Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 81 of 226
Found at i:29369994 original size:26 final size:25
Alignment explanation
Indices: 29369929--29370006 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 25
29369919 TTCATCTTGA
*
29369929 TTTTTCTTT-TT-C-TTTTCTTTGT
1 TTTTTCTTTGTTCCTTTTTTTTTGT
* *
29369951 TTTTTCTTTTTTCTTTTTTGTTTTGT
1 TTTTTCTTTGTTCCTTTTT-TTTTGT
*
29369977 TTTTGT-TTTGTTCCTTTTTTGTTGT
1 TTTT-TCTTTGTTCCTTTTTTTTTGT
29370002 TTTTT
1 TTTTT
29370007 TTAAGCATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.20
23 2 0.04
24 1 0.02
25 13 0.28
26 20 0.43
27 1 0.02
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (25 bp):
TTTTTCTTTGTTCCTTTTTTTTTGT
Found at i:29370005 original size:11 final size:10
Alignment explanation
Indices: 29369929--29370007 Score: 52
Period size: 11 Copynumber: 7.5 Consensus size: 10
29369919 TTCATCTTGA
*
29369929 TTTTTCTTTT
1 TTTTTGTTTT
*
29369939 TCTTTTCTTTGT
1 T-TTTTGTTT-T
*
29369951 TTTTTCTTTT
1 TTTTTGTTTT
*
29369961 TTCTT-TTTT
1 TTTTTGTTTT
*
29369970 GTTTTGTTTT
1 TTTTTGTTTT
*
29369980 TGTTTTGTTCCT
1 T-TTTTGTT-TT
29369992 TTTTTGTTGTT
1 TTTTTGTT-TT
29370003 TTTTT
1 TTTTT
29370008 TAAGCATAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
9 7 0.12
10 10 0.18
11 36 0.63
12 4 0.07
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:29375737 original size:18 final size:17
Alignment explanation
Indices: 29375684--29376048 Score: 225
Period size: 17 Copynumber: 20.7 Consensus size: 17
29375674 CAAAAAAAAA
*
29375684 TTTGAAACACGAGAATTT
1 TTTGAAACACGA-AAATT
* * *
29375702 TTTAAAACATGAAGATT
1 TTTGAAACACGAAAATT
*
29375719 TTTGGAACACGCAAAA-T
1 TTTGAAACACG-AAAATT
*
29375736 TTTGAAAACATGAAAATT
1 TTTG-AAACACGAAAATT
*
29375754 TTTGAAATACGAAAATT
1 TTTGAAACACGAAAATT
*
29375771 TTAGAAACACGAAAATT
1 TTTGAAACACGAAAATT
* *
29375788 TTTAAAACACGACAA-T
1 TTTGAAACACGAAAATT
* **
29375804 TTTGAAACATGGTCAATT
1 TTTGAAACA-CGAAAATT
* *
29375822 TTTGAAAATACGACAATT
1 TTTG-AAACACGAAAATT
* * *
29375840 TTTGAAATATGAGAATTTTT
1 TTTGAAACACGA-AA--ATT
* *
29375860 TTTAAAACACGGAAATTTT
1 TTTGAAACAC-GAAA-ATT
*
29375879 TTTGAAAACAAGAAAATT
1 TTTG-AAACACGAAAATT
** * **
29375897 TTCAAAATACGGGAATT
1 TTTGAAACACGAAAATT
*
29375914 TTTGAAAACACGGGAAATTTT
1 TTTG-AAACAC--GAAA-ATT
*
29375935 TTTAAAAACACGAAAATT
1 TTT-GAAACACGAAAATT
*
29375953 TTTGAAACACTG-GAATT
1 TTTGAAACAC-GAAAATT
* *
29375970 TTTAAAACACGAAGATT
1 TTTGAAACACGAAAATT
29375987 TTTGAAACACGAAAATT
1 TTTGAAACACGAAAATT
* **
29376004 TTAGAAACGTGAAAATT
1 TTTGAAACACGAAAATT
* *
29376021 TTTAAAACACGAGAA-T
1 TTTGAAACACGAAAATT
29376037 TTTGAAACACGA
1 TTTGAAACACGA
29376049 TTTTTTTAAA
Statistics
Matches: 267, Mismatches: 62, Indels: 38
0.73 0.17 0.10
Matches are distributed among these distances:
16 22 0.08
17 141 0.53
18 54 0.20
19 19 0.07
20 18 0.07
21 13 0.05
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (17 bp):
TTTGAAACACGAAAATT
Found at i:29375878 original size:19 final size:19
Alignment explanation
Indices: 29375856--29375955 Score: 89
Period size: 20 Copynumber: 5.3 Consensus size: 19
29375846 ATATGAGAAT
29375856 TTTTTTTAAAACACGGAAA
1 TTTTTTTAAAACACGGAAA
*
29375875 TTTTTTTGAAAACA-AGAAA
1 TTTTTTT-AAAACACGGAAA
* * * *
29375894 -ATTTTCAAAATACGGGAA
1 TTTTTTTAAAACACGGAAA
*
29375912 -TTTTTGAAAACACGGGAAA
1 TTTTTTTAAAACAC-GGAAA
*
29375931 TTTTTTTAAAAACACGAAAA
1 TTTTTTT-AAAACACGGAAA
29375951 TTTTT
1 TTTTT
29375956 GAAACACTGG
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
17 5 0.08
18 17 0.27
19 15 0.23
20 20 0.31
21 7 0.11
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (19 bp):
TTTTTTTAAAACACGGAAA
Found at i:29375932 original size:56 final size:55
Alignment explanation
Indices: 29375858--29375980 Score: 176
Period size: 56 Copynumber: 2.2 Consensus size: 55
29375848 ATGAGAATTT
* *
29375858 TTTTTAAAACAC-GGAAATTTTTTTGAAAACAAGAAAATTTTCAAAATACGGGAA
1 TTTTTAAAACACGGGAAATTTTTTTAAAAACAAGAAAATTTTCAAAACACGGGAA
* ** *
29375912 TTTTTGAAAACACGGGAAATTTTTTTAAAAACACGAAAATTTTTGAAACACTGGAA
1 TTTTT-AAAACACGGGAAATTTTTTTAAAAACAAGAAAATTTTCAAAACACGGGAA
29375968 TTTTTAAAACACG
1 TTTTTAAAACACG
29375981 AAGATTTTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
54 5 0.08
55 15 0.25
56 41 0.67
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (55 bp):
TTTTTAAAACACGGGAAATTTTTTTAAAAACAAGAAAATTTTCAAAACACGGGAA
Found at i:29376350 original size:5 final size:5
Alignment explanation
Indices: 29376340--29376364 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29376330 TAAAATTATT
29376340 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
29376365 ATTGAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:29376554 original size:7 final size:7
Alignment explanation
Indices: 29376542--29376566 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29376532 TTCTTCTTCT
29376542 TTTTTTC
1 TTTTTTC
29376549 TTTTTTC
1 TTTTTTC
29376556 TTTTTTC
1 TTTTTTC
29376563 TTTT
1 TTTT
29376567 CTTTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:29376571 original size:18 final size:18
Alignment explanation
Indices: 29376535--29376576 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
29376525 GAACCCCTTC
*
29376535 TTCTTCTTTTTTTCTTTT
1 TTCTTTTTTTTTTCTTTT
29376553 TTCTTTTTTCTTTTC-TTT
1 TTCTTTTTT-TTTTCTTTT
29376571 TTCTTT
1 TTCTTT
29376577 CCCTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TTCTTTTTTTTTTCTTTT
Found at i:29376573 original size:11 final size:11
Alignment explanation
Indices: 29376532--29376589 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
29376522 ATTGAACCCC
*
29376532 TTCTTCTTCTT
1 TTCTTTTTCTT
29376543 TT-TTTCTT-TT
1 TTCTTT-TTCTT
29376553 TTCTTTTTTCTT
1 TTC-TTTTTCTT
29376565 TTCTTTTTCTT
1 TTCTTTTTCTT
* *
29376576 TCCCTTTT-TT
1 TTCTTTTTCTT
29376586 TTCT
1 TTCT
29376590 GTTGGGCTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
10 10 0.26
11 20 0.53
12 8 0.21
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:29376649 original size:19 final size:19
Alignment explanation
Indices: 29376617--29376681 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 19
29376607 TGGGTCTGGC
29376617 CTGCTGGG-TGCGCTGGGT
1 CTGCTGGGCTGCGCTGGGT
29376635 CTGCTGGGCTGCGCTGGGCCT
1 CTGCTGGGCTGCGCTGGG--T
*
29376656 GGCTTGCTGGGCTGCGCTGGGC
1 --C-TGCTGGGCTGCGCTGGGT
29376678 CTGC
1 CTGC
29376682 CCTACTGGGC
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
18 8 0.20
19 12 0.30
20 1 0.03
21 1 0.03
23 1 0.03
24 17 0.43
ACGTcount: A:0.00, C:0.29, G:0.46, T:0.25
Consensus pattern (19 bp):
CTGCTGGGCTGCGCTGGGT
Found at i:29376667 original size:24 final size:24
Alignment explanation
Indices: 29376635--29376705 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
29376625 TGCGCTGGGT
*
29376635 CTGCTGGGCTGCGCTGGGCCTGGC
1 CTGCTGGGCTGCGCTGGGCCTGCC
*
29376659 TTGCTGGGCTGCGCTGGGCCTGCC
1 CTGCTGGGCTGCGCTGGGCCTGCC
*
29376683 CTACTGGGCTGCGCTGGGCCTGC
1 CTGCTGGGCTGCGCTGGGCCTGC
29376706 TGAAAATGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.01, C:0.34, G:0.42, T:0.23
Consensus pattern (24 bp):
CTGCTGGGCTGCGCTGGGCCTGCC
Found at i:29376745 original size:21 final size:20
Alignment explanation
Indices: 29376721--29376760 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
29376711 ATGGCCTGTT
*
29376721 TTCTTTTTTTTTTTTGCTTTG
1 TTCTTCTTTTTTTTT-CTTTG
29376742 TTCTTCTTTTTTTTTCTTT
1 TTCTTCTTTTTTTTTCTTT
29376761 TTGGGCTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.82
Consensus pattern (20 bp):
TTCTTCTTTTTTTTTCTTTG
Found at i:29376895 original size:10 final size:10
Alignment explanation
Indices: 29376879--29376944 Score: 71
Period size: 10 Copynumber: 6.5 Consensus size: 10
29376869 ACAAAATATT
29376879 TTCTTTTTT-
1 TTCTTTTTTC
29376888 TTCTTTTTTTC
1 TTC-TTTTTTC
*
29376899 TGTCTTTCTTC
1 T-TCTTTTTTC
* *
29376910 TTCTTCTTCC
1 TTCTTTTTTC
29376920 TTCTTTTTTC
1 TTCTTTTTTC
*
29376930 TTTTTTTTTC
1 TTCTTTTTTC
29376940 TTCTT
1 TTCTT
29376945 CTTCTTCTCC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
9 3 0.07
10 33 0.72
11 8 0.17
12 2 0.04
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:29376906 original size:16 final size:15
Alignment explanation
Indices: 29376887--29376947 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
29376877 TTTTCTTTTT
29376887 TTTCTTTTTTTCTGTC
1 TTTCTTTTTTTCT-TC
*
29376903 TTTCTTCTTCTTCTTC
1 TTTCTT-TTTTTCTTC
*
29376919 CTTC-TTTTTTCTT-
1 TTTCTTTTTTTCTTC
*
29376932 TTT-TTTTCTTCTTC
1 TTTCTTTTTTTCTTC
29376946 TT
1 TT
29376948 CTTCTCCGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 10 0.27
14 9 0.24
15 1 0.03
16 11 0.30
17 6 0.16
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTTTCTTC
Found at i:29376910 original size:3 final size:3
Alignment explanation
Indices: 29376904--29376952 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
29376894 TTTTCTGTCT
*
29376904 TTC TTC TTC TTC TTCC TTC TT- TT- TTC TT- TT- TTT TTC TTC TTC
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
29376946 TTC TTC T
1 TTC TTC T
29376953 CCGTTCGGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
2 8 0.19
3 31 0.74
4 3 0.07
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:29377357 original size:30 final size:30
Alignment explanation
Indices: 29377302--29377470 Score: 180
Period size: 30 Copynumber: 5.7 Consensus size: 30
29377292 AAATGCAGCA
* * * *
29377302 AAAGTTTTGGGGCCGAAACGTAATTTTGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
* * * *
29377332 AAAGCTTAAGGGTCCAAATGTAATTTTAAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
*
29377362 AAAGTTTAGGGGTCAAAATGTAATTTAGA-
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
** *
29377391 AAAGTTTAGGGGTTGAACTGTAATTTTGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
* * *
29377421 AAAGTTTATGGGTTAAAATGCAATTTT-AG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
29377450 AAAAGTTTAGGGGTCAAAATG
1 -AAAGTTTAGGGGTCAAAATG
29377471 CAAAAAAATT
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
29 27 0.23
30 88 0.77
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (30 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTGAG
Found at i:29377423 original size:59 final size:60
Alignment explanation
Indices: 29377350--29377463 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 60
29377340 AGGGTCCAAA
*
29377350 TGTAATTTTAAGAAAGTTTAGGGGTCAAAATGTAA-TTTAGAAAAGTTTAGGGGTTGAAC
1 TGTAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAGTTTAGGGGTTGAAC
* * *
29377409 TGTAATTTTGAGAAAGTTTATGGGTTAAAATGCAATTTTAGAAAAGTTTAGGGGT
1 TGTAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAGTTTAGGGGT
29377464 CAAAATGCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 31 0.62
60 19 0.38
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (60 bp):
TGTAATTTTAAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAGTTTAGGGGTTGAAC
Found at i:29377954 original size:44 final size:44
Alignment explanation
Indices: 29377878--29378408 Score: 557
Period size: 44 Copynumber: 12.0 Consensus size: 44
29377868 ATAAGACTTG
* *
29377878 TATCTTCGATCTTCTTC-TGCCAATACAGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGC
* * *
29377921 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGC
*
29377965 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGC
* * ** * *
29378009 TTTCTTTGATCTACTTCACCACCAATATATGAAGACAATATCTGC
1 TATCTTCGATCTACTTCA-TGCCAATACATGAAGACAAGATCTGC
* * * * ***
29378054 TTTCTTCGATCTACTTCACGCCAATACATGAAGATAAGACCCAT
1 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGC
* * *
29378098 TATCTTCGATCTACTTCATGTCAAAACATGAAGATAAGATCTGC
1 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGC
* * ***
29378142 TATC-TCTGATCTACTTCATGTCAATACATGAAGACAATATCCAT
1 TATCTTC-GATCTACTTCATGCCAATACATGAAGACAAGATCTGC
** * *** *
29378186 TATCTTCGATCTACTTCACCACCAGTATGGGAAGATAAGATCTGC
1 TATCTTCGATCTACTTCA-TGCCAATACATGAAGACAAGATCTGC
* * ***
29378231 TATC-TCTGATCTACTTCATGTCAATACATAAAGACAAGATCCAT
1 TATCTTC-GATCTACTTCATGCCAATACATGAAGACAAGATCTGC
* * *
29378275 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTTC
1 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGC
* ***
29378319 TATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCAT
1 TATCTTC-GATCTACTTCATGCCAATACATGAAGACAAGATCTGC
* *
29378363 TATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGC
1 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGC
29378407 TA
1 TA
29378409 CTTTTCAACC
Statistics
Matches: 407, Mismatches: 72, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
43 19 0.05
44 313 0.77
45 75 0.18
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (44 bp):
TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGC
Found at i:29378199 original size:177 final size:177
Alignment explanation
Indices: 29377878--29378380 Score: 692
Period size: 177 Copynumber: 2.8 Consensus size: 177
29377868 ATAAGACTTG
* * *** * * *
29377878 TATCTTCGATCTTCTTC-TGCCAATACAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGC
1 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATGT
* * * *
29377942 CAATACATGAAGACAAGATCTGTTATCT-TCGATCTACTTCACGCCAATACATGAAGACAAGATC
66 CAATACATGAAGATAAGATCTGCTATCTCT-GATCTACTTCATGTCAATACATGAAGACAAGATC
* * *
29378006 TGC-TT-TCTTTGATCTACTTCACCACCAATATATGAAGACAATATCTGC
130 --CATTATCTTCGATCTACTTCACCACCAATATAGGAAGACAAGATCTGC
* * * *
29378054 TTTCTTCGATCTACTTCACGCCAATACATGAAGATAAGACCCATTATCTTCGATCTACTTCATGT
1 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATGT
* *
29378119 CAAAACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAGACAATATCC
66 CAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCC
* * *
29378184 ATTATCTTCGATCTACTTCACCACCAGTATGGGAAGATAAGATCTGC
131 ATTATCTTCGATCTACTTCACCACCAATATAGGAAGACAAGATCTGC
* *
29378231 TATC-TCTGATCTACTTCATGTCAATACATAAAGACAAGATCCATTATCTTCGATCTACTTCATG
1 TATCTTC-GATCTACTTCATGCCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
*
29378295 TCAATACATGAAGATAAGATCTTCTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATC
65 TCAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATC
29378360 CATTATCTTCGATCTACTTCA
130 CATTATCTTCGATCTACTTCA
29378381 TGTCAATACA
Statistics
Matches: 289, Mismatches: 33, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
175 1 0.00
176 19 0.07
177 268 0.93
178 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (177 bp):
TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATGT
CAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCC
ATTATCTTCGATCTACTTCACCACCAATATAGGAAGACAAGATCTGC
Found at i:29379730 original size:22 final size:23
Alignment explanation
Indices: 29379699--29379746 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
29379689 AGCCTCTCCA
29379699 TTTTATTTTTCCAT-TTTTCATTT
1 TTTTATTTTT-CATCTTTTCATTT
29379722 TTTTA-TTTTCATCTTTTCATTT
1 TTTTATTTTTCATCTTTTCATTT
29379744 TTT
1 TTT
29379747 CACATCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 3 0.12
22 16 0.67
23 5 0.21
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTCATCTTTTCATTT
Found at i:29384367 original size:2 final size:2
Alignment explanation
Indices: 29384318--29384351 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
29384308 TAATTAAAAG
*
29384318 AT AT AA AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
29384352 GAAAATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29384687 original size:3 final size:3
Alignment explanation
Indices: 29384679--29384717 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
29384669 ATTACCAGAT
* *
29384679 TAA TAA TAA TAA CAAA TAA TAA TAA TAA TAA TAA CAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA
29384718 TGAAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:29387328 original size:27 final size:26
Alignment explanation
Indices: 29387288--29387361 Score: 112
Period size: 27 Copynumber: 2.8 Consensus size: 26
29387278 ACACACCGCA
*
29387288 GCTCTTTATGAGCTTCCCGTTTAAAG
1 GCTCTTTATGAGCTTCCCGATTAAAG
*
29387314 GCTCTTTCATGAGCTTCCTGATTAAAG
1 GCTCTTT-ATGAGCTTCCCGATTAAAG
*
29387341 GCTCTTTATGAGCTTTCCGAT
1 GCTCTTTATGAGCTTCCCGAT
29387362 ATGGCTAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.44
27 24 0.56
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (26 bp):
GCTCTTTATGAGCTTCCCGATTAAAG
Found at i:29391153 original size:5 final size:5
Alignment explanation
Indices: 29391138--29391166 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
29391128 CAATCCGGGC
29391138 CCAAA -CAAA CCAAA CCAAA CCAAA CCAAA
1 CCAAA CCAAA CCAAA CCAAA CCAAA CCAAA
29391167 TAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAA
Found at i:29392572 original size:3 final size:3
Alignment explanation
Indices: 29392564--29392621 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
29392554 TTTCTTGCCT
29392564 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29392612 TTA TTTA TTA
1 TTA -TTA TTA
29392622 CTTTTTTATA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29397254 original size:44 final size:43
Alignment explanation
Indices: 29397191--29398057 Score: 752
Period size: 44 Copynumber: 19.6 Consensus size: 43
29397181 ACAAGATACG
* * *
29397191 AATCTTATCTCCTTAAAGTTGCAGTGGGGTAGATTAAAGCTACA
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAGATTAAAGCTACA
*
29397235 AATCTTATTTCTCTGAAGTTGCAGTGG-GACAGATTAAAGCTACAAGTTA
1 AATCTTATCTC-CTGAAGTTGCAGTGGAG-CAGATTAAAGCTAC-----A
* * * *
29397284 CAAGTCTTATCTCCCTGAACTTGCAGTGGAGTAGATTAAAACCACA
1 -AA-TCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
29397330 GATCTTCTCTCACTGAAGTTGCAGTGGAGTAGATTAAAACCACA
1 AATCTTATCTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
** * * * *
29397374 GGTCTTCTCTCACTGAAGTTGCAGTGGACCAGATTGAAGTTACA
1 AATCTTATCTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
29397418 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
29397462 AATCTTATCTCCTTGATGTTGCAATAGAGAAAATTAAAGCTACA
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * *
29397506 AATCTTATTTCCCTGAAGTTGTAGTGGAACAGATTAAAGTTACA
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* *
29397550 AATCTTATCTCTCTGAAGGTGCAGTGGAGCAGAATAAAGCTACA
1 AATCTTATCTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
*
29397594 AATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTAAAGTTACA
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
29397638 AATCTTATTTCCTTAAAGTTGTAGTGGAGCAGATTGAAA-TTGCA
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAGATT-AAAGCTACA
* * *
29397682 AGTCTTATCTCCTTGAAGTTGTAGTGGAGTAGATTAAAGCTACA
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
29397726 TATCTTCTCTCCATAAAGTTGTAGTGGAGTAGATTAAAGCTACA
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * * * *
29397770 TATCTTCTCTCCATAAAGTTACAGTGGAGCAGACTGAAGTTGCA
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * *
29397814 AATTTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTGCA
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
29397858 AATCTTATCTCCCTAAAGTTACAGTGGAGTAGATTGAAGTTACA
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* *
29397902 AATCTTATCTCTCTGAAGTTGCAGTGGAGC-GATTGAAGTTACA
1 AATCTTATCTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * *
29397945 AATCTCATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCGACA
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * * * * *
29397989 AGTCTAATCTCTTTAAAGTTGTAATGGAGTAGATTGAAGCAACA
1 AATCTTATCTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
*
29398033 AATTCTGTACCT-CTGAAGTTGCAGT
1 AA-TCT-TATCTCCTGAAGTTGCAGT
29398058 AGGTTAGAAT
Statistics
Matches: 693, Mismatches: 104, Indels: 52
0.82 0.12 0.06
Matches are distributed among these distances:
43 50 0.07
44 589 0.85
45 13 0.02
46 4 0.01
49 1 0.00
50 2 0.00
51 32 0.05
52 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
Found at i:29397483 original size:132 final size:131
Alignment explanation
Indices: 29397191--29398057 Score: 914
Period size: 132 Copynumber: 6.5 Consensus size: 131
29397181 ACAAGATACG
* *
29397191 AATCTTATCTCCTTAAAGTTGCAGTGGGGTAGATTAAAGCTACAAATCTTATTTCTCTGAAGTTG
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTC-CTGAAGTTG
* * *
29397256 CAGTGG-GACAGATTAAAGCTACAAGTTACAAGTCTTATCTCCCTGAACTTGCAGTGGAGTAGAT
65 CAGTGGAG-CAGATT---G----AAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* *
29397320 TAAAACCACA
122 TAAAGCTACA
* * * * * ** *
29397330 GATCTTCTCTCAC-TGAAGTTGCAGTGGAGTAGATTAAAACCACAGGTCTTCTCTCACTGAAGTT
1 AATCTTATCTC-CTTAAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTC-CTGAAGTT
*
29397394 GCAGTGGACCAGATTGAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
64 GCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
29397459 ACA
129 ACA
* * * * * * *
29397462 AATCTTATCTCCTTGATGTTGCAATAGAGAAAATTAAAGCTACAAATCTTATTTCCCTGAAGTTG
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCT-CCTGAAGTTG
* * * * * *
29397527 TAGTGGAACAGATTAAAGTTACAAATCTTATCTCTCTGAAGGTGCAGTGGAGCAGAATAAAGCTA
65 CAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
29397592 CA
130 CA
* * * * * *
29397594 AATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTAAAGTTACAAATCTTATTTCCTTAAAGTTG
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCC-TGAAGTTG
* * * * * * *
29397659 TAGTGGAGCAGATTGAAATTGCAAGTCTTATCTCCTTGAAGTTGTAGTGGAGTAGATTAAAGCTA
65 CAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
29397724 CA
130 CA
* * * * * * * *
29397726 TATCTTCTCTCCATAAAGTTGTAGTGGAGTAGATTAAAGCTACATATCTTCTCTCCATAAAGTTA
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCC-TGAAGTTG
* * * * * *
29397791 CAGTGGAGCAGACTGAAGTTGCAAATTTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTG
65 CAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
29397856 CA
130 CA
* * * *
29397858 AATCTTATCTCCCTAAAGTTACAGTGGAGTAGATTGAAGTTACAAATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTC-CTGAAGTTG
* * *
29397923 CAGTGGAGC-GATTGAAGTTACAAATCTCATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCGA
65 CAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
29397987 CA
130 CA
* * * * * * * *
29397989 AGTCTAATCTCTTTAAAGTTGTAATGGAGTAGATTGAAGCAACAAATTCTGTACCT-CTGAAGTT
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGTAGATTAAAGCTACAAA-TCT-TATCTCCTGAAGTT
29398053 GCAGT
64 GCAGT
29398058 AGGTTAGAAT
Statistics
Matches: 613, Mismatches: 107, Indels: 24
0.82 0.14 0.03
Matches are distributed among these distances:
131 101 0.16
132 440 0.72
133 6 0.01
136 1 0.00
139 64 0.10
140 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (131 bp):
AATCTTATCTCCTTAAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCTGAAGTTGC
AGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
A
Found at i:29402203 original size:3 final size:3
Alignment explanation
Indices: 29402156--29402234 Score: 52
Period size: 3 Copynumber: 25.3 Consensus size: 3
29402146 TATTTTTTGC
* * * * * *
29402156 TAT TAT TGT TAT TTT TAA TAT TAC TAT TAC TAT TAT T-G TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
29402201 TAT TAT TACT TACCT TAT TAT TAT TAT AAT TAT T
1 TAT TAT TA-T TA--T TAT TAT TAT TAT TAT TAT T
29402235 TATTCATTCA
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
2 1 0.02
3 48 0.83
4 5 0.09
5 4 0.07
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:29402220 original size:30 final size:29
Alignment explanation
Indices: 29402155--29402227 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
29402145 TTATTTTTTG
29402155 CTATTATTGTTATTTTTAATATTACTATTA
1 CTATTATTGTTATTTTTAATATTAC-ATTA
*
29402185 CTATTATTG-TATTTATTATTATTAC-TTA
1 CTATTATTGTTATTT-TTAATATTACATTA
*
29402213 CCTTATTATTATTAT
1 -C-TATTATTGTTAT
29402228 AATTATTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 3 0.08
29 6 0.16
30 25 0.68
31 3 0.08
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (29 bp):
CTATTATTGTTATTTTTAATATTACATTA
Found at i:29402320 original size:27 final size:27
Alignment explanation
Indices: 29402282--29402335 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
29402272 TATATACATG
*
29402282 CATACTAGATGTGTCCATGGGCCGGGC
1 CATACCAGATGTGTCCATGGGCCGGGC
29402309 CATACCAGATGTGTCCATGGGCCGGGC
1 CATACCAGATGTGTCCATGGGCCGGGC
29402336 AGCCCGGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.33, T:0.20
Consensus pattern (27 bp):
CATACCAGATGTGTCCATGGGCCGGGC
Found at i:29402535 original size:40 final size:42
Alignment explanation
Indices: 29402473--29402554 Score: 125
Period size: 40 Copynumber: 2.0 Consensus size: 42
29402463 GGATACAATA
*
29402473 AAAATATATTTTTATTTTATTTTT-AATTTTAAAAT-ATTTT
1 AAAATATACTTTTATTTTATTTTTAAATTTTAAAATAATTTT
29402513 AAAA-ATACTTTTATTTTTATTTTTAAATTTTAAAATAATTTT
1 AAAATATACTTTTA-TTTTATTTTTAAATTTTAAAATAATTTT
29402555 TTGGTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
39 8 0.21
40 14 0.37
41 11 0.29
42 5 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (42 bp):
AAAATATACTTTTATTTTATTTTTAAATTTTAAAATAATTTT
Found at i:29402919 original size:17 final size:17
Alignment explanation
Indices: 29402881--29402922 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
29402871 ATACATACTT
*
29402881 ATATATATTTTTATATT
1 ATATATATTTTTATATC
*
29402898 TTATA-ATTTTTATATAC
1 ATATATATTTTTATAT-C
29402915 ATATATAT
1 ATATATAT
29402923 ACACATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 10 0.50
17 8 0.40
18 2 0.10
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATATATTTTTATATC
Found at i:29413274 original size:4 final size:4
Alignment explanation
Indices: 29413256--29413289 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
29413246 GGATTTTGGG
29413256 GAAA GTAAA -AAA GAAA GAAA GAAA GAAA GAAA GA
1 GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GA
29413290 GAATGTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 22 0.79
5 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:29427285 original size:19 final size:20
Alignment explanation
Indices: 29427240--29427285 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
29427230 ATTTTTTTTG
29427240 ATAAAAATACATAAAAATTT
1 ATAAAAATACATAAAAATTT
* *
29427260 ATTAAAAT-GATACAAAA-TT
1 ATAAAAATACATA-AAAATTT
29427279 ATAAAAA
1 ATAAAAA
29427286 ATATATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
ATAAAAATACATAAAAATTT
Found at i:29432179 original size:69 final size:71
Alignment explanation
Indices: 29432037--29432181 Score: 215
Period size: 69 Copynumber: 2.1 Consensus size: 71
29432027 ATAGTGATGC
* *
29432037 ATATACAATTTAAAACATGAATAGTCGAATGTGTATATACATTTATGCTTAACAAATATTATCAT
1 ATATACAATTTAAAACATGAATAGTCGAATGTGTATATACA-TTATGCCTAACAAATATTATCAC
29432102 CGAATGT
65 CGAATGT
* *
29432109 ATATACACTTT-AAACATGAATAGTCGAATGCT-TATATACA-TATGCCTAACAAGTATTATCAC
1 ATATACAATTTAAAACATGAATAGTCGAATG-TGTATATACATTATGCCTAACAAATATTATCAC
29432171 CGAATGT
65 CGAATGT
29432178 ATAT
1 ATAT
29432182 GTAACACACC
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
69 30 0.44
71 27 0.40
72 11 0.16
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (71 bp):
ATATACAATTTAAAACATGAATAGTCGAATGTGTATATACATTATGCCTAACAAATATTATCACC
GAATGT
Found at i:29433615 original size:50 final size:50
Alignment explanation
Indices: 29433553--29433735 Score: 222
Period size: 50 Copynumber: 3.7 Consensus size: 50
29433543 CAATGCAATA
* ** * * *
29433553 TCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATG
* *** * * *
29433603 TCCCAGAGATGGTCTTATGGGGGACCTCGCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATG
* * *
29433653 TCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATG
29433703 TCCCAGACATGGTCTTACATGAGACCTCTCATA
1 TCCCAGACATGGTCTTACATGAGACCTCTCATA
29433736 ATCTCAATGA
Statistics
Matches: 112, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 112 1.00
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATG
Found at i:29435203 original size:41 final size:41
Alignment explanation
Indices: 29435133--29435237 Score: 102
Period size: 41 Copynumber: 2.6 Consensus size: 41
29435123 CGGCTTTTAG
* * * * * * * *
29435133 CCTGCTAGACTTATAGTCCGAATTGTTTCACCTGCATTAAT
1 CCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCAAA
* *
29435174 CTTGCTAGACATAAAGTCTGAAATATTTCACCGGCGTCAAA
1 CCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCAAA
* *
29435215 CCTACTAGACGTAAAGTCTGAAA
1 CCTGCTAGACATAAAGTCTGAAA
29435238 CATTCGATCA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (41 bp):
CCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCAAA
Found at i:29435406 original size:75 final size:74
Alignment explanation
Indices: 29435319--29435459 Score: 167
Period size: 75 Copynumber: 1.9 Consensus size: 74
29435309 AATATATATA
* * * * *
29435319 CATAATCGAATCTTCCATAT-ACATATATAAATTTCATACTTAAATTCATTACAAGAACATACAC
1 CATAATCAAATC-T-CATATAACATATATAAATGTCATACCTAAATTCAATAAAAGAACATACAC
29435383 ATGTATACCTG
64 ATGTATACCTG
* * * *
29435394 CATAATCAAATCTCATATAAACTTATATAAATGTCCTTCCTAAATTCAATAAAAGAACATATACA
1 CATAATCAAATCTCATAT-AACATATATAAATGTCATACCTAAATTCAATAAAAGAACATACACA
29435459 T
65 T
29435460 ATATGTAAGC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 5 0.09
74 1 0.02
75 49 0.89
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (74 bp):
CATAATCAAATCTCATATAACATATATAAATGTCATACCTAAATTCAATAAAAGAACATACACAT
GTATACCTG
Found at i:29435770 original size:2 final size:2
Alignment explanation
Indices: 29435763--29435803 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29435753 AGAAATTTAC
29435763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29435804 CATGCTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29442779 original size:69 final size:71
Alignment explanation
Indices: 29442633--29442786 Score: 206
Period size: 69 Copynumber: 2.2 Consensus size: 71
29442623 ACTTAAAATT
* * * *
29442633 GAATGCATATACAATTTAAAACATGAATAGCCGAATGTGTATATACATATATGCTTAACAAATAT
1 GAATGTATATACAATTTAAAACATGAACAACCGAATGTGTATATACA-ATATGCCTAACAAATAT
*
29442698 TATCATC
65 TATCACC
* *
29442705 GAATGTATATACACTTT-AAACATGAACAACCGAATGCT-TATATAC-ATATGCCTAACAATTAT
1 GAATGTATATACAATTTAAAACATGAACAACCGAATG-TGTATATACAATATGCCTAACAAATAT
29442767 TATCACC
65 TATCACC
29442774 GAATGTATATACA
1 GAATGTATATACA
29442787 TGTTCTTCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
69 34 0.46
71 24 0.32
72 16 0.22
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.31
Consensus pattern (71 bp):
GAATGTATATACAATTTAAAACATGAACAACCGAATGTGTATATACAATATGCCTAACAAATATT
ATCACC
Found at i:29443186 original size:75 final size:75
Alignment explanation
Indices: 29443100--29443244 Score: 168
Period size: 75 Copynumber: 1.9 Consensus size: 75
29443090 ATATATATAC
* * * * *
29443100 ATAATCAAATCTTCCATATACA-TT-TATAAATTTCATACTTAAATTCATTACAAGAACATACAC
1 ATAATCAAATC-T-CATATAAACTTATATAAATGTCATACCTAAATTCAATAAAAGAACATACAC
*
29443163 ATGTATACCTGT
64 ATATATACCTGT
* * * *
29443175 ATAATCGAATCTCATATAAACTTATATAAATGTCCTTCCTAAATTCAATAAAAGAACATATACAT
1 ATAATCAAATCTCATATAAACTTATATAAATGTCATACCTAAATTCAATAAAAGAACATACACAT
29443240 ATATA
66 ATATA
29443245 TAAGCATGCT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
73 7 0.12
74 3 0.05
75 48 0.83
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.34
Consensus pattern (75 bp):
ATAATCAAATCTCATATAAACTTATATAAATGTCATACCTAAATTCAATAAAAGAACATACACAT
ATATACCTGT
Found at i:29443520 original size:8 final size:8
Alignment explanation
Indices: 29443507--29443540 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
29443497 ATTCGAGCAT
29443507 TATATACA
1 TATATACA
*
29443515 TATATATA
1 TATATACA
*
29443523 CATATACA
1 TATATACA
29443531 TATATACA
1 TATATACA
29443539 TA
1 TA
29443541 CTCATACCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
TATATACA
Found at i:29446793 original size:17 final size:17
Alignment explanation
Indices: 29446773--29446808 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29446763 ATTTTCAGAG
29446773 TTAGTCAAATAATTTCT
1 TTAGTCAAATAATTTCT
29446790 TTAGTCAAATAATTTCT
1 TTAGTCAAATAATTTCT
29446807 TT
1 TT
29446809 TGGACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (17 bp):
TTAGTCAAATAATTTCT
Found at i:29451550 original size:16 final size:17
Alignment explanation
Indices: 29451519--29451555 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
29451509 TTGTGAGGTT
29451519 TTTTTAAAGTAAAATTAA
1 TTTTTAAAGTAAAATT-A
29451537 TTTTT-AAG-AAAATTA
1 TTTTTAAAGTAAAATTA
29451552 TTTT
1 TTTT
29451556 ATTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 3 0.16
18 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTTTAAAGTAAAATTA
Found at i:29451580 original size:17 final size:16
Alignment explanation
Indices: 29451518--29451581 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 16
29451508 TTTGTGAGGT
29451518 TTTTTTAAAGTAAAATTA
1 TTTTTT-AA-TAAAATTA
* *
29451536 ATTTTTAAGAAAATTA
1 TTTTTTAATAAAATTA
*
29451552 TTTTATTTATAAAATTA
1 TTTT-TTAATAAAATTA
29451569 TTATTTTAATAAA
1 TT-TTTTAATAAA
29451582 TAAATTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 10 0.26
17 21 0.55
18 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTTTTAATAAAATTA
Found at i:29451991 original size:7 final size:7
Alignment explanation
Indices: 29451981--29452005 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29451971 TAACATCTAA
29451981 TATATAT
1 TATATAT
29451988 TATATAT
1 TATATAT
29451995 TATATAT
1 TATATAT
29452002 TATA
1 TATA
29452006 AGCTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:29457536 original size:3 final size:3
Alignment explanation
Indices: 29457528--29457599 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
29457518 TTTCGTTTGC
29457528 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29457576 ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
29457600 TAGCTATAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29461680 original size:20 final size:20
Alignment explanation
Indices: 29461655--29461693 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29461645 TCAAAAATCT
29461655 GAATAAAAATGAATG-TAATG
1 GAATAAAAAT-AATGATAATG
*
29461675 GAATAACAATAATGATAAT
1 GAATAAAAATAATGATAAT
29461694 CAAACAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (20 bp):
GAATAAAAATAATGATAATG
Found at i:29462257 original size:3 final size:3
Alignment explanation
Indices: 29462249--29462277 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29462239 GAACCATCAT
29462249 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29462278 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29462282 original size:3 final size:3
Alignment explanation
Indices: 29462276--29462322 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
29462266 ATAATAATAA
29462276 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29462323 CATTAAACCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29463075 original size:22 final size:22
Alignment explanation
Indices: 29463047--29463199 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
29463037 TTTATTGTTC
*
29463047 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
29463069 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
29463091 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
29463113 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
29463135 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
29463157 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
29463179 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
29463200 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:29463359 original size:17 final size:18
Alignment explanation
Indices: 29463328--29463361 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29463318 NNNNNNNNNA
29463328 AAAAATGGAAACAAAAAT
1 AAAAATGGAAACAAAAAT
*
29463346 AAAAAT-GAATCAAAAA
1 AAAAATGGAAACAAAAA
29463362 ATAACACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.12
Consensus pattern (18 bp):
AAAAATGGAAACAAAAAT
Found at i:29465040 original size:15 final size:15
Alignment explanation
Indices: 29465020--29465049 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29465010 CAATTGCTAA
29465020 CCTAAAATTGGATTT
1 CCTAAAATTGGATTT
29465035 CCTAAAATTGGATTT
1 CCTAAAATTGGATTT
29465050 TCCAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
CCTAAAATTGGATTT
Found at i:29466483 original size:150 final size:148
Alignment explanation
Indices: 29466213--29466856 Score: 809
Period size: 150 Copynumber: 4.3 Consensus size: 148
29466203 GCACCAACAT
* * * * *
29466213 CCTTATTTTGGCCCTTTATTCGTATTTTTTTCCAAATTTTTTTACTTTAAAAAATATACTATTTT
1 CCTTATTTCGGCCC-TTGTTCGTATTTTTTCCCAGATTTTATTACTTTAAAAAATATACTATTTT
* * *
29466278 CTAATTTTCTAATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
65 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTA-TGTGTTTT
29466343 TTAAATAAA-TT-AAAAAAC
129 TTAAATAAATTTAAAAAAAC
* *
29466361 CCTTATTTCGGCCCTTGTTCGTATTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATT
1 CCTTATTTCGGCCCTTGTTCGTATTTTTTCCCAGATTTTATTACTTT--A-AAAAATATACTATT
* * * *
29466426 TTC-ATATTTTATTATTTTACATTGTTTTAGTACATTATGTTTGAAATATATTAATTTACTGTAT
63 TTCTA-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTA-TGTGT
29466490 TTTTTAAATAAATTTAAAAAAAAC
126 TTTTTAAATAAATTT-AAAAAAAC
* * * * *
29466514 TCTTATTTCGGCCATTTGTTTGTATTTTTTCCCCCGATTTTATTGC-TTAAAAAA-ATACTATTT
1 CCTTATTTCGGCC-CTTGTTCGTATTTTTT-CCCAGATTTTATTACTTTAAAAAATATACTATTT
* *
29466577 TCTAATTTCATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATCCATTTA-GTGTTTT
64 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATGTGTTTT
29466641 TTAAATAAATTTTTGTAAAAAAAC
129 TTAAATAAA---TT-TAAAAAAAC
* * * *
29466665 CTTTATTTCGGCTCTTTGTTCGTATTTTTCCCCAGATTTTATTACTTTAAAAAATATA-TCATAT
1 CCTTATTTCGGC-CCTTGTTCGTATTTTTTCCCAGATTTTATTACTTTAAAAAATATACT-ATTT
29466729 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTGTTT
64 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTT-ATGTGTTT
29466794 TTTAAATAAATTTAAAAAAA-
128 TTTAAATAAATTTAAAAAAAC
* * *
29466814 ACTTATTTCGGCCCTTTATTCGTATTTTTTTCTCAGATTTTAT
1 CCTTATTTCGGCCC-TTGTTCGTA-TTTTTTCCCAGATTTTAT
29466857 CATTTTACAT
Statistics
Matches: 432, Mismatches: 42, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
147 28 0.06
148 29 0.07
149 20 0.05
150 174 0.40
151 53 0.12
152 63 0.15
153 20 0.05
154 32 0.07
155 13 0.03
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.51
Consensus pattern (148 bp):
CCTTATTTCGGCCCTTGTTCGTATTTTTTCCCAGATTTTATTACTTTAAAAAATATACTATTTTC
TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATGTGTTTTTT
AAATAAATTTAAAAAAAC
Found at i:29466855 original size:300 final size:298
Alignment explanation
Indices: 29466213--29466856 Score: 899
Period size: 302 Copynumber: 2.1 Consensus size: 298
29466203 GCACCAACAT
* * *
29466213 CCTTATTTTGGCCCTTTATTCGTATTTTTTTCCAAATTTTTTTACTTTAAAAAATATACTATTTT
1 CCTTATTTCGGCCCTTTATTCGTATTTTTTTCCAGATTTTATTACTTTAAAAAATATACTATTTT
*
29466278 CTAATTTTCTAATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
66 CTAATTTTCTAATTTTACATTATTTTAATACATTATGTTTGAAATGTATCCATTTAG-GTGTTTT
* *
29466343 TTAAATAAATTAAAAAACCCTTATTTCGGCCCTTGTTCGTATTTTTTCCCGGATTTTATTACTTT
130 TTAAATAAATTAAAAAACCCTTATTTCGGCCCTTGTTCGTATTTTTCCCCAGATTTTATTACTTT
* * *
29466408 CAATAAAAATATATTATTTTCATATTTTATTATTTTACATTGTTTTAGTACATTATGTTTGAAAT
195 -AATAAAAATATATCATATTCATATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
*
29466473 ATATTAATTTACTGTATTTTTTAAATAAATTTAAAAAAAA
259 ATATTAATTTAATGTATTTTTTAAATAAATTTAAAAAAAA
* * * * * *
29466513 CTCTTATTTCGGCCATTTGTTTGTATTTTTTCCCCCGATTTTATTGC-TTAAAAAA-ATACTATT
1 C-CTTATTTCGGCCCTTTATTCGTATTTTTT-TCCAGATTTTATTACTTTAAAAAATATACTATT
* *
29466576 TTCTAA-TTTCATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATCCATTTA-GTGTT
64 TTCTAATTTTC-TAATTTTACATTATTTTAATACATTATGTTTGAAATGTATCCATTTAGGTGTT
* *
29466639 TTTTAAATAAATTTTTGTAAAAAAACCTTTATTTCGGCTCTTTGTTCGTATTTTTCCCCAGATTT
128 TTTTAAATAAA----T-T-AAAAAACCCTTATTTCGGC-CCTTGTTCGTATTTTTCCCCAGATTT
29466704 TATTACTTT-A-AAAAATATATCATATTC-TAATTTTATTATTTTACATTATTTTAGTACATTAT
186 TATTACTTTAATAAAAATATATCATATTCAT-ATTTTATTATTTTACATTATTTTAGTACATTAT
* * *
29466766 GTTTGAAATGTATTCATTTAATGTGTTTTTTAAATAAATTTAAAAAAAA
250 GTTTGAAATATATTAATTTAATGTATTTTTTAAATAAATTTAAAAAAAA
29466815 -CTTATTTCGGCCCTTTATTCGTATTTTTTTCTCAGATTTTAT
1 CCTTATTTCGGCCCTTTATTCGTATTTTTTTC-CAGATTTTAT
29466857 CATTTTACAT
Statistics
Matches: 304, Mismatches: 28, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
298 16 0.05
299 5 0.02
300 94 0.31
301 34 0.11
302 103 0.34
303 2 0.01
304 18 0.06
305 32 0.11
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.51
Consensus pattern (298 bp):
CCTTATTTCGGCCCTTTATTCGTATTTTTTTCCAGATTTTATTACTTTAAAAAATATACTATTTT
CTAATTTTCTAATTTTACATTATTTTAATACATTATGTTTGAAATGTATCCATTTAGGTGTTTTT
TAAATAAATTAAAAAACCCTTATTTCGGCCCTTGTTCGTATTTTTCCCCAGATTTTATTACTTTA
ATAAAAATATATCATATTCATATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATAT
ATTAATTTAATGTATTTTTTAAATAAATTTAAAAAAAA
Found at i:29466930 original size:269 final size:271
Alignment explanation
Indices: 29466589--29467129 Score: 822
Period size: 269 Copynumber: 2.0 Consensus size: 271
29466579 TAATTTCATT
* * *
29466589 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATCCATTTAGTGTTTTTTAAATAAATTTT
1 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATCAATTAAGTATTTTTTAAATAAATTTT
* * * *
29466654 TGTAAAAAAACCTTTATTTCGGCTCTTTGTTCGTA-TTTTTCCCCAGATTTTATTACTTTAAAAA
66 AGT-AAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATTACTTTAAAAA
*
29466718 ATATA-TCATATTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCA
130 AAATACT-ATATTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCA
29466782 TTTAATGTGTTTTTT-AAATAAATTTAAAAAAAA-CTTATTTCGGCCCTTTATTCGTATTTTTTT
194 TTTAATGTGTTTTTTAAAATAAATTTAAAAAAAACCTTATTTCGGCCCTTTATTCGTATTTTTTT
*
29466845 CTCAGATTTTATC
259 CCCAGATTTTATC
* *
29466858 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAATTATGTTTTTAAATAAA-TT
1 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATCAATTAAGTAT-TTTTTAAATAAATTT
*
29466922 TAGTAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCGGATTTTATTACTTTAAAAA
65 TAGTAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATTACTTTAAAAA
* *
29466987 AAATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACGTTATGTTTGAAATGTATTCAT
130 AAATACTATATTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCAT
* *** * *
29467052 TTAGTGTGTTTTTTAAAATTTTTTTAAAAAAAACCCCTTATTTCGGCTCTTTGTTCGTATTTTTT
195 TTAATGTGTTTTTTAAAATAAATTTAAAAAAAA--CCTTATTTCGGCCCTTTATTCGTATTTTTT
29467117 TCCCAGATTTTAT
258 TCCCAGATTTTAT
29467130 TACTTTCAAT
Statistics
Matches: 245, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
268 28 0.11
269 150 0.61
270 28 0.11
273 39 0.16
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (271 bp):
ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATCAATTAAGTATTTTTTAAATAAATTTT
AGTAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATTACTTTAAAAAA
AATACTATATTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATT
TAATGTGTTTTTTAAAATAAATTTAAAAAAAACCTTATTTCGGCCCTTTATTCGTATTTTTTTCC
CAGATTTTATC
Found at i:29466961 original size:117 final size:116
Alignment explanation
Indices: 29466733--29466963 Score: 349
Period size: 117 Copynumber: 2.0 Consensus size: 116
29466723 TCATATTCTA
* * *
29466733 ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTGTTTTTTA
1 ATTTTATCATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCAATTAATATGTTTTTTA
*
29466798 AATAAATTTAAAAAAAACTTATTTCGGCCCTTTATTCGTATTTTTTTCTCAG
66 AATAAATTTAAAAAAAACTTACTTCGGCCCTTTATTCGTA-TTTTTTCTCAG
29466850 ATTTTATCATTTTACATTATTTTAGTACATTATGTTTGAAATGTATT-AATTAATTATG-TTTTT
1 ATTTTATCATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCAATTAA-TATGTTTTTT
* *
29466913 AAATAAATTTAGTAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTTC
65 AAATAAATTTA--AAAAAA-ACTTACTTCGGCCCTTTATTCGTATTTTTTC
29466964 CCCGGATTTT
Statistics
Matches: 104, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
116 21 0.20
117 49 0.47
118 13 0.12
119 21 0.20
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (116 bp):
ATTTTATCATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCAATTAATATGTTTTTTA
AATAAATTTAAAAAAAACTTACTTCGGCCCTTTATTCGTATTTTTTCTCAG
Found at i:29467035 original size:152 final size:158
Alignment explanation
Indices: 29466841--29467145 Score: 426
Period size: 154 Copynumber: 2.0 Consensus size: 158
29466831 ATTCGTATTT
*
29466841 TTTTCTCAGATTTTATCATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAATTA
1 TTTTCTCAGATTTTATCATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAAGTA
* *
29466906 TG-TTTTT-AAATAAATTTAGTAAAAAA-CCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCG
66 TGTTTTTTAAAATAAATTTA-AAAAAAACCCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCA
29466968 GATTTTATTACTTT-AA-AAAAAATACTA
130 GATTTTATTACTTTCAATAAAAAATACTA
* * * * *
29466995 TTTTCT-A-ATTTTATTATTTTACATTATTTTAGTACGTTATGTTTGAAATGTATTCATTTAGTG
1 TTTTCTCAGATTTTATCATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAAGTA
*** * * *
29467058 TGTTTTTTAAAATTTTTTTAAAAAAAACCCCTTATTTCGGCTCTTTGTTCGTATTTTTTTCCCAG
66 TGTTTTTTAAAATAAATTTAAAAAAAACCCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCAG
29467123 ATTTTATTACTTTCAATAAAAAA
131 ATTTTATTACTTTCAATAAAAAA
29467146 AACACACTAA
Statistics
Matches: 132, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
152 52 0.39
153 12 0.09
154 60 0.45
155 2 0.02
156 6 0.05
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (158 bp):
TTTTCTCAGATTTTATCATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAAGTA
TGTTTTTTAAAATAAATTTAAAAAAAACCCCTTACTTCGGCCCTTTGTTCGTATTTTTTCCCCAG
ATTTTATTACTTTCAATAAAAAATACTA
Found at i:29469916 original size:15 final size:17
Alignment explanation
Indices: 29469883--29469919 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
29469873 ATATAAATTT
29469883 AAAATTGTTAAGTCGAAA
1 AAAATTGTTAAGTC-AAA
29469901 AAAATT-TTAAGT-AAA
1 AAAATTGTTAAGTCAAA
29469916 AAAA
1 AAAA
29469920 AACTTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
17 6 0.32
18 6 0.32
ACGTcount: A:0.59, C:0.03, G:0.11, T:0.27
Consensus pattern (17 bp):
AAAATTGTTAAGTCAAA
Found at i:29469917 original size:16 final size:18
Alignment explanation
Indices: 29469883--29469920 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
29469873 ATATAAATTT
*
29469883 AAAATTGTTAAGTCGAAA
1 AAAATTGTTAAGTCAAAA
29469901 AAAATT-TTAAGT-AAAA
1 AAAATTGTTAAGTCAAAA
29469917 AAAA
1 AAAA
29469921 ACTTATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 6 0.32
18 6 0.32
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (18 bp):
AAAATTGTTAAGTCAAAA
Found at i:29469918 original size:17 final size:18
Alignment explanation
Indices: 29469883--29469921 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
29469873 ATATAAATTT
**
29469883 AAAATTGTTAAGTCGAAA
1 AAAATTGTTAAGTAAAAA
29469901 AAAATT-TTAAGTAAAAA
1 AAAATTGTTAAGTAAAAA
29469918 AAAA
1 AAAA
29469922 CTTATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (18 bp):
AAAATTGTTAAGTAAAAA
Found at i:29475115 original size:61 final size:60
Alignment explanation
Indices: 29475032--29475177 Score: 141
Period size: 61 Copynumber: 2.4 Consensus size: 60
29475022 ATACACTTTA
* * * * * * * *
29475032 TCAATTTGATCCTAAATATAAAAAATTTAACAAATTTAGCCTTCAATATTTACAAAATTTG
1 TCAATTTAATTCTAATTCTAAAAAA-TCAACAAACTTAGCCCTCAACATTTACAAAATTTG
* * * * *
29475093 AT-ATTTTAGTTCTAATTCTAAAATCATCAACTAACTTCGCCCTCAACATTTACAAAATTTG
1 -TCAATTTAATTCTAATTCTAAAA-AATCAACAAACTTAGCCCTCAACATTTACAAAATTTG
29475154 TCAATTTAATTCTAATTCTAAAAA
1 TCAATTTAATTCTAATTCTAAAAA
29475178 TTTCAAAAAG
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
60 1 0.02
61 63 0.95
62 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.38
Consensus pattern (60 bp):
TCAATTTAATTCTAATTCTAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTG
Found at i:29476506 original size:107 final size:107
Alignment explanation
Indices: 29476317--29476529 Score: 286
Period size: 107 Copynumber: 2.0 Consensus size: 107
29476307 ATTCATCACC
* *
29476317 CCTTCACCTACATGATGACCATAAAATATCTTTCTATCGTCCGTGGGACAAAATTGAGTATCCAC
1 CCTTCACCTACATGATGACCATAAAATATATTTCTATCGTCCATGGGACAAAATTGAGTATCCAC
* * *
29476382 GTTGTGTACGCGAGAATTCAATATGAAAGCATCTAATCTTCA
66 ATTGTGTACGCGAGAATTCAATACGAAACCATCTAATCTTCA
* * * *
29476424 CCTTCACCTGCATGAAT-AGCATACAATATATTTCT-TTGATCCATGGGACAAAATTGAGTATCC
1 CCTTCACCTACATG-ATGACCATAAAATATATTTCTATCG-TCCATGGGACAAAATTGAGTATCC
** *
29476487 ACATTGTGTTGGCGTGAATTCAATACGAAACCATCTAATCTTC
64 ACATTGTGTACGCGAGAATTCAATACGAAACCATCTAATCTTC
29476530 CTAACCTATA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 2 0.02
107 88 0.96
108 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (107 bp):
CCTTCACCTACATGATGACCATAAAATATATTTCTATCGTCCATGGGACAAAATTGAGTATCCAC
ATTGTGTACGCGAGAATTCAATACGAAACCATCTAATCTTCA
Found at i:29487210 original size:15 final size:15
Alignment explanation
Indices: 29487190--29487238 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
29487180 TTGATTTGAT
29487190 TTGATTTCAATCAAA
1 TTGATTTCAATCAAA
29487205 TTGATTT---TCAAA
1 TTGATTTCAATCAAA
29487217 TTGATTTCAATCAAA
1 TTGATTTCAATCAAA
29487232 TTGATTT
1 TTGATTT
29487239 TATTTTATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.39
15 19 0.61
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (15 bp):
TTGATTTCAATCAAA
Found at i:29487210 original size:20 final size:20
Alignment explanation
Indices: 29487185--29487258 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
29487175 ATATCTTGAT
29487185 TTGATTTGATTTCAATCAAA
1 TTGATTTGATTTCAATCAAA
29487205 TTGATTTTCAAATTGATTTCAATCAAA
1 TTGA---T----TTGATTTCAATCAAA
* * *
29487232 TTGATTTTATTTTATTCAAA
1 TTGATTTGATTTCAATCAAA
29487252 TTGATTT
1 TTGATTT
29487259 AAAGACTCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
20 23 0.52
23 1 0.02
24 1 0.02
27 19 0.43
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (20 bp):
TTGATTTGATTTCAATCAAA
Found at i:29487226 original size:11 final size:12
Alignment explanation
Indices: 29487200--29487239 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
29487190 TTGATTTCAA
29487200 TCAAATTGATTT
1 TCAAATTGATTT
29487212 TCAAATTGATTT
1 TCAAATTGATTT
29487224 CAATCAAATTGATTT
1 ---TCAAATTGATTT
29487239 T
1 T
29487240 ATTTTATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 13 0.52
15 12 0.48
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (12 bp):
TCAAATTGATTT
Found at i:29491909 original size:63 final size:62
Alignment explanation
Indices: 29491810--29491950 Score: 169
Period size: 63 Copynumber: 2.3 Consensus size: 62
29491800 TTTTAAGCCT
* *** * **
29491810 AAACAGTGAGTTACACAGCCTGGATACATGTTCATGTCCCT-ACCCGTGTGG-CTTTTATACCAC
1 AAACAGTGAGTTACACAGCCTGGACACATACCCATGTCCCTGA-CCGTATGGTCTCGT-T-CCAC
*
29491873 AAACAGTGAGTTACACAGCCTGGGCACATACCCATGTCCCTGACCGTATGGTCTCGTTCCAC
1 AAACAGTGAGTTACACAGCCTGGACACATACCCATGTCCCTGACCGTATGGTCTCGTTCCAC
29491935 AAACAGTGAGTTACAC
1 AAACAGTGAGTTACAC
29491951 GACCCAAACA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
62 20 0.29
63 44 0.65
64 4 0.06
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (62 bp):
AAACAGTGAGTTACACAGCCTGGACACATACCCATGTCCCTGACCGTATGGTCTCGTTCCAC
Found at i:29493388 original size:91 final size:91
Alignment explanation
Indices: 29493233--29493417 Score: 361
Period size: 91 Copynumber: 2.0 Consensus size: 91
29493223 CATGTCATAA
*
29493233 TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACTTGTAATTAATATATATTTCC
1 TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACCTGTAATTAATATATATTTCC
29493298 AACTTTCTTTGAAAATTCACTCATCT
66 AACTTTCTTTGAAAATTCACTCATCT
29493324 TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACCTGTAATTAATATATATTTCC
1 TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACCTGTAATTAATATATATTTCC
29493389 AACTTTCTTTGAAAATTCACTCATCT
66 AACTTTCTTTGAAAATTCACTCATCT
29493415 TTG
1 TTG
29493418 TACGTTGTGG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (91 bp):
TTGAATCTTGAATACATTCAAAACATCTAATAATATAAAGAAACCTGTAATTAATATATATTTCC
AACTTTCTTTGAAAATTCACTCATCT
Found at i:29496595 original size:27 final size:27
Alignment explanation
Indices: 29496548--29496600 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
29496538 ACGTGTTATA
*
29496548 AAAAAAAAGATGGAGAGAATAAAGAAC
1 AAAAAAAAGATGGAAAGAATAAAGAAC
* *
29496575 AAAAAAAATAT-GAAAGCAATAGAGAA
1 AAAAAAAAGATGGAAAG-AATAAAGAA
29496601 TGTACTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.68, C:0.04, G:0.19, T:0.09
Consensus pattern (27 bp):
AAAAAAAAGATGGAAAGAATAAAGAAC
Found at i:29496852 original size:17 final size:18
Alignment explanation
Indices: 29496830--29496873 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
29496820 GGGATTTAAA
*
29496830 TAATTAATTAAA-AATTT
1 TAATTAAGTAAATAATTT
29496847 TAATTATAGTAAATAATTT
1 TAATTA-AGTAAATAATTT
29496866 TCAATTAA
1 T-AATTAA
29496874 AATACCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 5 0.22
19 7 0.30
20 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TAATTAAGTAAATAATTT
Found at i:29497497 original size:2 final size:2
Alignment explanation
Indices: 29497490--29497527 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
29497480 TATTTTGAGC
29497490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29497528 TATTGTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29500005 original size:3 final size:3
Alignment explanation
Indices: 29499999--29500061 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
29499989 AATAGTATAG
29499999 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29500047 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
29500062 TGTGGGTGGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29502409 original size:10 final size:11
Alignment explanation
Indices: 29502381--29502414 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29502371 GATCTATCTC
29502381 TCAACAAAAATT
1 TCAA-AAAAATT
29502393 TCAAAAAAATT
1 TCAAAAAAATT
*
29502404 TCAAAATAATT
1 TCAAAAAAATT
29502415 ATTTAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (11 bp):
TCAAAAAAATT
Found at i:29508815 original size:15 final size:16
Alignment explanation
Indices: 29508795--29508824 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29508785 ATTTTCAAAT
29508795 TTAAAA-TTATTATTG
1 TTAAAATTTATTATTG
29508810 TTAAAATTTATTATT
1 TTAAAATTTATTATT
29508825 AAAAAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTAAAATTTATTATTG
Found at i:29508930 original size:16 final size:16
Alignment explanation
Indices: 29508874--29508931 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
29508864 TATTAAATTT
*
29508874 TTTAATAATTATTTATA
1 TTTAATAA-TATATATA
*
29508891 TTTAATAATATAAATA
1 TTTAATAATATATATA
* *
29508907 ATT-A-AATATATATG
1 TTTAATAATATATATA
29508921 TTTAATAATAT
1 TTTAATAATAT
29508932 TGAACACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
14 10 0.30
15 2 0.06
16 13 0.39
17 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTAATAATATATATA
Found at i:29509006 original size:17 final size:17
Alignment explanation
Indices: 29508986--29509020 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29508976 TGTTTTAAAA
29508986 ATTAAAATAAAAATATT
1 ATTAAAATAAAAATATT
* *
29509003 ATTAATATAATAATATT
1 ATTAAAATAAAAATATT
29509020 A
1 A
29509021 GGCTTAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAAATAAAAATATT
Found at i:29517040 original size:21 final size:20
Alignment explanation
Indices: 29517003--29517042 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29516993 ATTTTAAAAT
*
29517003 ATTTTTAAAATACTTTTTTG
1 ATTTTTAAAATAATTTTTTG
*
29517023 ATTTTTAAAATAAATTTTTG
1 ATTTTTAAAATAATTTTTTG
29517043 GTGTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTTAAAATAATTTTTTG
Found at i:29517049 original size:20 final size:20
Alignment explanation
Indices: 29517006--29517049 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
29516996 TTAAAATATT
** *
29517006 TTTAAAATACTTTTTTGATT
1 TTTAAAATAAATTTTTGATG
*
29517026 TTTAAAATAAATTTTTGGTG
1 TTTAAAATAAATTTTTGATG
29517046 TTTA
1 TTTA
29517050 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTAAAATAAATTTTTGATG
Found at i:29526614 original size:22 final size:22
Alignment explanation
Indices: 29526571--29526614 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
29526561 TTACCTTTAC
*
29526571 ATGCATTACATGCATTTCATAG
1 ATGCATTACATGCAATTCATAG
*
29526593 ATGCATTACCATGGAATT-ATAG
1 ATGCATTA-CATGCAATTCATAG
29526615 CTAATTCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (22 bp):
ATGCATTACATGCAATTCATAG
Found at i:29529657 original size:18 final size:19
Alignment explanation
Indices: 29529634--29529682 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
29529624 GTTGTAAAGT
*
29529634 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
29529652 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
29529671 TTTAATTTTTAT
1 TTT-ATTTTTAT
29529683 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:29529662 original size:22 final size:22
Alignment explanation
Indices: 29529633--29529682 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
29529623 AGTTGTAAAG
* *
29529633 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
29529654 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
29529677 TTTTAT
1 TTTTAT
29529683 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:29543684 original size:20 final size:20
Alignment explanation
Indices: 29543659--29543698 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29543649 AGTTAATTCG
29543659 TTATTGATCTTGACATTTAA
1 TTATTGATCTTGACATTTAA
29543679 TTATTGATCTTGACATTTAA
1 TTATTGATCTTGACATTTAA
29543699 GATTCAGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTATTGATCTTGACATTTAA
Found at i:29555120 original size:6 final size:6
Alignment explanation
Indices: 29555109--29555141 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
29555099 TATAGTAGTA
29555109 TTTATT TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTT
29555142 TTGAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:29557647 original size:30 final size:30
Alignment explanation
Indices: 29557607--29557668 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
29557597 TTTTATAAAT
*
29557607 AATTAATA-TTTAT-TACTTAAAAATATTTAC
1 AATTAATATTTTATATA-TT-AAAATATTAAC
*
29557637 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATATTTTATATATTAAAATATTAAC
29557667 AA
1 AA
29557669 CAAATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 7 0.25
32 2 0.07
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
AATTAATATTTTATATATTAAAATATTAAC
Found at i:29559718 original size:80 final size:82
Alignment explanation
Indices: 29559627--29559785 Score: 200
Period size: 82 Copynumber: 2.0 Consensus size: 82
29559617 GCATAAGCAA
** * * *
29559627 TTTTCAAAATATAACATA-AGCGGTCGCTCTCATAT-G-TGATCTTTAGAATTGCCTTTCGCC-A
1 TTTTCAAAATATAACATAGA-CGACCGCTCTCAGATAGCTGATCCTTAGAATTGCCTTTCACCAA
29559688 AACATTTAAACATAGGAGT
65 AACA-TTAAACATAGGAGT
* * *
29559707 TTTTTAAAATATAACATAGATGACCGTTCTCAGATAGCTGATCCTTAGAATTGCCTTTCACCAAA
1 TTTTCAAAATATAACATAGACGACCGCTCTCAGATAGCTGATCCTTAGAATTGCCTTTCACCAAA
29559772 ACATTAAACATAGG
66 ACATTAAACATAGG
29559786 TGATCTTCAA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
80 27 0.40
81 2 0.03
82 33 0.49
83 5 0.07
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (82 bp):
TTTTCAAAATATAACATAGACGACCGCTCTCAGATAGCTGATCCTTAGAATTGCCTTTCACCAAA
ACATTAAACATAGGAGT
Found at i:29563473 original size:244 final size:244
Alignment explanation
Indices: 29563044--29563531 Score: 949
Period size: 244 Copynumber: 2.0 Consensus size: 244
29563034 GTGAAATAGG
*
29563044 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCTAGAATTTTTAAAAATTATATATAGACAAGA
1 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
29563109 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
66 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
29563174 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
131 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
* *
29563239 TTAACATGCTGGATGCTGGGGTCCTTGCAGAGAGATGATTGTTCTAGCT
196 TTAACATGCTGGATGCTGGGGTCCATGCAAAGAGATGATTGTTCTAGCT
29563288 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
1 AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
29563353 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
66 GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
29563418 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
131 AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
29563483 TTAACATGCTGGATGCTGGGGTCCATGCAAAGAGATGATTGTTCTAGCT
196 TTAACATGCTGGATGCTGGGGTCCATGCAAAGAGATGATTGTTCTAGCT
29563532 GAACCTTTAC
Statistics
Matches: 241, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
244 241 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (244 bp):
AGAATTTACTCTGGAAGAAAGTAGAACTACAAGCAAGAATTTTTAAAAATTATATATAGACAAGA
GGGTAATCCAGGTTCTGTTCTTTCAAGCTAAGATTTGAGGTTTATTTGATTTTAAATAAAATAGT
AATCAATGATATCATGGTAAACAAATACTTCCATGACAATTTGATTTGGCATGGAATTGAATAGA
TTAACATGCTGGATGCTGGGGTCCATGCAAAGAGATGATTGTTCTAGCT
Found at i:29570947 original size:2 final size:2
Alignment explanation
Indices: 29570940--29570965 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29570930 CTATTAATTT
29570940 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
29570966 AATTCGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29576435 original size:26 final size:26
Alignment explanation
Indices: 29576406--29576458 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
29576396 TGATAAATAG
29576406 TCCAATTAAGACTAAAATGAGTTCAT
1 TCCAATTAAGACTAAAATGAGTTCAT
29576432 TCCAATTAAGACTAAAATGAGTTCAT
1 TCCAATTAAGACTAAAATGAGTTCAT
29576458 T
1 T
29576459 TAGATGGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (26 bp):
TCCAATTAAGACTAAAATGAGTTCAT
Found at i:29580463 original size:21 final size:21
Alignment explanation
Indices: 29580407--29580470 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
29580397 GCAATAATCA
29580407 AATTGCTGCTCCTGGTCAAAAT
1 AATT-CTGCTCCTGGTCAAAAT
* * *
29580429 TATTTTG-TGGCTGGTCAAAAT
1 AATTCTGCT-CCTGGTCAAAAT
*
29580450 AATTCTGCTTCTGGTCAAAAT
1 AATTCTGCTCCTGGTCAAAAT
29580471 GTGTGTGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.85
22 4 0.12
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (21 bp):
AATTCTGCTCCTGGTCAAAAT
Found at i:29581072 original size:33 final size:33
Alignment explanation
Indices: 29581030--29581094 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
29581020 ACGGGTGATG
29581030 GTACGCCTGCTATGATATCATCTGTTGGTCAAT
1 GTACGCCTGCTATGATATCATCTGTTGGTCAAT
29581063 GTACGCCTGCTATGATATCATCTGTTGGTCAA
1 GTACGCCTGCTATGATATCATCTGTTGGTCAA
29581095 GGTGTGTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (33 bp):
GTACGCCTGCTATGATATCATCTGTTGGTCAAT
Found at i:29584053 original size:7 final size:7
Alignment explanation
Indices: 29584030--29584126 Score: 83
Period size: 7 Copynumber: 14.0 Consensus size: 7
29584020 AATCAAAGTC
*
29584030 TAAATTT
1 TAAATCT
*
29584037 TAAA-CC
1 TAAATCT
*
29584043 TAAATAT
1 TAAATCT
29584050 TAAATCT
1 TAAATCT
*
29584057 TAAA-CAA
1 TAAATC-T
29584064 TAAAT-T
1 TAAATCT
29584070 ATAAATCT
1 -TAAATCT
*
29584078 TAAATAT
1 TAAATCT
*
29584085 TAAATCG
1 TAAATCT
29584092 TAAATCT
1 TAAATCT
*
29584099 TAAATAT
1 TAAATCT
*
29584106 TAAATTT
1 TAAATCT
29584113 TAAATCT
1 TAAATCT
29584120 TAAATCT
1 TAAATCT
29584127 ATTACTATTG
Statistics
Matches: 71, Mismatches: 14, Indels: 10
0.75 0.15 0.11
Matches are distributed among these distances:
6 5 0.07
7 65 0.92
8 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.40
Consensus pattern (7 bp):
TAAATCT
Found at i:29584074 original size:21 final size:21
Alignment explanation
Indices: 29584050--29584124 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
29584040 ACCTAAATAT
* *
29584050 TAAATCTTAAACAATAAATTA
1 TAAATCTTAAATATTAAATTA
**
29584071 TAAATCTTAAATATTAAATCG
1 TAAATCTTAAATATTAAATTA
*
29584092 TAAATCTTAAATATTAAATTT
1 TAAATCTTAAATATTAAATTA
29584113 TAAATCTTAAAT
1 TAAATCTTAAAT
29584125 CTATTACTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (21 bp):
TAAATCTTAAATATTAAATTA
Found at i:29585940 original size:9 final size:9
Alignment explanation
Indices: 29585926--29585955 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
29585916 GACTCAATCT
29585926 ATTATTTGA
1 ATTATTTGA
29585935 ATTATTTGA
1 ATTATTTGA
*
29585944 GTTATTTGA
1 ATTATTTGA
29585953 ATT
1 ATT
29585956 GTAAAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (9 bp):
ATTATTTGA
Found at i:29590206 original size:29 final size:29
Alignment explanation
Indices: 29590152--29590208 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
29590142 CATGTATAAT
* **
29590152 TAATAAAAATTTAATAAATTTTAAAAAAC
1 TAATAAAAATTCAATAAATTAAAAAAAAC
29590181 TAATAAAAATTCAATAAATTAAAAAAAA
1 TAATAAAAATTCAATAAATTAAAAAAAA
29590209 AATTAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (29 bp):
TAATAAAAATTCAATAAATTAAAAAAAAC
Found at i:29593705 original size:28 final size:27
Alignment explanation
Indices: 29593646--29593719 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 27
29593636 AAAAATAAAA
*
29593646 ATTTATCAAAATACTAT-AATTTTTTTT
1 ATTTACCAAAATA-TATAAATTTTTTTT
29593673 ATTTACCAAAATATATAAACTTTTTTTT
1 ATTTACCAAAATATATAAA-TTTTTTTT
29593701 ATTTACCAAAATATATAAA
1 ATTTACCAAAATATATAAA
29593720 AAAACCAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 3 0.07
27 14 0.32
28 27 0.61
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTACCAAAATATATAAATTTTTTTT
Found at i:29593739 original size:17 final size:18
Alignment explanation
Indices: 29593705--29593742 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
29593695 TTTTTTATTT
*
29593705 ACCAAAATATATAAAAAA
1 ACCAAAATATAAAAAAAA
29593723 ACCAAAAT-TAAAAAAAA
1 ACCAAAATATAAAAAAAA
29593740 ACC
1 ACC
29593743 TGACAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (18 bp):
ACCAAAATATAAAAAAAA
Found at i:29593823 original size:27 final size:27
Alignment explanation
Indices: 29593784--29593859 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
29593774 CACTGGTCAC
**
29593784 GCCAATGGTATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
29593811 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
*
29593838 GCCAATGCCATTGGCGACACCA
1 GCCAATGCCATTGGCGGCACCA
29593860 CTCGTATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAATGGT
Found at i:29594095 original size:3 final size:3
Alignment explanation
Indices: 29594077--29594150 Score: 130
Period size: 3 Copynumber: 24.3 Consensus size: 3
29594067 AAAATAAAAG
*
29594077 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29594123 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29594151 GTTGTTGTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:29594155 original size:3 final size:3
Alignment explanation
Indices: 29594149--29594186 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
29594139 ATTATTATTA
29594149 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
29594187 AGTATGAAGA
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:29598324 original size:4 final size:4
Alignment explanation
Indices: 29598317--29598400 Score: 57
Period size: 4 Copynumber: 20.0 Consensus size: 4
29598307 TCTTCCGTCC
* *
29598317 TTCT TTCT TTTT CTTC- TTCT TTCT TTCCT TT-T TTCT CTTC- TCCT TTCCTT
1 TTCT TTCT TTCT -TTCT TTCT TTCT TT-CT TTCT TTCT -TTCT TTCT TT-C-T
*
29598367 TTCT TTCT TTCCT CTCCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TT-CT -TTCT TTCT TTCT TTCT TTCT
29598401 CTCCTTCTGC
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
3 8 0.12
4 37 0.58
5 15 0.23
6 4 0.06
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTCT
Found at i:29598335 original size:16 final size:16
Alignment explanation
Indices: 29598274--29598342 Score: 66
Period size: 16 Copynumber: 4.0 Consensus size: 16
29598264 TTCTTCCCTC
29598274 TTCTTCTTCTTCTCTTT
1 TTCTTCTTCTT-TCTTT
* *
29598291 TTCTCTCTCCTTCCTTT
1 TTCT-TCTTCTTTCTTT
*
29598308 CTTCCGTCCTTCTTTCTTT
1 -TT-C-TTCTTCTTTCTTT
29598327 TTCTTCTTCTTTCTTT
1 TTCTTCTTCTTTCTTT
29598343 CCTTTTTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
16 12 0.29
17 9 0.21
18 10 0.24
19 10 0.24
20 1 0.02
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.65
Consensus pattern (16 bp):
TTCTTCTTCTTTCTTT
Found at i:29598342 original size:20 final size:19
Alignment explanation
Indices: 29598272--29598371 Score: 66
Period size: 20 Copynumber: 5.2 Consensus size: 19
29598262 CTTTCTTCCC
29598272 TCTTCTTCTTCTTCTCTTTT
1 TCTTCTTCTTCTT-TCTTTT
* *
29598292 TC-TC-TC-TCCTTC-CTT
1 TCTTCTTCTTCTTTCTTTT
*
29598307 TCTTCCGTCCTTCTTTCTTTT
1 TCTT-C-TTCTTCTTTCTTTT
29598328 TCTTCTTCTTTCTTTCCTTTT
1 TCTTCTTC-TTCTTT-CTTTT
* *
29598349 T-TCTCTTCTCCTTTCCTTT
1 TCT-TCTTCTTCTTTCTTTT
29598368 TCTT
1 TCTT
29598372 TCTTTCCTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 21
0.68 0.09 0.23
Matches are distributed among these distances:
15 4 0.06
16 3 0.05
17 4 0.06
18 2 0.03
19 11 0.18
20 21 0.34
21 17 0.27
ACGTcount: A:0.00, C:0.34, G:0.01, T:0.65
Consensus pattern (19 bp):
TCTTCTTCTTCTTTCTTTT
Found at i:29598355 original size:24 final size:24
Alignment explanation
Indices: 29598317--29598402 Score: 106
Period size: 24 Copynumber: 3.6 Consensus size: 24
29598307 TCTTCCGTCC
* *
29598317 TTCTTTCTTTTTCTTCTTCTTTCT
1 TTCTTTCTTTCTCTTCTCCTTTCT
29598341 TTCCTTT-TTTCTCTTCTCCTTTCCTT
1 TT-CTTTCTTTCTCTTCTCCTTT-C-T
29598367 TTCTTTCTTTC-C-TCTCCTTTCT
1 TTCTTTCTTTCTCTTCTCCTTTCT
29598389 TTCTTTCTTTCTCT
1 TTCTTTCTTTCTCT
29598403 CCTTCTGCCC
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
22 12 0.22
23 2 0.04
24 23 0.43
25 10 0.19
26 7 0.13
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (24 bp):
TTCTTTCTTTCTCTTCTCCTTTCT
Found at i:29598571 original size:19 final size:18
Alignment explanation
Indices: 29598536--29598575 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29598526 TTTTTTGTCA
**
29598536 GGTTTTTTTTTTAATTTT
1 GGTTTTTTTGATAATTTT
29598554 GGTTTTTTTGATATATTTT
1 GGTTTTTTTGATA-ATTTT
29598573 GGT
1 GGT
29598576 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.70
Consensus pattern (18 bp):
GGTTTTTTTGATAATTTT
Found at i:29598596 original size:28 final size:29
Alignment explanation
Indices: 29598564--29598635 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 29
29598554 GGTTTTTTTG
*
29598564 ATATATTTTGGTAAATAAAAAAAAGTT-T
1 ATATATTTTGGTAAATAAAAAAAACTTGT
**
29598592 ATATATTTTAATAAATAAAAAAAACTTGT
1 ATATATTTTGGTAAATAAAAAAAACTTGT
*
29598621 A-GTATTTTGGTAAAT
1 ATATATTTTGGTAAAT
29598636 TTTTATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 35 0.95
29 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.40
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAACTTGT
Found at i:29603975 original size:45 final size:45
Alignment explanation
Indices: 29603872--29603978 Score: 144
Period size: 46 Copynumber: 2.4 Consensus size: 45
29603862 TATGTGCCGA
*
29603872 TTACTGTTACTGTTACCAAATCGGCACTTTGTGTGTCGAAATACTG
1 TTACTGTTACTGTTA-CAAATCAGCACTTTGTGTGTCGAAATACTG
* * *
29603918 TTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTG-AATACTG
1 TTACTGTTACTGTTACA-AATCAGCACTTTGTGTGTCGAAATACTG
*
29603963 TTACTTTTACTGTTAC
1 TTACTGTTACTGTTAC
29603979 TGTTACCGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 23 0.43
46 31 0.57
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (45 bp):
TTACTGTTACTGTTACAAATCAGCACTTTGTGTGTCGAAATACTG
Found at i:29603999 original size:7 final size:6
Alignment explanation
Indices: 29603958--29604006 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
29603948 GTGTGTTGAA
* *
29603958 TACTGT TACTTT TACTGT TACTGT TACCGT TACTGAT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG-T TACTG
29604007 GTGTGTTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
6 25 0.68
7 12 0.32
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.49
Consensus pattern (6 bp):
TACTGT
Found at i:29609041 original size:16 final size:17
Alignment explanation
Indices: 29609013--29609044 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29609003 ATATAAAAAG
29609013 AAAATTGTAGTTAAATT
1 AAAATTGTAGTTAAATT
29609030 AAAATT-TAGTTAAAT
1 AAAATTGTAGTTAAAT
29609045 GTTTAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (17 bp):
AAAATTGTAGTTAAATT
Found at i:29609344 original size:12 final size:12
Alignment explanation
Indices: 29609310--29609348 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
29609300 TAAAATATAT
29609310 TAAATTTATTT-
1 TAAATTTATTTA
29609321 TATAATTT-TTTA
1 TA-AATTTATTTA
29609333 TAAATTTATTTA
1 TAAATTTATTTA
29609345 TAAA
1 TAAA
29609349 CAACATTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TAAATTTATTTA
Found at i:29614298 original size:15 final size:15
Alignment explanation
Indices: 29614278--29614308 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29614268 TTTTCAAATG
*
29614278 AACAACAATGAACAA
1 AACAACAAAGAACAA
29614293 AACAACAAAGAACAA
1 AACAACAAAGAACAA
29614308 A
1 A
29614309 GGCCCTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.19, G:0.06, T:0.03
Consensus pattern (15 bp):
AACAACAAAGAACAA
Found at i:29615660 original size:22 final size:23
Alignment explanation
Indices: 29615632--29615681 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
29615622 TTACGGAAGG
*
29615632 CTCAATGTCTCAAGACATGAA-C
1 CTCAATGTCTCAAGACATCAAGC
29615654 CTCAATGTCTCAAGACATCAAGC
1 CTCAATGTCTCAAGACATCAAGC
29615677 CTCAA
1 CTCAA
29615682 AGCTAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (23 bp):
CTCAATGTCTCAAGACATCAAGC
Found at i:29618436 original size:23 final size:24
Alignment explanation
Indices: 29618392--29618437 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
29618382 TTCAAACTCG
29618392 AGCCTAACCCATATTTTTAAACAA
1 AGCCTAACCCATATTTTTAAACAA
29618416 AGCCTAACCCATA-TTTTAAACA
1 AGCCTAACCCATATTTTTAAACA
29618438 TACATTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.28
Consensus pattern (24 bp):
AGCCTAACCCATATTTTTAAACAA
Found at i:29621032 original size:6 final size:6
Alignment explanation
Indices: 29621021--29621052 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
29621011 CATATATATC
29621021 TAGATA TAGATA TAGATA TAGATA TAGATA TA
1 TAGATA TAGATA TAGATA TAGATA TAGATA TA
29621053 ATTATAATAT
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:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
TAGATA
Found at i:29623650 original size:14 final size:16
Alignment explanation
Indices: 29623616--29623653 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
29623606 TTTCTAATAT
*
29623616 AAATTTAGCACTTATA
1 AAATTTAGCACGTATA
29623632 AAATTTAGCA-GTA-A
1 AAATTTAGCACGTATA
29623646 AAATTTAG
1 AAATTTAG
29623654 TATTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 2 0.10
16 10 0.48
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (16 bp):
AAATTTAGCACGTATA
Found at i:29624647 original size:2 final size:2
Alignment explanation
Indices: 29624640--29624676 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
29624630 TAAATATCTC
*
29624640 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29624677 CCACATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29625691 original size:27 final size:28
Alignment explanation
Indices: 29625660--29625721 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
29625650 GTAGGTGGTG
29625660 CCTATCTAG-TAGGCGCCACTA-GTGACT
1 CCTATCTAGATAGGCGCCAC-AGGTGACT
29625687 CCTATCT-GATAGGCGCCACAGGTGACT
1 CCTATCTAGATAGGCGCCACAGGTGACT
29625714 CCTATCTA
1 CCTATCTA
29625722 ATATGTGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (28 bp):
CCTATCTAGATAGGCGCCACAGGTGACT
Found at i:29626152 original size:54 final size:54
Alignment explanation
Indices: 29626094--29626264 Score: 158
Period size: 54 Copynumber: 3.2 Consensus size: 54
29626084 ATCACTAAAA
29626094 AATAACAAAGCCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATT
1 AATAACAAAGCCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATT
* * * *** * *
29626148 AATAACAAA---ATAAA-T-AACTA-TAACATTTTTTTAAAAGAAATTACATCACTAAA-A
1 AATAACAAAGCCCTAAACTAAAC-ACTAACA-ATTTGT-AACCTAA-T-C-CCA-TAAATT
29626202 AATAACAAAGCCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATT
1 AATAACAAAGCCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATT
29626256 AATAACAAA
1 AATAACAAA
29626265 ATAAATAACT
Statistics
Matches: 87, Mismatches: 16, Indels: 28
0.66 0.12 0.21
Matches are distributed among these distances:
49 8 0.09
50 6 0.07
51 8 0.09
52 1 0.01
53 5 0.06
54 31 0.36
55 5 0.06
56 1 0.01
57 8 0.09
58 6 0.07
59 8 0.09
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (54 bp):
AATAACAAAGCCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATT
Found at i:29626188 original size:108 final size:108
Alignment explanation
Indices: 29625900--29626320 Score: 623
Period size: 108 Copynumber: 4.0 Consensus size: 108
29625890 TTACAAAATA
* *
29625900 CTAAACTAAACACTAACAACTTATATAACCTAAT--CATAAATTACTAAC---A-AAATAACTAT
1 CTAAACTAAACACTAACAA-TT-TGTAACCTAATCCCATAAATTAATAACAAAATAAATAACTAT
* * * * * * *
29625959 AAAATTATTTAAAAAAAAATTACATTACTAAAAAATCACAAAACC
64 AACATTTTTTTAAAAGAAATTACATCACTAAAAAATAACAAAGCC
*
29626004 CTAAACTAAACACTAACAATTTG-----TAA-CCCATAAATTACTAACAAAATAAATAACTATAA
1 CTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTAATAACAAAATAAATAACTATAA
29626063 CATTTTTTTAAAAGAAATTACATCACTAAAAAATAACAAAGCC
66 CATTTTTTTAAAAGAAATTACATCACTAAAAAATAACAAAGCC
29626106 CTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTAATAACAAAATAAATAACTATAA
1 CTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTAATAACAAAATAAATAACTATAA
29626171 CATTTTTTTAAAAGAAATTACATCACTAAAAAATAACAAAGCC
66 CATTTTTTTAAAAGAAATTACATCACTAAAAAATAACAAAGCC
29626214 CTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTAATAACAAAATAAATAACTATAA
1 CTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTAATAACAAAATAAATAACTATAA
*
29626279 CATTTTTTTTAAAAGAAATTACATTACTAAAAAAATAACAAA
66 CA-TTTTTTTAAAAGAAATTACATCACT-AAAAAATAACAAA
29626321 ACACAAAACA
Statistics
Matches: 293, Mismatches: 10, Indels: 22
0.90 0.03 0.07
Matches are distributed among these distances:
97 3 0.01
98 14 0.05
101 1 0.00
102 72 0.25
103 2 0.01
104 19 0.06
107 3 0.01
108 142 0.48
109 24 0.08
110 13 0.04
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (108 bp):
CTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTAATAACAAAATAAATAACTATAA
CATTTTTTTAAAAGAAATTACATCACTAAAAAATAACAAAGCC
Found at i:29626226 original size:210 final size:210
Alignment explanation
Indices: 29625882--29626320 Score: 611
Period size: 210 Copynumber: 2.1 Consensus size: 210
29625872 AAATTCAATT
* *** *
29625882 TAAAAAAATTACAAAATACTAAACTAAACACTAACAACTTATATAACCTAATCATAAATTACTAA
1 TAAAAAAATAACAAAGCCCTAAACTAAACACTAACAACTTATATAACCTAATCATAAATTAATAA
* *
29625947 CAAAATAACTATAAAATTATTTAAAAAAAAATTACATTACTAAAAAATCACAAAACCCTAAACTA
66 CAAAATAACTATAAAATTATTTAAAAAAAAATTACATCACTAAAAAATAACAAAACCCTAAACTA
*
29626012 AACACTAACAATTTG-TAA-CCCATAAATTACTAACAAAATAAATAACTATAACA-TTTTTTTAA
131 AACACTAACAATTTGATAATCCCATAAATTAATAACAAAATAAATAACTATAACATTTTTTTTAA
29626074 AAGAAATTACATCAC
196 AAGAAATTACATCAC
*
29626089 T-AAAAAATAACAAAGCCCTAAACTAAACACTAACAA-TT-TGTAACCTAATCCCATAAATTAAT
1 TAAAAAAATAACAAAGCCCTAAACTAAACACTAACAACTTATATAACCTAAT--CATAAATTAAT
* * * * *
29626151 AACAAAATAAATAACTATAACATTTTTTTAAAAGAAATTACATCACTAAAAAATAACAAAGCCCT
64 AAC---A-AAATAACTATAAAATTATTTAAAAAAAAATTACATCACTAAAAAATAACAAAACCCT
29626216 AAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTAATAACAAAATAAATAACTATAACA
125 AAACTAAACACTAACAATTTG--A--TAATCCCATAAATTAATAACAAAATAAATAACTATAACA
*
29626281 TTTTTTTTAAAAGAAATTACATTAC
186 TTTTTTTTAAAAGAAATTACATCAC
29626306 TAAAAAAATAACAAA
1 TAAAAAAATAACAAA
29626321 ACACAAAACA
Statistics
Matches: 203, Mismatches: 15, Indels: 17
0.86 0.06 0.07
Matches are distributed among these distances:
204 10 0.05
205 2 0.01
206 44 0.22
207 1 0.00
209 1 0.00
210 71 0.35
215 3 0.01
216 34 0.17
217 24 0.12
218 13 0.06
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (210 bp):
TAAAAAAATAACAAAGCCCTAAACTAAACACTAACAACTTATATAACCTAATCATAAATTAATAA
CAAAATAACTATAAAATTATTTAAAAAAAAATTACATCACTAAAAAATAACAAAACCCTAAACTA
AACACTAACAATTTGATAATCCCATAAATTAATAACAAAATAAATAACTATAACATTTTTTTTAA
AAGAAATTACATCAC
Found at i:29626473 original size:72 final size:71
Alignment explanation
Indices: 29626378--29626516 Score: 269
Period size: 72 Copynumber: 1.9 Consensus size: 71
29626368 TATATTTTTA
29626378 AATTTTCATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAA
1 AATTTTCATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAA
29626443 CAAAAT
66 CAAAAT
29626449 AATTTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTA
1 AATTTT-CATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTA
29626514 ACA
65 ACA
29626517 CAACCAGTGG
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 6 0.09
72 61 0.91
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (71 bp):
AATTTTCATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAA
CAAAAT
Done.