAAATGTATCGATACAATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTATAAATGTATCGATAC-ATGCAGGCAAATTTGCCCAG
504017 ATGTATCGATACAACTATAAAATGTA-CGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATAC-ACTAT-AAATGTATCGATACATGCAGGCAAATTTGCCCAG
*
504069 ATGTA-CGATAGCACTATTCAATGTATCGATACATGCAGGCAAATTT
1 ATGTATCGATA-CACTA-TAAATGTATCGATACATGCAGGCAAATTT
504115 TTCATATTTC
Statistics
Matches: 140, Mismatches: 4, Indels: 12
0.90 0.03 0.08
Matches are distributed among these distances:
51 28 0.20
52 94 0.67
53 11 0.08
54 7 0.05
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTTGCCCAG
Done.