Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 153 of 193
Found at i:47593448 original size:22 final size:22
Alignment explanation
Indices: 47593400--47593447 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
47593390 AAAACTCAGG
*
47593400 TTTTAAAAAAAAAAAAAATTAA
1 TTTTAAAAAAAAAAAAAATCAA
47593422 TTTTAAAAAAGAAAAAATAA-CAA
1 TTTTAAAAAA-AAAAAA-AATCAA
47593445 TTT
1 TTT
47593448 ATTAAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 10 0.43
23 11 0.48
24 2 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
TTTTAAAAAAAAAAAAAATCAA
Found at i:47596753 original size:26 final size:27
Alignment explanation
Indices: 47596724--47596792 Score: 70
Period size: 30 Copynumber: 2.5 Consensus size: 27
47596714 ATTTATTTTT
*
47596724 TTTCA-TATATTTAAACCAAATCAAAA
1 TTTCAGTATAATTAAACCAAATCAAAA
*
47596750 TTTCATGGGTATAATTACACCAAATCAAAA
1 TTTCA---GTATAATTAAACCAAATCAAAA
47596780 TTT-ATGTATAATT
1 TTTCA-GTATAATT
47596793 TTAACATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 5 0.14
27 8 0.22
29 1 0.03
30 22 0.61
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (27 bp):
TTTCAGTATAATTAAACCAAATCAAAA
Found at i:47598109 original size:19 final size:19
Alignment explanation
Indices: 47598073--47598108 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
47598063 AATGAATAAA
*
47598073 AAATTTAAATAAATAAAAT
1 AAATATAAATAAATAAAAT
47598092 AAATATAAA-AAATAAAA
1 AAATATAAATAAATAAAA
47598109 AATATATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATATAAATAAATAAAAT
Found at i:47599146 original size:41 final size:38
Alignment explanation
Indices: 47599046--47599149 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
47599036 TTCAAAGCAA
* *
47599046 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
47599083 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
47599121 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
47599150 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:47599267 original size:12 final size:12
Alignment explanation
Indices: 47599252--47599288 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
47599242 ACAATTCATA
47599252 TCACTTTCAATT
1 TCACTTTCAATT
*
47599264 TCACTTTCACTT
1 TCACTTTCAATT
47599276 TCACTTTCAATT
1 TCACTTTCAATT
47599288 T
1 T
47599289 TGATCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:47599271 original size:6 final size:6
Alignment explanation
Indices: 47599252--47599284 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
47599242 ACAATTCATA
*
47599252 TCACTT TCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCA
47599285 ATTTTGATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.48
Consensus pattern (6 bp):
TCACTT
Found at i:47599463 original size:22 final size:22
Alignment explanation
Indices: 47599435--47599480 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
47599425 TAAACGTGTA
47599435 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
47599457 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
47599479 AT
1 AT
47599481 CACATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATTTCACATATACATTGTTC
Found at i:47599485 original size:18 final size:20
Alignment explanation
Indices: 47599439--47599488 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
47599429 CGTGTAATAT
47599439 TTCACATATACATTGTTCATA
1 TTCACATATACATTGTTCA-A
47599460 TTTCACATATACATTGTTC-A
1 -TTCACATATACATTGTTCAA
47599480 -TCACATATA
1 TTCACATATA
47599489 TATCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.32
20 1 0.04
22 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (20 bp):
TTCACATATACATTGTTCAA
Found at i:47603849 original size:73 final size:73
Alignment explanation
Indices: 47603726--47603871 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 73
47603716 AAGATTACCA
**
47603726 AGATTAATTGACACACTAATCTTGTGATTATCAATGCCAGGCACTGATGCCTCACCAAGAATGGA
1 AGATTAATTGACACACTAATCTTGTGATTATCAATGCCAGGCACCCATGCCTCACCAAGAATGGA
47603791 GATATTGT
66 GATATTGT
*
47603799 AGATTAATTGACACACTAATCTTGTGATTATCAATGCCAGGCACCCATGCCTCACCAAGAATGTA
1 AGATTAATTGACACACTAATCTTGTGATTATCAATGCCAGGCACCCATGCCTCACCAAGAATGGA
47603864 GATATTGT
66 GATATTGT
47603872 TTCCTGATCC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (73 bp):
AGATTAATTGACACACTAATCTTGTGATTATCAATGCCAGGCACCCATGCCTCACCAAGAATGGA
GATATTGT
Found at i:47609785 original size:22 final size:24
Alignment explanation
Indices: 47609729--47609786 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
47609719 TTTAAGATAT
47609729 TATTTATTATTTAATTTATGTTTTC
1 TATTTATT-TTTAATTTATGTTTTC
* *
47609754 TATTT-CTTTTAA-TTCTGTTTTC
1 TATTTATTTTTAATTTATGTTTTC
47609776 T-TTTATTTTTA
1 TATTTATTTTTA
47609787 TTGTTCCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 3 0.10
22 15 0.52
23 5 0.17
24 1 0.03
25 5 0.17
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.71
Consensus pattern (24 bp):
TATTTATTTTTAATTTATGTTTTC
Found at i:47612481 original size:6 final size:6
Alignment explanation
Indices: 47612470--47612529 Score: 113
Period size: 6 Copynumber: 10.2 Consensus size: 6
47612460 GGCAACCCAA
47612470 TTATTT TTA-TT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
47612517 TTATTT TTATTT T
1 TTATTT TTATTT T
47612530 CTTTTCTCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.09
6 48 0.91
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:47613913 original size:59 final size:60
Alignment explanation
Indices: 47613816--47613952 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
47613806 AAACTCTCAG
* ** * *
47613816 GGGTAAAATGGTAA-TTTTAGGAAAATTTGGGGTTAAAAAT-G-ATATTTTAGACATTCGA
1 GGGTAAAATGGTAATTTTTAGGAAAAATCAGGATCAAAAATGGAAT-TTTTAGACATTCGA
* * * *
47613874 GGGTAAAACGGTAATTTTTAGGAAAAATCAGGATCAAAAATGGAATTTTTGGATATTCGG
1 GGGTAAAATGGTAATTTTTAGGAAAAATCAGGATCAAAAATGGAATTTTTAGACATTCGA
*
47613934 GGGTAAAATGATAATTTTT
1 GGGTAAAATGGTAATTTTT
47613953 GAAAGTTTCG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 13 0.20
59 21 0.32
60 29 0.45
61 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (60 bp):
GGGTAAAATGGTAATTTTTAGGAAAAATCAGGATCAAAAATGGAATTTTTAGACATTCGA
Found at i:47613980 original size:30 final size:29
Alignment explanation
Indices: 47613938--47614133 Score: 141
Period size: 31 Copynumber: 6.5 Consensus size: 29
47613928 ATTCGGGGGT
47613938 AAAATGATAATTTTTGAAAGTTTCGAGGTCA
1 AAAAT-ATAATTTTTGAAAGTTT-GAGGTCA
* *
47613969 AAAATATAATTTTCAGAAAGTTTAGGGGT-A
1 AAAATATAATTTT-TGAAAGTTT-GAGGTCA
* * * *
47613999 AAATTGTAATTTTTGAAAGTTTTAGGGTTA
1 AAAATATAATTTTTGAAAGTTTGA-GGTCA
* *
47614029 AAAA-ATGGAATTTTGGAAAGTTTAGGGGT--
1 AAAATAT--AATTTTTGAAAGTTT-GAGGTCA
* * *
47614058 AAGATGTAATTTTTAGAAAGTTTGGGGGTCA
1 AAAATATAATTTTT-GAAAGTTT-GAGGTCA
*
47614089 AAAATATAATTTTAGAGAAGTTTGAGGGTC-
1 AAAATATAATTTTTGA-AAGTTTGA-GGTCA
47614119 AAAATATAATTTTTG
1 AAAATATAATTTTTG
47614134 GACTGTTTAG
Statistics
Matches: 131, Mismatches: 22, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
28 6 0.05
29 28 0.21
30 42 0.32
31 55 0.42
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAATATAATTTTTGAAAGTTTGAGGTCA
Found at i:47613997 original size:60 final size:57
Alignment explanation
Indices: 47613933--47614133 Score: 226
Period size: 60 Copynumber: 3.4 Consensus size: 57
47613923 TGGATATTCG
47613933 GGGGTAAAATGATAATTTTTGAAAGTTTCGAGGTCAAAAATATAATTTTCAGAAAGTTTA
1 GGGGTAAAATG-TAATTTTTGAAAGTTT-GAGGTCAAAAATATAATTTT-AGAAAGTTTA
* * *
47613993 GGGGTAAAATTGTAATTTTTGAAAGTTTTAGGGTTAAAAA-ATGGAATTTTGGAAAGTTTA
1 GGGGTAAAA-TGTAATTTTTGAAAGTTTGA-GGTCAAAAATAT--AATTTTAGAAAGTTTA
* *
47614053 GGGGTAAGATGTAATTTTTAGAAAGTTTGGGGGTCAAAAATATAATTTTAGAGAAGTTT-
1 GGGGTAAAATGTAATTTTT-GAAAGTTT-GAGGTCAAAAATATAATTTTAGA-AAGTTTA
*
47614112 GAGGGTCAAAATATAATTTTTG
1 G-GGGT-AAAATGTAATTTTTG
47614134 GACTGTTTAG
Statistics
Matches: 121, Mismatches: 10, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
59 22 0.18
60 77 0.64
61 22 0.18
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (57 bp):
GGGGTAAAATGTAATTTTTGAAAGTTTGAGGTCAAAAATATAATTTTAGAAAGTTTA
Found at i:47614145 original size:120 final size:120
Alignment explanation
Indices: 47613909--47614133 Score: 307
Period size: 120 Copynumber: 1.9 Consensus size: 120
47613899 AATCAGGATC
* *
47613909 AAAAATGGAATTTTTGGATATTCGGGGGTAAAATGATAATTTTTGAAAGTTTCGAGGTCAAAAAT
1 AAAAATGGAATTTTTGGAAATTCAGGGGTAAAATGATAATTTTTGAAAGTTTCGAGGTCAAAAAT
*
47613974 ATAATTTTCAGAAAGTTTAGGGGTAAAATTGTAATTTTTGAAAGTTTTAGGGTTA
66 ATAATTTTCAGAAAGTTTAGGGGTAAAATTATAATTTTTGAAAGTTTTAGGGTTA
* * * *
47614029 AAAAATGGAA-TTTTGGAAAGTTTAGGGGTAAGATG-TAATTTTTAGAAAGTTTGGGGGTCAAAA
1 AAAAATGGAATTTTTGGAAA-TTCAGGGGTAAAATGATAATTTTT-GAAAGTTTCGAGGTCAAAA
47614092 ATATAATTTT-AGAGAAGTTT-GAGGGTCAAAA-TATAATTTTTG
64 ATATAATTTTCAGA-AAGTTTAG-GGGT-AAAATTATAATTTTTG
47614134 GACTGTTTAG
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
119 20 0.22
120 69 0.74
121 4 0.04
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (120 bp):
AAAAATGGAATTTTTGGAAATTCAGGGGTAAAATGATAATTTTTGAAAGTTTCGAGGTCAAAAAT
ATAATTTTCAGAAAGTTTAGGGGTAAAATTATAATTTTTGAAAGTTTTAGGGTTA
Found at i:47615203 original size:3 final size:3
Alignment explanation
Indices: 47615195--47615255 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
47615185 ACTTTCATTT
* * * * *
47615195 TTA TTA TTA TTA ATA ATA TTA TTAA TTA CTA -TA TTA TTA TTTA ATG
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA
47615241 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
47615256 ATGCTATTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:47616839 original size:24 final size:22
Alignment explanation
Indices: 47616791--47616840 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
47616781 AGATTTAAGA
47616791 TATTTTTTATTATTTAATTTTG
1 TATTTTTTATTATTTAATTTTG
47616813 TATTTATTTATT-TTTATCATTTTG
1 TATTT-TTTATTATTTA--ATTTTG
47616837 TATT
1 TATT
47616841 GATCTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.36
23 6 0.24
24 10 0.40
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTATTTAATTTTG
Found at i:47617242 original size:6 final size:6
Alignment explanation
Indices: 47617233--47617324 Score: 79
Period size: 6 Copynumber: 15.8 Consensus size: 6
47617223 ATTTTTTTAA
* *
47617233 TTAATT TTAAAT TT-TAT TTAAAT TTAAAT TT--AT CTTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT
* *
47617279 TTATTTAT TTAAAT TT-ATT TTAAAT TTAAAT TT-AA- TTAAAT TTAAA
1 TTA--AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
47617325 ATGATATTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
4 4 0.06
5 14 0.20
6 45 0.64
7 2 0.03
8 5 0.07
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (6 bp):
TTAAAT
Found at i:47617333 original size:17 final size:17
Alignment explanation
Indices: 47617228--47617337 Score: 124
Period size: 17 Copynumber: 6.8 Consensus size: 17
47617218 TTTTGATTTT
*
47617228 TTTA-ATTAATTTTAAA
1 TTTATATTAAATTTAAA
47617244 TTT-TATTTAAATTTAAA
1 TTTATA-TTAAATTTAAA
*
47617261 TTTATCTTAAATTTAAA
1 TTTATATTAAATTTAAA
47617278 TTTAT-TT--ATTTAAA
1 TTTATATTAAATTTAAA
*
47617292 TTTATTTTAAATTTAAA
1 TTTATATTAAATTTAAA
47617309 TTTA-ATTAAATTTAAA
1 TTTATATTAAATTTAAA
* *
47617325 ATGATATTAAATT
1 TTTATATTAAATT
47617338 AATAAATTAA
Statistics
Matches: 82, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
14 12 0.15
15 2 0.02
16 19 0.23
17 48 0.59
18 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTATATTAAATTTAAA
Found at i:47617955 original size:21 final size:22
Alignment explanation
Indices: 47617921--47617963 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
47617911 CTATTATATA
47617921 TTTATTATACATTTAAGTCATT
1 TTTATTATACATTTAAGTCATT
*
47617943 TTTA-TATATATTTAAGTCATT
1 TTTATTATACATTTAAGTCATT
47617964 CTAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTATTATACATTTAAGTCATT
Found at i:47617970 original size:21 final size:21
Alignment explanation
Indices: 47617926--47617970 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
47617916 ATATATTTAT
* *
47617926 TATACATTTAAGTCATTTTTA
1 TATACATTTAAGTCATTCTAA
*
47617947 TATATATTTAAGTCATTCTAA
1 TATACATTTAAGTCATTCTAA
47617968 TAT
1 TAT
47617971 TTCGATAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (21 bp):
TATACATTTAAGTCATTCTAA
Found at i:47618077 original size:16 final size:16
Alignment explanation
Indices: 47618066--47618104 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
47618056 ACATTAATGG
47618066 TAATAAATATTAATAA
1 TAATAAATATTAATAA
*
47618082 TAATAAATA--AATAT
1 TAATAAATATTAATAA
47618096 TAATAAATA
1 TAATAAATA
47618105 AAAAGGGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATAAATATTAATAA
Found at i:47618081 original size:10 final size:10
Alignment explanation
Indices: 47618066--47618104 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
47618056 ACATTAATGG
47618066 TAATAAATAT
1 TAATAAATAT
47618076 TAAT-AATAAT
1 TAATAAAT-AT
*
47618086 AAATAAATAT
1 TAATAAATAT
47618096 TAATAAATA
1 TAATAAATA
47618105 AAAAGGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 19 0.76
11 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAATAAATAT
Found at i:47619154 original size:30 final size:29
Alignment explanation
Indices: 47619078--47619255 Score: 109
Period size: 29 Copynumber: 6.1 Consensus size: 29
47619068 GTTTATAGGT
* * *
47619078 CCCCGAAACTTCCAAAATTACCA-TTTTAC
1 CCCCAAAACTTTCAAAATT-CCATTTTTAA
* *
47619107 CCCCAAACCTTTTAAAATTCCATTTTTAA
1 CCCCAAAACTTTCAAAATTCCATTTTTAA
* *
47619136 CCCCAAAACTTCTAAAAATTAC-TATTTT-A
1 CCCCAAAACTT-TCAAAATTCCAT-TTTTAA
*
47619165 CCCCCAAACTTTCCAAAATTCCATTTTTAA
1 CCCCAAAACTTT-CAAAATTCCATTTTTAA
** *** *
47619195 CCTGATTTC-ATCAAAATTACCA-TTTT-A
1 CCCCAAAACTTTCAAAATT-CCATTTTTAA
*
47619222 CCCTC-GAACTTTCCAAAATTCCATTTTTAA
1 CCC-CAAAACTTT-CAAAATTCCATTTTTAA
47619252 CCCC
1 CCCC
47619256 GATTTTACCA
Statistics
Matches: 113, Mismatches: 24, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
27 4 0.04
28 19 0.17
29 69 0.61
30 21 0.19
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (29 bp):
CCCCAAAACTTTCAAAATTCCATTTTTAA
Found at i:47619378 original size:58 final size:59
Alignment explanation
Indices: 47619091--47619571 Score: 629
Period size: 59 Copynumber: 8.2 Consensus size: 59
47619081 CGAAACTTCC
* * * * * *
47619091 AAAATTACCATTTTACCCCCAAACCTTT-TAAAATTCCATTTTTAACCCCAAAACTT--CTA
1 AAAATTACCATTTTACCCTCGAA-CTTTCCAAAATTCCATTTTTAACCCC--GATTTCACCA
* * * * *
47619150 AAAATTACTATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA-CCTGATTTCATC-
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
47619207 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* *
47619266 AAAATTACCATTTCACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* *
47619325 AAAATTATCATTTTACCCTCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
47619383 AAAATTACCATTTTACCCTCGAAC-TTCCAAAATTTCATTTTTAACCTCGATTTTACCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
47619441 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * * *
47619500 AAAATTACCATTTTACCCTCAAAGC-CTCAAAAATTCCATTTTTAACCCCGATTTCA-CT
1 AAAATTACCATTTTACCCTCGAA-CTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
47619558 AAAATTACCATTTT
1 AAAATTACCATTTT
47619572 GCCCCCGGGT
Statistics
Matches: 382, Mismatches: 33, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
56 3 0.01
57 42 0.11
58 139 0.36
59 197 0.52
60 1 0.00
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:47619577 original size:29 final size:29
Alignment explanation
Indices: 47619149--47619578 Score: 209
Period size: 29 Copynumber: 14.8 Consensus size: 29
47619139 CAAAACTTCT
* *
47619149 AAAAATTACTATTTTACCCCCAAACTTTC-C
1 AAAAATTACCATTTTACCCCC-GA-TTTCAC
* *
47619179 -AAAATT-CCATTTTTA-ACCTGATTTCATC
1 AAAAATTACCA-TTTTACCCCCGATTTCA-C
*
47619207 -AAAATTACCATTTTACCCTCGAACTTTC-C
1 AAAAATTACCATTTTACCCCCG-A-TTTCAC
* *
47619236 -AAAATT-CCATTTTTAACCCCGATTTTACC
1 AAAAATTACCA-TTTTACCCCCGATTTCA-C
* *
47619265 AAAAATTACCATTTCACCCTCGAACTTTC-C
1 AAAAATTACCATTTTACCCCCG-A-TTTCAC
*
47619295 -AAAATT-CCATTTTTAACCCCGATTTCACC
1 AAAAATTACCA-TTTTACCCCCGATTTCA-C
* * * *
47619324 CAAAATTATCATTTTACCCTCGAACTTC-C
1 AAAAATTACCATTTTACCCCCG-ATTTCAC
* *
47619353 -AAAATT-CCATTTTTAACCTCGATTTCACC
1 AAAAATTACCA-TTTTACCCCCGATTTCA-C
* *
47619382 AAAAATTACCATTTTACCCTCGAACTTC-C
1 AAAAATTACCATTTTACCCCCG-ATTTCAC
* * * *
47619411 -AAAATT-TCATTTTTAACCTCGATTTTACC
1 AAAAATTACCA-TTTTACCCCCGATTTCA-C
*
47619440 AAAAATTACCATTTTACCCCCAAACTTTC-C
1 AAAAATTACCATTTTACCCCC-GA-TTTCAC
*
47619470 -AAAATT-CCATTTTTAACCCCGATTTCATC
1 AAAAATTACCA-TTTTACCCCCGATTTCA-C
* * *** *
47619499 AAAAATTACCATTTTACCCTCAAAGCCTC
1 AAAAATTACCATTTTACCCCCGATTTCAC
*
47619528 AAAAATT-CCATTTTTAACCCCGATTTCAC
1 AAAAATTACCA-TTTTACCCCCGATTTCAC
* *
47619557 TAAAATTACCATTTTGCCCCCG
1 AAAAATTACCATTTTACCCCCG
47619579 GGTATCCAAA
Statistics
Matches: 306, Mismatches: 54, Indels: 81
0.69 0.12 0.18
Matches are distributed among these distances:
26 4 0.01
27 23 0.08
28 63 0.21
29 102 0.33
30 81 0.26
31 27 0.09
32 6 0.02
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGATTTCAC
Found at i:47619589 original size:175 final size:174
Alignment explanation
Indices: 47619091--47619571 Score: 684
Period size: 175 Copynumber: 2.7 Consensus size: 174
47619081 CGAAACTTCC
* * *
47619091 AAAATTACCATTTTACCCCCAAACCTTT-TAAAATTCCATTTTTAACCCCAAAACTTC-T-AAAA
1 AAAATTACCATTTTACCCCCAAA-CTTTCCAAAATTCCATTTTTAACCCC--GATTTCATCAAAA
* * *
47619153 ATTACTATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA-CCTGATTTCA-TCAAAATTACC
63 ATTACCATTTTACCCTCAAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCACT-AAAATTACC
47619216 ATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCA
126 ATTTTACCCTCGAAC-TTCCAAAATTCCATTTTTAACCCCGATTTTACCA
* * * * *
47619266 AAAATTACCATTTCACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATT
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAATT
* * * *
47619331 ATCATTTTACCCTCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTT
66 ACCATTTTACCCTCAAACTTCCAAAATTCCATTTTTAACCCCGATTTCA-CTAAAATTACCATTT
* *
47619396 TACCCTCGAACTTCCAAAATTTCATTTTTAACCTCGATTTTACCA
130 TACCCTCGAACTTCCAAAATTCCATTTTTAACCCCGATTTTACCA
47619441 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAATT
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAATT
* *
47619506 ACCATTTTACCCTCAAAGCCTCAAAAATTCCATTTTTAACCCCGATTTCACTAAAATTACCATTT
66 ACCATTTTACCCTCAAA-CTTCCAAAATTCCATTTTTAACCCCGATTTCACTAAAATTACCATTT
47619571 T
130 T
47619572 GCCCCCGGGT
Statistics
Matches: 271, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
173 4 0.01
174 24 0.09
175 190 0.70
176 53 0.20
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.35
Consensus pattern (174 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAATT
ACCATTTTACCCTCAAACTTCCAAAATTCCATTTTTAACCCCGATTTCACTAAAATTACCATTTT
ACCCTCGAACTTCCAAAATTCCATTTTTAACCCCGATTTTACCA
Found at i:47619615 original size:117 final size:118
Alignment explanation
Indices: 47619091--47619578 Score: 634
Period size: 117 Copynumber: 4.2 Consensus size: 118
47619081 CGAAACTTCC
* * * * *
47619091 AAAATTACCATTTTACCCCCAAACCTTT-TAAAATTCCATTTTTAACCCCAAAACTT--CTAAAA
1 AAAATTACCATTTTACCCCCGAA-CTTTCCAAAATTCCATTTTTAACCCC--GATTTCACCAAAA
* * * *
47619153 ATTACTATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA-CCTGATTTCATC-
63 ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCT
* *
47619207 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATT
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
* * *
47619272 ACCATTTCACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC
66 ACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCT
* * *
47619325 AAAATTATCATTTTACCCTCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
* * * * *
47619389 ACCATTTTACCCTCGAAC-TTCCAAAATTTCATTTTTAACCTCGATTTTACCA
66 ACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCT
* *
47619441 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAATT
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
* *
47619506 ACCATTTTACCCTCAAAGC-CTCAAAAATTCCATTTTTAACCCCGATTTCA-CT
66 ACCATTTTACCCTCAAA-CTTTCCAAAATTCCATTTTTAACCCCGATTTCACCT
*
47619558 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
47619579 GGTATCCAAA
Statistics
Matches: 331, Mismatches: 34, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
114 3 0.01
115 4 0.01
116 135 0.41
117 139 0.42
118 50 0.15
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (118 bp):
AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
ACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCT
Found at i:47628510 original size:18 final size:18
Alignment explanation
Indices: 47628462--47628512 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
47628452 TCACATTAGC
*
47628462 AAAAAAA-ATTTAAATTT
1 AAAAAAATAATTAAATTT
*
47628479 AAAAACATAATTAAATTT
1 AAAAAAATAATTAAATTT
*
47628497 AAAAAAATAGTTAAAT
1 AAAAAAATAATTAAAT
47628513 ATTTTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 6 0.21
18 23 0.79
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAAAAATAATTAAATTT
Found at i:47629840 original size:17 final size:17
Alignment explanation
Indices: 47629818--47629850 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
47629808 AAAATTTAAT
47629818 AATTTTATATTTTAAAG
1 AATTTTATATTTTAAAG
47629835 AATTTTATATTTTAAA
1 AATTTTATATTTTAAA
47629851 AAAATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTTATATTTTAAAG
Found at i:47631251 original size:15 final size:14
Alignment explanation
Indices: 47631231--47631261 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
47631221 CTTATATTAG
47631231 CAATAATGCTCATAT
1 CAATAATGCTCA-AT
47631246 CAATAATGCTCAAT
1 CAATAATGCTCAAT
47631260 CA
1 CA
47631262 TTTATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.29
Consensus pattern (14 bp):
CAATAATGCTCAAT
Found at i:47633668 original size:31 final size:31
Alignment explanation
Indices: 47633607--47633669 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
47633597 AATAGCGTAG
** *
47633607 TGACTTAAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
*
47633638 TGACTTAAATGAAAACTTTCAAATAATTCAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
47633669 T
1 T
47633670 ACTATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAATTCAA
Found at i:47635558 original size:78 final size:78
Alignment explanation
Indices: 47635466--47635627 Score: 324
Period size: 78 Copynumber: 2.1 Consensus size: 78
47635456 ATTGAAATCA
47635466 TTCACGCTGGACATCCCAAACTTTTGTATTCTATTTTCATCAAAAATAAAGTTTAACTTTTCTCA
1 TTCACGCTGGACATCCCAAACTTTTGTATTCTATTTTCATCAAAAATAAAGTTTAACTTTTCTCA
47635531 TCTCAACTGGACT
66 TCTCAACTGGACT
47635544 TTCACGCTGGACATCCCAAACTTTTGTATTCTATTTTCATCAAAAATAAAGTTTAACTTTTCTCA
1 TTCACGCTGGACATCCCAAACTTTTGTATTCTATTTTCATCAAAAATAAAGTTTAACTTTTCTCA
47635609 TCTCAACTGGACT
66 TCTCAACTGGACT
47635622 TTCACG
1 TTCACG
47635628 TTGGCATTTA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 84 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.38
Consensus pattern (78 bp):
TTCACGCTGGACATCCCAAACTTTTGTATTCTATTTTCATCAAAAATAAAGTTTAACTTTTCTCA
TCTCAACTGGACT
Found at i:47640789 original size:29 final size:30
Alignment explanation
Indices: 47640757--47640813 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
47640747 TAGTTTAATA
47640757 TACAATTATATACAT-AAACTTT-GATTTTG
1 TACAATTATATACATGAAA-TTTCGATTTTG
*
47640786 TACAATTTTATACATGAAATTTCGATTT
1 TACAATTATATACATGAAATTTCGATTT
47640814 GATTCAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (30 bp):
TACAATTATATACATGAAATTTCGATTTTG
Found at i:47647262 original size:33 final size:33
Alignment explanation
Indices: 47647225--47647297 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
47647215 AGCTTTTGTG
47647225 AAATATTTT-TA-AGAAATC-TGTCAAACAACAAA
1 AAATATTTTATACAG-AATCAT-TCAAACAACAAA
*
47647257 CAAATATTTTATACAGAATCATTCAAACATCAAA
1 -AAATATTTTATACAGAATCATTCAAACAACAAA
47647291 AAATATT
1 AAATATT
47647298 AATTTTTGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 16 0.44
34 17 0.47
35 3 0.08
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (33 bp):
AAATATTTTATACAGAATCATTCAAACAACAAA
Found at i:47647431 original size:24 final size:24
Alignment explanation
Indices: 47647386--47647431 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
47647376 GTTTAGTGCG
* * *
47647386 TAAATAAAAGTGCCTTCAAATAAA
1 TAAATAAAAATACATTCAAATAAA
*
47647410 TAAATAAAAATACATTCTAATA
1 TAAATAAAAATACATTCAAATA
47647432 GTATAAGCTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (24 bp):
TAAATAAAAATACATTCAAATAAA
Found at i:47650133 original size:80 final size:80
Alignment explanation
Indices: 47650000--47650160 Score: 268
Period size: 80 Copynumber: 2.0 Consensus size: 80
47649990 GCTGCCCACT
* *
47650000 TGTTGGGGATCATGGAGTTTCAAGCCTGTTGTCATCAACATCTTCCGTCCTTTCAAAGGTTAGGC
1 TGTTGGGGATCATGGAGTTTCAAGCCTGTTGTCATCAACAACTTCCGTCCTTTCAAAGGTTAAGC
47650065 TTCAGGGTTTAAGCA
66 TTCAGGGTTTAAGCA
* *
47650080 TGTTGGGGATCATGGAGTTTCAAGCCTGTTGTCATCAGCAACTTTCGTCCTTTCAAAGGTTAAGC
1 TGTTGGGGATCATGGAGTTTCAAGCCTGTTGTCATCAACAACTTCCGTCCTTTCAAAGGTTAAGC
* *
47650145 TTCCGGGTTTGAGCA
66 TTCAGGGTTTAAGCA
47650160 T
1 T
47650161 AACGGATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (80 bp):
TGTTGGGGATCATGGAGTTTCAAGCCTGTTGTCATCAACAACTTCCGTCCTTTCAAAGGTTAAGC
TTCAGGGTTTAAGCA
Found at i:47654699 original size:21 final size:21
Alignment explanation
Indices: 47654675--47654714 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
47654665 TAACCGTTTA
*
47654675 ATAATTTTCATCAA-CCAATTC
1 ATAATCTT-ATCAATCCAATTC
47654696 ATAATCTTATCAATCCAAT
1 ATAATCTTATCAATCCAAT
47654715 CAATTGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATCTTATCAATCCAATTC
Found at i:47668420 original size:28 final size:28
Alignment explanation
Indices: 47668376--47668435 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
47668366 ATATTTATAT
*
47668376 TATATTATTTTAATATTTAATAA-TTTTA
1 TATATTATTTTAATATTGAA-AATTTTTA
*
47668404 TATATT-TTTTATTTATTGAAAATTTTTA
1 TATATTATTTTA-ATATTGAAAATTTTTA
47668432 TATA
1 TATA
47668436 ATCATCTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TATATTATTTTAATATTGAAAATTTTTA
Found at i:47668433 original size:26 final size:27
Alignment explanation
Indices: 47668375--47668434 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
47668365 AATATTTATA
*
47668375 TTATATTATTTTAATATTTAATAATTT
1 TTATATTATTTTAATATTGAATAATTT
*
47668402 TATATATT-TTTTATTTATTGAA-AATTT
1 T-TATATTATTTTA-ATATTGAATAATTT
47668429 TTATAT
1 TTATAT
47668435 AATCATCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 12 0.41
28 12 0.41
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTATATTATTTTAATATTGAATAATTT
Found at i:47670077 original size:2 final size:2
Alignment explanation
Indices: 47670070--47670100 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47670060 ATTTAATGAT
47670070 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47670101 TATTTGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47671136 original size:3 final size:3
Alignment explanation
Indices: 47671128--47671170 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
47671118 CTTTTTCTCA
47671128 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
47671171 CATTGAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:47671522 original size:17 final size:18
Alignment explanation
Indices: 47671481--47671525 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
47671471 ATTTATCATG
47671481 CATATTAAT-TTTTGAAT
1 CATATTAATATTTTGAAT
*
47671498 CGAT-TTAATATTTTTAA-
1 C-ATATTAATATTTTGAAT
47671515 CATATTAATAT
1 CATATTAATAT
47671526 AAAATATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 2 0.08
17 14 0.58
18 8 0.33
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (18 bp):
CATATTAATATTTTGAAT
Found at i:47671935 original size:15 final size:17
Alignment explanation
Indices: 47671915--47671948 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
47671905 TCATAAAAAA
47671915 ATAATT-GATTGA-ATT
1 ATAATTCGATTGATATT
47671930 ATAATTCGATTGATATT
1 ATAATTCGATTGATATT
47671947 AT
1 AT
47671949 TTTTAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
ATAATTCGATTGATATT
Found at i:47672155 original size:14 final size:15
Alignment explanation
Indices: 47672136--47672166 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
47672126 ATTTATTTTA
47672136 AAATTATTTA-AATT
1 AAATTATTTATAATT
47672150 AAATTATTTATAATT
1 AAATTATTTATAATT
47672165 AA
1 AA
47672167 GAGGGCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTATTTATAATT
Found at i:47679999 original size:3 final size:3
Alignment explanation
Indices: 47679985--47680016 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
47679975 GGGTTTTTCA
47679985 CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
47680017 TTTTCTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:47681529 original size:16 final size:17
Alignment explanation
Indices: 47681486--47681529 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
47681476 TTAAAAATAG
47681486 CCTAAAAT-AAACTGAA
1 CCTAAAATAAAACTGAA
*
47681502 CCTAAAGTAAAACT-AA
1 CCTAAAATAAAACTGAA
*
47681518 CGTAAAATAAAA
1 CCTAAAATAAAA
47681530 AGTAAATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.59, C:0.16, G:0.07, T:0.18
Consensus pattern (17 bp):
CCTAAAATAAAACTGAA
Found at i:47684759 original size:59 final size:58
Alignment explanation
Indices: 47684691--47685122 Score: 407
Period size: 59 Copynumber: 7.4 Consensus size: 58
47684681 TGACTTTTGG
* * *
47684691 GGGTAAAAT-GTAATTTTTAGTGAAATCGGGGTCAAGAAATGGAATTTTAGAAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAA-AAATGGAATTTTGGAAAGTT-GA
* *
47684750 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAATA-TTCGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAA-AGTT-GA
* * *
47684809 GGGGAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTGA
* * * * *
47684868 GGGTAAAATGGTAATTTTT-G-GAAGTTTTGGGGTTAAAAATAGG-ATTTTAG-AACTTTA
1 GGGTAAAATGGTAATTTTTGGTGAA--ATCGGGGTTAAAAAT-GGAATTTTGGAAAGTTGA
* *
47684925 GGGGT-AAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGG
1 -GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTGA
** * * * ** *
47684984 GGGTAAAATAATAATTTTT--AGAAGTTTCGGGGTCAAAAATTAAATTTTGGAAAGTTTA
1 GGGTAAAATGGTAATTTTTGGTGAA--ATCGGGGTTAAAAATGGAATTTTGGAAAGTTGA
** * * *
47685042 GGGGTAAAGCGGTAATTTTTGGTGAAA-CTAGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 -GGGTAAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTGGAAAGTTGA
47685101 GGGGTAAAATGGTAATTTTTGG
1 -GGGTAAAATGGTAATTTTTGG
47685123 AATTTTTGGG
Statistics
Matches: 310, Mismatches: 43, Indels: 40
0.79 0.11 0.10
Matches are distributed among these distances:
56 2 0.01
57 40 0.13
58 18 0.06
59 218 0.70
60 29 0.09
61 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTGA
Found at i:47684856 original size:30 final size:31
Alignment explanation
Indices: 47684695--47684850 Score: 120
Period size: 30 Copynumber: 5.2 Consensus size: 31
47684685 TTTTGGGGGT
* *
47684695 AAAAT-GTAATTTTTAGTGAAATCGGGGTCA
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
*
47684725 AGAAATGG-AA-TTTT--AGAAAGTTCGAGGG-T-
1 A-AAATGGTAATTTTTGGTGAAA--TCG-GGGTTA
47684754 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
* **
47684785 AAAATGG-GA-TTTT-G-GAATATTCGGGG-GG
1 AAAATGGTAATTTTTGGTGAA-A-TCGGGGTTA
47684813 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
47684844 AAAATGG
1 AAAATGG
47684851 GATTTTGGAA
Statistics
Matches: 99, Mismatches: 9, Indels: 35
0.69 0.06 0.24
Matches are distributed among these distances:
27 3 0.03
28 19 0.19
29 17 0.17
30 27 0.27
31 25 0.25
32 8 0.08
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTA
Found at i:47684871 original size:30 final size:30
Alignment explanation
Indices: 47684837--47685228 Score: 142
Period size: 30 Copynumber: 13.3 Consensus size: 30
47684827 TGGTGAAATC
*
47684837 GGGGTTAAAAATGGGATTTTGGAAAGTTT-
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
47684866 GGGGGT-AAAATGGTAATTTTTGG-AAGTTTT
1 GGGGTTAAAAATGG-AA-TTTTGGAAAGTTTA
* *
47684896 GGGGTTAAAAATAGG-ATTTTAG-AACTTTA
1 GGGGTTAAAAAT-GGAATTTTGGAAAGTTTA
*
47684925 GGGG-T--AAATGGTAATTTTGGGTGAAA---TC
1 GGGGTTAAAAATGG-AATTTT--G-GAAAGTTTA
*
47684953 GGGGTTAAAAATGGAATTTTGGAAAGTTTG
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * *
47684983 GGGGTAAAATAAT--AATTTT-TAGAAGTTTC
1 GGGGTTAAA-AATGGAATTTTGGA-AAGTTTA
* **
47685012 GGGGTCAAAAATTAAATTTTGGAAAGTTTA
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
** *
47685042 GGGG-T-AAAGCGGTAATTTTTGGTGAAA--CTA
1 GGGGTTAAAAATGG-AA-TTTT-G-GAAAGTTTA
*
47685072 -GGGTTAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
47685101 GGGG-T-AAAATGGTAATTTTTGG-AATTTTT
1 GGGGTTAAAAATGG-AA-TTTTGGAAAGTTTA
* *
47685130 GGGGTCAAAACGAT--AATTTTTTGTGAAA-CTT-
1 GGGGTTAAAA--ATGGAA--TTTTG-GAAAGTTTA
*
47685161 -GGGTTAAAAATGGGATTTTGGAAAGTTT-
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * *
47685189 GGGGGT-AAAATAGTAATTTTTGG-AAGTTTC
1 GGGGTTAAAAAT-GGAA-TTTTGGAAAGTTTA
*
47685219 GAGGTTAAAA
1 GGGGTTAAAA
47685229 TGATAAATTT
Statistics
Matches: 277, Mismatches: 38, Indels: 94
0.68 0.09 0.23
Matches are distributed among these distances:
25 2 0.01
26 4 0.01
27 17 0.06
28 43 0.16
29 81 0.29
30 82 0.30
31 35 0.13
32 9 0.03
33 4 0.01
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (30 bp):
GGGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:47685090 original size:89 final size:88
Alignment explanation
Indices: 47685005--47685241 Score: 280
Period size: 89 Copynumber: 2.7 Consensus size: 88
47684995 TAATTTTTAG
* * * *
47685005 AAGTTTCGGGGTCAAAAATTAAATTTTGGAAAGTTTAGGGGT-AAAGCGGTAATTTTTGGTGAAA
1 AAGTTTAGGGGT-AAAAATTAATTTTTGG-AAGTTTAGGGGTCAAAACGATAATTTTTGGTGAAA
47685069 CTAGGGTTAAAAATGGGATTTTGGA
64 CTAGGGTTAAAAATGGGATTTTGGA
* * *
47685094 AAGTTTAGGGGT-AAAATGGTAATTTTTGGAATTTTTGGGGTCAAAACGATAATTTTTTGTGAAA
1 AAGTTTAGGGGTAAAAAT--TAATTTTTGGAAGTTTAGGGGTCAAAACGATAATTTTTGGTGAAA
*
47685158 CTTGGGTTAAAAATGGGATTTTGGA
64 CTAGGGTTAAAAATGGGATTTTGGA
* * * * * * *
47685183 AAGTTTGGGGGTAAAATAGTAATTTTTGGAAGTTTCGAGGTTAAAATGATAAATTTTGG
1 AAGTTTAGGGGTAAAA-ATTAATTTTTGGAAGTTTAGGGGTCAAAACGATAATTTTTGG
47685242 GGTCAAAAAT
Statistics
Matches: 126, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
87 5 0.04
88 10 0.08
89 107 0.85
90 3 0.02
91 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (88 bp):
AAGTTTAGGGGTAAAAATTAATTTTTGGAAGTTTAGGGGTCAAAACGATAATTTTTGGTGAAACT
AGGGTTAAAAATGGGATTTTGGA
Found at i:47685107 original size:234 final size:234
Alignment explanation
Indices: 47684690--47685139 Score: 604
Period size: 234 Copynumber: 1.9 Consensus size: 234
47684680 TTGACTTTTG
*
47684690 GGGGTAAAATGTAATTTTTAGTGAAATCGGGGTCAAGAAATGGAATTTTAGAAAGTTCGAGGGTA
1 GGGGTAAAATGTAATTTTGAGTGAAATCGGGGTCAAGAAATGGAATTTTAGAAAGTTCGAGGGTA
** * * ** * *
47684755 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAATATTCGGGGGGAAAATGG
66 AAATAATAATTTTT-GAGAAATCGGGGTCAAAAATGAAATTTTGGAATATTCAGGGGGAAAACGG
* *
47684820 TAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTGGGGGTAAAATGGTAATTT
130 TAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
*
47684885 TTGGAAGTTTTGGGGTTAAAAATAGGATTTTAGAACTTTA
195 TTGGAAGTTTTGGGGTCAAAAATAGGATTTTAGAACTTTA
* * * * *
47684925 GGGGT-AAATGGTAATTTTGGGTGAAATCGGGGTTAA-AAATGGAATTTTGGAAAGTTTGGGGGT
1 GGGGTAAAAT-GTAATTTTGAGTGAAATCGGGGTCAAGAAATGGAATTTTAGAAAGTTCGAGGGT
* * * * *
47684988 AAAATAATAATTTTT-AGAAGTTTCGGGGTCAAAAATTAAATTTTGGAA-AGTTTAGGGGTAAAG
65 AAAATAATAATTTTTGAGAA--ATCGGGGTCAAAAATGAAATTTTGGAATA-TTCAGGGGGAAAA
47685051 CGGTAATTTTTGGTGAAA-CTAGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTA
127 CGGTAATTTTTGGTGAAATC-AGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTA
*
47685115 ATTTTTGGAATTTTTGGGGTCAAAA
191 ATTTTTGGAAGTTTTGGGGTCAAAA
47685140 CGATAATTTT
Statistics
Matches: 187, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
232 3 0.02
233 2 0.01
234 154 0.82
235 28 0.15
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (234 bp):
GGGGTAAAATGTAATTTTGAGTGAAATCGGGGTCAAGAAATGGAATTTTAGAAAGTTCGAGGGTA
AAATAATAATTTTTGAGAAATCGGGGTCAAAAATGAAATTTTGGAATATTCAGGGGGAAAACGGT
AATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTT
TGGAAGTTTTGGGGTCAAAAATAGGATTTTAGAACTTTA
Found at i:47685240 original size:30 final size:30
Alignment explanation
Indices: 47685175--47685241 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
47685165 TAAAAATGGG
*
47685175 ATTTTGGAAAGTTTGGGGGTAAAATAGTAA
1 ATTTTGGAAAGTTTGAGGGTAAAATAGTAA
* *
47685205 TTTTTGG-AAGTTTCGAGGTTAAAAT-GATAA
1 ATTTTGGAAAGTTT-GAGGGTAAAATAG-TAA
47685235 ATTTTGG
1 ATTTTGG
47685242 GGTCAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.33, C:0.01, G:0.27, T:0.39
Consensus pattern (30 bp):
ATTTTGGAAAGTTTGAGGGTAAAATAGTAA
Found at i:47687137 original size:13 final size:13
Alignment explanation
Indices: 47687128--47687152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47687118 AAATAAATTT
47687128 AATCTTTAAAATA
1 AATCTTTAAAATA
47687141 AATCTTTAAAAT
1 AATCTTTAAAAT
47687153 GGGTTTAATT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
AATCTTTAAAATA
Found at i:47687140 original size:18 final size:17
Alignment explanation
Indices: 47687096--47687143 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
47687086 TTTAAATATG
47687096 AATTC-AAATAAATTTA
1 AATTCAAAATAAATTTA
47687112 AATTCAAAATAAATTTA
1 AATTCAAAATAAATTTA
* *
47687129 ATCTTTAAAATAAAT
1 A-ATTCAAAATAAAT
47687144 CTTTAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.18
17 12 0.43
18 11 0.39
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTCAAAATAAATTTA
Found at i:47687768 original size:49 final size:49
Alignment explanation
Indices: 47687715--47687819 Score: 176
Period size: 49 Copynumber: 2.1 Consensus size: 49
47687705 GTATCTCATT
47687715 AGGAAGATGACCGCCTC-TGTTGTTTTAATTTGCTTCTCTGGATCTCCTC
1 AGGAAGATGACCGCCTCGT-TTGTTTTAATTTGCTTCTCTGGATCTCCTC
* *
47687764 AGGAAGATGATCGCCTCGTTTGTTTTAATTTGCTTCTTTGGATCTCCTC
1 AGGAAGATGACCGCCTCGTTTGTTTTAATTTGCTTCTCTGGATCTCCTC
47687813 AGGAAGA
1 AGGAAGA
47687820 CAAATTTGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 52 0.98
50 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (49 bp):
AGGAAGATGACCGCCTCGTTTGTTTTAATTTGCTTCTCTGGATCTCCTC
Found at i:47687940 original size:249 final size:248
Alignment explanation
Indices: 47687498--47688110 Score: 931
Period size: 249 Copynumber: 2.5 Consensus size: 248
47687488 ACCTGGTCTT
* * *
47687498 CTTCTCTGTG-TCTCATCAAGAAGATGACCGCCTCGTTTGTTTCAATTCGTTTCTCTGGATCTCC
1 CTTCTCTG-GATCTCCTCAAGAAGATGA-CGCCTCGTTTGTTTCAATTTGCTTCTCTGGATCTCC
* * * * * *
47687562 TCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAAGAAGCTAACCTTTTTATTGCTTCG
64 TCAGGAAGACAAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCTTTTTATTGCTTCG
* * * *
47687627 ACCCGCTTCTCCGTATCTCATCAGGGAGCTGGGTTCGAAGATTTGCTCGCGTGGAGCATTGAGTT
129 ACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTGGATCGCGTGGAGCATTGAGTT
* *
47687692 GGTATTCTTTTATGTATCTCATTAGGAAGATGACCGCCTCTGTTGTTTTAATTTG
194 GGTATTCTTCTATGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTTG
* * *
47687747 CTTCTCTGGATCTCCTCAGGAAGATGATCGCCTCGTTTGTTTTAATTTGCTTCTTTGGATCTCCT
1 CTTCTCTGGATCTCCTCAAGAAGATGA-CGCCTCGTTTGTTTCAATTTGCTTCTCTGGATCTCCT
47687812 CAGGAAGACAAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCTTTTTATTGCTTCGA
65 CAGGAAGACAAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCTTTTTATTGCTTCGA
** * * * **
47687877 CTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGATCGTGTTGAGTGTTGAGTTG
130 CCCGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTGGATCGCGTGGAGCATTGAGTTG
*
47687942 GTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTTG
195 GTATTCTTCTATGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTTG
*
47687996 CTTCTCTGGATCTCCTCAAGAAGATGACTGCCTCGTTTATTTCAATTTGCTTCTCTGGATCTCCT
1 CTTCTCTGGATCTCCTCAAGAAGATGAC-GCCTCGTTTGTTTCAATTTGCTTCTCTGGATCTCCT
*
47688061 CAGGAAGACAAATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACC
65 CAGGAAGACAAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACC
47688111 GCCTCGCTTG
Statistics
Matches: 330, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
248 2 0.01
249 328 0.99
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (248 bp):
CTTCTCTGGATCTCCTCAAGAAGATGACGCCTCGTTTGTTTCAATTTGCTTCTCTGGATCTCCTC
AGGAAGACAAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCTTTTTATTGCTTCGAC
CCGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTGGATCGCGTGGAGCATTGAGTTGG
TATTCTTCTATGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTTG
Found at i:47688000 original size:49 final size:49
Alignment explanation
Indices: 47687947--47688068 Score: 176
Period size: 49 Copynumber: 2.5 Consensus size: 49
47687937 AGTTGGTATT
* *
47687947 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTGTTGT-TTT-AATTTG
1 CTTCTCTGGATCTCCTCAGGAAGATGACCGCCTC-GTT-TATTTCAATTTG
* *
47687996 CTTCTCTGGATCTCCTCAAGAAGATGACTGCCTCGTTTATTTCAATTTG
1 CTTCTCTGGATCTCCTCAGGAAGATGACCGCCTCGTTTATTTCAATTTG
47688045 CTTCTCTGGATCTCCTCAGGAAGA
1 CTTCTCTGGATCTCCTCAGGAAGA
47688069 CAAATTTGGT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
47 1 0.02
48 6 0.09
49 59 0.89
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (49 bp):
CTTCTCTGGATCTCCTCAGGAAGATGACCGCCTCGTTTATTTCAATTTG
Found at i:47688141 original size:86 final size:86
Alignment explanation
Indices: 47687996--47688190 Score: 264
Period size: 86 Copynumber: 2.3 Consensus size: 86
47687986 TTTTAATTTG
* * * * * * *
47687996 CTTCTCTGGATCTCCTCAAGAAGATGACTGCCTCGTTTATTTCAATTTGCTTCTCTGGATCTCCT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTATTTCAATTCGCTTATCTGGATCTCCT
*
47688061 CAGGAAGACAAATTTGGTCTA
66 CAGGAAGACAAATTTGGTCCA
* * *
47688082 CTTCTCTGTATCTCATTAGGAAGATGACCGCCTCGCTTGTTTCAATTCGTTTATCTGGATCTCCT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTATTTCAATTCGCTTATCTGGATCTCCT
*
47688147 CAGGAAGACGAATTTGGTCCA
66 CAGGAAGACAAATTTGGTCCA
**
47688168 CTTCTCTGTGCCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
47688191 CTAACCTTTT
Statistics
Matches: 94, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 94 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (86 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTATTTCAATTCGCTTATCTGGATCTCCT
CAGGAAGACAAATTTGGTCCA
Found at i:47694594 original size:3 final size:3
Alignment explanation
Indices: 47694586--47694613 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47694576 ATATCATTGA
47694586 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
47694614 GAAGAATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:47700661 original size:29 final size:29
Alignment explanation
Indices: 47700584--47700795 Score: 129
Period size: 30 Copynumber: 7.3 Consensus size: 29
47700574 CAAGAAATTG
* *
47700584 AATTTTGGAA-AGTTTAGGGGTAAAATAGT
1 AATTTTGGAAGA-TTCAGGGGTAAAATGGT
47700613 AATTTTTGGTGAA-A-TC-GGGGTTAAAATGG-
1 AA-TTTT-G-GAAGATTCAGGGG-TAAAATGGT
*
47700642 GATTTTGGAAGATTCAGGGGTAAAATGGT
1 AATTTTGGAAGATTCAGGGGTAAAATGGT
* *
47700671 AATTTTTGGAAG-TT-TGGGGTCAAAAATAG-
1 AA-TTTTGGAAGATTCAGGGGT--AAAATGGT
* **
47700700 AATTTTGGACGGGTCAGGGGTAAAATGGT
1 AATTTTGGAAGATTCAGGGGTAAAATGGT
* * *
47700729 AATTTTTGGAAGTTTTAGGGTTAAAAATGG-
1 AA-TTTTGGAAGATTCAGGGGT-AAAATGGT
* * *
47700759 GATTTTAGAA-AGTTTAGGGGTAAAATGGT
1 AATTTTGGAAGA-TTCAGGGGTAAAATGGT
47700788 AATTTTGG
1 AATTTTGG
47700796 GTGAAATCGG
Statistics
Matches: 144, Mismatches: 21, Indels: 36
0.72 0.10 0.18
Matches are distributed among these distances:
26 3 0.02
27 2 0.01
28 40 0.28
29 40 0.28
30 47 0.33
31 8 0.06
32 4 0.03
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (29 bp):
AATTTTGGAAGATTCAGGGGTAAAATGGT
Found at i:47700673 original size:58 final size:58
Alignment explanation
Indices: 47700540--47700809 Score: 246
Period size: 58 Copynumber: 4.6 Consensus size: 58
47700530 TTGACTTTCG
* * *
47700540 GGGGTAAAAAT-GTAATTTTTGGTGAAATTGGGGTCAAGAAATTGAATTTTGGAAAGTTTA
1 GGGGT-AAAATGGTAATTTTTGGTGAAATTGGGGT-TA-AAATGGAATTTTGGAAAGTTCA
* * *
47700600 GGGGTAAAATAGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGG-AAGATTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAATGGAATTTTGGAAAG-TTCA
* * * ** *
47700658 GGGGTAAAATGGTAATTTTT-G-GAAGTTTGGGGTCAAAAATAGAATTTTGGACGGGTCA
1 GGGGTAAAATGGTAATTTTTGGTGAA-ATTGGGGT-TAAAATGGAATTTTGGAAAGTTCA
* * * * *
47700716 GGGGTAAAATGGTAATTTTT-G-GAAGTTTTAGGGTTAAAAATGGGATTTTAGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAA--ATTGGGGTT-AAAATGGAATTTTGGAAAGTTCA
* *
47700775 GGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT
47700810 CGTACTGTGT
Statistics
Matches: 173, Mismatches: 28, Indels: 19
0.79 0.13 0.09
Matches are distributed among these distances:
56 3 0.02
57 10 0.06
58 74 0.43
59 55 0.32
60 28 0.16
61 3 0.02
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAATGGAATTTTGGAAAGTTCA
Found at i:47701285 original size:13 final size:13
Alignment explanation
Indices: 47701276--47701300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47701266 AAATAAATTT
47701276 AATCTTTAAAATA
1 AATCTTTAAAATA
47701289 AATCTTTAAAAT
1 AATCTTTAAAAT
47701301 GGATTTAATT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
AATCTTTAAAATA
Found at i:47701288 original size:18 final size:17
Alignment explanation
Indices: 47701244--47701291 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
47701234 TTTAAATATG
47701244 AATTC-AAATAAATTTA
1 AATTCAAAATAAATTTA
47701260 AATTCAAAATAAATTTA
1 AATTCAAAATAAATTTA
* *
47701277 ATCTTTAAAATAAAT
1 A-ATTCAAAATAAAT
47701292 CTTTAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.18
17 12 0.43
18 11 0.39
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTCAAAATAAATTTA
Found at i:47702174 original size:30 final size:30
Alignment explanation
Indices: 47702133--47702189 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
47702123 ACTCATACAT
*
47702133 AAAATAATAATATA-ATATAAACTATTACTA
1 AAAATAATAATACACATAT-AACTATTACTA
*
47702163 AAAATATTAATACACATATAACTATTA
1 AAAATAATAATACACATATAACTATTA
47702190 TTATAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAATAATAATACACATATAACTATTACTA
Found at i:47702435 original size:12 final size:12
Alignment explanation
Indices: 47702420--47702453 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
47702410 TATAACTATT
47702420 ATTATAGTATAG
1 ATTATAGTATAG
47702432 ATTATAGTAATAG
1 ATTATAGT-ATAG
47702445 A-TATAGTAT
1 ATTATAGTAT
47702454 TACATGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 14 0.67
13 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (12 bp):
ATTATAGTATAG
Found at i:47705792 original size:23 final size:22
Alignment explanation
Indices: 47705762--47705886 Score: 135
Period size: 23 Copynumber: 5.5 Consensus size: 22
47705752 ACGCTAGCGC
47705762 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
47705785 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
*
47705808 GCTTACTGATTTGCA-TTATGTGC
1 GCTTACTG-TTTGCACTT-TGTGT
* * *
47705831 GCCTACTGATTGCACTGTGTGT
1 GCTTACTGTTTGCACTTTGTGT
* * *
47705853 GCCTACTGGATTGCACTGTGTGT
1 GCTTACT-GTTTGCACTTTGTGT
47705876 GCTTACTGTTT
1 GCTTACTGTTT
47705887 TCCCAGCACT
Statistics
Matches: 91, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
22 21 0.23
23 67 0.74
24 3 0.03
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (22 bp):
GCTTACTGTTTGCACTTTGTGT
Found at i:47705883 original size:45 final size:46
Alignment explanation
Indices: 47705765--47705883 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 46
47705755 CTAGCGCGCT
* * * *
47705765 TACTG-TTTCGCACTTTGTGTGCTTACTGTTTCGCACTTTGTGTGCT
1 TACTGATTT-GCACTATGTGTGCTTACTGATTCGCACTGTGTGTGCC
* * *
47705811 TACTGATTTGCATTATGTGCGCCTACTGATT-GCACTGTGTGTGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTCGCACTGTGTGTGCC
*
47705856 TACTGGA-TTGCACTGTGTGTGCTTACTG
1 TACT-GATTTGCACTATGTGTGCTTACTG
47705884 TTTTCCCAGC
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
45 33 0.55
46 24 0.40
47 3 0.05
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.42
Consensus pattern (46 bp):
TACTGATTTGCACTATGTGTGCTTACTGATTCGCACTGTGTGTGCC
Found at i:47708142 original size:388 final size:389
Alignment explanation
Indices: 47707420--47708201 Score: 1332
Period size: 388 Copynumber: 2.0 Consensus size: 389
47707410 TTCCCCGCGA
* * *
47707420 ACTTTTCCACGCTAATAGGTCTTAGCCTGACATCCCCTTTCTCTAAAGATCTTTGGCGAACTTGC
1 ACTTTTCCACGCTAATAGGTCTTAGCCTGACATCCCCTTTCTCTAAAGATCTCTAGCGAACTTAC
*
47707485 CAATTAGACCGTTTAGCTTAGAATTTGCTTAATTGACTCACTCATTGTACCCATTGTTATTTTAT
66 CAATTAGACCGTTTAGCTTAGAATTTGCTTAATTGACTCACTCATTGTACCCATTGTTAGTTTAT
*
47707550 TTGTCAATCGTTAGGTGAACTAAGAATGACAGAACCCATTTCTTGAATAGAGTACCTCTTCTATT
131 TTGTCAATCGTTAGGTGAACTAAGAATGACAGAACCCATTTCTTGAATAGAGTACCTCTTCTATC
*
47707615 TCCTCTACCTTGATAAGACCACACACAAATACTAAATTCCTCTTTCAATCATAAATTGGCAAATT
196 TCCTCTACCTTGATAAGACCACACACAAATACCAAATTCCTCTTTCAATCATAAATTGGCAAATT
** *
47707680 CCCTTATTAACAGGCTTACTCGTATTCTCAGGCGCATCGAATTCATCCAACTATACTACTCTTCG
261 CCCTTATTAACAGGCTTACTCGTATTCTCAAACGCATCGAATTCATCCAACTATACTACTCTTCA
* * * * *
47707745 TGCGGGTCATACACTGATCTTCCTTTTCTTGCCCTATCAACGTCCTAGTTCATCTTCTTGGCGG
326 CGCGGGTCATACAATGATCTCCCTTTTCTTGCCCTATCAACATCCTAGTTCATCATCTTGGCGG
* *
47707809 ACTTTTCCACGCTAATAGGTCTTAGCCTGACTTCCCCTTTCTCTGAAGATCTCTAGCGAACTTAC
1 ACTTTTCCACGCTAATAGGTCTTAGCCTGACATCCCCTTTCTCTAAAGATCTCTAGCGAACTTAC
* *
47707874 CAATTAGACTGTTTAGCTTAGAATTTGCTTAATTGACTCACTCATTGTACCTATTGTTAGTTTAT
66 CAATTAGACCGTTTAGCTTAGAATTTGCTTAATTGACTCACTCATTGTACCCATTGTTAGTTTAT
*
47707939 TTGTCAATTGTTA-GTGAACTAAGAATGACAGAACCCATTTCTTGAATAGAGTACCTCTTCTATC
131 TTGTCAATCGTTAGGTGAACTAAGAATGACAGAACCCATTTCTTGAATAGAGTACCTCTTCTATC
*
47708003 TCCTCTACCTTGATAAGACCACACACAAATACCAAATTCCTCTTTCAATCATAAATTGGCAGATT
196 TCCTCTACCTTGATAAGACCACACACAAATACCAAATTCCTCTTTCAATCATAAATTGGCAAATT
* *
47708068 CCCTTATTAACAGGCTTACTCGTATTCTCAAATGCGTCGAATTCATCCAACTATACTACTCTTCA
261 CCCTTATTAACAGGCTTACTCGTATTCTCAAACGCATCGAATTCATCCAACTATACTACTCTTCA
* * *
47708133 CGTGGGTCATACAATGATCTCCCTTTTCTTGCCCTGTCAACATCTTAGTTCATCATCTTGGCGG
326 CGCGGGTCATACAATGATCTCCCTTTTCTTGCCCTATCAACATCCTAGTTCATCATCTTGGCGG
47708197 ACTTT
1 ACTTT
47708202 ATCTAACGCC
Statistics
Matches: 368, Mismatches: 25, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
388 234 0.64
389 134 0.36
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.35
Consensus pattern (389 bp):
ACTTTTCCACGCTAATAGGTCTTAGCCTGACATCCCCTTTCTCTAAAGATCTCTAGCGAACTTAC
CAATTAGACCGTTTAGCTTAGAATTTGCTTAATTGACTCACTCATTGTACCCATTGTTAGTTTAT
TTGTCAATCGTTAGGTGAACTAAGAATGACAGAACCCATTTCTTGAATAGAGTACCTCTTCTATC
TCCTCTACCTTGATAAGACCACACACAAATACCAAATTCCTCTTTCAATCATAAATTGGCAAATT
CCCTTATTAACAGGCTTACTCGTATTCTCAAACGCATCGAATTCATCCAACTATACTACTCTTCA
CGCGGGTCATACAATGATCTCCCTTTTCTTGCCCTATCAACATCCTAGTTCATCATCTTGGCGG
Found at i:47713580 original size:36 final size:36
Alignment explanation
Indices: 47713540--47713615 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
47713530 GAGATAATTG
* * **
47713540 TTCTGCATGGAATTATGTGTTTCCTTCCTGATAAAA
1 TTCTGAATCGAATTATGTGTTTCCTTCCCAATAAAA
*
47713576 TTCTGAATCGAATTATGTGTTTCTTTCCCAATAAAA
1 TTCTGAATCGAATTATGTGTTTCCTTCCCAATAAAA
47713612 TTCT
1 TTCT
47713616 AAGGTTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (36 bp):
TTCTGAATCGAATTATGTGTTTCCTTCCCAATAAAA
Found at i:47722715 original size:27 final size:27
Alignment explanation
Indices: 47722677--47722728 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
47722667 GGTACAAGGG
47722677 GTGGTGCCTACCTGACAGGCGGCACTA
1 GTGGTGCCTACCTGACAGGCGGCACTA
* *
47722704 GTGGTGTCTACCTGTCAGGCGGCAC
1 GTGGTGCCTACCTGACAGGCGGCAC
47722729 CAACCCGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.29, G:0.35, T:0.21
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACTA
Found at i:47724128 original size:27 final size:27
Alignment explanation
Indices: 47724096--47724162 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
47724086 AAATTTGACA
47724096 AGTGGTGCTTTTAGGGTAGGC-GACACT
1 AGTGGTGCTTTTAGGGTAGGCAG-CACT
**
47724123 AGTGGTGCCTACT-GGGTAGGCAGCACT
1 AGTGGTG-CTTTTAGGGTAGGCAGCACT
*
47724150 AGTGGTGCATTTA
1 AGTGGTGCTTTTA
47724163 TCAAAACTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
26 2 0.06
27 26 0.81
28 4 0.12
ACGTcount: A:0.19, C:0.16, G:0.36, T:0.28
Consensus pattern (27 bp):
AGTGGTGCTTTTAGGGTAGGCAGCACT
Found at i:47727157 original size:26 final size:26
Alignment explanation
Indices: 47727108--47727157 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
47727098 TCTGTTTAAA
**
47727108 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
47727134 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
47727158 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:47730485 original size:17 final size:17
Alignment explanation
Indices: 47730455--47730488 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47730445 CTTACAATAA
*
47730455 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
*
47730472 TTAAATAACGTTTAAAT
1 TTAAATAACATTTAAAT
47730489 GAATTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:47730947 original size:20 final size:20
Alignment explanation
Indices: 47730910--47730947 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
47730900 AAAAAAATTA
*
47730910 TTATTTAAATATTTTTTTAT
1 TTATTTAAATATTATTTTAT
47730930 TTATTT-AATATTAATTTT
1 TTATTTAAATATT-ATTTT
47730948 TTTTTGTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTAAATATTATTTTAT
Found at i:47743136 original size:30 final size:28
Alignment explanation
Indices: 47743069--47743138 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
47743059 TTTTAATAGT
*
47743069 ATATATTTTTATAATTTTAAAGAATTAA
1 ATATAATTTTATAATTTTAAAGAATTAA
* *
47743097 ATCAAAATTTTATAATTTTAGAGAAATTAA
1 AT-ATAATTTTATAATTTTAAAG-AATTAA
47743127 AGTATAATTTTA
1 A-TATAATTTTA
47743139 GCTGGGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.06
29 17 0.49
30 15 0.43
31 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (28 bp):
ATATAATTTTATAATTTTAAAGAATTAA
Found at i:47745038 original size:29 final size:30
Alignment explanation
Indices: 47744988--47745045 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
47744978 AAATGGTCAT
* *
47744988 TAAATTATTCGATAATTTTTATTTAAGTCC
1 TAAACTATTCGATAAGTTTTATTTAAGTCC
47745018 TAAACTATTCG-TAAGTTTTATTTAAGTC
1 TAAACTATTCGATAAGTTTTATTTAAGTC
47745046 ATTAGACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (30 bp):
TAAACTATTCGATAAGTTTTATTTAAGTCC
Found at i:47745055 original size:30 final size:31
Alignment explanation
Indices: 47744983--47745056 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 31
47744973 ATACAAAATG
* *
47744983 GTCATTAAATTATTCGATAATTTTTATTTAA
1 GTCATTAAACTATTCGATAAGTTTTATTTAA
*
47745014 GTC-CTAAACTATTCG-TAAGTTTTATTTAA
1 GTCATTAAACTATTCGATAAGTTTTATTTAA
*
47745043 GTCATTAGACTATT
1 GTCATTAAACTATT
47745057 ATTTTTTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 16 0.43
30 18 0.49
31 3 0.08
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.47
Consensus pattern (31 bp):
GTCATTAAACTATTCGATAAGTTTTATTTAA
Found at i:47750345 original size:65 final size:65
Alignment explanation
Indices: 47750241--47750373 Score: 239
Period size: 65 Copynumber: 2.0 Consensus size: 65
47750231 AGTTTTTAAG
* *
47750241 CCTGGCTCAATTGATTTGTACCGGTTCACAAATCAACCAATTTAATACCTATATTTGGATCGATA
1 CCTGGCTCAATTGATTCGTACCGGTTCACAAATCAACCAATTTAACACCTATATTTGGATCGATA
*
47750306 CCTGGCTCAATTGATTCGTACTGGTTCACAAATCAACCAATTTAACACCTATATTTGGATCGATA
1 CCTGGCTCAATTGATTCGTACCGGTTCACAAATCAACCAATTTAACACCTATATTTGGATCGATA
47750371 CCT
1 CCT
47750374 AGATCGGTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (65 bp):
CCTGGCTCAATTGATTCGTACCGGTTCACAAATCAACCAATTTAACACCTATATTTGGATCGATA
Found at i:47750806 original size:7 final size:7
Alignment explanation
Indices: 47750794--47750831 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
47750784 TAAATGTCAT
47750794 TTTCCTA
1 TTTCCTA
47750801 TTTCCTA
1 TTTCCTA
47750808 TTTCCTA
1 TTTCCTA
47750815 TTTCCTA
1 TTTCCTA
47750822 TTTCCTA
1 TTTCCTA
47750829 TTT
1 TTT
47750832 TTAACTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTCCTA
Found at i:47752172 original size:3 final size:3
Alignment explanation
Indices: 47752164--47752196 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
47752154 CAAATTCAAC
47752164 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
47752197 CAAATTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:47754667 original size:42 final size:42
Alignment explanation
Indices: 47754608--47754702 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
47754598 TGATGTATAA
* *
47754608 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
1 AAAGGAAGACTCATGTCTCGAGATCAGAATGAGAATATGATT
*
47754650 AAAGGAAGACTCATGTCTCGGGATCAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATCAGAATGAGAATATGATT
47754692 AAAGGAAGACT
1 AAAGGAAGACT
47754703 TATGACTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATCAGAATGAGAATATGATT
Found at i:47762125 original size:13 final size:14
Alignment explanation
Indices: 47762104--47762132 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
47762094 CTCAAAGTAG
47762104 AAATCAAGGTATGA
1 AAATCAAGGTATGA
47762118 AAAT-AAGGTATGA
1 AAATCAAGGTATGA
47762131 AA
1 AA
47762133 TTCTCTACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (14 bp):
AAATCAAGGTATGA
Found at i:47766730 original size:35 final size:35
Alignment explanation
Indices: 47766684--47766753 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
47766674 AAAATCATTT
47766684 AATTTAGACAAACAAACTTATTACACACTCAAATG
1 AATTTAGACAAACAAACTTATTACACACTCAAATG
47766719 AATTTAGACAAACAAACTTATTACACACTCAAATG
1 AATTTAGACAAACAAACTTATTACACACTCAAATG
47766754 TAAACAGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.26
Consensus pattern (35 bp):
AATTTAGACAAACAAACTTATTACACACTCAAATG
Found at i:47769299 original size:6 final size:6
Alignment explanation
Indices: 47769288--47769313 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
47769278 AAGTTATAAA
47769288 AAATAT AAATAT AAATAT AAATAT AA
1 AAATAT AAATAT AAATAT AAATAT AA
47769314 TTTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:47772357 original size:21 final size:21
Alignment explanation
Indices: 47772331--47772374 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
47772321 TCAAAACCAA
47772331 GGGTTGGTGGAGGTGAAAGAT
1 GGGTTGGTGGAGGTGAAAGAT
47772352 GGGTTGGTGGAGGTGAAAGAT
1 GGGTTGGTGGAGGTGAAAGAT
47772373 GG
1 GG
47772375 TTCACCCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.55, T:0.23
Consensus pattern (21 bp):
GGGTTGGTGGAGGTGAAAGAT
Found at i:47779241 original size:29 final size:29
Alignment explanation
Indices: 47779209--47779466 Score: 137
Period size: 29 Copynumber: 8.8 Consensus size: 29
47779199 TGGATACCCG
*
47779209 GGGGTAAAATGGTGATTTTTGGTGAAATC
1 GGGGTAAAATGGTAATTTTTGGTGAAATC
*
47779238 GGGGTTAAAAATGG-AA-TTTT-G-AAAAGTTC
1 GGGG-T-AAAATGGTAATTTTTGGTGAAA--TC
*
47779267 GGGGGTAAAATGGTAATTTTTGGTGAAATTA
1 -GGGGTAAAATGGTAATTTTTGGTGAAA-TC
* ***
47779298 GGGTTAAAAATGG-AA-TTTT-AAAAAATTC
1 GGGGT-AAAATGGTAATTTTTGGTGAAA-TC
*
47779326 AAGGGTAAAATGGTAATTTTTGGTGAAATC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATC
* ** *
47779356 GGGGTTAAAAGTGG-AATTTTAGAAG-ATTC
1 GGGG-TAAAA-TGGTAATTTTTGGTGAAATC
*
47779385 GGGGGTAAAATGGTAATTTTCGGTGAAATC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATC
**
47779415 GGGGTTAAAAATGG--ATTTTT--AAAAGATTC
1 GGGG-T-AAAATGGTAATTTTTGGTGAA-A-TC
47779444 GGGGGTAAAATGGTAATTTTTGG
1 -GGGGTAAAATGGTAATTTTTGG
47779467 AAGTTTCGGG
Statistics
Matches: 175, Mismatches: 26, Indels: 53
0.69 0.10 0.21
Matches are distributed among these distances:
27 5 0.03
28 31 0.18
29 53 0.30
30 53 0.30
31 30 0.17
32 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATC
Found at i:47779475 original size:30 final size:29
Alignment explanation
Indices: 47779207--47779477 Score: 132
Period size: 30 Copynumber: 9.2 Consensus size: 29
47779197 TTTGGATACC
* *
47779207 CGGGGGTAAAATGGTGATTTTTGGTGAA-AT
1 CGGGGGTAAAATGGTAATTTTT-G-GAAGTT
* *
47779237 CGGGGTTAAAAATGG-AA-TTTTGAAAAGTT
1 CGGGGGT-AAAATGGTAATTTTTG-GAAGTT
*
47779266 CGGGGGTAAAATGGTAATTTTTGGTGAAATT
1 CGGGGGTAAAATGGTAATTTTT-G-GAAGTT
* * *** *
47779297 -AGGGTTAAAAATGG-AATTTTAAAAAATT
1 CGGGGGT-AAAATGGTAATTTTTGGAAGTT
** *
47779325 CAAGGGTAAAATGGTAATTTTTGGTGAA-AT
1 CGGGGGTAAAATGGTAATTTTT-G-GAAGTT
* *
47779355 CGGGGTTAAAAGTGG-AA-TTTTAGAAGATT
1 CGGGGGTAAAA-TGGTAATTTTTGGAAG-TT
* *
47779384 CGGGGGTAAAATGGTAATTTTCGGTGAA-AT
1 CGGGGGTAAAATGGTAATTTT-TG-GAAGTT
* **
47779414 CGGGGTTAAAAATGG--ATTTTTAAAAGATT
1 CGGGGGT-AAAATGGTAATTTTTGGAAG-TT
47779443 CGGGGGTAAAATGGTAATTTTTGGAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGAAG-TT
47779473 CGGGG
1 CGGGG
47779478 TCGAAATGCA
Statistics
Matches: 181, Mismatches: 38, Indels: 44
0.69 0.14 0.17
Matches are distributed among these distances:
27 5 0.03
28 32 0.18
29 52 0.29
30 58 0.32
31 31 0.17
32 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (29 bp):
CGGGGGTAAAATGGTAATTTTTGGAAGTT
Found at i:47779478 original size:59 final size:59
Alignment explanation
Indices: 47779207--47779466 Score: 414
Period size: 59 Copynumber: 4.4 Consensus size: 59
47779197 TTTGGATACC
*
47779207 CGGGGGTAAAATGGTGATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAG-TT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-AAAAGATT
** *
47779266 CGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTAAAAAATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
** * *
47779325 CAAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAGTGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
47779384 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGATTTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
47779443 CGGGGGTAAAATGGTAATTTTTGG
1 CGGGGGTAAAATGGTAATTTTTGG
47779467 AAGTTTCGGG
Statistics
Matches: 182, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
58 4 0.02
59 178 0.98
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:47781143 original size:16 final size:16
Alignment explanation
Indices: 47781124--47781154 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47781114 CAGGGCATGG
47781124 TGGAGCAGGTGGTGGA
1 TGGAGCAGGTGGTGGA
*
47781140 TGGAGCTGGTGGTGG
1 TGGAGCAGGTGGTGG
47781155 CAGCAGCACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.06, G:0.58, T:0.23
Consensus pattern (16 bp):
TGGAGCAGGTGGTGGA
Found at i:47781438 original size:6 final size:6
Alignment explanation
Indices: 47781411--47781489 Score: 83
Period size: 6 Copynumber: 13.2 Consensus size: 6
47781401 ATGTTTAGTG
* * *
47781411 TTTAAA TTTTAA TTTTAA TTTAAA TTTAAA -GTAAA TTTAAA TAATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
47781460 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA T
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA T
47781490 CAATTTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 48 0.76
7 1 0.02
8 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:47781438 original size:11 final size:11
Alignment explanation
Indices: 47781411--47781499 Score: 63
Period size: 11 Copynumber: 7.6 Consensus size: 11
47781401 ATGTTTAGTG
47781411 TTTAAATTTTAA
1 TTTAAA-TTTAA
*
47781423 TTTTAATTTAAA
1 TTTAAATTT-AA
* *
47781435 TTTAAAGTAAA
1 TTTAAATTTAA
47781446 TTTAAATAATTAAA
1 TTTAAAT--TT-AA
47781460 TTTAAATTTAA
1 TTTAAATTTAA
**
47781471 GATAAATTTAAA
1 TTTAAATTT-AA
*
47781483 TTTAAA-TCAA
1 TTTAAATTTAA
47781493 TTTAAAT
1 TTTAAAT
47781500 CCAAATTGAA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
10 8 0.13
11 21 0.35
12 21 0.35
13 1 0.02
14 9 0.15
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:47781447 original size:17 final size:16
Alignment explanation
Indices: 47781427--47781499 Score: 87
Period size: 17 Copynumber: 4.6 Consensus size: 16
47781417 TTTTAATTTT
47781427 AATTTAAATTTAAAGTA
1 AATTTAAATTT-AAGTA
*
47781444 AATTTAAA--TAATTA
1 AATTTAAATTTAAGTA
47781458 AATTTAAATTTAAGATA
1 AATTTAAATTTAAG-TA
* *
47781475 AATTTAAATTTAAATC
1 AATTTAAATTTAAGTA
47781491 AATTTAAAT
1 AATTTAAAT
47781500 CCAAATTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
14 12 0.24
15 1 0.02
16 13 0.27
17 23 0.47
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.42
Consensus pattern (16 bp):
AATTTAAATTTAAGTA
Found at i:47787172 original size:24 final size:25
Alignment explanation
Indices: 47787144--47787193 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
47787134 CTTAAATTCA
* *
47787144 TTTAAATTTATCAAT-TTTTTTATT
1 TTTAAAATTATAAATATTTTTTATT
47787168 TTTAAAATTATAAATATTTTTTATT
1 TTTAAAATTATAAATATTTTTTATT
47787193 T
1 T
47787194 AATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTAAAATTATAAATATTTTTTATT
Found at i:47789783 original size:32 final size:32
Alignment explanation
Indices: 47789747--47789810 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
47789737 CAGAAAAGTG
47789747 AAAAG-AGAGAGAAAAAGAAATAACTGAAAAAA
1 AAAAGAAGA-AGAAAAAGAAATAACTGAAAAAA
* * *
47789779 AAAAGAAGAAGCAGAAGAAGTAACTGAAAAAA
1 AAAAGAAGAAGAAAAAGAAATAACTGAAAAAA
47789811 TAACCCAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.69, C:0.05, G:0.20, T:0.06
Consensus pattern (32 bp):
AAAAGAAGAAGAAAAAGAAATAACTGAAAAAA
Found at i:47790931 original size:29 final size:26
Alignment explanation
Indices: 47790894--47790947 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
47790884 ATTCTTTTAA
47790894 AAAGATTTACAAAACTAAAACTAAAAATC
1 AAAGATTTA-AAAA-TAAAA-TAAAAATC
* *
47790923 AAAGTTTTAGAAATAAAATAAAAAT
1 AAAGATTTAAAAATAAAATAAAAAT
47790948 AAAAAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 5 0.22
28 3 0.13
29 8 0.35
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (26 bp):
AAAGATTTAAAAATAAAATAAAAATC
Found at i:47796124 original size:20 final size:20
Alignment explanation
Indices: 47796099--47796147 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
47796089 ATTGCCAACG
47796099 AAAATATCGATTTATT-AATA
1 AAAATATCGATTT-TTAAATA
* *
47796119 AAAATAT-TATTTTTAAATG
1 AAAATATCGATTTTTAAATA
47796138 AAAATATCGA
1 AAAATATCGA
47796148 ACTCAATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.08
19 14 0.58
20 8 0.33
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (20 bp):
AAAATATCGATTTTTAAATA
Found at i:47797929 original size:23 final size:24
Alignment explanation
Indices: 47797903--47797953 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
47797893 TAATTCCATT
* *
47797903 AAATAAATTA-TTAAAAATATAAA
1 AAATAAAATATTTAAAAATAAAAA
*
47797926 AAATAAAATATTTTAAAATAAAAA
1 AAATAAAATATTTAAAAATAAAAA
47797950 AAAT
1 AAAT
47797954 TCAGTTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAAATATTTAAAAATAAAAA
Found at i:47798994 original size:13 final size:13
Alignment explanation
Indices: 47798963--47798997 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
47798953 TATTTCATTG
47798963 TAAAAAATACAAA
1 TAAAAAATACAAA
*
47798976 TGAAAAAATTCAAA
1 T-AAAAAATACAAA
47798990 TAAAAAAT
1 TAAAAAAT
47798998 GGGATTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (13 bp):
TAAAAAATACAAA
Found at i:47805301 original size:195 final size:194
Alignment explanation
Indices: 47804908--47805355 Score: 510
Period size: 195 Copynumber: 2.3 Consensus size: 194
47804898 TACCAGTACT
* * * **
47804908 CGATGCTGCTCACACGAGCTATCGAGGACTCGCAACGTATGCGGTACCCCAGCCATCGATATGGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACAGT
* * * * *
47804973 GCCTGTCTGTATTGTAAATTGTTCCTTAACGATGCTGCTCACACGAGCTATCGAGAATATGCGTA
66 ACCTG-CTGCATTATAAACTGTTCCTTAACGATGCTGCTCACACGAGCTATCGAGAATATGCCTA
***
47805038 AAGCATAGTCCCAAACATCGCAAGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGGGTCA
130 AAGCATAGTCCCAAACATCGCAAGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCAACTCA
*
47805103 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACAGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACAGT
* * *
47805168 ATCTG-TGCA-TAT-AACTGTT-CTCTACCGATGCTGCTCACACGAGCTGTCGAGAATATGCACT
66 ACCTGCTGCATTATAAACTGTTCCT-TAACGATGCTGCTCACACGAGCTATCGAGAATATGC-CT
* * * ** * * * * * * * *
47805229 TATGCATAGATCTCAGCCATCGTAGGGCCTGTAATCCGTTCTTGGATTCTTTTCTCATTTC-CAA
129 AAAGCATAG-TCCCAAACATCGCAAGGCCTATAATCCATT-TAGGATCCATATCTC-TTTCTC-A
47805293 ACTCA
190 ACTCA
* *
47805298 CGATGCTGGTCATACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
47805356 CGTCGGTTTC
Statistics
Matches: 214, Mismatches: 33, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
190 2 0.01
191 40 0.19
192 10 0.05
193 26 0.12
194 12 0.06
195 124 0.58
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (194 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACAGT
ACCTGCTGCATTATAAACTGTTCCTTAACGATGCTGCTCACACGAGCTATCGAGAATATGCCTAA
AGCATAGTCCCAAACATCGCAAGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCAACTCA
Found at i:47807952 original size:20 final size:19
Alignment explanation
Indices: 47807927--47807964 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
47807917 TGCCATCGCA
*
47807927 CTGTACATTTATGATCATTT
1 CTGTACATTGATGA-CATTT
47807947 CTGTACATTGATGACATT
1 CTGTACATTGATGACATT
47807965 GTTTCCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (19 bp):
CTGTACATTGATGACATTT
Found at i:47813050 original size:20 final size:22
Alignment explanation
Indices: 47813020--47813061 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
47813010 AGATTATAAA
47813020 TATACTCT-AAAATTATATTTG
1 TATACTCTAAAAATTATATTTG
47813041 TATA-TCTAAAAAATTATATTT
1 TATACTCT-AAAAATTATATTT
47813062 TCAAACAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 4 0.21
22 12 0.63
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
TATACTCTAAAAATTATATTTG
Found at i:47815458 original size:56 final size:56
Alignment explanation
Indices: 47815372--47815496 Score: 250
Period size: 56 Copynumber: 2.2 Consensus size: 56
47815362 TAATATAATT
47815372 TTTTTCATACCTTTGTTGCAGTCAACAAAATTCTCATTTGTACACTCATCCCTTTG
1 TTTTTCATACCTTTGTTGCAGTCAACAAAATTCTCATTTGTACACTCATCCCTTTG
47815428 TTTTTCATACCTTTGTTGCAGTCAACAAAATTCTCATTTGTACACTCATCCCTTTG
1 TTTTTCATACCTTTGTTGCAGTCAACAAAATTCTCATTTGTACACTCATCCCTTTG
47815484 TTTTTCATACCTT
1 TTTTTCATACCTT
47815497 GGAATGGTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 69 1.00
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.45
Consensus pattern (56 bp):
TTTTTCATACCTTTGTTGCAGTCAACAAAATTCTCATTTGTACACTCATCCCTTTG
Found at i:47827072 original size:7 final size:7
Alignment explanation
Indices: 47827028--47827098 Score: 67
Period size: 7 Copynumber: 10.4 Consensus size: 7
47827018 ATTTAAAATA
47827028 AAATATT
1 AAATATT
47827035 AAAT-TT
1 AAATATT
47827041 -AA-ATT
1 AAATATT
* *
47827046 AAAAAAT
1 AAATATT
* *
47827053 AAAAAAT
1 AAATATT
47827060 ATAATATT
1 A-AATATT
47827068 AAATATT
1 AAATATT
*
47827075 AAATATC
1 AAATATT
47827082 AAATATT
1 AAATATT
47827089 AAATATT
1 AAATATT
47827096 AAA
1 AAA
47827099 AAATATTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
5 4 0.07
6 4 0.07
7 42 0.76
8 5 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (7 bp):
AAATATT
Found at i:47827287 original size:25 final size:24
Alignment explanation
Indices: 47827259--47827306 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
47827249 ATTTAAATAC
*
47827259 TTAATATTATAAT-TTTTTGTTTTAT
1 TTAA-ATT-TAATGTTTTTATTTTAT
47827284 TTAAATTTAATGTTTTTATTTTA
1 TTAAATTTAATGTTTTTATTTTA
47827307 AATATGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (24 bp):
TTAAATTTAATGTTTTTATTTTAT
Found at i:47827319 original size:20 final size:19
Alignment explanation
Indices: 47827278--47827320 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
47827268 TAATTTTTTG
* *
47827278 TTTTATTTAAATTTAATGT
1 TTTTATTTAAATATAATAT
*
47827297 TTTTATTTTAAATATGATAT
1 TTTTA-TTTAAATATAATAT
47827317 TTTT
1 TTTT
47827321 TCATTACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTATTTAAATATAATAT
Found at i:47827956 original size:2 final size:2
Alignment explanation
Indices: 47827940--47827980 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
47827930 CATACTTTGT
*
47827940 TA TA T- TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47827981 CGATATAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:47833467 original size:45 final size:45
Alignment explanation
Indices: 47833404--47833497 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
47833394 ACGTATAAAC
*
47833404 TAAAAAAATAAGGTTATTTGCTTCAAAAT-AAAAAATAAAATAAT
1 TAAAAAAATAAGCTTATTTGCTTCAAAATAAAAAAATAAAATAAT
*
47833448 TAAAAAATATAATCTTATTTGCTTCAAAATAAAAAAATAAAATAAT
1 TAAAAAA-ATAAGCTTATTTGCTTCAAAATAAAAAAATAAAATAAT
47833494 TAAA
1 TAAA
47833498 TTAAATTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 7 0.15
45 20 0.43
46 19 0.41
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (45 bp):
TAAAAAAATAAGCTTATTTGCTTCAAAATAAAAAAATAAAATAAT
Found at i:47833936 original size:29 final size:29
Alignment explanation
Indices: 47833907--47833963 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
47833897 CTTTTACAAT
* * *
47833907 TTCGAATAT-TTTTTTATTTTTTAAAAAA
1 TTCGAACATATTTTTGAATTTTTAAAAAA
*
47833935 TTCTAACATATTTTTGAATTTTTAAAAAA
1 TTCGAACATATTTTTGAATTTTTAAAAAA
47833964 ATTATATAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (29 bp):
TTCGAACATATTTTTGAATTTTTAAAAAA
Found at i:47837887 original size:23 final size:23
Alignment explanation
Indices: 47837850--47837903 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
47837840 AAAAATCACG
*
47837850 GACAAAAATAGTTTTACTATAAT
1 GACAAAAATAATTTTACTATAAT
*
47837873 GACAAAGATAATTTTACTATAAT
1 GACAAAAATAATTTTACTATAAT
47837896 GACAAAAA
1 GACAAAAA
47837904 AATGAAGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (23 bp):
GACAAAAATAATTTTACTATAAT
Found at i:47838132 original size:24 final size:24
Alignment explanation
Indices: 47838104--47838154 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
47838094 AGTTTTACTC
*
47838104 AAACAAATAAACAAAATTTAATTG
1 AAACAAATAAACAAAATTTAACTG
*
47838128 AAACAAATAAACAAAGTTTAACTG
1 AAACAAATAAACAAAATTTAACTG
47838152 AAA
1 AAA
47838155 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.10, G:0.06, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAAAATTTAACTG
Found at i:47838556 original size:18 final size:18
Alignment explanation
Indices: 47838535--47838576 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
47838525 ATAAATTTAG
47838535 TTTTTAAT-ATTTATATTT
1 TTTTTAATAATTTA-ATTT
**
47838553 TTTTTGTTAATTTAATTT
1 TTTTTAATAATTTAATTT
47838571 TTTTTA
1 TTTTTA
47838577 GTTAAATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTAATAATTTAATTT
Found at i:47838565 original size:19 final size:19
Alignment explanation
Indices: 47838543--47838581 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
47838533 AGTTTTTAAT
47838543 ATTTATATTTTTTTT-GTTA
1 ATTTA-ATTTTTTTTAGTTA
47838562 ATTTAATTTTTTTTAGTTA
1 ATTTAATTTTTTTTAGTTA
47838581 A
1 A
47838582 ATTTCATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
ATTTAATTTTTTTTAGTTA
Found at i:47838584 original size:20 final size:19
Alignment explanation
Indices: 47838538--47838590 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
47838528 AATTTAGTTT
47838538 TTAATATTTATATTTTTTTTG
1 TTAA-ATTTA-ATTTTTTTTG
47838559 TT-AATTTAATTTTTTTTAG
1 TTAAATTTAATTTTTTTT-G
*
47838578 TTAAATTTCATTT
1 TTAAATTTAATTT
47838591 CTAAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.31
19 8 0.28
20 10 0.34
21 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (19 bp):
TTAAATTTAATTTTTTTTG
Found at i:47843511 original size:3 final size:3
Alignment explanation
Indices: 47843503--47843540 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
47843493 TCAATCATGC
47843503 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47843541 TGGGCCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47846008 original size:77 final size:77
Alignment explanation
Indices: 47845881--47846025 Score: 200
Period size: 77 Copynumber: 1.9 Consensus size: 77
47845871 TTCGATTAGT
* * * * * *
47845881 ATGGATATTATTGTCAATACAAGATGATGTGAGTTCGAGTGTGTTGAAGTGTATTATTCTTCTGT
1 ATGGATATTATTGTCAATACAAAAGGATGTGAGTTCGAGTGTGCTAAAGTGCATTATTCTTCTAT
47845946 TTATGTATTGAC
66 TTATGTATTGAC
* * * *
47845958 ATGGATATTGTTGTCAATACAAAAGGATGTGATTTTGAGTGTGCTAAAGTGCATTATTTTTCTAT
1 ATGGATATTATTGTCAATACAAAAGGATGTGAGTTCGAGTGTGCTAAAGTGCATTATTCTTCTAT
47846023 TTA
66 TTA
47846026 CGTGTTGAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
77 58 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.43
Consensus pattern (77 bp):
ATGGATATTATTGTCAATACAAAAGGATGTGAGTTCGAGTGTGCTAAAGTGCATTATTCTTCTAT
TTATGTATTGAC
Found at i:47856500 original size:18 final size:20
Alignment explanation
Indices: 47856477--47856515 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
47856467 TCCTCTCCCA
*
47856477 TTTCCT-TTTT-TCTTTTTT
1 TTTCCTCTTTTGTATTTTTT
47856495 TTTCCTCTTTTGTATTTTTT
1 TTTCCTCTTTTGTATTTTTT
47856515 T
1 T
47856516 ATTTTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTCCTCTTTTGTATTTTTT
Found at i:47856869 original size:205 final size:205
Alignment explanation
Indices: 47856488--47857003 Score: 747
Period size: 207 Copynumber: 2.5 Consensus size: 205
47856478 TTCCTTTTTT
*
47856488 CTTTTTTTTTCCTCTTTTGTATTTTTTTATTTTTCATAGATAAGAATTAAAAATAAAAATTTATG
1 CTTTTTTTTCCCTCTTTTGTATTTTTTTATTTTTCATAGATAAGAATTAAAAATAAAAATTTATG
* * * * *
47856553 TCAACTCAA-TAAATGATTCCAGTGTAAA-AAGGATATTATTCATCTTAAGAGACTCGAATTCGA
66 TGAATTCAACTAATTG-TTCCAGTGTAAAGAA-GATATTATTCAACTTAAAAGACTCGAATTCGA
* *
47856616 ACACTTGTGTGTGCATTGTCAAACTATCAATATCCTCTTCCATTATTTTTTTTCTTTTG-TTTTT
129 ACACCTGTGTGTACATTGTCAAACTATCAATATCCTCTTCCATTATTTTTTTTCTTTTGTTTTTT
47856680 TTCAAACTTCTC
194 TTCAAACTTCTC
47856692 CTTTTTTTTCCCTCTTTTGTATTTTTTTATTTTTCATAGATAAGAATTAAAAATAAAAATTTATG
1 CTTTTTTTTCCCTCTTTTGTATTTTTTTATTTTTCATAGATAAGAATTAAAAATAAAAATTTATG
* * * * *
47856757 TGAATTTAACTAGTTGTTCCAATAGTAAAGAAGATATTATTCAAAC-TAAAAGTCTTGAATTC-A
66 TGAATTCAACTAATTGTTCCAGT-GTAAAGAAGATATTATTC-AACTTAAAAGACTCGAATTCGA
* *
47856820 AGCACCTGTGTGTATATTGTCAAACTATTAATATCCTCTTCCATTATTTTTTTTCTTTTGTTTTT
129 A-CACCTGTGTGTACATTGTCAAACTATCAATATCCTCTTCCATTATTTTTTTTCTTTTG--TTT
47856885 TTTTTCAAACTTCTC
191 TTTTTCAAACTTCTC
*
47856900 C-TTTTTTTCCCTCTTTTGTATTTTTTTATTTTTCATAGATAATAATTAAAAATAAAAATTTATG
1 CTTTTTTTTCCCTCTTTTGTATTTTTTTATTTTTCATAGATAAGAATTAAAAATAAAAATTTATG
* * *
47856964 TGAATTCAACGAATGGTTCCAGTGGTAAAGAGGATATTAT
66 TGAATTCAACTAATTGTTCCAGT-GTAAAGAAGATATTAT
47857004 CCATTTTAGA
Statistics
Matches: 281, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
204 78 0.28
205 86 0.31
206 4 0.01
207 95 0.34
208 18 0.06
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (205 bp):
CTTTTTTTTCCCTCTTTTGTATTTTTTTATTTTTCATAGATAAGAATTAAAAATAAAAATTTATG
TGAATTCAACTAATTGTTCCAGTGTAAAGAAGATATTATTCAACTTAAAAGACTCGAATTCGAAC
ACCTGTGTGTACATTGTCAAACTATCAATATCCTCTTCCATTATTTTTTTTCTTTTGTTTTTTTT
CAAACTTCTC
Found at i:47864909 original size:12 final size:13
Alignment explanation
Indices: 47864886--47864951 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
47864876 AGTTTAACAT
47864886 TGTTTTTGAAAAG
1 TGTTTTTGAAAAG
* *
47864899 TGTTTTTAAAAAA
1 TGTTTTTGAAAAG
* *
47864912 T-TCTGTGAAAAAG
1 TGTTTTTG-AAAAG
47864925 TGTTTTTGAAAAG
1 TGTTTTTGAAAAG
**
47864938 TACTTTTGAAAAG
1 TGTTTTTGAAAAG
47864951 T
1 T
47864952 TTGGTTTAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
12 3 0.07
13 34 0.83
14 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.42
Consensus pattern (13 bp):
TGTTTTTGAAAAG
Found at i:47864949 original size:26 final size:26
Alignment explanation
Indices: 47864889--47864951 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
47864879 TTAACATTGT
*
47864889 TTTTGAAAAGTGTTTTTAAAAAATTC
1 TTTTGAAAAGTGTTTTTAAAAAATAC
* * *
47864915 -TGTGAAAAAGTGTTTTTGAAAAGTAC
1 TTTTG-AAAAGTGTTTTTAAAAAATAC
47864941 TTTTGAAAAGT
1 TTTTGAAAAGT
47864952 TTGGTTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 3 0.10
26 24 0.80
27 3 0.10
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.41
Consensus pattern (26 bp):
TTTTGAAAAGTGTTTTTAAAAAATAC
Done.