Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008708.1 Hibiscus syriacus cultivar Beakdansim tig00111754_pilon, whole genome shotgun sequence
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: 1112311
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:2817 original size:7 final size:7
Alignment explanation
Indices: 2796--2863 Score: 54
Period size: 7 Copynumber: 9.4 Consensus size: 7
2786 AAAAGGGAAC
2796 AAAT-AA
1 AAATGAA
2802 AAGATGAA
1 AA-ATGAA
2810 AAATGAAAA
1 AAATG--AA
2819 AAATGAA
1 AAATGAA
2826 AAA-GAAAA
1 AAATG--AA
2834 AAATGAA
1 AAATGAA
2841 AAATGAA
1 AAATGAA
2848 AAA--AA
1 AAATGAA
2853 GAAATGAA
1 -AAATGAA
2861 AAA
1 AAA
2864 ATAAAAGAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 19
0.73 0.00 0.27
Matches are distributed among these distances:
5 2 0.04
6 6 0.12
7 25 0.48
8 11 0.21
9 8 0.15
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.10
Consensus pattern (7 bp):
AAATGAA
Found at i:2819 original size:16 final size:16
Alignment explanation
Indices: 2800--2864 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
2790 GGGAACAAAT
*
2800 AAAAGATGAAAAATGA
1 AAAAAATGAAAAATGA
2816 AAAAAATGAAAAA-GA
1 AAAAAATGAAAAATGA
2831 AAAAAATGAAAAATGA
1 AAAAAATGAAAAATGA
2847 AAAAAA-G--AAATGA
1 AAAAAATGAAAAATGA
2860 AAAAA
1 AAAAA
2865 TAAAAGAGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
13 11 0.23
15 16 0.34
16 20 0.43
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (16 bp):
AAAAAATGAAAAATGA
Found at i:2827 original size:24 final size:21
Alignment explanation
Indices: 2796--2877 Score: 80
Period size: 21 Copynumber: 3.8 Consensus size: 21
2786 AAAAGGGAAC
2796 AAATAAAAGATGAAAAATGAAAA
1 AAATAAAAGA-GAAAAATG-AAA
*
2819 AAATGAAAAAGAAAAAAATG-AA
1 AAAT--AAAAGAGAAAAATGAAA
2841 AAATGAAAA-A-AAGAAATGAAA
1 AAAT-AAAAGAGAA-AAATGAAA
2862 AAATAAAAGAGAAAAA
1 AAATAAAAGAGAAAAA
2878 GGAGGGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
19 2 0.04
20 10 0.20
21 14 0.27
22 8 0.16
23 4 0.08
24 7 0.14
25 6 0.12
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (21 bp):
AAATAAAAGAGAAAAATGAAA
Found at i:2840 original size:31 final size:29
Alignment explanation
Indices: 2800--2864 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 29
2790 GGGAACAAAT
*
2800 AAAAGATGAAAAATGAAAAAAATGAAAAAGA
1 AAAAAATGAAAAATGAAAAAAA-G-AAAAGA
*
2831 AAAAAATGAAAAATGAAAAAAAGAAATGA
1 AAAAAATGAAAAATGAAAAAAAGAAAAGA
2860 AAAAA
1 AAAAA
2865 TAAAAGAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 10 0.31
30 1 0.03
31 21 0.66
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (29 bp):
AAAAAATGAAAAATGAAAAAAAGAAAAGA
Found at i:2877 original size:15 final size:15
Alignment explanation
Indices: 2800--2877 Score: 83
Period size: 15 Copynumber: 5.3 Consensus size: 15
2790 GGGAACAAAT
*
2800 AAAAGATGAAAAATGA
1 AAAAAATGAAAAA-GA
2816 AAAAAATGAAAAAGA
1 AAAAAATGAAAAAGA
2831 AAAAAATGAAAAATGA
1 AAAAAATGAAAAA-GA
*
2847 AAAAAA-G-AAATG-
1 AAAAAATGAAAAAGA
2859 AAAAAAT-AAAAGAGA
1 AAAAAATGAAAA-AGA
2874 AAAA
1 AAAA
2878 GGAGGGTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
12 6 0.11
13 4 0.07
14 4 0.07
15 20 0.37
16 20 0.37
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (15 bp):
AAAAAATGAAAAAGA
Found at i:4318 original size:105 final size:105
Alignment explanation
Indices: 4098--4352 Score: 314
Period size: 105 Copynumber: 2.4 Consensus size: 105
4088 CTCGCTTGAG
*
4098 GGATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
1 GGATCAACATTTCC--TGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
* * * * **
4163 TGAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
64 TGAGAAAAACATGTTCCTTTCAAATCCACCACAAAAAGAGGT
* * * * *
4205 GAACCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTCCTAAATGAGAAAGTTCATAATG
1 GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
* * **
4270 AGAAAAACATGTT-CTTTCTAAGTCCACCGCAAAAAGATTT
66 AGAAAAACATGTTCCTTTC-AAATCCACCACAAAAAGAGGT
**
4310 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATC
1 GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATC
4353 CACGTGAAAA
Statistics
Matches: 126, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
104 5 0.04
105 110 0.87
107 11 0.09
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (105 bp):
GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
AGAAAAACATGTTCCTTTCAAATCCACCACAAAAAGAGGT
Found at i:4531 original size:3 final size:3
Alignment explanation
Indices: 4516--4558 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
4506 AGTTAAAAAA
*
4516 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4559 AGTGTGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 36 0.97
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:6271 original size:2 final size:2
Alignment explanation
Indices: 6264--6297 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6254 CCTTACGTAA
6264 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
6298 TCCCAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7084 original size:30 final size:29
Alignment explanation
Indices: 7024--7085 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
7014 TAAATAATAT
*
7024 TTTAGTCATTTGAGTTTTTATTTATTTTA
1 TTTAGTCATTTGAGTTTCTATTTATTTTA
* *
7053 TTTAGGTCCTTTGAGTTTCTGTTT-TTGTTA
1 TTTA-GTCATTTGAGTTTCTATTTATT-TTA
7083 TTT
1 TTT
7086 TCATCCTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.65
Consensus pattern (29 bp):
TTTAGTCATTTGAGTTTCTATTTATTTTA
Found at i:7225 original size:30 final size:30
Alignment explanation
Indices: 7149--7227 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
7139 TGTTTTTGCC
*
7149 ATTTTAGTCTTTTAAATTTCATCTTGTGAT
1 ATTTTAGTCTTTTAAATTTCATATTGTGAT
* ** * *
7179 A-TTTGGTCTTCAAAATTT-ATATTTTTACT
1 ATTTTAGTCTTTTAAATTTCATATTGTGA-T
7208 ATTTTAGTCTTTTAAATTTC
1 ATTTTAGTCTTTTAAATTTC
7228 TGTTTCTGTC
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
28 6 0.16
29 16 0.43
30 15 0.41
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (30 bp):
ATTTTAGTCTTTTAAATTTCATATTGTGAT
Found at i:7272 original size:30 final size:30
Alignment explanation
Indices: 7207--7272 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
7197 ATATTTTTAC
* *
7207 TATTTTAGTCTTTTAAATTTCTGTTTCTGT
1 TATTTTAGTCCTTTAAATTTCTATTTCTGT
* * *
7237 CATTTTAGTCCTTTAATTTTTTAATTT-TGT
1 TATTTTAGTCCTTTAAATTTCT-ATTTCTGT
7267 TATTTT
1 TATTTT
7273 GATTCTTAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.18, C:0.09, G:0.08, T:0.65
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAATTTCTATTTCTGT
Found at i:7377 original size:22 final size:22
Alignment explanation
Indices: 7352--7405 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
7342 TGATTTGTAA
* *
7352 TATTTATTTGTTTTATTTCAGT
1 TATTTATTTGTCTTATTTAAGT
*
7374 TATTTGAATT-TCTTATTTAAGT
1 TATTT-ATTTGTCTTATTTAAGT
*
7396 TATTAATTTG
1 TATTTATTTG
7406 AAGCAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 3 0.12
22 19 0.76
23 3 0.12
ACGTcount: A:0.24, C:0.04, G:0.09, T:0.63
Consensus pattern (22 bp):
TATTTATTTGTCTTATTTAAGT
Found at i:9958 original size:12 final size:12
Alignment explanation
Indices: 9941--9966 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9931 TTGCATTAAT
9941 TTTCAACAATTG
1 TTTCAACAATTG
9953 TTTCAACAATTG
1 TTTCAACAATTG
9965 TT
1 TT
9967 GGCGCCACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTCAACAATTG
Found at i:10797 original size:23 final size:23
Alignment explanation
Indices: 10761--10807 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
10751 AAATGTGCCA
**
10761 AAAGACAGAAGAAAATTTGTCAT
1 AAAGACAGAAGAAAACGTGTCAT
* *
10784 AAAGACATATGAAAACGTGTCAT
1 AAAGACAGAAGAAAACGTGTCAT
10807 A
1 A
10808 TATGCAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (23 bp):
AAAGACAGAAGAAAACGTGTCAT
Found at i:11112 original size:2 final size:2
Alignment explanation
Indices: 11107--11145 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11097 GTGTGTGAAT
11107 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11146 CATTAAGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12181 original size:2 final size:2
Alignment explanation
Indices: 12174--12208 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12164 TGGGAAATTG
12174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12209 CCTTTGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13469 original size:24 final size:24
Alignment explanation
Indices: 13437--13484 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
13427 TAAAGGAAAA
13437 TCCACCGTTACGTTCCTATTTAGG
1 TCCACCGTTACGTTCCTATTTAGG
*
13461 TCCACCGTTACGTTCCTTTTTAGG
1 TCCACCGTTACGTTCCTATTTAGG
13485 GAAGATTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.29, G:0.17, T:0.40
Consensus pattern (24 bp):
TCCACCGTTACGTTCCTATTTAGG
Found at i:13665 original size:27 final size:27
Alignment explanation
Indices: 13634--13694 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
13624 TAATAATAGA
*
13634 AAATTTTCGTAGAAAATAGACACAAAT
1 AAATTTTCATAGAAAATAGACACAAAT
* * *
13661 AAA-TTTCATATAAAGTAGATACAAAT
1 AAATTTTCATAGAAAATAGACACAAAT
13687 AGAATTTT
1 A-AATTTT
13695 AAGGTAGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 20 0.71
27 5 0.18
28 3 0.11
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTTTCATAGAAAATAGACACAAAT
Found at i:16512 original size:17 final size:17
Alignment explanation
Indices: 16490--16523 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16480 GTTTTGTTAA
* *
16490 AATATATTAAATTATAT
1 AATATATAAAAATATAT
16507 AATATATAAAAATATAT
1 AATATATAAAAATATAT
16524 TAAAATTAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATATAAAAATATAT
Found at i:16582 original size:9 final size:9
Alignment explanation
Indices: 16570--16597 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
16560 TTTTTCGGAT
16570 TTTTTTATA
1 TTTTTTATA
16579 TTTTTTATA
1 TTTTTTATA
16588 TTTTTTATA
1 TTTTTTATA
16597 T
1 T
16598 ATGTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTATA
Found at i:23754 original size:2 final size:2
Alignment explanation
Indices: 23747--23801 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
23737 TTAATCCTTC
* * *
23747 AT AT AT AT AT AT AT AT TT TT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23789 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
23802 ACTCATTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:23772 original size:20 final size:20
Alignment explanation
Indices: 23747--23801 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
23737 TTAATCCTTC
*
23747 ATATATATATATATATTTTT
1 ATATATATATATATATATTT
23767 ATATATATATATATATATTT
1 ATATATATATATATATATTT
23787 ATATATATATATATA
1 ATATATATATATATA
23802 ACTCATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATATATATATATATTT
Found at i:24183 original size:44 final size:44
Alignment explanation
Indices: 24120--24289 Score: 301
Period size: 44 Copynumber: 3.9 Consensus size: 44
24110 GAGTTTGTCC
24120 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
24164 CATCTCAAATTAGACTTACTCTATTTTCTCG---ACACGTTCTT
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
*
24205 CATCTCAAATTAGTCTTACTCTATTTTCTCGACCACACGTTCTT
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
*
24249 CATCTCAAATTAGACTTACTCTTTTTTCTCGACCACACGTT
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTT
24290 ATTCGTTCGT
Statistics
Matches: 120, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
41 40 0.33
44 80 0.67
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.40
Consensus pattern (44 bp):
CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
Found at i:24263 original size:85 final size:85
Alignment explanation
Indices: 24120--24281 Score: 306
Period size: 85 Copynumber: 1.9 Consensus size: 85
24110 GAGTTTGTCC
24120 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
24185 TATTTTCTCGACACGTTCTT
66 TATTTTCTCGACACGTTCTT
*
24205 CATCTCAAATTAGTCTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
*
24270 TTTTTTCTCGAC
66 TATTTTCTCGAC
24282 CACACGTTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (85 bp):
CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
TATTTTCTCGACACGTTCTT
Found at i:26166 original size:44 final size:44
Alignment explanation
Indices: 26103--26306 Score: 369
Period size: 44 Copynumber: 4.7 Consensus size: 44
26093 CGACCCAACC
26103 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAAT
1 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAAT
*
26147 TAGACTTACTCTTTTTTCTCG---ACACGTTCTTCATCTCAAAT
1 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAAT
26188 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAAT
1 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAAT
26232 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAAT
1 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAAT
*
26276 TAGACTTACTCTTTTTTCTCGACCACACGTT
1 TAGACTTACTCTATTTTCTCGACCACACGTT
26307 ATTCGTTCGT
Statistics
Matches: 154, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
41 40 0.26
44 114 0.74
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.40
Consensus pattern (44 bp):
TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAAT
Found at i:26249 original size:85 final size:86
Alignment explanation
Indices: 26103--26306 Score: 365
Period size: 85 Copynumber: 2.4 Consensus size: 86
26093 CGACCCAACC
*
26103 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTCTTTTTTCTCG
1 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTCTATTTTCTCG
26168 -ACACGTTCTTCATCTCAAAT
66 CACACGTTCTTCATCTCAAAT
26188 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTCTATTTTCTCG
1 TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTCTATTTTCTCG
26253 ACCACACGTTCTTCATCTCAAAT
66 --CACACGTTCTTCATCTCAAAT
*
26276 TAGACTTACTCTTTTTTCTCGACCACACGTT
1 TAGACTTACTCTATTTTCTCGACCACACGTT
26307 ATTCGTTCGT
Statistics
Matches: 114, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
85 64 0.56
88 50 0.44
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.40
Consensus pattern (86 bp):
TAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTCTATTTTCTCG
CACACGTTCTTCATCTCAAAT
Found at i:32983 original size:36 final size:36
Alignment explanation
Indices: 32942--33082 Score: 153
Period size: 36 Copynumber: 3.9 Consensus size: 36
32932 AAGTCTCTAC
* *
32942 AGGTTCAGTTCTAATCAAGCTGGTAATTCCTTATAT
1 AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
* * **
32978 AGGTTCAGCACCGATCAA-CTAATAATTCCTTAT-T
1 AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
33012 GCAGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
1 --AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
* ** *
33050 AGGTTCAACAATGATC-AGCTGATAATTCCTTAT
1 AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTAT
33083 GGACCTAAGG
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
34 1 0.01
35 29 0.33
36 43 0.49
37 13 0.15
38 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (36 bp):
AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
Found at i:33066 original size:72 final size:72
Alignment explanation
Indices: 32941--33082 Score: 221
Period size: 72 Copynumber: 2.0 Consensus size: 72
32931 GAAGTCTCTA
* * *
32941 CAGGTTCAGTTCTAATCAAGCTGGTAATTCCTTATATAGGTTCAGCACCGATCAACTAATAATTC
1 CAGGTTCAGCTCTAATCAAGCTGGTAATTCCTTATATAGGTTCAACAACGATCAACTAATAATTC
33006 CTTATTG
66 CTTATTG
* * * *
33013 CAGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATATAGGTTCAACAATGATCAGCTGATAATTC
1 CAGGTTCAGCTCTAATCAAGCTGGTAATTCCTTATATAGGTTCAACAACGATCAACTAATAATTC
33078 CTTAT
66 CTTAT
33083 GGACCTAAGG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (72 bp):
CAGGTTCAGCTCTAATCAAGCTGGTAATTCCTTATATAGGTTCAACAACGATCAACTAATAATTC
CTTATTG
Found at i:33077 original size:35 final size:35
Alignment explanation
Indices: 32959--33082 Score: 142
Period size: 35 Copynumber: 3.5 Consensus size: 35
32949 GTTCTAATCA
* *
32959 AGCTGGTAATTCCTTATATAGGTTCAGCACCGATC
1 AGCTGATAATTCCTTATATAGGTTCAGCACTGATC
* * *
32994 AACTAATAATTCCTTAT-TGCAGGTTCAGCTCTGATC
1 AGCTGATAATTCCTTATAT--AGGTTCAGCACTGATC
* * *
33030 AAGCTGGTAATTCCTTATATAGGTTCAACAATGATC
1 -AGCTGATAATTCCTTATATAGGTTCAGCACTGATC
33066 AGCTGATAATTCCTTAT
1 AGCTGATAATTCCTTAT
33083 GGACCTAAGG
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
34 1 0.01
35 30 0.41
36 27 0.37
37 14 0.19
38 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (35 bp):
AGCTGATAATTCCTTATATAGGTTCAGCACTGATC
Found at i:33641 original size:14 final size:14
Alignment explanation
Indices: 33622--33649 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33612 CCGATGGCAT
33622 ATTGCATTCATCTA
1 ATTGCATTCATCTA
33636 ATTGCATTCATCTA
1 ATTGCATTCATCTA
33650 GTAGTTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTGCATTCATCTA
Found at i:50735 original size:14 final size:16
Alignment explanation
Indices: 50716--50748 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
50706 TTAAAATATC
50716 TATTTGATA-CTG-TT
1 TATTTGATATCTGATT
50730 TATTTGATATCTGATT
1 TATTTGATATCTGATT
50746 TAT
1 TAT
50749 GGCACACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 3 0.18
16 5 0.29
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (16 bp):
TATTTGATATCTGATT
Found at i:59355 original size:115 final size:115
Alignment explanation
Indices: 59153--59974 Score: 1204
Period size: 115 Copynumber: 7.2 Consensus size: 115
59143 TTTTAAAGAC
* * * * * *
59153 AAGTGGAACAACTCTGCCCCCATTCAGTGGATCAAGCTCCTCCAATATTTGATATTCCCTTCATA
1 AAGTGGAACAAGTCTGCCCCCATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
* *
59218 GTAAGCGTAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAAAGT
66 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
*
59268 AAGTGGAACAAGTCTGCCCCCATTCAGTGGATCAAACTCCTGTAAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTCTGCCCCCATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
59333 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
66 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
** * * *
59383 AAGTGGAACAAGTCTGCCCTGATTCAAG-GAATCGAACTACT-TCAAGATCTGATATTCCCTTCA
1 AAGTGGAACAAGTCTGCCCCCATTC-AGTGGATCAAACTCCTCT-AAGATCTGATATTCCCTTCA
* * *
59446 GAGTAAGCGGAACATGTATCTCTTTCCCAAGATTTGATATTCCCTTAAGAGT
64 GAGTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* *
59498 AAGTGGAACAAGTTTGCCCCCATTCAGTGGATCAAACTCCTCCAAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTCTGCCCCCATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
**
59563 GTAAGCGGAACATATCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
66 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* *
59613 AAGTGGAACAAGTCTGCCCCCATTCAGTGGATCAAACTCCTTTAAGATCTGATATTCCTTTCAGA
1 AAGTGGAACAAGTCTGCCCCCATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
59678 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
66 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
** * * * *
59728 AAGTGGAACAAGTCTGCCCTGATTCAAG-GAATCGAACTCCT-TAAAGATTTGATATTCCTTTCA
1 AAGTGGAACAAGTCTGCCCCCATTC-AGTGGATCAAACTCCTCT-AAGATCTGATATTCCCTTCA
** * * * *
59791 GAGTAAGCAAAATAGATATCTCTTTCCCAATATTTGATATTCCCTTCAGAGT
64 GAGTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* *
59843 AAGTGGAACAAGTCTTCCCCCATTCAGTGGATCAAACTCCTCTAAGATCTGATATTTCCTTCAGA
1 AAGTGGAACAAGTCTGCCCCCATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
* ** *
59908 GTAAGCGGAACAGGTCT-TTTTTTTCAAGATTTGATATTCCCTTCTGAGT
66 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
59957 AAGTGGAACAAGTCTGCC
1 AAGTGGAACAAGTCTGCC
59975 TCAATTCAAT
Statistics
Matches: 636, Mismatches: 63, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
114 50 0.08
115 581 0.91
116 5 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (115 bp):
AAGTGGAACAAGTCTGCCCCCATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
Found at i:59784 original size:345 final size:345
Alignment explanation
Indices: 59153--59974 Score: 1364
Period size: 345 Copynumber: 2.4 Consensus size: 345
59143 TTTTAAAGAC
* * * * * *
59153 AAGTGGAACAACTCTGCCCCCATTCAGTGGATCAAGCTCCTCCAATATTTGATATTCCCTTCATA
1 AAGTGGAACAAGTTTGCCCCCATTCAGTGGATCAAACTCCTCCAAGATCTGATATTCCCTTCAGA
* *
59218 GTAAGCGTAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAAAGTAAGTGGAACAAGTCT
66 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
59283 GCCCCCATTCAGTGGATCAAACTCCTGTAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGT
131 GCCCCCATTCAGTGGATCAAACTCCTGTAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGT
59348 CTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
196 CTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
* *
59413 ATCGAACTACTTCAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAT-G-TATCTCTTTCCCAA
261 ATCGAACTACTTAAAGATCTGATATTCCCTTCAGAGTAAGC--AAAATAGATATCTCTTTCCCAA
59476 GATTTGATATTCCCTTAAGAGT
324 GATTTGATATTCCCTTAAGAGT
59498 AAGTGGAACAAGTTTGCCCCCATTCAGTGGATCAAACTCCTCCAAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTTTGCCCCCATTCAGTGGATCAAACTCCTCCAAGATCTGATATTCCCTTCAGA
**
59563 GTAAGCGGAACATATCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
66 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
* *
59628 GCCCCCATTCAGTGGATCAAACTCCTTTAAGATCTGATATTCCTTTCAGAGTAAGCGGAACAGGT
131 GCCCCCATTCAGTGGATCAAACTCCTGTAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGT
59693 CTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
196 CTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
* * * *
59758 ATCGAACTCCTTAAAGATTTGATATTCCTTTCAGAGTAAGCAAAATAGATATCTCTTTCCCAATA
261 ATCGAACTACTTAAAGATCTGATATTCCCTTCAGAGTAAGCAAAATAGATATCTCTTTCCCAAGA
*
59823 TTTGATATTCCCTTCAGAGT
326 TTTGATATTCCCTTAAGAGT
* *
59843 AAGTGGAACAAGTCTT-CCCCCATTCAGTGGATCAAACTCCTCTAAGATCTGATATTTCCTTCAG
1 AAGTGGAACAAGT-TTGCCCCCATTCAGTGGATCAAACTCCTCCAAGATCTGATATTCCCTTCAG
* ** *
59907 AGTAAGCGGAACAGGTCT-TTTTTTTCAAGATTTGATATTCCCTTCTGAGTAAGTGGAACAAGTC
65 AGTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTC
59971 TGCC
130 TGCC
59975 TCAATTCAAT
Statistics
Matches: 447, Mismatches: 27, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
343 4 0.01
344 47 0.11
345 394 0.88
346 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (345 bp):
AAGTGGAACAAGTTTGCCCCCATTCAGTGGATCAAACTCCTCCAAGATCTGATATTCCCTTCAGA
GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
GCCCCCATTCAGTGGATCAAACTCCTGTAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGT
CTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
ATCGAACTACTTAAAGATCTGATATTCCCTTCAGAGTAAGCAAAATAGATATCTCTTTCCCAAGA
TTTGATATTCCCTTAAGAGT
Found at i:60281 original size:14 final size:13
Alignment explanation
Indices: 60246--60284 Score: 55
Period size: 11 Copynumber: 3.1 Consensus size: 13
60236 TTATTTATAT
60246 TATTATTATAAT-
1 TATTATTATAATA
60258 TA-TATTATAATA
1 TATTATTATAATA
60270 TATTATTAATAATA
1 TATTATT-ATAATA
60284 T
1 T
60285 TAAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.38
12 4 0.17
13 4 0.17
14 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTATTATAATA
Found at i:60574 original size:26 final size:26
Alignment explanation
Indices: 60506--60651 Score: 179
Period size: 26 Copynumber: 5.7 Consensus size: 26
60496 GGGTTTCCAG
*
60506 AACAGGCCACCACCACTTGGACCACTC
1 AACA-GCCACCACCGCTTGGACCACTC
* **
60533 -A-TGCCACTTCCGCTTGGACCACTC
1 AACAGCCACCACCGCTTGGACCACTC
*
60557 AACAGCCACCACCACTTGGACCACTC
1 AACAGCCACCACCGCTTGGACCACTC
*
60583 AACAACCACCACCGCTTGGACCACTC
1 AACAGCCACCACCGCTTGGACCACTC
* * *
60609 GACAACCACCATCGCTTGGACCACTC
1 AACAGCCACCACCGCTTGGACCACTC
*
60635 AACAGCCACCACTGCTT
1 AACAGCCACCACCGCTT
60652 CCAACCACTC
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
24 19 0.19
25 1 0.01
26 81 0.80
ACGTcount: A:0.27, C:0.44, G:0.14, T:0.15
Consensus pattern (26 bp):
AACAGCCACCACCGCTTGGACCACTC
Found at i:63603 original size:7 final size:7
Alignment explanation
Indices: 63591--63622 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
63581 TATCCTAATC
63591 AAATATT
1 AAATATT
63598 AAATATT
1 AAATATT
63605 AAATATT
1 AAATATT
63612 AAATATT
1 AAATATT
63619 AAAT
1 AAAT
63623 TTGATAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATATT
Found at i:63721 original size:2 final size:2
Alignment explanation
Indices: 63716--63771 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
63706 ATGTGTGTGA
63716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63758 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
63772 CAAGTTGAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64306 original size:2 final size:2
Alignment explanation
Indices: 64299--64339 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
64289 TTATGCATTC
64299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64340 CTTTTTATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:69406 original size:15 final size:15
Alignment explanation
Indices: 69376--69404 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
69366 ATATTGAATA
69376 AAAAATATATTTTTT
1 AAAAATATATTTTTT
69391 AAAAATA-ATTTTTT
1 AAAAATATATTTTTT
69405 TATCAGATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAAAATATATTTTTT
Found at i:75522 original size:227 final size:228
Alignment explanation
Indices: 75076--75542 Score: 891
Period size: 227 Copynumber: 2.0 Consensus size: 228
75066 CCCTTGTGGC
*
75076 TTCATAATATAGAAAACGGTAAACTACTCCAATGGTCACTAATGTTTGGATAATTTTTCGTTTTC
1 TTCAT-ATATTGAAAACGGTAAACTACTCCAATGGTCACTAATGTTTGGATAATTTTTCGTTTTC
75141 ACCACTGATGTTTCAAAAGTTACAAATCGGTCACTACCGTTATCATTTGTTTTAAATTGGTCACT
65 ACCACTGATGTTTCAAAAGTTACAAATCGGTCACTACCGTTATCATTTG-TTTAAATTGGTCACT
75206 CGCTGTTAACAGGCATGACGAAAAACAAACGTGACCTGTTAACATAACAGCAGTTAACAGGCTTA
129 CGCTGTTAACAGGCATGACGAAAAACAAACGTGACCTGTTAACATAACAGCAGTTAACAGGCTTA
75271 CCTGGATGGTATAGTTACACAAATAGTCCATGTTA
194 CCTGGATGGTATAGTTACACAAATAGTCCATGTTA
*
75306 TTCATATATTGAAAACGGTAAACTACTCCAATGGTCACTAATGTTTGGATAATTTTTCGTTTTTA
1 TTCATATATTGAAAACGGTAAACTACTCCAATGGTCACTAATGTTTGGATAATTTTTCGTTTTCA
75371 CCACTGATGTTTCAAAAGTTACAAATCGGTCACTACCGTTATCATTTG-TTAAATTGGTCACTCG
66 CCACTGATGTTTCAAAAGTTACAAATCGGTCACTACCGTTATCATTTGTTTAAATTGGTCACTCG
75435 CTGTTAACAGGCATGACGAAAAACAAACGTGACCTGTTAACATAACAGCAGTTAACAGGCTTACC
131 CTGTTAACAGGCATGACGAAAAACAAACGTGACCTGTTAACATAACAGCAGTTAACAGGCTTACC
75500 TGGATGGTATAGTTACACAAATAGTCCATGTTA
196 TGGATGGTATAGTTACACAAATAGTCCATGTTA
75533 TTCATATATT
1 TTCATATATT
75543 CTTTCAATTT
Statistics
Matches: 235, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
227 124 0.53
229 106 0.45
230 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (228 bp):
TTCATATATTGAAAACGGTAAACTACTCCAATGGTCACTAATGTTTGGATAATTTTTCGTTTTCA
CCACTGATGTTTCAAAAGTTACAAATCGGTCACTACCGTTATCATTTGTTTAAATTGGTCACTCG
CTGTTAACAGGCATGACGAAAAACAAACGTGACCTGTTAACATAACAGCAGTTAACAGGCTTACC
TGGATGGTATAGTTACACAAATAGTCCATGTTA
Found at i:76422 original size:19 final size:20
Alignment explanation
Indices: 76383--76422 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
76373 GGTTTGCGTA
76383 TATGAAAAATACTGATTAAT
1 TATGAAAAATACTGATTAAT
* *
76403 TATGTAAAATA-TGTTTAAT
1 TATGAAAAATACTGATTAAT
76422 T
1 T
76423 TAAGGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (20 bp):
TATGAAAAATACTGATTAAT
Found at i:77290 original size:177 final size:180
Alignment explanation
Indices: 76997--77360 Score: 533
Period size: 177 Copynumber: 2.0 Consensus size: 180
76987 TTAAATGTTT
*
76997 TTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATAATTATAAAATAAAAATTTAGATAA
1 TTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATAATTATAAAAT-AAAATTTAGATAA
*
77062 ATTTTTTAATTAATTAATAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTG
65 ATTTTTTAATTAATT-ATAATATTGATTTAGATTTAAAAGTTATAGGATCTTAAATTATTAATTG
* * *
77127 TGTTTTAAAT-GTTAGGGTTTAACCCATATGTTATATATAATATATTTAATA
129 AGTTTTAAATGGTTAGGGCTGAACCCATATGTTATATATAATATATTTAATA
* * *
77178 TTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AATTTTATAT-
1 TTTAATTCAAAAAAAAGTTTACAATTAATTTAAAT-A-ATATAATTATAAAATAAAATTTAGATA
* *
77240 ATTTTTTTAAATTAA-T-TAATATTGATTTAGGTTTAAAAGTTATAGGATCTTAAATTATTAATT
64 AATTTTTT-AATTAATTATAATATTGATTTAGATTTAAAAGTTATAGGATCTTAAATTATTAATT
* *
77303 GAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATA
128 GAGTTTTAAATGGTTAGGGCTGAACCCATATGTTATATATAATATATTTAATA
77356 TTTAA
1 TTTAA
77361 AATTTAATTT
Statistics
Matches: 167, Mismatches: 12, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
177 55 0.33
178 42 0.25
179 8 0.05
180 39 0.23
181 8 0.05
182 15 0.09
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (180 bp):
TTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATAATTATAAAATAAAATTTAGATAAA
TTTTTTAATTAATTATAATATTGATTTAGATTTAAAAGTTATAGGATCTTAAATTATTAATTGAG
TTTTAAATGGTTAGGGCTGAACCCATATGTTATATATAATATATTTAATA
Found at i:79185 original size:29 final size:29
Alignment explanation
Indices: 79152--79239 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
79142 ATTGATTTAC
79152 TTTCTGTTATTTACATTTCTTCCTTTAAA
1 TTTCTGTTATTTACATTTCTTCCTTTAAA
* * *
79181 TTTCTGTTATTTTA-ATTTGTGCC-TTAAT
1 TTTCTGTTA-TTTACATTTCTTCCTTTAAA
* * *
79209 TTTCAG-CATTTACATTTCAGTCCTTTAAA
1 TTTCTGTTATTTACATTTC-TTCCTTTAAA
79238 TT
1 TT
79240 CCAGCTTTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
26 4 0.09
27 5 0.11
28 11 0.24
29 22 0.48
30 4 0.09
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTCTGTTATTTACATTTCTTCCTTTAAA
Found at i:86656 original size:2 final size:2
Alignment explanation
Indices: 86649--86681 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
86639 TTAATCCTTC
86649 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 A
86682 ATCATTAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:87052 original size:44 final size:44
Alignment explanation
Indices: 86989--87158 Score: 301
Period size: 44 Copynumber: 3.9 Consensus size: 44
86979 GAGTTTGTCC
86989 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
87033 CATCTCAAATTAGACTTACTCTATTTTCTCG---ACACGTTCTT
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
*
87074 CATCTCAAATTAGTCTTACTCTATTTTCTCGACCACACGTTCTT
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
*
87118 CATCTCAAATTAGACTTACTCTTTTTTCTCGACCACACGTT
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTT
87159 ATTCGTTCGT
Statistics
Matches: 120, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
41 40 0.33
44 80 0.67
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.40
Consensus pattern (44 bp):
CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTT
Found at i:87132 original size:85 final size:85
Alignment explanation
Indices: 86989--87150 Score: 306
Period size: 85 Copynumber: 1.9 Consensus size: 85
86979 GAGTTTGTCC
86989 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
87054 TATTTTCTCGACACGTTCTT
66 TATTTTCTCGACACGTTCTT
*
87074 CATCTCAAATTAGTCTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
1 CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
*
87139 TTTTTTCTCGAC
66 TATTTTCTCGAC
87151 CACACGTTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (85 bp):
CATCTCAAATTAGACTTACTCTATTTTCTCGACCACACGTTCTTCATCTCAAATTAGACTTACTC
TATTTTCTCGACACGTTCTT
Found at i:95060 original size:32 final size:31
Alignment explanation
Indices: 95024--95100 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
95014 CGGGGCCGTG
*
95024 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
95056 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
95087 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
95101 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:95083 original size:63 final size:63
Alignment explanation
Indices: 94977--95100 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
94967 CCCTAAGGGA
* * * ** *
94977 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGCTTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
95040 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
95101 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 47 0.92
64 3 0.06
ACGTcount: A:0.26, C:0.30, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:96018 original size:9 final size:9
Alignment explanation
Indices: 96000--96088 Score: 79
Period size: 9 Copynumber: 9.3 Consensus size: 9
95990 GGTCGGGTCG
*
96000 GGTCAGACC
1 GGTCAAACC
96009 GGTCAAACC
1 GGTCAAACC
* *
96018 GATTCAGACC
1 G-GTCAAACC
96028 GGTCAAACC
1 GGTCAAACC
*
96037 GGTTCGAACC
1 GG-TCAAACC
96047 GGTCAAACC
1 GGTCAAACC
96056 GGTCAGAACC
1 GGTCA-AACC
*
96066 GGTTGAAAACC
1 GG-T-CAAACC
*
96077 GGTTAAACC
1 GGTCAAACC
96086 GGT
1 GGT
96089 TTCCAGCAGC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
9 36 0.55
10 22 0.33
11 7 0.11
12 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:96057 original size:19 final size:19
Alignment explanation
Indices: 96006--96068 Score: 85
Period size: 19 Copynumber: 3.3 Consensus size: 19
95996 GTCGGGTCAG
*
96006 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
96024 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
96044 ACCGGTCAAACCGG-TCAGA
1 ACCGGTCAAACCGGTTC-GA
96063 ACCGGT
1 ACCGGT
96069 TGAAAACCGG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 2 0.05
19 38 0.93
20 1 0.02
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:96087 original size:20 final size:21
Alignment explanation
Indices: 96051--96089 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
96041 CGAACCGGTC
96051 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
96072 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
96090 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:102369 original size:32 final size:31
Alignment explanation
Indices: 102331--102407 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
102321 CGGGGTCGTG
*
102331 GGGCCTACCTAAGAACACATCTTAGGGCCACA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCACA
** * *
102363 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCACA
*
102394 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
102408 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.30, C:0.31, G:0.25, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCACA
Found at i:103590 original size:32 final size:31
Alignment explanation
Indices: 103554--103630 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
103544 CGGGGCCGTG
*
103554 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
103586 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
103617 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
103631 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:103613 original size:63 final size:63
Alignment explanation
Indices: 103507--103630 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
103497 CCCTAAGGGA
* * * ** *
103507 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGCTTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
103570 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
103631 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 47 0.92
64 3 0.06
ACGTcount: A:0.26, C:0.30, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:104430 original size:7 final size:7
Alignment explanation
Indices: 104418--104448 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
104408 GTCAAAGAAA
104418 GTCAACG
1 GTCAACG
104425 GTCAACG
1 GTCAACG
104432 GTCAACG
1 GTCAACG
104439 GTCAACG
1 GTCAACG
104446 GTC
1 GTC
104449 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:104455 original size:5 final size:5
Alignment explanation
Indices: 104445--104524 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
104435 AACGGTCAAC
* *
104445 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
* *
104494 GGTCA GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
104525 AGACCGGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 49 0.80
7 12 0.20
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:104466 original size:22 final size:22
Alignment explanation
Indices: 104438--104524 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
104428 AACGGTCAAC
104438 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
104460 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
104482 GGTCAACGGTCGGGTCAGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
104504 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
104525 AGACCGGTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:104568 original size:19 final size:19
Alignment explanation
Indices: 104527--104590 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
104517 GTCGGGTCAG
*
104527 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
104545 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
*
104565 ACCGGTTGAAACCGG-TCAGA
1 ACCGG-TCAAACCGGTTC-GA
104585 ACCGGT
1 ACCGGT
104591 TGAAAACCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:104578 original size:20 final size:21
Alignment explanation
Indices: 104553--104611 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
104543 CAGACCGGTC
104553 AAACCGGTTCGAACCGGTTG-
1 AAACCGGTTCGAACCGGTTGA
104573 AAACCGG-TCAGAACCGGTTGA
1 AAACCGGTTC-GAACCGGTTGA
*
104594 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCGAACCGGTT
104612 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 2 0.06
20 25 0.71
21 7 0.20
22 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCGAACCGGTTGA
Found at i:110434 original size:36 final size:36
Alignment explanation
Indices: 110393--110533 Score: 135
Period size: 36 Copynumber: 3.9 Consensus size: 36
110383 AAGTCTCTGC
*
110393 AGGTTCAGTTCTAATCAAGCTGGTAATTCCTTATAT
1 AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATAT
** * **
110429 AGGTTCAGCACCGATCAA-CTAATAATTCCTTAT-T
1 AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATAT
*
110463 GCAGGTTCAATTCTGATCAAGCTGGTAATTCCTTATAT
1 --AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATAT
**** *
110501 AGGTTCAACAATGATC-AGCTGATAATTCCTTAT
1 AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTAT
110534 GGACCTAAGG
Statistics
Matches: 85, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
34 1 0.01
35 29 0.34
36 41 0.48
37 13 0.15
38 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (36 bp):
AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATAT
Found at i:110507 original size:72 final size:72
Alignment explanation
Indices: 110390--110533 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 72
110380 ATGAAGTCTC
* * *
110390 TGCAGGTTCAGTTCTAATCAAGCTGGTAATTCCTTATATAGGTTCAGCACCGATCAACTAATAAT
1 TGCAGGTTCAATTCTAATCAAGCTGGTAATTCCTTATATAGGTTCAACAACGATCAACTAATAAT
110455 TCCTTAT
66 TCCTTAT
* * * *
110462 TGCAGGTTCAATTCTGATCAAGCTGGTAATTCCTTATATAGGTTCAACAATGATCAGCTGATAAT
1 TGCAGGTTCAATTCTAATCAAGCTGGTAATTCCTTATATAGGTTCAACAACGATCAACTAATAAT
110527 TCCTTAT
66 TCCTTAT
110534 GGACCTAAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (72 bp):
TGCAGGTTCAATTCTAATCAAGCTGGTAATTCCTTATATAGGTTCAACAACGATCAACTAATAAT
TCCTTAT
Found at i:110528 original size:35 final size:35
Alignment explanation
Indices: 110410--110533 Score: 133
Period size: 35 Copynumber: 3.5 Consensus size: 35
110400 GTTCTAATCA
* * *
110410 AGCTGGTAATTCCTTATATAGGTTCAGCACCGATC
1 AGCTGATAATTCCTTATATAGGTTCAACACTGATC
* * **
110445 AACTAATAATTCCTTAT-TGCAGGTTCAATTCTGATC
1 AGCTGATAATTCCTTATAT--AGGTTCAACACTGATC
* *
110481 AAGCTGGTAATTCCTTATATAGGTTCAACAATGATC
1 -AGCTGATAATTCCTTATATAGGTTCAACACTGATC
110517 AGCTGATAATTCCTTAT
1 AGCTGATAATTCCTTAT
110534 GGACCTAAGG
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
34 1 0.01
35 30 0.42
36 25 0.35
37 14 0.20
38 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (35 bp):
AGCTGATAATTCCTTATATAGGTTCAACACTGATC
Found at i:111783 original size:20 final size:20
Alignment explanation
Indices: 111707--111777 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 20
111697 AAGAAAGTAT
111707 AATAAAA-ATTTAGAAGATATAA
1 AATAAAATATTTA-AA-ATAT-A
*
111729 AATTAAATTATTAGTAAAATATA
1 AA-TAAAATATT--TAAAATATA
111752 AATAAAATATTTAAATATATA
1 AATAAAATATTTAAA-ATATA
111773 AATAA
1 AATAA
111778 TTATTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
20 4 0.10
21 10 0.24
22 10 0.24
23 7 0.17
24 7 0.17
25 2 0.05
26 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AATAAAATATTTAAAATATA
Found at i:117723 original size:23 final size:23
Alignment explanation
Indices: 117693--117762 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
117683 AAAAAATGAA
117693 AAAGCATGTTCGGGATCCAACTC
1 AAAGCATGTTCGGGATCCAACTC
117716 AAAGCATGTTCGGGATCCAACTC
1 AAAGCATGTTCGGGATCCAACTC
*
117739 AAAGCATGTTCGGGATCTAACTC
1 AAAGCATGTTCGGGATCCAACTC
117762 A
1 A
117763 TTCACGGTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (23 bp):
AAAGCATGTTCGGGATCCAACTC
Found at i:146156 original size:70 final size:68
Alignment explanation
Indices: 146073--146317 Score: 366
Period size: 70 Copynumber: 3.5 Consensus size: 68
146063 ATATATGTGG
146073 TTTTGAAATATATATATAATATATAATTTTGATAAATATATAATATAGTATTTGAAAATATGTTA
1 TTTTGAAA-ATATATATAATATATAATTTTGA-AAATATATAATATAGT-TTTGAAAATATGTTA
*
146138 TATACT
63 TATAAT
*
146144 TTTTGAAAATATATATAATATATAATTTTGAAAAATATATAATATAGTTTTTGAAAATATATTAT
1 TTTTGAAAATATATATAATATATAATTTTG-AAAATATATAATATAG-TTTTGAAAATATGTTAT
146209 ATAAT
64 ATAAT
*
146214 TTTTGAAAATATATATAATGTATAATTTTGGAAAATATATAATATAGGTTTTGAAAATATGTTAT
1 TTTTGAAAATATATATAATATATAATTTT-GAAAATATATAATATA-GTTTTGAAAATATGTTAT
*
146279 ATATT
64 ATAAT
146284 TTTTGAAAATATATA-ATATATATAATTTTTGAAA
1 TTTTGAAAATATATATA-ATATATAA-TTTTGAAA
146318 GCATAATAGA
Statistics
Matches: 162, Mismatches: 6, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
69 1 0.01
70 145 0.90
71 16 0.10
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (68 bp):
TTTTGAAAATATATATAATATATAATTTTGAAAATATATAATATAGTTTTGAAAATATGTTATAT
AAT
Found at i:146179 original size:48 final size:47
Alignment explanation
Indices: 146086--146317 Score: 198
Period size: 48 Copynumber: 5.0 Consensus size: 47
146076 TGAAATATAT
* * *
146086 ATATAATATATAATTTTGATAA-ATATATAATATAGT-A-TTTG-AAA
1 ATATATTATATATTTTTGAAAATATATATAATATA-TAATTTTGAAAA
*
146130 ATATGTTATATACTTTTTGAAAATATATATAATATATAATTTTGAAAA
1 ATATATTATATA-TTTTTGAAAATATATATAATATATAATTTTGAAAA
* *
146178 ATATATAATATAGTTTTTGAAAATATAT-T-ATATA-ATTTTTGAAAA
1 ATATATTATATA-TTTTTGAAAATATATATAATATATAATTTTGAAAA
* * * **
146223 TATATATAATGTATAATTTTGGAAA-ATATATAATATA-GGTTTTG-AAA
1 -ATATAT--TATATATTTTTGAAAATATATATAATATATAATTTTGAAAA
*
146270 ATATGTTATATATTTTTTGAAAATATATA-ATATATATAATTTTTGAAA
1 ATATATTATATA-TTTTTGAAAATATATATA-ATATATAA-TTTTGAAA
146318 GCATAATAGA
Statistics
Matches: 152, Mismatches: 20, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
44 15 0.10
45 28 0.18
46 43 0.28
47 17 0.11
48 47 0.31
49 2 0.01
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (47 bp):
ATATATTATATATTTTTGAAAATATATATAATATATAATTTTGAAAA
Found at i:146304 original size:22 final size:22
Alignment explanation
Indices: 146084--146304 Score: 208
Period size: 22 Copynumber: 9.6 Consensus size: 22
146074 TTTGAAATAT
*
146084 ATATATAATATATAATTTTGATAA
1 ATATATAATATAT-TTTTTGA-AA
* *
146108 ATATATAATATAGTATTTGAAA
1 ATATATAATATATTTTTTGAAA
* * *
146130 ATATGTTATATACTTTTTGAAAA
1 ATATATAATATATTTTTTG-AAA
*
146153 TATATATAATATATAATTTTGAAAA
1 -ATATATAATATAT-TTTTTG-AAA
*
146178 ATATATAATATAGTTTTTGAAA
1 ATATATAATATATTTTTTGAAA
* *
146200 ATATATTATATAATTTTTGAAAA
1 ATATATAATATATTTTTTG-AAA
* *
146223 TATATATAATGTATAATTTTGGAAA
1 -ATATATAA--TATATTTTTTGAAA
**
146248 ATATATAATATAGGTTTTGAAA
1 ATATATAATATATTTTTTGAAA
* *
146270 ATATGTTATATATTTTTTGAAA
1 ATATATAATATATTTTTTGAAA
146292 ATATATAATATAT
1 ATATATAATATAT
146305 ATAATTTTTG
Statistics
Matches: 164, Mismatches: 26, Indels: 16
0.80 0.13 0.08
Matches are distributed among these distances:
22 77 0.47
23 16 0.10
24 49 0.30
25 12 0.07
26 10 0.06
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (22 bp):
ATATATAATATATTTTTTGAAA
Found at i:146350 original size:16 final size:16
Alignment explanation
Indices: 146329--146376 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
146319 CATAATAGAA
146329 TTTTGAAAATAAATAT
1 TTTTGAAAATAAATAT
146345 TTTTGAAAAT--ATAGT
1 TTTTGAAAATAAATA-T
*
146360 GTTTGAAAATATAATAT
1 TTTTGAAAATA-AATAT
146377 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 10 0.37
17 1 0.04
18 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (16 bp):
TTTTGAAAATAAATAT
Found at i:146392 original size:22 final size:20
Alignment explanation
Indices: 146367--146420 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
146357 AGTGTTTGAA
*
146367 AATATAATATATATTTTTTTT
1 AATATAATATATA-TGTTTTT
*
146388 GA-ATAATATATA-GTTTTT
1 AATATAATATATATGTTTTT
146406 AATATATATATATAT
1 AATATA-ATATATAT
146421 ATATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.22
19 3 0.11
20 17 0.63
21 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
AATATAATATATATGTTTTT
Found at i:146398 original size:18 final size:18
Alignment explanation
Indices: 146373--146437 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
146363 TGAAAATATA
**
146373 ATATATATTTTTTTTGAAT
1 ATATATATAGTTTTT-AAT
146392 A-ATATATAGTTTTTAAT
1 ATATATATAGTTTTTAAT
* *
146409 ATATATATA-TATATATAT
1 ATATATATAGTTTTTA-AT
146427 ATATATATAGT
1 ATATATATAGT
146438 ATACAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 8 0.21
18 29 0.74
19 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
ATATATATAGTTTTTAAT
Found at i:146416 original size:20 final size:20
Alignment explanation
Indices: 146367--146419 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
146357 AGTGTTTGAA
**
146367 AATATAATATATATTTTTTTT
1 AATAT-ATATATATAGTTTTT
*
146388 GA-ATA-ATATATAGTTTTT
1 AATATATATATATAGTTTTT
146406 AATATATATATATA
1 AATATATATATATA
146420 TATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 12 0.46
19 4 0.15
20 9 0.35
21 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
AATATATATATATAGTTTTT
Found at i:146448 original size:2 final size:2
Alignment explanation
Indices: 146407--146440 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
146397 ATAGTTTTTA
146407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
146441 CAATATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:146479 original size:21 final size:20
Alignment explanation
Indices: 146448--146509 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
146438 ATACAATATA
146448 TTACTTTTTTAATTTT-ATTT
1 TTACTTTTTT-ATTTTCATTT
146468 TTACTCTTTTTATTTTCATTT
1 TTACT-TTTTTATTTTCATTT
146489 CTT--TTTATTTATTTTCATTT
1 -TTACTTT-TTTATTTTCATTT
146509 T
1 T
146510 GGTTTAGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.08
20 24 0.63
21 9 0.24
22 2 0.05
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (20 bp):
TTACTTTTTTATTTTCATTT
Found at i:146480 original size:15 final size:16
Alignment explanation
Indices: 146460--146498 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
146450 ACTTTTTTAA
*
146460 TTTTATTTTTA-CTCT
1 TTTTATTTTCATCTCT
*
146475 TTTTATTTTCATTTCT
1 TTTTATTTTCATCTCT
146491 TTTTATTT
1 TTTTATTT
146499 ATTTTCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTTCATCTCT
Found at i:149337 original size:106 final size:104
Alignment explanation
Indices: 149155--149366 Score: 282
Period size: 106 Copynumber: 2.0 Consensus size: 104
149145 TAAGGCTCGA
*
149155 CCAGGTGATTTTAGGGATTAGGTTTTCGACTTTCGTCCCCAAAGATGCTACGTGATTTAGGTGTT
1 CCAGGTGATTTTAGGGATTAGGTTTTCGACTTTCGTCCCCAAAGATGCTACGCGATTTAGGTGTT
* * * *
149220 CTTCGCTAG-TTTTGGTGAGTCCGTTTCTTTCTCTCCAG
66 CTCCGCTAGTTTTTGGTGAGACCATTTCGTTCTCTCCAG
* * * * *
149258 CCAGGTGATTTTGGGGATTAGGTTTCATTCGGCTTTCGTCCCCAAAGCTGCTACGCGTTTTGGGT
1 CCAGGTGATTTTAGGGATTAGG-TT--TTCGACTTTCGTCCCCAAAGATGCTACGCGATTTAGGT
*
149323 GTTCTCCTCTAGTTTTTTGGTGAGACCATTTCGTTCTCTCCAG
63 GTTCTCCGCTAG-TTTTTGGTGAGACCATTTCGTTCTCTCCAG
149366 C
1 C
149367 TGTGATTTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
103 21 0.23
104 2 0.02
106 43 0.46
108 27 0.29
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (104 bp):
CCAGGTGATTTTAGGGATTAGGTTTTCGACTTTCGTCCCCAAAGATGCTACGCGATTTAGGTGTT
CTCCGCTAGTTTTTGGTGAGACCATTTCGTTCTCTCCAG
Found at i:151968 original size:364 final size:362
Alignment explanation
Indices: 151416--152148 Score: 1193
Period size: 364 Copynumber: 2.0 Consensus size: 362
151406 TTCATTCACG
* **
151416 TTTA-ATCCATTAATGAGAAACAAGTGGATGGGGAAATTACAACATTATATTAGCACTAAACACT
1 TTTATATCCATTAACGAGAAACAAGTGGATAAGGAAATTACAACATTATATTAGCACTAAACACT
151480 AGCAAGAGTGACGAAACGTATCTATCAAATGCTAAATTTGCGTCTACATATTTAGATTGAACAAA
66 AGCAAGAGTGACGAAACGTATCTATCAAATGCTAAATTTGCGTCTACATATTTAGATTGAACAAA
* *
151545 ATGATTTCCACGTGAGACCACCGAGACTTCGTCCTCTTTGAAAATAAGTGTCTACTATCATTGCT
131 ATGATTTCCACGTGAGACCACCGACACTTCGTCCTCTTTGAAAATAAGTGGCTACTATCATTGCT
* *
151610 GCCACTGCATCACTTTTCTCTCCCCTGCTTTATATATTTAATGTTTTAGATAGTTTTTTACTAGA
196 GCCACTGCATCACTTCTCTCTCCCCTGCTTTATACATTTAATG-TTTAGATAG-TTTTTA-TAGA
151675 AAAATT-AAAAATATTAATATTTTTCAG-TAGCATCTTTTATTGACCGTATATTAAGACTGTCGT
258 AAAATTAAAAAATATTAATATTTTT-AGATAGCATCTTTTATTGACCGTATATTAAGACTGTCGT
**
151738 ACGAAAAAATTACTTACGAGTTAGAAACAGATAGTTATACA
322 ACGAAAAAATTACCCACGAGTTAGAAACAGATAGTTATACA
*
151779 TTTATATCCATTAACGAGAAATAAGTGGATAAGGAAATTACAACATTATATTAGCACTAAACACT
1 TTTATATCCATTAACGAGAAACAAGTGGATAAGGAAATTACAACATTATATTAGCACTAAACACT
151844 AGCAAGAGTGACGAAACGTATCTATCAAATGCTAAATTTGCGTCTACATATTTAGATTGAACAAA
66 AGCAAGAGTGACGAAACGTATCTATCAAATGCTAAATTTGCGTCTACATATTTAGATTGAACAAA
151909 ATGATTTCCACGTGAGACCACCGACACTTCGTCCTCTTTGAAAATAAGTGGCTACTATCATTGCT
131 ATGATTTCCACGTGAGACCACCGACACTTCGTCCTCTTTGAAAATAAGTGGCTACTATCATTGCT
* * * * *
151974 GCCACTGCATCACTTCTCTCTCCCCTGTTTTATACGTTTAATGTTTAGGTAGTTTTTATTGGAAA
196 GCCACTGCATCACTTCTCTCTCCCCTGCTTTATACATTTAATGTTTAGATAGTTTTTATAGAAAA
* * * *
152039 ATTAAAAAAATATTAATATTTTTAGATAGTATTTTTTATTGATCGTATATTAAGACTGTTGTACG
261 ATT-AAAAAATATTAATATTTTTAGATAGCATCTTTTATTGACCGTATATTAAGACTGTCGTACG
* * * *
152104 GAAGAATTACCCACGTGTTAGAAACAGGTAGTTATACA
325 AAAAAATTACCCACGAGTTAGAAACAGATAGTTATACA
152142 TTTATAT
1 TTTATAT
152149 GAGCTAGAAT
Statistics
Matches: 343, Mismatches: 23, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
361 8 0.02
362 8 0.02
363 104 0.30
364 223 0.65
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (362 bp):
TTTATATCCATTAACGAGAAACAAGTGGATAAGGAAATTACAACATTATATTAGCACTAAACACT
AGCAAGAGTGACGAAACGTATCTATCAAATGCTAAATTTGCGTCTACATATTTAGATTGAACAAA
ATGATTTCCACGTGAGACCACCGACACTTCGTCCTCTTTGAAAATAAGTGGCTACTATCATTGCT
GCCACTGCATCACTTCTCTCTCCCCTGCTTTATACATTTAATGTTTAGATAGTTTTTATAGAAAA
ATTAAAAAATATTAATATTTTTAGATAGCATCTTTTATTGACCGTATATTAAGACTGTCGTACGA
AAAAATTACCCACGAGTTAGAAACAGATAGTTATACA
Found at i:154381 original size:39 final size:39
Alignment explanation
Indices: 154278--154430 Score: 155
Period size: 39 Copynumber: 3.9 Consensus size: 39
154268 CCTGTACACA
* * *
154278 CAGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGCTTA
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATG
* * *** *
154317 CAATAAGGTCTTATTATGTGCACAAAGCAGAGGAGTC-TG
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAG-CATG
* * * *
154356 CAGTAAGGGCTTACCCTGAGTACAAAGCAAATGAGCATG
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATG
* *
154395 CAGTAAGGATTTACCCTGAGCACAAAGCCGAGGAGC
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGC
154431 CCGCGGAAAG
Statistics
Matches: 91, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
38 1 0.01
39 89 0.98
40 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATG
Found at i:155242 original size:18 final size:19
Alignment explanation
Indices: 155207--155241 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
155197 GGATGTCAAA
155207 AAAATAAATATGACTTTTC
1 AAAATAAATATGACTTTTC
155226 AAAA-AAAT-TGACTTTT
1 AAAATAAATATGACTTTT
155242 TGGTCAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (19 bp):
AAAATAAATATGACTTTTC
Found at i:155928 original size:23 final size:26
Alignment explanation
Indices: 155884--155930 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
155874 GACATTACTT
*
155884 ATTTTATTTCTTGTATTCATCTTAAA
1 ATTTTATTTCATGTATTCATCTTAAA
155910 ATTTTATTT-ATGT-TT-ATCTTA
1 ATTTTATTTCATGTATTCATCTTA
155931 TATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 3 0.15
26 9 0.45
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.62
Consensus pattern (26 bp):
ATTTTATTTCATGTATTCATCTTAAA
Found at i:156348 original size:27 final size:27
Alignment explanation
Indices: 156318--156378 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
156308 TAATAATAGA
*
156318 AAATTTTCGTAAAAAGTACACACAAAT
1 AAATTTTCATAAAAAGTACACACAAAT
* * *
156345 AAA-TTTCATATAAAGTAGATACAAAT
1 AAATTTTCATAAAAAGTACACACAAAT
156371 AGAATTTT
1 A-AATTTT
156379 AAGGTAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 20 0.71
27 5 0.18
28 3 0.11
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTTTCATAAAAAGTACACACAAAT
Found at i:159852 original size:49 final size:48
Alignment explanation
Indices: 159780--159872 Score: 114
Period size: 49 Copynumber: 1.9 Consensus size: 48
159770 GTGACCCCCC
* * **
159780 AGGGGCGGATCTCCATGGAGCCCGGGGTATTCCGGGCAACCCCTCATCT
1 AGGGGCGGACCTCCATGGAGCCC-GGGTATCCCAAGCAACCCCTCATCT
* * *
159829 AGGGGTGGACCTCTATGGTGCCCGGGTATCCCAAGCAACCCCTC
1 AGGGGCGGACCTCCATGGAGCCCGGGTATCCCAAGCAACCCCTC
159873 CATAAATGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
48 18 0.49
49 19 0.51
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.18
Consensus pattern (48 bp):
AGGGGCGGACCTCCATGGAGCCCGGGTATCCCAAGCAACCCCTCATCT
Found at i:160461 original size:3 final size:3
Alignment explanation
Indices: 160435--160536 Score: 58
Period size: 3 Copynumber: 35.3 Consensus size: 3
160425 ATACACTATC
* * * *
160435 ATT ATT -TT ACT AAT ATT ATT -TT ATT ATT ATT AATT A-G AGT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
*
160477 ATT ATT AATT ATT -TT ATT ATT -TT GTT ATT ACTT -TT ATT -TT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
*
160520 AGTT ATT ATT ACT ATT A
1 A-TT ATT ATT ATT ATT A
160537 ATTTTGAGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
2 14 0.18
3 53 0.68
4 11 0.14
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:160465 original size:14 final size:14
Alignment explanation
Indices: 160435--160529 Score: 61
Period size: 14 Copynumber: 6.4 Consensus size: 14
160425 ATACACTATC
* *
160435 ATTATTTTACTAAT
1 ATTATTTTATTATT
160449 ATTATTTTATTATT
1 ATTATTTTATTATT
**
160463 ATTAATTAGAGTTTATT
1 ATT-ATTTTA--TTATT
160480 ATTAATTATT-TTATT
1 ATT-ATT-TTATTATT
160495 ATT-TTGTTATTACTT
1 ATTATT-TTATTA-TT
160510 -TTATTTTATTAGTT
1 ATTATTTTATTA-TT
160524 ATTATT
1 ATTATT
160530 ACTATTAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
13 4 0.06
14 28 0.43
15 21 0.32
17 12 0.18
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (14 bp):
ATTATTTTATTATT
Found at i:160540 original size:25 final size:25
Alignment explanation
Indices: 160475--160541 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
160465 TAATTAGAGT
*
160475 TTATTATTA--ATTATTTTATTATT
1 TTATTATTACTATTATTTTATTATG
* *
160498 TTGTTATTACTTTTATTTTATTA-G
1 TTATTATTACTATTATTTTATTATG
160522 TTATTATTACTATTAATTTT
1 TTATTATTACTATT-ATTTT
160542 GAGTTTCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 8 0.22
24 12 0.33
25 16 0.44
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (25 bp):
TTATTATTACTATTATTTTATTATG
Found at i:165443 original size:11 final size:11
Alignment explanation
Indices: 165417--165522 Score: 61
Period size: 13 Copynumber: 8.9 Consensus size: 11
165407 GTTGTATTAC
165417 TATTAATTATTTT
1 TATT-ATTA-TTT
*
165430 TATTTTTATTT
1 TATTATTATTT
*
165441 TATTATTATTA
1 TATTATTATTT
* *
165452 TCTTATTATTAG
1 TATTATTATT-T
*
165464 TAGTATTTATTAT
1 TATTA-TTATT-T
*
165477 TACTATTA-TT
1 TATTATTATTT
*
165487 TATTATTACTAT
1 TATTATTA-TTT
165499 TATTTATTAATATT
1 TA-TTATT-AT-TT
165513 TATTATTATT
1 TATTATTATT
165523 ATAATTATTT
Statistics
Matches: 74, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
10 8 0.11
11 23 0.31
12 14 0.19
13 25 0.34
14 4 0.05
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTATTATTT
Found at i:165448 original size:3 final size:3
Alignment explanation
Indices: 165411--165531 Score: 93
Period size: 3 Copynumber: 39.3 Consensus size: 3
165401 GTTGTTGTTG
* * * *
165411 TAT TAC TAT TAAT TAT TTT TAT TTT TAT T-T TAT TAT TAT TA- TCT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
165455 TAT TAT TAG TAG TATT TAT TAT TAC TAT TATT TAT TAT TAC TAT TATT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T
* *
165503 TAT TAA TATT TAT TAT TAT TAT AAT TAT T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT T
165532 TCAAAAAAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 14
0.74 0.14 0.11
Matches are distributed among these distances:
2 3 0.03
3 77 0.83
4 13 0.14
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:165475 original size:16 final size:16
Alignment explanation
Indices: 165411--165532 Score: 112
Period size: 16 Copynumber: 7.9 Consensus size: 16
165401 GTTGTTGTTG
*
165411 TATTACTATTAATTAT
1 TATTACTATTATTTAT
* * *
165427 TTTTATTTTTA-TT-T
1 TATTACTATTATTTAT
*
165441 TATTATTATTATCTTAT
1 TATTACTATTAT-TTAT
* *
165458 TATTAGTAGTATTTAT
1 TATTACTATTATTTAT
165474 TATTACTATTATTTAT
1 TATTACTATTATTTAT
165490 TATTACTATTATTTAT
1 TATTACTATTATTTAT
*
165506 TAATA-T-TTA-TTAT
1 TATTACTATTATTTAT
165519 TATTA-TAATTATTT
1 TATTACT-ATTATTT
165533 CAAAAAAATA
Statistics
Matches: 89, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
13 9 0.10
14 13 0.15
15 6 0.07
16 50 0.56
17 11 0.12
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTACTATTATTTAT
Found at i:165521 original size:29 final size:27
Alignment explanation
Indices: 165429--165531 Score: 99
Period size: 26 Copynumber: 3.9 Consensus size: 27
165419 TTAATTATTT
*
165429 TTATTT-TTATT-TTATTATTATTATC
1 TTATTTATTATTATTATTATTATTATA
* *
165454 TTA-TTATTAGTAGTATTTATTATTACTA
1 TTATTTATTATTATTA-TTATTATTA-TA
*
165482 TTATTTATTATTACTATTATTTATTA-A
1 TTATTTATTATTATTATTA-TTATTATA
*
165509 -TATTTATTATTATTATAATTATT
1 TTATTTATTATTATTATTATTATT
165532 TCAAAAAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
24 2 0.03
25 12 0.18
26 18 0.28
27 10 0.15
28 7 0.11
29 16 0.25
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATTTATTATTATTATTATTATTATA
Found at i:166074 original size:2 final size:2
Alignment explanation
Indices: 166069--166093 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
166059 TTAATCATTA
166069 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 A
166094 ATGATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:168641 original size:14 final size:15
Alignment explanation
Indices: 168618--168650 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
168608 AATTTGTGCC
*
168618 TTTACTTTTCAG-CA
1 TTTACATTTCAGTCA
168632 TTTACATTTCAGTCA
1 TTTACATTTCAGTCA
168647 TTTA
1 TTTA
168651 AATTCCAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (15 bp):
TTTACATTTCAGTCA
Found at i:168707 original size:24 final size:24
Alignment explanation
Indices: 168661--168707 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
168651 AATTCCAGAT
* * *
168661 TTTAATTTTTATGTGCTGTTTTAA
1 TTTAAGTTTTATATGCTGATTTAA
*
168685 TTTAAGTTTTATATTCTGATTTA
1 TTTAAGTTTTATATGCTGATTTA
168708 TTTCATTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.23, C:0.04, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTAAGTTTTATATGCTGATTTAA
Found at i:169180 original size:139 final size:139
Alignment explanation
Indices: 168911--169183 Score: 372
Period size: 139 Copynumber: 2.0 Consensus size: 139
168901 GTTTGTTTAA
* * * *
168911 TTTCACATTTAGTCGTTAAATTAGGAGAAATTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCA
1 TTTCACATTTAGTCCTTAAATTAGGAGAAATCTTAATTTGGTCATCGATTTTGCTCGAGGTTCCA
* * * *
168976 AATTAATTATTCGATATGTTATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATTT
66 AATTAATTATTCGATATGTCATAATTGATTAAAATTAATTAAGATTAATATTAGAACCTCAATTT
169041 TAGGCCTAT
131 TAGGCCTAT
* **
169050 TTTCATATTTAGTCCTTAAATTAGGAGAAATCTTAATTTTTTCATCGATTTTGCTCGAGGTTCCA
1 TTTCACATTTAGTCCTTAAATTAGGAGAAATCTTAATTTGGTCATCGATTTTGCTCGAGGTTCCA
** *
169115 TTTTAATTATTTGA-AT-TGCATAATTGATTAAAATTAATTTAAG-TTAATATTAGAACCTACAA
66 AATTAATTATTCGATATGT-CATAATTGATTAAAATTAA-TTAAGATTAATATTAGAACCT-CAA
169177 TTTTAGG
128 TTTTAGG
169184 TTTAATCAAT
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
137 1 0.01
138 34 0.29
139 82 0.70
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.43
Consensus pattern (139 bp):
TTTCACATTTAGTCCTTAAATTAGGAGAAATCTTAATTTGGTCATCGATTTTGCTCGAGGTTCCA
AATTAATTATTCGATATGTCATAATTGATTAAAATTAATTAAGATTAATATTAGAACCTCAATTT
TAGGCCTAT
Found at i:171778 original size:53 final size:54
Alignment explanation
Indices: 171693--171801 Score: 175
Period size: 53 Copynumber: 2.0 Consensus size: 54
171683 GATTAGCTCA
* *
171693 ACAATAAATAATTTGTAAGCTTTTTTCATATAGACCCCAAACAAACAAGTCTAAC
1 ACAATAAATAATTTATAAGC-TTTTTCATATAGACCCAAAACAAACAAGTCTAAC
*
171748 ACAATAAATAGTTTATAAGC-TTTTCATATAGACCCAAAACAAACAAGTCTAAC
1 ACAATAAATAATTTATAAGCTTTTTCATATAGACCCAAAACAAACAAGTCTAAC
171801 A
1 A
171802 TCTTAATGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 33 0.65
55 18 0.35
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (54 bp):
ACAATAAATAATTTATAAGCTTTTTCATATAGACCCAAAACAAACAAGTCTAAC
Found at i:180959 original size:115 final size:115
Alignment explanation
Indices: 180825--181040 Score: 285
Period size: 115 Copynumber: 1.9 Consensus size: 115
180815 GGTTTGAGAA
* * * *
180825 CAAAAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAA-AGCAGCAAAAGGTCG
1 CAAAAACGCCGCAAAAGGTCAAGATATATAGCGACGTTTTTGGAACAAACA-CAGAAAAAGGTC-
*
180889 AGATATATAAC-GACATTTTTGGA-ACAAACGCCGCTAAAGGTCAGATCTATC
64 AAATATATAACAG-CATTTTTGGATACAAACGCCGCTAAAGGTCAGATCTATC
* * *
180940 CAAAAACGCCGCAAAAGGTCGAGATATATAGTGACGTTTTTGGAACAAACACAGAAAAATGTCAA
1 CAAAAACGCCGCAAAAGGTCAAGATATATAGCGACGTTTTTGGAACAAACACAGAAAAAGGTCAA
* * *
181005 ATCTATAGCAGCATTTTTGGATACAAATGCCGCTAA
66 ATATATAACAGCATTTTTGGATACAAACGCCGCTAA
181041 TTACCTTTCT
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
114 18 0.21
115 68 0.78
116 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (115 bp):
CAAAAACGCCGCAAAAGGTCAAGATATATAGCGACGTTTTTGGAACAAACACAGAAAAAGGTCAA
ATATATAACAGCATTTTTGGATACAAACGCCGCTAAAGGTCAGATCTATC
Found at i:182630 original size:21 final size:21
Alignment explanation
Indices: 182605--182648 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
182595 CCAAAATAAC
182605 CATGAATCGAATGCTCAAAAG
1 CATGAATCGAATGCTCAAAAG
182626 CATGAATCGAATGCTCAAAAG
1 CATGAATCGAATGCTCAAAAG
182647 CA
1 CA
182649 ACTACGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (21 bp):
CATGAATCGAATGCTCAAAAG
Found at i:190249 original size:23 final size:24
Alignment explanation
Indices: 190219--190271 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
190209 TCCTTCGGGA
*
190219 CATAGTGGTCATTCGGGAC-ATTT
1 CATAGTGGTCATTAGGGACAATTT
*
190242 CATAGTGGTCCTTAGGGACAAATTT
1 CATAGTGGTCATTAGGGAC-AATTT
190267 CATAG
1 CATAG
190272 CCCCTAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 17 0.65
25 9 0.35
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (24 bp):
CATAGTGGTCATTAGGGACAATTT
Found at i:194553 original size:18 final size:18
Alignment explanation
Indices: 194530--194573 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
194520 AAGAAGCTAT
194530 CCAAGCTTAGAAACCGAG
1 CCAAGCTTAGAAACCGAG
194548 CCAAGCTTAGAAACCGAG
1 CCAAGCTTAGAAACCGAG
194566 CCAAGCTT
1 CCAAGCTT
194574 TGGGTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.30, G:0.20, T:0.14
Consensus pattern (18 bp):
CCAAGCTTAGAAACCGAG
Found at i:197870 original size:16 final size:16
Alignment explanation
Indices: 197851--197881 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
197841 TAATTTTAAA
*
197851 AATTTTGAATTAAATT
1 AATTTTGAATAAAATT
197867 AATTTTGAATAAAAT
1 AATTTTGAATAAAAT
197882 GATAAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
AATTTTGAATAAAATT
Found at i:198469 original size:31 final size:31
Alignment explanation
Indices: 198425--198500 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
198415 TTTCAAAAGT
* * **
198425 AAAAAA-TGATCACTAATGTTATTGATTTAG
1 AAAAAATTGGTCACTAATATTATCAATTTAG
*
198455 AAAAAATTGGTCACTAATATTATCAATTTAT
1 AAAAAATTGGTCACTAATATTATCAATTTAG
*
198486 AACAAATTGGTCACT
1 AAAAAATTGGTCACT
198501 CGATCGTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 6 0.15
31 33 0.85
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (31 bp):
AAAAAATTGGTCACTAATATTATCAATTTAG
Found at i:205007 original size:21 final size:22
Alignment explanation
Indices: 204983--205037 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
204973 TTATTAATGC
204983 ATGCATGTATGTATAA-TATGT-
1 ATGCATGTATGTATAATTAT-TA
*
205004 ATGCATATATGTATAATTTATTA
1 ATGCATGTATGTATAA-TTATTA
205027 ATGCATGTATG
1 ATGCATGTATG
205038 ATATGTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 15 0.52
22 1 0.03
23 13 0.45
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (22 bp):
ATGCATGTATGTATAATTATTA
Found at i:205216 original size:7 final size:7
Alignment explanation
Indices: 205206--205283 Score: 59
Period size: 7 Copynumber: 11.3 Consensus size: 7
205196 TAGTTTATAG
205206 AAACCCT
1 AAACCCT
205213 AAACCCT
1 AAACCCT
* *
205220 AAATCAT
1 AAACCCT
*
205227 AAACCAT
1 AAACCCT
*
205234 ACACCCT
1 AAACCCT
**
205241 -AACTTT
1 AAACCCT
*
205247 AAACCAT
1 AAACCCT
*
205254 AAACACT
1 AAACCCT
*
205261 AAACACT
1 AAACCCT
*
205268 AAACCAT
1 AAACCCT
205275 AAACCCT
1 AAACCCT
205282 AA
1 AA
205284 TATAATTATA
Statistics
Matches: 55, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
6 3 0.05
7 52 0.95
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:205239 original size:21 final size:21
Alignment explanation
Indices: 205206--205283 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
205196 TAGTTTATAG
*
205206 AAACCCTAAACCCTAAATCAT
1 AAACCATAAACCCTAAATCAT
* * *
205227 AAACCATACACCCTAACT-TT
1 AAACCATAAACCCTAAATCAT
*
205247 AAACCATAAACACTAAA-CACT
1 AAACCATAAACCCTAAATCA-T
205268 AAACCATAAACCCTAA
1 AAACCATAAACCCTAA
205284 TATAATTATA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 15 0.33
21 31 0.67
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCATAAACCCTAAATCAT
Found at i:205251 original size:41 final size:41
Alignment explanation
Indices: 205206--205283 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
205196 TAGTTTATAG
* * *
205206 AAACCCTAAACCCTAAATCA-TAAACCATACACCCTAACTTT
1 AAACCATAAACACTAAA-CACTAAACCATAAACCCTAACTTT
205247 AAACCATAAACACTAAACACTAAACCATAAACCCTAA
1 AAACCATAAACACTAAACACTAAACCATAAACCCTAA
205284 TATAATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 31 0.94
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (41 bp):
AAACCATAAACACTAAACACTAAACCATAAACCCTAACTTT
Found at i:205438 original size:13 final size:13
Alignment explanation
Indices: 205406--205432 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
205396 TAATTTACAT
205406 TTAAATAATTTTA
1 TTAAATAATTTTA
205419 TTAAATAATTTTA
1 TTAAATAATTTTA
205432 T
1 T
205433 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:205569 original size:48 final size:49
Alignment explanation
Indices: 205475--205569 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
205465 TATATATATA
* *
205475 TATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
1 TATAGATAAACTATATAAAGTAAATTACATATATAGTTTATAGAAACAC
205524 TATAGATAAACTATATAAAGT-AATATA-ATATATAGTTTATAGAAAC
1 TATAGATAAACTATATAAAGTAAAT-TACATATATAGTTTATAGAAAC
205570 CCTAAATCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 21 0.49
49 22 0.51
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.36
Consensus pattern (49 bp):
TATAGATAAACTATATAAAGTAAATTACATATATAGTTTATAGAAACAC
Found at i:205582 original size:49 final size:49
Alignment explanation
Indices: 205480--205583 Score: 140
Period size: 48 Copynumber: 2.1 Consensus size: 49
205470 ATATATATAT
* * *
205480 ATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATAG
1 ATAAACTATATAAAGTAAATTACATATATAGTTTATAGAAACACTAAAC
*
205529 ATAAACTATATAAAGT-AATATA-ATATATAGTTTATAGAAACCCTAAATC
1 ATAAACTATATAAAGTAAAT-TACATATATAGTTTATAGAAACACTAAA-C
205578 ATAAAC
1 ATAAAC
205584 CATAAACTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
48 25 0.51
49 24 0.49
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.33
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATTACATATATAGTTTATAGAAACACTAAAC
Found at i:205596 original size:21 final size:22
Alignment explanation
Indices: 205566--205630 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 22
205556 TAGTTTATAG
*
205566 AAACCCTAAATCATAAACCA-T
1 AAACACTAAATCATAAACCACT
** *
205587 AAACTTTAAATCACAAA-CACT
1 AAACACTAAATCATAAACCACT
205608 AAACACTAAATCATAAACC-CT
1 AAACACTAAATCATAAACCACT
205629 AA
1 AA
205631 TGTAAATGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.06
21 33 0.92
22 1 0.03
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (22 bp):
AAACACTAAATCATAAACCACT
Found at i:209733 original size:35 final size:36
Alignment explanation
Indices: 209652--209758 Score: 189
Period size: 35 Copynumber: 3.0 Consensus size: 36
209642 CAAAATCGTC
*
209652 ATTTCTAATACTAGTGGGATACCCTAATTTGAGCAT
1 ATTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
*
209688 ATTTCTAATACTAGTGGGATAACCTAATTT-AGCGT
1 ATTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
209723 ATTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
1 ATTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
209759 TATCAACATT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 34 0.51
36 33 0.49
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (36 bp):
ATTTCTAATACTAGTGGGATAACCTAATTTGAGCAT
Found at i:210350 original size:31 final size:31
Alignment explanation
Indices: 210315--210377 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
210305 AATTCGATGA
* *
210315 ATTCAATATGTCTTTCTCACTAGAAAGTCCC
1 ATTCAATATGTCCTTCTCACTAGAAACTCCC
*
210346 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTAGAAACTCCC
210377 A
1 A
210378 AACTCTTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (31 bp):
ATTCAATATGTCCTTCTCACTAGAAACTCCC
Found at i:214022 original size:36 final size:36
Alignment explanation
Indices: 213970--214075 Score: 162
Period size: 35 Copynumber: 3.0 Consensus size: 36
213960 CAAAATCATC
*
213970 ATTTTCAATACTAGTGGGATAACCTAATTTGAGCAT
1 ATTTCCAATACTAGTGGGATAACCTAATTTGAGCAT
214006 ATTTCCAATACTAGTGGGATAACCTAATTT-AGCAT
1 ATTTCCAATACTAGTGGGATAACCTAATTTGAGCAT
* * *
214041 ATTTCTAATACTGGTGGGATAACCT-AGTTGAGCAT
1 ATTTCCAATACTAGTGGGATAACCTAATTTGAGCAT
214076 TATCAACAAG
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 3 0.05
35 33 0.51
36 29 0.45
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (36 bp):
ATTTCCAATACTAGTGGGATAACCTAATTTGAGCAT
Found at i:229487 original size:21 final size:21
Alignment explanation
Indices: 229450--229489 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
229440 TATGCTGAAA
**
229450 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTGCGGAGTATG
229471 CTCCACCTGTTGCGGAGTA
1 CTCCACCTGTTGCGGAGTA
229490 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGTTGCGGAGTATG
Found at i:238081 original size:14 final size:14
Alignment explanation
Indices: 238062--238101 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
238052 AGAACCTTGG
238062 ATGATAATATGAGA
1 ATGATAATATGAGA
238076 ATGAT-A-AT-AGA
1 ATGATAATATGAGA
238087 ATGATAATATGAGA
1 ATGATAATATGAGA
238101 A
1 A
238102 AATGAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.35
12 3 0.13
13 3 0.13
14 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.28
Consensus pattern (14 bp):
ATGATAATATGAGA
Found at i:238501 original size:31 final size:31
Alignment explanation
Indices: 238465--238537 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
238455 ATTACGAATG
238465 TTATTGATTTAGAAAAAATCGATCACTAATA
1 TTATTGATTTAGAAAAAATCGATCACTAATA
238496 TTATTGATTTAGAAAAAATCGATCACTAATA
1 TTATTGATTTAGAAAAAATCGATCACTAATA
*
238527 TTATCGATTTA
1 TTATTGATTTA
238538 TAACAAATTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (31 bp):
TTATTGATTTAGAAAAAATCGATCACTAATA
Found at i:244143 original size:58 final size:58
Alignment explanation
Indices: 244066--244197 Score: 187
Period size: 58 Copynumber: 2.3 Consensus size: 58
244056 ATTAGGTGAC
* * *
244066 CATTTTATAACTTTTAATAG-TCGATGACTCAACAAAATAGCATCATATAGTTGAGAGAT
1 CATTTTGTAAC-TTTAATAGTTAGATGACTCAAC-AAATAACATCATATAGTTGAGAGAT
*
244125 CATTTTGTAACTTTAATAGTTAGATGACTCAACAAATAACATCTTATAGTTGAGAGAT
1 CATTTTGTAACTTTAATAGTTAGATGACTCAACAAATAACATCATATAGTTGAGAGAT
244183 CATTTTTGT-ACTTTA
1 CA-TTTTGTAACTTTA
244198 CCCTAAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
58 39 0.58
59 28 0.42
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (58 bp):
CATTTTGTAACTTTAATAGTTAGATGACTCAACAAATAACATCATATAGTTGAGAGAT
Found at i:245092 original size:32 final size:32
Alignment explanation
Indices: 245051--245116 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
245041 CAATCGATAA
245051 ATAAAATAATTATTACTTCTTGAAATATGATT
1 ATAAAATAATTATTACTTCTTGAAATATGATT
*
245083 ATAAAATAATTATTATTTCTTGAAATATGATT
1 ATAAAATAATTATTACTTCTTGAAATATGATT
245115 AT
1 AT
245117 CTACTTGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (32 bp):
ATAAAATAATTATTACTTCTTGAAATATGATT
Found at i:247225 original size:15 final size:15
Alignment explanation
Indices: 247207--247236 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
247197 GGGGTTCTAT
*
247207 CACCGTGCTTTCTGA
1 CACCATGCTTTCTGA
247222 CACCATGCTTTCTGA
1 CACCATGCTTTCTGA
247237 TTTATTGACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (15 bp):
CACCATGCTTTCTGA
Found at i:254718 original size:22 final size:22
Alignment explanation
Indices: 254693--254787 Score: 97
Period size: 23 Copynumber: 4.3 Consensus size: 22
254683 CACCACAACT
254693 CACATAATTTG-CACCGAAGTG-C
1 CACATAATTTGTC-CCGAA-TGAC
254715 CACAT-ATTTGTCCCGAATGAC
1 CACATAATTTGTCCCGAATGAC
* * *
254736 CACATAGTTTTATCCCGAAGGAC
1 CACATA-ATTTGTCCCGAATGAC
*
254759 CACATAGTTTTGTCCCGAATGAC
1 CACATA-ATTTGTCCCGAATGAC
254782 CACATA
1 CACATA
254788 GAACCCTCGA
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.03
21 16 0.25
22 6 0.09
23 40 0.62
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (22 bp):
CACATAATTTGTCCCGAATGAC
Found at i:254754 original size:23 final size:23
Alignment explanation
Indices: 254725--254788 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
254715 CACATATTTG
254725 TCCCGAATGACCACATAGTTTTA
1 TCCCGAATGACCACATAGTTTTA
* *
254748 TCCCGAAGGACCACATAGTTTTG
1 TCCCGAATGACCACATAGTTTTA
254771 TCCCGAATGACCACATAG
1 TCCCGAATGACCACATAG
254789 AACCCTCGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (23 bp):
TCCCGAATGACCACATAGTTTTA
Found at i:260940 original size:2 final size:2
Alignment explanation
Indices: 260933--260977 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
260923 TTATTCAAAT
260933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
260975 TA T
1 TA T
260978 GGTAATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:262319 original size:3 final size:3
Alignment explanation
Indices: 262311--262349 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
262301 GAAATGCCCC
262311 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
262350 TGGTTTCTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.