Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 115 of 126
Found at i:34343437 original size:81 final size:81
Alignment explanation
Indices: 34343302--34343464 Score: 256
Period size: 81 Copynumber: 2.0 Consensus size: 81
34343292 ACTCACGATG
** *
34343302 ACACATAGTCATCGAACCTCATAGTCCGTAAAGGATTCATATACTCACGATGACACATAATCATC
1 ACACATAGTCATCGAACCTCATAACCCGTAAAAGATTCATATACTCACGATGACACATAATCATC
34343367 -AGACCTCATAATCTGT
66 GA-ACCTCATAATCTGT
* * *
34343383 ACACATAGTCATCGGACCTCATAACCCGTAAAAGATTTATATACTCACGATGACACATAGTCATC
1 ACACATAGTCATCGAACCTCATAACCCGTAAAAGATTCATATACTCACGATGACACATAATCATC
34343448 GAACCTCATAATCTGT
66 GAACCTCATAATCTGT
34343464 A
1 A
34343465 AAGGTTTCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
81 74 0.99
82 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (81 bp):
ACACATAGTCATCGAACCTCATAACCCGTAAAAGATTCATATACTCACGATGACACATAATCATC
GAACCTCATAATCTGT
Found at i:34343466 original size:52 final size:52
Alignment explanation
Indices: 34343383--34343505 Score: 185
Period size: 52 Copynumber: 2.4 Consensus size: 52
34343373 CATAATCTGT
34343383 ACACATAGTCATCGGACCTCATAACCCGTAAAAGATTT-ATATACTCACGATG
1 ACACATAGTCATCGGACCTCATAACCCGT-AAAGATTTCATATACTCACGATG
* * * * *
34343435 ACACATAGTCATCGAACCTCATAATCTGTAAAGGTTTCATATATTCACGATG
1 ACACATAGTCATCGGACCTCATAACCCGTAAAGATTTCATATACTCACGATG
34343487 ACACATAGTCATCGGACCT
1 ACACATAGTCATCGGACCT
34343506 TTTGCATTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 7 0.11
52 57 0.89
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (52 bp):
ACACATAGTCATCGGACCTCATAACCCGTAAAGATTTCATATACTCACGATG
Found at i:34343488 original size:133 final size:133
Alignment explanation
Indices: 34343250--34343505 Score: 406
Period size: 133 Copynumber: 1.9 Consensus size: 133
34343240 GCTCATGATG
* **
34343250 ACACATGGTCATCGGACCTCATAATTCGTAAAGAATTCATATACTCACGATGACACATAGTCATC
1 ACACATAGTCATCGGACCTCATAACCCGTAAAGAATTCATATACTCACGATGACACATAGTCATC
*
34343315 GAACCTCATAGTCCGTAAAGGATTCATATACTCACGATGACACATAATCATCAGACCTCATAATC
66 GAACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATAATCATCAGACCTCATAATC
34343380 TGT
131 TGT
*
34343383 ACACATAGTCATCGGACCTCATAACCCGTAAA-AGATTTATATACTCACGATGACACATAGTCAT
1 ACACATAGTCATCGGACCTCATAACCCGTAAAGA-ATTCATATACTCACGATGACACATAGTCAT
* * * * *
34343447 CGAACCTCATAATCTGTAAAGGTTTCATATATTCACGATGACACATAGTCATCGGACCT
65 CGAACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATAATCATCAGACCT
34343506 TTTGCATTTA
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
132 1 0.01
133 111 0.99
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27
Consensus pattern (133 bp):
ACACATAGTCATCGGACCTCATAACCCGTAAAGAATTCATATACTCACGATGACACATAGTCATC
GAACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATAATCATCAGACCTCATAATC
TGT
Found at i:34346502 original size:3 final size:3
Alignment explanation
Indices: 34346496--34346552 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
34346486 GTTGAGGAGG
34346496 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
34346544 GAA GAA GAA
1 GAA GAA GAA
34346553 ATGAATTTGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:34347268 original size:66 final size:66
Alignment explanation
Indices: 34347172--34347296 Score: 151
Period size: 66 Copynumber: 1.9 Consensus size: 66
34347162 TGGCGGTACG
* * * *
34347172 ATTGATTACTGTAGCGATGAGATAAAATACTACAACAGTAAAATTAAAAACAACGGTGACGGCGA
1 ATTGATTACTATAACGATGAAATAAAATACTACAACAATAAAATTAAAAACAACGGTGACGGCGA
34347237 T
66 T
** ** * * *
34347238 ATTGATTACTATAACGATGAAATAGGATACTGTAACAATTAGATTAAAAATAACGGTGA
1 ATTGATTACTATAACGATGAAATAAAATACTACAACAATAAAATTAAAAACAACGGTGA
34347297 GATGTGTATT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 48 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (66 bp):
ATTGATTACTATAACGATGAAATAAAATACTACAACAATAAAATTAAAAACAACGGTGACGGCGA
T
Found at i:34364396 original size:31 final size:32
Alignment explanation
Indices: 34364351--34364410 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
34364341 AATATTACTA
*
34364351 TAGTGACAGCAATGAAGGCTGAAACAGGACTG
1 TAGTGACAGAAATGAAGGCTGAAACAGGACTG
* *
34364383 TAGTG-CAGAAATGAAGGTTGAAATAGGA
1 TAGTGACAGAAATGAAGGCTGAAACAGGA
34364411 GGGGAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.40, C:0.10, G:0.32, T:0.18
Consensus pattern (32 bp):
TAGTGACAGAAATGAAGGCTGAAACAGGACTG
Found at i:34374520 original size:29 final size:28
Alignment explanation
Indices: 34374481--34374935 Score: 203
Period size: 29 Copynumber: 15.5 Consensus size: 28
34374471 ATCGAGATTA
34374481 AAAATGGAATTTTAAAAGATTCGGGGGT
1 AAAATGGAATTTTAAAAGATTCGGGGGT
* * ** * *
34374509 ATAATGGTAATTTTCAGTGAAATCGGGGTT
1 AAAATGG-AATTTTAAAAG-ATTCGGGGGT
*
34374539 AAAAATGGAATTTTAAAAGCTTCGGGGGT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
**** * * *
34374568 AAAATGGTAATTTTTGGTGAAATCAGGGTT
1 AAAATGG-AATTTTAAAAG-ATTCGGGGGT
*
34374598 AAAAATAGAATTTTAAAAGATTCGGGGGT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
**** * * *
34374627 AAAATGGTAATTTTTGGTGAAATCAGGGTT
1 AAAATGG-AATTTTAAAAG-ATTCGGGGGT
*
34374657 AAAAATGGAATTTTAAAAGCTTCGGGGGT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
** *
34374686 AAAATGGTAATTTTCGGTGAA-ATT-GGGGTT
1 AAAATGG-AATTTT---AAAAGATTCGGGGGT
**
34374716 AAAAATGGAATTTTAAAAGATTCTAGGGT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
**** * * *
34374745 AAAATGGTAATTTTCGGTGAAATCGAGGTT
1 AAAATGG-AATTTTAAAAG-ATTCGGGGGT
* ** * *
34374775 AAAAACGGAATTTTAGGAGCTTCAGGGGT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
**** * *
34374804 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGG-AATTTTAAAAG-ATTCGGGGGT
34374834 AAAAATGGAATTTTAAAAGATTCGGGGGT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
**** * * *
34374863 AAAATGGTAATTTTCGGTGAAATCAGGGTT
1 AAAATGG-AATTTTAAAAG-ATTCGGGGGT
34374893 AAAAATGGAATTTTAAAAGATTCGGGGGT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
34374922 AAAATGGTAATTTT
1 AAAATGG-AATTTT
34374936 CGAAAGTTTT
Statistics
Matches: 305, Mismatches: 96, Indels: 51
0.67 0.21 0.11
Matches are distributed among these distances:
27 2 0.01
28 56 0.18
29 100 0.33
30 97 0.32
31 48 0.16
32 2 0.01
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTAAAAGATTCGGGGGT
Found at i:34374549 original size:59 final size:59
Alignment explanation
Indices: 34374444--34374937 Score: 756
Period size: 59 Copynumber: 8.4 Consensus size: 59
34374434 TATGGATACC
* * * * *
34374444 CGGGGGCAAAATGGTAATTTT-GATGTAATCGAGATTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * *
34374502 CGGGGGTATAATGGTAATTTTCAGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * *
34374561 CGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATAGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * *
34374620 CGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
34374679 CGGGGGTAAAATGGTAATTTTCGGTGAAATTGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
** * * ** *
34374738 CTAGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAACGGAATTTTAGGAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
34374797 CAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
34374856 CGGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
34374915 CGGGGGTAAAATGGTAATTTTCG
1 CGGGGGTAAAATGGTAATTTTCG
34374938 AAAGTTTTAG
Statistics
Matches: 396, Mismatches: 39, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
58 19 0.05
59 377 0.95
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:34374957 original size:30 final size:30
Alignment explanation
Indices: 34374888--34375084 Score: 247
Period size: 30 Copynumber: 6.6 Consensus size: 30
34374878 GGTGAAATCA
* * *
34374888 GGGTTAAAAATGGAATTTT--AAAAGATTCG
1 GGGTT-AAAATGTAATTTTGGAAAAGTTTTG
* * *
34374917 GGGGTAAAATGGTAATTTTCG-AAAGTTTTA
1 GGGTTAAAAT-GTAATTTTGGAAAAGTTTTG
34374947 GGGTTAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTTG
* *
34374977 GGGTCAAAATGTAATTTCGGAAAAGTTTTG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTTG
* *
34375007 GGGTCAAAATATAATTTTGGAAAAGTTTTG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTTG
*
34375037 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTTG
*
34375067 GGGTCAAAATGTAATTTT
1 GGGTTAAAATGTAATTTT
34375085 TGGATTGTTT
Statistics
Matches: 148, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.03
29 20 0.14
30 123 0.83
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTTG
Found at i:34374993 original size:177 final size:176
Alignment explanation
Indices: 34374446--34374993 Score: 697
Period size: 177 Copynumber: 3.1 Consensus size: 176
34374436 TGGATACCCG
* * * * *
34374446 GGGGCAAAATGGTAA-TTTTGATGTAATCGAGATTAAAAATGGAATTTTAAAAGATTCGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTA
* * *
34374510 TAATGGTAATTTTCAGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTTCGGGGGTAAAATGG
66 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGG
* *
34374575 TAATTTTTGGTGAAA-TCAGGGTTAAAAATAGAATTTT--AAAAGATTCG
131 TAA-TTTT--CGAAATTCAGGGTTAAAAAT-GAATTTTGGAAAAGATTCA
* *
34374622 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGCTTCGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTA
* **
34374687 AAATGGTAATTTTCGGTGAAATTGGGGTTAAAAATGGAATTTTAAAAGATTCTAGGGTAAAATGG
66 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGG
* *
34374752 TAATTTTCGGTGAAA-TC-GAGGTTAAAAACGGAATTTTAGG---AGCTTCA
131 TAATTTTC---GAAATTCAG-GGTTAAAAA-TGAATTTT-GGAAAAGATTCA
34374799 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTA
*
34374864 AAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGG
66 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGG
* **
34374929 TAATTTTCGAAAGTTTTAGGGTT-AAAATGTAATTTTGGAAAAG-TTTT
131 TAATTTTCGAAA--TTCAGGGTTAAAAATG-AATTTTGGAAAAGATTCA
34374976 GGGGTCAAAAT-GTAATTT
1 GGGGT-AAAATGGTAATTT
34374994 CGGAAAAGTT
Statistics
Matches: 327, Mismatches: 27, Indels: 35
0.84 0.07 0.09
Matches are distributed among these distances:
174 4 0.01
175 3 0.01
176 29 0.09
177 283 0.87
178 8 0.02
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (176 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTA
AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGG
TAATTTTCGAAATTCAGGGTTAAAAATGAATTTTGGAAAAGATTCA
Found at i:34376865 original size:12 final size:14
Alignment explanation
Indices: 34376846--34376883 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
34376836 TTTAGACTAT
34376846 TGTAATTGGGCC-C
1 TGTAATTGGGCCTC
*
34376859 T-TAATTGGGCCTT
1 TGTAATTGGGCCTC
34376872 TGTAATTGGGCC
1 TGTAATTGGGCC
34376884 GTGGGCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 10 0.45
13 2 0.09
14 10 0.45
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (14 bp):
TGTAATTGGGCCTC
Found at i:34376984 original size:6 final size:6
Alignment explanation
Indices: 34376961--34377068 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
34376951 TATTTGGACT
* * **
34376961 TTTAAA TTTTAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA
1 TTTAAA TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
* * *
34377011 TTCAAA -TTAAA TTTAAATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
34377059 --TAAA TTTAAA
1 TTTAAA TTTAAA
34377069 ATCAATTTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 53 0.64
7 14 0.17
8 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:34377032 original size:25 final size:25
Alignment explanation
Indices: 34377004--34377053 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
34376994 TTTTATTTAA
* *
34377004 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
34377029 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
34377054 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:34377032 original size:31 final size:31
Alignment explanation
Indices: 34376997--34377060 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
34376987 TTTTAATTTT
*
34376997 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
34377028 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
34377059 TA
1 TA
34377061 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:34377047 original size:42 final size:43
Alignment explanation
Indices: 34376975--34377068 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
34376965 AATTTTAATG
* * ** *
34376975 TTAAATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
*
34377017 TTAAATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
34377059 -TAAATTTAAA
1 TTAAATTTAAA
34377069 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 10 0.22
42 31 0.69
43 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (43 bp):
TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:34377070 original size:17 final size:16
Alignment explanation
Indices: 34376998--34377068 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
34376988 TTTAATTTTT
34376998 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
34377016 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
34377029 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
34377046 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
34377062 ATTTAAA
1 ATTTAAA
34377069 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:34377987 original size:23 final size:22
Alignment explanation
Indices: 34377954--34378004 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
34377944 CTTTATTTGA
34377954 TAAAATA-TTTTGATATAACAAAT
1 TAAAATATTTTTGA-AT-ACAAAT
* *
34377977 TAAAATGTTTTTGAATACAAGT
1 TAAAATATTTTTGAATACAAAT
34377999 TAAAAT
1 TAAAAT
34378005 TGACAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 8 0.32
24 6 0.24
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (22 bp):
TAAAATATTTTTGAATACAAAT
Found at i:34378001 original size:22 final size:24
Alignment explanation
Indices: 34377961--34378004 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
34377951 TGATAAAATA
34377961 TTTTGATATAACAAATTAAAATGT
1 TTTTGATATAACAAATTAAAATGT
*
34377985 TTTTGA-AT-ACAAGTTAAAAT
1 TTTTGATATAACAAATTAAAAT
34378005 TGACAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAATGT
Found at i:34393032 original size:127 final size:123
Alignment explanation
Indices: 34392746--34393001 Score: 413
Period size: 125 Copynumber: 2.0 Consensus size: 123
34392736 CGAGACAAGC
34392746 CCTCCATTGCACCAAGATCTCACGCCCAAGTAACTTCGAAATCATAAGCCACAAGACCCTCACAC
1 CCTCCATTGCACCAAGATCTCACGCCC-A-TAACTTCGAAATCATAAGCCACAAGACCCTCACAC
* * *
34392811 GAAGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACTCAGAAGCGCCAAGATTAGG
64 GAAGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACCCAGAAACCCCAAGATTAGG
*
34392871 CCTCCATTGCACCAAGATCTCACGCCCAAGTAACTTCGGAATCATAAGCCACAAGACCCTCACAC
1 CCTCCATTGCACCAAGATCTCACGCCC-A-TAACTTCGAAATCATAAGCCACAAGACCCTCACA-
*
34392936 CCTAAGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACCCAGAAACCCCAAGATTAGG
63 -CGAAGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACCCAGAAACCCCAAGATTAGG
34392998 CCTC
1 CCTC
34393002 TTCACGCCTT
Statistics
Matches: 124, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
125 63 0.51
127 61 0.49
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (123 bp):
CCTCCATTGCACCAAGATCTCACGCCCATAACTTCGAAATCATAAGCCACAAGACCCTCACACGA
AGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACCCAGAAACCCCAAGATTAGG
Found at i:34407732 original size:4 final size:4
Alignment explanation
Indices: 34407711--34407805 Score: 82
Period size: 4 Copynumber: 23.0 Consensus size: 4
34407701 TTAAAAATAT
* * *
34407711 TTTA TTTA TATA TATA TTTA TTTTA TTTTA TTTA GTTA TTTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA -TTTA TTTA TTTA
* * * * * *
34407762 GTTA GTTA GTTA TTTA TTTA CTTA TTTA CTTC TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
34407806 CATCGTAAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
4 65 0.84
5 12 0.16
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:34411923 original size:20 final size:21
Alignment explanation
Indices: 34411884--34411923 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
34411874 GAGAATTGTT
*
34411884 TTTATTTTGATTACTTTAAAA
1 TTTATTTTGATTAATTTAAAA
34411905 TTTATTTTG-TTAATTTAAA
1 TTTATTTTGATTAATTTAAA
34411924 TATTCTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTATTTTGATTAATTTAAAA
Found at i:34413014 original size:40 final size:40
Alignment explanation
Indices: 34412967--34413049 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
34412957 CTACTATTAG
34412967 TCCTATACTAAGCGTAAAATTTTAAATTCAATCCATATTC
1 TCCTATACTAAGCGTAAAATTTTAAATTCAATCCATATTC
34413007 TCCTATACTAAGCGTAAAATTTTAAATTCAATCCATATTC
1 TCCTATACTAAGCGTAAAATTTTAAATTCAATCCATATTC
34413047 TCC
1 TCC
34413050 AATTGGATCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (40 bp):
TCCTATACTAAGCGTAAAATTTTAAATTCAATCCATATTC
Found at i:34427395 original size:12 final size:12
Alignment explanation
Indices: 34427381--34427421 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
34427371 TTTACTTAAT
*
34427381 TTTTTTTTGAAT
1 TTTTTTTTGAAA
*
34427393 TTTTTTTATAAAA
1 TTTTTTT-TGAAA
34427406 TTTTTTTTGAAA
1 TTTTTTTTGAAA
34427418 TTTT
1 TTTT
34427422 ATCAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (12 bp):
TTTTTTTTGAAA
Found at i:34427395 original size:26 final size:26
Alignment explanation
Indices: 34427366--34427423 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
34427356 GATTTAAGAT
* *
34427366 TTTTATTTACTTAATTTTTTTTTG-AA
1 TTTTATTTA-TAAAATTTTTTTTGAAA
*
34427392 TTTTTTTTATAAAATTTTTTTTGAAA
1 TTTTATTTATAAAATTTTTTTTGAAA
34427418 TTTTAT
1 TTTTAT
34427424 CAAATAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTTATTTATAAAATTTTTTTTGAAA
Found at i:34427885 original size:16 final size:16
Alignment explanation
Indices: 34427864--34427894 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34427854 AATTCTAATA
*
34427864 TATATTTTTAAAAATT
1 TATATTATTAAAAATT
34427880 TATATTATTAAAAAT
1 TATATTATTAAAAAT
34427895 ATTTATCAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATTATTAAAAATT
Found at i:34441469 original size:7 final size:7
Alignment explanation
Indices: 34441457--34441522 Score: 68
Period size: 7 Copynumber: 9.7 Consensus size: 7
34441447 AATTGAACCC
34441457 AATTTTA
1 AATTTTA
34441464 AATTTTA
1 AATTTTA
34441471 AATTTTA
1 AATTTTA
34441478 AATTTTA
1 AATTTTA
*
34441485 AATTATTTT
1 AA-T-TTTA
*
34441494 AAGTTTA
1 AATTTTA
34441501 AA-TTT-
1 AATTTTA
34441506 -ATTTTA
1 AATTTTA
34441512 AA-TTTA
1 AATTTTA
34441518 AATTT
1 AATTT
34441523 AATTTAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 9 0.18
7 31 0.62
8 1 0.02
9 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:34441494 original size:17 final size:17
Alignment explanation
Indices: 34441458--34441521 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
34441448 ATTGAACCCA
34441458 ATTTTAAATTTT-AA--
1 ATTTTAAATTTTAAATT
34441472 ATTTTAAATTTTAAATT
1 ATTTTAAATTTTAAATT
*
34441489 ATTTT-AAGTTTAAATTT
1 ATTTTAAATTTTAAA-TT
34441506 ATTTTAAA-TTTAAATT
1 ATTTTAAATTTTAAATT
34441522 TAATTTAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 12 0.27
15 2 0.05
16 10 0.23
17 18 0.41
18 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTTAAATT
Found at i:34441506 original size:6 final size:6
Alignment explanation
Indices: 34441460--34441530 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
34441450 TGAACCCAAT
* * *
34441460 TTTAAA TTTTAAA TTTTAAA TTTTAAA -TT-AT TTTAAG TTTAAA TTT-AT
1 TTTAAA -TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
34441508 TTTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
34441531 AAAAAGGGTC
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
4 1 0.02
5 13 0.24
6 21 0.38
7 20 0.36
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:34441522 original size:17 final size:17
Alignment explanation
Indices: 34441472--34441530 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
34441462 TAAATTTTAA
34441472 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
*
34441489 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
34441506 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
34441523 AATTTAAA
1 ATTTTAAA
34441531 AAAAAGGGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 6 0.16
17 32 0.84
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:34443449 original size:29 final size:29
Alignment explanation
Indices: 34443192--34443440 Score: 245
Period size: 29 Copynumber: 8.5 Consensus size: 29
34443182 TATTTTCTTT
* * *
34443192 AAAAATCCCATTTTGACCCTTAAACTTATCC
1 AAAAATCACATTTTTACCCCTAAAC-T-TCC
* * *
34443223 -AAAATTACA-TTTAACCTCTAAACTTCTC
1 AAAAATCACATTTTTACCCCTAAACTTC-C
* ** **
34443251 CAAAATTGCATTTTTA-CCCTCGCACTTCTC
1 AAAAATCACATTTTTACCCCT-AAACTTC-C
* * *
34443281 AAAAATTACAATTTTGCCCCTAAACTTCC
1 AAAAATCACATTTTTACCCCTAAACTTCC
*
34443310 AAAAATCACATTTTTACCCTTAAACTTCC
1 AAAAATCACATTTTTACCCCTAAACTTCC
*
34443339 AAAAATCACATTTTTACCCCCCAAACTTCC
1 AAAAATCACATTTTTA-CCCCTAAACTTCC
34443369 AAAAATCACA-TTTTACCCCTAAACTTCC
1 AAAAATCACATTTTTACCCCTAAACTTCC
*
34443397 AAAAATCACATTTTTACCCCTAAACTTTCT
1 AAAAATCACATTTTTACCCCTAAAC-TTCC
*
34443427 AAAAATCATATTTT
1 AAAAATCACATTTT
34443441 GACTCTAAAG
Statistics
Matches: 185, Mismatches: 25, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.01
28 24 0.13
29 83 0.45
30 72 0.39
31 4 0.02
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATCACATTTTTACCCCTAAACTTCC
Found at i:34443449 original size:58 final size:56
Alignment explanation
Indices: 34443192--34443449 Score: 232
Period size: 59 Copynumber: 4.4 Consensus size: 56
34443182 TATTTTCTTT
* * * *
34443192 AAAAATCCCATTTTGACCCTTAAACTTATCC-AAAATTACA-TTTAACCTCTAAACTTCTC
1 AAAAATCACATTTT-ACCC-TAAAC-T-TCCAAAAATCACATTTTTACCCCTAAACTTC-C
* ** ** * * *
34443251 CAAAATTGCATTTTTACCCTCGCACTTCTCAAAAATTACAATTTTGCCCCTAAACTTCC
1 AAAAATCACA-TTTTACCCT-AAACTTC-CAAAAATCACATTTTTACCCCTAAACTTCC
*
34443310 AAAAATCACATTTTTACCCTTAAACTTCCAAAAATCACATTTTTACCCCCCAAACTTCC
1 AAAAATCACA-TTTTACCC-TAAACTTCCAAAAATCACATTTTTA-CCCCTAAACTTCC
*
34443369 AAAAATCACATTTTACCCCTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTTCT
1 AAAAATCACATTTTA-CCCTAAACTTCCAAAAATCACATTTTTACCCCTAAAC-TTCC
* *
34443427 AAAAATCATATTTTGACTCTAAA
1 AAAAATCACATTTT-ACCCTAAA
34443450 GTCTTCGAAA
Statistics
Matches: 168, Mismatches: 21, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
57 10 0.06
58 69 0.41
59 70 0.42
60 19 0.11
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (56 bp):
AAAAATCACATTTTACCCTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCC
Found at i:34448067 original size:23 final size:23
Alignment explanation
Indices: 34448022--34448071 Score: 57
Period size: 26 Copynumber: 2.1 Consensus size: 23
34448012 ATATAACACT
34448022 AATTATTATGTGATAATTGTAAATAA
1 AATTATTATGTGATAA-T-TAAA-AA
*
34448048 AATTATTATGTGGTAA-TAAAAA
1 AATTATTATGTGATAATTAAAAA
34448070 AA
1 AA
34448072 GTAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
23 4 0.17
26 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (23 bp):
AATTATTATGTGATAATTAAAAA
Found at i:34449483 original size:21 final size:22
Alignment explanation
Indices: 34449442--34449484 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
34449432 TTCAGATACC
*
34449442 AAATTATAAACAATGATTAAAA
1 AAATCATAAACAATGATTAAAA
*
34449464 AAATCATAAA-AATTATTAAAA
1 AAATCATAAACAATGATTAAAA
34449485 TTTCTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATCATAAACAATGATTAAAA
Found at i:34454385 original size:16 final size:17
Alignment explanation
Indices: 34454359--34454399 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
34454349 ATTTTTGCTT
34454359 TTTTTTAATAT-T-ATAA
1 TTTTTT-ATATGTGATAA
34454375 TATTTTTATATGTGATAA
1 T-TTTTTATATGTGATAA
34454393 TTTTTTA
1 TTTTTTA
34454400 GTGCCTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTTTTATATGTGATAA
Found at i:34455134 original size:24 final size:24
Alignment explanation
Indices: 34455118--34455192 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
34455108 AGTTTGACTC
34455118 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
34455142 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
34455166 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
34455190 AAA
1 AAA
34455193 TATTATTTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:34457169 original size:24 final size:24
Alignment explanation
Indices: 34457141--34457191 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
34457131 AGTTTGACTC
*
34457141 AAACAAATAAACAGAATTTAATTA
1 AAACAAATAAACAGAATTTAACTA
* *
34457165 AAACAATTAAACAGAGTTTAACTA
1 AAACAAATAAACAGAATTTAACTA
34457189 AAA
1 AAA
34457192 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTA
Found at i:34457624 original size:22 final size:22
Alignment explanation
Indices: 34457586--34457651 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
34457576 TTATATTGTA
* *
34457586 TAATTTTATGATATTAAAAATG
1 TAATTTTATAATTTTAAAAATG
* * *
34457608 TAATTTTATTATTTTAATAATT
1 TAATTTTATAATTTTAAAAATG
34457630 TATATTTTTATAAATTTTAAAA
1 TA-A-TTTTAT-AATTTTAAAA
34457652 TGTTAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
22 20 0.57
23 1 0.03
24 6 0.17
25 8 0.23
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
TAATTTTATAATTTTAAAAATG
Found at i:34463971 original size:6 final size:6
Alignment explanation
Indices: 34463960--34463991 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
34463950 TTCACTTACA
34463960 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC
34463992 AAGATTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:34465981 original size:22 final size:19
Alignment explanation
Indices: 34465934--34465986 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
34465924 ATTGATAACA
34465934 TTTTAATAATAATAAATGT
1 TTTTAATAATAATAAATGT
* *
34465953 TTCTAATAATAATGAATTATTT
1 TTTTAATAATAAT-AA--ATGT
34465975 TTTTAATAATAA
1 TTTTAATAATAA
34465987 GGTAATAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.43
20 2 0.07
22 14 0.50
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TTTTAATAATAATAAATGT
Found at i:34467159 original size:58 final size:59
Alignment explanation
Indices: 34467053--34467303 Score: 364
Period size: 59 Copynumber: 4.3 Consensus size: 59
34467043 CCCATTCTTT
* * *
34467053 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATCCCATTTTTAACCCCGATTTCA
* *
34467112 CCCAAAATTACCATTTTA-CCCCAAACTCTCCAAAATCCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATCCCATTTTTAACCCCGATTTCA
* * *
34467170 TCC-AAAATTACCGTTTTACCCCCAAACTCTCTAAAATCCCATTTTTAACCCAGATTTCA
1 -CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATCCCATTTTTAACCCCGATTTCA
** * *
34467229 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTT-ACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATCCCATTTTTAACCCCGATTTCA
34467287 CCAAAAATTACCATTTT
1 CCAAAAATTACCATTTT
34467304 GCCCTCGAAA
Statistics
Matches: 173, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
58 79 0.46
59 94 0.54
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.32
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATCCCATTTTTAACCCCGATTTCA
Found at i:34467285 original size:117 final size:117
Alignment explanation
Indices: 34467053--34467303 Score: 371
Period size: 117 Copynumber: 2.1 Consensus size: 117
34467043 CCCATTCTTT
* * * * *
34467053 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCTATTTTTAACCCCGATTTCACCCAAA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATCCCATTTTTAACCCAGATTTCACCAAAA
* *
34467118 ATTACCATTTTACCCCAAACTCTCCAAAATCCCATTTTTAACCTCGATTTCA
66 ATTACCATTTTACCCCAAACTCTCCAAAATCCCATTTTTAACCCCAATTTCA
* *
34467170 TCC-AAAATTACCGTTTTACCCCCAAACTCTCTAAAATCCCATTTTTAACCCAGATTTCACCAAA
1 -CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATCCCATTTTTAACCCAGATTTCACCAAA
* *
34467234 AATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTT-ACCCCAATTTCA
65 AATTACCATTTTACCCC-AAACTCTCCAAAATCCCATTTTTAACCCCAATTTCA
34467287 CCAAAAATTACCATTTT
1 CCAAAAATTACCATTTT
34467304 GCCCTCGAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
116 2 0.02
117 94 0.79
118 23 0.19
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.32
Consensus pattern (117 bp):
CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATCCCATTTTTAACCCAGATTTCACCAAAA
ATTACCATTTTACCCCAAACTCTCCAAAATCCCATTTTTAACCCCAATTTCA
Found at i:34469804 original size:13 final size:12
Alignment explanation
Indices: 34469786--34469828 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
34469776 TAAATAAATG
*
34469786 ATTTATGTAATAA
1 ATTTATATAAT-A
34469799 ATTTATATAATA
1 ATTTATATAATA
34469811 ATTTGATATAATA
1 ATTT-ATATAATA
34469824 ATTTA
1 ATTTA
34469829 ATGGTACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 6 0.21
13 22 0.79
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (12 bp):
ATTTATATAATA
Found at i:34480831 original size:52 final size:52
Alignment explanation
Indices: 34480753--34480857 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
34480743 GACCCCCCCC
*
34480753 AAAGAGCTGCTACAGACAGCAAGCTCACAACCAAAACCACAAAA-ACAGAACA
1 AAAGAGCTACTACAGACAGCAAGCTCACAACCAAAACCA-AAAATACAGAACA
* **
34480805 AAAGAGTTACTACAGACAGCAAGCTCACAGTCAAAACCAAAAATACAGAACA
1 AAAGAGCTACTACAGACAGCAAGCTCACAACCAAAACCAAAAATACAGAACA
34480857 A
1 A
34480858 TCGATCTGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
51 4 0.08
52 44 0.92
ACGTcount: A:0.52, C:0.26, G:0.13, T:0.09
Consensus pattern (52 bp):
AAAGAGCTACTACAGACAGCAAGCTCACAACCAAAACCAAAAATACAGAACA
Found at i:34484033 original size:17 final size:17
Alignment explanation
Indices: 34484011--34484049 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
34484001 AGGTGGAGAA
* *
34484011 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
34484028 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
34484045 CTTGT
1 CTTGT
34484050 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:34487170 original size:17 final size:17
Alignment explanation
Indices: 34487148--34487186 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
34487138 AGGTGGAGAA
* *
34487148 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
34487165 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
34487182 CTTGT
1 CTTGT
34487187 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:34492681 original size:10 final size:10
Alignment explanation
Indices: 34492666--34492695 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
34492656 TCAAATAAAT
34492666 TTTCCTTTTA
1 TTTCCTTTTA
34492676 TTTCCTTTTA
1 TTTCCTTTTA
*
34492686 TTTTCTTTTA
1 TTTCCTTTTA
34492696 GGTCAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCCTTTTA
Found at i:34500506 original size:16 final size:18
Alignment explanation
Indices: 34500472--34500513 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
34500462 GATATAAAAA
*
34500472 TCATATTTCACTTCAATTC
1 TCAT-TTTCACATCAATTC
34500491 T-ATTTTCACATC-ATTC
1 TCATTTTCACATCAATTC
34500507 TCATTTT
1 TCATTTT
34500514 TGTCCCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 13 0.62
18 2 0.10
19 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (18 bp):
TCATTTTCACATCAATTC
Found at i:34504893 original size:11 final size:11
Alignment explanation
Indices: 34504879--34504960 Score: 65
Period size: 11 Copynumber: 7.5 Consensus size: 11
34504869 ATATCCAAAC
34504879 AATAATAACAA
1 AATAATAACAA
* *
34504890 AATAGTAATAA
1 AATAATAACAA
* **
34504901 TATAATAGTAA
1 AATAATAACAA
* *
34504912 AATGATAGCAA
1 AATAATAACAA
*
34504923 AATAATAAAAA
1 AATAATAACAA
*
34504934 AATAATGACAA
1 AATAATAACAA
* *
34504945 AACAATAAAAA
1 AATAATAACAA
34504956 AATAA
1 AATAA
34504961 CAATAATTTT
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 54 1.00
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (11 bp):
AATAATAACAA
Found at i:34511828 original size:20 final size:20
Alignment explanation
Indices: 34511784--34511834 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
34511774 ACATTATAAC
*
34511784 AAAAGAAGAAAGAAAAAATAG
1 AAAAG-AGAAAAAAAAAATAG
*
34511805 AAAATAGAAAAAAAGAAATA-
1 AAAAGAGAAAAAAA-AAATAG
34511825 AAAAGAGAAA
1 AAAAGAGAAA
34511835 TAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (20 bp):
AAAAGAGAAAAAAAAAATAG
Found at i:34511833 original size:12 final size:12
Alignment explanation
Indices: 34511784--34511852 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 12
34511774 ACATTATAAC
* *
34511784 AAAAGAAGAAAG
1 AAAAAAAGAAAT
34511796 AAAAAATAGAAAAT
1 AAAAAA-AG-AAAT
34511810 AGAAAAAAAGAAAT
1 --AAAAAAAGAAAT
*
34511824 AAAAAGAGAAAT
1 AAAAAAAGAAAT
34511836 AATATAAAAGAAA-
1 AA-A-AAAAGAAAT
34511849 AAAA
1 AAAA
34511853 TGAAAATATG
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
11 1 0.02
12 19 0.40
13 5 0.11
14 14 0.30
15 2 0.04
16 6 0.13
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (12 bp):
AAAAAAAGAAAT
Found at i:34513456 original size:2 final size:2
Alignment explanation
Indices: 34513449--34513482 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34513439 CTAATTCTTC
34513449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34513483 CAATTTCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34514263 original size:25 final size:26
Alignment explanation
Indices: 34514235--34514288 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
34514225 ATGGAGAAGC
**
34514235 AAAAGATAATGGAAAAT-AAAGAAAA
1 AAAAGATAAAAGAAAATAAAAGAAAA
* *
34514260 AAAAGTTAAAAGAACATAAAAGAAAA
1 AAAAGATAAAAGAAAATAAAAGAAAA
34514286 AAA
1 AAA
34514289 CTAAATTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (26 bp):
AAAAGATAAAAGAAAATAAAAGAAAA
Found at i:34519846 original size:13 final size:13
Alignment explanation
Indices: 34519823--34519856 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
34519813 AAAAATAAAA
*
34519823 AAAATTATAATATT
1 AAAA-TATAATAAT
34519837 AAAATATAATAAT
1 AAAATATAATAAT
34519850 AAAATAT
1 AAAATAT
34519857 TTAAATTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:34526907 original size:17 final size:17
Alignment explanation
Indices: 34526885--34526942 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
34526875 AATGGGATAA
*
34526885 AAATTTATTTTGAATTT
1 AAATTTATTTTAAATTT
** *
34526902 AAATTTACATAAAATTT
1 AAATTTATTTTAAATTT
*
34526919 AAATTTATTATAAATTT
1 AAATTTATTTTAAATTT
34526936 AAATTTA
1 AAATTTA
34526943 AAATTAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:34526954 original size:5 final size:6
Alignment explanation
Indices: 34526897--34526952 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
34526887 ATTTATTTTG
* *
34526897 AATTTA AATTTA CA-TAA AATTTA AATTT- -ATTATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA
*
34526943 AAATTA AATT
1 AATTTA AATT
34526953 AATGTCCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.08
5 4 0.10
6 30 0.75
7 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:34538284 original size:200 final size:200
Alignment explanation
Indices: 34537933--34538455 Score: 645
Period size: 200 Copynumber: 2.6 Consensus size: 200
34537923 GTAGTTCAAC
* * * * * * *
34537933 AAAAC-AGTGAGGCGGTAATCTTTCTGATGAGATATAGAGAAGTATATCAACTCAACGCTGAACA
1 AAAACAAGCGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCAACGCTCAACG
* ** * *
34537997 CAAGTAAATCTTCGAACCCAATTTCCTGATGAGACACTTAGAAGAAGGTCGAAGCAATAAAATGG
66 CGAGTAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGAAGGTCGAAGCAATAAAATAG
* *
34538062 TTAGGTTCCTGATGAGATACAGAGAAGTGGACCAAATTTGTC-TTCTTGAGGAGATCCAGAGAAG
131 TTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTTC-TGAGGAGATCCAGAGAAG
*
34538126 CGAATT
195 CAAATT
* * *
34538132 AAAACAAGCGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGAATACCAACTCAATGCTCAACG
1 AAAACAAGCGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCAACGCTCAACG
** * *
34538197 CGAGCCAATCTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGCAATAAAATAG
66 CGAGTAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGAAGGTCGAAGCAATAAAATAG
* * *
34538262 TTAGCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTTCTGAGGAGATCTAGATAAGC
131 TTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTTCTGAGGAGATCCAGAGAAGC
34538327 AAATT
196 AAATT
* * * * * * *
34538332 AAAACAATCGAGGCAGTCATCTTCTTGATGAGACATTGAGAAGAAGACCAAATCAAACCAACGCT
1 AAAACAAGCGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGAATACC-AA-C---TCAACGCT
* * * * *
34538397 CAATGTGAATAAATCTTCGAACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAG
61 CAACGCGAGTAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGAAGGTCGAAG
34538456 TCAACGAGAC
Statistics
Matches: 274, Mismatches: 43, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
199 5 0.02
200 206 0.75
201 5 0.02
202 1 0.00
205 57 0.21
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (200 bp):
AAAACAAGCGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCAACGCTCAACG
CGAGTAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGAAGGTCGAAGCAATAAAATAG
TTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTTCTGAGGAGATCCAGAGAAGC
AAATT
Found at i:34538823 original size:17 final size:17
Alignment explanation
Indices: 34538801--34538841 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
34538791 AATGGGATAA
*
34538801 AAATTTATTTTTAAATT
1 AAATTTATTTTGAAATT
*
34538818 AAATTTATTTTGAATTT
1 AAATTTATTTTGAAATT
34538835 AAATTTA
1 AAATTTA
34538842 CATAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
AAATTTATTTTGAAATT
Found at i:34538850 original size:17 final size:17
Alignment explanation
Indices: 34538812--34538876 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
34538802 AATTTATTTT
* *
34538812 TAAA-TTAAATTTATTT
1 TAAATTTAAATTTAATA
*
34538828 TGAATTTAAATTTACATA
1 TAAATTTAAATTTA-ATA
*
34538846 -AAATTTAAATTTATTA
1 TAAATTTAAATTTAATA
34538862 TAAATTTAAATTTAA
1 TAAATTTAAATTTAA
34538877 AATTAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 5 0.12
17 34 0.85
18 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TAAATTTAAATTTAATA
Found at i:34538887 original size:5 final size:6
Alignment explanation
Indices: 34538810--34538885 Score: 63
Period size: 6 Copynumber: 13.3 Consensus size: 6
34538800 AAAATTTATT
* * * *
34538810 TTTAAA -TTAAA TTT-AT TTTGAA TTTAAA TTTACA -TAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
34538855 TTT--A TTATAAA TTTAAA TTTAAA ATTAAA TT
1 TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TT
34538886 AATTTCCAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
4 3 0.05
5 13 0.24
6 36 0.65
7 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:34542444 original size:6 final size:6
Alignment explanation
Indices: 34542435--34542473 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
34542425 AATAGGAATA
*
34542435 GGAAGG GGAAGG GGAAGG GGAAGG GGAATG GGAATGG GG
1 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGAA-GG GG
34542474 GCGGCTAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 27 0.90
7 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.64, T:0.05
Consensus pattern (6 bp):
GGAAGG
Found at i:34542450 original size:18 final size:18
Alignment explanation
Indices: 34542429--34542469 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
34542419 AATAGGAATA
34542429 GGAATAGGAAGGGGAAGG
1 GGAATAGGAAGGGGAAGG
** *
34542447 GGAAGGGGAAGGGGAATG
1 GGAATAGGAAGGGGAAGG
34542465 GGAAT
1 GGAAT
34542470 GGGGGCGGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.56, T:0.07
Consensus pattern (18 bp):
GGAATAGGAAGGGGAAGG
Found at i:34554757 original size:50 final size:50
Alignment explanation
Indices: 34554696--34554792 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
34554686 GAGAAATGGC
34554696 TTCTATTTATAGATTCTCAAAGGAGCAAAACGGTTCAAAAAATTCAATAG
1 TTCTATTTATAGATTCTCAAAGGAGCAAAACGGTTCAAAAAATTCAATAG
*
34554746 TTCTATTTATAGATTCTCAAAGGGGCAAAACGGTTCAAAAAATTCAA
1 TTCTATTTATAGATTCTCAAAGGAGCAAAACGGTTCAAAAAATTCAA
34554793 CAGTCATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (50 bp):
TTCTATTTATAGATTCTCAAAGGAGCAAAACGGTTCAAAAAATTCAATAG
Found at i:34554812 original size:14 final size:14
Alignment explanation
Indices: 34554790--34554838 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
34554780 TCAAAAAATT
*
34554790 CAACAGTCATATTG
1 CAACGGTCATATTG
* *
34554804 CAACGGTCAAATTC
1 CAACGGTCATATTG
*
34554818 CAACGATCATATTG
1 CAACGGTCATATTG
*
34554832 TAACGGT
1 CAACGGT
34554839 TAGATTCTAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (14 bp):
CAACGGTCATATTG
Found at i:34554845 original size:28 final size:28
Alignment explanation
Indices: 34554785--34554864 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
34554775 ACGGTTCAAA
*
34554785 AAATT-CAACAGTCATATTGCAACGGTC
1 AAATTCCAACAGTCATATTGTAACGGTC
*
34554812 AAATTCCAAC-GATCATATTGTAACGGTT
1 AAATTCCAACAG-TCATATTGTAACGGTC
* * *
34554840 AGATTCTAACAGTTATATTGTAACG
1 AAATTCCAACAGTCATATTGTAACG
34554865 ATCATATTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.13
28 38 0.84
29 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (28 bp):
AAATTCCAACAGTCATATTGTAACGGTC
Found at i:34558526 original size:29 final size:28
Alignment explanation
Indices: 34558463--34558527 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 28
34558453 TATATCTTTA
*
34558463 TAATTTTTAAATAATTAAATCAAATTTT
1 TAATTTTTAAAAAATTAAATCAAATTTT
34558491 TATATTTTTAAAGAAATTAAAAT-ATAA-TTT
1 TA-ATTTTTAAA-AAATT-AAATCA-AATTTT
34558521 TAATTTT
1 TAATTTT
34558528 ACTAATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
28 2 0.06
29 14 0.44
30 10 0.31
31 6 0.19
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (28 bp):
TAATTTTTAAAAAATTAAATCAAATTTT
Found at i:34560075 original size:24 final size:24
Alignment explanation
Indices: 34560007--34560075 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
34559997 AGAAATAATC
* * * *
34560007 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTA
*
34560031 TTTCAATTAAACTCTATTTATTTA
1 TTTCAATTAAACTCTGTTTATTTA
34560055 TTTCAATTAAACTCTGTTTAT
1 TTTCAATTAAACTCTGTTTAT
34560076 ATGTTTGAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTA
Found at i:34562029 original size:24 final size:24
Alignment explanation
Indices: 34562002--34562088 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
34561992 AGAGATAATC
*
34562002 TTTTAGTTAAACTCTATTTAATTG
1 TTTTAGTTAAACTCTATTTATTTG
* *
34562026 TTTTATTTAAGCTCTATTTATTTG
1 TTTTAGTTAAACTCTATTTATTTG
* * *
34562050 TTTCAATTAAACTCTGTTTATTTG
1 TTTTAGTTAAACTCTATTTATTTG
* *
34562074 TTTGAGTCAAACTCT
1 TTTTAGTTAAACTCT
34562089 TATTAGTCTA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.54
Consensus pattern (24 bp):
TTTTAGTTAAACTCTATTTATTTG
Found at i:34565755 original size:54 final size:54
Alignment explanation
Indices: 34565673--34565775 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
34565663 AAAATAAACA
* * *
34565673 TAATAATTAGGGTTTAATTCAATTGATAGAGTTTATCCATGTGCTTGAATAGCT
1 TAATAATTAGGGGTTAATTCAATGGATAGAGTTTATCCATGAGCTTGAATAGCT
*
34565727 TAATAATTAGGGGTTAATTCAGTGGATAGAGTTTATCCATGAGCTTGAA
1 TAATAATTAGGGGTTAATTCAATGGATAGAGTTTATCCATGAGCTTGAA
34565776 AGAGATTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (54 bp):
TAATAATTAGGGGTTAATTCAATGGATAGAGTTTATCCATGAGCTTGAATAGCT
Found at i:34567135 original size:16 final size:14
Alignment explanation
Indices: 34567098--34567142 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 14
34567088 TAATACAATG
34567098 TGTAATTTTATATA
1 TGTAATTTTATATA
*
34567112 TG-AATTTTAGTTTTA
1 TGTAATTTTA--TATA
34567127 TGTAATTTTATATA
1 TGTAATTTTATATA
34567141 TG
1 TG
34567143 AAATATCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.27
14 7 0.27
15 5 0.19
16 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (14 bp):
TGTAATTTTATATA
Found at i:34571655 original size:24 final size:26
Alignment explanation
Indices: 34571600--34571652 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
34571590 AAACCACTAA
*
34571600 TAATTTTCTTTCACAAAAATAAACAT
1 TAATTTTCTTTCACAAAAAAAAACAT
34571626 TAATTTT-TTT-ACAAAAGAAAAACAT
1 TAATTTTCTTTCACAAAA-AAAAACAT
34571651 TA
1 TA
34571653 TTTAGTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 12 0.48
26 7 0.28
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (26 bp):
TAATTTTCTTTCACAAAAAAAAACAT
Found at i:34576221 original size:12 final size:13
Alignment explanation
Indices: 34576188--34576233 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
34576178 ATATAAAAGT
34576188 TATTTTATAATAA
1 TATTTTATAATAA
34576201 TATTTTATAATTAA
1 TATTTTATAA-TAA
*
34576215 -ATTTATATAAAAA
1 TATTT-TATAATAA
34576228 TATTTT
1 TATTTT
34576234 TGGTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTTTATAATAA
Found at i:34580376 original size:45 final size:45
Alignment explanation
Indices: 34580326--34580416 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
34580316 ACAGACAGAG
*
34580326 TACCCTTAAATAAAGTGTAATATGTGTACCACGGACTAGAAGATT
1 TACCCTTAAATAAAGTGTAATATGTGTACCACCGACTAGAAGATT
34580371 TACCCTTAAATAAAGTGTAATATGTGTACCACCGACTAGAAGATT
1 TACCCTTAAATAAAGTGTAATATGTGTACCACCGACTAGAAGATT
34580416 T
1 T
34580417 TCTGGATCAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (45 bp):
TACCCTTAAATAAAGTGTAATATGTGTACCACCGACTAGAAGATT
Found at i:34593103 original size:18 final size:18
Alignment explanation
Indices: 34593068--34593103 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
34593058 TTTTGATGTA
*
34593068 TTTTAATAAATAATTAAT
1 TTTTAATAAATAAGTAAT
*
34593086 TTTTAATAATTAAGTAAT
1 TTTTAATAAATAAGTAAT
34593104 AATTCGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTAATAAATAAGTAAT
Found at i:34605328 original size:16 final size:17
Alignment explanation
Indices: 34605291--34605328 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
34605281 GAAATGATTT
34605291 TAATTTTATATAATTAA
1 TAATTTTATATAATTAA
34605308 TAATTTTAT-TACATT-A
1 TAATTTTATATA-ATTAA
34605324 TAATT
1 TAATT
34605329 CAATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATTTTATATAATTAA
Found at i:34609206 original size:37 final size:37
Alignment explanation
Indices: 34609156--34609227 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
34609146 TCAATCCAAT
*
34609156 GACTTTAGAAATATGATGAACA-CTTTTAATTAATAAC
1 GACTTTAGAAATATGATGAACATC-TCTAATTAATAAC
34609193 GACTTTAGAAATATGATGAACATCTCTAATTAATA
1 GACTTTAGAAATATGATGAACATCTCTAATTAATA
34609228 GGCTAATCGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 32 0.97
38 1 0.03
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (37 bp):
GACTTTAGAAATATGATGAACATCTCTAATTAATAAC
Found at i:34612637 original size:2 final size:2
Alignment explanation
Indices: 34612630--34612660 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34612620 TTCTATTTTA
*
34612630 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34612661 CTTTACCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:34613115 original size:19 final size:20
Alignment explanation
Indices: 34613082--34613119 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
34613072 TTTTTTAATT
34613082 AATTTATAATAATTTTTATA
1 AATTTATAATAATTTTTATA
*
34613102 AATTT-TAATGATTTTTAT
1 AATTTATAATAATTTTTAT
34613120 TATTTTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
AATTTATAATAATTTTTATA
Found at i:34629225 original size:30 final size:29
Alignment explanation
Indices: 34629189--34629349 Score: 120
Period size: 30 Copynumber: 5.5 Consensus size: 29
34629179 ACTTTCAGGG
34629189 TAAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAATGG-AATTTTTGGTGAAATCGAGGT
* *
34629219 TAAAATGGGA-TTTT-G-GAAAGTTC-AGGGG
1 TAAAATGGAATTTTTGGTGAAA--TCGA-GGT
* **
34629247 CAAAATGGTAATTTTTGGTGAAATTAAGGT
1 TAAAATGG-AATTTTTGGTGAAATCGAGGT
** *
34629277 TAAAATGGAA-TTTT-G-GAAAGTTTAGGGG
1 TAAAATGGAATTTTTGGTGAAA-TCGA-GGT
34629305 TAAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAATGG-AATTTTTGGTGAAATCGAGGT
34629335 TAAAAATGGAATTTT
1 T-AAAATGGAATTTT
34629350 GGAAAGTTTG
Statistics
Matches: 104, Mismatches: 12, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
26 8 0.08
27 6 0.06
28 29 0.28
29 6 0.06
30 35 0.34
31 12 0.12
32 8 0.08
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.35
Consensus pattern (29 bp):
TAAAATGGAATTTTTGGTGAAATCGAGGT
Found at i:34629251 original size:28 final size:27
Alignment explanation
Indices: 34629219--34629712 Score: 227
Period size: 29 Copynumber: 17.0 Consensus size: 27
34629209 AAATCGAGGT
*
34629219 TAAAATGGGATTTTGGAAAGTTCAGGGG
1 TAAAATGGAATTTTGGAAAGTT-AGGGG
* * *
34629247 CAAAATGGTAATTTTTGGTGAAA-TTAAGGT
1 TAAAATGG-AA-TTTT-G-GAAAGTTAGGGG
34629277 TAAAATGGAATTTTGGAAAGTTTAGGGG
1 TAAAATGGAATTTTGGAAAG-TTAGGGG
* *
34629305 TAAAATGGTAATTTTTGGTGAAA--TCGAGGT
1 TAAAATGG-AA-TTTT-G-GAAAGTTAG-GGG
*
34629335 TAAAAATGGAATTTTGGAAAGTTTGGGGG
1 T-AAAATGGAATTTTGGAAAG-TTAGGGG
* * *
34629364 TAAAATGATAATTTTGG-AAGTTTCGAGG
1 TAAAATG-GAATTTTGGAAAG-TTAGGGG
*
34629392 TCAAAAATGGAATTTTGGAAAGTTTGGAGG
1 T--AAAATGGAATTTTGGAAAGTTAGG-GG
**
34629422 TAAAATGGTAATTTTTGGTGAAA--CCGGGG
1 TAAAATGG-AA-TTTT-G-GAAAGTTAGGGG
*
34629451 TTAAAAATGGAATTTTGGAAAGTTTGGGGG
1 -T-AAAATGGAATTTTGGAAAG-TTAGGGG
* * **
34629481 TAAAATGGTAATTCTAG-AAGTTTCAGGAT
1 TAAAATGG-AATTTTGGAAAG-TT-AGGGG
* * *
34629510 TAAAAATGGAAGTTTGGGAAGTTTGGGG
1 T-AAAATGGAATTTTGGAAAGTTAGGGG
*
34629538 ATAAAATGGTAATTTTTGG-AAGCTTCGGGG
1 -TAAAATGG-AA-TTTTGGAAAG-TTAGGGG
*
34629568 TCAAAATGGAATTTTTGG-AAGTTTGGGGG
1 T-AAAATGGAA-TTTTGGAAAG-TTAGGGG
*
34629597 TAAAATGGTAATTTTTGG-AAGCTTCGGGG
1 TAAAATGG-AA-TTTTGGAAAG-TTAGGGG
* *
34629626 TTAAAATGGAATTTTGGGAAGTTTGGGGG
1 -TAAAATGGAATTTTGGAAAG-TTAGGGG
* *
34629655 TAAAATGATAATTTTTGG-AAGCTTCGGGG
1 TAAAATG-GAA-TTTTGGAAAG-TTAGGGG
* *
34629684 TCAAAAATGGAATTTTGGTAAGTTCGGGG
1 T--AAAATGGAATTTTGGAAAGTTAGGGG
34629713 ACTAGAGAGC
Statistics
Matches: 376, Mismatches: 44, Indels: 91
0.74 0.09 0.18
Matches are distributed among these distances:
26 4 0.01
27 9 0.02
28 91 0.24
29 138 0.37
30 97 0.26
31 25 0.07
32 12 0.03
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (27 bp):
TAAAATGGAATTTTGGAAAGTTAGGGG
Found at i:34629405 original size:117 final size:116
Alignment explanation
Indices: 34629186--34629712 Score: 601
Period size: 117 Copynumber: 4.5 Consensus size: 116
34629176 TTGACTTTCA
* ** *
34629186 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGGATTTTGGAAAGTTCAGGGGCAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAA
* * *
34629250 AATGGTAATTTTTGGTGAA-ATT-AAGGTTAAAATGGAATTTTGGAAAGTTTAG
66 AATGGTAATTTTT-G-GAAGTTTCGAGGTAAAAATGGAATTTTGGAAAGTTT-G
34629302 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAA
*
34629367 AATGATAA-TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTGGAAAGTTTG
66 AATGGTAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTGGAAAGTTTG
* *
34629418 GAGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTA
1 G-GGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTA
* * * *
34629483 AAATGGTAA-TTCTAGAAGTTTC-AGGATTAAAAATGGAAGTTTGGGAAGTTTG
65 AAATGGTAATTTTTGGAAGTTTCGAGG--TAAAAATGGAATTTTGGAAAGTTTG
* * *
34629535 GGGATAAAATGGTAATTTTT-G-GAAGCTTCG-GGGTCAAAATGGAATTTTTGG-AAGTTTGGGG
1 GGG-TAAAATGGTAATTTTTGGTGAA--ATCGAGGTTAAAAATGGAA-TTTTGGAAAGTTTGGGG
* * * *
34629596 GTAAAATGGTAATTTTTGGAAGCTTCGGGGTTAAAATGGAATTTTGGGAAGTTTGG
62 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTGGAAAGTTT-G
* * * * * *
34629652 GGGTAAAATGATAATTTTT-G-GAAGCTTCGGGGTCAAAAATGGAATTTTGGTAAGTTCGGGG
1 GGGTAAAATGGTAATTTTTGGTGAA--ATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGG
34629713 ACTAGAGAGC
Statistics
Matches: 365, Mismatches: 30, Indels: 31
0.86 0.07 0.07
Matches are distributed among these distances:
114 3 0.01
115 6 0.02
116 137 0.38
117 216 0.59
118 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (116 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAA
AATGGTAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTGGAAAGTTTG
Found at i:34629515 original size:175 final size:172
Alignment explanation
Indices: 34629212--34629713 Score: 589
Period size: 175 Copynumber: 2.9 Consensus size: 172
34629202 TTTGGTGAAA
* * * * ****
34629212 TCGAGGTTAAAATGGGATTTTGGAAAGTTCAGGGGCAAAATGGTAATTTTTGGTGAAATTAAGGT
1 TCGAGGTCAAAATGGAATTTTGGAAAGTT-TGGGGTAAAATGGTAATTTTTGGTGAAACCGGGGT
* * ** *
34629277 TAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAT
65 TAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTAGAAG-ATTC-AGGTTAAAAAT
* *
34629342 GGAATTTTGGAAAGTTTGGGGGTAAAATGATAA-TTTTGGAAGTT
128 GGAATTTTGGAAAGTTTGGGGATAAAATGATAATTTTTGGAAGCT
34629386 TCGAGGTCAAAAATGGAATTTTGGAAAGTTTGGAGGTAAAATGGTAATTTTTGGTGAAACCGGGG
1 TCGAGGTC-AAAATGGAATTTTGGAAAGTTTGG-GGTAAAATGGTAATTTTTGGTGAAACCGGGG
* *
34629451 TTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTCTAGAAGTTTCAGGATTAAAAA
64 TT-AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTAGAAGATTCAGG-TTAAAAA
* * *
34629516 TGGAAGTTTGGGAAGTTTGGGGATAAAATGGTAATTTTTGGAAGCT
127 TGGAATTTTGGAAAGTTTGGGGATAAAATGATAATTTTTGGAAGCT
* *
34629562 TCGGGGTCAAAATGGAATTTTTGG-AAGTTTGGGGGTAAAATGGTAATTTTT-G-GAAGCTTCGG
1 TCGAGGTCAAAATGGAA-TTTTGGAAAGTTT-GGGGTAAAATGGTAATTTTTGGTGAAAC--CGG
* * * * * *
34629624 GGTTAAAATGGAATTTTGGGAAGTTTGGGGGTAAAATGATAATTTTTGGAAGCTTCGGGGTCAAA
62 GGTTAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAA-TTTTAGAAGATTC-AGGTTAAA
* *
34629689 AATGGAATTTTGGTAAGTTCGGGGA
125 AATGGAATTTTGGAAAGTTTGGGGA
34629714 CTAGAGAGCA
Statistics
Matches: 285, Mismatches: 32, Indels: 21
0.84 0.09 0.06
Matches are distributed among these distances:
173 4 0.01
174 49 0.17
175 163 0.57
176 69 0.24
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (172 bp):
TCGAGGTCAAAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTT
AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTAGAAGATTCAGGTTAAAAATGGA
ATTTTGGAAAGTTTGGGGATAAAATGATAATTTTTGGAAGCT
Found at i:34629673 original size:58 final size:58
Alignment explanation
Indices: 34629186--34629712 Score: 563
Period size: 58 Copynumber: 9.0 Consensus size: 58
34629176 TTGACTTTCA
* * * **
34629186 GGGTAAAATGGTAATTTTTGGTGAA--ATCGAGGTTAAAATGGGATTTTGGAAAGTTCAG
1 GGGTAAAATGGTAATTTTT-G-GAAGCTTCGGGGTTAAAATGGAATTTTGGAAAGTTTGG
* * ** *
34629244 GGGCAAAATGGTAATTTTTGGTGAA-ATT-AAGGTTAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTT-G-GAAGCTTCGGGGTTAAAATGGAATTTTGGAAAGTTTGG
* *
34629302 GGGTAAAATGGTAATTTTTGGTGAA--ATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTT-G-GAAGCTTCGGGGTT-AAAATGGAATTTTGGAAAGTTTGG
* * * *
34629361 GGGTAAAATGATAA-TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGT-TAAAATGGAATTTTGGAAAGTTTGG
* *
34629419 AGGTAAAATGGTAATTTTTGGTGAAAC--CGGGGTTAAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTT-G-GAAGCTTCGGGGTT-AAAATGGAATTTTGGAAAGTTTGG
* * * * * * *
34629478 GGGTAAAATGGTAA-TTCTAGAAGTTTCAGGATTAAAAATGGAAGTTTGGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTT-AAAATGGAATTTTGGAAAGTTTGG
* *
34629536 GGATAAAATGGTAATTTTTGGAAGCTTCGGGGTCAAAATGGAATTTTTGG-AAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTTAAAATGGAA-TTTTGGAAAGTTTGG
*
34629594 GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTTAAAATGGAATTTTGGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTTAAAATGGAATTTTGGAAAGTTTGG
* * * *
34629652 GGGTAAAATGATAATTTTTGGAAGCTTCGGGGTCAAAAATGGAATTTTGGTAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGT-TAAAATGGAATTTTGGAAAGTTTGG
34629711 GG
1 GG
34629713 ACTAGAGAGC
Statistics
Matches: 412, Mismatches: 41, Indels: 31
0.85 0.08 0.06
Matches are distributed among these distances:
56 6 0.01
57 8 0.02
58 269 0.65
59 125 0.30
60 1 0.00
61 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTTAAAATGGAATTTTGGAAAGTTTGG
Found at i:34631506 original size:6 final size:6
Alignment explanation
Indices: 34631489--34631548 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
34631479 TAGTTTATCT
* * **
34631489 AATTTA ATTTTA AATTTA AATTTA TAA--TA AATTTA AATTT- TATGCA
1 AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA
34631535 AATTTA AATTTA AA
1 AATTTA AATTTA AA
34631549 ATAAATCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
4 2 0.05
5 4 0.10
6 34 0.81
7 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:34631521 original size:17 final size:17
Alignment explanation
Indices: 34631499--34631554 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
34631489 AATTTAATTT
34631499 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
34631516 TAAATTTAAATTT-T-A
1 TAAATTTAAATTTATAA
*
34631531 TGCAAATTTAAATTTAAAA
1 T--AAATTTAAATTTATAA
34631550 TAAAT
1 TAAAT
34631555 CTAACTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 2 0.06
16 1 0.03
17 29 0.85
19 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:34631572 original size:34 final size:35
Alignment explanation
Indices: 34631499--34631574 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
34631489 AATTTAATTT
* * * * **
34631499 TAAATTTAAATTTATAATAAATTTAAATTTTATGC
1 TAAATTTAAATTTAAAATAAATCTAAACTTAAAAC
34631534 -AAATTTAAATTTAAAATAAATCT-AACTTAAAAC
1 TAAATTTAAATTTAAAATAAATCTAAACTTAAAAC
34631567 TAAATTTA
1 TAAATTTA
34631575 TATCTTATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 6 0.18
34 28 0.82
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAATTTAAATTTAAAATAAATCTAAACTTAAAAC
Found at i:34648909 original size:32 final size:33
Alignment explanation
Indices: 34648873--34648948 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
34648863 GCTCTCACGC
*
34648873 GTCCACAGCTCGCCAT-CCCCTGTCCGCCTGAT
1 GTCCACAGCTCGCCATCCCCCTGTCCACCTGAT
*
34648905 GTCCACAGCTCGTCATCCCCCTGTCCACCTGAT
1 GTCCACAGCTCGCCATCCCCCTGTCCACCTGAT
34648938 GTCCACAGCTC
1 GTCCACAGCTC
34648949 ATCCGCGTCC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 15 0.37
33 26 0.63
ACGTcount: A:0.14, C:0.46, G:0.17, T:0.22
Consensus pattern (33 bp):
GTCCACAGCTCGCCATCCCCCTGTCCACCTGAT
Found at i:34648958 original size:82 final size:81
Alignment explanation
Indices: 34648822--34648999 Score: 270
Period size: 82 Copynumber: 2.2 Consensus size: 81
34648812 CGCCTGTCCA
* * *
34648822 ATGTCCACAGCTCGCATCCTCCTGTCCAGCTGATGTCAGCAGCTCTCACGCGTCCACAGCTCGCC
1 ATGTCCACAGCTCGCATCCCCCTGTCCACCTGATGTCAGCAGCTCTCACGCGTCCACAACTCGCC
34648887 ATCCCCTGTCCGCCTG
66 ATCCCCTGTCCGCCTG
34648903 ATGTCCACAGCTCGTCATCCCCCTGTCCACCTGATGTCCA-CAGCTCATC-CGCGTCCACAACTC
1 ATGTCCACAGCTCG-CATCCCCCTGTCCACCTGATGT-CAGCAGCTC-TCACGCGTCCACAACTC
* *
34648966 GTCATCCCCTGTCCGCTTG
63 GCCATCCCCTGTCCGCCTG
34648985 ATGTCCACAGCTCGC
1 ATGTCCACAGCTCGC
34649000 CATCTCCTTA
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
81 15 0.17
82 70 0.79
83 4 0.04
ACGTcount: A:0.16, C:0.43, G:0.18, T:0.23
Consensus pattern (81 bp):
ATGTCCACAGCTCGCATCCCCCTGTCCACCTGATGTCAGCAGCTCTCACGCGTCCACAACTCGCC
ATCCCCTGTCCGCCTG
Found at i:34650037 original size:14 final size:14
Alignment explanation
Indices: 34650000--34650056 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
34649990 TAGTAAAATT
34650000 AATAATAA-AATAAA
1 AATAATAATAAT-AA
* *
34650014 AATTATATAATATTCA
1 AA-TA-ATAATAATAA
34650030 AATAATAATAATAA
1 AATAATAATAATAA
*
34650044 AATAATAACAATA
1 AATAATAATAATA
34650057 TTATAGCGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 22 0.63
15 4 0.11
16 7 0.20
17 2 0.06
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:34660545 original size:96 final size:91
Alignment explanation
Indices: 34660282--34660557 Score: 322
Period size: 90 Copynumber: 3.0 Consensus size: 91
34660272 GACAGGAGTT
* * * * *
34660282 CATTTTTTTTCATTTCAATGACAATGGTAAAATTTCAGTTTTGGTTTCTCTAATAAACTTAAATT
1 CATTTTTTTTCATTTCAATGATAATGGTAAAATTTTAGTTTT-G-ATCTCTATTAAACTCAAATT
* * *
34660347 TAATATTTAATCTTTATATTTTTACATT
64 TAAGATTTAATCTTTATATTTTTATATG
* * * * * *
34660375 CA-TTTTTTTCATTTCAATTATGATGGTAAAATTTTATTTTTTTAT-TTTTTTAAACTCAAATTT
1 CATTTTTTTTCATTTCAATGATAATGGTAAAATTTTA-GTTTTGATCTCTATTAAACTCAAATTT
*
34660438 AAGATTTAATCTTTATATTTTTATGTG
65 AAGATTTAATCTTTATATTTTTATATG
*
34660465 CACTTTTGTTTTCCATTTCAATGATAATGGTAAAATTTTAGTTTTGATCCCTCTATTGAACTCAA
1 CA-TTTT-TTTT-CATTTCAATGATAATGGTAAAATTTTAGTTTTGAT--CTCTATTAAACTCAA
34660530 ATTTAAGATTTAATCTTTATATTTTTAT
61 ATTTAAGATTTAATCTTTATATTTTTAT
34660558 TTGACATAAT
Statistics
Matches: 153, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
90 39 0.25
91 1 0.01
92 33 0.22
93 16 0.10
94 25 0.16
96 39 0.25
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (91 bp):
CATTTTTTTTCATTTCAATGATAATGGTAAAATTTTAGTTTTGATCTCTATTAAACTCAAATTTA
AGATTTAATCTTTATATTTTTATATG
Found at i:34663703 original size:27 final size:27
Alignment explanation
Indices: 34663665--34663719 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
34663655 AAATTTCGAG
*
34663665 TGGTGCTTATGGGGTAGGCGACACCAA
1 TGGTGCCTATGGGGTAGGCGACACCAA
**
34663692 TGGTGCCTATGGGGTAGGTTACACCAA
1 TGGTGCCTATGGGGTAGGCGACACCAA
34663719 T
1 T
34663720 TCGTACTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (27 bp):
TGGTGCCTATGGGGTAGGCGACACCAA
Found at i:34677188 original size:17 final size:17
Alignment explanation
Indices: 34677166--34677208 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
34677156 GACATGAGTA
34677166 GGTTGAAATAGTTAAAT
1 GGTTGAAATAGTTAAAT
34677183 GGTTGAAATAGTTAAAT
1 GGTTGAAATAGTTAAAT
34677200 GGTTGAAAT
1 GGTTGAAAT
34677209 TGTAGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.35
Consensus pattern (17 bp):
GGTTGAAATAGTTAAAT
Found at i:34677208 original size:9 final size:9
Alignment explanation
Indices: 34677166--34677218 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
34677156 GACATGAGTA
34677166 GGTTGAAAT
1 GGTTGAAAT
*
34677175 AGTT-AAAT
1 GGTTGAAAT
34677183 GGTTGAAAT
1 GGTTGAAAT
*
34677192 AGTT-AAAT
1 GGTTGAAAT
34677200 GGTTGAAAT
1 GGTTGAAAT
* *
34677209 TGTAGAAAT
1 GGTTGAAAT
34677218 G
1 G
34677219 ATTATATGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
8 14 0.40
9 21 0.60
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.34
Consensus pattern (9 bp):
GGTTGAAAT
Found at i:34678819 original size:19 final size:20
Alignment explanation
Indices: 34678795--34678844 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
34678785 TATAGCATTC
34678795 ATATTATTTTGA-TAAAAAT
1 ATATTATTTTGAGTAAAAAT
***
34678814 ATATTATAAAGAGTAAAAAT
1 ATATTATTTTGAGTAAAAAT
34678834 ATATTTATTTT
1 ATA-TTATTTT
34678845 ATTTTATTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
19 9 0.39
20 10 0.43
21 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
ATATTATTTTGAGTAAAAAT
Found at i:34708965 original size:20 final size:20
Alignment explanation
Indices: 34708916--34708967 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
34708906 GTAACATATC
34708916 TAATATTATT-AAATAATGT
1 TAATATTATTAAAATAATGT
34708935 TAAT-TGATATTAAAATTAAT-T
1 TAATAT--TATTAAAA-TAATGT
34708956 TAATATTATTAA
1 TAATATTATTAA
34708968 TATTTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 1 0.04
19 4 0.14
20 10 0.36
21 8 0.29
22 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
TAATATTATTAAAATAATGT
Found at i:34709038 original size:18 final size:18
Alignment explanation
Indices: 34709011--34709053 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
34709001 ATAATGTTAT
*
34709011 ATAATATTAATTTAATTA
1 ATAATATTAAGTTAATTA
* *
34709029 ATAATGTTAAGTTATTTA
1 ATAATATTAAGTTAATTA
*
34709047 ATTATAT
1 ATAATAT
34709054 CTGATGATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
ATAATATTAAGTTAATTA
Found at i:34711110 original size:14 final size:14
Alignment explanation
Indices: 34711083--34711118 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
34711073 GCAGCTGTTT
34711083 TCTTTCTT-CTTTC
1 TCTTTCTTCCTTTC
34711096 TCTTTCTTCCTTTC
1 TCTTTCTTCCTTTC
*
34711110 TCTTCCTTC
1 TCTTTCTTC
34711119 ACGCAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTTTCTTCCTTTC
Found at i:34716699 original size:17 final size:19
Alignment explanation
Indices: 34716665--34716707 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
34716655 CAATCTCCTT
34716665 TTGAACAGTAGTCTT-CCC
1 TTGAACAGTAGTCTTCCCC
*
34716683 TTGAGCAGTAG-CTTCCCC
1 TTGAACAGTAGTCTTCCCC
34716701 TTGAACA
1 TTGAACA
34716708 ATGGTGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (19 bp):
TTGAACAGTAGTCTTCCCC
Found at i:34718389 original size:19 final size:19
Alignment explanation
Indices: 34718365--34718405 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
34718355 CAACTAAGGA
*
34718365 AATAATATCTCTTAATTAG
1 AATAATATATCTTAATTAG
34718384 AATAATATATCTTAATTAG
1 AATAATATATCTTAATTAG
34718403 AAT
1 AAT
34718406 CTCTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (19 bp):
AATAATATATCTTAATTAG
Found at i:34719765 original size:15 final size:16
Alignment explanation
Indices: 34719747--34719777 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34719737 CTGTTTCATT
34719747 TGATT-TTGTTTTCTA
1 TGATTCTTGTTTTCTA
34719762 TGATTCTTGTTTTCTA
1 TGATTCTTGTTTTCTA
34719778 CAGTTAGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.65
Consensus pattern (16 bp):
TGATTCTTGTTTTCTA
Found at i:34724376 original size:33 final size:34
Alignment explanation
Indices: 34724339--34724411 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 34
34724329 AACTTCATAG
*
34724339 ACTTAGCTAACTT-TATAAAAATGTGACTGAATA
1 ACTTAGCTAACTTATATAAAAATGAGACTGAATA
* *
34724372 ACTTAGCTAACTTGAATGTAAAAATGAGGCTGAATA
1 ACTTAGCTAACTT--ATATAAAAATGAGACTGAATA
34724408 ACTT
1 ACTT
34724412 TAATGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 13 0.38
36 21 0.62
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (34 bp):
ACTTAGCTAACTTATATAAAAATGAGACTGAATA
Found at i:34727170 original size:18 final size:18
Alignment explanation
Indices: 34727147--34727193 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
34727137 TCTTATTGCA
34727147 TAAATAGGAAACCTATTC
1 TAAATAGGAAACCTATTC
34727165 TAAATAGGAAACCTATTC
1 TAAATAGGAAACCTATTC
34727183 TAAATAGGAAA
1 TAAATAGGAAA
34727194 TAACTTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (18 bp):
TAAATAGGAAACCTATTC
Found at i:34733547 original size:28 final size:28
Alignment explanation
Indices: 34733494--34733547 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
34733484 AAACCTAAAC
* *
34733494 CTCCTAAGATTTAGTCAACTATCTTGCA
1 CTCCTAAGATCTACTCAACTATCTTGCA
34733522 CTCCTAAGATCTACTCATACTA-CTTG
1 CTCCTAAGATCTACTCA-ACTATCTTG
34733548 ACATGCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (28 bp):
CTCCTAAGATCTACTCAACTATCTTGCA
Found at i:34734365 original size:21 final size:22
Alignment explanation
Indices: 34734341--34734381 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
34734331 TATTCTCTAA
34734341 CTATCAAAAAG-TTCATCTACT
1 CTATCAAAAAGATTCATCTACT
**
34734362 CTATCATCAAGATTCATCTA
1 CTATCAAAAAGATTCATCTA
34734382 AATAGGGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (22 bp):
CTATCAAAAAGATTCATCTACT
Found at i:34735312 original size:13 final size:13
Alignment explanation
Indices: 34735294--34735318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34735284 CTTTTCAATC
34735294 TTTTTTTCTATTT
1 TTTTTTTCTATTT
34735307 TTTTTTTCTATT
1 TTTTTTTCTATT
34735319 GTCAAGTAAT
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:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTCTATTT
Found at i:34736088 original size:120 final size:122
Alignment explanation
Indices: 34735960--34736256 Score: 431
Period size: 122 Copynumber: 2.5 Consensus size: 122
34735950 AGTAACTCCC
*
34735960 AACATTATATTTTTGTTTGAATGATTTGATTTGTGTTAAAAAGTAATATTAAGATTGGTTTGGTA
1 AACATTATATTTTTGTTTGAATGATTAGATTTGTGTTAAAAAGTAATATTAAGATTGGTTTGGTA
* * * * * * * *
34736025 GTGTATG-TTTTTTTTATATTGTAATAATAATTTGTATGTTTTTAGATGTAA-ATTT
66 GTATATGTTTTTTTTTACATTGTAATAATAAATTATATATTTTAAGATATAACATTA
*
34736080 AACATTATATTTTTTGTTTGAATGATTAGATTTGTGTT-GAAAGTAATATTAAGATTGGTTTGGT
1 AACATTATA-TTTTTGTTTGAATGATTAGATTTGTGTTAAAAAGTAATATTAAGATTGGTTTGGT
34736144 AGTATATGTTTTTTTTTTACATTGTAATAATAAATTATATATTTTAAGATATAACATTA
65 AGTATATG-TTTTTTTTTACATTGTAATAATAAATTATATATTTTAAGATATAACATTA
* * *
34736203 AACATTAGATTTTTGTTTGGATTATTAGATTTGTGTTAAAAA-TAATATTAAGAT
1 AACATTATATTTTTGTTTGAATGATTAGATTTGTGTTAAAAAGTAATATTAAGAT
34736257 ATAATTTAAA
Statistics
Matches: 158, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
120 41 0.26
121 27 0.17
122 76 0.48
123 14 0.09
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (122 bp):
AACATTATATTTTTGTTTGAATGATTAGATTTGTGTTAAAAAGTAATATTAAGATTGGTTTGGTA
GTATATGTTTTTTTTTACATTGTAATAATAAATTATATATTTTAAGATATAACATTA
Found at i:34738282 original size:16 final size:16
Alignment explanation
Indices: 34738261--34738293 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34738251 TGTGTCTCAT
34738261 ATTTTTCTTTCAGTTA
1 ATTTTTCTTTCAGTTA
*
34738277 ATTTTTTTTTCAGTTA
1 ATTTTTCTTTCAGTTA
34738293 A
1 A
34738294 AATCTGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (16 bp):
ATTTTTCTTTCAGTTA
Found at i:34741121 original size:9 final size:8
Alignment explanation
Indices: 34741107--34741146 Score: 50
Period size: 7 Copynumber: 5.2 Consensus size: 8
34741097 CCCAATCACC
34741107 AAAAGAAGA
1 AAAAGAA-A
34741116 AAAAG-AA
1 AAAAGAAA
34741123 AAAAG-AA
1 AAAAGAAA
34741130 AAAAG-AA
1 AAAAGAAA
34741137 AAAAGAAA
1 AAAAGAAA
34741145 AA
1 AA
34741147 CAATAGTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 20 0.67
8 5 0.17
9 5 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:34741125 original size:7 final size:7
Alignment explanation
Indices: 34741115--34741146 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
34741105 CCAAAAGAAG
34741115 AAAAAGA
1 AAAAAGA
34741122 AAAAAGA
1 AAAAAGA
34741129 AAAAAGA
1 AAAAAGA
34741136 AAAAAGA
1 AAAAAGA
34741143 AAAA
1 AAAA
34741147 CAATAGTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:34741130 original size:13 final size:13
Alignment explanation
Indices: 34741107--34741146 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 13
34741097 CCCAATCACC
34741107 AAAAGAAGAAAAAG
1 AAAA-AAGAAAAAG
34741121 AAAAAAGAAAAAAG
1 AAAAAAG-AAAAAG
34741135 AAAAAAGAAAAA
1 AAAAAAGAAAAA
34741147 CAATAGTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:34744583 original size:5 final size:5
Alignment explanation
Indices: 34744573--34744604 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
34744563 ATGACGAAGA
34744573 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AA
1 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AA
34744605 ACCTGAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (5 bp):
AAGGG
Found at i:34750541 original size:17 final size:17
Alignment explanation
Indices: 34750519--34750557 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
34750509 AGGTGGAGAA
* *
34750519 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
34750536 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
34750553 CTTGT
1 CTTGT
34750558 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:34751742 original size:2 final size:2
Alignment explanation
Indices: 34751735--34751760 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34751725 TCCGATTTAA
34751735 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
34751761 TCTAAATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34755599 original size:48 final size:48
Alignment explanation
Indices: 34755499--34755601 Score: 161
Period size: 48 Copynumber: 2.1 Consensus size: 48
34755489 TCTTTCAGTT
*
34755499 AAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTAATTGTTTCAATT
1 AAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTAATTGTTTCAATC
* * * *
34755547 AAACTCTGTTTATTTGTTTCAATTAAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTAATTGTTTCAATC
34755595 AAACTCT
1 AAACTCT
34755602 TATTAGTCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.50
Consensus pattern (48 bp):
AAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTAATTGTTTCAATC
Found at i:34755601 original size:24 final size:24
Alignment explanation
Indices: 34755491--34755589 Score: 171
Period size: 24 Copynumber: 4.1 Consensus size: 24
34755481 AGAAATAATC
*
34755491 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
34755515 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
34755539 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
*
34755563 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
34755587 TTT
1 TTT
34755590 GAGTCAAACT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:34759076 original size:16 final size:16
Alignment explanation
Indices: 34759057--34759087 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34759047 ATTATTATTC
34759057 CATCCTTTCAATTTTT
1 CATCCTTTCAATTTTT
34759073 CATCCTTTCAATTTT
1 CATCCTTTCAATTTT
34759088 CTTTGCTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (16 bp):
CATCCTTTCAATTTTT
Found at i:34761483 original size:24 final size:24
Alignment explanation
Indices: 34761456--34761526 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
34761446 AAAGTTTGAC
34761456 TGAAACAAATAAACAGAGTTTAAT
1 TGAAACAAATAAACAGAGTTTAAT
*
34761480 TGAAATAAATAAACAGAGTTTAAT
1 TGAAACAAATAAACAGAGTTTAAT
34761504 TGAAACAAATAAAC-GAAGTTTAA
1 TGAAACAAATAAACAG-AGTTTAA
34761527 CTGGAAGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 1 0.02
24 43 0.98
ACGTcount: A:0.55, C:0.07, G:0.13, T:0.25
Consensus pattern (24 bp):
TGAAACAAATAAACAGAGTTTAAT
Found at i:34764326 original size:13 final size:13
Alignment explanation
Indices: 34764310--34764334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34764300 AAAAAATACC
34764310 CAAAAAAAGAAAA
1 CAAAAAAAGAAAA
34764323 CAAAAAAAGAAA
1 CAAAAAAAGAAA
34764335 GAAAGTCTCT
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:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
CAAAAAAAGAAAA
Found at i:34765974 original size:6 final size:6
Alignment explanation
Indices: 34765963--34766000 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
34765953 ATAATATTAG
34765963 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TA
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TA
34766001 GTTTGTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TAATTT
Found at i:34766386 original size:15 final size:17
Alignment explanation
Indices: 34766366--34766400 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
34766356 CAACATTTTA
34766366 TTATTAAAAA-AAG-AT
1 TTATTAAAAATAAGTAT
34766381 TTATTAAAAATAAGTAT
1 TTATTAAAAATAAGTAT
34766398 TTA
1 TTA
34766401 CTTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 3 0.17
17 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (17 bp):
TTATTAAAAATAAGTAT
Found at i:34768226 original size:43 final size:43
Alignment explanation
Indices: 34768145--34768229 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
34768135 ATTAACATAT
* *
34768145 TAAATTATATTACTTGACTCCTGTTAATATGGTTACATGTTAC
1 TAAATTATATTACTTGACTCCTATTAATATGCTTACATGTTAC
*
34768188 TAAATTATATTACTTGACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCCTATTAATATGCTT-ACATGTTA
34768230 TTAATTGTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 2 0.05
43 36 0.95
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCCTATTAATATGCTTACATGTTAC
Done.