Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 84 of 120
Found at i:24354172 original size:50 final size:50
Alignment explanation
Indices: 24354092--24354220 Score: 168
Period size: 50 Copynumber: 2.6 Consensus size: 50
24354082 GACGAATGCT
* * ** *
24354092 ATACCCTTAAAGTTGTAGAGGAACGGATTGAAGCCGCAATGGCAAATCTC
1 ATACACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGGCAAATCTC
* *
24354142 ATACACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGTAATGGCGAATCTC
1 ATACACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGGCAAATCTC
* * *
24354192 ATTCACCTAAAACTGTAGAGGGGCAGATT
1 ATACACTTAAAGCTGTAGAGGGGCAGATT
24354221 AAAGTCACAA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (50 bp):
ATACACTTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGGCAAATCTC
Found at i:24354238 original size:50 final size:50
Alignment explanation
Indices: 24354117--24354245 Score: 143
Period size: 50 Copynumber: 2.6 Consensus size: 50
24354107 TAGAGGAACG
* * * * *
24354117 GATTGAAGCCGCAATGGCAAATCTCATACACTTAAAGCTGTAGAGGGGCA
1 GATTAAAGCCACAATGGCGAATCTCATACACCTAAAACTGTAGAGGGGCA
* ** *
24354167 GATTGAAGCCGTAATGGCGAATCTCATTCACCTAAAACTGTAGAGGGGCA
1 GATTAAAGCCACAATGGCGAATCTCATACACCTAAAACTGTAGAGGGGCA
* *
24354217 GATTAAAGTCACAA-GGACGAATCTTATAC
1 GATTAAAGCCACAATGG-CGAATCTCATAC
24354246 TCTTGAAGCT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
49 2 0.03
50 65 0.97
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (50 bp):
GATTAAAGCCACAATGGCGAATCTCATACACCTAAAACTGTAGAGGGGCA
Found at i:24354331 original size:40 final size:40
Alignment explanation
Indices: 24354282--24354411 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
24354272 ACAACCCCCA
24354282 ATCTTTTACCCTAACTAGAGGGAAGATTGAAGACCATCCG
1 ATCTTTTACCCTAACTAGAGGGAAGATTGAAGACCATCCG
* ** * * * *
24354322 ATCTCTTACCCCGACCATG-GGGTAGATTGAAG-CAATCCA
1 ATCTTTTACCCTAACTA-GAGGGAAGATTGAAGACCATCCG
* *
24354361 ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCAG
1 ATCTTTTACCCTAACTAGAGGGAAGATTGAAGACCATCCG
24354401 ATCTTTTACCC
1 ATCTTTTACCC
24354412 CTGCCATGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
38 1 0.01
39 30 0.42
40 40 0.56
41 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (40 bp):
ATCTTTTACCCTAACTAGAGGGAAGATTGAAGACCATCCG
Found at i:24354376 original size:79 final size:79
Alignment explanation
Indices: 24354279--24354449 Score: 263
Period size: 79 Copynumber: 2.2 Consensus size: 79
24354269 GTTACAACCC
*
24354279 CCAATCTTTTACCCTAACTAGAGGGAAGATTGAAGACCATCCGATCTCTTACCCC-GACCATGGG
1 CCAATCTTTTACCCTAACTAGAGGGAAGATTGAAGACCATCAGATCTCTTACCCCTG-CCATGGG
* * *
24354343 GTAGATTGAAGCAAT
65 GCAGATTAAAACAAT
* *
24354358 CCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCAGATCTTTTACCCCTGCCATGGGG
1 CCAATCTTTTACCCTAACTAGAGGGAAGATTGAAGACCATCAGATCTCTTACCCCTGCCATGGGG
24354423 CAGATTAAAACAAT
66 CAGATTAAAACAAT
*
24354437 TCAATCTTTTACC
1 CCAATCTTTTACC
24354450 GTTAAAACTA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 83 0.99
80 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (79 bp):
CCAATCTTTTACCCTAACTAGAGGGAAGATTGAAGACCATCAGATCTCTTACCCCTGCCATGGGG
CAGATTAAAACAAT
Found at i:24354424 original size:40 final size:39
Alignment explanation
Indices: 24354305--24354449 Score: 120
Period size: 39 Copynumber: 3.7 Consensus size: 39
24354295 ACTAGAGGGA
* * * *
24354305 AGATTGAAGACCATCCGATCTCTTACCCC-GACCATGGGGT
1 AGATTGAAGACAAT-CAATCTTTTACCCCTG-CCATGGGGC
**
24354345 AGATTGAAG-CAATCCAATCTTTTA-CCCTAAC-TAGAGGGC
1 AGATTGAAGACAAT-CAATCTTTTACCCCTGCCAT-G-GGGC
*
24354384 AGATTGAAGACCATCAGATCTTTTACCCCTGCCATGGGGC
1 AGATTGAAGACAATCA-ATCTTTTACCCCTGCCATGGGGC
*
24354424 AGATT-AAAACAATTCAATCTTTTACC
1 AGATTGAAGACAA-TCAATCTTTTACC
24354450 GTTAAAACTA
Statistics
Matches: 86, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
37 1 0.01
38 5 0.06
39 41 0.48
40 32 0.37
41 6 0.07
42 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (39 bp):
AGATTGAAGACAATCAATCTTTTACCCCTGCCATGGGGC
Found at i:24356354 original size:26 final size:26
Alignment explanation
Indices: 24356306--24356355 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
24356296 TACTTATATA
*
24356306 TATATATATATATATAGTTTATTCCT
1 TATATATATATATATAGTATATTCCT
*
24356332 TATATATATAGTATGTA-TATATTC
1 TATATATATA-TATATAGTATATTC
24356356 ATCATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (26 bp):
TATATATATATATATAGTATATTCCT
Found at i:24356362 original size:26 final size:26
Alignment explanation
Indices: 24356307--24356363 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
24356297 ACTTATATAT
* * *
24356307 ATATATATATATATAGTTTATTCCTT
1 ATATATATATATATAGTATATTCATC
*
24356333 ATATATATAGTATGTA-TATATTCATC
1 ATATATATA-TATATAGTATATTCATC
24356359 ATATA
1 ATATA
24356364 ATTTCCTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (26 bp):
ATATATATATATATAGTATATTCATC
Found at i:24356407 original size:70 final size:72
Alignment explanation
Indices: 24356313--24356499 Score: 220
Period size: 78 Copynumber: 2.6 Consensus size: 72
24356303 ATATATATAT
*
24356313 ATATATATAGTTTATTCCTTATATATATAGTATGTATATATTCATC-ATATA-A-TTTCCTTAAA
1 ATATATATAGTTTATT-CTTATATATATAGTATGTATATATTCACCGATATACACTTTCCTTAAA
24356375 TTATATGC
65 TTATATGC
* * *
24356383 ATATATATAGTTTATTTTTCATATATATAGTATATATATATATTCGCCGTATATACACTGTTTCC
1 ATATATATAGTTTATTCTT-ATATATATAG--TATGTATATATTCACCG-ATATACAC--TTTCC
*
24356448 TTAAATTATATGT
60 TTAAATTATATGC
* *
24356461 ATATATATAGCTTATTGTT-TATATATAGTATGTATATAT
1 ATATATATAGTTTATTCTTATATATATAGTATGTATATAT
24356500 ATATTTTTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
69 2 0.02
70 26 0.26
72 13 0.13
74 15 0.15
75 1 0.01
76 9 0.09
78 34 0.34
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (72 bp):
ATATATATAGTTTATTCTTATATATATAGTATGTATATATTCACCGATATACACTTTCCTTAAAT
TATATGC
Found at i:24361442 original size:18 final size:18
Alignment explanation
Indices: 24361409--24361443 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24361399 CTGATATGGA
*
24361409 TGATACATTTGAGGTGGG
1 TGATACATTGGAGGTGGG
*
24361427 TGATACATTGGGGGTGG
1 TGATACATTGGAGGTGG
24361444 AGGTGGGTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.06, G:0.43, T:0.31
Consensus pattern (18 bp):
TGATACATTGGAGGTGGG
Found at i:24361447 original size:24 final size:24
Alignment explanation
Indices: 24361419--24361470 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
24361409 TGATACATTT
24361419 GAGGTGGGTGATACATTGGGGGTG
1 GAGGTGGGTGATACATTGGGGGTG
24361443 GAGGTGGGTGATACATTGGGGGTG
1 GAGGTGGGTGATACATTGGGGGTG
24361467 GAGG
1 GAGG
24361471 ATGCATCTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.17, C:0.04, G:0.56, T:0.23
Consensus pattern (24 bp):
GAGGTGGGTGATACATTGGGGGTG
Found at i:24365098 original size:17 final size:19
Alignment explanation
Indices: 24365076--24365112 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
24365066 TATCATGAAA
24365076 ATAAAAA-TAA-AAATAAT
1 ATAAAAATTAACAAATAAT
24365093 ATAAAAATTAACAAATAAT
1 ATAAAAATTAACAAATAAT
24365112 A
1 A
24365113 AATTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
ATAAAAATTAACAAATAAT
Found at i:24374038 original size:39 final size:39
Alignment explanation
Indices: 24373993--24374076 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
24373983 TTTTTTATTT
* *
24373993 ATAAAATCAAATAATAATTGTTAAATATCATTATTTTTA
1 ATAAAATCAAATAATAATTGTCAAATATAATTATTTTTA
* *
24374032 ATAAAATCAAATAATTATTGTCAAGTATAATTATTTTTA
1 ATAAAATCAAATAATAATTGTCAAATATAATTATTTTTA
*
24374071 GTAAAA
1 ATAAAA
24374077 AATTTAAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (39 bp):
ATAAAATCAAATAATAATTGTCAAATATAATTATTTTTA
Found at i:24374882 original size:16 final size:16
Alignment explanation
Indices: 24374863--24374908 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
24374853 TAAGTTTTAA
24374863 AGTTTGGGAATTTTCG
1 AGTTTGGGAATTTTCG
* *
24374879 AGTTTTGGAATTGTCG
1 AGTTTGGGAATTTTCG
*
24374895 ATTTTGGAGAATTT
1 AGTTTGG-GAATTT
24374909 CAAGTTTAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.22, C:0.04, G:0.28, T:0.46
Consensus pattern (16 bp):
AGTTTGGGAATTTTCG
Found at i:24375952 original size:24 final size:24
Alignment explanation
Indices: 24375920--24375967 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
24375910 GCAATTTTAT
24375920 GGTGATGGTAATGAAGGTAGTGAG
1 GGTGATGGTAATGAAGGTAGTGAG
** *
24375944 GGTGATGGTGGTGAAGGTGGTGAG
1 GGTGATGGTAATGAAGGTAGTGAG
24375968 ATTGCTCGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.52, T:0.25
Consensus pattern (24 bp):
GGTGATGGTAATGAAGGTAGTGAG
Found at i:24376004 original size:38 final size:38
Alignment explanation
Indices: 24375953--24376036 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
24375943 GGGTGATGGT
*
24375953 GGTGAAGGTGGTGAGATTGCTCGCAGTAAAGGTGGTGA-
1 GGTG-AGGTGGTGAGATTGCTCGCAGTAAAGGTGGTAAG
* * * *
24375991 GGTGAGGATGGTGAGGTTGCTTGTAGTATAGGTGGTAAG
1 GGTGAGG-TGGTGAGATTGCTCGCAGTAAAGGTGGTAAG
24376030 GGTGAGG
1 GGTGAGG
24376037 GTGAGGGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 3 0.08
38 29 0.74
39 7 0.18
ACGTcount: A:0.21, C:0.05, G:0.48, T:0.26
Consensus pattern (38 bp):
GGTGAGGTGGTGAGATTGCTCGCAGTAAAGGTGGTAAG
Found at i:24376039 original size:6 final size:6
Alignment explanation
Indices: 24376028--24376057 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
24376018 ATAGGTGGTA
24376028 AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG
1 AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG
24376058 GTAAGGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.67, T:0.17
Consensus pattern (6 bp):
AGGGTG
Found at i:24376081 original size:57 final size:57
Alignment explanation
Indices: 24375986--24376160 Score: 192
Period size: 57 Copynumber: 2.9 Consensus size: 57
24375976 CAGTAAAGGT
* * * * *
24375986 GGTGA-GGTGAGGATGGTGAGGTTGCTT-GTAGTATAGGTGGTAAGGGTGAGGGTGAG
1 GGTGAGGGTGAGGGTGGTAAGGTTG-TTGGCAATAAAGGTGGTAAGGGTGAGGGTGAG
24376042 GGTGAGGGTGAGGGTGGTAAGGTTGTTGGCAATAAAGGTGGTAAGGGTGAGGGTGAG
1 GGTGAGGGTGAGGGTGGTAAGGTTGTTGGCAATAAAGGTGGTAAGGGTGAGGGTGAG
*
24376099 GGTGAGGGTGAGGGTGAGGGTGAGGGTGAGGGTGTTGGCAATAAAGGTGGTAAGGGTGAGGG
1 GGTGAGGGTGAGGGT---GGT-A-----AGGTTGTTGGCAATAAAGGTGGTAAGGGTGAGGG
24376161 AGGTAAGCGT
Statistics
Matches: 102, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
56 7 0.07
57 58 0.57
60 3 0.03
61 1 0.01
66 33 0.32
ACGTcount: A:0.21, C:0.02, G:0.54, T:0.23
Consensus pattern (57 bp):
GGTGAGGGTGAGGGTGGTAAGGTTGTTGGCAATAAAGGTGGTAAGGGTGAGGGTGAG
Found at i:24376096 original size:6 final size:6
Alignment explanation
Indices: 24376085--24376132 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
24376075 AAAGGTGGTA
24376085 AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG
1 AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG
24376133 TTGGCAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.17, C:0.00, G:0.67, T:0.17
Consensus pattern (6 bp):
AGGGTG
Found at i:24379500 original size:17 final size:19
Alignment explanation
Indices: 24379464--24379502 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
24379454 CCACATCAGC
*
24379464 AAATGAATTGAAACTTAAA
1 AAATGAATTGAAAATTAAA
24379483 AAAT-AATT-AAAATTAAA
1 AAATGAATTGAAAATTAAA
24379500 AAA
1 AAA
24379503 AATATTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 4 0.21
19 4 0.21
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATGAATTGAAAATTAAA
Found at i:24379915 original size:11 final size:11
Alignment explanation
Indices: 24379899--24379923 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24379889 GAACTTGAGA
24379899 ATTTTTTTATT
1 ATTTTTTTATT
24379910 ATTTTTTTATT
1 ATTTTTTTATT
24379921 ATT
1 ATT
24379924 GTGTCGGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
ATTTTTTTATT
Found at i:24387214 original size:22 final size:23
Alignment explanation
Indices: 24387186--24387247 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 23
24387176 CTTTAAAATA
* *
24387186 AAAAATTTTAATTTAATTCT-TT
1 AAAAATTTTAATTTAATTATCGT
* *
24387208 AAAAA-TTAAATTTTATTATCGT
1 AAAAATTTTAATTTAATTATCGT
*
24387230 AAAAATTATAATTTAATT
1 AAAAATTTTAATTTAATT
24387248 TCGCTTCCTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 11 0.35
22 11 0.35
23 9 0.29
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (23 bp):
AAAAATTTTAATTTAATTATCGT
Found at i:24389226 original size:21 final size:22
Alignment explanation
Indices: 24389200--24389241 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
24389190 AGTTTTAGCA
*
24389200 ATTTATTATG-TCTCTTTCAAG
1 ATTTATGATGATCTCTTTCAAG
*
24389221 ATTTATGGTGATCTCTTTCAA
1 ATTTATGATGATCTCTTTCAA
24389242 TAATGTCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTTATGATGATCTCTTTCAAG
Found at i:24390213 original size:23 final size:23
Alignment explanation
Indices: 24390185--24390233 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
24390175 AAAATTTAAT
* * *
24390185 TTTTATATTTTTATTTTTAAGAA
1 TTTTATATTTCTACTTTTAAAAA
*
24390208 TTTTATCTTTCTACTTTTAAAAA
1 TTTTATATTTCTACTTTTAAAAA
24390231 TTT
1 TTT
24390234 AAAATTCTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTATATTTCTACTTTTAAAAA
Found at i:24392117 original size:24 final size:24
Alignment explanation
Indices: 24392059--24392105 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
24392049 TTTGGTGCAG
24392059 AATCAGCAGCACTTTCAACAACAC
1 AATCAGCAGCACTTTCAACAACAC
*
24392083 AATCAGCAGCATTTTCAACAACA
1 AATCAGCAGCACTTTCAACAACA
24392106 ACATCAACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.30, G:0.09, T:0.19
Consensus pattern (24 bp):
AATCAGCAGCACTTTCAACAACAC
Found at i:24397595 original size:5 final size:5
Alignment explanation
Indices: 24397585--24397614 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
24397575 ATGATGATAA
24397585 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG
1 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG
24397615 AAGAATAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
GGAAG
Found at i:24401210 original size:22 final size:22
Alignment explanation
Indices: 24401182--24401230 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
24401172 TGCACATAGA
*
24401182 TATGAAAGCCCTTTATGAGTAG
1 TATGAAAGCCCTTTAAGAGTAG
*
24401204 TATGAAAGCCCTTTAAGGGTAG
1 TATGAAAGCCCTTTAAGAGTAG
24401226 TATGA
1 TATGA
24401231 GACTCTGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (22 bp):
TATGAAAGCCCTTTAAGAGTAG
Found at i:24401564 original size:28 final size:28
Alignment explanation
Indices: 24401504--24401571 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
24401494 TAAATGGACA
* *
24401504 ATCTTGCAAGTAGGAGTCCATCAAGATT
1 ATCTTACAAGTAGGAGTCCATCAAGACT
* * *
24401532 GTCTTATAAGTGGGAGTCCATCAAGACT
1 ATCTTACAAGTAGGAGTCCATCAAGACT
24401560 ATCTTACAAGTA
1 ATCTTACAAGTA
24401572 TGAATCTGCC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (28 bp):
ATCTTACAAGTAGGAGTCCATCAAGACT
Found at i:24405890 original size:2 final size:2
Alignment explanation
Indices: 24405883--24405915 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24405873 CTTCATTGCA
24405883 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
24405916 GATTTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:24411109 original size:11 final size:11
Alignment explanation
Indices: 24411093--24411117 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24411083 CCAACATTAT
24411093 TATTATTTAGC
1 TATTATTTAGC
24411104 TATTATTTAGC
1 TATTATTTAGC
24411115 TAT
1 TAT
24411118 ACTAAAGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
TATTATTTAGC
Found at i:24411489 original size:22 final size:21
Alignment explanation
Indices: 24411464--24411538 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
24411454 TAAAATTTAA
*
24411464 ATAATATAATTTTTATAACTTT
1 ATAATATAATTTTT-TAAATTT
* *** *
24411486 ATAAAATACATAAATTAATTTT
1 ATAATATA-ATTTTTTAAATTT
24411508 ATAATATAATTTTTTAAAATTT
1 ATAATATAATTTTTT-AAATTT
24411530 ATAATATAA
1 ATAATATAA
24411539 ATAAATATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.83
23 3 0.07
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATATAATTTTTTAAATTT
Found at i:24411828 original size:23 final size:23
Alignment explanation
Indices: 24411801--24411845 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24411791 AAATTCGAAT
**
24411801 TTCAAATTATTCGAATCGAGTTA
1 TTCAAATTAAACGAATCGAGTTA
*
24411824 TTCAAGTTAAACGAATCGAGTT
1 TTCAAATTAAACGAATCGAGTT
24411846 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (23 bp):
TTCAAATTAAACGAATCGAGTTA
Found at i:24412445 original size:68 final size:70
Alignment explanation
Indices: 24412373--24412518 Score: 172
Period size: 71 Copynumber: 2.1 Consensus size: 70
24412363 TTGCCGTGTA
* * **
24412373 AATTTTACTGTATT-TTAAACTTTTGCTTATATTTTT-TTATAATCTTGTTGTGTTATTGTT-GT
1 AATTTTACTGT-TTATTAAACTTTTACTTATATTTTTATTATAATCTTGTTATGTTATCATTAGT
24412435 TACTTG
65 TACTTG
* * * *
24412441 AATTTATATTGTTTACTTGAACTTTTACTTATTTTTTTATTATAATCTTGTTATGTTATCATTAT
1 AATTT-TACTGTTTA-TTAAACTTTTACTTATATTTTTATTATAATCTTGTTATGTTATCATTAG
24412506 TTACTTG
64 TTACTTG
24412513 AATTTT
1 AATTTT
24412519 TTCACTTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
68 7 0.11
69 5 0.08
70 19 0.29
71 22 0.34
72 12 0.18
ACGTcount: A:0.23, C:0.08, G:0.09, T:0.60
Consensus pattern (70 bp):
AATTTTACTGTTTATTAAACTTTTACTTATATTTTTATTATAATCTTGTTATGTTATCATTAGTT
ACTTG
Found at i:24418600 original size:17 final size:17
Alignment explanation
Indices: 24418578--24418666 Score: 97
Period size: 17 Copynumber: 5.2 Consensus size: 17
24418568 CCAACTTTTA
*
24418578 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
**
24418595 ATTTTAAATTCGAATTT
1 ATTTTAAATTTAAATTT
*
24418612 ATTTTAAATTTAAATTC
1 ATTTTAAATTTAAATTT
* *
24418629 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
* * *
24418646 ATTTTGAATTAAAAATT
1 ATTTTAAATTTAAATTT
24418663 ATTT
1 ATTT
24418667 AATATTAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 61 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:24418610 original size:23 final size:23
Alignment explanation
Indices: 24418587--24418646 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
24418577 AATTTTAAAT
*
24418587 TTTAATTT-ATTTTAAATTCGAA
1 TTTAATTTAAATTTAAATTCGAA
* *
24418609 TTTATTTTAAATTTAAATTC-AT
1 TTTAATTTAAATTTAAATTCGAA
*
24418631 TTTGAGTTTAAATTTA
1 TTT-AATTTAAATTTA
24418647 TTTTGAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTAATTTAAATTTAAATTCGAA
Found at i:24420784 original size:59 final size:59
Alignment explanation
Indices: 24420713--24420996 Score: 248
Period size: 59 Copynumber: 4.9 Consensus size: 59
24420703 AAAGTCCCTC
* ** * *
24420713 AACTGTTCAAAAATTATATTTTGACCCTCGAATTTTTCTAAAATTACATTTTGACCTTGA
1 AACT-TTCAAAAATTACATTTTGACCCTCGAAACTTTCAAAAATTACATTTTGACCATGA
* * *
24420773 AACTTTCAAAAATTAAATTTTTG-CCCCCGAAACTTCCAAAAATTACATTTTTGACCATG-
1 AACTTTCAAAAATTACA-TTTTGACCCTCGAAACTTTCAAAAATTACA-TTTTGACCATGA
* ***
24420832 AACTTTCAAAAATTACATTTTGACCCT--AAACTTTCAAAAATTACATTTTTACCCCAA
1 AACTTTCAAAAATTACATTTTGACCCTCGAAACTTTCAAAAATTACATTTTGACCATGA
* * * * * *
24420889 AACTTACAAAAATTACATTTTTACCCT--TAACTTTTAGAAATTACATTTTTGATCC-CGA
1 AACTTTCAAAAATTACATTTTGACCCTCGAAACTTTCAAAAATTACA-TTTTGA-CCATGA
*
24420947 AAC-TTCTAAAAATTACATTTTTG-CCC-CTAAAC-TTCTAAAAATTACATTTT
1 AACTTTC-AAAAATTACA-TTTTGACCCTCGAAACTTTC-AAAAATTACATTTT
24420997 TAACCCCGAA
Statistics
Matches: 187, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
56 7 0.04
57 59 0.32
58 34 0.18
59 68 0.36
60 19 0.10
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (59 bp):
AACTTTCAAAAATTACATTTTGACCCTCGAAACTTTCAAAAATTACATTTTGACCATGA
Found at i:24420795 original size:30 final size:30
Alignment explanation
Indices: 24420713--24421027 Score: 294
Period size: 29 Copynumber: 10.7 Consensus size: 30
24420703 AAAGTCCCTC
*
24420713 AACTGTTCAAAAATTATA-TTTTGACCCTCGA
1 AACT-TTCAAAAATTACATTTTTGACCCT-GA
** * *
24420744 ATTTTTCTAAAATTACA-TTTTGACCTTGA
1 AACTTTCAAAAATTACATTTTTGACCCTGA
* * *
24420773 AACTTTCAAAAATTAAATTTTTGCCCCCGA
1 AACTTTCAAAAATTACATTTTTGACCCTGA
* *
24420803 AACTTCCAAAAATTACATTTTTGACCATG-
1 AACTTTCAAAAATTACATTTTTGACCCTGA
24420832 AACTTTCAAAAATTACA-TTTTGACCCT-A
1 AACTTTCAAAAATTACATTTTTGACCCTGA
**
24420860 AACTTTCAAAAATTACATTTTT-ACCCCAA
1 AACTTTCAAAAATTACATTTTTGACCCTGA
* *
24420889 AACTTACAAAAATTACATTTTT-ACCCT-T
1 AACTTTCAAAAATTACATTTTTGACCCTGA
* *
24420917 AACTTTTAGAAATTACATTTTTGATCCC-GA
1 AACTTTCAAAAATTACATTTTTGA-CCCTGA
*
24420947 AAC-TTCTAAAAATTACATTTTTGCCCCT-A
1 AACTTTC-AAAAATTACATTTTTGACCCTGA
* *
24420976 AAC-TTCTAAAAATTACATTTTTAACCCCGA
1 AACTTTC-AAAAATTACATTTTTGACCCTGA
** *
24421006 ATTTTTCCAAAATTACCATTTT
1 AACTTTCAAAAATTA-CATTTT
24421028 ACCCCGAGAG
Statistics
Matches: 236, Mismatches: 36, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
28 49 0.21
29 93 0.39
30 83 0.35
31 11 0.05
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTCAAAAATTACATTTTTGACCCTGA
Found at i:24423243 original size:21 final size:22
Alignment explanation
Indices: 24423195--24423244 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
24423185 ATTAATTACC
24423195 ATATTATTTAAAAATAGTATTT
1 ATATTATTTAAAAATAGTATTT
24423217 AT-TTATTTAAAAA-A-TATTT
1 ATATTATTTAAAAATAGTATTT
24423236 AATATTATT
1 -ATATTATT
24423245 CGTTTCACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.19
20 3 0.12
21 16 0.62
22 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTATTTAAAAATAGTATTT
Found at i:24429106 original size:58 final size:58
Alignment explanation
Indices: 24428779--24429209 Score: 541
Period size: 59 Copynumber: 7.4 Consensus size: 58
24428769 TTGACTTTCG
** *
24428779 GGGGTAAAAAT-GTAATTTTTTGGTGAAATCGGGGTCGAAAATGGGATTTTAGGAAAGTT-T
1 GGGGT-AAAATGGTAA--TTTTGGTGAAATCGGGGTTAAAAATGGGATTTT-GGAAAGTTCA
* * * *
24428839 GAGGGTAAAAGGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 G-GGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* * *
24428899 GGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAGTGGAATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* *
24428958 GGGGTAAAATGGTAATTTTGGTGAAAT-TGGGTTAAAAATGGGATTTAGGAAAGTTC-
1 GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* *
24429014 GGGG-ATAAATGGTAATTTTGGTGAAATCGAGGTTAAAAGTGGGATTTTGGAAAGTTCA
1 GGGGTA-AAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* * *
24429072 GGGGTGAAATGGTAATTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* * * *
24429130 GGGGTAAAAGGGTAATTTTTGGGGAAATCAGGGTTAAAAATGAGATTTTGGAAAGTTC-
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
24429188 GGAGGTAAAATGGTAATTTTGG
1 GG-GGTAAAATGGTAATTTTGG
24429210 ACAGTCCAAG
Statistics
Matches: 327, Mismatches: 34, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
55 1 0.00
56 25 0.08
57 50 0.15
58 85 0.26
59 122 0.37
60 36 0.11
61 8 0.02
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
Found at i:24429206 original size:29 final size:27
Alignment explanation
Indices: 24428807--24429210 Score: 184
Period size: 29 Copynumber: 13.9 Consensus size: 27
24428797 TTTGGTGAAA
*
24428807 TCGGGGTCGAAAATGGGATTTTAGGAAAGT
1 TCGGGGT--AAAATGGAATTTT-GGAAAGT
* * *
24428837 TTGAGGGTAAAAGGGTAATTTTTGGTAAA-A
1 TCG-GGGTAAAATGG-AA-TTTTGG-AAAGT
* *
24428867 TCAGGGTTAAAAATGGGATTTTGGAAAGTT
1 TC-GGGGT-AAAATGGAATTTTGGAAAG-T
*
24428897 TAGGGGTAAAATGGTAATTTTGGGTGAAA--
1 TCGGGGTAAAATGG-AATTTT--G-GAAAGT
24428926 TCGGGGTTAAAAGTGGAATTTTGGAAAGT
1 TCGGGG-TAAAA-TGGAATTTTGGAAAGT
24428955 TCGGGGGTAAAATGGTAATTTTGGTGAAA-T
1 TC-GGGGTAAAATGG-AATTTT-G-GAAAGT
* * *
24428985 T-GGGTTAAAAATGGGATTTAGGAAAGT
1 TCGGGGT-AAAATGGAATTTTGGAAAGT
24429012 TCGGGG-ATAAATGGTAATTTTGGTGAAA--
1 TCGGGGTA-AAATGG-AATTTT-G-GAAAGT
* *
24429040 TCGAGGTTAAAAGTGGGATTTTGGAAAGT
1 TCG-GGGTAAAA-TGGAATTTTGGAAAGT
* *
24429069 TCAGGGGTGAAATGGTAATTTTGGTAAA-A
1 TC-GGGGTAAAATGG-AATTTTGG-AAAGT
*
24429098 TCGGGGTTAAAAATGGGATTTTGGAAAGTT
1 TCGGGG-T-AAAATGGAATTTTGGAAAG-T
* *
24429128 TAGGGGTAAAAGGGTAATTTTTGGGGAAA--
1 TCGGGGTAAAATGG-AA-TTTT--GGAAAGT
*
24429157 TCAGGGTTAAAAAT-GAGATTTTGGAAAGT
1 TC-GGGGT-AAAATGGA-ATTTTGGAAAGT
24429186 TCGGAGGTAAAATGGTAATTTTGGA
1 TCGG-GGTAAAATGG-AATTTTGGA
24429211 CAGTCCAAGG
Statistics
Matches: 288, Mismatches: 35, Indels: 103
0.68 0.08 0.24
Matches are distributed among these distances:
26 5 0.02
27 22 0.08
28 56 0.19
29 103 0.36
30 63 0.22
31 30 0.10
32 9 0.03
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.31
Consensus pattern (27 bp):
TCGGGGTAAAATGGAATTTTGGAAAGT
Found at i:24431070 original size:17 final size:15
Alignment explanation
Indices: 24431020--24431074 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 15
24431010 ATGGACATTT
24431020 AATTT-AATTT-T-A
1 AATTTAAATTTATAA
24431032 AATTTAAATTTATAA
1 AATTTAAATTTATAA
24431047 TAGATTTAAATTGTATACA
1 -A-ATTTAAATT-TATA-A
24431066 AATTTAAAT
1 AATTTAAAT
24431075 CCAAAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 1 0.03
15 1 0.03
16 1 0.03
17 17 0.47
18 5 0.14
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (15 bp):
AATTTAAATTTATAA
Found at i:24437427 original size:21 final size:21
Alignment explanation
Indices: 24437395--24437442 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
24437385 CTGTTAGGGA
24437395 AACCAA-TATCATTACAAAAC
1 AACCAATTATCATTACAAAAC
* *
24437415 AACCAATTATCATTAGAAAGC
1 AACCAATTATCATTACAAAAC
24437436 AACCAAT
1 AACCAAT
24437443 GAAAAAGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.52, C:0.23, G:0.04, T:0.21
Consensus pattern (21 bp):
AACCAATTATCATTACAAAAC
Found at i:24438794 original size:22 final size:22
Alignment explanation
Indices: 24438769--24438811 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
24438759 TAGGAAAAAT
24438769 TCTGCCTTCTGGCACGACTTTC
1 TCTGCCTTCTGGCACGACTTTC
* * *
24438791 TCTGTCTTTTGGCACGTCTTT
1 TCTGCCTTCTGGCACGACTTT
24438812 GTTCTTTCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.30, G:0.19, T:0.44
Consensus pattern (22 bp):
TCTGCCTTCTGGCACGACTTTC
Found at i:24443923 original size:26 final size:26
Alignment explanation
Indices: 24443894--24443957 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
24443884 ACCTTAGCGC
* *
24443894 GCTCTCCG-TTATTTAGCATGTATTGT
1 GCTCTCCGTTTA-TTAGCACGTATAGT
*
24443920 GCTCTCCGTTTATTAGCACGTGTAGT
1 GCTCTCCGTTTATTAGCACGTATAGT
*
24443946 GCTCTCCATTTA
1 GCTCTCCGTTTA
24443958 GCACATTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 30 0.91
27 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (26 bp):
GCTCTCCGTTTATTAGCACGTATAGT
Found at i:24446276 original size:19 final size:18
Alignment explanation
Indices: 24446231--24446277 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
24446221 CAACGTCAGC
*
24446231 AAAAAA-AATTAAACTTA
1 AAAAAATAATTAAAATTA
*
24446248 AAAACATAATTAAAATTA
1 AAAAAATAATTAAAATTA
24446266 AAAAAATTAATT
1 AAAAAA-TAATT
24446278 TTTTGGGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATAATTAAAATTA
Found at i:24456500 original size:13 final size:13
Alignment explanation
Indices: 24456482--24456506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24456472 CCCATAATTA
24456482 ATATATATATATT
1 ATATATATATATT
24456495 ATATATATATAT
1 ATATATATATAT
24456507 ATTCCAACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATATATATT
Found at i:24456502 original size:15 final size:14
Alignment explanation
Indices: 24456478--24456509 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
24456468 GAGGCCCATA
24456478 ATTAATATATATAT
1 ATTAATATATATAT
24456492 ATTATATATATATAT
1 ATTA-ATATATATAT
24456507 ATT
1 ATT
24456510 CCAACTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTAATATATATAT
Found at i:24457453 original size:17 final size:18
Alignment explanation
Indices: 24457426--24457459 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
24457416 GATTCAAAAA
24457426 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
24457444 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
24457460 TAATTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:24459781 original size:10 final size:10
Alignment explanation
Indices: 24459768--24459863 Score: 76
Period size: 10 Copynumber: 9.9 Consensus size: 10
24459758 TTTTAAAAAA
24459768 TTTTATAATT
1 TTTTATAATT
24459778 TTTT-T-A-T
1 TTTTATAATT
* *
24459785 TTCTAT-ATA
1 TTTTATAATT
24459794 TTTTATAATT
1 TTTTATAATT
**
24459804 TTTTATAAAA
1 TTTTATAATT
*
24459814 TTTTACAATT
1 TTTTATAATT
24459824 TTTT-TATATT
1 TTTTATA-ATT
*
24459834 TTTTACAATT
1 TTTTATAATT
24459844 TTTATATAATT
1 TTT-TATAATT
*
24459855 TTTTCTAAT
1 TTTTATAAT
24459864 ATTTAATATT
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
7 4 0.06
8 3 0.04
9 7 0.10
10 43 0.64
11 10 0.15
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:24459786 original size:26 final size:27
Alignment explanation
Indices: 24459743--24459808 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
24459733 TTACATTTTG
24459743 TATAATTTTTTACGATTT-TAAAAAATTT
1 TATAATTTTTTA-GATTTCT-AAAAATTT
* * *
24459771 TATAATTTTTT-TATTTCTATATATTT
1 TATAATTTTTTAGATTTCTAAAAATTT
24459797 TATAATTTTTTA
1 TATAATTTTTTA
24459809 TAAAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 21 0.64
27 1 0.03
28 11 0.33
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (27 bp):
TATAATTTTTTAGATTTCTAAAAATTT
Found at i:24459929 original size:16 final size:18
Alignment explanation
Indices: 24459908--24459946 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
24459898 TATTTATAGC
24459908 TTTTATTTATTT-TA-TT
1 TTTTATTTATTTCTACTT
*
24459924 TTTTATTTTTTTCTACTT
1 TTTTATTTATTTCTACTT
24459942 TTTTA
1 TTTTA
24459947 ATAAAAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 2 0.10
18 7 0.35
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTATTTATTTCTACTT
Found at i:24460121 original size:84 final size:85
Alignment explanation
Indices: 24459956--24460120 Score: 194
Period size: 84 Copynumber: 2.0 Consensus size: 85
24459946 AATAAAAAGA
* *
24459956 GGTTTAATTTTTTTTTTTGAAAAATTTGAAGATTTTTTGATACATTTTGAAAGTTCAAATGCTTA
1 GGTTTAA-TTTTTTTTTTGAAAAATTTGAAGATTTTTTGATACATTTTAAAAGTTCAAATACTTA
* * * *
24460021 ATTGAGTGTAAAAAAAATAGG
65 AATAACTGAAAAAAAAATAGG
* * *
24460042 GGTTTAA-TTTTTTTTT-AAAGATTT-AAGAGTTTTTTTTATGCATTTTAAAAGTTCAAATAC-T
1 GGTTTAATTTTTTTTTTGAAAAATTTGAAGA--TTTTTTGATACATTTTAAAAGTTCAAATACTT
24460103 AAATAACTGAAAAAAAAA
64 AAATAACTGAAAAAAAAA
24460121 AAAACAAAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
82 4 0.06
83 22 0.32
84 35 0.51
86 7 0.10
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (85 bp):
GGTTTAATTTTTTTTTTGAAAAATTTGAAGATTTTTTGATACATTTTAAAAGTTCAAATACTTAA
ATAACTGAAAAAAAAATAGG
Found at i:24476017 original size:18 final size:19
Alignment explanation
Indices: 24475985--24476025 Score: 59
Period size: 17 Copynumber: 2.2 Consensus size: 19
24475975 AAAAAATTGA
24475985 AAAATAAAAATATGAAAATG
1 AAAATAAAAATATG-AAATG
24476005 AAAA-AAAAA-ATGAAATG
1 AAAATAAAAATATGAAATG
24476022 AAAA
1 AAAA
24476026 CTTTTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
19 5 0.24
20 4 0.19
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAATAAAAATATGAAATG
Found at i:24477928 original size:22 final size:23
Alignment explanation
Indices: 24477894--24477942 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
24477884 TCAAAAATAC
24477894 TTTTGAGATGAAAAAATTAAAAA
1 TTTTGAGATGAAAAAATTAAAAA
24477917 TTTTGA-ATGAAAAAATTAAAAA
1 TTTTGAGATGAAAAAATTAAAAA
24477939 TTTT
1 TTTT
24477943 AACTTATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (23 bp):
TTTTGAGATGAAAAAATTAAAAA
Found at i:24487076 original size:18 final size:18
Alignment explanation
Indices: 24487053--24487091 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
24487043 AGTGATTTTT
24487053 AAAAGCACTTTT-AACATA
1 AAAAGCACTTTTGAAC-TA
24487071 AAAAGCACTTTTGAACTA
1 AAAAGCACTTTTGAACTA
24487089 AAA
1 AAA
24487092 GTAATGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (18 bp):
AAAAGCACTTTTGAACTA
Found at i:24492838 original size:94 final size:94
Alignment explanation
Indices: 24492677--24492866 Score: 371
Period size: 94 Copynumber: 2.0 Consensus size: 94
24492667 TCATCCATCA
*
24492677 CAAAAACGAACAACACGTGGCCACGATTACTTTTCATCAACCATTTAATGTCTATGAGAGGATAT
1 CAAAAACGAACAACACGTGACCACGATTACTTTTCATCAACCATTTAATGTCTATGAGAGGATAT
24492742 TATTTACCCATGTTTTGGGCTATGAATTC
66 TATTTACCCATGTTTTGGGCTATGAATTC
24492771 CAAAAACGAACAACACGTGACCACGATTACTTTTCATCAACCATTTAATGTCTATGAGAGGATAT
1 CAAAAACGAACAACACGTGACCACGATTACTTTTCATCAACCATTTAATGTCTATGAGAGGATAT
24492836 TATTTACCCATGTTTTGGGCTATGAATTC
66 TATTTACCCATGTTTTGGGCTATGAATTC
24492865 CA
1 CA
24492867 CTATTGTGAA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (94 bp):
CAAAAACGAACAACACGTGACCACGATTACTTTTCATCAACCATTTAATGTCTATGAGAGGATAT
TATTTACCCATGTTTTGGGCTATGAATTC
Found at i:24495526 original size:19 final size:19
Alignment explanation
Indices: 24495504--24495555 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
24495494 GTCACTTACT
24495504 GTAATCAAATTTGTCTACC
1 GTAATCAAATTTGTCTACC
24495523 GTAATCAAATTTGTCTACC
1 GTAATCAAATTTGTCTACC
24495542 GTAATCAAATTTGT
1 GTAATCAAATTTGT
24495556 TATTAACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (19 bp):
GTAATCAAATTTGTCTACC
Found at i:24498729 original size:27 final size:27
Alignment explanation
Indices: 24498673--24498730 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
24498663 TAAATGTATT
*
24498673 TATATTAATTTTTAATTTTTAATTTAA
1 TATATTAATTTTTAATTATTAATTTAA
* * *
24498700 TATATTTATTATTT-ATTATTATTTTTA
1 TATATTAATT-TTTAATTATTAATTTAA
24498727 TATA
1 TATA
24498731 ATCGCGTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TATATTAATTTTTAATTATTAATTTAA
Found at i:24499749 original size:20 final size:20
Alignment explanation
Indices: 24499721--24499760 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
24499711 AACGTCTTCC
* *
24499721 ATTAGAAATTTTGATATTTG
1 ATTACAAATATTGATATTTG
24499741 ATTACAAATATTGATATTTG
1 ATTACAAATATTGATATTTG
24499761 GATGTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTACAAATATTGATATTTG
Found at i:24500418 original size:32 final size:32
Alignment explanation
Indices: 24500373--24500448 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
24500363 TTAACAGAAA
* *
24500373 CCATGTCAACATCG-TTCGTTGATGTGACAATAT
1 CCATGTCATCATCGATT-GTTGACGTGACAAT-T
*
24500406 -CATGTCATCATCGATTGTTGACGTGGCAATT
1 CCATGTCATCATCGATTGTTGACGTGACAATT
24500437 CCATGTCATCAT
1 CCATGTCATCAT
24500449 TGAAGGCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 1 0.03
32 35 0.92
33 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (32 bp):
CCATGTCATCATCGATTGTTGACGTGACAATT
Found at i:24500722 original size:16 final size:16
Alignment explanation
Indices: 24500692--24500724 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
24500682 ATAAAATTTT
24500692 ATAAACTTTATAAAAA
1 ATAAACTTTATAAAAA
24500708 ATAAA-TTTATCAAAAA
1 ATAAACTTTAT-AAAAA
24500724 A
1 A
24500725 CCATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAACTTTATAAAAA
Found at i:24503478 original size:21 final size:22
Alignment explanation
Indices: 24503454--24503506 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
24503444 TTGTGTTAGC
24503454 TCTACCGATACAAGT-ATGAAA
1 TCTACCGATACAAGTCATGAAA
* *
24503475 TCTACCGATATAAGTCATGCAA
1 TCTACCGATACAAGTCATGAAA
24503497 -CTACCGATAC
1 TCTACCGATAC
24503507 CGAAAACTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
TCTACCGATACAAGTCATGAAA
Found at i:24532407 original size:52 final size:52
Alignment explanation
Indices: 24532328--24532432 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
24532318 AATAGGTAAG
24532328 CAAAAGAGGATTTCACATGATAATGAGCTTTAAAAGTGGGTGATCTAGTGAA
1 CAAAAGAGGATTTCACATGATAATGAGCTTTAAAAGTGGGTGATCTAGTGAA
*
24532380 CAAAAGAGGATTTCACATGATAGTGAGCTTTAAAAGTGGGTGATCTAGTGAA
1 CAAAAGAGGATTTCACATGATAATGAGCTTTAAAAGTGGGTGATCTAGTGAA
24532432 C
1 C
24532433 TTGCCTTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (52 bp):
CAAAAGAGGATTTCACATGATAATGAGCTTTAAAAGTGGGTGATCTAGTGAA
Found at i:24533087 original size:25 final size:26
Alignment explanation
Indices: 24533026--24533087 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
24533016 ACGACCAATG
*
24533026 CTTGATGTCGTAGCGTGACATGATGA
1 CTTGATGTCGTAGCGTGACATGATAA
* *
24533052 CTTGATCTCGTTGCGATGACAT-A-AA
1 CTTGATGTCGTAGCG-TGACATGATAA
24533077 CTTGATGTCGT
1 CTTGATGTCGT
24533088 GATGTGCCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 11 0.35
26 14 0.45
27 6 0.19
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (26 bp):
CTTGATGTCGTAGCGTGACATGATAA
Found at i:24537731 original size:41 final size:41
Alignment explanation
Indices: 24537686--24537816 Score: 138
Period size: 41 Copynumber: 3.2 Consensus size: 41
24537676 AGTAAAAATT
* * *
24537686 TTCCTTTTTAAACGATCTTATGCTTTACCGAGTCATAAGTC
1 TTCCTTTTTAAACAATCTTATGCTCTACCGAGACATAAGTC
* *
24537727 TTCCTTTTTAAACAATCTTATTCTCTATCGAGACATAAGTC
1 TTCCTTTTTAAACAATCTTATGCTCTACCGAGACATAAGTC
* * * ** *
24537768 TTCC-TTTTAACATAATCTCATGCCCTTTTCGAGACATGAGTC
1 TTCCTTTTTAA-ACAATCTTATGCTC-TACCGAGACATAAGTC
24537810 TTCCTTT
1 TTCCTTT
24537817 AAATATAATC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 6 0.08
41 50 0.66
42 18 0.24
43 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (41 bp):
TTCCTTTTTAAACAATCTTATGCTCTACCGAGACATAAGTC
Found at i:24538168 original size:21 final size:21
Alignment explanation
Indices: 24538125--24538175 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
24538115 CCTATGACAG
*
24538125 TTCTACC-AATACAAGTGAGAC
1 TTCTACCGAA-ACAAGTCAGAC
* *
24538146 TTTTACCGAAACAAGTCATAC
1 TTCTACCGAAACAAGTCAGAC
24538167 TTCTACCGA
1 TTCTACCGA
24538176 TACTAAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (21 bp):
TTCTACCGAAACAAGTCAGAC
Found at i:24545867 original size:123 final size:123
Alignment explanation
Indices: 24545700--24546068 Score: 594
Period size: 123 Copynumber: 3.0 Consensus size: 123
24545690 TCCCCACATA
* * *
24545700 GAATCCCACTTCCTCTTATTTGTAGAAAATTTTTGCTTAATGTCACTTGAATCCAACTTCACAAC
1 GAATCCCTCTTCCTCTTATTTGAAGAAAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAAC
* * * *
24545765 ATCATCATCACTATGTGTGCATTCCTTACATTCAAGAGAACCCTCCATGATTGCACTT
66 ATCATCATCACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
* *
24545823 GAATCCCTCTTCCTCTTATTTGAAGAAAAATTTTCCTTAATGTCACTTGAATCCAATTTCACAAC
1 GAATCCCTCTTCCTCTTATTTGAAGAAAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAAC
* *
24545888 ATCATCATCACTGTGTGTACATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
66 ATCATCATCACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
** *
24545946 GAATCCCTCTTCCTCTTATTTGAAGAATTTTTTTCCTTAACGTCACTTGAATCCAACTTCACAAC
1 GAATCCCTCTTCCTCTTATTTGAAGAAAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAAC
* *
24546011 ATCATCATCAGTATGTGTGCGTTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
66 ATCATCATCACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
24546069 TTCACCTCAT
Statistics
Matches: 226, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 226 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (123 bp):
GAATCCCTCTTCCTCTTATTTGAAGAAAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAAC
ATCATCATCACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
Found at i:24549795 original size:138 final size:138
Alignment explanation
Indices: 24549631--24549931 Score: 462
Period size: 138 Copynumber: 2.2 Consensus size: 138
24549621 ATTTTGATTA
* *
24549631 AAATTAATTAATATAATTATTTATATTAATAAATTTGGTAAATTATATAC-AATTAATATTTTGT
1 AAATTAATTAATATAATTATTTATATTAATAAATTCGATAAA-TATATACAAATTAATATTTTGT
* *
24549695 ATGAATCAAATTCATATATTAATTATATTCTTCCCAAAAGAATATTAA-TTTCTATTTCTTTTAT
65 ATGAATAAAATTCATATATTAATTATATTCTTCCCAAAAGAATATTAATTTTC-ATGTCTTTTAT
24549759 ATTTTAACCG
129 ATTTTAACCG
24549769 AAATTAATTAATATAATTATTTATATTAATAAATTCGATAAATATATACAAATTAATATTTTGTA
1 AAATTAATTAATATAATTATTTATATTAATAAATTCGATAAATATATACAAATTAATATTTTGTA
* * *
24549834 TTAATAAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTGTAT
66 TGAATAAAATTCATATATTAATTATATTCTTCCCAAAAGAATATTAATTTTCATGTCTTTTATAT
* *
24549899 TTTTATCG
131 TTTAACCG
* * *
24549907 AAATTAATTATTATAACTGTTTATA
1 AAATTAATTAATATAATTATTTATA
24549932 GATAAAGGAT
Statistics
Matches: 149, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
137 7 0.05
138 138 0.93
139 4 0.03
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (138 bp):
AAATTAATTAATATAATTATTTATATTAATAAATTCGATAAATATATACAAATTAATATTTTGTA
TGAATAAAATTCATATATTAATTATATTCTTCCCAAAAGAATATTAATTTTCATGTCTTTTATAT
TTTAACCG
Found at i:24552603 original size:28 final size:28
Alignment explanation
Indices: 24552563--24552619 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
24552553 AAATGCAGCT
24552563 ATTACAAGTAAGATCCAGATGGATTTAA
1 ATTACAAGTAAGATCCAGATGGATTTAA
24552591 ATTACAAGTAAGATCCAGATGGATTTAA
1 ATTACAAGTAAGATCCAGATGGATTTAA
24552619 A
1 A
24552620 CATAGCAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.28
Consensus pattern (28 bp):
ATTACAAGTAAGATCCAGATGGATTTAA
Found at i:24554291 original size:15 final size:15
Alignment explanation
Indices: 24554271--24554300 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24554261 ATTAGATTTA
24554271 CTATTCATTTAACAT
1 CTATTCATTTAACAT
24554286 CTATTCATTTAACAT
1 CTATTCATTTAACAT
24554301 TCCACATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (15 bp):
CTATTCATTTAACAT
Found at i:24558650 original size:42 final size:42
Alignment explanation
Indices: 24558546--24558818 Score: 404
Period size: 42 Copynumber: 6.5 Consensus size: 42
24558536 TGATGCATAA
* * * * *
24558546 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGGATTTG-TAT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGAT-T
* * *
24558588 AAATAGAAGACTCATGTCTCGAGATGAGAGTGAGATTATGATT
1 AAA-GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
24558631 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
*
24558673 AAAGGAAGACTCATCTCTCGAGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
*
24558715 AAAGGAAGACTCATGTCTCAAGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
*
24558757 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* *
24558799 AAAGGAAGACTTATGACTCG
1 AAAGGAAGACTCATGTCTCG
24558819 TTAGAGCATA
Statistics
Matches: 211, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
42 178 0.84
43 32 0.15
44 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
Found at i:24565220 original size:16 final size:16
Alignment explanation
Indices: 24565194--24565235 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
24565184 AAATGCAACT
*
24565194 ACAATACAAATG-TGAG
1 ACAATA-AAATGCAGAG
24565210 ACAAGTAAAATGCAGAG
1 ACAA-TAAAATGCAGAG
24565227 ACAATAAAA
1 ACAATAAAA
24565236 ATGTAATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.14
Consensus pattern (16 bp):
ACAATAAAATGCAGAG
Found at i:24568603 original size:22 final size:19
Alignment explanation
Indices: 24568574--24568613 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
24568564 TTTTATATGG
24568574 AATTTTGAATTGAAGAATTTT
1 AATTTTGAATT-AA-AATTTT
24568595 AATTATTGAATTAAAATTT
1 AATT-TTGAATTAAAATTT
24568614 AGTATAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (19 bp):
AATTTTGAATTAAAATTTT
Found at i:24570389 original size:52 final size:52
Alignment explanation
Indices: 24570311--24570601 Score: 458
Period size: 52 Copynumber: 5.6 Consensus size: 52
24570301 AAATGCAAAA
*
24570311 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
24570363 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
** * *
24570415 AGGTTTGATGACTATGTGTCATCATGAGTATATGAATCCTTTAAGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
24570467 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
24570519 AGGTCCGATGACTATGTGTCATCGTGAGCATATGGATCCTTTTACGGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATG
* * *
24570571 AGGTCCAATGACTTTGTGTCATTGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
24570602 TAAATGAGAA
Statistics
Matches: 222, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
52 212 0.95
53 10 0.05
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:24571563 original size:21 final size:21
Alignment explanation
Indices: 24571537--24571587 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
24571527 AGCCACACTC
24571537 GTATCGATAATATTATCTCAA
1 GTATCGATAATATTATCTCAA
24571558 GTATCGATAATATTATCTCAA
1 GTATCGATAATATTATCTCAA
24571579 GTATCGATA
1 GTATCGATA
24571588 GAAGTCTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
GTATCGATAATATTATCTCAA
Found at i:24576868 original size:23 final size:23
Alignment explanation
Indices: 24576838--24576938 Score: 116
Period size: 23 Copynumber: 4.3 Consensus size: 23
24576828 GCTGGGCAAT
24576838 AGAGAGCACACACAATGCTAAAC
1 AGAGAGCACACACAATGCTAAAC
*
24576861 AGAGAGCACACA-AAGTGCTAATC
1 AGAGAGCACACACAA-TGCTAAAC
*
24576884 AGAGAGCACACACAGTGCTAATAAC
1 AGAGAGCACACACAATGCT-A-AAC
* *
24576909 AGAGAGCACGAGAC-GTGCTAAAC
1 AGAGAGCAC-ACACAATGCTAAAC
24576932 AGAGAGC
1 AGAGAGC
24576939 GTGCTAGTGT
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
22 2 0.03
23 45 0.65
24 3 0.04
25 16 0.23
26 3 0.04
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.10
Consensus pattern (23 bp):
AGAGAGCACACACAATGCTAAAC
Found at i:24576927 original size:48 final size:46
Alignment explanation
Indices: 24576838--24576938 Score: 132
Period size: 48 Copynumber: 2.2 Consensus size: 46
24576828 GCTGGGCAAT
*
24576838 AGAGAGCACACACAATGCTAAACAGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACACAATGCTAAACAGAGAGCACACAAAGTGCTAAAC
* * *
24576884 AGAGAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGCTAAAC
1 AGAGAGCACACACAATGCT-A-AACAGAGAGCAC-ACAAAGTGCTAAAC
24576932 AGAGAGC
1 AGAGAGC
24576939 GTGCTAGTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 18 0.38
47 1 0.02
48 28 0.58
49 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.10
Consensus pattern (46 bp):
AGAGAGCACACACAATGCTAAACAGAGAGCACACAAAGTGCTAAAC
Found at i:24580243 original size:47 final size:41
Alignment explanation
Indices: 24580122--24580285 Score: 229
Period size: 41 Copynumber: 4.0 Consensus size: 41
24580112 TTATGCTCTA
* * * *
24580122 TCGAGGCATAAGTCTTCCTTTTTCCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATT-CATAATCTCATTCTCATC
* * * *
24580164 TCGAGACATAAGTATTTCGTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
*
24580205 TCGATACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
*
24580246 TCGAGACATGAGTCTTCCTTATTCATAATCTCATGCTCAT
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCAT
24580286 TCCGACTCAT
Statistics
Matches: 109, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
41 91 0.83
42 18 0.17
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
Found at i:24580297 original size:41 final size:40
Alignment explanation
Indices: 24580132--24580304 Score: 195
Period size: 41 Copynumber: 4.2 Consensus size: 40
24580122 TCGAGGCATA
* * * *
24580132 AGTCTTCCTTTTTCCATATTCTCATTCTCATCTCGAGACATA
1 AGTCTTCCTTATT-CATAATCTCATTCTCATCTCGA-TCATG
* * *
24580174 AGTATTTCGTATTCATAATCTCATTCTCATCTCGATACATG
1 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAT-CATG
*
24580215 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGA-TCATG
*
24580256 AGTCTTCCTTATTCATAATCTCATGCTCAT-TCCGACTCATG
1 AGTCTTCCTTATTCATAATCTCATTCTCATCT-CGA-TCATG
*
24580297 ACTCTTCC
1 AGTCTTCC
24580305 ATTTTACAAT
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 103 0.91
42 9 0.08
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (40 bp):
AGTCTTCCTTATTCATAATCTCATTCTCATCTCGATCATG
Found at i:24580303 original size:82 final size:83
Alignment explanation
Indices: 24580134--24580304 Score: 231
Period size: 82 Copynumber: 2.1 Consensus size: 83
24580124 GAGGCATAAG
* * * *
24580134 TCTTCCTTTTTCCATATTCTCATTCTCATCTCGAGACATAAGTATTTCGTATTCATAATCTCATT
1 TCTTCCTTATTCCATAATCTCATTCTCATCTCGAGACATAAGTATTCCGTATTCATAATCTCATG
*
24580199 CTCATCTCGATACATGAG
66 CTCATCTCGATACATGAC
* * *
24580217 TCTTCCTTATT-CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCATAATCTCATG
1 TCTTCCTTATTCCATAATCTCATTCTCATCTCGAGACATAAGTATTCCGTATTCATAATCTCATG
24580281 CTCAT-TCCGACT-CATGAC
66 CTCATCT-CGA-TACATGAC
24580299 TCTTCC
1 TCTTCC
24580305 ATTTTACAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
81 1 0.01
82 66 0.85
83 11 0.14
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.41
Consensus pattern (83 bp):
TCTTCCTTATTCCATAATCTCATTCTCATCTCGAGACATAAGTATTCCGTATTCATAATCTCATG
CTCATCTCGATACATGAC
Found at i:24585181 original size:42 final size:42
Alignment explanation
Indices: 24585076--24585210 Score: 202
Period size: 42 Copynumber: 3.2 Consensus size: 42
24585066 TTGATGTATA
* * *
24585076 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGGATT-TG-TAT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGA-GATTATGAT-T
24585118 AAATGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
1 AAA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
24585161 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
24585203 AAAGGAAG
1 AAAGGAAG
24585211 GCTTGTGACT
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
42 54 0.62
43 32 0.37
44 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
Found at i:24599046 original size:34 final size:34
Alignment explanation
Indices: 24599008--24599074 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
24598998 AAAAAATTAT
24599008 ATTGTTGTTTTGGTCCAGTTTTTTTACTGTTTTA
1 ATTGTTGTTTTGGTCCAGTTTTTTTACTGTTTTA
* ***
24599042 ATTGTTGTTTTTGTGTTGTTTTTTTACTGTTTT
1 ATTGTTGTTTTGGTCCAGTTTTTTTACTGTTTT
24599075 GGTTGTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.67
Consensus pattern (34 bp):
ATTGTTGTTTTGGTCCAGTTTTTTTACTGTTTTA
Found at i:24599081 original size:34 final size:34
Alignment explanation
Indices: 24599025--24599124 Score: 130
Period size: 34 Copynumber: 2.9 Consensus size: 34
24599015 TTTTGGTCCA
** *
24599025 GTTTTTTTACTGTTTTAATTGTTGTTTTTGTGTT
1 GTTTTTTTACTGTTTTGGTTGTTATTTTTGTGTT
*
24599059 GTTTTTTTACTGTTTTGGTTGTTATTTTCGTGTT
1 GTTTTTTTACTGTTTTGGTTGTTATTTTTGTGTT
*
24599093 -TTTTTTGCTACTATTTTGGTTGTTATTTTTGT
1 GTTTTTT--TACTGTTTTGGTTGTTATTTTTGT
24599125 TGTTTGGATG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
33 6 0.10
34 30 0.52
35 22 0.38
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (34 bp):
GTTTTTTTACTGTTTTGGTTGTTATTTTTGTGTT
Found at i:24599092 original size:20 final size:21
Alignment explanation
Indices: 24599050--24599094 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
24599040 TAATTGTTGT
*
24599050 TTTTGTGTTGTTTTTTTACTG
1 TTTTGTGTTGTTATTTTACTG
24599071 TTTTG-GTTGTTATTTT-CGTG
1 TTTTGTGTTGTTATTTTAC-TG
24599091 TTTT
1 TTTT
24599095 TTTTGCTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.04, C:0.04, G:0.20, T:0.71
Consensus pattern (21 bp):
TTTTGTGTTGTTATTTTACTG
Found at i:24601128 original size:137 final size:138
Alignment explanation
Indices: 24600864--24601234 Score: 577
Period size: 137 Copynumber: 2.7 Consensus size: 138
24600854 AAAAAAAAAG
* * * *
24600864 AATTATATTCTTTTCAAAAGATTATTAATTTTCATATTTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
*
24600929 TATAAATGTTTATATTAATAAATTTAGTAAAATATATACAATTAATATTTTGTATTAATCAAATT
66 TATAAATGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATTAATCAAATT
24600994 CATATATT
131 CATATATT
* * *
24601002 AATTATATTCTTTCCAAAACAAAATTAATTTTCATGCCTTTTATATTTTGA-CTGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATC-GAAATTAATTA
* *
24601066 ATA-AAATGTTTATATTAATAAATTCCGTAAAATATATACAATTAATGTTTTGTATTAATCAAAT
65 ATATAAATGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATTAATCAAAT
24601130 TCATATATT
130 TCATATATT
* * *
24601139 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTGTATTTTAATCGAAATTAACTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
*
24601204 TATAACA-GTTTATATTAATAAATTCGGTAAA
66 TATAA-ATGTTTATATTAATAAATTCAGTAAA
24601235 GAATATTAAT
Statistics
Matches: 212, Mismatches: 17, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
137 127 0.60
138 84 0.40
139 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
TATAAATGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATTAATCAAATT
CATATATT
Found at i:24601240 original size:77 final size:77
Alignment explanation
Indices: 24601155--24601311 Score: 233
Period size: 77 Copynumber: 2.0 Consensus size: 77
24601145 ATTCTTTCCA
* * * * * *
24601155 AAAGAATATTAATTTTCATGTCTTTTGTATTTTAATCGAAATTAACTAATATAACAGTTTATATT
1 AAAGAATATTAATCTCCACGTCTTTTATATTTTAACCGAAACTAACTAATATAACAGTTTATATT
24601220 AATAAATTCGGT
66 AATAAATTCGGT
* * *
24601232 AAAGAATATTAATCTCCACGTCTTTTATATTTTGACCGAAACTAATTAATATAACTGTTTATATT
1 AAAGAATATTAATCTCCACGTCTTTTATATTTTAACCGAAACTAACTAATATAACAGTTTATATT
24601297 AATAAATTCGGT
66 AATAAATTCGGT
24601309 AAA
1 AAA
24601312 ATATATACAA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.41
Consensus pattern (77 bp):
AAAGAATATTAATCTCCACGTCTTTTATATTTTAACCGAAACTAACTAATATAACAGTTTATATT
AATAAATTCGGT
Found at i:24604289 original size:20 final size:20
Alignment explanation
Indices: 24604261--24604298 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24604251 ATTTGATTTT
*
24604261 AAGGTTTGGGTTAAGGTTTC
1 AAGGCTTGGGTTAAGGTTTC
*
24604281 AAGGCTTGGGTTTAGGTT
1 AAGGCTTGGGTTAAGGTT
24604299 AGGTCAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.05, G:0.37, T:0.39
Consensus pattern (20 bp):
AAGGCTTGGGTTAAGGTTTC
Found at i:24613926 original size:19 final size:19
Alignment explanation
Indices: 24613904--24613969 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
24613894 TCCTAAAAAT
24613904 AAATAAATTAAAATTATAA
1 AAATAAATTAAAATTATAA
24613923 AAATAAA-TAAAATTTATAA
1 AAATAAATTAAAA-TTATAA
* *
24613942 AAAAAATATTAAAAATTCTAA
1 AAATAA-ATT-AAAATTATAA
*
24613963 GAATAAA
1 AAATAAA
24613970 GTGAGAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 5 0.13
19 18 0.46
20 2 0.05
21 10 0.26
22 4 0.10
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATAAATTAAAATTATAA
Found at i:24615415 original size:34 final size:34
Alignment explanation
Indices: 24615367--24615435 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
24615357 TCATTTCCGA
*
24615367 TACAAAATCAGCTAAAAACCTAGTTACATGCCAT
1 TACAAAATCAGCTAAAAACCTAATTACATGCCAT
*
24615401 TACAAAATCGGCTAAAAACCTAATTACATGCCAT
1 TACAAAATCAGCTAAAAACCTAATTACATGCCAT
24615435 T
1 T
24615436 TATCGAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (34 bp):
TACAAAATCAGCTAAAAACCTAATTACATGCCAT
Found at i:24616541 original size:22 final size:23
Alignment explanation
Indices: 24616514--24616565 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
24616504 GTATATGCAT
24616514 ATAAATAGTATAATCTTGAATC-
1 ATAAATAGTATAATCTTGAATCA
*
24616536 ATAAATAGTATGATCTTGAATCA
1 ATAAATAGTATAATCTTGAATCA
24616559 ATAAATA
1 ATAAATA
24616566 AAACAATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (23 bp):
ATAAATAGTATAATCTTGAATCA
Found at i:24620781 original size:30 final size:30
Alignment explanation
Indices: 24620747--24620835 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 30
24620737 GAGAAAAATT
24620747 AGGGTTAAAAATGGGATTTTGGAAAGTTCG
1 AGGGTTAAAAATGGGATTTTGGAAAGTTCG
* *
24620777 AGGG-T-AAAATGGTAATTTTTTATGAAA--TC-
1 AGGGTTAAAAATGG-GA--TTTT-GGAAAGTTCG
*
24620806 AAGGTTAAAAATGGGATTTTGGAAAGTTCG
1 AGGGTTAAAAATGGGATTTTGGAAAGTTCG
24620836 GGAGTAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 18
0.66 0.07 0.26
Matches are distributed among these distances:
27 4 0.09
28 11 0.24
29 7 0.16
30 8 0.18
31 11 0.24
32 4 0.09
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (30 bp):
AGGGTTAAAAATGGGATTTTGGAAAGTTCG
Found at i:24620899 original size:30 final size:31
Alignment explanation
Indices: 24620865--24620933 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 31
24620855 TGGTGAAATC
24620865 GGGGTCAAAAATGG-AA-CTTTGGAAAGTTTA
1 GGGGTCAAAAATGGTAATCTTTGG-AAGTTTA
* *
24620895 GGGGT--AAAATGGTAATTTTTGGAAGTTTC
1 GGGGTCAAAAATGGTAATCTTTGGAAGTTTA
*
24620924 GAGGTCAAAA
1 GGGGTCAAAA
24620934 TGTAATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
28 7 0.22
29 12 0.38
30 10 0.31
31 3 0.09
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.29
Consensus pattern (31 bp):
GGGGTCAAAAATGGTAATCTTTGGAAGTTTA
Found at i:24620916 original size:59 final size:58
Alignment explanation
Indices: 24620742--24620916 Score: 233
Period size: 59 Copynumber: 3.0 Consensus size: 58
24620732 ATTTCGAGAA
* **
24620742 AAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTTATG
1 AAATCAGGGTTAAAAATGGGATTTTGGAAAGTTCG-GGGTAAAATGGTAATTTTTGGTG
* *
24620801 AAATCAAGGTTAAAAATGGGATTTTGGAAAGTTCGGGAGTAAAATGGTAACTTTTGGTG
1 AAATCAGGGTTAAAAATGGGATTTTGGAAAGTTCGGG-GTAAAATGGTAATTTTTGGTG
* * * * *
24620860 AAATCGGGGTCAAAAATGGAACTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGG
1 AAATCAGGGTTAAAAATGGGATTTTGGAAAG-TTCGGGGTAAAATGGTAATTTTTGG
24620917 AAGTTTCGAG
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
58 2 0.02
59 95 0.93
60 5 0.05
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (58 bp):
AAATCAGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTTGGTG
Found at i:24620921 original size:29 final size:30
Alignment explanation
Indices: 24620882--24620942 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
24620872 AAAATGGAAC
*
24620882 TTTGGAAAGTTTAGGGGT-AAAATGGTAATT
1 TTTGGAAAGTTTAGAGGTCAAAAT-GTAATT
*
24620912 TTTGG-AAGTTTCGAGGTCAAAATGTAATT
1 TTTGGAAAGTTTAGAGGTCAAAATGTAATT
24620941 TT
1 TT
24620943 CTAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.39
Consensus pattern (30 bp):
TTTGGAAAGTTTAGAGGTCAAAATGTAATT
Found at i:24621268 original size:10 final size:10
Alignment explanation
Indices: 24621253--24621302 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
24621243 TACTGGGCCA
24621253 AATTAAAAAT
1 AATTAAAAAT
24621263 AATTAAAAAT
1 AATTAAAAAT
*
24621273 -ATGAAAAGGACT
1 AATTAAAA--A-T
24621285 AATT-AAAAT
1 AATTAAAAAT
24621294 AATTAAAAA
1 AATTAAAAA
24621303 ATGCAGAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
9 11 0.33
10 15 0.45
11 1 0.03
12 4 0.12
13 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (10 bp):
AATTAAAAAT
Found at i:24623533 original size:200 final size:200
Alignment explanation
Indices: 24623179--24623905 Score: 1197
Period size: 200 Copynumber: 3.6 Consensus size: 200
24623169 ATTCCACTAG
* *
24623179 TTTATTGACTTCGACCTGGTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCGT
1 TTTATTG-CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGT
* * * *
24623244 TGAGCGTTGAGTTGGTATTCTTTTCTGTATCTCATCAGGGAGATGACCGCCTCGCTTGTTTTAAT
65 TGAGCCTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGAT
* * *
24623309 TCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCT
130 TCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTATATCTCATCAGGAAGCT
24623374 AACCAT
195 AACCAT
24623380 TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTT
1 TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTT
* *
24623445 GAGCCTTGAGTTGGTATTCTTCTCTGTATCTTATCAGGAAGATGTCCGCCTCGCTTGTTTTGATT
66 GAGCCTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATT
* * *
24623510 CGCTTCTCTAGATCTCTTCAGGAAGACGAATCTGGTCCACTTCTCTATATCTTATCAGGAAGCTA
131 CGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTATATCTCATCAGGAAGCTA
24623575 ACCAT
196 ACCAT
*
24623580 TTTATTGCTTCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTT
1 TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTT
* * * *
24623645 GAGCGTTGAGTTGGTATTCTTCTCTGTATGTTATCAGGAAGATGACCGCCTCACTTGTTTTGATT
66 GAGCCTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATT
* *
24623710 CGCTTCTCTGGATATCCTCAGGAAGACGAATCTGGTCCACTTCTCTCTATCTCATCAGGAAGCTA
131 CGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTATATCTCATCAGGAAGCTA
24623775 ACCAT
196 ACCAT
* *
24623780 TTTATCGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGTTCGAAGATTGGCTCGTGTT
1 TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTT
* *
24623845 GAGCGC-TGAGTTGGTATTCTTCTCTGTTTCTCATCAGGAAGATGACTGCCTCGC-TGTTTTG
66 GAGC-CTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTG
24623906 TTGAACTACT
Statistics
Matches: 492, Mismatches: 33, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
199 7 0.01
200 478 0.97
201 7 0.01
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (200 bp):
TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTT
GAGCCTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATT
CGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTATATCTCATCAGGAAGCTA
ACCAT
Found at i:24624162 original size:49 final size:49
Alignment explanation
Indices: 24624109--24624330 Score: 195
Period size: 50 Copynumber: 4.6 Consensus size: 49
24624099 TCCCTTCAAA
*
24624109 TCTTCGTGGTACTAGATCCACCGTTGCGGCTTAGATCTTTCTCTTTATG
1 TCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGATCTTTCTCTTTATG
* * * * *
24624158 TCTTCTTGGTACTGGATTCACCGTTGCGGCTT-GAAACTTTC-CTGTCT-
1 TCTTCGTGGTACTGGATCCACCGTTGCGGCTTAG-ATCTTTCTCTTTATG
* ** * * * *
24624205 TCTT-GAGGTACACGATCCACCGTTGTGACTTAGACCTTTCCCTTT-TG
1 TCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGATCTTTCTCTTTATG
* * *
24624252 CATCATT-GTGGTACTGGATCCACCGTCGCGGCCTTAGATCTTTCTCTTCATA
1 --TC-TTCGTGGTACTGGATCCACCGTTGCGG-CTTAGATCTTTCTCTTTATG
* *
24624304 TCTTCGTGGTGCTGGATCCGCCGTTGC
1 TCTTCGTGGTACTGGATCCACCGTTGC
24624331 AGTTTTATGT
Statistics
Matches: 135, Mismatches: 28, Indels: 19
0.74 0.15 0.10
Matches are distributed among these distances:
46 27 0.20
47 8 0.06
48 5 0.04
49 39 0.29
50 41 0.30
51 14 0.10
52 1 0.01
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (49 bp):
TCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGATCTTTCTCTTTATG
Found at i:24624313 original size:50 final size:49
Alignment explanation
Indices: 24624096--24624330 Score: 196
Period size: 49 Copynumber: 4.8 Consensus size: 49
24624086 CGACTTAAGC
* *
24624096 CTTTCCCTTCAAATCTTCGTGGTACTAGATCCACCGTTGCGGCTTAGAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGAT
* * * * * *
24624145 CTTTCTCTTTATGTCTTCTTGGTACTGGATTCACCGTTGCGGCTT-GAAA
1 CTTTCCCTTCATATCTTCGTGGTACTGGATCCACCGTTGCGGCTTAG-AT
* ** * * *
24624194 CTTT-CCTGTC-T-TCTT-GAGGTACACGATCCACCGTTGTGACTTAGAC
1 CTTTCCCT-TCATATCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGAT
* *
24624240 CTTTCCCTT-TTGCATCATT-GTGGTACTGGATCCACCGTCGCGGCCTTAGAT
1 CTTTCCCTTCAT--ATC-TTCGTGGTACTGGATCCACCGTTGCGG-CTTAGAT
* * *
24624291 CTTTCTCTTCATATCTTCGTGGTGCTGGATCCGCCGTTGC
1 CTTTCCCTTCATATCTTCGTGGTACTGGATCCACCGTTGC
24624331 AGTTTTATGT
Statistics
Matches: 144, Mismatches: 30, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
46 27 0.19
47 8 0.06
48 4 0.03
49 48 0.33
50 42 0.29
51 14 0.10
52 1 0.01
ACGTcount: A:0.14, C:0.28, G:0.20, T:0.37
Consensus pattern (49 bp):
CTTTCCCTTCATATCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGAT
Found at i:24626065 original size:21 final size:20
Alignment explanation
Indices: 24626039--24626084 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
24626029 CCTTTACGGT
24626039 TTTTTTTATCTTGACTTTTTC
1 TTTTTTTATCTT-ACTTTTTC
* *
24626060 TTTTTTTTTCTTTCTTTTTC
1 TTTTTTTATCTTACTTTTTC
24626080 TTTTT
1 TTTTT
24626085 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTTTATCTTACTTTTTC
Found at i:24626069 original size:10 final size:10
Alignment explanation
Indices: 24626054--24626089 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
24626044 TTATCTTGAC
24626054 TTTTTCTTTT
1 TTTTTCTTTT
*
24626064 TTTTTCTTTC
1 TTTTTCTTTT
24626074 TTTTTCTTTT
1 TTTTTCTTTT
24626084 TATTTT
1 T-TTTT
24626090 AAAATGTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:24630667 original size:29 final size:28
Alignment explanation
Indices: 24630635--24630756 Score: 72
Period size: 30 Copynumber: 4.2 Consensus size: 28
24630625 TAAAAATGAG
24630635 ATTTTGGAAGGTTCGGGTGTAAAATGGTA
1 ATTTTGGAAGGTTCGGGT-TAAAATGGTA
* ** *
24630664 ATTTTTGGTGAA-ATTAAGGTTAAAAATGG-G
1 A-TTTT-G-GAAGGTTCGGGTT-AAAATGGTA
*
24630694 ATTTTGGAAAGTTCGAGAG-TAAAATGGTA
1 ATTTTGGAAGGTTCG-G-GTTAAAATGGTA
* *
24630723 ATTTTTGGAAGTTTCGGCGTCAAAAT-GTA
1 A-TTTTGGAAGGTTCGG-GTTAAAATGGTA
24630752 ATTTT
1 ATTTT
24630757 CTAAAATTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
27 3 0.04
28 14 0.20
29 14 0.20
30 24 0.34
31 13 0.18
32 3 0.04
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (28 bp):
ATTTTGGAAGGTTCGGGTTAAAATGGTA
Found at i:24630688 original size:59 final size:60
Alignment explanation
Indices: 24630613--24630730 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 60
24630603 ATAATTTCAA
* * *
24630613 GAAATTCAAGGTTAAAAATGAGATTTTGGAAGGTTCGGGTGTAAAATGGTAATTTTTGGT
1 GAAATTCAAGGTTAAAAATGAGATTTTGGAAAGTTCGAGAGTAAAATGGTAATTTTTGGT
*
24630673 GAAATT-AAGGTTAAAAATGGGATTTTGGAAAGTTCGAGAGTAAAATGGTAATTTTTGG
1 GAAATTCAAGGTTAAAAATGAGATTTTGGAAAGTTCGAGAGTAAAATGGTAATTTTTGG
24630731 AAGTTTCGGC
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
59 48 0.89
60 6 0.11
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (60 bp):
GAAATTCAAGGTTAAAAATGAGATTTTGGAAAGTTCGAGAGTAAAATGGTAATTTTTGGT
Found at i:24630731 original size:30 final size:30
Alignment explanation
Indices: 24630636--24630756 Score: 71
Period size: 29 Copynumber: 4.1 Consensus size: 30
24630626 AAAAATGAGA
* *
24630636 TTTTGGAAGGTTCG-GGTGTAAAATGGTAAT
1 TTTTGGAAAGTTCGAGGT-AAAAATGGTAAT
* *
24630666 TTTTGGTGAAA-TT-AAGGTTAAAAATGG-GA-
1 TTTT-G-GAAAGTTCGAGG-TAAAAATGGTAAT
24630695 TTTTGGAAAGTTCGAGAGT-AAAATGGTAAT
1 TTTTGGAAAGTTCGAG-GTAAAAATGGTAAT
*
24630725 TTTTGG-AAGTTTCG-GCGTCAAAAT-GTAAT
1 TTTTGGAAAG-TTCGAG-GTAAAAATGGTAAT
24630754 TTT
1 TTT
24630757 CTAAAATTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
27 4 0.05
28 10 0.14
29 22 0.30
30 21 0.29
31 12 0.16
32 4 0.05
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAGTTCGAGGTAAAAATGGTAAT
Found at i:24631972 original size:15 final size:15
Alignment explanation
Indices: 24631952--24632000 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
24631942 TCTTTATTAA
24631952 TATTATTAATATATT
1 TATTATTAATATATT
*
24631967 TATTATTAA-CTATT
1 TATTATTAATATATT
*
24631981 TATCA-TAATA-A-T
1 TATTATTAATATATT
24631993 TATTATTA
1 TATTATTA
24632001 TAACATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 5 0.18
13 6 0.21
14 8 0.29
15 9 0.32
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATTAATATATT
Found at i:24636832 original size:21 final size:21
Alignment explanation
Indices: 24636808--24636856 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
24636798 TTCTTATGTG
*
24636808 TATTTTTGGTTGTATTGGTGT
1 TATTTTTGGTTATATTGGTGT
* *
24636829 TATTTTTTGTTATTTTGGTGT
1 TATTTTTGGTTATATTGGTGT
*
24636850 TGTTTTT
1 TATTTTT
24636857 ACTATTTTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.08, C:0.00, G:0.22, T:0.69
Consensus pattern (21 bp):
TATTTTTGGTTATATTGGTGT
Found at i:24636876 original size:20 final size:20
Alignment explanation
Indices: 24636839--24636878 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
24636829 TATTTTTTGT
* **
24636839 TATTTTGGTGTTGTTTTTAC
1 TATTTTGGTGCTACTTTTAC
24636859 TATTTTGGTGCTACTTTTAC
1 TATTTTGGTGCTACTTTTAC
24636879 AGTTATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.60
Consensus pattern (20 bp):
TATTTTGGTGCTACTTTTAC
Found at i:24636899 original size:12 final size:12
Alignment explanation
Indices: 24636880--24636962 Score: 71
Period size: 12 Copynumber: 7.0 Consensus size: 12
24636870 TACTTTTACA
24636880 GTTATTTTTGTT
1 GTTATTTTTGTT
* *
24636892 GTTGTTTTTGCT
1 GTTATTTTTGTT
*
24636904 GCTATTTTTGTCT
1 GTTATTTTTGT-T
*
24636917 -TTA-TTTTGCT
1 GTTATTTTTGTT
*
24636927 GTTATTTTTGCT
1 GTTATTTTTGTT
* * *
24636939 GCTGTTTTGGTT
1 GTTATTTTTGTT
24636951 GTTATTTTTGTT
1 GTTATTTTTGTT
24636963 ATTTGGATGT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
10 1 0.02
11 8 0.15
12 44 0.81
13 1 0.02
ACGTcount: A:0.06, C:0.07, G:0.19, T:0.67
Consensus pattern (12 bp):
GTTATTTTTGTT
Found at i:24636923 original size:24 final size:23
Alignment explanation
Indices: 24636882--24636936 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
24636872 CTTTTACAGT
*
24636882 TATTTTTGTTGTTGTTTTTGCTGC
1 TATTTTTGTTGTT-ATTTTGCTGC
*
24636906 TATTTTTGTCT-TTATTTTGCTGT
1 TATTTTTGT-TGTTATTTTGCTGC
24636929 TATTTTTG
1 TATTTTTG
24636937 CTGCTGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 16 0.57
24 11 0.39
25 1 0.04
ACGTcount: A:0.07, C:0.07, G:0.16, T:0.69
Consensus pattern (23 bp):
TATTTTTGTTGTTATTTTGCTGC
Found at i:24636935 original size:35 final size:34
Alignment explanation
Indices: 24636880--24636966 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
24636870 TACTTTTACA
* *
24636880 GTTATTTTTGTTGTTGTTTTTGCTGCTATTTTTGTCT
1 GTTA-TTTTG-TGTTATTTTTGCTGCTATTTTGGT-T
*
24636917 -TTATTTTGCTGTTATTTTTGCTGCTGTTTTGGTT
1 GTTATTTTG-TGTTATTTTTGCTGCTATTTTGGTT
24636951 GTTATTTT-TGTTATTT
1 GTTATTTTGTGTTATTT
24636967 GGATGTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 8 0.18
34 1 0.02
35 33 0.73
36 3 0.07
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (34 bp):
GTTATTTTGTGTTATTTTTGCTGCTATTTTGGTT
Found at i:24637806 original size:23 final size:24
Alignment explanation
Indices: 24637779--24637833 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
24637769 TCGTGCATAA
24637779 TTTTAAATAATA-ATATACTA-TTT
1 TTTTAAATAATAGA-ATACTACTTT
* * *
24637802 TTTTAATTATTAGAATATTACTTT
1 TTTTAAATAATAGAATACTACTTT
24637826 TTTTAAAT
1 TTTTAAAT
24637834 TGATTGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTAAATAATAGAATACTACTTT
Found at i:24638041 original size:52 final size:53
Alignment explanation
Indices: 24637943--24638064 Score: 147
Period size: 52 Copynumber: 2.3 Consensus size: 53
24637933 TCTTATTCTT
* *
24637943 TTGAATCGATTTTTTTATATGATTAAATCGATTGTTATGTTAGAATA-CTACTA
1 TTGAATCGA-TTGTTTATATGATTAAATCGATTGTTATATTAGAATATCTACTA
* * * * *
24637996 TTGAATCGATTGTTTATATGTTTAAATCGATTGTTTTATTGGAATATTGCTTCTT
1 TTGAATCGATTGTTTATATGATTAAATCGATTGTTATATTAGAATA-T-CTACTA
24638051 TTGAATCGATTGTT
1 TTGAATCGATTGTT
24638065 ACGTAGTACG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
52 32 0.54
53 9 0.15
55 18 0.31
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (53 bp):
TTGAATCGATTGTTTATATGATTAAATCGATTGTTATATTAGAATATCTACTA
Found at i:24640789 original size:21 final size:21
Alignment explanation
Indices: 24640765--24640813 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
24640755 CCTATGATAG
* * *
24640765 TTCTACCAATACAAGTGAAGC
1 TTCTACCAAAACAAATCAAGC
*
24640786 TTCTACCAAAACAAATCATGC
1 TTCTACCAAAACAAATCAAGC
24640807 TTCTACC
1 TTCTACC
24640814 GGTACTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.27
Consensus pattern (21 bp):
TTCTACCAAAACAAATCAAGC
Found at i:24641564 original size:28 final size:28
Alignment explanation
Indices: 24641532--24641587 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
24641522 GATATCTGAT
24641532 TTACTCCCTGTTGATCC-AAAGGTCATGC
1 TTACTCCCTGTTGA-CCTAAAGGTCATGC
*
24641560 TTACTCCCTGTTGACCTAAAGGTTATGC
1 TTACTCCCTGTTGACCTAAAGGTCATGC
24641588 CTGTTACCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (28 bp):
TTACTCCCTGTTGACCTAAAGGTCATGC
Found at i:24654877 original size:5 final size:5
Alignment explanation
Indices: 24654856--24654892 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
24654846 TAATCATTTG
*
24654856 TGTTT TGATTA TGTTT TGTTT TGTTT TGTTT TGTTT T
1 TGTTT TG-TTT TGTTT TGTTT TGTTT TGTTT TGTTT T
24654893 TCAGAGTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.05, C:0.00, G:0.19, T:0.76
Consensus pattern (5 bp):
TGTTT
Found at i:24655200 original size:15 final size:15
Alignment explanation
Indices: 24655180--24655244 Score: 112
Period size: 15 Copynumber: 4.3 Consensus size: 15
24655170 AACCACTACT
24655180 TCCACCTGGGCAGTA
1 TCCACCTGGGCAGTA
*
24655195 TCCACCTGGGCAATA
1 TCCACCTGGGCAGTA
24655210 TCCACCTGGGCAGTA
1 TCCACCTGGGCAGTA
*
24655225 TCCACCTGCGCAGTA
1 TCCACCTGGGCAGTA
24655240 TCCAC
1 TCCAC
24655245 AAGGACAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.20
Consensus pattern (15 bp):
TCCACCTGGGCAGTA
Found at i:24655396 original size:18 final size:17
Alignment explanation
Indices: 24655369--24655402 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
24655359 CTGGGCATCC
24655369 ACTACCTCCTCCAGGTT
1 ACTACCTCCTCCAGGTT
*
24655386 ACTATCCTCCTGCAGGT
1 ACTA-CCTCCTCCAGGT
24655403 CAAGGTCAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.18, C:0.38, G:0.15, T:0.29
Consensus pattern (17 bp):
ACTACCTCCTCCAGGTT
Found at i:24656117 original size:18 final size:19
Alignment explanation
Indices: 24656077--24656119 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
24656067 AAAATTTAAA
**
24656077 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTAC
24656096 AAAATTCAAAAT-ATTTAC
1 AAAATTCAAAATAATTTAC
24656114 AAAATT
1 AAAATT
24656120 TTCAGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAC
Found at i:24662186 original size:12 final size:12
Alignment explanation
Indices: 24662171--24662213 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
24662161 AGTAACCAAT
*
24662171 GAAGTGCCAAAA
1 GAAGTGGCAAAA
24662183 GAAGTGGCAAAA
1 GAAGTGGCAAAA
24662195 GAAGTGGCAAAA
1 GAAGTGGCAAAA
*
24662207 AAAGTGG
1 GAAGTGG
24662214 GAGTTGCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.49, C:0.09, G:0.33, T:0.09
Consensus pattern (12 bp):
GAAGTGGCAAAA
Found at i:24667048 original size:21 final size:20
Alignment explanation
Indices: 24667022--24667060 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
24667012 TACTGATATA
*
24667022 TATATATATATAGAATTTTTT
1 TATATATAAATA-AATTTTTT
24667043 TATATATAAATAAATTTT
1 TATATATAAATAAATTTT
24667061 ATATCCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TATATATAAATAAATTTTTT
Found at i:24672133 original size:9 final size:9
Alignment explanation
Indices: 24672110--24672142 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
24672100 ATTTAGTTTT
24672110 AATTTT-AA
1 AATTTTAAA
24672118 AATTTTAAA
1 AATTTTAAA
*
24672127 AACTTTAAA
1 AATTTTAAA
24672136 AATTTTA
1 AATTTTA
24672143 TTTAAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (9 bp):
AATTTTAAA
Found at i:24673488 original size:16 final size:16
Alignment explanation
Indices: 24673463--24673502 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
24673453 TCACGATACT
*
24673463 ATAATGAAATGACTTC
1 ATAATTAAATGACTTC
* *
24673479 ATAATTAAATGAGTTT
1 ATAATTAAATGACTTC
24673495 ATAATTAA
1 ATAATTAA
24673503 TAGGCGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (16 bp):
ATAATTAAATGACTTC
Done.