Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 9 of 210
Found at i:2877823 original size:17 final size:19
Alignment explanation
Indices: 2877785--2877824 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2877775 TGAGGTACAC
2877785 ATTCTCAATGATATCCACCA
1 ATTCTCAATGATAT-CACCA
2877805 ATTCTCAATGAT-T-ACCA
1 ATTCTCAATGATATCACCA
2877822 ATT
1 ATT
2877825 TGACAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (19 bp):
ATTCTCAATGATATCACCA
Found at i:2878037 original size:89 final size:89
Alignment explanation
Indices: 2877886--2878063 Score: 275
Period size: 89 Copynumber: 2.0 Consensus size: 89
2877876 AACTGTAACA
* *
2877886 ACAATAATAATATAAACCGAACTAATACTCAATCATCATATTCATAATTTTTTAATTTTATAAAA
1 ACAATAATAATATAAACCGAACTAATACACAACCATCATATTCATAATTTTTTAATTTTATAAAA
2877951 TATGACTACTTTGAGTGACTAATC
66 TATGACTACTTTGAGTGACTAATC
* ** *
2877975 ACAATAATAATATGAATTGAACTAATACACAACCATCATATTCATAATTTTTTAGTTTTATAAAA
1 ACAATAATAATATAAACCGAACTAATACACAACCATCATATTCATAATTTTTTAATTTTATAAAA
* * *
2878040 TATGGCTACTTTGGGTGGCTAATC
66 TATGACTACTTTGAGTGACTAATC
2878064 TGATTTGAGA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.37
Consensus pattern (89 bp):
ACAATAATAATATAAACCGAACTAATACACAACCATCATATTCATAATTTTTTAATTTTATAAAA
TATGACTACTTTGAGTGACTAATC
Found at i:2893680 original size:9 final size:9
Alignment explanation
Indices: 2893663--2893700 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2893653 TTATTTAGTC
2893663 ATTTT-AAA
1 ATTTTAAAA
2893671 ATTTTAAAA
1 ATTTTAAAA
2893680 ATTTTAAAA
1 ATTTTAAAA
**
2893689 ATGATAAAA
1 ATTTTAAAA
2893698 ATT
1 ATT
2893701 AATTTACACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
8 5 0.19
9 21 0.81
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:2894145 original size:13 final size:13
Alignment explanation
Indices: 2894127--2894151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2894117 TTGTCTAAAC
2894127 TTAACTATATTTG
1 TTAACTATATTTG
2894140 TTAACTATATTT
1 TTAACTATATTT
2894152 ATAAATAGTT
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:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTAACTATATTTG
Found at i:2896230 original size:21 final size:21
Alignment explanation
Indices: 2896206--2896270 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
2896196 CCTTCTAGGT
*
2896206 TTCAGTTCAGCTCTTTTGAGC
1 TTCAGTTTAGCTCTTTTGAGC
* * ** * *
2896227 TTCAGTTTAACCCTAATGGGT
1 TTCAGTTTAGCTCTTTTGAGC
2896248 TTCAGTTTAGCTCTTTTGAGC
1 TTCAGTTTAGCTCTTTTGAGC
2896269 TT
1 TT
2896271 TAGATTAACC
Statistics
Matches: 31, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCAGTTTAGCTCTTTTGAGC
Found at i:2896237 original size:42 final size:42
Alignment explanation
Indices: 2896180--2896313 Score: 169
Period size: 42 Copynumber: 3.2 Consensus size: 42
2896170 TTAACTCATA
* * *
2896180 TGAGTTTCAGATTAACCCTTCTAGGTTTCAGTTCAGCTCTTT
1 TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTCAGCTCTTT
* * *
2896222 TGAGCTTCAGTTTAACCCTAATGGGTTTCAGTTTAGCTCTTT
1 TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTCAGCTCTTT
* * * * *
2896264 TGAGCTTTAGATTAACCTTTATGGGTTTCCGTTCAGCTCCTA
1 TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTCAGCTCTTT
2896306 TGAGCTTC
1 TGAGCTTC
2896314 CGTTCAACTC
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (42 bp):
TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTCAGCTCTTT
Found at i:2896332 original size:84 final size:84
Alignment explanation
Indices: 2896180--2896342 Score: 195
Period size: 84 Copynumber: 1.9 Consensus size: 84
2896170 TTAACTCATA
* * * * *
2896180 TGAGTTTCAGATTAACCCTTCTAGGTTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTAATG
1 TGAGTTTCAGATTAACCCTTATAGGTTTCAGTTCAGCTCCTATGAGCTTCAGTTCAACCCTAACG
2896245 GG-TTTCAGTTTAGCTCTTT
66 GGTTTTC-GTTTAGCTCTTT
* * * * * *
2896264 TGAGCTTT-AGATTAACCTTTATGGGTTTCCGTTCAGCTCCTATGAGCTTCCGTTCAACTCTTAC
1 TGAG-TTTCAGATTAACCCTTATAGGTTTCAGTTCAGCTCCTATGAGCTTCAGTTCAACCCTAAC
2896328 GGGTTTTCGTTTAGC
65 GGGTTTTCGTTTAGC
2896343 ACTTATGTGT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 59 0.89
85 7 0.11
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (84 bp):
TGAGTTTCAGATTAACCCTTATAGGTTTCAGTTCAGCTCCTATGAGCTTCAGTTCAACCCTAACG
GGTTTTCGTTTAGCTCTTT
Found at i:2903850 original size:21 final size:21
Alignment explanation
Indices: 2903826--2903887 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
2903816 CATAGAATTC
2903826 TATTAAATATAAAATTATATT
1 TATTAAATATAAAATTATATT
* *
2903847 TATTAACT-TGAAAATTAT-TA
1 TATTAAATAT-AAAATTATATT
* * *
2903867 TATTTAATATATACTTATATT
1 TATTAAATATAAAATTATATT
2903888 AATAAAAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (21 bp):
TATTAAATATAAAATTATATT
Found at i:2903976 original size:21 final size:19
Alignment explanation
Indices: 2903952--2903995 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 19
2903942 AGGGTGAAAG
2903952 ATATAATAAAATATTAAAAAT
1 ATATAATAAAA-A-TAAAAAT
2903973 ATATAATAAAAATAAAAAT
1 ATATAATAAAAATAAAAAT
2903992 ATAT
1 ATAT
2903996 GTCAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.48
20 1 0.04
21 11 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATAATAAAAATAAAAAT
Found at i:2911853 original size:21 final size:23
Alignment explanation
Indices: 2911817--2911860 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2911807 TAAAATTTAA
*
2911817 ATTTTATTTCGAA-TTTTAAAAT
1 ATTTTAATTCGAATTTTTAAAAT
2911839 ATTTTAATT-GAATTTTTAAAAT
1 ATTTTAATTCGAATTTTTAAAAT
2911861 TAGAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
ATTTTAATTCGAATTTTTAAAAT
Found at i:2912887 original size:12 final size:12
Alignment explanation
Indices: 2912867--2912896 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2912857 AAGATGAAAG
*
2912867 TTCAACTTCAGT
1 TTCAGCTTCAGT
2912879 TTCAGCTTCAGT
1 TTCAGCTTCAGT
2912891 TTCAGC
1 TTCAGC
2912897 CTCTTTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (12 bp):
TTCAGCTTCAGT
Found at i:2915849 original size:1 final size:1
Alignment explanation
Indices: 2915843--2915915 Score: 92
Period size: 1 Copynumber: 73.0 Consensus size: 1
2915833 AGATGAAACC
** ** *
2915843 AAAAAAAAAAAAAAAAAAAAAAGGAAAAAGCAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
2915908 AAAGAAAA
1 AAAAAAAA
2915916 GAAACAAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.92, C:0.01, G:0.05, T:0.01
Consensus pattern (1 bp):
A
Found at i:2919709 original size:19 final size:19
Alignment explanation
Indices: 2919685--2919797 Score: 145
Period size: 19 Copynumber: 5.8 Consensus size: 19
2919675 AATCATATAT
*
2919685 TCTAAGATTGCATGTCATA
1 TCTAAGATTGCATATCATA
** *
2919704 TCTAAGATTATATATCATC
1 TCTAAGATTGCATATCATA
2919723 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2919742 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
* **
2919763 TATTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2919782 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
2919798 CTCAAAAATT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 63 0.80
21 16 0.20
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2919772 original size:40 final size:40
Alignment explanation
Indices: 2919687--2919796 Score: 161
Period size: 40 Copynumber: 2.8 Consensus size: 40
2919677 TCATATATTC
* * *
2919687 TAAGATTGCATGTCATATCTAAGATT--ATATATCATCTC
1 TAAGATTGCATATCATATCTAAGATTGCATATATCATATA
2919725 TAAGATTGCATATCATATCTAAGATTGCATATATCATATA
1 TAAGATTGCATATCATATCTAAGATTGCATATATCATATA
**
2919765 TTGGATTGCATATCATATCTAAGATTGCATAT
1 TAAGATTGCATATCATATCTAAGATTGCATAT
2919797 CCTCAAAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 25 0.38
40 40 0.62
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (40 bp):
TAAGATTGCATATCATATCTAAGATTGCATATATCATATA
Found at i:2920112 original size:23 final size:24
Alignment explanation
Indices: 2920064--2920113 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
2920054 TGATGAAATC
* *
2920064 AAATATTATATTTTAACTTCTTAA
1 AAATATTATAATTTAACTTCTGAA
2920088 AAAT-TTATAATTTAA-TTCTCGAA
1 AAATATTATAATTTAACTTCT-GAA
2920111 AAA
1 AAA
2920114 AAATTCACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATATTATAATTTAACTTCTGAA
Found at i:2926251 original size:25 final size:24
Alignment explanation
Indices: 2926197--2926251 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
2926187 GTTCGGGTTT
*
2926197 ATTCGGCCTAAAAAATATATTTAA
1 ATTCGGCCTAAAAAAAATATTTAA
2926221 AGTTCGGCCTAAATAAAAA-ATATTAA
1 A-TTCGGCCTAAA-AAAAATAT-TTAA
2926247 ATTCG
1 ATTCG
2926252 AGTTCGACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.04
25 17 0.63
26 9 0.33
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (24 bp):
ATTCGGCCTAAAAAAAATATTTAA
Found at i:2926527 original size:21 final size:22
Alignment explanation
Indices: 2926478--2926528 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
2926468 TAAGTAATAG
*
2926478 CAACAAAATGGCAGTAAAACTA
1 CAACAAAATGGCAGTAAAACAA
*
2926500 CATCAAAATGGCA-TAAAACAA
1 CAACAAAATGGCAGTAAAACAA
*
2926521 TAACAAAA
1 CAACAAAA
2926529 CAATAGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.14
Consensus pattern (22 bp):
CAACAAAATGGCAGTAAAACAA
Found at i:2927549 original size:25 final size:24
Alignment explanation
Indices: 2927495--2927549 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
2927485 GTTCGGGTTT
*
2927495 ATTCGGCCTAAAAAATATATTTAA
1 ATTCGGCCTAAAAAAAATATTTAA
2927519 AGTTCGGCCTAAATAAAAA-ATATTAA
1 A-TTCGGCCTAAA-AAAAATAT-TTAA
2927545 ATTCG
1 ATTCG
2927550 AGTTCGACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.04
25 17 0.63
26 9 0.33
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (24 bp):
ATTCGGCCTAAAAAAAATATTTAA
Found at i:2927825 original size:21 final size:22
Alignment explanation
Indices: 2927776--2927826 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
2927766 TAAGTAATAG
*
2927776 CAACAAAATGGCAGTAAAACTA
1 CAACAAAATGGCAGTAAAACAA
*
2927798 CATCAAAATGGCA-TAAAACAA
1 CAACAAAATGGCAGTAAAACAA
*
2927819 TAACAAAA
1 CAACAAAA
2927827 CAATAGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.14
Consensus pattern (22 bp):
CAACAAAATGGCAGTAAAACAA
Found at i:2934603 original size:15 final size:15
Alignment explanation
Indices: 2934583--2934611 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2934573 TGGTTGGCAA
2934583 AAATGAGTCTACAAT
1 AAATGAGTCTACAAT
2934598 AAATGAGTCTACAA
1 AAATGAGTCTACAA
2934612 GTGATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (15 bp):
AAATGAGTCTACAAT
Found at i:2937031 original size:22 final size:22
Alignment explanation
Indices: 2937005--2937092 Score: 79
Period size: 22 Copynumber: 3.8 Consensus size: 22
2936995 ATTAATCCTT
*
2937005 TCTCAATTTTCTCTCAATTTGC
1 TCTCAATTTTCTCTCAATTTCC
*
2937027 TCTCAAATTAATCCTTTCTCAATTTCC
1 TCTC-AATT--T--TCTCTCAATTTCC
*
2937054 TCTCAATTTCCTCTCAATTTCC
1 TCTCAATTTTCTCTCAATTTCC
*
2937076 T-TCCAAATTTCTCTCAA
1 TCT-CAATTTTCTCTCAA
2937093 ATCCATATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
21 1 0.02
22 28 0.52
23 4 0.07
24 1 0.02
25 1 0.02
26 4 0.07
27 15 0.28
ACGTcount: A:0.23, C:0.31, G:0.01, T:0.45
Consensus pattern (22 bp):
TCTCAATTTTCTCTCAATTTCC
Found at i:2937043 original size:38 final size:38
Alignment explanation
Indices: 2936992--2937092 Score: 140
Period size: 38 Copynumber: 2.8 Consensus size: 38
2936982 TTTTTTTTCA
*
2936992 CAAATTAATCCTTTCTCAATTTTCTCTCAATTTGCTCT
1 CAAATTAATCCTTTCTCAATTTTCTCTCAATTTCCTCT
*
2937030 CAAATTAATCCTTTCTCAATTTCCTCTCAATTTCCTCT
1 CAAATTAATCCTTTCTCAATTTTCTCTCAATTTCCTCT
*
2937068 C-AATT--TCC-TTC-CAAATTTCTCTCAA
1 CAAATTAATCCTTTCTCAATTTTCTCTCAA
2937093 ATCCATATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
33 12 0.20
34 3 0.05
35 3 0.05
37 4 0.07
38 37 0.63
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.45
Consensus pattern (38 bp):
CAAATTAATCCTTTCTCAATTTTCTCTCAATTTCCTCT
Found at i:2937094 original size:11 final size:11
Alignment explanation
Indices: 2937005--2937076 Score: 81
Period size: 11 Copynumber: 6.1 Consensus size: 11
2936995 ATTAATCCTT
*
2937005 TCTCAATTTTC
1 TCTCAATTTCC
*
2937016 TCTCAATTTGC
1 TCTCAATTTCC
2937027 TCTCAAATTAATCC
1 TCTC-AATT--TCC
2937041 TTTCTCAATTTCC
1 --TCTCAATTTCC
2937054 TCTCAATTTCC
1 TCTCAATTTCC
2937065 TCTCAATTTCC
1 TCTCAATTTCC
2937076 T
1 T
2937077 TCCAAATTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
11 37 0.69
12 4 0.07
13 3 0.06
14 2 0.04
15 4 0.07
16 4 0.07
ACGTcount: A:0.21, C:0.31, G:0.01, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:2937121 original size:51 final size:51
Alignment explanation
Indices: 2937054--2937153 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
2937044 CTCAATTTCC
2937054 TCTCAATTTCCTCTCAATTT-C-CTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTCCTCTCAATTTGCTCTT--AAATTTCTCTCAAATCCATATTTAA
* * *
2937105 TCTCAATTTGCTCTCAATTTGCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTCCTCTCAATTTGCTCTTAAATTTCTCTCAAATCCATATTT
2937154 TTAAATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 40 0.91
52 1 0.02
53 3 0.07
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAATTTCCTCTCAATTTGCTCTTAAATTTCTCTCAAATCCATATTTAA
Found at i:2937125 original size:11 final size:11
Alignment explanation
Indices: 2937105--2937129 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2937095 CCATATTTAA
2937105 TCTCAATTTGC
1 TCTCAATTTGC
2937116 TCTCAATTTGC
1 TCTCAATTTGC
2937127 TCT
1 TCT
2937130 TAAATTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (11 bp):
TCTCAATTTGC
Found at i:2937140 original size:11 final size:12
Alignment explanation
Indices: 2937109--2937145 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
2937099 ATTTAATCTC
*
2937109 AATTTGCTC-TC
1 AATTTGCTCTTA
2937120 AATTTGCTCTTA
1 AATTTGCTCTTA
2937132 AATTT-CTCTTA
1 AATTTGCTCTTA
2937143 AAT
1 AAT
2937146 CCCTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (12 bp):
AATTTGCTCTTA
Found at i:2937184 original size:17 final size:18
Alignment explanation
Indices: 2937162--2937203 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2937152 TTTTAAATAA
2937162 TTTAAAAAAATTAT-ATT
1 TTTAAAAAAATTATAATT
* *
2937179 TTTAAATAAATTTTAATT
1 TTTAAAAAAATTATAATT
2937197 TTTAAAA
1 TTTAAAA
2937204 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAAAAAATTATAATT
Found at i:2939390 original size:615 final size:615
Alignment explanation
Indices: 2938205--2939435 Score: 2081
Period size: 615 Copynumber: 2.0 Consensus size: 615
2938195 GCAAGTTATG
2938205 CTCGATTACCTACCTCTCTTGAAGATATACAGCTTCTATTGGACCAACGGTTGGAAGCACTAGTA
1 CTCGATTACCTACCTCTCTTGAAGATATACAGCTTCTATTGGACCAACGGTTGGAAGCACTAGTA
2938270 AGTATTAAATAAAATAGATATTTCCATAATGAGATAGTCGATTGGTATTTAGTATTTAGTACATA
66 AGTATTAAATAAAATAGATATTTCCATAATGAGATAGTCGATTGGTATTTAGTATTTAGTACATA
2938335 ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACCATACGAGGATCCGGCAATTCGGGC
131 ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACCATACGAGGATCCGGCAATTCGGGC
2938400 AGTAATTCCGGATGAGTACTTCCAAAATCGAAACAGTTGGCATGTGAAAGTCCCATTGGTCAACT
196 AGTAATTCCGGATGAGTACTTCCAAAATCGAAACAGTTGGCATGTGAAAGTCCCATTGGTCAACT
* * * *
2938465 TTGCGATTGTGGCGATGCACCAGTCGGACAGAGTATTACGGGAATTTGGATTCCGACAACCGATT
261 TTGCGACTGTAGAGATGCACCAGTCGAACAGAGTATTACGGGAATTTGGATTCCGACAACCGATT
* *
2938530 CCCGTGGCACTTGAGGTGTTGGATGATCATCACAAAATCGACCTATGGCAATTGCATACGGATTG
326 CCCGTGGCACCTGAGGTGTTGGATGATCATCACAAAATCGACCTACGGCAATTGCATACGGATTG
2938595 GCCGAGATTCTGGTCACACTACATCCAAATGTGAGAAGATCGGTATGACTATATACCTACTTGGG
391 GCCGAGATTCTGGTCACACTACATCCAAATGTGAGAAGATCGGTATGACTATATACCTACTTGGG
* * * * * * * *
2938660 AGCCGATCATCGTTCCAGAGTTAGTGTCCGTGCCAGAATACATGCCATGATTTAGGATCCATGGG
456 AACCGATCATCCTTCCAGAATTAGCGTCCATGCCAGAATACATACCATGATTTAGGATCAATGGA
* * *
2938725 AAGCCGTATTTACTCTCGCCAGAGGAGAGGCAGCGGCAATTACATGTCCAAAGGGAACGACGTAG
521 AAGCCATATTTACTCTCGCCAGAGGAGAGGCAGCGACAATTACATGTCCAAAGGGAACAACGTAG
2938790 CCCTTTAAATCCAAGAAGAAGGGACGACGA
586 CCCTTTAAATCCAAGAAGAAGGGACGACGA
2938820 CTCGATTACCTACCTCTCTTGAAGATATACAGCTTCTATTGGACCAACGGTTGGAAGCACTAGTA
1 CTCGATTACCTACCTCTCTTGAAGATATACAGCTTCTATTGGACCAACGGTTGGAAGCACTAGTA
2938885 AGTATTAAATAAAATAGATATTTCCATAATGAGATAGTCGATTGGTATTTAGTATTTAGTACATA
66 AGTATTAAATAAAATAGATATTTCCATAATGAGATAGTCGATTGGTATTTAGTATTTAGTACATA
*
2938950 ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACTATACGAGGATCCGGCAATTCGGGC
131 ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACCATACGAGGATCCGGCAATTCGGGC
** * * *
2939015 AGTAATTTTGGATGAGTACTTCCAAAATTGAAACGGTTGGCATGTGAAAGTCTCATTGGTCAACT
196 AGTAATTCCGGATGAGTACTTCCAAAATCGAAACAGTTGGCATGTGAAAGTCCCATTGGTCAACT
* * *
2939080 TTGCGACTGTAGAGATGCACTAGTCGAACAGAGTATTACGGTAATTTGGATTCTGACAACCGATT
261 TTGCGACTGTAGAGATGCACCAGTCGAACAGAGTATTACGGGAATTTGGATTCCGACAACCGATT
*
2939145 CCTC-TGGCACCTGAGGTGTTGGATGATCATCACAAAATTGACCTACGGCAATTGCATACGGATT
326 CC-CGTGGCACCTGAGGTGTTGGATGATCATCACAAAATCGACCTACGGCAATTGCATACGGATT
* * *
2939209 GGCTGAGATTCTGGTCACACTACATCCAAATGTGGGAAGATTGGTATGACTATATACCTA-TTCG
390 GGCCGAGATTCTGGTCACACTACATCCAAATGTGAGAAGATCGGTATGACTATATACCTACTT-G
* * *
2939273 GGAACCGATTATCCTTCCAGAATTAGCGTGCATGCC-GTAATACATACCATGGTTTAGGATCAAT
454 GGAACCGATCATCCTTCCAGAATTAGCGTCCATGCCAG-AATACATACCATGATTTAGGATCAAT
* *
2939337 GGAAAGCCATATTTACTCTCGCCAGAGGAGAGGCAGCGACAATTGCGTGTCCAAAGGGAACAACG
518 GGAAAGCCATATTTACTCTCGCCAGAGGAGAGGCAGCGACAATTACATGTCCAAAGGGAACAACG
* *
2939402 TATCCCTTTAAATCCAAGAAGAAGGGACGGCGA
583 TAGCCCTTTAAATCCAAGAAGAAGGGACGACGA
2939435 C
1 C
2939436 GCAAGCCCAT
Statistics
Matches: 576, Mismatches: 37, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
614 3 0.01
615 572 0.99
616 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (615 bp):
CTCGATTACCTACCTCTCTTGAAGATATACAGCTTCTATTGGACCAACGGTTGGAAGCACTAGTA
AGTATTAAATAAAATAGATATTTCCATAATGAGATAGTCGATTGGTATTTAGTATTTAGTACATA
ACTAATATTTCCATCATGGTCATATAGTTTGAATGGACACCATACGAGGATCCGGCAATTCGGGC
AGTAATTCCGGATGAGTACTTCCAAAATCGAAACAGTTGGCATGTGAAAGTCCCATTGGTCAACT
TTGCGACTGTAGAGATGCACCAGTCGAACAGAGTATTACGGGAATTTGGATTCCGACAACCGATT
CCCGTGGCACCTGAGGTGTTGGATGATCATCACAAAATCGACCTACGGCAATTGCATACGGATTG
GCCGAGATTCTGGTCACACTACATCCAAATGTGAGAAGATCGGTATGACTATATACCTACTTGGG
AACCGATCATCCTTCCAGAATTAGCGTCCATGCCAGAATACATACCATGATTTAGGATCAATGGA
AAGCCATATTTACTCTCGCCAGAGGAGAGGCAGCGACAATTACATGTCCAAAGGGAACAACGTAG
CCCTTTAAATCCAAGAAGAAGGGACGACGA
Found at i:2939884 original size:12 final size:11
Alignment explanation
Indices: 2939853--2939878 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2939843 ATTTTCTTTA
2939853 TTTTAAAATAC
1 TTTTAAAATAC
2939864 TTTTAAAATAC
1 TTTTAAAATAC
2939875 TTTT
1 TTTT
2939879 TTAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:2939899 original size:41 final size:41
Alignment explanation
Indices: 2939852--2939993 Score: 160
Period size: 40 Copynumber: 3.4 Consensus size: 41
2939842 TATTTTCTTT
*
2939852 ATTTTAAAATACTTTTAAAATACTTTTTTAAATTTTGTTAA
1 ATTTTAAAATAATTTTAAAATACTTTTTTAAATTTTGTTAA
* * * * *
2939893 ATTTTAAAAAAATTTTAAAA-AATTTTTTTAATTTTTTTTA
1 ATTTTAAAATAATTTTAAAATACTTTTTTAAATTTTGTTAA
* *
2939933 ATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTGTTTTAA
1 ATTTTAAAATAATTTTAAAATAC-TTTTTTAAATTTTG--TTAA
*
2939977 TTTTTAAAATAAATTTT
1 ATTTTAAAAT-AATTTT
2939994 TGGTATTTAT
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
40 34 0.42
41 19 0.23
42 11 0.14
44 12 0.15
45 5 0.06
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (41 bp):
ATTTTAAAATAATTTTAAAATACTTTTTTAAATTTTGTTAA
Found at i:2939935 original size:29 final size:30
Alignment explanation
Indices: 2939903--2939968 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
2939893 ATTTTAAAAA
**
2939903 AATTTTAAAAAATTTTTTTAAT-TTTTTTT
1 AATTTTAAAAAATTTTTAAAATATTTTTTT
*
2939932 AATTTTAAAATATTTTTAAAATACTTTTTTT
1 AATTTTAAAAAATTTTTAAAATA-TTTTTTT
2939963 AATTTT
1 AATTTT
2939969 TGTTTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 19 0.59
31 13 0.41
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
AATTTTAAAAAATTTTTAAAATATTTTTTT
Found at i:2940951 original size:21 final size:20
Alignment explanation
Indices: 2940893--2940952 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
2940883 TCTGATCAAT
2940893 AAATGACACATAAGTGCCTG
1 AAATGACACATAAGTGCCTG
* * *
2940913 AAACGACACACGAGGTGCCT-
1 AAATGACACA-TAAGTGCCTG
2940933 AATATGACACATAAAGTGCC
1 AA-ATGACACAT-AAGTGCC
2940953 AGATCGGCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
AAATGACACATAAGTGCCTG
Found at i:2941686 original size:13 final size:13
Alignment explanation
Indices: 2941668--2941694 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2941658 TACTACTTAA
2941668 TTTCCTACCAAAC
1 TTTCCTACCAAAC
2941681 TTTCCTACCAAAC
1 TTTCCTACCAAAC
2941694 T
1 T
2941695 CACATTTAAC
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:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (13 bp):
TTTCCTACCAAAC
Found at i:2942211 original size:16 final size:16
Alignment explanation
Indices: 2942190--2942271 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
2942180 ATTTTCCCTT
2942190 TTCTTTCTTTCTTTTC
1 TTCTTTCTTTCTTTTC
* * *
2942206 TTCTTTCCTTCCTTCC
1 TTCTTTCTTTCTTTTC
* *
2942222 TTCTCTGTTTCTTTT-
1 TTCTTTCTTTCTTTTC
* *
2942237 TGCTTTTGTTTC-TTTC
1 TTC-TTTCTTTCTTTTC
2942253 TT-TTTCATTTCTTTT-
1 TTCTTTC-TTTCTTTTC
2942268 TTCT
1 TTCT
2942272 AATAATATAA
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
14 3 0.06
15 11 0.22
16 35 0.71
ACGTcount: A:0.01, C:0.24, G:0.04, T:0.71
Consensus pattern (16 bp):
TTCTTTCTTTCTTTTC
Found at i:2942773 original size:16 final size:16
Alignment explanation
Indices: 2942752--2942787 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2942742 ATTTTCCCTT
* *
2942752 TTCTTTCTTTCTTTTC
1 TTCTTTCCTTCCTTTC
2942768 TTCTTTCCTTCCTTTC
1 TTCTTTCCTTCCTTTC
2942784 TTCT
1 TTCT
2942788 CTGTTTCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTTCCTTCCTTTC
Found at i:2943202 original size:49 final size:48
Alignment explanation
Indices: 2943080--2943204 Score: 214
Period size: 48 Copynumber: 2.6 Consensus size: 48
2943070 AAATAGTTTA
* *
2943080 TATTAATGTAATAGAATACAAAATAGTTTAATTTGAATATTTTGATAT
1 TATTGATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTGATAT
*
2943128 TATTGATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATAT
1 TATTGATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTGATAT
2943176 TATTTGATGTAATAAAATACAAAATAGTT
1 TA-TTGATGTAATAAAATACAAAATAGTT
2943205 AATATTCTTA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
48 47 0.64
49 26 0.36
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.43
Consensus pattern (48 bp):
TATTGATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTGATAT
Found at i:2943378 original size:37 final size:37
Alignment explanation
Indices: 2943327--2943398 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
2943317 NNNNNNNNNA
* *
2943327 AATCATTACTTAATTAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
2943364 AATCACTACATAATTAAAAACATTACATAATTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
2943399 GAAATTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:2943392 original size:17 final size:17
Alignment explanation
Indices: 2943330--2943395 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
2943320 NNNNNNAAAT
*
2943330 CATTACTTAATTAAAAA
1 CATTACATAATTAAAAA
** *
2943347 CATTACATAAGTCTTTGAAT
1 CATTACATAA---TTAAAAA
*
2943367 CACTACATAATTAAAAA
1 CATTACATAATTAAAAA
2943384 CATTACATAATT
1 CATTACATAATT
2943396 CTTGAAATTA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 24 0.65
20 13 0.35
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (17 bp):
CATTACATAATTAAAAA
Found at i:2943577 original size:38 final size:39
Alignment explanation
Indices: 2943526--2943603 Score: 124
Period size: 38 Copynumber: 2.0 Consensus size: 39
2943516 TACTTAGAGT
*
2943526 TAGACTTTAGTTTTATTTTTATT-GAGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTAG-GTTGGGTAATTGGG
2943564 TAGACTTTAGTTTTAGTTTTATTAGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTAGGTTGGGTAATTGGG
2943603 T
1 T
2943604 TGGGTTGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 25 0.68
39 12 0.32
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTAGGTTGGGTAATTGGG
Found at i:2947165 original size:124 final size:124
Alignment explanation
Indices: 2946869--2947258 Score: 618
Period size: 124 Copynumber: 3.1 Consensus size: 124
2946859 CCCAAACATG
2946869 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTATTTCAGAAATTTTTCTTATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTATTTCAGAAATTTTTCTTATAAAGCATCCTGC
*
2946934 TTGAAGCGTTTTTATACTATTTGCTCATAAACGTCATTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCATAAACG----TCAACTCGAAATTATTTTTTCAGGAC
* * ** * * *
2946997 CTACTGTAGCAAAAGCGCATCCACGTGGAAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTATTTCAGAAATTTTTCTTATAAAGCATCCTGC
* * *
2947062 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTTTTCAAGAC
66 TTGAAGCGTTTTTATACTATTTGCTCATAAACGTCAACTCGAAATTATTTTTTCAGGAC
*
2947121 TTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTATTTCAGAAATTTTTCTTATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTATTTCAGAAATTTTTCTTATAAAGCATCCTGC
*
2947186 TTGAAGCGTTTTTATACTATTTGCTCATAAACGTCAACTCGAAATTATATTTTCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCATAAACGTCAACTCGAAATTATTTTTTCAGGAC
*
2947245 CTACTGTATCAAAA
1 CTACTGTAGCAAAA
2947259 ACGCATCTGC
Statistics
Matches: 237, Mismatches: 25, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
124 147 0.62
128 90 0.38
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTATTTCAGAAATTTTTCTTATAAAGCATCCTGC
TTGAAGCGTTTTTATACTATTTGCTCATAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:2947636 original size:41 final size:43
Alignment explanation
Indices: 2947554--2947639 Score: 131
Period size: 41 Copynumber: 2.0 Consensus size: 43
2947544 GCGTCCCCAG
2947554 GGGAGCGCTTATGTGGCAGCAAATTAACGTGCCCTTAAGGGAGC
1 GGGAGCGCTTATGTGGCAGCAAA-TAACGTGCCCTTAAGGGAGC
* *
2947598 GGGAGCGCTTATGTGGTAGC-AA-AACGTGCCCTTGAGGGAGC
1 GGGAGCGCTTATGTGGCAGCAAATAACGTGCCCTTAAGGGAGC
2947639 G
1 G
2947640 ATTTATGTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
41 19 0.47
43 2 0.05
44 19 0.47
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (43 bp):
GGGAGCGCTTATGTGGCAGCAAATAACGTGCCCTTAAGGGAGC
Found at i:2949986 original size:973 final size:974
Alignment explanation
Indices: 2948087--2950035 Score: 3891
Period size: 973 Copynumber: 2.0 Consensus size: 974
2948077 TTTTAAAAAT
2948087 TAATTATTAATATGACATACACATGACAATCTATGGTATGCCGCAACATCCGTCTATTATAGAGT
1 TAATTATTAATATGACATACACATGACAATCTATGGTATGCCGCAACATCCGTCTATTATAGAGT
2948152 GATTTGACAAACAATGAATATTTAAAGATTAAAAGAGATAAAAAAATTAATTAATTAATTAAAAT
66 GATTTGACAAACAATGAATATTTAAAGATTAAAAGAGATAAAAAAATTAATTAATTAATTAAAAT
2948217 GATTATCCTTAAGAGGTCAAATAAGTCATTATGCCTGAATTGTATTACAACTACATTCTGTGTGG
131 GATTATCCTTAAGAGGTCAAATAAGTCATTATGCCTGAATTGTATTACAACTACATTCTGTGTGG
2948282 AGGACTATTATAACACATTTAGAACGTGGATGAAAAAAATTATATAATAAATTTATAAAAGAAAT
196 AGGACTATTATAACACATTTAGAACGTGGATGAAAAAAATTATATAATAAATTTATAAAAGAAAT
2948347 TGATATAAATATGTAATGTGATTTTGGTTGGAATGGTAAAATTGATATATTAAATTTTATGATGT
261 TGATATAAATATGTAATGTGATTTTGGTTGGAATGGTAAAATTGATATATTAAATTTTATGATGT
2948412 TTTGGTTAAAATATTATGATTTTAATTTTGAATATGTATTTTTTCTAGATTTATTAAAATATAAA
326 TTTGGTTAAAATATTATGATTTTAATTTTGAATATGTATTTTTTCTAGATTTATTAAAATATAAA
2948477 AAATACATAAATAGTCTTAAAATAATATTTTTTTATTTTATAAATTTAATAATTTTTTTATAATT
391 AAATACATAAATAGTCTTAAAATAATATTTTTTTATTTTATAAATTTAATAATTTTTTTATAATT
2948542 CCACAATTGAATTGAAATTTGATTAATTGGTGATACAAATTCAATTAAATTATTAATTATAGTAT
456 CCACAATTGAATTGAAATTTGATTAATTGGTGATACAAATTCAATTAAATTATTAATTATAGTAT
2948607 AAATATACCAAATTGCTATTAATGATGCTTTTTTTTAATTAAGATGCTATTCATGTTTAATGAAA
521 AAATATACCAAATTGCTATTAATGATGCTTTTTTTTAATTAAGATGCTATTCATGTTTAATGAAA
2948672 CTTTATCTTAAAAAAAGAAATAATTAAAGATTTAAATTAAACATATCATATCTTCTTCTTTTTTT
586 CTTTATCTTAAAAAAAGAAATAATTAAAGATTTAAATTAAACATATCATATCTTCTTCTTTTTTT
2948737 ACATAATGTCTAAAGCTACTCAAAAGTCTCTCTCCAACCTATACATAGAAACATAATGCGCTTCA
651 ACATAATGTCTAAAGCTACTCAAAAGTCTCTCTCCAACCTATACATAGAAACATAATGCGCTTCA
2948802 ACACACTCGAACTCACGTCCTTTTCCATTGGCAACAATAGCTATGCCACTCGAATTAAAACTCAA
716 ACACACTCGAACTCACGTCCTTTTCCATTGGCAACAATAGCTATGCCACTCGAATTAAAACTCAA
2948867 TTGACTTCTTTATTTTTAATATATCTATAATTAGTTAGATATAAATAATAAAATAAATTTTAGTA
781 TTGACTTCTTTATTTTTAATATATCTATAATTAGTTAGATATAAATAATAAAATAAATTTTAGTA
2948932 TTTATTTGTAGATGTTTATGAGATGAATTAGATTTGGCAGGGATTATATATGATATTATAATATT
846 TTTATTTGTAGATGTTTATGAGATGAATTAGATTTGGCAGGGATTATATATGATATTATAATATT
2948997 TCATACGAGTCTAAATCTCACTCAACTTGAAATATTAATTTTAAATTTTATTCAAATTCACTCG
911 TCATACGAGTCTAAATCTCACTCAACTTGAAATATTAATTTTAAATTTTATTCAAATTCACTCG
2949061 TAATTATTAATA-GACATACACATGACAATCTATGGTATGCCGCAACATCCGTCTATTATAGAGT
1 TAATTATTAATATGACATACACATGACAATCTATGGTATGCCGCAACATCCGTCTATTATAGAGT
2949125 GATTTGACAAACAATGAATATTTAAAGATTAAAAGAGATAAAAAAATTAATTAATTAATTAAAAT
66 GATTTGACAAACAATGAATATTTAAAGATTAAAAGAGATAAAAAAATTAATTAATTAATTAAAAT
2949190 GATTATCCTTAAGAGGTCAAATAAGTCATTATGCCTGAATTGTATTACAACTACATTCTGTGTGG
131 GATTATCCTTAAGAGGTCAAATAAGTCATTATGCCTGAATTGTATTACAACTACATTCTGTGTGG
2949255 AGGACTATTATAACACATTTAGAACGTGGATGAAAAAAATTATATAATAAATTTATAAAAGAAAT
196 AGGACTATTATAACACATTTAGAACGTGGATGAAAAAAATTATATAATAAATTTATAAAAGAAAT
2949320 TGATATAAATATGTAATGTGATTTTGGTTGGAATGGTAAAATTGATATATTAAATTTTATGATGT
261 TGATATAAATATGTAATGTGATTTTGGTTGGAATGGTAAAATTGATATATTAAATTTTATGATGT
2949385 TTTGGTTAAAATATTATGATTTTAATTTTGAATATGTATTTTTTCTAGATTTATTAAAATATAAA
326 TTTGGTTAAAATATTATGATTTTAATTTTGAATATGTATTTTTTCTAGATTTATTAAAATATAAA
2949450 AAATACATAAATAGTCTTAAAATAATATTTTTTTATTTTATAAATTTAATAATTTTTTTATAATT
391 AAATACATAAATAGTCTTAAAATAATATTTTTTTATTTTATAAATTTAATAATTTTTTTATAATT
2949515 CCACAATTGAATTGAAATTTGATTAATTGGTGATACAAATTCAATTAAATTATTAATTATAGTAT
456 CCACAATTGAATTGAAATTTGATTAATTGGTGATACAAATTCAATTAAATTATTAATTATAGTAT
2949580 AAATATACCAAATTGCTATTAATGATGCTTTTTTTTAATTAAGATGCTATTCATGTTTAATGAAA
521 AAATATACCAAATTGCTATTAATGATGCTTTTTTTTAATTAAGATGCTATTCATGTTTAATGAAA
2949645 CTTTATCTTAAAAAAAGAAATAATTAAAGATTTAAATTAAACATATCATATCTTCTTCTTTTTTT
586 CTTTATCTTAAAAAAAGAAATAATTAAAGATTTAAATTAAACATATCATATCTTCTTCTTTTTTT
2949710 ACATAATGTCTAAAGCTACTCAAAAGTCTCTCTCCAACCTATACATAGAAACATAATGCGCTTCA
651 ACATAATGTCTAAAGCTACTCAAAAGTCTCTCTCCAACCTATACATAGAAACATAATGCGCTTCA
2949775 ACACACTCGAACTCACGTCCTTTTCCATTGGCAACAATAGCTATGCCACTCGAATTAAAACTCAA
716 ACACACTCGAACTCACGTCCTTTTCCATTGGCAACAATAGCTATGCCACTCGAATTAAAACTCAA
2949840 TTGACTTCTTTATTTTTAATATATCTATAATTAGTTAGATATAAATAATAAAATAAATTTTAGTA
781 TTGACTTCTTTATTTTTAATATATCTATAATTAGTTAGATATAAATAATAAAATAAATTTTAGTA
2949905 TTTATTTGTAGATGTTTATGAGATGAATTAGATTTGGCAGGGATTATATATGATATTATAATATT
846 TTTATTTGTAGATGTTTATGAGATGAATTAGATTTGGCAGGGATTATATATGATATTATAATATT
2949970 TCATACGAGTCTAAATCTCACTCAACTTGAAATATTAATTTTAAATTTTATTCAAATTCACTCG
911 TCATACGAGTCTAAATCTCACTCAACTTGAAATATTAATTTTAAATTTTATTCAAATTCACTCG
2950034 TA
1 TA
2950036 TTTACCATTA
Statistics
Matches: 975, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
973 963 0.99
974 12 0.01
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (974 bp):
TAATTATTAATATGACATACACATGACAATCTATGGTATGCCGCAACATCCGTCTATTATAGAGT
GATTTGACAAACAATGAATATTTAAAGATTAAAAGAGATAAAAAAATTAATTAATTAATTAAAAT
GATTATCCTTAAGAGGTCAAATAAGTCATTATGCCTGAATTGTATTACAACTACATTCTGTGTGG
AGGACTATTATAACACATTTAGAACGTGGATGAAAAAAATTATATAATAAATTTATAAAAGAAAT
TGATATAAATATGTAATGTGATTTTGGTTGGAATGGTAAAATTGATATATTAAATTTTATGATGT
TTTGGTTAAAATATTATGATTTTAATTTTGAATATGTATTTTTTCTAGATTTATTAAAATATAAA
AAATACATAAATAGTCTTAAAATAATATTTTTTTATTTTATAAATTTAATAATTTTTTTATAATT
CCACAATTGAATTGAAATTTGATTAATTGGTGATACAAATTCAATTAAATTATTAATTATAGTAT
AAATATACCAAATTGCTATTAATGATGCTTTTTTTTAATTAAGATGCTATTCATGTTTAATGAAA
CTTTATCTTAAAAAAAGAAATAATTAAAGATTTAAATTAAACATATCATATCTTCTTCTTTTTTT
ACATAATGTCTAAAGCTACTCAAAAGTCTCTCTCCAACCTATACATAGAAACATAATGCGCTTCA
ACACACTCGAACTCACGTCCTTTTCCATTGGCAACAATAGCTATGCCACTCGAATTAAAACTCAA
TTGACTTCTTTATTTTTAATATATCTATAATTAGTTAGATATAAATAATAAAATAAATTTTAGTA
TTTATTTGTAGATGTTTATGAGATGAATTAGATTTGGCAGGGATTATATATGATATTATAATATT
TCATACGAGTCTAAATCTCACTCAACTTGAAATATTAATTTTAAATTTTATTCAAATTCACTCG
Found at i:2951403 original size:14 final size:14
Alignment explanation
Indices: 2951383--2951423 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
2951373 TTTGATTGCC
2951383 AGTAAAATGTTTTT
1 AGTAAAATGTTTTT
*
2951397 CGTAAAATGATTTTT
1 AGTAAAATG-TTTTT
2951412 AG-AAAATGTTTT
1 AGTAAAATGTTTT
2951424 ATTTTTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 14 0.58
15 6 0.25
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (14 bp):
AGTAAAATGTTTTT
Found at i:2954000 original size:21 final size:21
Alignment explanation
Indices: 2953959--2954001 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2953949 ACCTCAAATT
* *
2953959 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
2953980 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
2954001 C
1 C
2954002 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:2957468 original size:43 final size:43
Alignment explanation
Indices: 2957403--2957485 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
2957393 TAAAAGTAAT
* *
2957403 TATTTATTATAATCTTTCTAATGGTTATCAGTTAAGGTATTGC
1 TATTTATTATAATATTTCTAATGGTTATCAGTTAAAGTATTGC
* * *
2957446 TATTTATTTTAATATTTTTAATGGTTGTCAGTTAAAGTAT
1 TATTTATTATAATATTTCTAATGGTTATCAGTTAAAGTAT
2957486 AACTATCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (43 bp):
TATTTATTATAATATTTCTAATGGTTATCAGTTAAAGTATTGC
Found at i:2959218 original size:19 final size:21
Alignment explanation
Indices: 2959191--2959230 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
2959181 GTTAAATTAT
*
2959191 ATTTTATTTTT-TAT-TTAAA
1 ATTTAATTTTTATATATTAAA
2959210 ATTTAATTTTTATATATTAAA
1 ATTTAATTTTTATATATTAAA
2959231 TTAAAGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAATTTTTATATATTAAA
Found at i:2963997 original size:26 final size:26
Alignment explanation
Indices: 2963934--2963989 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 26
2963924 TTTAAGAAAT
* *
2963934 TTATTGTTATT-TT-TATTATTATAC
1 TTATTCTTATTATTGTATTATCATAC
2963958 TTATTCTTATTATTGTATTATCATA-
1 TTATTCTTATTATTGTATTATCATAC
2963983 TT-TTCTT
1 TTATTCTT
2963990 TATATATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 15 0.54
25 4 0.14
26 9 0.32
ACGTcount: A:0.23, C:0.07, G:0.04, T:0.66
Consensus pattern (26 bp):
TTATTCTTATTATTGTATTATCATAC
Found at i:2965649 original size:20 final size:20
Alignment explanation
Indices: 2965624--2965663 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2965614 GAGTCATCCC
2965624 TCGTCTTGTAGTGCCACGTA
1 TCGTCTTGTAGTGCCACGTA
2965644 TCGTCTTGTAGTGCCACGTA
1 TCGTCTTGTAGTGCCACGTA
2965664 ACTGTTAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (20 bp):
TCGTCTTGTAGTGCCACGTA
Found at i:2966634 original size:2 final size:2
Alignment explanation
Indices: 2966627--2966661 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2966617 TTAATACTTC
2966627 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 A
2966662 GCAGCTAGTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2967242 original size:16 final size:16
Alignment explanation
Indices: 2967221--2967255 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2967211 ACATAATCAA
*
2967221 TGTTCCGCATTATACT
1 TGTTCCGCACTATACT
2967237 TGTTCCGCACTATACT
1 TGTTCCGCACTATACT
2967253 TGT
1 TGT
2967256 GAGCCTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (16 bp):
TGTTCCGCACTATACT
Found at i:2968692 original size:16 final size:16
Alignment explanation
Indices: 2968671--2968703 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2968661 GTAAACATAA
2968671 TTTGTTTAATATTAGG
1 TTTGTTTAATATTAGG
2968687 TTTGTTTAATATTAGG
1 TTTGTTTAATATTAGG
2968703 T
1 T
2968704 GTTGGATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TTTGTTTAATATTAGG
Found at i:2970770 original size:43 final size:43
Alignment explanation
Indices: 2970722--2970937 Score: 423
Period size: 43 Copynumber: 5.0 Consensus size: 43
2970712 AAACTTCGAC
2970722 TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
1 TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
2970765 TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
1 TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
2970808 TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
1 TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
2970851 TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
1 TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
*
2970894 TGTATATGTAATAAAGTTGAGGGTTTTGAACTTTGATGCGTAT
1 TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
2970937 T
1 T
2970938 CTTATTCAAG
Statistics
Matches: 172, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 172 1.00
ACGTcount: A:0.28, C:0.05, G:0.24, T:0.44
Consensus pattern (43 bp):
TGTATATGTAATAAAGTTGATGGTTTTGAACTTTGATGCGTAT
Found at i:2978370 original size:19 final size:18
Alignment explanation
Indices: 2978354--2978388 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2978344 TTTGAAAAGT
2978354 AATTAAATTTTTAAAAAA
1 AATTAAATTTTTAAAAAA
*
2978372 AATTAAA-ATTTAAAAAA
1 AATTAAATTTTTAAAAAA
2978389 TTTAAAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTAAATTTTTAAAAAA
Found at i:2979460 original size:23 final size:24
Alignment explanation
Indices: 2979429--2979474 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2979419 AGATTTAAAA
*
2979429 ATTTCAAA-CAAACCTTATCCATT
1 ATTTAAAACCAAACCTTATCCATT
**
2979452 ATTTAAAACCAAATTTTATCCAT
1 ATTTAAAACCAAACCTTATCCAT
2979475 AACTTTAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (24 bp):
ATTTAAAACCAAACCTTATCCATT
Found at i:2984163 original size:1 final size:1
Alignment explanation
Indices: 2984157--2984289 Score: 266
Period size: 1 Copynumber: 133.0 Consensus size: 1
2984147 CCCAAAGAAC
2984157 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2984222 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2984287 AAA
1 AAA
2984290 CCAGAGAGGC
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 132 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2995010 original size:50 final size:50
Alignment explanation
Indices: 2994927--2995026 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
2994917 AGATCAAGTA
* *
2994927 GCACAAGTAAGATCCATATAGAACTACTTTTCTTTTATTTGACATTGATT
1 GCACAAGTAAGATCCATATAGAACCACTCTTCTTTTATTTGACATTGATT
*
2994977 GCACAAGT-AGAATCCATATATAACCACTCTTCTTTTATTTGACATTGATT
1 GCACAAGTAAG-ATCCATATAGAACCACTCTTCTTTTATTTGACATTGATT
2995027 AGAATAAAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 2 0.04
50 44 0.96
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (50 bp):
GCACAAGTAAGATCCATATAGAACCACTCTTCTTTTATTTGACATTGATT
Found at i:2995184 original size:38 final size:38
Alignment explanation
Indices: 2995142--2995214 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
2995132 TCCCGAAAAG
2995142 GTTTCCATGTAAAATTTTTGCGTGTTTTATTTTTCATT
1 GTTTCCATGTAAAATTTTTGCGTGTTTTATTTTTCATT
2995180 GTTTCCATGTAAAATTTTTGCGTGTTTTATTTTTC
1 GTTTCCATGTAAAATTTTTGCGTGTTTTATTTTTC
2995215 TTTCTCATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.18, C:0.11, G:0.14, T:0.58
Consensus pattern (38 bp):
GTTTCCATGTAAAATTTTTGCGTGTTTTATTTTTCATT
Found at i:3001138 original size:6 final size:6
Alignment explanation
Indices: 3001128--3001161 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3001118 GCGTGGGATA
*
3001128 TGGAAA TGGAAT TGGAAT TGGAAT TGGAAT TGGA
1 TGGAAT TGGAAT TGGAAT TGGAAT TGGAAT TGGA
3001162 TCGAGTTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (6 bp):
TGGAAT
Found at i:3001441 original size:72 final size:72
Alignment explanation
Indices: 3001324--3001543 Score: 359
Period size: 72 Copynumber: 3.1 Consensus size: 72
3001314 TGGCTTTCAT
*
3001324 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTTGGAAGCGGTAGCAGCTCTTACCCTAGTCTGAA
1 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTTGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
3001389 TAGCAGC
66 TAGCAGC
* * * * *
3001396 TCTTCGGGTTCTACAGTGGTTAATGGGCTCTTTGGAAGCAGTAGCAGGTCTCACCCTAGTCTCAA
1 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTTGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
3001461 TAGCAGC
66 TAGCAGC
* *
3001468 TCTTCGGGTGCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
1 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTTGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
*
3001533 TAACAGC
66 TAGCAGC
3001540 TCTT
1 TCTT
3001544 ACCCTAGCCT
Statistics
Matches: 134, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 134 1.00
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.30
Consensus pattern (72 bp):
TCTTCGGGTTCTACATTGGGTAATGGGCTCTTTGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
TAGCAGC
Found at i:3001544 original size:24 final size:24
Alignment explanation
Indices: 3001512--3001557 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3001502 GAAGCAGTAG
*
3001512 CAGCTCTTACCCTAGTCTGAATAA
1 CAGCTCTTACCCTAGCCTGAATAA
3001536 CAGCTCTTACCCTAGCCTGAAT
1 CAGCTCTTACCCTAGCCTGAAT
3001558 CCTGGTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.33, G:0.13, T:0.28
Consensus pattern (24 bp):
CAGCTCTTACCCTAGCCTGAATAA
Found at i:3002548 original size:6 final size:6
Alignment explanation
Indices: 3002529--3002592 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
3002519 GACTGCCCCA
* * * * *
3002529 GCTCCT GCTCCC GCTTCC GCTCCC GCTCCA GCTCCA GCTCCC GCTCCT
1 GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC
* *
3002577 GCTCCT GCTCCA GCTC
1 GCTCCC GCTCCC GCTC
3002593 TGGCTGTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.05, C:0.55, G:0.17, T:0.23
Consensus pattern (6 bp):
GCTCCC
Found at i:3002556 original size:18 final size:18
Alignment explanation
Indices: 3002526--3002592 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
3002516 GATGACTGCC
* *
3002526 CCAGCTCCTGCTCCCGCTT
1 CCAGCTCCCGCTCCAGC-T
3002545 CC-GCTCCCGCTCCAGCT
1 CCAGCTCCCGCTCCAGCT
*
3002562 CCAGCTCCCGCTCCTGCT
1 CCAGCTCCCGCTCCAGCT
* *
3002580 CCTGCTCCAGCTC
1 CCAGCTCCCGCTC
3002593 TGGCTGTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
17 3 0.07
18 37 0.88
19 2 0.05
ACGTcount: A:0.06, C:0.55, G:0.16, T:0.22
Consensus pattern (18 bp):
CCAGCTCCCGCTCCAGCT
Found at i:3002580 original size:12 final size:12
Alignment explanation
Indices: 3002521--3002592 Score: 74
Period size: 12 Copynumber: 6.0 Consensus size: 12
3002511 CAAGTGATGA
*
3002521 CTGCCCCAGCTC
1 CTGCTCCAGCTC
*
3002533 CTGCTCCCGCTTC
1 CTGCTCCAGC-TC
*
3002546 C-GCTCCCGCTC
1 CTGCTCCAGCTC
*
3002557 CAGCTCCAGCTC
1 CTGCTCCAGCTC
* *
3002569 CCGCTCCTGCTC
1 CTGCTCCAGCTC
3002581 CTGCTCCAGCTC
1 CTGCTCCAGCTC
3002593 TGGCTGTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
11 3 0.06
12 45 0.88
13 3 0.06
ACGTcount: A:0.06, C:0.56, G:0.17, T:0.22
Consensus pattern (12 bp):
CTGCTCCAGCTC
Found at i:3016609 original size:21 final size:22
Alignment explanation
Indices: 3016583--3016628 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3016573 ACACGTATTG
* * *
3016583 TTTTTTGAAATTTTTAGATTTT
1 TTTTTTAAAATTTATACATTTT
3016605 TTTTTTAAAATTTATACATTTT
1 TTTTTTAAAATTTATACATTTT
3016627 TT
1 TT
3016629 AGATTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTTTAAAATTTATACATTTT
Found at i:3017386 original size:10 final size:10
Alignment explanation
Indices: 3017371--3017395 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3017361 ACCTACAATC
3017371 TATATATTTA
1 TATATATTTA
3017381 TATATATTTA
1 TATATATTTA
3017391 TATAT
1 TATAT
3017396 GCCCTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATATTTA
Found at i:3034934 original size:16 final size:15
Alignment explanation
Indices: 3034908--3034944 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
3034898 AACATTATTA
3034908 TATAAATAAAAAAAT
1 TATAAATAAAAAAAT
*
3034923 TATAATATAAAATAAT
1 TATAA-ATAAAAAAAT
3034939 TATAAA
1 TATAAA
3034945 ACCAAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TATAAATAAAAAAAT
Found at i:3038107 original size:30 final size:32
Alignment explanation
Indices: 3038033--3038116 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 32
3038023 AATTAATAAT
* * *
3038033 AAATTTATATTTAGGTCAC-TAAACTATTTAA
1 AAATTTCTATTTAAGTTACTTAAACTATTTAA
3038064 AAATTTCTATTTAAGTTA-TTAAACTATTT-A
1 AAATTTCTATTTAAGTTACTTAAACTATTTAA
** *
3038094 ATTTTTTTATTTAAGTTACTTAA
1 AAATTTCTATTTAAGTTACTTAA
3038117 TTGTTAAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 16 0.36
31 29 0.64
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (32 bp):
AAATTTCTATTTAAGTTACTTAAACTATTTAA
Found at i:3040073 original size:19 final size:21
Alignment explanation
Indices: 3040049--3040088 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3040039 GATCAGAGAG
3040049 TAAATT-CATC-ATTTATGTT
1 TAAATTCCATCTATTTATGTT
*
3040068 TAAATTCCATCTATTTCTGTT
1 TAAATTCCATCTATTTATGTT
3040089 GTTAAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.53
Consensus pattern (21 bp):
TAAATTCCATCTATTTATGTT
Found at i:3040889 original size:20 final size:19
Alignment explanation
Indices: 3040866--3040911 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
3040856 AGAGTATAGA
3040866 TTATTTAAAAATTGAATTTT
1 TTATTTAAAAATTG-ATTTT
*
3040886 TTATATAAAAATTGATTTT
1 TTATTTAAAAATTGATTTT
*
3040905 TTTTTTA
1 TTATTTA
3040912 TCATCAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (19 bp):
TTATTTAAAAATTGATTTT
Found at i:3040903 original size:19 final size:20
Alignment explanation
Indices: 3040866--3040906 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3040856 AGAGTATAGA
*
3040866 TTATTTAAAAATTGAATTTT
1 TTATATAAAAATTGAATTTT
3040886 TTATATAAAAATTG-ATTTT
1 TTATATAAAAATTGAATTTT
3040905 TT
1 TT
3040907 TTTTATCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTATATAAAAATTGAATTTT
Found at i:3044696 original size:234 final size:235
Alignment explanation
Indices: 3044437--3044905 Score: 931
Period size: 234 Copynumber: 2.0 Consensus size: 235
3044427 TCCTTCTCTA
3044437 TCTACCATTTTTTTTTTCAAATTAAGTGATAAAAATTAAAAGAAAGTAAAGTTTCGCTTTTTTTT
1 TCTACCATTTTTTTTTTCAAATTAAGTGATAAAAATTAAAAGAAAGTAAAGTTTCGCTTTTTTTT
3044502 CCCCATTCCAGCTCGCGATTTGAGGTTAGTAGCTTCGTTTTGCTTAATTTTTTTTGGTTTAATCC
66 CCCCATTCCAGCTCGCGATTTGAGGTTAGTAGCTTCGTTTTGCTTAATTTTTTTTGGTTTAATCC
3044567 GTTTTATTTAATTAAAGCTGTTTAATGATTTTATTAGTTCGATTCTGCTTCGATCGATCTCTAAA
131 GTTTTATTTAATTAAAGCTGTTTAATGATTTTATTAGTTCGATTCTGCTTCGATCGATCTCTAAA
3044632 ATAAGGAAAGTTTTGCTTTTTTTATTGCGAATTTTGTTTT
196 ATAAGGAAAGTTTTGCTTTTTTTATTGCGAATTTTGTTTT
3044672 TCTACCA-TTTTTTTTTCAAATTAAGTGATAAAAATTAAAAGAAAGTAAAGTTTCGCTTTTTTTT
1 TCTACCATTTTTTTTTTCAAATTAAGTGATAAAAATTAAAAGAAAGTAAAGTTTCGCTTTTTTTT
3044736 CCCCATTCCAGCTCGCGATTTGAGGTTAGTAGCTTCGTTTTGCTTAATTTTTTTTGGTTTAATCC
66 CCCCATTCCAGCTCGCGATTTGAGGTTAGTAGCTTCGTTTTGCTTAATTTTTTTTGGTTTAATCC
3044801 GTTTTATTTAATTAAAGCTGTTTAATGATTTTATTAGTTCGATTCTGCTTCGATCGATCTCTAAA
131 GTTTTATTTAATTAAAGCTGTTTAATGATTTTATTAGTTCGATTCTGCTTCGATCGATCTCTAAA
3044866 ATAAGGAAAGTTTTGCTTTTTTTATTGCGAATTTTGTTTT
196 ATAAGGAAAGTTTTGCTTTTTTTATTGCGAATTTTGTTTT
3044906 ATTTTGAAGT
Statistics
Matches: 234, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
234 227 0.97
235 7 0.03
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (235 bp):
TCTACCATTTTTTTTTTCAAATTAAGTGATAAAAATTAAAAGAAAGTAAAGTTTCGCTTTTTTTT
CCCCATTCCAGCTCGCGATTTGAGGTTAGTAGCTTCGTTTTGCTTAATTTTTTTTGGTTTAATCC
GTTTTATTTAATTAAAGCTGTTTAATGATTTTATTAGTTCGATTCTGCTTCGATCGATCTCTAAA
ATAAGGAAAGTTTTGCTTTTTTTATTGCGAATTTTGTTTT
Found at i:3051515 original size:21 final size:21
Alignment explanation
Indices: 3051489--3051528 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3051479 AAAAATGAGT
3051489 AAATTAATCTCTTTACTTTGC
1 AAATTAATCTCTTTACTTTGC
3051510 AAATTAATCTCTTTACTTT
1 AAATTAATCTCTTTACTTT
3051529 TGATAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (21 bp):
AAATTAATCTCTTTACTTTGC
Found at i:3059766 original size:3 final size:3
Alignment explanation
Indices: 3059758--3059786 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3059748 AGAGAGAGAG
3059758 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
3059787 GGTTAATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3060081 original size:25 final size:24
Alignment explanation
Indices: 3060015--3060081 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
3060005 GTGAAAATTA
*
3060015 AAATTTAATTTTTATA-ATAATAG
1 AAATTTAATTTTTATAGTTAATAG
*
3060038 AAATTTAA-TTTCATCAGTTGAATAG
1 AAATTTAATTTTTAT-AGTT-AATAG
3060063 -AATTTATATTTTTATAGTT
1 AAATTTA-ATTTTTATAGTT
3060082 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 5 0.14
23 9 0.25
24 7 0.19
25 10 0.28
26 5 0.14
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.49
Consensus pattern (24 bp):
AAATTTAATTTTTATAGTTAATAG
Found at i:3066873 original size:20 final size:20
Alignment explanation
Indices: 3066848--3066888 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3066838 GAAATTAAAC
3066848 CATCCAAGAAAGCTGAATAG
1 CATCCAAGAAAGCTGAATAG
3066868 CATCCAAGAAAGCTGAATAG
1 CATCCAAGAAAGCTGAATAG
3066888 C
1 C
3066889 TTCCTCACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.15
Consensus pattern (20 bp):
CATCCAAGAAAGCTGAATAG
Found at i:3068135 original size:2 final size:2
Alignment explanation
Indices: 3068128--3068155 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3068118 AACTGCAGCC
3068128 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
3068156 TCTACCAGTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3080306 original size:20 final size:17
Alignment explanation
Indices: 3080266--3080297 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3080256 ATATAAAATT
3080266 TTTAAAAAAATATTTAA
1 TTTAAAAAAATATTTAA
3080283 TTT-AAAAAATATTTA
1 TTTAAAAAAATATTTA
3080298 TTATATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.80
17 3 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAAAAATATTTAA
Found at i:3080332 original size:39 final size:40
Alignment explanation
Indices: 3080288--3080364 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
3080278 TTTAATTTAA
*
3080288 AAAATATTTATTATATTTAT-TCGTGTTTTTTAATATGAT
1 AAAATATTTATTATATTTATGTAGTGTTTTTTAATATGAT
3080327 AAAATATTTATTATATTTATGGTAGTGTTTTTTAATAT
1 AAAATATTTATTATATTTAT-GTAGTGTTTTTTAATAT
3080365 AAATATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 20 0.57
41 15 0.43
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.56
Consensus pattern (40 bp):
AAAATATTTATTATATTTATGTAGTGTTTTTTAATATGAT
Found at i:3090103 original size:72 final size:70
Alignment explanation
Indices: 3089988--3090130 Score: 196
Period size: 72 Copynumber: 2.0 Consensus size: 70
3089978 TCTCGGATTT
* * * *
3089988 GAAAAAAGGATCATGACCAGTAAGTTAGGACACGGTCTTTTCTTAATTCCTGAGATCGTTTAAAA
1 GAAAAAAGGATCACGACCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
3090053 CTTGA
66 CTTGA
* * *
3090058 GAAAAAAGGGGATCACGCCCAGTAAGTTAGGACATGATCTCTTCTTGATTCCCGAGATCGTTTAA
1 GAAAAAA--GGATCACGACCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAA
*
3090123 TACTTGA
64 AACTTGA
3090130 G
1 G
3090131 TTTGAAAAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 7 0.11
72 56 0.89
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (70 bp):
GAAAAAAGGATCACGACCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGA
Found at i:3090769 original size:3 final size:3
Alignment explanation
Indices: 3090753--3090820 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
3090743 TAAATGAGTA
* * * *
3090753 AAT AAT AGT TAT AAT AAT AAT AAT AAT ACAG AACT AAT AGT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AAT
3090799 -AT AAT AAT -AT AAT AAT GAAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AA
3090821 ATAAATAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
2 5 0.10
3 39 0.76
4 7 0.14
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3090828 original size:18 final size:20
Alignment explanation
Indices: 3090796--3090835 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
3090786 CTAATAGTAT
*
3090796 AATATAATAATATAATAATG
1 AATATAATAATATAAAAATG
3090816 AATA-AATAA-ATAAAAATG
1 AATATAATAATATAAAAATG
3090834 AA
1 AA
3090836 AATACAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AATATAATAATATAAAAATG
Found at i:3091788 original size:38 final size:38
Alignment explanation
Indices: 3091737--3091816 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
3091727 ACTTTCATTT
3091737 TCATATGCTTATCAAAGATAAGTATTGTATTAACCAAA
1 TCATATGCTTATCAAAGATAAGTATTGTATTAACCAAA
*
3091775 TCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATATGCTTATCAAAGATAAGTATTGTATTAACCAAA
3091813 TCAT
1 TCAT
3091817 TTATTGAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (38 bp):
TCATATGCTTATCAAAGATAAGTATTGTATTAACCAAA
Found at i:3091822 original size:21 final size:22
Alignment explanation
Indices: 3091797--3091840 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3091787 CAAATATAAG
*
3091797 TATTGTAT-TAACCAAATCATT
1 TATTGAATATAACCAAATCATT
3091818 TATTGAATATAACCAAATCATT
1 TATTGAATATAACCAAATCATT
3091840 T
1 T
3091841 TCATATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTGAATATAACCAAATCATT
Found at i:3092155 original size:21 final size:21
Alignment explanation
Indices: 3092131--3092170 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3092121 CGTGTCAATA
3092131 TTTA-ATTACAAATATTTAATT
1 TTTATATT-CAAATATTTAATT
*
3092152 TTTATATTTAAATATTTAA
1 TTTATATTCAAATATTTAA
3092171 ATATAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATATTCAAATATTTAATT
Found at i:3092450 original size:13 final size:13
Alignment explanation
Indices: 3092429--3092466 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3092419 ACAATCAAAT
*
3092429 TTCTCAAAAGCAG
1 TTCTCAAAAGCAC
*
3092442 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
3092455 TTCTCAAAAGCA
1 TTCTCAAAAGCA
3092467 ATAAAGAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:3094892 original size:38 final size:41
Alignment explanation
Indices: 3094849--3094932 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 41
3094839 ATTGATATTT
* *
3094849 ATAAAACTTAAA-GTTAA-AATATATATTATA-ATATTATA
1 ATAAAACTTAAATATTAATAATATATATTATATATATTAAA
*
3094887 ATAAAACTTAAATATTAATTATATATATTATATTATATTAAA
1 ATAAAACTTAAATATTAATAATATATATTATA-TATATTAAA
3094929 ATAA
1 ATAA
3094933 TTAAGAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
38 12 0.31
39 4 0.10
40 12 0.31
42 11 0.28
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (41 bp):
ATAAAACTTAAATATTAATAATATATATTATATATATTAAA
Found at i:3094972 original size:14 final size:12
Alignment explanation
Indices: 3094935--3095071 Score: 79
Period size: 12 Copynumber: 11.0 Consensus size: 12
3094925 TAAAATAATT
3094935 AAGAAAGAGAAA
1 AAGAAAGAGAAA
*
3094947 AAGAATGAGAAA
1 AAGAAAGAGAAA
* *
3094959 AAGAAGGAGAGA
1 AAGAAAGAGAAA
3094971 AAGAAACGA-AACA
1 AAGAAA-GAGAA-A
*
3094984 GAGAAAGA-AAGA
1 AAGAAAGAGAA-A
*
3094996 AAGGAAAGAAAAA
1 AA-GAAAGAGAAA
3095009 AAGAAAGA-AAGA
1 AAGAAAGAGAA-A
3095021 AA-AATAGGAGAAA
1 AAGAA-A-GAGAAA
3095034 AAGAAAGA-AAA
1 AAGAAAGAGAAA
*
3095045 GAA-AAAGGGAAAGA
1 -AAGAAAGAG-AA-A
3095059 AAGAAAGGAGAAA
1 AAGAAA-GAGAAA
3095072 TTAGGGTTTT
Statistics
Matches: 100, Mismatches: 10, Indels: 29
0.72 0.07 0.21
Matches are distributed among these distances:
11 11 0.11
12 47 0.47
13 28 0.28
14 12 0.12
15 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.27, T:0.01
Consensus pattern (12 bp):
AAGAAAGAGAAA
Found at i:3094988 original size:17 final size:16
Alignment explanation
Indices: 3094966--3095064 Score: 58
Period size: 17 Copynumber: 5.9 Consensus size: 16
3094956 AAAAAGAAGG
3094966 AGAGAAAGAAACGAAAC
1 AGAGAAAGAAA-GAAAC
*
3094983 AGAGAAAGAAAGAAAGG
1 AGAGAAAGAAAGAAA-C
* * *
3095000 AAAGAAAAAAAGAAAG
1 AGAGAAAGAAAGAAAC
*
3095016 AAAGAAA-AATAGGAGAA-
1 AGAGAAAGAA-A-GA-AAC
* *
3095033 AAAGAAAGAAAAGAAAA
1 AGAGAAAG-AAAGAAAC
*
3095050 AGGGAAAGAAAGAAA
1 AGAGAAAGAAAGAAA
3095065 GGAGAAATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
15 2 0.03
16 22 0.31
17 41 0.59
18 3 0.04
19 2 0.03
ACGTcount: A:0.72, C:0.02, G:0.25, T:0.01
Consensus pattern (16 bp):
AGAGAAAGAAAGAAAC
Found at i:3094994 original size:21 final size:20
Alignment explanation
Indices: 3094954--3095065 Score: 82
Period size: 21 Copynumber: 5.1 Consensus size: 20
3094944 AAAAAGAATG
*
3094954 AGAAAAAGAAGGAGAGAAAGAA
1 AGAAAAAG-A-GAAAGAAAGAA
*
3094976 ACGAAACAGAGAAAGAAAGAA
1 A-GAAAAAGAGAAAGAAAGAA
*
3094997 AGGAAAGAA-AAAAAGAAAGAA
1 A-GAAA-AAGAGAAAGAAAGAA
3095018 AGAAAAATAGGAGAAAAAGAAAGAAA
1 AG-AAAA-A-GAG--AAAGAAAG-AA
*
3095044 AGAAAAAGGGAAAGAAAGAA
1 AGAAAAAGAGAAAGAAAGAA
3095064 AG
1 AG
3095066 GAGAAATTAG
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
20 6 0.08
21 39 0.53
22 3 0.04
23 9 0.12
24 1 0.01
25 12 0.16
26 4 0.05
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.01
Consensus pattern (20 bp):
AGAAAAAGAGAAAGAAAGAA
Found at i:3094996 original size:25 final size:25
Alignment explanation
Indices: 3094935--3095048 Score: 85
Period size: 25 Copynumber: 4.6 Consensus size: 25
3094925 TAAAATAATT
* *
3094935 AAGAAAGAGAA-AAA-GAATGAGAAA
1 AAGAAAGA-AAGAAAGGAAAGAAAAA
* * *
3094959 AAGAAGGAGAGAAA-GAAACGAAACA
1 AAGAAAGAAAGAAAGGAAA-GAAAAA
*
3094984 GAGAAAGAAAGAAAGGAAAGAAAAA
1 AAGAAAGAAAGAAAGGAAAGAAAAA
*
3095009 AAGAAAGAAAGAAA--AATAGGAGAAA
1 AAGAAAGAAAGAAAGGAA-A-GAAAAA
3095034 AAGAAAGAAAAGAAA
1 AAGAAAG-AAAGAAA
3095049 AAGGGAAAGA
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
23 3 0.04
24 14 0.19
25 45 0.62
26 11 0.15
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (25 bp):
AAGAAAGAAAGAAAGGAAAGAAAAA
Found at i:3095065 original size:25 final size:24
Alignment explanation
Indices: 3094985--3095065 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 24
3094975 AACGAAACAG
*
3094985 AGAAAGAAAGAAAGGAA-AGAAAAAA
1 AGAAAGAAAGAAA--AATAGGAAAAA
3095010 AGAAAGAAAGAAAAATAGGAGAAAA
1 AGAAAGAAAGAAAAATAGGA-AAAA
*
3095035 AGAAAGAAAAGAAAAA-GGGAAAGAA
1 AGAAAG-AAAGAAAAATAGGAAA-AA
3095060 AGAAAG
1 AGAAAG
3095066 GAGAAATTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
23 2 0.04
24 5 0.10
25 34 0.68
26 9 0.18
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (24 bp):
AGAAAGAAAGAAAAATAGGAAAAA
Found at i:3099632 original size:29 final size:28
Alignment explanation
Indices: 3099596--3099655 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
3099586 ATCGTAATAT
*
3099596 TTATTATGT-AATTTATATTACATAAAAA
1 TTATTATGTGAATTT-TATAACATAAAAA
* *
3099624 TTATATATGTGTATTTTATAACATAAATA
1 TTAT-TATGTGAATTTTATAACATAAAAA
3099653 TTA
1 TTA
3099656 GAAAATTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 19 0.70
30 4 0.15
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (28 bp):
TTATTATGTGAATTTTATAACATAAAAA
Found at i:3108118 original size:29 final size:30
Alignment explanation
Indices: 3108086--3108156 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
3108076 AAATCAATTT
*
3108086 TTCATGTATAAAATTGCATA-AAATCAAAG
1 TTCATGTATAAAATTGCATATAAACCAAAG
* *
3108115 TTCATGTATACAATTGCATATTAAACCATAG
1 TTCATGTATAAAATTGCATA-TAAACCAAAG
3108146 TTCATGTATAA
1 TTCATGTATAA
3108157 TTTTGGGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 19 0.53
31 17 0.47
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (30 bp):
TTCATGTATAAAATTGCATATAAACCAAAG
Found at i:3108523 original size:31 final size:32
Alignment explanation
Indices: 3108478--3108537 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
3108468 ATTTAATAGA
*
3108478 GAGTGATCAAAAATAAAAATAATCTAAAATAT
1 GAGTGATCAAAAATAAAAATAACCTAAAATAT
* * *
3108510 GAGTGA-CTAAAATAGAAATTACCTAAAA
1 GAGTGATCAAAAATAAAAATAACCTAAAA
3108538 CGTTATAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 18 0.75
32 6 0.25
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.23
Consensus pattern (32 bp):
GAGTGATCAAAAATAAAAATAACCTAAAATAT
Found at i:3108757 original size:4 final size:4
Alignment explanation
Indices: 3108748--3108775 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3108738 AAAAACAGAA
3108748 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3108776 GTTTGTTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:3112887 original size:107 final size:106
Alignment explanation
Indices: 3112762--3112977 Score: 414
Period size: 107 Copynumber: 2.0 Consensus size: 106
3112752 TATTTATTAA
3112762 ATTTTTTATATAGTCATCTTAATATTTTTTAATATTTACATTATAATAGTATTATATATTACTAT
1 ATTTTTTATATAGTCATCTTAATATTTTTTAATATTTACATTATAATAGTATTATATATTACTAT
3112827 AGGTTTAATTTTCATGTTATATAAATTATATAATATAAAAC
66 AGGTTTAATTTTCATGTTATATAAATTATATAATATAAAAC
*
3112868 ATTTTTTGTATATGTCATCTTAATATTTTTTAATATTTACATTATAATAGTATTATATATTACTA
1 ATTTTTTATATA-GTCATCTTAATATTTTTTAATATTTACATTATAATAGTATTATATATTACTA
3112933 TAGGTTTAATTTTCATGTTATATAAATTATATAATATAAAAC
65 TAGGTTTAATTTTCATGTTATATAAATTATATAATATAAAAC
3112975 ATT
1 ATT
3112978 ACAAACTTAA
Statistics
Matches: 108, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
106 11 0.10
107 97 0.90
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (106 bp):
ATTTTTTATATAGTCATCTTAATATTTTTTAATATTTACATTATAATAGTATTATATATTACTAT
AGGTTTAATTTTCATGTTATATAAATTATATAATATAAAAC
Found at i:3113686 original size:23 final size:26
Alignment explanation
Indices: 3113636--3113698 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
3113626 ATCATAAGTC
*
3113636 ATTAGGAATTTATTTATTTTGGTGAAA
1 ATTAGGAATTTA-TTATTTTGATGAAA
*
3113663 ATTAGGAATTTA-T-TTTTGATAAAAA
1 ATTAGGAATTTATTATTTTGAT-GAAA
*
3113688 ATTAGAAATTT
1 ATTAGGAATTT
3113699 CCATTTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 6 0.19
25 14 0.44
27 12 0.38
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (26 bp):
ATTAGGAATTTATTATTTTGATGAAA
Found at i:3119219 original size:25 final size:25
Alignment explanation
Indices: 3119185--3119248 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
3119175 TTTATATAAT
* *
3119185 TAATCAGAGAGCACTGACGTGCTAG
1 TAATCAGAGAGCACTGACATGCTAA
*
3119210 TAATCAGAGAACACTGACATGCTAA
1 TAATCAGAGAGCACTGACATGCTAA
3119235 TAATCAGAGAGCAC
1 TAATCAGAGAGCAC
3119249 GCTAAACTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (25 bp):
TAATCAGAGAGCACTGACATGCTAA
Found at i:3122048 original size:23 final size:23
Alignment explanation
Indices: 3122001--3122051 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
3121991 ACTTACTTTC
* * * *
3122001 TTACAGTAGTAATTTTTGGGGTA
1 TTACAGTAATAATTTTCGAGATA
3122024 TTACAGTAATAATTTTCGAGATA
1 TTACAGTAATAATTTTCGAGATA
3122047 TTACA
1 TTACA
3122052 TATATTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (23 bp):
TTACAGTAATAATTTTCGAGATA
Found at i:3124700 original size:80 final size:80
Alignment explanation
Indices: 3124582--3124742 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
3124572 TCAATAATAA
*
3124582 TTTATTCATTTAACAACATAAATCTTAAAATTATATATTGATTTTGATCTAGTGTGAAATGTGAT
1 TTTATTCATTTAACAACATAAATCTTAAAATTATATATTAATTTTGATCTAGTGTGAAATGTGAT
3124647 AAATAAATTTTAATT
66 AAATAAATTTTAATT
3124662 TTTATTCATTTAACAACATAAATCTTAAAATTATATATTAATTTTGATCTAGTGTGAAATGTGAT
1 TTTATTCATTTAACAACATAAATCTTAAAATTATATATTAATTTTGATCTAGTGTGAAATGTGAT
3124727 AAATAAATTTTAATT
66 AAATAAATTTTAATT
3124742 T
1 T
3124743 ATATAAGTAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.45
Consensus pattern (80 bp):
TTTATTCATTTAACAACATAAATCTTAAAATTATATATTAATTTTGATCTAGTGTGAAATGTGAT
AAATAAATTTTAATT
Found at i:3125147 original size:273 final size:273
Alignment explanation
Indices: 3124660--3125208 Score: 1098
Period size: 273 Copynumber: 2.0 Consensus size: 273
3124650 TAAATTTTAA
3124660 TTTTTATTCATTTAACAACATAAATCTTAAAATTATATATTAATTTTGATCTAGTGTGAAATGTG
1 TTTTTATTCATTTAACAACATAAATCTTAAAATTATATATTAATTTTGATCTAGTGTGAAATGTG
3124725 ATAAATAAATTTTAATTTATATAAGTAATCTGTTCAAACAAAATGCTGACTTCTACATAGCCTCC
66 ATAAATAAATTTTAATTTATATAAGTAATCTGTTCAAACAAAATGCTGACTTCTACATAGCCTCC
3124790 TTTACTATTGTTAAAGTCATCAACTCCATTGGTTCGAGGTTGTCAGCTGACCGAAATTTTTAGCC
131 TTTACTATTGTTAAAGTCATCAACTCCATTGGTTCGAGGTTGTCAGCTGACCGAAATTTTTAGCC
3124855 TTCCACTTGCAGCATATACAGAGTATCTTTGACTTTTCTTAGGAAATGCTTGTAATAGATCATGT
196 TTCCACTTGCAGCATATACAGAGTATCTTTGACTTTTCTTAGGAAATGCTTGTAATAGATCATGT
3124920 ATGTAAAACCATT
261 ATGTAAAACCATT
3124933 TTTTTATTCATTTAACAACATAAATCTTAAAATTATATATTAATTTTGATCTAGTGTGAAATGTG
1 TTTTTATTCATTTAACAACATAAATCTTAAAATTATATATTAATTTTGATCTAGTGTGAAATGTG
3124998 ATAAATAAATTTTAATTTATATAAGTAATCTGTTCAAACAAAATGCTGACTTCTACATAGCCTCC
66 ATAAATAAATTTTAATTTATATAAGTAATCTGTTCAAACAAAATGCTGACTTCTACATAGCCTCC
3125063 TTTACTATTGTTAAAGTCATCAACTCCATTGGTTCGAGGTTGTCAGCTGACCGAAATTTTTAGCC
131 TTTACTATTGTTAAAGTCATCAACTCCATTGGTTCGAGGTTGTCAGCTGACCGAAATTTTTAGCC
3125128 TTCCACTTGCAGCATATACAGAGTATCTTTGACTTTTCTTAGGAAATGCTTGTAATAGATCATGT
196 TTCCACTTGCAGCATATACAGAGTATCTTTGACTTTTCTTAGGAAATGCTTGTAATAGATCATGT
3125193 ATGTAAAACCATT
261 ATGTAAAACCATT
3125206 TTT
1 TTT
3125209 GGTCTCCCTA
Statistics
Matches: 276, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
273 276 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (273 bp):
TTTTTATTCATTTAACAACATAAATCTTAAAATTATATATTAATTTTGATCTAGTGTGAAATGTG
ATAAATAAATTTTAATTTATATAAGTAATCTGTTCAAACAAAATGCTGACTTCTACATAGCCTCC
TTTACTATTGTTAAAGTCATCAACTCCATTGGTTCGAGGTTGTCAGCTGACCGAAATTTTTAGCC
TTCCACTTGCAGCATATACAGAGTATCTTTGACTTTTCTTAGGAAATGCTTGTAATAGATCATGT
ATGTAAAACCATT
Found at i:3129024 original size:13 final size:13
Alignment explanation
Indices: 3129006--3129030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3128996 CACATTGAGA
3129006 GGGGTGTATTTAG
1 GGGGTGTATTTAG
3129019 GGGGTGTATTTA
1 GGGGTGTATTTA
3129031 TATCCTGGAG
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:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
GGGGTGTATTTAG
Found at i:3133054 original size:5 final size:5
Alignment explanation
Indices: 3133044--3133082 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
3133034 TCCTAAGATG
* *
3133044 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
3133083 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:3133949 original size:92 final size:92
Alignment explanation
Indices: 3133792--3133978 Score: 356
Period size: 92 Copynumber: 2.0 Consensus size: 92
3133782 TTTAAGGCCA
3133792 CTTTTCTCACGCATTTTGACATTAACCTGTACTCAACATTCACATACACCAATATATCCCAACCA
1 CTTTTCTCACGCATTTTGACATTAACCTGTACTCAACATTCACATACACCAATATATCCCAACCA
3133857 AGCAATCAATACAAGCTAAAACATGTT
66 AGCAATCAATACAAGCTAAAACATGTT
* *
3133884 CTTTTCTCACGCATTTTGACATTAATCTGTACTCAACATTCACGTACACCAATATATCCCAACCA
1 CTTTTCTCACGCATTTTGACATTAACCTGTACTCAACATTCACATACACCAATATATCCCAACCA
3133949 AGCAATCAATACAAGCTAAAACATGTT
66 AGCAATCAATACAAGCTAAAACATGTT
3133976 CTT
1 CTT
3133979 GACTGTATGA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.36, C:0.28, G:0.07, T:0.29
Consensus pattern (92 bp):
CTTTTCTCACGCATTTTGACATTAACCTGTACTCAACATTCACATACACCAATATATCCCAACCA
AGCAATCAATACAAGCTAAAACATGTT
Found at i:3157102 original size:13 final size:13
Alignment explanation
Indices: 3157084--3157108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3157074 TTTGGCAATG
3157084 CTTTTGAAAAGTA
1 CTTTTGAAAAGTA
3157097 CTTTTGAAAAGT
1 CTTTTGAAAAGT
3157109 TTGGTTTAAA
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:3158105 original size:15 final size:14
Alignment explanation
Indices: 3158085--3158114 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3158075 CTAGTCTTCC
3158085 TTTCTTTTTCTTTTT
1 TTTCTTTTT-TTTTT
3158100 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
3158114 T
1 T
3158115 CTAAATTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:3165753 original size:25 final size:25
Alignment explanation
Indices: 3165719--3165768 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3165709 CTCAATAGAT
*
3165719 AATTTTACTTTTATTTAAAAATTAA
1 AATTTTACTTTTATATAAAAATTAA
3165744 AATTTTACTTTTATATAAAAATTAA
1 AATTTTACTTTTATATAAAAATTAA
3165769 CTTAAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTTTACTTTTATATAAAAATTAA
Found at i:3166608 original size:17 final size:18
Alignment explanation
Indices: 3166570--3166608 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3166560 TCAATTGAAT
*
3166570 AAATTATTTAAAAAATTAA
1 AAATTATTT-AAAAATAAA
3166589 AAATTATTT-AAAATAAA
1 AAATTATTTAAAAATAAA
3166606 AAA
1 AAA
3166609 AATCAATTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTATTTAAAAATAAA
Found at i:3166609 original size:19 final size:19
Alignment explanation
Indices: 3166570--3166611 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3166560 TCAATTGAAT
*
3166570 AAATTATTTAAAAAATTAA
1 AAATTATTTAAAAAATAAA
3166589 AAATTATTTAAAATAA-AAA
1 AAATTATTTAAAA-AATAAA
3166608 AAAT
1 AAAT
3166612 CAATTCGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTATTTAAAAAATAAA
Found at i:3193279 original size:4 final size:4
Alignment explanation
Indices: 3193270--3193319 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
3193260 GCAACAACAC
3193270 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3193318 TG
1 TG
3193320 GAACTAATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:3214672 original size:156 final size:154
Alignment explanation
Indices: 3214388--3214851 Score: 615
Period size: 156 Copynumber: 3.0 Consensus size: 154
3214378 TGCTGCAATA
* *
3214388 GTAGACCCGTGGACGCACATGCTTCAACTGAATGACCAGATGAAACATTGGGTAATTCAGCCCTT
1 GTAGACCAGTGGAAGCACATGCTTCAACTGAATGACCAGATGAAACATTGGGTAATTCAG-CCTT
* * *
3214453 GGGTTGAATGACATGGCCGCAGGTCCAGCATTATCTCTAGTGCTACTTTTCTGGGGATTCAAGAA
65 TGGTTGAAAGACATGGCCGCAGGTCCAGCATT-TCTCTAGCGCTACTTTTCTGGGGATTCAAGAA
3214518 AAAATCAAGATCATTGACTTGTAACG
129 AAAATCAAGATCATTGACTTGTAACG
* *
3214544 GTAGACCAGTGTAAGCACATGCTTCAACTGAATGACCAGAT-AAACCATTGGGTGATTCAGCCTT
1 GTAGACCAGTGGAAGCACATGCTTCAACTGAATGACCAGATGAAA-CATTGGGTAATTCAGCCTT
* * * *
3214608 TCGGTTAAAAGACCTGGCCGCAGGTGCAGCATCTTCTCTAGCACTACTTTTCTGGGGATTCAAGA
65 T-GGTTGAAAGACATGGCCGCAGGTCCAGCAT-TTCTCTAGCGCTACTTTTCTGGGGATTCAAGA
** * * * *
3214673 AAAAATCTGGACCATTGACATGTGACT
128 AAAAATCAAGATCATTGACTTGTAACG
* ** * *
3214700 GTAGACCAGCGGATTCACATGCTTCAACTGAACGACCAGATGAAACATTCGGTAATTCAGCCTTT
1 GTAGACCAGTGGAAGCACATGCTTCAACTGAATGACCAGATGAAACATTGGGTAATTCAGCCTTT
* * *
3214765 GGATTGGACGACATGGCCTCAGGTCCAGCATTTTCTCTAGCGCTACTTTTCTGGGGATTCAAGAA
66 GG-TTGAAAGACATGGCCGCAGGTCCAGCA-TTTCTCTAGCGCTACTTTTCTGGGGATTCAAGAA
* *
3214830 AAAAGCAAGATCATTGAATTGT
129 AAAATCAAGATCATTGACTTGT
3214852 GACATAGTCT
Statistics
Matches: 265, Mismatches: 37, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
155 9 0.03
156 251 0.95
157 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (154 bp):
GTAGACCAGTGGAAGCACATGCTTCAACTGAATGACCAGATGAAACATTGGGTAATTCAGCCTTT
GGTTGAAAGACATGGCCGCAGGTCCAGCATTTCTCTAGCGCTACTTTTCTGGGGATTCAAGAAAA
AATCAAGATCATTGACTTGTAACG
Found at i:3227472 original size:104 final size:105
Alignment explanation
Indices: 3227344--3227552 Score: 411
Period size: 104 Copynumber: 2.0 Consensus size: 105
3227334 TATAATGATT
3227344 GTTTAAATAAAGTATAAAAGTTTTTTAGTATATTAACGAGGCTTTCGTTTTTATGAATTAAGACC
1 GTTTAAATAAAGTATAAAAGTTTTTTAGTATATTAACGAGGCTTTCGTTTTTATGAATTAAGACC
3227409 ATATAGGGTGGAAGTGGAGGTGCTCATGGGCCGGGTCGGG
66 ATATAGGGTGGAAGTGGAGGTGCTCATGGGCCGGGTCGGG
3227449 GTTTAAAT-AAGTATAAAAGTTTTTTAGTATATTAACGAGGCTTTCGTTTTTATGAATTAAGACC
1 GTTTAAATAAAGTATAAAAGTTTTTTAGTATATTAACGAGGCTTTCGTTTTTATGAATTAAGACC
3227513 ATATAGGGTGGAAGTGGAGGTGCTCATGGGCCGGGTCGGG
66 ATATAGGGTGGAAGTGGAGGTGCTCATGGGCCGGGTCGGG
3227553 CCCAAAAAAA
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
104 96 0.92
105 8 0.08
ACGTcount: A:0.28, C:0.10, G:0.29, T:0.33
Consensus pattern (105 bp):
GTTTAAATAAAGTATAAAAGTTTTTTAGTATATTAACGAGGCTTTCGTTTTTATGAATTAAGACC
ATATAGGGTGGAAGTGGAGGTGCTCATGGGCCGGGTCGGG
Found at i:3228975 original size:12 final size:12
Alignment explanation
Indices: 3228957--3229079 Score: 149
Period size: 12 Copynumber: 10.2 Consensus size: 12
3228947 TTTTAATTTA
3228957 TTTCTTTTCTTC
1 TTTCTTTTCTTC
*
3228969 CTTCTTTTCTTC
1 TTTCTTTTCTTC
*
3228981 TTTCTTTTCCTC
1 TTTCTTTTCTTC
*
3228993 TTTCTTCTCTTC
1 TTTCTTTTCTTC
* *
3229005 CTTCTTCTCTTC
1 TTTCTTTTCTTC
* *
3229017 TTTCTTCTCCTC
1 TTTCTTTTCTTC
*
3229029 TTTCTTTTCCTC
1 TTTCTTTTCTTC
3229041 TTTCTTTTCTTCC
1 TTTCTTTTCTT-C
*
3229054 TTT-TTTTCTAC
1 TTTCTTTTCTTC
3229065 TTTCTTTTCTTC
1 TTTCTTTTCTTC
3229077 TTT
1 TTT
3229080 AGCAGGTCCT
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
11 4 0.04
12 89 0.92
13 4 0.04
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCTTTTCTTC
Found at i:3229561 original size:6 final size:6
Alignment explanation
Indices: 3229550--3229575 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3229540 GATATAGGGG
3229550 ATGAAA ATGAAA ATGAAA ATGAAA AT
1 ATGAAA ATGAAA ATGAAA ATGAAA AT
3229576 AACATCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.19
Consensus pattern (6 bp):
ATGAAA
Found at i:3232949 original size:13 final size:13
Alignment explanation
Indices: 3232933--3232957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3232923 AATTGTGTTC
3232933 TTAAAATTAAAAT
1 TTAAAATTAAAAT
3232946 TTAAAATTAAAA
1 TTAAAATTAAAA
3232958 ACTCATAAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAATTAAAAT
Found at i:3235812 original size:31 final size:27
Alignment explanation
Indices: 3235745--3235835 Score: 78
Period size: 31 Copynumber: 3.1 Consensus size: 27
3235735 AATAAGTAAA
*
3235745 TTTTTAACATAAAAAATTAATTTATATT
1 TTTTTAAC-TAAATAATTAATTTATATT
3235773 TTAATTTAACGTATAATAATTAATTTATATAAT
1 TT--TTTAAC-TA-AATAATTAATTTATAT--T
3235806 TTTTTAA-TAAAATAAATTAATTTA-ATT
1 TTTTTAACT-AAAT-AATTAATTTATATT
3235833 TTT
1 TTT
3235836 AATATAAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
27 4 0.07
28 2 0.04
29 6 0.11
30 19 0.35
31 20 0.37
33 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (27 bp):
TTTTTAACTAAATAATTAATTTATATT
Found at i:3238346 original size:22 final size:21
Alignment explanation
Indices: 3238321--3238362 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3238311 TTTAATGTTT
* *
3238321 ATTTTTATTTTCTGTCACTTTA
1 ATTTTAATTTT-TATCACTTTA
3238343 ATTTTAATTTTTATCACTTT
1 ATTTTAATTTTTATCACTTT
3238363 GACCCTCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTTAATTTTTATCACTTTA
Found at i:3238539 original size:25 final size:22
Alignment explanation
Indices: 3238487--3238540 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 22
3238477 GATTATTAAA
*
3238487 AACATAAAAAATAAATTATTTT
1 AACAAAAAAAATAAATTATTTT
**
3238509 TCCAAAAAAACATATAATTACTTTT
1 AACAAAAAAA-ATA-AATTA-TTTT
3238534 AACAAAA
1 AACAAAA
3238541 TTATCTACAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 3 0.12
24 5 0.21
25 9 0.38
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (22 bp):
AACAAAAAAAATAAATTATTTT
Found at i:3248911 original size:19 final size:20
Alignment explanation
Indices: 3248877--3248915 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3248867 AATTCGGAAA
3248877 AAGAAAAATATTAAATAAAAC
1 AAGAAAAATA-TAAATAAAAC
3248898 AAGAAAAATA-AAATAAAA
1 AAGAAAAATATAAATAAAA
3248916 TGAACTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
AAGAAAAATATAAATAAAAC
Found at i:3249749 original size:17 final size:17
Alignment explanation
Indices: 3249729--3249770 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
3249719 TATATGTTAT
3249729 AAATTATATAATATAAA
1 AAATTATATAATATAAA
*
3249746 AAATAATATAATATAAA
1 AAATTATATAATATAAA
*
3249763 ACATTATA
1 AAATTATA
3249771 AACGGGCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTATATAATATAAA
Done.