Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 100 of 125
Found at i:30145200 original size:11 final size:11
Alignment explanation
Indices: 30145173--30145268 Score: 90
Period size: 11 Copynumber: 8.5 Consensus size: 11
30145163 CTTTGTTTAT
30145173 TTTAAACTTACAA
1 TTTAAA-TTA-AA
*
30145186 ATTAAATTTAAA
1 TTTAAA-TTAAA
30145198 -TTAAATTCAAA
1 TTTAAATT-AAA
*
30145209 CTTAAATTAAA
1 TTTAAATTAAA
30145220 TTTAAA-TAAA
1 TTTAAATTAAA
30145230 TTTAAATTTAAA
1 TTTAAA-TTAAA
30145242 -TTAAATTAAAA
1 TTTAAATT-AAA
*
30145253 TTTAAAATAAA
1 TTTAAATTAAA
30145264 TTTAA
1 TTTAA
30145269 TTTCAAAGTA
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
10 14 0.19
11 32 0.44
12 19 0.26
13 8 0.11
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:30145253 original size:17 final size:16
Alignment explanation
Indices: 30145187--30145282 Score: 104
Period size: 17 Copynumber: 5.8 Consensus size: 16
30145177 AACTTACAAA
30145187 TTAAATTTAAATTAAAT
1 TTAAA-TTAAATTAAAT
*
30145204 TCAAACTTAAATTAAAT
1 TTAAA-TTAAATTAAAT
30145221 TTAAA-TAAATTTAAAT
1 TTAAATTAAA-TTAAAT
30145237 TTAAATTAAATTAAAAT
1 TTAAATTAAATT-AAAT
* *
30145254 TTAAAATAAATTTAAT
1 TTAAATTAAATTAAAT
*
30145270 TTCAAAGTAAATT
1 TT-AAATTAAATT
30145283 CTAAAATGGT
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.06
16 18 0.26
17 47 0.68
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (16 bp):
TTAAATTAAATTAAAT
Found at i:30145281 original size:28 final size:29
Alignment explanation
Indices: 30145232--30145289 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
30145222 TAAATAAATT
*
30145232 TAAATTTAAATTAAATTAAAATT-TAAAA
1 TAAATTTAAATTAAAGTAAAATTCTAAAA
*
30145260 TAAATTTAATTTCAAAGT-AAATTCTAAAA
1 TAAATTTAAATT-AAAGTAAAATTCTAAAA
30145289 T
1 T
30145290 GGTTTGGGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAATTTAAATTAAAGTAAAATTCTAAAA
Found at i:30145664 original size:38 final size:37
Alignment explanation
Indices: 30145617--30145748 Score: 115
Period size: 38 Copynumber: 3.5 Consensus size: 37
30145607 AAACGATCTT
30145617 GCTCATACTTCAATTTCAGAGATAAAGACGTGTTATCCA
1 GCTC-TACTTCAATTTCAGAGATAAAGACGTG-TATCCA
* ** *** **
30145656 ACTCTACTTCAATTTCAAGAGGAT-GGGAAAAG-ATCTT
1 GCTCTACTTCAATTTC-AGA-GATAAAGACGTGTATCCA
30145693 GCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
1 GCTC-TACTTCAATTTCAGAGATAAAGACGTG-TATCCA
*
30145732 GCTTTACTTCAATTTCA
1 GCTCTACTTCAATTTCA
30145749 AGAGGATAGG
Statistics
Matches: 70, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
36 3 0.04
37 12 0.17
38 37 0.53
39 15 0.21
40 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (37 bp):
GCTCTACTTCAATTTCAGAGATAAAGACGTGTATCCA
Found at i:30145685 original size:76 final size:76
Alignment explanation
Indices: 30145558--30146578 Score: 1324
Period size: 76 Copynumber: 13.8 Consensus size: 76
30145548 TGCTCTTTAG
* * * *
30145558 AGAGATAAAGACTTGTTATCTAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCAT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
30145623 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
30145634 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
30145699 ACTTCAATTTC
66 ACTTCAATTTC
* *
30145710 AGAGATAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--CTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
30145773 --TT--ACTTC
66 ACTTCAATTTC
*
30145780 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
30145839 ACTTCAATTTC
66 ACTTCAATTTC
* * * **
30145850 AGAGATAAAGACTTGGTATCCAGCTTTAATTCAATTTCAAGAGGATGGGAAACTATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
30145915 ATTTCAATTTC
66 ACTTCAATTTC
* *
30145926 AGAGATAAAGACTTGTTATCCAGCCTTACTTCAATTTCAAGAGGATAGGAAAAGATGTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
30145991 ACTTCAATTTC
66 ACTTCAATTTC
* * * **
30146002 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATGGGCAACTATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
30146067 ACTTCAATTTC
66 ACTTCAATTTC
* *
30146078 AGAGATAAAGACTTGATATCCAGCCTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
30146143 ACATCAATTTC
66 ACTTCAATTTC
* *
30146154 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAATAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
30146219 ACTTTAATTTC
66 ACTTCAATTTC
* * **
30146230 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATGGGAAACTATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
30146295 ACTTCAATTTC
66 ACTTCAATTTC
* * * * * * *
30146306 AGAGATAAAGACTTGTTATCCAACTTTACTCCCATTTCAAGAGGATAGGGAATGATGTTGTTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
30146371 ACTTCAATTTT
66 ACTTCAATTTC
* * * * * *
30146382 AGAGATAATGACTCGTTTATCCAACTCTACTTCAATTTCAAGCGGAT-------GACCTTGCTCT
1 AGAGATAAAGACTTG-TTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCT
30146440 TACTTCAATTTC
65 TACTTCAATTTC
* * *
30146452 AGAGATAAAGACATGTTATCCA-CTCTACTTCAATTTCAAGAGGAT--G--ACG---TTGCTCTT
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
30146509 ACTTCAGTTTC
66 ACTTCAATTTC
* * * *
30146520 AGAGATGAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTG
1 AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
30146579 GTGTGGTCTG
Statistics
Matches: 843, Mismatches: 79, Indels: 47
0.87 0.08 0.05
Matches are distributed among these distances:
64 53 0.06
66 3 0.00
68 84 0.10
69 7 0.01
70 40 0.05
71 1 0.00
72 4 0.00
74 3 0.00
75 3 0.00
76 618 0.73
77 27 0.03
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:30146497 original size:68 final size:67
Alignment explanation
Indices: 30146367--30146564 Score: 297
Period size: 68 Copynumber: 2.9 Consensus size: 67
30146357 ATGATGTTGT
* *
30146367 TCTTACTTCAATTTTAGAGATAATGACTCGTTTATCCAACTCTACTTCAATTTCAAGCGGATGAC
1 TCTTACTTCAATTTCAGAGATAAAGACT-G-TTATCC-ACTCTACTTCAATTTCAAGCGGATGAC
30146432 CTTGC
63 CTTGC
* *
30146437 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGT
1 TCTTACTTCAATTTCAGAGATAAAGAC-TGTTATCCACTCTACTTCAATTTCAAGCGGATGACCT
30146502 TGC
65 TGC
* *
30146505 TCTTACTTCAGTTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGCGGAT
1 TCTTACTTCAATTTCAGAGATAAAGAC-TGTTATCCACTCTACTTCAATTTCAAGCGGAT
30146565 AGGAAAAGAT
Statistics
Matches: 119, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
68 86 0.72
69 6 0.05
70 26 0.22
71 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (67 bp):
TCTTACTTCAATTTCAGAGATAAAGACTGTTATCCACTCTACTTCAATTTCAAGCGGATGACCTT
GC
Found at i:30146520 original size:31 final size:31
Alignment explanation
Indices: 30146409--30146527 Score: 98
Period size: 31 Copynumber: 3.7 Consensus size: 31
30146399 TATCCAACTC
* *
30146409 TACTTCAATTTCAAGCGGATGACCTTGCTCT
1 TACTTCAATTTCAAGAGGATGACGTTGCTCT
** * * *
30146440 TACTTCAATTTCAGAGATAAAGACATGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT
30146476 CTACTTCAATTTCAAGAGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACGTTGCTCT
*
30146508 TACTTCAGTTTC-AGA-GATGA
1 TACTTCAATTTCAAGAGGATGA
30146528 AGACGTGTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
29 5 0.07
30 3 0.04
31 24 0.35
32 10 0.14
33 1 0.01
34 1 0.01
35 1 0.01
36 11 0.16
37 13 0.19
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (31 bp):
TACTTCAATTTCAAGAGGATGACGTTGCTCT
Found at i:30158707 original size:29 final size:29
Alignment explanation
Indices: 30158673--30158766 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
30158663 GTGAAATGGT
*
30158673 AATTTTGGTATAATCGGGGTTAAAAATGA
1 AATTTTGGTAAAATCGGGGTTAAAAATGA
* ** *
30158702 AATTTTAG-AAGGTTCGGGGGT-AAAATGGTA
1 AATTTTGGTAA-AATCGGGGTTAAAAAT-G-A
* * *
30158732 ATTTTTGGTAAAATCGAGGTTAAAAATGG
1 AATTTTGGTAAAATCGGGGTTAAAAATGA
30158761 AATTTT
1 AATTTT
30158767 AGAAGGTTCG
Statistics
Matches: 47, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
28 6 0.13
29 20 0.43
30 14 0.30
31 7 0.15
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AATTTTGGTAAAATCGGGGTTAAAAATGA
Found at i:30158722 original size:30 final size:29
Alignment explanation
Indices: 30158686--30158844 Score: 81
Period size: 29 Copynumber: 5.4 Consensus size: 29
30158676 TTTGGTATAA
*
30158686 TCGGGGTTAAAAATGAAATTTTAGAAGGT
1 TCGGGGGTAAAAATGAAATTTTAGAAGGT
* * **
30158715 TCGGGGGT-AAAATGGTAATTTTTGGTAA-AA
1 TCGGGGGTAAAAAT-G-AAATTTTAG-AAGGT
* * *
30158745 TCGAGGTTAAAAATGGAATTTTAGAAGGT
1 TCGGGGGTAAAAATGAAATTTTAGAAGGT
* * * ** **
30158774 TCGAGGGT-AAAATGGTAATTTTTGGTGAAA
1 TCGGGGGTAAAAAT-GAAATTTTAGAAG-GT
* * *
30158804 TCGAGGTTAAAAATGGAATTTTAGAAGGT
1 TCGGGGGTAAAAATGAAATTTTAGAAGGT
*
30158833 TTGGGGGTAAAA
1 TCGGGGGTAAAA
30158845 TGGTAATTTT
Statistics
Matches: 93, Mismatches: 29, Indels: 16
0.67 0.21 0.12
Matches are distributed among these distances:
28 12 0.13
29 39 0.42
30 30 0.32
31 12 0.13
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.31
Consensus pattern (29 bp):
TCGGGGGTAAAAATGAAATTTTAGAAGGT
Found at i:30158753 original size:59 final size:58
Alignment explanation
Indices: 30158660--30158872 Score: 318
Period size: 59 Copynumber: 3.6 Consensus size: 58
30158650 TTGGATACCC
* * * *
30158660 GGGGTGAAATGGTAATTTTGGTATAATCGGGGTTAAAAATGAAATTTTAGAAGGTTCG
1 GGGGTAAAATGGTAATTTTGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTCG
30158718 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTCG
1 GGGGTAAAATGGTAA-TTTTGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTCG
* * *
30158777 AGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTTG
1 GGGGTAAAATGGTAA-TTTTGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTCG
* * *
30158836 GGGGTAAAATGGTAATTTTGGTGAAATAGGGGTTAAA
1 GGGGTAAAATGGTAATTTTGGTAAAATCGAGGTTAAA
30158873 TGTAATTTCC
Statistics
Matches: 144, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
58 34 0.24
59 110 0.76
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTCG
Found at i:30158778 original size:29 final size:29
Alignment explanation
Indices: 30158690--30158833 Score: 114
Period size: 30 Copynumber: 4.9 Consensus size: 29
30158680 GTATAATCGG
* *
30158690 GGTTAAAAATGAAATTTTAGAAGGTTCGG
1 GGTTAAAAATGGAATTTTAGAAGGTTCGA
* * **
30158719 GGGT-AAAATGGTAATTTTTGGTAA-AATCGA
1 GGTTAAAAATGG-AA-TTTTAG-AAGGTTCGA
30158749 GGTTAAAAATGGAATTTTAGAAGGTTCGA
1 GGTTAAAAATGGAATTTTAGAAGGTTCGA
* * ** **
30158778 GGGT-AAAATGGTAATTTTTGGTGAAATCGA
1 GGTTAAAAATGG-AATTTTAGAAG-GTTCGA
30158808 GGTTAAAAATGGAATTTTAGAAGGTT
1 GGTTAAAAATGGAATTTTAGAAGGTT
30158834 TGGGGGTAAA
Statistics
Matches: 85, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
28 15 0.18
29 26 0.31
30 28 0.33
31 16 0.19
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.33
Consensus pattern (29 bp):
GGTTAAAAATGGAATTTTAGAAGGTTCGA
Found at i:30158844 original size:29 final size:29
Alignment explanation
Indices: 30158702--30158854 Score: 123
Period size: 29 Copynumber: 5.2 Consensus size: 29
30158692 TTAAAAATGA
*
30158702 AATTTTAGAAGGTTCGGGGGTAAAATGGT
1 AATTTTAGAAGGTTCGAGGGTAAAATGGT
* ** *
30158731 AATTTTTGGTAA-AATCGAGGTTAAAAATGG-
1 AA-TTTTAG-AAGGTTCGAGGGT-AAAATGGT
30158761 AATTTTAGAAGGTTCGAGGGTAAAATGGT
1 AATTTTAGAAGGTTCGAGGGTAAAATGGT
* ** ** *
30158790 AATTTTTGGTGAAATCGAGGTTAAAAATGG-
1 AATTTTAGAAG-GTTCGAGGGT-AAAATGGT
* *
30158820 AATTTTAGAAGGTTTGGGGGTAAAATGGT
1 AATTTTAGAAGGTTCGAGGGTAAAATGGT
30158849 AATTTT
1 AATTTT
30158855 GGTGAAATAG
Statistics
Matches: 93, Mismatches: 23, Indels: 16
0.70 0.17 0.12
Matches are distributed among these distances:
28 16 0.17
29 33 0.35
30 28 0.30
31 16 0.17
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
AATTTTAGAAGGTTCGAGGGTAAAATGGT
Found at i:30158867 original size:29 final size:29
Alignment explanation
Indices: 30158778--30158880 Score: 72
Period size: 28 Copynumber: 3.6 Consensus size: 29
30158768 GAAGGTTCGA
* *
30158778 GGGTAAAATGGTAATTTTTGGTGAAATCGA
1 GGGTAAAATGGTAA-TTTTGGTGAAATAGG
* * * *
30158808 GGTTAAAAATGG-AATTTT--AGAAGGTTTGG
1 GGGT-AAAATGGTAATTTTGGTGAA--ATAGG
30158837 GGGTAAAATGGTAATTTTGGTGAAATA-G
1 GGGTAAAATGGTAATTTTGGTGAAATAGG
*
30158865 GGGTTAAAT-GTAATTT
1 GGGTAAAATGGTAATTT
30158881 CCTAAAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
27 10 0.18
28 16 0.28
29 16 0.28
30 5 0.09
31 10 0.18
ACGTcount: A:0.34, C:0.01, G:0.30, T:0.35
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTGGTGAAATAGG
Found at i:30159056 original size:15 final size:15
Alignment explanation
Indices: 30159031--30159065 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
30159021 TGTAATTAAA
30159031 TAAAA-GTAATTTCC
1 TAAAATGTAATTTCC
30159045 TAAAATGTAATTTCC
1 TAAAATGTAATTTCC
30159060 TAAAAT
1 TAAAAT
30159066 TTTACGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (15 bp):
TAAAATGTAATTTCC
Found at i:30159166 original size:177 final size:177
Alignment explanation
Indices: 30158870--30159214 Score: 645
Period size: 177 Copynumber: 1.9 Consensus size: 177
30158860 AATAGGGGTT
* *
30158870 AAATGTAATTTCCTAAAATTTTAGGGTTAAAATGTAATTTTCGGACTGTTTGGGGACCTATACCA
1 AAATGTAATTTCCTAAAATTTTACGGTCAAAATGTAATTTTCGGACTGTTTGGGGACCTATACCA
* * *
30158935 AAGAGTGGGTGACACGTGGCAGCCCCACAGGCATCCAACAGTGAAGGGATTAAATTGTAAATCTT
66 AAGAGTGGGTGACACGTGGCAACCCCACAAGCATCCAACAGTCAAGGGATTAAATTGTAAATCTT
30159000 GAAAAATTCTTGGGCTAATTTTGTAATTAAATAAAAGTAATTTCCTA
131 GAAAAATTCTTGGGCTAATTTTGTAATTAAATAAAAGTAATTTCCTA
30159047 AAATGTAATTTCCTAAAATTTTACGGTCAAAATGTAATTTTCGGACTGTTTGGGGACCTATACCA
1 AAATGTAATTTCCTAAAATTTTACGGTCAAAATGTAATTTTCGGACTGTTTGGGGACCTATACCA
30159112 AAGAGTGGGTGACACGTGGCAACCCCACAAGCATCCAACAGTCAAGGGATTAAATTGTAAATCTT
66 AAGAGTGGGTGACACGTGGCAACCCCACAAGCATCCAACAGTCAAGGGATTAAATTGTAAATCTT
30159177 GAAAAATTCTTGGGCTAATTTTGTAATTAAATAAAAGT
131 GAAAAATTCTTGGGCTAATTTTGTAATTAAATAAAAGT
30159215 TGATTTAGGG
Statistics
Matches: 163, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
177 163 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (177 bp):
AAATGTAATTTCCTAAAATTTTACGGTCAAAATGTAATTTTCGGACTGTTTGGGGACCTATACCA
AAGAGTGGGTGACACGTGGCAACCCCACAAGCATCCAACAGTCAAGGGATTAAATTGTAAATCTT
GAAAAATTCTTGGGCTAATTTTGTAATTAAATAAAAGTAATTTCCTA
Found at i:30159342 original size:162 final size:161
Alignment explanation
Indices: 30159169--30159480 Score: 527
Period size: 162 Copynumber: 1.9 Consensus size: 161
30159159 GATTAAATTG
* * * *
30159169 TAAATCTTGAAAAATTCTTGGGCTAATTTTGTAATTAAATAAAAGTTGATTTA-GGGATTAAATT
1 TAAACCTTGAAAAATTCTCGGGCCAATTTTATAATTAAATAAAAGTTGATTTAGGGGA-TAAATT
*
30159233 AAAACAAATTAAACATGTCAGGGACTAAATGCATAAATAAGCCAAAAAGTGACACGTGGCAGCCC
65 AAAACAAATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAAA-TGACACGTGGCAGCCC
*
30159298 CTGGTGCAGTCAAACAGTCAAAAGACTGATTTA
129 CTGGTGCAGTCAAACAATCAAAAGACTGATTTA
30159331 TAAACCTTGAAAAATTCTCGGGCCAATTTTATAATTAAATAAAAGTTGATTTAGGGGATAAATTA
1 TAAACCTTGAAAAATTCTCGGGCCAATTTTATAATTAAATAAAAGTTGATTTAGGGGATAAATTA
* *
30159396 AAACAAATTAAAAATGTCAGGGACTACATGCATAAATAAGCCAAAAATGACACGTGGCAGCCTCT
66 AAACAAATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAAATGACACGTGGCAGCCCCT
30159461 GGTGCAGTCAAACAATCAAA
131 GGTGCAGTCAAACAATCAAA
30159481 GGATTAAATT
Statistics
Matches: 141, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
161 36 0.26
162 101 0.72
163 4 0.03
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (161 bp):
TAAACCTTGAAAAATTCTCGGGCCAATTTTATAATTAAATAAAAGTTGATTTAGGGGATAAATTA
AAACAAATTAAAAATGTCAGGGACTAAATGCATAAATAAGCCAAAAATGACACGTGGCAGCCCCT
GGTGCAGTCAAACAATCAAAAGACTGATTTA
Found at i:30161059 original size:5 final size:5
Alignment explanation
Indices: 30161051--30161103 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
30161041 TTAAACTTAC
30161051 AAATT AAATTT AAATT AAATT CAAACTT AAATT AAATTT AAA-T AAATT
1 AAATT AAA-TT AAATT AAATT -AAA-TT AAATT AAA-TT AAATT AAATT
*
30161099 TAATT
1 AAATT
30161104 TCAAAGTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
4 4 0.10
5 20 0.48
6 16 0.38
7 2 0.05
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:30161065 original size:6 final size:6
Alignment explanation
Indices: 30161040--30161101 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
30161030 CTTTGTTTAT
* * * *
30161040 TTTAAA CTTACAA ATTAAA TTTAAA -TTAAA TTCAAA CTTAAA -TTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
30161087 TTTAAA --TAAA TTTAA
1 TTTAAA TTTAAA TTTAA
30161102 TTTCAAAGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.09
5 10 0.22
6 26 0.58
7 5 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:30161082 original size:17 final size:16
Alignment explanation
Indices: 30161051--30161088 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
30161041 TTAAACTTAC
*
30161051 AAATTAAATTTAAATT
1 AAATTAAACTTAAATT
30161067 AAATTCAAACTTAAATT
1 AAATT-AAACTTAAATT
30161084 AAATT
1 AAATT
30161089 TAAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTAAACTTAAATT
Found at i:30161098 original size:10 final size:11
Alignment explanation
Indices: 30161040--30161101 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
30161030 CTTTGTTTAT
30161040 TTTAAACTTACAA
1 TTTAAA-TTA-AA
*
30161053 ATTAAATTTAAA
1 TTTAAA-TTAAA
30161065 -TTAAATTCAAA
1 TTTAAATT-AAA
*
30161076 CTTAAATTAAA
1 TTTAAATTAAA
30161087 TTTAAA-TAAA
1 TTTAAATTAAA
30161097 TTTAA
1 TTTAA
30161102 TTTCAAAGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
10 11 0.25
11 16 0.36
12 9 0.20
13 8 0.18
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:30161497 original size:38 final size:37
Alignment explanation
Indices: 30161450--30161581 Score: 115
Period size: 38 Copynumber: 3.5 Consensus size: 37
30161440 AAACGATTTT
30161450 GCTCATACTTCAATTTCAGAGATAAAGACGTGTTATCCA
1 GCTC-TACTTCAATTTCAGAGATAAAGACGTG-TATCCA
* ** *** **
30161489 ACTCTACTTCAATTTCAAGAGGAT-GGGAAAAG-ATCTT
1 GCTCTACTTCAATTTC-AGA-GATAAAGACGTGTATCCA
30161526 GCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
1 GCTC-TACTTCAATTTCAGAGATAAAGACGTG-TATCCA
*
30161565 GCTTTACTTCAATTTCA
1 GCTCTACTTCAATTTCA
30161582 AGAGGATAGG
Statistics
Matches: 70, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
36 3 0.04
37 12 0.17
38 37 0.53
39 15 0.21
40 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (37 bp):
GCTCTACTTCAATTTCAGAGATAAAGACGTGTATCCA
Found at i:30161518 original size:76 final size:76
Alignment explanation
Indices: 30161391--30162183 Score: 931
Period size: 76 Copynumber: 10.8 Consensus size: 76
30161381 TGCTCTTTAG
* * * *
30161391 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGATGATAGGAAACGATTTTGCTCAT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
30161456 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
30161467 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
30161532 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
30161543 AGAGATAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--CTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
*
30161606 --TT--ACTTC
66 ACTTCAATTTC
** * * *
30161613 ------AAAGACTTAATATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
30161672 ACTTCAATTTC
66 ACTTCAATTTC
* * * * *
30161683 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAATAGGATGGGAAACTATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
30161748 ACTTCAATTTC
66 ACTTCAATTTC
* * *
30161759 AGAGATAAAGACTTGTTATCCAGCCTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
30161824 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
30161835 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATGGGAAACTATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
30161900 ACTTCAATTTC
66 ACTTCAATTTC
* * * * * * *
30161911 AGAGATAAAGACTTGTTATCCAACTTTACTCCCATTTCAAGAGGAAAGGGAATGATGTTGTTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
30161976 ACTTCAATTTC
66 ACTTCAATTTC
* * * * *
30161987 AAAGATAACGACTCGTGTATCCAACTCTACTTCAATTTCAAGCGGAT--G--AC---CTTGCTCT
1 AGAGATAAAGACTTGT-TATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCT
30162045 TACTTCAATTTC
65 TACTTCAATTTC
** *
30162057 AGAGATAAAGACAGGTTATCC-ACTCTACTTCAATTTCAAGAGGAT-GG---CG---TTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
30162114 ACTTCAATTTC
66 ACTTCAATTTC
* * * * *
30162125 AGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTG
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTG
30162184 GTGTGGTCTG
Statistics
Matches: 629, Mismatches: 66, Indels: 45
0.85 0.09 0.06
Matches are distributed among these distances:
64 51 0.08
66 3 0.00
68 86 0.14
69 8 0.01
70 38 0.06
72 3 0.00
73 1 0.00
74 3 0.00
75 4 0.01
76 407 0.65
77 25 0.04
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
ACTTCAATTTC
Found at i:30161609 original size:38 final size:38
Alignment explanation
Indices: 30161493--30161911 Score: 229
Period size: 38 Copynumber: 11.3 Consensus size: 38
30161483 TATCCAACTC
* *
30161493 TACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAGGAAAATATCTTGCTCT
* ** **
30161531 TACTTCAATTTC-AGA-GATAAAGACGTGATATCCAGCT-T
1 TACTTCAATTTCAAGAGGAT-AGGA--AAATATCTTGCTCT
* *
30161569 TACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTT
1 TACTTCAATTTCAAGAGGATAGGAAAATATCTTGCTCT
* * **
30161607 TACTTC-A----AAGA--CT----TAATATCCAGCT-T
1 TACTTCAATTTCAAGAGGATAGGAAAATATCTTGCTCT
* *
30161633 TACTTCAATTTCAAGAGAATAGGAAAAGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAGGAAAATATCTTGCTCT
* ** **
30161671 TACTTCAATTTC-AGA-GATAAAGACTTGATATCCAGCT-T
1 TACTTCAATTTCAAGAGGAT-AGGA--AAATATCTTGCTCT
* * *
30161709 TACTTCAATTTCAATAGGATGGGAAACTATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAGGAAAATATCTTGCTCT
* *** **
30161747 TACTTCAATTTC-AGA-GATAAAGACTTGTTATCCAGC-CT
1 TACTTCAATTTCAAGAGGAT-AGGA--AAATATCTTGCTCT
*
30161785 TACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAGGAAAATATCTTGCTCT
* ** **
30161823 TACTTCAATTTC-AGA-GATAAAGACTTGATATCCAGCT-T
1 TACTTCAATTTCAAGAGGAT-AGGA--AAATATCTTGCTCT
* *
30161861 TACTTCAATTTCAAGAGGATGGGAAACTATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAGGAAAATATCTTGCTCT
30161899 TACTTCAATTTCA
1 TACTTCAATTTCA
30161912 GAGATAAAGA
Statistics
Matches: 279, Mismatches: 66, Indels: 72
0.67 0.16 0.17
Matches are distributed among these distances:
26 7 0.03
27 9 0.03
31 5 0.02
33 5 0.02
36 11 0.04
37 56 0.20
38 126 0.45
39 48 0.17
40 12 0.04
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (38 bp):
TACTTCAATTTCAAGAGGATAGGAAAATATCTTGCTCT
Found at i:30161655 original size:64 final size:64
Alignment explanation
Indices: 30161549--30161678 Score: 224
Period size: 64 Copynumber: 2.0 Consensus size: 64
30161539 TTTCAGAGAT
* * *
30161549 AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTTACTTC
1 AAAGACGTAATATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAAGATCTTGCTCTTACTTC
*
30161613 AAAGACTTAATATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAAGATCTTGCTCTTACTTC
1 AAAGACGTAATATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAAGATCTTGCTCTTACTTC
30161677 AA
1 AA
30161679 TTTCAGAGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (64 bp):
AAAGACGTAATATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAAGATCTTGCTCTTACTTC
Found at i:30161940 original size:38 final size:37
Alignment explanation
Indices: 30161613--30161949 Score: 185
Period size: 38 Copynumber: 8.9 Consensus size: 37
30161603 CTTTTACTTC
*
30161613 AAAGACTTAATATCCAGCTTTACTTCAATTTCAAGAGA-
1 AAAGACTT-GTATCCAGCTTTACTTCAATTTC-AGAGAT
* *** **
30161651 ATAGGAAAAG-ATCTTGCTCTTACTTCAATTTCAGAGAT
1 A-AAGACTTGTATCCAGCT-TTACTTCAATTTCAGAGAT
*
30161689 AAAGACTTGATATCCAGCTTTACTTCAATTTCAATAGGAT
1 AAAGACTTG-TATCCAGCTTTACTTCAATTTC-AGA-GAT
* **
30161729 GGGAA-AC---TATCTTGCTCTTACTTCAATTTCAGAGAT
1 --AAAGACTTGTATCCAGCT-TTACTTCAATTTCAGAGAT
*
30161765 AAAGACTTGTTATCCAGCCTTACTTCAATTTCAAGAGGAT
1 AAAGACTTG-TATCCAGCTTTACTTCAATTTC-AGA-GAT
* *** **
30161805 -AGGAAAAG-ATCTTGCTCTTACTTCAATTTCAGAGAT
1 AAAGACTTGTATCCAGCT-TTACTTCAATTTCAGAGAT
30161841 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGAT
1 AAAGACTTG-TATCCAGCTTTACTTCAATTTC-AGA-GAT
* **
30161881 GGGAA-AC---TATCTTGCTCTTACTTCAATTTCAGAGAT
1 --AAAGACTTGTATCCAGCT-TTACTTCAATTTCAGAGAT
* * *
30161917 AAAGACTTGTTATCCAACTTTACTCCCATTTCA
1 AAAGACTTG-TATCCAGCTTTACTTCAATTTCA
30161950 AGAGGAAAGG
Statistics
Matches: 224, Mismatches: 44, Indels: 62
0.68 0.13 0.19
Matches are distributed among these distances:
34 4 0.02
35 4 0.02
36 9 0.04
37 46 0.21
38 105 0.47
39 39 0.17
40 9 0.04
41 4 0.02
42 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (37 bp):
AAAGACTTGTATCCAGCTTTACTTCAATTTCAGAGAT
Found at i:30162102 original size:68 final size:67
Alignment explanation
Indices: 30161972--30162169 Score: 288
Period size: 68 Copynumber: 2.9 Consensus size: 67
30161962 ATGATGTTGT
* * *
30161972 TCTTACTTCAATTTCAAAGATAACGACTCGTGTATCCAACTCTACTTCAATTTCAAGCGGATGAC
1 TCTTACTTCAATTTCAGAGATAAAGAC-GGT-TATCC-ACTCTACTTCAATTTCAAGCGGATGAC
30162037 CTTGC
63 CTTGC
* * *
30162042 TCTTACTTCAATTTCAGAGATAAAGACAGGTTATCCACTCTACTTCAATTTCAAGAGGATGGCGT
1 TCTTACTTCAATTTCAGAGATAAAGAC-GGTTATCCACTCTACTTCAATTTCAAGCGGATGACCT
30162107 TGC
65 TGC
*
30162110 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGCGGAT
1 TCTTACTTCAATTTCAGAGATAAAGACG-GTTATCCACTCTACTTCAATTTCAAGCGGAT
30162170 AGGAAAAGAT
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
67 1 0.01
68 85 0.72
69 5 0.04
70 27 0.23
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (67 bp):
TCTTACTTCAATTTCAGAGATAAAGACGGTTATCCACTCTACTTCAATTTCAAGCGGATGACCTT
GC
Found at i:30162120 original size:31 final size:31
Alignment explanation
Indices: 30162014--30162132 Score: 98
Period size: 31 Copynumber: 3.7 Consensus size: 31
30162004 TATCCAACTC
* *
30162014 TACTTCAATTTCAAGCGGATGACCTTGCTCT
1 TACTTCAATTTCAAGAGGATGACGTTGCTCT
** * * *
30162045 TACTTCAATTTCAGAGATAAAGACAGGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT
*
30162081 CTACTTCAATTTCAAGAGGATGGCGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACGTTGCTCT
30162113 TACTTCAATTTC-AGA-GATGA
1 TACTTCAATTTCAAGAGGATGA
30162133 AGACGTGTTA
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
29 4 0.06
30 3 0.04
31 25 0.37
32 10 0.15
33 1 0.01
34 1 0.01
35 1 0.01
36 10 0.15
37 13 0.19
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (31 bp):
TACTTCAATTTCAAGAGGATGACGTTGCTCT
Found at i:30165870 original size:41 final size:41
Alignment explanation
Indices: 30165807--30165884 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
30165797 GACTCAGACA
30165807 CAAGACCAGAAGGTATAGAGAAGCTTAACCATTGAACCACT
1 CAAGACCAGAAGGTATAGAGAAGCTTAACCATTGAACCACT
30165848 CAAGACCAGAAGGTAT-GTAGAAGCTTAACCATTGAAC
1 CAAGACCAGAAGGTATAG-AGAAGCTTAACCATTGAAC
30165885 TACTAAGCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (41 bp):
CAAGACCAGAAGGTATAGAGAAGCTTAACCATTGAACCACT
Found at i:30166683 original size:2 final size:2
Alignment explanation
Indices: 30166670--30166731 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
30166660 TGTTTTTATC
*
30166670 AT AT AC 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 AT AT
30166712 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
30166732 GAAATTGTAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30170825 original size:29 final size:29
Alignment explanation
Indices: 30170783--30170849 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
30170773 CACAACAACA
*
30170783 ATATTATTTGATTCTATCAACAGCTTCCG
1 ATATTATATGATTCTATCAACAGCTTCCG
30170812 ATATTATATGATTCTATCAACAGCTTCCG
1 ATATTATATGATTCTATCAACAGCTTCCG
30170841 ATATTATAT
1 ATATTATAT
30170850 TGGATCTGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (29 bp):
ATATTATATGATTCTATCAACAGCTTCCG
Found at i:30173976 original size:82 final size:81
Alignment explanation
Indices: 30173681--30173973 Score: 347
Period size: 81 Copynumber: 3.6 Consensus size: 81
30173671 TAAAAAATAA
* * * * *
30173681 AATTGAATAAATATGTTTCAAGATTTATTCCT-ACTATTCAACAAATTTTATTCTATTTTGATTT
1 AATTGAATAAATCTGTTTCAGGATTTATTCTTGTC-GTTCAACAAATTTTATTCTATTTTGATTT
*
30173745 GTTTCCAAACAATAATT
65 GTTTCCAAACAAGAATT
* * * **
30173762 AATTGAATAAATCTGTTTCGGGATTTATTCCTGTCCTTCAACCGATTTTATTCTATTTTGATTTG
1 AATTGAATAAATCTGTTTCAGGATTTATTCTTGTCGTTCAACAAATTTTATTCTATTTTGATTTG
30173827 TTTCCAAACAAGAATT
66 TTTCCAAACAAGAATT
* * * *
30173843 ATTTGAATAAATCTGTTT-TGGAATTTATTCTTGCCGTTCAACAAATTTTATTCCATTTTGATTT
1 AATTGAATAAATCTGTTTCAGG-ATTTATTCTTGTCGTTCAACAAATTTTATTCTATTTTGA-TT
* *
30173907 TGTTTCCAAACTAGAAAT
64 TGTTTCCAAACAAGAATT
* * * *
30173925 AATTAAATAATTCTGTTTCAGGATTTAATATTGTCGTTCAACAGAATTT
1 AATTGAATAAATCTGTTTCAGGATTTATTCTTGTCGTTCAACA-AATTT
30173974 ATTTTGATTT
Statistics
Matches: 182, Mismatches: 25, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
80 2 0.01
81 121 0.66
82 52 0.29
83 7 0.04
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.45
Consensus pattern (81 bp):
AATTGAATAAATCTGTTTCAGGATTTATTCTTGTCGTTCAACAAATTTTATTCTATTTTGATTTG
TTTCCAAACAAGAATT
Found at i:30176637 original size:32 final size:33
Alignment explanation
Indices: 30176601--30176666 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
30176591 ATCGAAATAA
*
30176601 AATAG-AAGTGATAACTATACATTTAAAA-AATT
1 AATAGTAA-TGATAACTACACATTTAAAATAATT
* *
30176633 AATAGTTATGATAATTACACATTTAAAATAATT
1 AATAGTAATGATAACTACACATTTAAAATAATT
30176666 A
1 A
30176667 TAATTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 23 0.79
33 6 0.21
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.35
Consensus pattern (33 bp):
AATAGTAATGATAACTACACATTTAAAATAATT
Found at i:30176674 original size:16 final size:17
Alignment explanation
Indices: 30176643--30176675 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30176633 AATAGTTATG
30176643 ATAATTACACATTTAAA
1 ATAATTACACATTTAAA
*
30176660 ATAATTATA-ATTTAAA
1 ATAATTACACATTTAAA
30176676 TTACAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATTACACATTTAAA
Found at i:30176680 original size:29 final size:32
Alignment explanation
Indices: 30176609--30176671 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
30176599 AAAATAGAAG
* * *
30176609 TGATAACTATACATTTAAAAAATTAATAGTTA
1 TGATAATTACACATTTAAAAAATTAATAATTA
30176641 TGATAATTACACATTTAAAATAATT-ATAATT
1 TGATAATTACACATTTAAAA-AATTAATAATT
30176672 TAAATTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (32 bp):
TGATAATTACACATTTAAAAAATTAATAATTA
Found at i:30176917 original size:23 final size:27
Alignment explanation
Indices: 30176870--30176921 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
30176860 TTATGAGCAT
30176870 ATTAATTATCACTTAATTAATATTATA
1 ATTAATTATCACTTAATTAATATTATA
30176897 ATTAATTAT-A-TTAATTAATTATTAT
1 ATTAATTATCACTTAATTAA-TATTAT
30176922 TATGAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 8 0.33
26 7 0.29
27 9 0.38
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTAATTATCACTTAATTAATATTATA
Found at i:30176933 original size:26 final size:25
Alignment explanation
Indices: 30176882--30176935 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
30176872 TAATTATCAC
* *
30176882 TTAATTAATATTATAATTAATTATA
1 TTAATTAATATTATAATGAATAATA
*
30176907 TTAATTAATTATTATTATGAATAATA
1 TTAATTAA-TATTATAATGAATAATA
30176933 TTA
1 TTA
30176936 CTTTTCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTAATTAATATTATAATGAATAATA
Found at i:30178189 original size:14 final size:13
Alignment explanation
Indices: 30178166--30178195 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
30178156 GCAGTGAAAT
30178166 GGGTGGGGGGTGG
1 GGGTGGGGGGTGG
30178179 GGGTGGGGGGGTGG
1 GGGT-GGGGGGTGG
30178193 GGG
1 GGG
30178196 AGATATTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.00, C:0.00, G:0.87, T:0.13
Consensus pattern (13 bp):
GGGTGGGGGGTGG
Found at i:30179371 original size:20 final size:21
Alignment explanation
Indices: 30179329--30179374 Score: 58
Period size: 24 Copynumber: 2.1 Consensus size: 21
30179319 TCTTGTATTG
30179329 TAAATAAGTTGTAGATTTTTTTAA
1 TAAATAAGTTGTAGA---TTTTAA
30179353 TAAATAAGTTGTAGA-TTTAA
1 TAAATAAGTTGTAGATTTTAA
30179373 TA
1 TA
30179375 GTTGTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
24 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (21 bp):
TAAATAAGTTGTAGATTTTAA
Found at i:30179876 original size:2 final size:2
Alignment explanation
Indices: 30179869--30179905 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
30179859 GACGTACCAA
30179869 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 A
30179906 AAAAAGACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30181428 original size:2 final size:2
Alignment explanation
Indices: 30181421--30181454 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30181411 GGCTAAGCAT
30181421 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30181455 GTAAGGGAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30191387 original size:43 final size:43
Alignment explanation
Indices: 30191334--30191441 Score: 155
Period size: 42 Copynumber: 2.5 Consensus size: 43
30191324 TGCTATAGAA
* *
30191334 CATGGTCTTTAGCGGCGCTTTTTCAACAAACGCCACTAAAGAC
1 CATGTTCTTTAGCGGCGCTTTCTCAACAAACGCCACTAAAGAC
* * *
30191377 CATGTTCTTTAGCGGCGC-TTCTCCACAAATGCCGCTAAAGAC
1 CATGTTCTTTAGCGGCGCTTTCTCAACAAACGCCACTAAAGAC
*
30191419 CATGTTCTTTAGCGGTGCTTTCT
1 CATGTTCTTTAGCGGCGCTTTCT
30191442 TTAGCGGCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 37 0.64
43 21 0.36
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (43 bp):
CATGTTCTTTAGCGGCGCTTTCTCAACAAACGCCACTAAAGAC
Found at i:30191443 original size:15 final size:15
Alignment explanation
Indices: 30191423--30191454 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30191413 AAAGACCATG
*
30191423 TTCTTTAGCGGTGCT
1 TTCTTTAGCGGCGCT
30191438 TTCTTTAGCGGCGCT
1 TTCTTTAGCGGCGCT
30191453 TT
1 TT
30191455 TCCCACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.22, G:0.25, T:0.47
Consensus pattern (15 bp):
TTCTTTAGCGGCGCT
Found at i:30191473 original size:58 final size:58
Alignment explanation
Indices: 30191381--30191529 Score: 264
Period size: 58 Copynumber: 2.6 Consensus size: 58
30191371 AAAGACCATG
* *
30191381 TTCTTTAGCGGCGCTTCT-CCACAAATGCCGCTAAAGACCATGTTCTTTAGCGGTGCT
1 TTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGTGCT
30191438 TTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGTGCT
1 TTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGTGCT
*
30191496 TTCTTTAGCGGCGCTTTTCTCACAAACGCCGCTA
1 TTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
30191530 GCGGTGCTTT
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
57 17 0.19
58 71 0.81
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.32
Consensus pattern (58 bp):
TTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGTGCT
Found at i:30191501 original size:15 final size:15
Alignment explanation
Indices: 30191481--30191512 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30191471 AAAGACCATG
*
30191481 TTCTTTAGCGGTGCT
1 TTCTTTAGCGGCGCT
30191496 TTCTTTAGCGGCGCT
1 TTCTTTAGCGGCGCT
30191511 TT
1 TT
30191513 TCTCACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.22, G:0.25, T:0.47
Consensus pattern (15 bp):
TTCTTTAGCGGCGCT
Found at i:30191534 original size:42 final size:42
Alignment explanation
Indices: 30191486--30191614 Score: 179
Period size: 42 Copynumber: 3.0 Consensus size: 42
30191476 CCATGTTCTT
30191486 TAGCGGTGCTTTCTTTAGCGGCGCTTTTCTCACAAACGCCGC
1 TAGCGGTGCTTTCTTTAGCGGCGCTTTTCTCACAAACGCCGC
30191528 TAGCGGTGCTTTCTTTAGCGGCGCTTTTCTCACAAACGCCGC
1 TAGCGGTGCTTTCTTTAGCGGCGCTTTTCTCACAAACGCCGC
** ** * *
30191570 TA-AAGAACATGGTCTTTAGCGGCGCTATTCTCACAAACGCCGC
1 TAGCGGTGC-T-TTCTTTAGCGGCGCTTTTCTCACAAACGCCGC
30191613 TA
1 TA
30191615 AAGAACATAG
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
41 2 0.03
42 45 0.57
43 32 0.41
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.29
Consensus pattern (42 bp):
TAGCGGTGCTTTCTTTAGCGGCGCTTTTCTCACAAACGCCGC
Found at i:30191601 original size:43 final size:42
Alignment explanation
Indices: 30191497--30191657 Score: 191
Period size: 43 Copynumber: 3.8 Consensus size: 42
30191487 AGCGGTGCTT
** ** *
30191497 TCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAGCGGTGC-TT
1 TCTTTAGCGGCGCTTTTCTCACAAACGCCGCTA-AAGAACATG
30191539 TCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACATGG
1 TCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACAT-G
*
30191582 TCTTTAGCGGCGCTATTCTCACAAACGCCGCTAAAGAACATAG
1 TCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACAT-G
* * * *
30191625 TCTTTTGCGACGCTTTCCT-ACAAACGCCACTAA
1 TCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAA
30191658 CATTAACAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
41 2 0.02
42 47 0.45
43 56 0.53
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (42 bp):
TCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACATG
Found at i:30191648 original size:85 final size:85
Alignment explanation
Indices: 30191497--30191657 Score: 200
Period size: 85 Copynumber: 1.9 Consensus size: 85
30191487 AGCGGTGCTT
* ** ** * * *
30191497 TCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAGCGGTGCTTTCTTTAGCGGCGCTTTTCTCACA
1 TCTTTAGCGGCGCTATTCTCACAAACGCCGCTAGAAGAACTGTCTTTAGCGACGCTTTCCTCACA
*
30191562 AACGCCGCTAAAGAACATGG
66 AACGCCACTAAAGAACATGG
*
30191582 TCTTTAGCGGCGCTATTCTCACAAACGCCGCTA-AAGAACATAGTCTTTTGCGACGCTTTCCT-A
1 TCTTTAGCGGCGCTATTCTCACAAACGCCGCTAGAAGAAC-T-GTCTTTAGCGACGCTTTCCTCA
30191645 CAAACGCCACTAA
64 CAAACGCCACTAA
30191658 CATTAACAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 2 0.03
85 46 0.72
86 16 0.25
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (85 bp):
TCTTTAGCGGCGCTATTCTCACAAACGCCGCTAGAAGAACTGTCTTTAGCGACGCTTTCCTCACA
AACGCCACTAAAGAACATGG
Found at i:30196416 original size:29 final size:30
Alignment explanation
Indices: 30196369--30196427 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
30196359 TTTGGTCTAA
30196369 TGTGCAATTTTAGACATG-AACTTTGATTT
1 TGTGCAATTTTAGACATGAAACTTTGATTT
* * *
30196398 TGTGCAATTTTATATATGAAATTTTGATTT
1 TGTGCAATTTTAGACATGAAACTTTGATTT
30196428 GTTTCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTTTAGACATGAAACTTTGATTT
Found at i:30203220 original size:21 final size:21
Alignment explanation
Indices: 30203195--30203240 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
30203185 CTACAATTTT
*
30203195 ATAATATTTT-AATAATTTCTA
1 ATAATATTTTAAATAA-ATCTA
*
30203216 ATAATTTTTTAAATAAATCTA
1 ATAATATTTTAAATAAATCTA
30203237 ATAA
1 ATAA
30203241 AAATTACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATATTTTAAATAAATCTA
Found at i:30203408 original size:26 final size:24
Alignment explanation
Indices: 30203363--30203410 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
30203353 TTTACCATTT
*
30203363 AGGTTTAAAAATGTTGTGAAAACG
1 AGGTTTAAAAATATTGTGAAAACG
*
30203387 AGGTTTATAAAATAATTTTGAAAA
1 AGGTTTA-AAAAT-ATTGTGAAAA
30203411 TTTTTATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 5 0.25
26 8 0.40
ACGTcount: A:0.46, C:0.02, G:0.19, T:0.33
Consensus pattern (24 bp):
AGGTTTAAAAATATTGTGAAAACG
Found at i:30205070 original size:31 final size:30
Alignment explanation
Indices: 30205034--30205115 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
30205024 CATTTATTTG
**
30205034 TTTTATTTAGATTTAATTTTGTTTTACTTAT
1 TTTTATTTAGATTTAATTTT-CATTACTTAT
** *
30205065 TTTTATTTTTATTTAATTTTCATTATTTAT
1 TTTTATTTAGATTTAATTTTCATTACTTAT
*
30205095 TTTAGATTTAGATTTAATTTT
1 TTT-TATTTAGATTTAATTTT
30205116 TTTCTTTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 10 0.24
31 32 0.76
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (30 bp):
TTTTATTTAGATTTAATTTTCATTACTTAT
Found at i:30205095 original size:18 final size:17
Alignment explanation
Indices: 30205063--30205096 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30205053 TGTTTTACTT
*
30205063 ATTTTTATTTTTATTTA
1 ATTTTCATTTTTATTTA
30205080 ATTTTCATTATTTATTT
1 ATTTTCATT-TTTATTT
30205097 TAGATTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTTCATTTTTATTTA
Found at i:30216561 original size:18 final size:18
Alignment explanation
Indices: 30216521--30216562 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
30216511 TTTTTAGTTG
30216521 TAATTAACTTAAAATTTT
1 TAATTAACTTAAAATTTT
* *
30216539 CAATTAAC-TAAATTTATT
1 TAATTAACTTAAAATT-TT
30216557 TAATTA
1 TAATTA
30216563 TAAATTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTAACTTAAAATTTT
Found at i:30218813 original size:3 final size:3
Alignment explanation
Indices: 30218805--30218829 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30218795 TCTCTACCTT
30218805 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
30218830 TAGTGTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:30226766 original size:27 final size:27
Alignment explanation
Indices: 30226706--30226766 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
30226696 GGTGCTTAGG
*
30226706 GTTTTGAGTTCAGAGTTAAAGATTTAA
1 GTTTTGGGTTCAGAGTTAAAGATTTAA
30226733 GTTTTGGGTTCA-AGTTTAAAGATTTAA
1 GTTTTGGGTTCAGAG-TTAAAGATTTAA
30226760 GTTTTGG
1 GTTTTGG
30226767 ATTTAGGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (27 bp):
GTTTTGGGTTCAGAGTTAAAGATTTAA
Found at i:30228570 original size:19 final size:19
Alignment explanation
Indices: 30228546--30228583 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30228536 AAAACCAAGA
*
30228546 TTTTTACAATATTCATTTT
1 TTTTTAAAATATTCATTTT
*
30228565 TTTTTAAAATTTTCATTTT
1 TTTTTAAAATATTCATTTT
30228584 AAATCATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTAAAATATTCATTTT
Found at i:30240542 original size:18 final size:18
Alignment explanation
Indices: 30240486--30240542 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
30240476 CATTATAAAT
*
30240486 AAAATTAAAATA-TAGCAA
1 AAAATTAAAAAACTAG-AA
* * *
30240504 AAAAATAATAAAACAAAAA
1 AAAATTAA-AAAACTAGAA
30240523 AAAATTAAAAAACTAGAA
1 AAAATTAAAAAACTAGAA
30240541 AA
1 AA
30240543 TGAAACATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 17 0.57
19 12 0.40
20 1 0.03
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (18 bp):
AAAATTAAAAAACTAGAA
Found at i:30241065 original size:2 final size:2
Alignment explanation
Indices: 30241058--30241094 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
30241048 AGAACATCGC
30241058 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
30241095 ATTACATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30260012 original size:24 final size:24
Alignment explanation
Indices: 30259996--30260070 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
30259986 AGTTTGACTC
30259996 AAACAAATAAACAGAGTTCAATTG
1 AAACAAATAAACAGAGTTCAATTG
30260020 AAACAAATAAACAGAGTTCAATTG
1 AAACAAATAAACAGAGTTCAATTG
* * *
30260044 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTCAATTG
30260068 AAA
1 AAA
30260071 GATTATTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTCAATTG
Found at i:30262004 original size:24 final size:24
Alignment explanation
Indices: 30261976--30262032 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
30261966 TAGACTAATA
*
30261976 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
30262000 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
30262024 AGAGTTTAA
1 AGAGTTTAA
30262033 TTGAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:30262033 original size:24 final size:24
Alignment explanation
Indices: 30261988--30262038 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
30261978 AGTTTGACTC
30261988 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
30262012 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
30262036 AAA
1 AAA
30262039 AATTATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:30263489 original size:27 final size:27
Alignment explanation
Indices: 30263459--30263553 Score: 129
Period size: 27 Copynumber: 3.5 Consensus size: 27
30263449 ACGAGGGCAA
* * *
30263459 TTCCTTCAGGGTTCGCCAATAATACCG
1 TTCCTTCAGAGTTCGCCAAGAATATCG
*
30263486 TTCCTTCAGAGCTT-GCCAAGAATATTG
1 TTCCTTCAGAG-TTCGCCAAGAATATCG
*
30263513 TTCCTTCAGAGCTCGCCAAGAATATCG
1 TTCCTTCAGAGTTCGCCAAGAATATCG
30263540 TTCCTTCAGAGTTC
1 TTCCTTCAGAGTTC
30263554 ACCACAAAGG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.02
27 56 0.95
28 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (27 bp):
TTCCTTCAGAGTTCGCCAAGAATATCG
Found at i:30277733 original size:7 final size:7
Alignment explanation
Indices: 30277721--30277745 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30277711 TGCTTGTTAA
30277721 GGTGATT
1 GGTGATT
30277728 GGTGATT
1 GGTGATT
30277735 GGTGATT
1 GGTGATT
30277742 GGTG
1 GGTG
30277746 TGGGAGGGCT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (7 bp):
GGTGATT
Found at i:30281269 original size:6 final size:6
Alignment explanation
Indices: 30281258--30281306 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
30281248 TATCACTTTC
30281258 ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG
1 ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG ATTGGG
30281306 A
1 A
30281307 GAATTAAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.18, C:0.00, G:0.49, T:0.33
Consensus pattern (6 bp):
ATTGGG
Found at i:30289825 original size:13 final size:15
Alignment explanation
Indices: 30289802--30289833 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
30289792 GTATTTCTGT
30289802 TTTTGTATTTTAA-A
1 TTTTGTATTTTAATA
30289816 TTTT-TATTTTAATA
1 TTTTGTATTTTAATA
30289830 TTTT
1 TTTT
30289834 AATCATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTGTATTTTAATA
Found at i:30290598 original size:89 final size:89
Alignment explanation
Indices: 30290447--30290609 Score: 204
Period size: 89 Copynumber: 1.8 Consensus size: 89
30290437 TTGAGTGCAA
* * ** ** *
30290447 AAAAAAAAAACAAAGGTTTAATTACTTTTTTTGAAAAAATTTGAGGGTCTTTTGGATATATTTTG
1 AAAAAAAAAACAAAGGTTTAATTACTTTCTTTGAAAAAATTTAAGACTCTTTTCAATATATTTTA
30290512 AAAGTTTAAGTACCTAATCGAGTG
66 AAAGTTTAAGTACCTAATCGAGTG
* * *
30290536 AAAAAAAAAGC-AAGAGTTTAATTGCTTTCTTTGAAAAAATTTAAAGACT-TTTTCAATGTATTT
1 AAAAAAAAAACAAAG-GTTTAATTACTTTCTTTGAAAAAATTT-AAGACTCTTTTCAATATATTT
30290599 TAAAAGTTTAA
64 TAAAAGTTTAA
30290610 ATACTCAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
88 3 0.05
89 56 0.90
90 3 0.05
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (89 bp):
AAAAAAAAAACAAAGGTTTAATTACTTTCTTTGAAAAAATTTAAGACTCTTTTCAATATATTTTA
AAAGTTTAAGTACCTAATCGAGTG
Found at i:30290629 original size:89 final size:89
Alignment explanation
Indices: 30290446--30290635 Score: 197
Period size: 89 Copynumber: 2.1 Consensus size: 89
30290436 ATTGAGTGCA
* * ** **
30290446 AAAAAAAAAAACAAAGGTTTAATTACTTTTTTTGAAAAAATTTGAGGGTCTTTTGGATATATTTT
1 AAAAAAAAAAACAAAGGTTTAATTACTTTCTTTGAAAAAATTTAAGACTCTTTTCAATATATTTT
* * *
30290511 GAAAGTTTAAGTACCTAATCGAGT
66 AAAAGTTTAAATACCTAATCGAAT
* * * *
30290535 GAAAAAAAAAGC-AAGAGTTTAATTGCTTTCTTTGAAAAAATTTAAAGACT-TTTTCAATGTATT
1 AAAAAAAAAAACAAAG-GTTTAATTACTTTCTTTGAAAAAATTT-AAGACTCTTTTCAATATATT
*
30290598 TTAAAAGTTTAAATA-CTCAATTGAAT
64 TTAAAAGTTTAAATACCT-AATCGAAT
30290624 AAAAAAACAAAA
1 AAAAAAA-AAAA
30290636 ACTTAATTAT
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
88 5 0.06
89 70 0.86
90 6 0.07
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (89 bp):
AAAAAAAAAAACAAAGGTTTAATTACTTTCTTTGAAAAAATTTAAGACTCTTTTCAATATATTTT
AAAAGTTTAAATACCTAATCGAAT
Found at i:30290883 original size:16 final size:17
Alignment explanation
Indices: 30290862--30290894 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30290852 TAAAAATTTA
30290862 GGAATTA-TGATTATAT
1 GGAATTACTGATTATAT
*
30290878 GGAATTACTGGTTATAT
1 GGAATTACTGATTATAT
30290895 TTGGGCCGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.42
Consensus pattern (17 bp):
GGAATTACTGATTATAT
Found at i:30293457 original size:52 final size:53
Alignment explanation
Indices: 30293380--30293489 Score: 136
Period size: 53 Copynumber: 2.1 Consensus size: 53
30293370 CTACAGATTA
* * * *
30293380 TTAACTATTCTAAATAGTGTTTTTCTCATGTAA-ACCTGTTCTGCTCTTATTG
1 TTAACTATTCTAAATAGTGTTTTTCTCAAGTAATACCAGTTCTACTCCTATTG
*
30293432 TTAACT-TTCTAAATAGT-TCTATTTCTCAAGTAATAGCAGTTCTACTCCTATTG
1 TTAACTATTCTAAATAGTGT-T-TTTCTCAAGTAATACCAGTTCTACTCCTATTG
30293485 TTAAC
1 TTAAC
30293490 CATATTACTG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
50 1 0.02
51 12 0.24
52 17 0.34
53 20 0.40
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.45
Consensus pattern (53 bp):
TTAACTATTCTAAATAGTGTTTTTCTCAAGTAATACCAGTTCTACTCCTATTG
Found at i:30293540 original size:51 final size:52
Alignment explanation
Indices: 30293473--30293571 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
30293463 AATAGCAGTT
* *
30293473 CTACTCCTATTGTTAACCATA-TTACTGATGCTTTTTCTCATGTAACACCAA
1 CTACTCCTATTGTTAACCATAGTAACTGATGCCTTTTCTCATGTAACACCAA
* *
30293524 CTACTCCTATTGTTAACCTTAGTAACTGGTGCCTTTTCTCATGTAACA
1 CTACTCCTATTGTTAACCATAGTAACTGATGCCTTTTCTCATGTAACA
30293572 GCTGTATTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 20 0.47
52 23 0.53
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.39
Consensus pattern (52 bp):
CTACTCCTATTGTTAACCATAGTAACTGATGCCTTTTCTCATGTAACACCAA
Found at i:30302751 original size:2 final size:2
Alignment explanation
Indices: 30302744--30302771 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30302734 AACTTGTTAA
30302744 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30302772 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:30302805 original size:2 final size:2
Alignment explanation
Indices: 30302771--30302797 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30302761 TCTCTCTCTC
30302771 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30302798 TCATATATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30306977 original size:19 final size:19
Alignment explanation
Indices: 30306953--30306989 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30306943 ATTCATTGAA
* *
30306953 TAAAAATATAACTATAAAG
1 TAAAAATAAAAATATAAAG
30306972 TAAAAATAAAAATATAAA
1 TAAAAATAAAAATATAAA
30306990 ATAATTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (19 bp):
TAAAAATAAAAATATAAAG
Found at i:30323145 original size:5 final size:5
Alignment explanation
Indices: 30323135--30323179 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
30323125 AAATTATAAT
30323135 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG
1 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG
30323180 GAGGCCCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
AAGGG
Found at i:30324008 original size:31 final size:31
Alignment explanation
Indices: 30323965--30324059 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 31
30323955 TTTTTTAGAT
30323965 TCAA-TTTG-GTACCAAATTAGGAAAAAGTA
1 TCAAGTTTGAGTACCAAATTAGGAAAAAGTA
30323994 TCAAGTTTGAGTACCAAATT-GGATAAAA--A
1 TCAAGTTTGAGTACCAAATTAGGA-AAAAGTA
* * * * *
30324023 -AAAGTTTAAGTAACAAATTAAGAAAAAGTG
1 TCAAGTTTGAGTACCAAATTAGGAAAAAGTA
30324053 TCAAGTT
1 TCAAGTT
30324060 CAGATACCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
28 20 0.38
29 7 0.13
30 7 0.13
31 19 0.36
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.27
Consensus pattern (31 bp):
TCAAGTTTGAGTACCAAATTAGGAAAAAGTA
Found at i:30324157 original size:18 final size:17
Alignment explanation
Indices: 30324129--30324182 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
30324119 AAATAAATAT
*
30324129 ATAAAAAATTCATAAAA
1 ATAATAAATTCATAAAA
30324146 ATATATAAATTC-TAGAAA
1 ATA-ATAAATTCATA-AAA
30324164 A-AATAAATT-ATAAAA
1 ATAATAAATTCATAAAA
30324179 ATAA
1 ATAA
30324183 AATTTACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 4 0.12
16 11 0.34
17 6 0.19
18 11 0.34
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (17 bp):
ATAATAAATTCATAAAA
Found at i:30324312 original size:19 final size:20
Alignment explanation
Indices: 30324269--30324312 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
30324259 AATTATAAGA
30324269 AAAAATTGTAAAAAATTATT
1 AAAAATTGTAAAAAATTATT
* **
30324289 TAAAATT-TAAAATTTTATT
1 AAAAATTGTAAAAAATTATT
30324308 AAAAA
1 AAAAA
30324313 ATAATATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAAATTGTAAAAAATTATT
Found at i:30325812 original size:60 final size:60
Alignment explanation
Indices: 30325732--30325923 Score: 255
Period size: 60 Copynumber: 3.2 Consensus size: 60
30325722 ACTGAAGTCA
* * *
30325732 AAAATAGAATTTTGG-AAAG-TTCAGGGGTTAAAATGTAATTTTAGAAAAGTTTTTAGGTT
1 AAAATATAATTTTGGAAAAGTTTTA-GGGTTAAAATGTAATTTTAGAAAAGTTTTTAGGTC
* * * * *
30325791 AAAATATAATATTGGAAAAGTTTTAGGGTCAAAATGTAATATTAGAAAAATTTTAAGGTC
1 AAAATATAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTTTAGGTC
* *
30325851 AAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAG-TTTTAGGGTC
1 AAAATATAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTTTA-GGTC
30325911 AAAATATAATTTT
1 AAAATATAATTTT
30325924 TGGATAGTTT
Statistics
Matches: 114, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
59 17 0.15
60 94 0.82
61 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (60 bp):
AAAATATAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTTTAGGTC
Found at i:30325822 original size:90 final size:90
Alignment explanation
Indices: 30325728--30325937 Score: 241
Period size: 90 Copynumber: 2.3 Consensus size: 90
30325718 CAAAACTGAA
* *
30325728 GTCAAAAATAGAATTTTGGAAAGTTCAGGGGTTAAAATGTAATTTTAGAAAAGTTTTTA-GGTTA
1 GTCAAAAATAGAATTTTGGAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAG-TTTTAGGGTTA
30325792 AAATATAATATTGGAAAAGTTTTAGG
65 AAATATAATATTGGAAAAGTTTTAGG
* * * * *
30325818 GTC-AAAAT-GTAATATTAGAAAAATTTTA-AGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGT
1 GTCAAAAATAG-AAT-TTTG-GAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGT
* *
30325880 TAAAATGTAATTTTGGAAAAGTTTTAGG
63 TAAAATATAATATTGGAAAAGTTTTAGG
* *
30325908 GTCAAAATATA-ATTTTTGGATAGTTTAGGG
1 GTCAAAA-ATAGAATTTTGGAAAGTTTAGGG
30325938 ACCTACAGAG
Statistics
Matches: 97, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
88 1 0.01
89 19 0.20
90 64 0.66
91 11 0.11
92 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (90 bp):
GTCAAAAATAGAATTTTGGAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTTAA
AATATAATATTGGAAAAGTTTTAGG
Found at i:30325933 original size:30 final size:30
Alignment explanation
Indices: 30325739--30325923 Score: 223
Period size: 30 Copynumber: 6.2 Consensus size: 30
30325729 TCAAAAATAG
* *
30325739 AATTTTGG-AAAG-TTCAGGGGTTAAAATGT
1 AATTTTGGAAAAGTTTTA-GGGTCAAAATGT
* * *
30325768 AATTTTAGAAAAGTTTTTA-GGTTAAAATAT
1 AATTTTGGAAAAG-TTTTAGGGTCAAAATGT
*
30325798 AATATTGGAAAAGTTTTAGGGTCAAAATGT
1 AATTTTGGAAAAGTTTTAGGGTCAAAATGT
* * * *
30325828 AATATTAGAAAAATTTTAAGGTCAAAATGT
1 AATTTTGGAAAAGTTTTAGGGTCAAAATGT
*
30325858 AATTTTGGAAAAGTTTTAGGGTTAAAATGT
1 AATTTTGGAAAAGTTTTAGGGTCAAAATGT
*
30325888 AATTTTGGAAAAGTTTTAGGGTCAAAATAT
1 AATTTTGGAAAAGTTTTAGGGTCAAAATGT
30325918 AATTTT
1 AATTTT
30325924 TGGATAGTTT
Statistics
Matches: 135, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
29 12 0.09
30 120 0.89
32 3 0.02
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTTAGGGTCAAAATGT
Found at i:30327850 original size:11 final size:11
Alignment explanation
Indices: 30327796--30327860 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
30327786 TTTTCTTTTT
30327796 TTAAAATTATAA
1 TTAAAATTA-AA
*
30327808 -TAATATTAAA
1 TTAAAATTAAA
*
30327818 TTAAAATTGAAT
1 TTAAAATT-AAA
*
30327830 TTAGAA-TAAA
1 TTAAAATTAAA
30327840 TTAAAATTAAA
1 TTAAAATTAAA
* *
30327851 ATAAATTTAA
1 TTAAAATTAA
30327861 TTTCAAAATG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
10 9 0.21
11 26 0.62
12 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
TTAAAATTAAA
Found at i:30328279 original size:91 final size:92
Alignment explanation
Indices: 30328110--30329030 Score: 1431
Period size: 91 Copynumber: 10.1 Consensus size: 92
30328100 AAGTAGGGTT
* * * * * * *
30328110 TGATGTCGGGGTTTTATCTTGCTCTTACTTCAATTTCAAAGAGATAAAGACTTGATATCCATCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
*
30328175 TACTAT-AACTTCAAGAGGATAGGAAAA
66 TACT-TCAATTTCAAGAGGATAGGAAAA
* *
30328202 -GATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGCGACAAAGGCTTGATATCCAGCTC
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
30328266 TACTTCAATTTCAAGAGGATAGGAAAA
66 TACTTCAATTTCAAGAGGATAGGAAAA
* * * * * *
30328293 TGATGTTGGTGTTTCATCTTGCTCTTACTTCAATTCCAGAGGGACGAAGGCTTGTTATCCAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
*
30328358 TACTTCAATTTCAAAAGGATAGGAAAA
66 TACTTCAATTTCAAGAGGATAGGAAAA
* * *
30328385 -GATGTCGCTGCTTCATCTTACTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
30328449 TACTTCAATTTCAAGAGGATAGGAAAA
66 TACTTCAATTTCAAGAGGATAGGAAAA
* * *
30328476 -GATGTCGGTGCTTCATCTTACTCTTACTTCAATTTCAGAGCGACAAAGGCTTGATATCCAGCTC
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
30328540 TACTTCAATTTCAAGAGGATAGGAAAA
66 TACTTCAATTTCAAGAGGATAGGAAAA
* * * *
30328567 TGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
30328632 TACTTCAATTTCAAGAGGATAGGAAAA
66 TACTTCAATTTCAAGAGGATAGGAAAA
* *
30328659 -GATGTCGGTGCTTCATTTTGCTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
*
30328723 TACTTCAATTTCAAAAGGATAGGAAAA
66 TACTTCAATTTCAAGAGGATAGGAAAA
*
30328750 -GATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCTAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
30328814 TACTTCAATTTCAAGAGGATAGGAAAA
66 TACTTCAATTTCAAGAGGATAGGAAAA
* * *
30328841 TGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGATATCCAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
*
30328906 TACTTCAATTTTAAGAGGATAGGAAAA
66 TACTTCAATTTCAAGAGGATAGGAAAA
* ** * *
30328933 TGATGTTGGTGCTTCATCTTATTCTTACTTCAATTTCAGAGGGACGAAGGCTTGATATCCAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
30328998 TACTTCAATTTCAAGAGGATAGGAAAA
66 TACTTCAATTTCAAGAGGATAGGAAAA
30329025 TGATGT
1 TGATGT
30329031 TGGTTGATCT
Statistics
Matches: 768, Mismatches: 57, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
90 1 0.00
91 418 0.54
92 349 0.45
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (92 bp):
TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
TACTTCAATTTCAAGAGGATAGGAAAA
Found at i:30328433 original size:183 final size:183
Alignment explanation
Indices: 30328110--30329030 Score: 1434
Period size: 183 Copynumber: 5.0 Consensus size: 183
30328100 AAGTAGGGTT
* * * * * * *
30328110 TGATGTCGGGGTTTTATCTTGCTCTTACTTCAATTTCAAAGAGATAAAGACTTGATATCCATCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
*
30328175 TACTAT-AACTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCA
66 TACT-TCAATTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCA
* *
30328239 GAGCGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAA
130 GAGAGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
* * * * * *
30328293 TGATGTTGGTGTTTCATCTTGCTCTTACTTCAATTCCAGAGGGACGAAGGCTTGTTATCCAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
* * * *
30328358 TACTTCAATTTCAAAAGGATAGGAAAAGATGTCGCTGCTTCATCTTACTCTTACTTCAATTTCAA
66 TACTTCAATTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAG
30328423 AGAGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
131 AGAGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
* * *
30328476 -GATGTCGGTGCTTCATCTTACTCTTACTTCAATTTCAGAGCGACAAAGGCTTGATATCCAGCTC
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
*
30328540 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
66 TACTTCAATTTCAAGAGGATAGGAAAA-GATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCA
* * *
30328605 GAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
130 GAGAGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
* *
30328659 -GATGTCGGTGCTTCATTTTGCTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
*
30328723 TACTTCAATTTCAAAAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAG
66 TACTTCAATTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAG
*
30328788 AGAGACAAAGGCTTGATATCTAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
131 AGAGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
* * *
30328841 TGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGATATCCAGCTT
1 TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
* * **
30328906 TACTTCAATTTTAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTATTCTTACTTCAATTTCA
66 TACTTCAATTTCAAGAGGATAGGAAAA-GATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCA
* *
30328971 GAGGGACGAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
130 GAGAGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
30329025 TGATGT
1 TGATGT
30329031 TGGTTGATCT
Statistics
Matches: 676, Mismatches: 58, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
182 169 0.25
183 416 0.62
184 91 0.13
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (183 bp):
TGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTT
TACTTCAATTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAG
AGAGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAA
Found at i:30328600 original size:274 final size:274
Alignment explanation
Indices: 30328111--30329030 Score: 1572
Period size: 274 Copynumber: 3.4 Consensus size: 274
30328101 AGTAGGGTTT
* * * * * * *
30328111 GATGTCGGGGTTTTATCTTGCTCTTACTTCAATTTCAAAGAGATAAAGACTTGATATCCATCTTT
1 GATGTCGGTGCTTCATCTTACTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTTT
*
30328176 ACTAT-AACTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAG
66 ACT-TCAATTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAG
*
30328240 AGCGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGT
130 AGCGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGC
*
30328305 TTCATCTTGCTCTTACTTCAATTCCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTC
195 TTCATCTTGCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTC
*
30328370 AAAAGGATAGGAAAA
260 AAGAGGATAGGAAAA
*
30328385 GATGTCGCTGCTTCATCTTACTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTTT
1 GATGTCGGTGCTTCATCTTACTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTTT
*
30328450 ACTTCAATTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTACTCTTACTTCAATTTCAGA
66 ACTTCAATTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGA
30328515 GCGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCT
131 GCGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCT
30328580 TCATCTTGCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCA
196 TCATCTTGCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCA
30328645 AGAGGATAGGAAAA
261 AGAGGATAGGAAAA
* *
30328659 GATGTCGGTGCTTCATTTTGCTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTTT
1 GATGTCGGTGCTTCATCTTACTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTTT
*
30328724 ACTTCAATTTCAAAAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGA
66 ACTTCAATTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGA
* * *
30328789 GAGACAAAGGCTTGATATCTAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCT
131 GCGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCT
* *
30328854 TCATCTTGCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGATATCCAGCTTTACTTCAATTTTA
196 TCATCTTGCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCA
30328919 AGAGGATAGGAAAA
261 AGAGGATAGGAAAA
* * * * *
30328933 TGATGTTGGTGCTTCATCTTATTCTTACTTCAATTTCAGAGGGACGAAGGCTTGATATCCAGCTT
1 -GATGTCGGTGCTTCATCTTACTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTT
30328998 TACTTCAATTTCAAGAGGATAGGAAAATGATGT
65 TACTTCAATTTCAAGAGGATAGGAAAA-GATGT
30329031 TGGTTGATCT
Statistics
Matches: 612, Mismatches: 31, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
273 1 0.00
274 523 0.85
275 83 0.14
276 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (274 bp):
GATGTCGGTGCTTCATCTTACTCTTACTTCAATTTCAAAGAGACAAAGGCTTGATATCCAGCTTT
ACTTCAATTTCAAGAGGATAGGAAAAGATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGA
GCGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCT
TCATCTTGCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCA
AGAGGATAGGAAAA
Found at i:30341120 original size:90 final size:90
Alignment explanation
Indices: 30341025--30341188 Score: 222
Period size: 90 Copynumber: 1.8 Consensus size: 90
30341015 GCAAAACCGA
* * * *
30341025 GGTTAAAAATGGAAT-TTTGGAAAGTTCGGGGGTTAAAATGTAATATTGGAAAAGTTTTAGGGTT
1 GGTT-AAAATGGAATATTAGAAAAGTTCGAGGGTTAAAATGTAATATTGGAAAAGTTTTAGGGTC
30341089 AAAATGTAATATTGGAAAAGTTTTAG
65 AAAATGTAATATTGGAAAAGTTTTAG
* ** * * *
30341115 GGTTAAAATGTAATATTAGAAAAGTTTTAGGGTTAAGATGTAATTTTGGAAAAGTTTTGGGGTCA
1 GGTTAAAATGGAATATTAGAAAAGTTCGAGGGTTAAAATGTAATATTGGAAAAGTTTTAGGGTCA
30341180 AAATGTAAT
66 AAATGTAAT
30341189 TTTTAGACAG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
89 9 0.14
90 54 0.86
ACGTcount: A:0.38, C:0.01, G:0.26, T:0.35
Consensus pattern (90 bp):
GGTTAAAATGGAATATTAGAAAAGTTCGAGGGTTAAAATGTAATATTGGAAAAGTTTTAGGGTCA
AAATGTAATATTGGAAAAGTTTTAG
Found at i:30341191 original size:30 final size:30
Alignment explanation
Indices: 30341054--30341188 Score: 225
Period size: 30 Copynumber: 4.5 Consensus size: 30
30341044 GAAAGTTCGG
30341054 GGGTTAAAATGTAATATTGGAAAAGTTTTA
1 GGGTTAAAATGTAATATTGGAAAAGTTTTA
30341084 GGGTTAAAATGTAATATTGGAAAAGTTTTA
1 GGGTTAAAATGTAATATTGGAAAAGTTTTA
*
30341114 GGGTTAAAATGTAATATTAGAAAAGTTTTA
1 GGGTTAAAATGTAATATTGGAAAAGTTTTA
* * *
30341144 GGGTTAAGATGTAATTTTGGAAAAGTTTTG
1 GGGTTAAAATGTAATATTGGAAAAGTTTTA
*
30341174 GGGTCAAAATGTAAT
1 GGGTTAAAATGTAAT
30341189 TTTTAGACAG
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 98 1.00
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (30 bp):
GGGTTAAAATGTAATATTGGAAAAGTTTTA
Found at i:30341201 original size:60 final size:60
Alignment explanation
Indices: 30341025--30341188 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 60
30341015 GCAAAACCGA
* ** *
30341025 GGTTAAAAATGGAATTTTGG-AAAGTTCGGGGGTTAAAATGTAATATTGGAAAAGTTTTAG
1 GGTT-AAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATATTAGAAAAGTTTTAG
* *
30341085 GGTTAAAATGTAATATTGGAAAAGTTTTAGGGTTAAAATGTAATATTAGAAAAGTTTTAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATATTAGAAAAGTTTTAG
* *
30341145 GGTTAAGATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAAT
1 GGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAAT
30341189 TTTTAGACAG
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
59 13 0.14
60 80 0.86
ACGTcount: A:0.38, C:0.01, G:0.26, T:0.35
Consensus pattern (60 bp):
GGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATATTAGAAAAGTTTTAG
Found at i:30341551 original size:21 final size:22
Alignment explanation
Indices: 30341517--30341557 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
30341507 TTTTATAAAT
30341517 ATTACTTTAATTCTTTTTTTTC
1 ATTACTTTAATTCTTTTTTTTC
*
30341539 ATTA-TTTCATTCTTTTTTT
1 ATTACTTTAATTCTTTTTTT
30341558 AAAAAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTACTTTAATTCTTTTTTTTC
Found at i:30341816 original size:9 final size:9
Alignment explanation
Indices: 30341804--30341828 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30341794 ACTCCTTTCC
30341804 CTTCTTTTT
1 CTTCTTTTT
30341813 CTTCTTTTT
1 CTTCTTTTT
30341822 CTTCTTT
1 CTTCTTT
30341829 CTTTTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
CTTCTTTTT
Found at i:30343001 original size:17 final size:16
Alignment explanation
Indices: 30342979--30343076 Score: 88
Period size: 17 Copynumber: 5.8 Consensus size: 16
30342969 TTCTTTTTTT
*
30342979 TTAAATTTATAATAATA
1 TTAAATTTAAAATAA-A
*
30342996 TTAAATTTAAATTAAA
1 TTAAATTTAAAATAAA
*
30343012 TTAAAATTAAAATTAAAA
1 TTAAATTTAAAA-T-AAA
* *
30343030 TTGAATTTAGAATAAA
1 TTAAATTTAAAATAAA
*
30343046 TTTAAAATTAAAATAAA
1 -TTAAATTTAAAATAAA
*
30343063 TTTAATTTTAAAAT
1 -TTAAATTTAAAAT
30343077 GGTTTGAGCC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
16 14 0.21
17 40 0.61
18 12 0.18
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:30343011 original size:11 final size:11
Alignment explanation
Indices: 30342995--30343070 Score: 66
Period size: 11 Copynumber: 6.8 Consensus size: 11
30342985 TTATAATAAT
30342995 ATTAAATTTAA
1 ATTAAATTTAA
*
30343006 ATTAAATTAAA
1 ATTAAATTTAA
*
30343017 ATTAAAATTAAA
1 ATT-AAATTTAA
*
30343029 ATTGAATTTAGA
1 ATTAAATTTA-A
30343041 A-TAAATTTAAA
1 ATTAAATTT-AA
*
30343052 ATTAAA-ATAA
1 ATTAAATTTAA
*
30343062 ATTTAATTT
1 ATTAAATTT
30343071 TAAAATGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
10 7 0.13
11 28 0.53
12 18 0.34
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:30350935 original size:21 final size:20
Alignment explanation
Indices: 30350888--30350938 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
30350878 TTTGATTAAA
*
30350888 ATTATTAAACCTAAATTTTT
1 ATTATTAAACATAAATTTTT
30350908 ATATATTAAACA-ATAATATTTT
1 AT-TATTAAACATA-AAT-TTTT
30350930 ATTATTAAA
1 ATTATTAAA
30350939 TTAGTTTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 18 0.67
22 6 0.22
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATTAAACATAAATTTTT
Found at i:30356346 original size:19 final size:19
Alignment explanation
Indices: 30356322--30356358 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30356312 TAATATAACT
30356322 TAATTTAATTTCATAAATC
1 TAATTTAATTTCATAAATC
*
30356341 TAATTTAATTTCGTAAAT
1 TAATTTAATTTCATAAAT
30356359 GACATAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (19 bp):
TAATTTAATTTCATAAATC
Found at i:30356861 original size:25 final size:24
Alignment explanation
Indices: 30356832--30356887 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
30356822 TTACTCTACT
*
30356832 AAATAAAAA-AAATTAATAACAAATC
1 AAATAAAAATAAATT-A-AACAAAAC
30356857 AAATAAAAATTAAATTAAACAAAAC
1 AAATAAAAA-TAAATTAAACAAAAC
30356882 AAATAA
1 AAATAA
30356888 CTTATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 22 0.79
26 1 0.04
27 5 0.18
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (24 bp):
AAATAAAAATAAATTAAACAAAAC
Found at i:30357148 original size:4 final size:4
Alignment explanation
Indices: 30357141--30357177 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
30357131 AAACTTCATC
*
30357141 TCTT TCTT TCTT TCTT TCTT TCTTT TCTT TCCT TCTT
1 TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT TCTT
30357178 CTCCTGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:30364545 original size:90 final size:89
Alignment explanation
Indices: 30364170--30364542 Score: 500
Period size: 90 Copynumber: 4.2 Consensus size: 89
30364160 TATTTACTTA
* * * *
30364170 ACCAATAAATAATACGGATTAAAATTGATTTACAGATAC-AAATAATACGAACATTTTAGAAAAT
1 ACCAACAAATAATACGGACTAAAATTGATTTATAGATACAAAATAATACGAACATTTTAAAAAAT
***
30364234 TGATATACGAAAATATAAAATGCA
66 TGATATACGAAAATATAAAATTTG
* *
30364258 ACCAACAAATAATATGGACTAAAATTGATTTATAGATACAAAATAATACGATCATTTTAAAAAAT
1 ACCAACAAATAATACGGACTAAAATTGATTTATAGATACAAAATAATACGAACATTTTAAAAAAT
* *
30364323 T-AGTATGCTAAAATATAAAATTTG
66 TGA-TATACGAAAATATAAAATTTG
* *
30364347 ACCAACAAATAATATGGACTAAAATTAATTTATAGATACAAAAATAATACGAACATTTTAAAAAA
1 ACCAACAAATAATACGGACTAAAATTGATTTATAGATAC-AAAATAATACGAACATTTTAAAAAA
**
30364412 TTGATATATAAAAATATAAAATTTG
65 TTGATATACGAAAATATAAAATTTG
* * * * *
30364437 ATCAACAAATAATACGAACTAAAATTGACTTATA-AGTACCAAAATAATACGAATATTTTACAAA
1 ACCAACAAATAATACGGACTAAAATTGATTTATAGA-TA-CAAAATAATACGAACATTTTAAAAA
30364501 ATTGATATACGAAAATATAAAATTTG
64 ATTGATATACGAAAATATAAAATTTG
*
30364527 ACTAACAAATAATACG
1 ACCAACAAATAATACG
30364543 AACCAATTTT
Statistics
Matches: 252, Mismatches: 27, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
88 36 0.14
89 79 0.31
90 135 0.54
91 2 0.01
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (89 bp):
ACCAACAAATAATACGGACTAAAATTGATTTATAGATACAAAATAATACGAACATTTTAAAAAAT
TGATATACGAAAATATAAAATTTG
Found at i:30364567 original size:179 final size:179
Alignment explanation
Indices: 30364170--30364574 Score: 507
Period size: 179 Copynumber: 2.3 Consensus size: 179
30364160 TATTTACTTA
* * * * *
30364170 ACCAATAAATAATACGGATTAAAATTGATTTACAGATAC--AAATAATACGAACATTTTAGAAAA
1 ACCAACAAATAATACGAACTAAAATTAATTTACAGATACAAAAATAATACGAACATTTTAAAAAA
* * * *
30364233 TTGATATACGAAAATATAAAATGCAACCAACAAATAATATGGACTAAAATTGATTTATAGATACA
66 TTGATATACAAAAATATAAAATGCAACCAACAAATAATACGAACTAAAATTGACTTATAGATACA
* *
30364298 AAATAATACGATCATTTTAAAAAATTAGTATGCTAAAATATAAAATTTG
131 AAATAATACGATCATTTTAAAAAATTAGTATACGAAAATATAAAATTTG
* * *
30364347 ACCAACAAATAATATGGACTAAAATTAATTTATAGATACAAAAATAATACGAACATTTTAAAAAA
1 ACCAACAAATAATACGAACTAAAATTAATTTACAGATACAAAAATAATACGAACATTTTAAAAAA
* *** *
30364412 TTGATATATAAAAATATAAAATTTGATCAACAAATAATACGAACTAAAATTGACTTATA-AGTAC
66 TTGATATACAAAAATATAAAATGCAACCAACAAATAATACGAACTAAAATTGACTTATAGA-TA-
*
30364476 CAAAATAATACGAAT-ATTTTACAAAATT-GATATACGAAAATATAAAATTTG
129 CAAAATAATACG-ATCATTTTAAAAAATTAG-TATACGAAAATATAAAATTTG
* * * * *
30364527 ACTAACAAATAATACGAAC-CAATTTTATTTACATATACAAAAATAATA
1 ACCAACAAATAATACGAACTAAAATTAATTTACAGATACAAAAATAATA
30364575 GGCTTTTTTA
Statistics
Matches: 196, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
177 34 0.17
178 1 0.01
179 100 0.51
180 59 0.30
181 2 0.01
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (179 bp):
ACCAACAAATAATACGAACTAAAATTAATTTACAGATACAAAAATAATACGAACATTTTAAAAAA
TTGATATACAAAAATATAAAATGCAACCAACAAATAATACGAACTAAAATTGACTTATAGATACA
AAATAATACGATCATTTTAAAAAATTAGTATACGAAAATATAAAATTTG
Found at i:30364931 original size:13 final size:13
Alignment explanation
Indices: 30364908--30364932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30364898 CATTATTTAA
30364908 TTTTATTATTATG
1 TTTTATTATTATG
30364921 TTTTATTATTAT
1 TTTTATTATTAT
30364933 TTATTTTTTG
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTATTATTATG
Found at i:30372117 original size:261 final size:261
Alignment explanation
Indices: 30371496--30372279 Score: 976
Period size: 261 Copynumber: 3.0 Consensus size: 261
30371486 TCTCTCAGTT
**
30371496 GATGAAACTCAATTTGAATCACTCAAATCGCAGTCTTTACGATCCACCATTTCGC-TCTCTTCCC
1 GATGAAACTCAATTTGAATCACTCAAATCGCAGTCTTTACGATCCACGGTTTC-CTTCTCTTCCC
* * * * * **
30371560 AAGTTAGTTCAGAGTCACCCTCACCGATTAGCATGTCTCCCTTGCATTCCAGTTCTTCAGAATCA
65 AAGTTAGTTCACAGTCACCTTCACCAACTAGCATGTCTCCATCACATTCCAGTTCTTCAGAATCA
* *
30371625 CCGAAGTACAAAGTGAGTGAGTTGGTGAAGGAAAGGAGTCCCCGCCAGTCTTTTCCTCCTACTT-
130 CCAAAGTACAAAGTGAGTGAATTGGTGAAGGAAAGGAGTCCCCGCCAGTCTTTTCCTCCTACTTC
* * ** * * * * * *
30371689 --CATCTGCACTGAAACCAACAAGTGGTAAAGCTTCAGTGAAT-CTATCATATTCTCAGAAGGAA
195 ACCATCAGTACCAAAACCAACAAGTAGTAAAGCTTCGGTGAATGC-ATCACATTCTCGGCAGGAT
**
30371751 AAT
259 AGC
* * *
30371754 GATGAGACTCAATTTGAATCACTCAAATCGCACTCTTTACGATCCACAGG-TTCATTCTCTTCCC
1 GATGAAACTCAATTTGAATCACTCAAATCGCAGTCTTTACGATCCAC-GGTTTCCTTCTCTTCCC
* *
30371818 AAGTTAGTTCACAGTCACTTTCACCAACTAGCATGTCTCCATCACATTCCAGTTATGT-AGAATC
65 AAGTTAGTTCACAGTCACCTTCACCAACTAGCATGTCTCCATCACATTCCAGTTCT-TCAGAATC
* *
30371882 ACCAAAGTACAAAGCGAGTGAATTGATGAAGGAAAGGAG-CCTCCGCCAGTCTTTTCCTCCTACT
129 ACCAAAGTACAAAGTGAGTGAATTGGTGAAGGAAAGGAGTCC-CCGCCAGTCTTTTCCTCCTACT
*
30371946 TCACCATCAGTACCAAAACCAACAAGTAGTAAAGCTTCGGTGAATGCATCACATTCTTGGCAGGA
193 TCACCATCAGTACCAAAACCAACAAGTAGTAAAGCTTCGGTGAATGCATCACATTCTCGGCAGGA
30372011 TAGC
258 TAGC
* * * * *
30372015 GGTGAAACTCAATTCGAATCACTCAAA-C-CATGGTCTTTTCGATCCACGGTTTCCTTGTCTTCT
1 GATGAAACTCAATTTGAATCACTCAAATCGCA--GTCTTTACGATCCACGGTTTCCTTCTCTTCC
* * * *
30372078 CAAGTCAGTTCACAGTCACCTTCACCAACTAGGATGTCTCCGTCACATTCCAGTCCTTCAGAATC
64 CAAGTTAGTTCACAGTCACCTTCACCAACTAGCATGTCTCCATCACATTCCAGTTCTTCAGAATC
** * * * *
30372143 ACCAAAGTATGAAGTAAGCGAATTGGTGAAGGAAAGAAGTCCCCGCCAGTCTTTCCCTCCTACTT
129 ACCAAAGTACAAAGTGAGTGAATTGGTGAAGGAAAGGAGTCCCCGCCAGTCTTTTCCTCCTACTT
** * *
30372208 CACCATCAGTACCAAAACCAATGAGTAGTAAAGCTTTGGTGAATGCATCACATTCTCGGCAGTAT
194 CACCATCAGTACCAAAACCAACAAGTAGTAAAGCTTCGGTGAATGCATCACATTCTCGGCAGGAT
*
30372273 AGT
259 AGC
30372276 GATG
1 GATG
30372280 GCTCTGTGTT
Statistics
Matches: 453, Mismatches: 60, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
257 2 0.00
258 168 0.37
259 3 0.01
260 4 0.01
261 273 0.60
262 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (261 bp):
GATGAAACTCAATTTGAATCACTCAAATCGCAGTCTTTACGATCCACGGTTTCCTTCTCTTCCCA
AGTTAGTTCACAGTCACCTTCACCAACTAGCATGTCTCCATCACATTCCAGTTCTTCAGAATCAC
CAAAGTACAAAGTGAGTGAATTGGTGAAGGAAAGGAGTCCCCGCCAGTCTTTTCCTCCTACTTCA
CCATCAGTACCAAAACCAACAAGTAGTAAAGCTTCGGTGAATGCATCACATTCTCGGCAGGATAG
C
Found at i:30380574 original size:30 final size:31
Alignment explanation
Indices: 30380540--30380597 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
30380530 ATTAATAATT
30380540 TGATAA-AATT-TTTCACAAAAAAAATATATA
1 TGATAAGAATTATTTCA-AAAAAAAATATATA
* *
30380570 TGATAAGATTTATTTCAAAAAGAAATAT
1 TGATAAGAATTATTTCAAAAAAAAATAT
30380598 CATGACATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.25
31 13 0.54
32 5 0.21
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.34
Consensus pattern (31 bp):
TGATAAGAATTATTTCAAAAAAAAATATATA
Found at i:30381841 original size:28 final size:27
Alignment explanation
Indices: 30381785--30381848 Score: 65
Period size: 30 Copynumber: 2.2 Consensus size: 27
30381775 ATTAATAATT
* *
30381785 TGATAAGATTTTTCACAAAATAATTATA
1 TGATAAGATTTTTCAAAAAAGAA-TATA
30381813 TGATAAGATTTATTTCAAAAAAGAAATATCA
1 TGATAAGA-TT-TTTCAAAAAAG-AATAT-A
30381844 TGATA
1 TGATA
30381849 TAAGATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.27
29 2 0.07
30 12 0.40
31 8 0.27
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (27 bp):
TGATAAGATTTTTCAAAAAAGAATATA
Found at i:30383633 original size:21 final size:20
Alignment explanation
Indices: 30383604--30383655 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
30383594 TTTTTTTGAG
30383604 TATTATTATTATAAATGTTTAA
1 TATT-TTATTATAAAT-TTTAA
**
30383626 TATTTTATGCTAAATTTTAA
1 TATTTTATTATAAATTTTAA
30383646 -ATTTGTATTA
1 TATTT-TATTA
30383656 GGACAGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 9 0.36
22 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (20 bp):
TATTTTATTATAAATTTTAA
Found at i:30384690 original size:507 final size:503
Alignment explanation
Indices: 30382636--30385351 Score: 3066
Period size: 504 Copynumber: 5.4 Consensus size: 503
30382626 CATATTTCAT
* * * *
30382636 AATTTTTATTAGTACATG-ATTCGCATTTCATAATTAATGCATATTATAATCATTATATAATTTA
1 AATTTGTATTAGTACA-GAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATA
* *
30382700 TTTCTATTGTTATTTTACATATGTTAAGAATTTGAATGGTTTGCTGTAATTTATTCTGTTTTGAT
65 TTTCTATTATTATTTTACATATGTTAAGAATTTGAATGGTTTGCTGTAATCTATTCTGTTTTGAT
* *
30382765 TTGCTTTTGATTTGGGTTTTTTGATTTTCTATTTCTACAGATTATTTTGAGTTTGTTTTGGTTTT
130 TTGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTACAGATTGTTTTGAGTTTGTTTTGGTTTT
* ** * * * * * *
30382830 GTGATTTCCCATTTCTGTA-GG-CTAGTTTGATTTATGGTTTTTTATCTACTCAACTTCTGAGTG
195 ATGATTTTTCATTT-T-TATGGTTTAGTTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTG
* * * * * * **
30382893 GATGGTTGAGTACTATTTTTTTTAAATTGTTATAATAAGTTATG-TTAGCATATTTATTTAAAAA
258 GGTGGTTGAGTACTGTCTCTTTTAAATTGTTATAATAAATGATGCCGA-CATATTTATTT---AA
* * * *
30382957 AAAGAATTTGAATAATTTTCGATACAATATGGTATCAGAGTTAAAGAGAAGTAAATATTTTTAAG
319 AAAGAATTTGAATAATTTTCGAGACAATATGATATCAGAGTTAAAGAG-AGTAGATATTTCTAAG
* * * * *
30383022 TTTTGAAAATATTCAATTTGTTTTTAATATTTTTGAGTTCTAGTTTAACTGTCTTTATTAATATA
383 TTTTAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCTA-TTTAACTGTCTTTATTAATGTA
* ** * *
30383087 TTATTGTTATTGCTGAGTATTATTATTTTAAAGGATTAATTTTGGATACTAAAGTTTA
447 TTATTATT-TTTTTGAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
* * * * *
30383145 AATTTTTATTAGTACGGAATCCATATTTCATAAATAATGCATATTATAATTATTATATAATATAT
1 AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATAT
* * * * * * * *
30383210 TTATATTTTTATTTAACAAATGTTAAGAATTTGAATGGTTTGTTGTAAACTGTTCTCTTTTGATT
66 TTCTATTATTATTTTACATATGTTAAGAATTTGAATGGTTTGCTGTAATCTATTCTGTTTTGATT
* * * * *
30383275 TGCTTTTGATTTGGATTTGTTGATTTTCTATTTCTTCAGATTATTTTGAGTTTGTTTAGGTTTTG
131 TGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTACAGATTGTTTTGAGTTTGTTTTGGTTTTA
* * * *
30383340 TGGTTTTTCATTTCTATGGGTTAGTTTGATTTATTATTTTCTATCCAC-TAACTTTTGAGTGGGT
196 TGATTTTTCATTTTTATGGTTTAGTTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTGGGT
* * * *
30383404 GATTGAGTATTGTCTCTTTTAAATTGTTATAATAAATTATGCCGACATATTTATTAAAAAAAGAA
261 GGTTGAGTACTGTCTCTTTTAAATTGTTATAATAAATGATGCCGACATATTTATT-TAAAAAGAA
* * * * * * * * * *
30383469 TATGAATAATTTTCGATACAATTTGGTATCAGAGTCAAGGAAGAATAAATATTT-TTATTATTTA
325 TTTGAATAATTTTCGAGACAATATGATATCAGAGTTAAAG-AGAGTAGATATTTCTAAGT-TTTA
* *
30383533 AAAATATTCT-ATTTGTTTTCAATATTTTCGAGTTC----TAACTGTCTTTATTAATATATTTTT
388 AAAATATT-TAATTTGTTTTCAATATTTTCGAGTTCTATTTAACTGTCTTTATTAATGTATTATT
* * * *
30383593 ATTTTTTTGAGTATTATTATTATAAATGTTTAATATTT-TATGCTAAATTTTA
452 ATTTTTTTGAGTATTATTATTTTAAAGGATTAAT-TTTGGATGCTAAATTTTA
* *
30383645 AATTTGTATTAGGACAGAATCCACATTTCATTATTAATGCATATTATAATCATTATATAATATA-
1 AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATAT
* * * * * *
30383709 TTCGTATTATTATTTTATATATGTTAAGAATTTGAATGGTTTGTTGTAATCTGTTATGTTTAGGT
66 TTC-TATTATTATTTTACATATGTTAAGAATTTGAATGGTTTGCTGTAATCTATTCTGTTTTGAT
* * *
30383774 TTGCTTTTTA-TTGGAGTTTGTTGATTTTCTATTTTTACAGATTGTTTTGAGTTTATTTTGG-TT
130 TTGCTTTTGATTTGG-GTTTGTTGATTTTCTATTTCTACAGATTGTTTTGAGTTTGTTTTGGTTT
* * * * * * *
30383837 TATGATTTTTCATTTTTATGGTTTGGTTTGATATT-TGATTTTTTATTCACTCAACTTCTAAGTT
194 TATGATTTTTCATTTTTATGGTTTAGTTTGAT-TTATGATTTTCTATCCACTTAACTTTTGAGTG
* * * *
30383901 GGTGGTTGAATACTGTCTCATTTAAATTGATATAATAAATGATGCCGACATATTTATTCAAAAA-
258 GGTGGTTGAGTACTGTCTCTTTTAAATTGTTATAATAAATGATGCCGACATATTTATTTAAAAAG
* * * * * *
30383965 AA-TTGTATAATTTTCGAGATAATATGATATCAGA-ATCAAGA-AGGAGCATATACTTTTAAGTT
323 AATTTGAATAATTTTCGAGACAATATGATATCAGAGTTAAAGAGAGTAG-ATAT--TTCTAAGTT
* * * * * * * *
30384027 TTAAAAATATTCAATTTATTTTTAATATTTCCAAGATCTGTTTTAACTGTTTTTATTAATGTATT
385 TTAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCT-ATTTAACTGTCTTTATTAATGTATT
* * *
30384092 ATTATTTTTGCTGAGTATTATTATTTTAAATGATTAATTTTGGATACTAAATTTTA
449 ATTATTTTT-TTGAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
*
30384148 AATTTGTATTAGTACAGAATCCACATTTTATAATTAATGCATATTATAATCATTATATAATATAT
1 AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATAT
* * *
30384213 TTCTATTGTTATTTTACATATGTTAAGAATTTAAATGGTTTGCTGTAATTTATTCTGTTTTGATT
66 TTCTATTATTATTTTACATATGTTAAGAATTTGAATGGTTTGCTGTAATCTATTCTGTTTTGATT
* * * *
30384278 TGCTTTTAATTTGGGTTTGCTTGTTTTTC-ATTTTTATAGATTGTTTTGAGTTTGTTTTGGTTTT
131 TGCTTTTGATTTGGGTTTG-TTGATTTTCTATTTCTACAGATTGTTTTGAGTTTGTTTTGGTTTT
* * * * * * * * *
30384342 TTTATTTTTTATTTTTATGGTTTGGTTTTATTTGTGGTTTTCTATCCACTTAATTTTTCAGTGGG
195 ATGATTTTTCATTTTTATGGTTTAGTTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTGGG
* *
30384407 TGGTTAAGTACTGTCTCTTTTAAAATT-TTATAATAAATGATGCCGACATATTTATTTAAAAATT
260 TGGTTGAGTACTGTCTCTTTT-AAATTGTTATAATAAATGATGCCGACATATTTATTTAAAAA-G
** * * * *
30384471 TTTTTTAATAATTTTC-AGGACAATCTAATATCAGAGTTAAAGAGATGTAGGTATTTCTAAGTTT
323 AATTTGAATAATTTTCGA-GACAATATGATATCAGAGTTAAAGAGA-GTAGATATTTCTAAGTTT
*
30384535 TAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCTGATTTAATTGTCTTTATTAATGTATTA
386 TAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCT-ATTTAACTGTCTTTATTAATGTATTA
*
30384600 TTATATTTTTTGAGTATTATTATTTTAAAGGATTAAATTTGGATGCTAAATTTTA
450 TTAT-TTTTTTGAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
* * *
30384655 AATTTTTATTAGTACAGAATCCAAATTTCATAATTAATGCATATTATAAT-AGATATATAATATA
1 AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCA-TTATATAATATA
* * * * * *
30384719 TTTCTATTATTATTTTAAATATGTTAAGAATTTGAATGGTTTGTTGTAATATGTTATATTTTGAT
65 TTTCTATTATTATTTTACATATGTTAAGAATTTGAATGGTTTGCTGTAATCTATTCTGTTTTGAT
* * *
30384784 TTGCTTTTGA-TTGGGTTTGTTGATATTCCATTTCTATAGATTGTTTTGAGTTTGTTTTGGTTTT
130 TTGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTACAGATTGTTTTGAGTTTGTTTTGGTTTT
* * ** * *
30384848 ATGGTTTTTTATTTTTATTATTT-GTTTTGATTTGTGATTTTCTATCCACTTAATTTTTGAGTGG
195 ATGATTTTTCATTTTTATGGTTTAG-TTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTGG
* ** * * * *
30384912 GTGGTTGAGTATTGTCT-TTCTTAAATTACTATAAAAAATGATGTCGACACATTTA-TTAAAAAA
259 GTGGTTGAGTACTGTCTCTT-TTAAATTGTTATAATAAATGATGCCGACATATTTATTTAAAAAG
* * * * * *
30384975 AATTTGAATAATTTTCG-GTACAATCTAATATCAGAGTCAAGGAAGAGTAGGTATTTCAAAGTTT
323 AATTTGAATAATTTTCGAG-ACAATATGATATCAGAGTTAAAG-AGAGTAGATATTTCTAAGTTT
* * * * *
30385039 TGAAAATATTTAATTTGTTTTCAATATTTTTGAGTTCTAATTTAACTATCTTTATTGATGTATTG
386 TAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCT-ATTTAACTGTCTTTATTAATGTATTA
30385104 TTATTTTTGCTT-AGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
450 TTATTTTT--TTGAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
* * * *
30385159 AATTTGTATTAGTAC-GAAATCTACCTTTCATAATTAATGCATATTATAATCATTAAAAAATATA
1 AATTTGTATTAGTACAG-AATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATA
* * * * * *
30385223 TTTTTATTATTATTTTAGATATGTTTAA-ATTTTGGATGGTTTGCTATAATCTATTCTGTTTAGA
65 TTTCTATTATTATTTTACATATG-TTAAGAATTTGAATGGTTTGCTGTAATCTATTCTGTTTTGA
* ** * *
30385287 TTTGCTTTTGATTTGGGTTTGTTGGTTTTCTATTTCTGTAGATTGTTTTGAATTTATTTTGGTTT
129 TTTGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTACAGATTGTTTTGAGTTTGTTTTGGTTT
30385352 GTACTTTTCT
Statistics
Matches: 1893, Mismatches: 261, Indels: 110
0.84 0.12 0.05
Matches are distributed among these distances:
494 2 0.00
495 5 0.00
496 2 0.00
497 60 0.03
498 5 0.00
499 52 0.03
500 258 0.14
501 29 0.02
502 31 0.02
503 201 0.11
504 386 0.20
505 87 0.05
506 227 0.12
507 264 0.14
508 70 0.04
509 211 0.11
510 3 0.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (503 bp):
AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATAT
TTCTATTATTATTTTACATATGTTAAGAATTTGAATGGTTTGCTGTAATCTATTCTGTTTTGATT
TGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTACAGATTGTTTTGAGTTTGTTTTGGTTTTA
TGATTTTTCATTTTTATGGTTTAGTTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTGGGT
GGTTGAGTACTGTCTCTTTTAAATTGTTATAATAAATGATGCCGACATATTTATTTAAAAAGAAT
TTGAATAATTTTCGAGACAATATGATATCAGAGTTAAAGAGAGTAGATATTTCTAAGTTTTAAAA
ATATTTAATTTGTTTTCAATATTTTCGAGTTCTATTTAACTGTCTTTATTAATGTATTATTATTT
TTTTGAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
Found at i:30385150 original size:504 final size:503
Alignment explanation
Indices: 30382636--30385882 Score: 3064
Period size: 504 Copynumber: 6.5 Consensus size: 503
30382626 CATATTTCAT
* * * *
30382636 AATTTTTATTAGTACATG-ATTCGCATTTCATAATTAATGCATATTATAATCATTATATAATTTA
1 AATTTGTATTAGTACA-GAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATA
* * *
30382700 TTTCTATTGTTATTTTACATATGTTAAGAATTTGAATGGTTTGCTGTAATTTATTCTGTTTTGAT
65 TTTCTATTATTATTTTAAATATGTTAAGAATTTGAATGGTTTGCTGTAATATATTCTGTTTTGAT
* * *
30382765 TTGCTTTTGATTTGGGTTTTTTGATTTTCTATTTCTACAGATTATTTTGAGTTTGTTTTGGTTTT
130 TTGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTATAGATTGTTTTGAGTTTGTTTTGGTTTT
* ** * * * * * * *
30382830 GTGATTTCCCATTTCTGTA-GGCTAGTTTGATTTATGGTTTTTTATCTACTCAACTTCTGAGTGG
195 ATGATTTTTCATTT-T-TATGGTTTGTTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTGG
* * * * * * * **
30382894 ATGGTTGAGTACTATTTTTTTTAAATTGTTATAATAAGTTATG-TTAGCATATTTATTTAAAAAA
258 GTGGTTGAGTACTGTCTCTTTTAAATTATTATAATAAATGATGCCGA-CATATTTA-TT--AAAA
* * *
30382958 AAGAATTTGAATAATTTTCGATACAATATGGTATCAGAGTTAAAG-AGAAGTAAATATTTTTAAG
319 AA-AATTTGAATAATTTTCGGTACAATATGATATCAGAGTCAAAGAAG-AGTAAATA-TTTTAAG
* * * * * *
30383022 TTTTGAAAATATTCAATTTGTTTTTAATATTTTTGAGTTCTAGTTTAACTGTCTTTATTAATATA
381 TTTTAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCTAATTTAACTGTCTTTATTAATGTA
* * * * *
30383087 TTATTGTTATTGCTGAGTATTATTATTTTAAAGGATTAATTTTGGATACTAAAGTTTA
446 TTATTATTTTTGCTTAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
* * * * *
30383145 AATTTTTATTAGTACGGAATCCATATTTCATAAATAATGCATATTATAATTATTATATAATATAT
1 AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATAT
* * * * * *
30383210 TTATATTTTTA-TTTAACAAATGTTAAGAATTTGAATGGTTTGTTGTAA-ACTGTTCTCTTTTGA
66 TTCTATTATTATTTTAA-ATATGTTAAGAATTTGAATGGTTTGCTGTAATA-TATTCTGTTTTGA
* * *
30383273 TTTGCTTTTGATTTGGATTTGTTGATTTTCTATTTCT-TCAGATTATTTTGAGTTTGTTTAGGTT
129 TTTGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTAT-AGATTGTTTTGAGTTTGTTTTGGTT
* * * * *
30383337 TTGTGGTTTTTCATTTCTATGGGTTAGTTTGATTTATTATTTTCTATCCAC-TAACTTTTGAGTG
193 TTATGATTTTTCATTTTTAT-GGTTTGTTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTG
* * * *
30383401 GGTGATTGAGTATTGTCTCTTTTAAATTGTTATAATAAATTATGCCGACATATTTATTAAAAAAA
257 GGTGGTTGAGTACTGTCTCTTTTAAATTATTATAATAAATGATGCCGACATATTTATT-AAAAAA
* * * * * * * *
30383466 GAATATGAATAATTTTCGATACAATTTGGTATCAGAGTCAAGGAAGAATAAATATTTTTATTATT
321 -AATTTGAATAATTTTCGGTACAATATGATATCAGAGTCAAAGAAGAGTAAATATTTTAAGT-TT
*
30383531 TAAAAATATTCT-ATTTGTTTTCAATATTTTCGAGTTC-----TAACTGTCTTTATTAATATATT
384 TAAAAATATT-TAATTTGTTTTCAATATTTTCGAGTTCTAATTTAACTGTCTTTATTAATGTATT
* * * * *
30383590 TTTATTTTT--TTGAGTATTATTATTATAAATGTTTAATATTT-TATGCTAAATTTTA
448 ATTATTTTTGCTT-AGTATTATTATTTTAAAGGATTAAT-TTTGGATGCTAAATTTTA
* *
30383645 AATTTGTATTAGGACAGAATCCACATTTCATTATTAATGCATATTATAATCATTATATAATATA-
1 AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATAT
* * * * * * *
30383709 TTCGTATTATTATTTTATATATGTTAAGAATTTGAATGGTTTGTTGTAATCTGTTATGTTTAGGT
66 TTC-TATTATTATTTTAAATATGTTAAGAATTTGAATGGTTTGCTGTAATATATTCTGTTTTGAT
* * * *
30383774 TTGCTTTTTA-TTGGAGTTTGTTGATTTTCTATTTTTACAGATTGTTTTGAGTTTATTTTGG-TT
130 TTGCTTTTGATTTGG-GTTTGTTGATTTTCTATTTCTATAGATTGTTTTGAGTTTGTTTTGGTTT
* * * * * *
30383837 TATGATTTTTCATTTTTATGGTTTGGTTTGATATT-TGATTTTTTATTCACTCAACTTCTAAGTT
194 TATGATTTTTCATTTTTATGGTTT-GTTTGAT-TTATGATTTTCTATCCACTTAACTTTTGAGTG
* * *
30383901 GGTGGTTGAATACTGTCTCATTTAAATTGA-TATAATAAATGATGCCGACATATTTATTCAAAAA
257 GGTGGTTGAGTACTGTCTCTTTTAAATT-ATTATAATAAATGATGCCGACATATTTATTAAAAAA
* * * * *
30383965 AA-TTGTATAATTTTCGAG-ATAATATGATATCAGAATC-AAGAAGGAGCATATACTTTTAAGTT
321 AATTTGAATAATTTTCG-GTACAATATGATATCAGAGTCAAAGAA-GAGTAAATA-TTTTAAGTT
* * * * * * ** *
30384027 TTAAAAATATTCAATTTATTTTTAATATTTCCAAGATCTGTTTTAACTGTTTTTATTAATGTATT
383 TTAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCTAATTTAACTGTCTTTATTAATGTATT
* * *
30384092 ATTATTTTTGCTGAGTATTATTATTTTAAATGATTAATTTTGGATACTAAATTTTA
448 ATTATTTTTGCTTAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
*
30384148 AATTTGTATTAGTACAGAATCCACATTTTATAATTAATGCATATTATAATCATTATATAATATAT
1 AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATAT
* * * *
30384213 TTCTATTGTTATTTTACATATGTTAAGAATTTAAATGGTTTGCTGTAATTTATTCTGTTTTGATT
66 TTCTATTATTATTTTAAATATGTTAAGAATTTGAATGGTTTGCTGTAATATATTCTGTTTTGATT
* * *
30384278 TGCTTTTAATTTGGGTTTGCTTGTTTTTC-ATTTTTATAGATTGTTTTGAGTTTGTTTTGGTTTT
131 TGCTTTTGATTTGGGTTTG-TTGATTTTCTATTTCTATAGATTGTTTTGAGTTTGTTTTGGTTTT
* * * * * * * *
30384342 TTTATTTTTTATTTTTATGGTTTGGTTTTATTTGTGGTTTTCTATCCACTTAATTTTTCAGTGGG
195 ATGATTTTTCATTTTTATGGTTT-GTTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTGGG
* *
30384407 TGGTTAAGTACTGTCTCTTTTAAAATT-TTATAATAAATGATGCCGACATATTTATTTAAAAATT
259 TGGTTGAGTACTGTCTCTTTT-AAATTATTATAATAAATGATGCCGACATATTTA-TTAAAAA-A
** * * * * **
30384471 TTTTTTAATAATTTTCAGG-ACAATCTAATATCAGAGTTAAAG-AGATGTAGGTATTTCTAAGTT
321 AATTTGAATAATTTTC-GGTACAATATGATATCAGAGTCAAAGAAGA-GTAAATATTT-TAAGTT
* *
30384534 TTAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCTGATTTAATTGTCTTTATTAATGTATT
383 TTAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCTAATTTAACTGTCTTTATTAATGTATT
*
30384599 ATTATATTTT--TTGAGTATTATTATTTTAAAGGATTAAATTTGGATGCTAAATTTTA
448 ATTAT-TTTTGCTT-AGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
* * *
30384655 AATTTTTATTAGTACAGAATCCAAATTTCATAATTAATGCATATTATAAT-AGATATATAATATA
1 AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCA-TTATATAATATA
* * * *
30384719 TTTCTATTATTATTTTAAATATGTTAAGAATTTGAATGGTTTGTTGTAATATGTTATATTTTGAT
65 TTTCTATTATTATTTTAAATATGTTAAGAATTTGAATGGTTTGCTGTAATATATTCTGTTTTGAT
* *
30384784 TTGCTTTTGA-TTGGGTTTGTTGATATTCCATTTCTATAGATTGTTTTGAGTTTGTTTTGGTTTT
130 TTGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTATAGATTGTTTTGAGTTTGTTTTGGTTTT
* * ** * *
30384848 ATGGTTTTTTATTTTTATTATTTGTTTTGATTTGTGATTTTCTATCCACTTAATTTTTGAGTGGG
195 ATGATTTTTCATTTTTATGGTTTG-TTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTGGG
* * * * *
30384913 TGGTTGAGTATTGTCT-TTCTTAAATTACTATAAAAAATGATGTCGACACATTTATTAAAAAAAA
259 TGGTTGAGTACTGTCTCTT-TTAAATTATTATAATAAATGATGCCGACATATTTATTAAAAAAAA
* * * ** * *
30384977 TTTGAATAATTTTCGGTACAATCTAATATCAGAGTCAAGGAAGAGTAGGTATTTCAAAGTTTTGA
323 TTTGAATAATTTTCGGTACAATATGATATCAGAGTCAAAGAAGAGTAAATATTT-TAAGTTTTAA
* * * *
30385042 AAATATTTAATTTGTTTTCAATATTTTTGAGTTCTAATTTAACTATCTTTATTGATGTATTGTTA
387 AAATATTTAATTTGTTTTCAATATTTTCGAGTTCTAATTTAACTGTCTTTATTAATGTATTATTA
30385107 TTTTTGCTTAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
452 TTTTTGCTTAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
* * * *
30385159 AATTTGTATTAGTAC-GAAATCTACCTTTCATAATTAATGCATATTATAATCATTAAAAAATATA
1 AATTTGTATTAGTACAG-AATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATA
* * * * * * *
30385223 TTTTTATTATTATTTTAGATATGTTTAA-ATTTTGGATGGTTTGCTATAATCTATTCTGTTTAGA
65 TTTCTATTATTATTTTAAATATG-TTAAGAATTTGAATGGTTTGCTGTAATATATTCTGTTTTGA
* * * *
30385287 TTTGCTTTTGATTTGGGTTTGTTGGTTTTCTATTTCTGTAGATTGTTTTGAATTTATTTTGG-TT
129 TTTGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTATAGATTGTTTTGAGTTTGTTTTGGTTT
* * * ** **** * * * * ** * *
30385351 TGT-ACTTTTC-TATCCACTCAACT-TTCGA-GT-GGATAGTT-TAGT--ACTGTCTCTTTTAAA
194 TATGATTTTTCATTTTTA-TGGTTTGTTTGATTTATGAT-TTTCTA-TCCACT-TAACTTTTGAG
* ** * ** * * * * * * *
30385408 T-TGT-AATAAAAAATG---ATATTAGCA-TATT-TATTAAA--A-----A-TTA-TTGTT----
255 TGGGTGGTTGAGTACTGTCTCTTTTA-AATTATTATAATAAATGATGCCGACATATTTATTAAAA
* * * ** * * * * **
30385453 ----GTTGAATAAATTTCAGTACAATCGGATAAT-AGTGTCAAGGATGAATAGGTATTTCTAAGT
319 AAAATTTGAATAATTTTCGGTACAATATGAT-ATCAGAGTCAAAGAAGAGTAAATATTT-TAAGT
* * * * * *
30385513 TTT-TAAATATTTAATTT-TTTTTAATGTTTTCGAGTTCTAGTTTAACTTTCTTTGTTAATGTAT
382 TTTAAAAATATTTAATTTGTTTTCAATATTTTCGAGTTCTAATTTAACTGTCTTTATTAATGTAT
* *
30385576 TATTATTATTG-TTGAGTATTATTATTTTAAAGGATTAATTTTGAATGCTAAATTTTA
447 TATTATTTTTGCTT-AGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
* *
30385633 AATTTGTATTAGTACGGAATCCACATTTTATAATTAATGCATATTATAATCATTATATAATATAT
1 AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATAT
* * * * * * **
30385698 TAT-TATTATTATTTTACATATGTTAAGAATTTAAATGATTTTCTGTAATCTGTTCTGTTTAAAT
66 T-TCTATTATTATTTTAAATATGTTAAGAATTTGAATGGTTTGCTGTAATATATTCTGTTTTGAT
* ** ** * * *
30385762 TTGTTTTTGATTTGGGTTTACTGGCTTTCCATTTCTACATATTGTTTTGAGTTTGTTTTGGGTTT
130 TTGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTATAGATTGTTTTGAGTTTGTTTT-GGTTT
* * * * *
30385827 T-TGGA-TTTCCATTTTTGTGGTTTGTTTTGATTTGTAATTTTCTATCCACTCAACTT
194 TAT-GATTTTTCATTTTTATGGTTTG-TTTGATTTATGATTTTCTATCCACTTAACTT
30385883 CTGTTTAAAA
Statistics
Matches: 2303, Mismatches: 350, Indels: 199
0.81 0.12 0.07
Matches are distributed among these distances:
473 6 0.00
474 245 0.11
475 18 0.01
476 60 0.03
477 5 0.00
478 4 0.00
479 4 0.00
480 7 0.00
481 3 0.00
484 4 0.00
485 1 0.00
486 1 0.00
491 1 0.00
493 5 0.00
494 6 0.00
495 2 0.00
496 4 0.00
497 70 0.03
498 17 0.01
499 61 0.03
500 251 0.11
501 39 0.02
502 34 0.01
503 207 0.09
504 384 0.17
505 93 0.04
506 231 0.10
507 268 0.12
508 69 0.03
509 203 0.09
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (503 bp):
AATTTGTATTAGTACAGAATCCACATTTCATAATTAATGCATATTATAATCATTATATAATATAT
TTCTATTATTATTTTAAATATGTTAAGAATTTGAATGGTTTGCTGTAATATATTCTGTTTTGATT
TGCTTTTGATTTGGGTTTGTTGATTTTCTATTTCTATAGATTGTTTTGAGTTTGTTTTGGTTTTA
TGATTTTTCATTTTTATGGTTTGTTTGATTTATGATTTTCTATCCACTTAACTTTTGAGTGGGTG
GTTGAGTACTGTCTCTTTTAAATTATTATAATAAATGATGCCGACATATTTATTAAAAAAAATTT
GAATAATTTTCGGTACAATATGATATCAGAGTCAAAGAAGAGTAAATATTTTAAGTTTTAAAAAT
ATTTAATTTGTTTTCAATATTTTCGAGTTCTAATTTAACTGTCTTTATTAATGTATTATTATTTT
TGCTTAGTATTATTATTTTAAAGGATTAATTTTGGATGCTAAATTTTA
Found at i:30394640 original size:48 final size:48
Alignment explanation
Indices: 30394588--30394733 Score: 135
Period size: 48 Copynumber: 3.1 Consensus size: 48
30394578 TTTAATATAA
30394588 ATTTTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACT
1 ATTTTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACT
*** * * * * ** *
30394636 ATTTTTAAACTATACATTTTAT-TATTTATTATG-TA-TAATTTTTAA--
1 ATTTTTATTTTA-ATATTATATATATTTAATGTGTTACT-ATAATAAACT
30394681 A--TTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACT
1 ATTTTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACT
30394727 ATTTTTA
1 ATTTTTA
30394734 AACTATACAT
Statistics
Matches: 69, Mismatches: 20, Indels: 18
0.64 0.19 0.17
Matches are distributed among these distances:
42 7 0.10
43 15 0.22
44 7 0.10
45 2 0.03
46 2 0.03
47 7 0.10
48 22 0.32
49 7 0.10
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (48 bp):
ATTTTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACT
Found at i:30394690 original size:91 final size:91
Alignment explanation
Indices: 30394591--30394772 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
30394581 AATATAAATT
30394591 TTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACTATTTTTAAACTATACATTTT
1 TTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACTATTTTTAAACTATACATTTT
30394656 ATTATTTATTATGTATAATTTTTAAA
66 ATTATTTATTATGTATAATTTTTAAA
30394682 TTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACTATTTTTAAACTATACATTTT
1 TTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACTATTTTTAAACTATACATTTT
30394747 ATTATTTATTATGTATAATTTTTAAA
66 ATTATTTATTATGTATAATTTTTAAA
30394773 CATCCACACA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (91 bp):
TTTATTTTAATATTATATATATTTAATGTGTTACTATAATAAACTATTTTTAAACTATACATTTT
ATTATTTATTATGTATAATTTTTAAA
Found at i:30394733 original size:43 final size:43
Alignment explanation
Indices: 30394595--30394734 Score: 133
Period size: 43 Copynumber: 3.1 Consensus size: 43
30394585 TAAATTTTTA
30394595 TTTTAATATTATATATATTTAATGTGTTACTATAATAAACTAT
1 TTTTAATATTATATATATTTAATGTGTTACTATAATAAACTAT
* * * * * *
30394638 TTTTAA-ACTATACAT-TTTATTATTTATTATGTATAATTTTTAAA-TTT
1 TTTTAATATTATATATATTTA--ATGTGTTA-CTATAA----TAAACTAT
30394685 ATTTTAATATTATATATATTTAATGTGTTACTATAATAAACTAT
1 -TTTTAATATTATATATATTTAATGTGTTACTATAATAAACTAT
30394729 TTTTAA
1 TTTTAA
30394735 ACTATACATT
Statistics
Matches: 74, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
41 4 0.05
42 7 0.09
43 22 0.30
44 7 0.09
47 7 0.09
48 16 0.22
49 7 0.09
50 4 0.05
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (43 bp):
TTTTAATATTATATATATTTAATGTGTTACTATAATAAACTAT
Found at i:30394765 original size:44 final size:44
Alignment explanation
Indices: 30394625--30394765 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 44
30394615 AATGTGTTAC
30394625 TATAATAAACTATTTTTAAACTATACATTTTATTATTTATTATG
1 TATAATAAACTATTTTTAAACTATACATTTTATTATTTATTATG
* * * * * *
30394669 TATAATTTTTAAA-TTTATTTTAATATTATATATATTTA--ATGTGTTA-C
1 TATAA----TAAACTAT-TTTTAA-ACTATACAT-TTTATTATTTATTATG
30394716 TATAATAAACTATTTTTAAACTATACATTTTATTATTTATTATG
1 TATAATAAACTATTTTTAAACTATACATTTTATTATTTATTATG
30394760 TATAAT
1 TATAAT
30394766 TTTTAAACAT
Statistics
Matches: 74, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
41 4 0.05
42 7 0.09
43 16 0.22
44 13 0.18
47 7 0.09
48 16 0.22
49 7 0.09
50 4 0.05
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (44 bp):
TATAATAAACTATTTTTAAACTATACATTTTATTATTTATTATG
Found at i:30394868 original size:33 final size:32
Alignment explanation
Indices: 30394831--30394926 Score: 92
Period size: 32 Copynumber: 3.0 Consensus size: 32
30394821 GGAAATATAT
30394831 GATAAGATTTATTTCCTAAAAAATATATTATGA
1 GATAAGATTTATTTCCTAAAAAA-ATATTATGA
* *
30394864 GATAAGATTTGTTAT--AAAAAAAATATTATGA
1 GATAAGATTTATT-TCCTAAAAAAATATTATGA
* *
30394895 -A-AAGGTTGATTTCCTTAAACAAAATATTATGA
1 GATAAGATTTATTTCC-TAAA-AAAATATTATGA
30394927 AACGATTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
28 1 0.02
29 7 0.13
30 1 0.02
31 12 0.23
32 18 0.35
33 12 0.23
34 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.36
Consensus pattern (32 bp):
GATAAGATTTATTTCCTAAAAAAATATTATGA
Found at i:30395387 original size:18 final size:19
Alignment explanation
Indices: 30395353--30395388 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30395343 TAAATAATTA
30395353 TTTAAAAATTCTATTTATT
1 TTTAAAAATTCTATTTATT
*
30395372 TTTAAATATT-TATTTAT
1 TTTAAAAATTCTATTTAT
30395389 GTATCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAAAAATTCTATTTATT
Found at i:30400532 original size:59 final size:59
Alignment explanation
Indices: 30400425--30400601 Score: 223
Period size: 59 Copynumber: 3.0 Consensus size: 59
30400415 TTTGCCTAAT
* * * * *
30400425 AACAAATTTAGCTCTCTAATGTTTAC-ATATTCTATCAATTTAATTCTAAATCTAAAATTC
1 AACAAATTTAGCCCTC-AATATTTACAAAATT-TGTCAATTTAATTCTAATTCTAAAATTC
* *
30400485 AACAAATTTAGCCCTCAATATTTACAAAATTTGTCATTTTAGTTCTAATTCTAAAAATTC
1 AACAAATTTAGCCCTCAATATTTACAAAATTTGTCAATTTAATTCTAATTCT-AAAATTC
* * *
30400545 AATACATTTA-CCCTCAATATTTACAAAATTTGTCAATTTAATTCTATTTCTAAAATT
1 AACAAATTTAGCCCTCAATATTTACAAAATTTGTCAATTTAATTCTAATTCTAAAATT
30400602 TTAAAAAAGG
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
58 6 0.06
59 63 0.61
60 34 0.33
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.42
Consensus pattern (59 bp):
AACAAATTTAGCCCTCAATATTTACAAAATTTGTCAATTTAATTCTAATTCTAAAATTC
Found at i:30407828 original size:22 final size:21
Alignment explanation
Indices: 30407803--30407849 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 21
30407793 TTTAAATGTG
30407803 TTTAATAATT-ATTTTATTTTTA
1 TTTAAT-ATTAATTTTA-TTTTA
30407825 TTTAATATTAAATTTTATTTTA
1 TTTAATATT-AATTTTATTTTA
30407847 TTT
1 TTT
30407850 CACTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.13
22 14 0.61
23 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTAATATTAATTTTATTTTA
Found at i:30408424 original size:21 final size:21
Alignment explanation
Indices: 30408404--30408442 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30408394 TGAATGATAT
30408404 TAAA-AAAAACATAAAGAATA
1 TAAAGAAAAACATAAAGAATA
* *
30408424 TAAAGAAAAATATATAGAA
1 TAAAGAAAAACATAAAGAA
30408443 GATGGAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (21 bp):
TAAAGAAAAACATAAAGAATA
Found at i:30409245 original size:3 final size:3
Alignment explanation
Indices: 30409237--30409263 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
30409227 ATAAATTTAA
30409237 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
30409264 TTCCTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30431615 original size:19 final size:20
Alignment explanation
Indices: 30431588--30431625 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
30431578 TAAAAATATC
30431588 ATATCAATAAT-TTAACAAA
1 ATATCAATAATATTAACAAA
*
30431607 ATATTAATAATATTAACAA
1 ATATCAATAATATTAACAA
30431626 CTAGATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATCAATAATATTAACAAA
Found at i:30434027 original size:17 final size:18
Alignment explanation
Indices: 30434007--30434042 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
30433997 ATTTATTAAG
*
30434007 ATATTTTTTTTATT-TTT
1 ATATTTATTTTATTGTTT
30434024 ATATTTATTTTATTGTTT
1 ATATTTATTTTATTGTTT
30434042 A
1 A
30434043 AGTTTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
ATATTTATTTTATTGTTT
Found at i:30435322 original size:17 final size:15
Alignment explanation
Indices: 30435291--30435343 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
30435281 AATTAAATTT
*
30435291 AACTAAAAAAT-AAA
1 AACTAAAATATAAAA
30435305 AACTAAAATGATAAAA
1 AACTAAAAT-ATAAAA
* *
30435321 AAATATAAATATTAAA
1 AACTA-AAATATAAAA
30435337 AACTAAA
1 AACTAAA
30435344 TTTGATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 8 0.25
15 4 0.12
16 16 0.50
17 4 0.12
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.21
Consensus pattern (15 bp):
AACTAAAATATAAAA
Found at i:30440013 original size:76 final size:76
Alignment explanation
Indices: 30439883--30440038 Score: 249
Period size: 76 Copynumber: 2.1 Consensus size: 76
30439873 TCAAAACGTT
* * * *
30439883 TTAATGACTTCTCAATATAGCAATATCGTAAATTAAGTATTTTCATTAGTCAATTTGTCAGTTTA
1 TTAATGACTTCTCAATATAGCAATATCGTAAACTAAGTACTTTCATTAGCCAATTTGTCAATTTA
30439948 GTCATTAAATG
66 GTCATTAAATG
* * *
30439959 TTAATGAGTTCTCAATATAGCAATCTTGTAAACTAAGTACTTTCATTAGCCAATTTGTCAATTTA
1 TTAATGACTTCTCAATATAGCAATATCGTAAACTAAGTACTTTCATTAGCCAATTTGTCAATTTA
30440024 GTCATTAAATG
66 GTCATTAAATG
30440035 TTAA
1 TTAA
30440039 CTTTGATGAG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (76 bp):
TTAATGACTTCTCAATATAGCAATATCGTAAACTAAGTACTTTCATTAGCCAATTTGTCAATTTA
GTCATTAAATG
Found at i:30442076 original size:23 final size:23
Alignment explanation
Indices: 30442063--30442172 Score: 150
Period size: 23 Copynumber: 4.8 Consensus size: 23
30442053 TACTGTTCAA
*
30442063 CACTGTGTGTGCTTACTGATTCG
1 CACTGTGTGTGCTTACTGATTTG
* * *
30442086 CACTATATGTGCCTACTGATTTG
1 CACTGTGTGTGCTTACTGATTTG
*
30442109 CACTGCGTGTGCTTACT-ATTTTG
1 CACTGTGTGTGCTTACTGA-TTTG
*
30442132 CACTGTGTGTGCCTACTGATTTG
1 CACTGTGTGTGCTTACTGATTTG
30442155 CACTGTGTGTGCTTACTG
1 CACTGTGTGTGCTTACTG
30442173 TTTCCCCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
22 1 0.01
23 72 0.97
24 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (23 bp):
CACTGTGTGTGCTTACTGATTTG
Found at i:30442120 original size:46 final size:47
Alignment explanation
Indices: 30442063--30442176 Score: 171
Period size: 46 Copynumber: 2.5 Consensus size: 47
30442053 TACTGTTCAA
30442063 CACTGTGTGTGCTTACTGA-TTCGCACTATATGTGCCTACTGATTTG
1 CACTGTGTGTGCTTACTGATTTCGCACTATATGTGCCTACTGATTTG
* * * *
30442109 CACTGCGTGTGCTTACT-ATTTTGCACTGTGTGTGCCTACTGATTTG
1 CACTGTGTGTGCTTACTGATTTCGCACTATATGTGCCTACTGATTTG
30442155 CACTGTGTGTGCTTACTG-TTTC
1 CACTGTGTGTGCTTACTGATTTC
30442177 CCCAGCACTT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
45 1 0.02
46 59 0.98
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (47 bp):
CACTGTGTGTGCTTACTGATTTCGCACTATATGTGCCTACTGATTTG
Done.