Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 150 of 362
Found at i:49778915 original size:10 final size:10
Alignment explanation
Indices: 49778916--49778941 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
49778906 TTGAAATTTT
49778916 TTTTTTGAAA
1 TTTTTTGAAA
49778926 TTTTTTGAAA
1 TTTTTTGAAA
49778936 TTTTTT
1 TTTTTT
49778942 ACTTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (10 bp):
TTTTTTGAAA
Found at i:49778917 original size:14 final size:14
Alignment explanation
Indices: 49778900--49778931 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
49778890 TTTTTTCAGA
49778900 TTTTTTTTGAAATT
1 TTTTTTTTGAAATT
49778914 TTTTTTTTGAAATT
1 TTTTTTTTGAAATT
49778928 TTTT
1 TTTT
49778932 GAAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (14 bp):
TTTTTTTTGAAATT
Found at i:49779113 original size:16 final size:16
Alignment explanation
Indices: 49779092--49779132 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
49779082 GTATACGAAA
49779092 TTTTTTTTCTATACTC
1 TTTTTTTTCTATACTC
49779108 TTTTTTTTCTATACTC
1 TTTTTTTTCTATACTC
49779124 TTCTTTTTT
1 TT-TTTTTT
49779133 TTTCTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTTCTATACTC
Found at i:49785067 original size:45 final size:45
Alignment explanation
Indices: 49785018--49785281 Score: 402
Period size: 45 Copynumber: 5.9 Consensus size: 45
49785008 TCGGCCATGG
* * * * *
49785018 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
49785063 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
49785108 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
49785153 TGCTTCCTCAAAGTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
49785198 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * * **
49785243 TTCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
49785282 TCCACCTCTT
Statistics
Matches: 202, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 202 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:49792903 original size:13 final size:12
Alignment explanation
Indices: 49792887--49793020 Score: 64
Period size: 12 Copynumber: 11.0 Consensus size: 12
49792877 TTTTTTCGCT
49792887 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
49792900 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
49792914 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
49792925 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
49792939 -TTTCTTTTTC-
1 TTTTCTTTTTCA
**
49792949 TTTTGCAATTTC-
1 TTTT-CTTTTTCA
*
49792961 TTTTCTTTTGCA
1 TTTTCTTTTTCA
* *
49792973 ATTTC-TTTTCT
1 TTTTCTTTTTCA
*
49792984 TTTTC-TTTTCT
1 TTTTCTTTTTCA
*
49792995 TTTTGTTTCTTTCA
1 TTTT-CTT-TTTCA
*
49793009 ATTTCTTTTTCA
1 TTTTCTTTTTCA
49793021 ATCTCTTTCT
Statistics
Matches: 93, Mismatches: 17, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
11 26 0.28
12 37 0.40
13 11 0.12
14 16 0.17
15 3 0.03
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:49792908 original size:28 final size:27
Alignment explanation
Indices: 49792866--49793019 Score: 70
Period size: 28 Copynumber: 5.6 Consensus size: 27
49792856 TCAAGCTCTC
*
49792866 TTTCAATTTCTTTTT-TTCGCTTTTTCTT
1 TTTCAATTTCTTTTTCTT--CATTTTCTT
49792894 TTTCAATTT-TCTTTTCTTCATTTTCTT
1 TTTCAATTTCT-TTTTCTTCATTTTCTT
** ** *
49792921 TTTCTCTCACTTTTTCGATTTCTTTTTCTT
1 TTTCAATTTCTTTTTC---TTCATTTTCTT
* * *
49792951 TTGCAATTTCTTTTCTTTTGCAATTTC-T
1 TTTCAATTTCTTTT-TCTT-CATTTTCTT
**
49792979 TTTCTTTTTC-TTTTCTT--TTTGT-TT
1 TTTCAATTTCTTTTTCTTCATTT-TCTT
49793003 CTTTCAATTTCTTTTTC
1 -TTTCAATTTCTTTTTC
49793020 AATCTCTTTC
Statistics
Matches: 93, Mismatches: 21, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
23 2 0.02
24 2 0.02
25 8 0.09
26 8 0.09
27 22 0.24
28 24 0.26
29 7 0.08
30 19 0.20
31 1 0.01
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTTCTTCATTTTCTT
Found at i:49792916 original size:14 final size:14
Alignment explanation
Indices: 49792887--49792923 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
49792877 TTTTTTCGCT
49792887 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
49792900 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
49792914 TTTTCTTTTT
1 TTTTCTTTTT
49792924 CTCTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:49792952 original size:17 final size:17
Alignment explanation
Indices: 49792938--49792986 Score: 89
Period size: 17 Copynumber: 2.8 Consensus size: 17
49792928 CACTTTTTCG
49792938 ATTTCTTTTTCTTTTGCA
1 ATTTC-TTTTCTTTTGCA
49792956 ATTTCTTTTCTTTTGCA
1 ATTTCTTTTCTTTTGCA
49792973 ATTTCTTTTCTTTT
1 ATTTCTTTTCTTTT
49792987 TCTTTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 26 0.84
18 5 0.16
ACGTcount: A:0.10, C:0.16, G:0.04, T:0.69
Consensus pattern (17 bp):
ATTTCTTTTCTTTTGCA
Found at i:49792990 original size:11 final size:11
Alignment explanation
Indices: 49792974--49792998 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
49792964 TCTTTTGCAA
49792974 TTTCTTTTCTT
1 TTTCTTTTCTT
49792985 TTTCTTTTCTT
1 TTTCTTTTCTT
49792996 TTT
1 TTT
49792999 GTTTCTTTCA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:49792998 original size:17 final size:17
Alignment explanation
Indices: 49792887--49792997 Score: 82
Period size: 17 Copynumber: 6.2 Consensus size: 17
49792877 TTTTTTCGCT
49792887 TTTTCTTTTTCAATTTTC
1 TTTTCTTTTTC-ATTTTC
*
49792905 TTTTCTTCATTTTCTTTTTC
1 TTTTC-T--TTTTCATTTTC
**
49792925 TCTCACTTTTTCGA-TTTC
1 T-TTTCTTTTTC-ATTTTC
* *
49792943 TTTTTCTTTTGCAATTTC
1 -TTTTCTTTTTCATTTTC
* *
49792961 TTTTCTTTTGCAATTTC
1 TTTTCTTTTTCATTTTC
49792978 TTTTCTTTTTC-TTTTC
1 TTTTCTTTTTCATTTTC
49792994 TTTT
1 TTTT
49792998 TGTTTCTTTC
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
16 8 0.10
17 28 0.36
18 25 0.32
19 2 0.03
20 7 0.09
21 7 0.09
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTCTTTTTCATTTTC
Found at i:49793019 original size:6 final size:6
Alignment explanation
Indices: 49792885--49792998 Score: 63
Period size: 6 Copynumber: 19.0 Consensus size: 6
49792875 CTTTTTTTCG
* * * **
49792885 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * **
49792936 CGATTT CTTTTT CTTTTG CAATTT C-TTTT CTTTTG CAATTT C-TTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
49792982 CTTTTT C-TTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT
49792999 GTTTCTTTCA
Statistics
Matches: 78, Mismatches: 25, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
5 13 0.17
6 53 0.68
7 9 0.12
8 3 0.04
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:49794073 original size:1 final size:1
Alignment explanation
Indices: 49794069--49794125 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
49794059 TTGTCACTTC
* ** ***
49794069 TTTTTTTTTTTCTTTTTTTGATTTTTTTGAATTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
49794126 AAATCCAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.05, C:0.02, G:0.04, T:0.89
Consensus pattern (1 bp):
T
Found at i:49794094 original size:35 final size:34
Alignment explanation
Indices: 49794055--49794121 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
49794045 TTAACTCGAT
*
49794055 TTTTTTGTCACTTCTTTTTTTTTTTCTTTTTTTGA
1 TTTTTT-TCAATTCTTTTTTTTTTTCTTTTTTTGA
* * *
49794090 TTTTTTTGAATTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTCAATTCTTTTTTTTTTTCTTTTTTT
49794122 TTTTAAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 22 0.79
35 6 0.21
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.84
Consensus pattern (34 bp):
TTTTTTTCAATTCTTTTTTTTTTTCTTTTTTTGA
Found at i:49798841 original size:11 final size:11
Alignment explanation
Indices: 49798825--49798854 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
49798815 TTGTAGATTC
49798825 AAAAAAAATCG
1 AAAAAAAATCG
*
49798836 AAAAAAAATTG
1 AAAAAAAATCG
49798847 AAAAAAAA
1 AAAAAAAA
49798855 AATTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:49798871 original size:13 final size:14
Alignment explanation
Indices: 49798836--49798869 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
49798826 AAAAAAATCG
49798836 AAAAAAAA-TTGAA
1 AAAAAAAATTTGAA
49798849 AAAAAAAATTTGAA
1 AAAAAAAATTTGAA
49798863 AAAAAAA
1 AAAAAAA
49798870 TTGCATACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (14 bp):
AAAAAAAATTTGAA
Found at i:49807989 original size:33 final size:33
Alignment explanation
Indices: 49807951--49808013 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
49807941 GATTACTCAC
49807951 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
49807984 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
49808014 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:49808060 original size:14 final size:14
Alignment explanation
Indices: 49808016--49808066 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
49808006 TCTCTTTCAA
49808016 TTTCTTTTTTC-GCT
1 TTTCTTTTTTCAG-T
49808030 TTT-TCTTTTTCAGT
1 TTTCT-TTTTTCAGT
49808044 TTTCTTTTCTTCA-T
1 TTTCTTTT-TTCAGT
49808058 TTTCTTTTT
1 TTTCTTTTT
49808067 CTCTCACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.06
14 25 0.76
15 6 0.18
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTCTTTTTTCAGT
Found at i:49808108 original size:18 final size:18
Alignment explanation
Indices: 49808028--49808113 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 18
49808018 TCTTTTTTCG
49808028 CTTTTTCTTTTTCAGTTTT
1 CTTTTTCTTTTTCA-TTTT
* *
49808047 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
49808067 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
49808085 CTTTTTCTTTTTCATTTT
1 CTTTTTCTTTTTCATTTT
*
49808103 CTTTTTGTTTT
1 CTTTTTCTTTT
49808114 CTTTCAATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
17 1 0.02
18 32 0.62
19 3 0.06
20 8 0.15
21 8 0.15
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.72
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:49808130 original size:6 final size:6
Alignment explanation
Indices: 49808028--49808117 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
49808018 TCTTTTTTCG
* * * **
49808028 CTTTTT CTTTTT CAGTTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * *
49808079 CGATTT CTTTTT CTTTTT CATTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
49808118 CAATTTCTTT
Statistics
Matches: 62, Mismatches: 19, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
5 4 0.06
6 46 0.74
7 9 0.15
8 3 0.05
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:49808149 original size:63 final size:63
Alignment explanation
Indices: 49808028--49808149 Score: 138
Period size: 63 Copynumber: 1.9 Consensus size: 63
49808018 TCTTTTTTCG
* * ** * *
49808028 CTTTTTCTTTTTCAGTTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTTTCGATTTCTTTTT
1 CTTTTTCATTTTCAGTTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTCTCCATTTCTTTTT
* * * *
49808091 CTTTTTCATTTTC-TTTTTGTTTTCTTTCAATTTCTTTTTCAATCTCTTTCTCCTTTTCT
1 CTTTTTCATTTTCAGTTTTCTTTTC-TTCAATTTCTTTTTCAATCACTTTCTCCATTTCT
49808150 CGCTCAATGG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
62 9 0.19
63 39 0.81
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.69
Consensus pattern (63 bp):
CTTTTTCATTTTCAGTTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTCTCCATTTCTTTTT
Found at i:49809210 original size:11 final size:11
Alignment explanation
Indices: 49809195--49809229 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
49809185 TTTTTGCTCG
49809195 ATTTTTTTTCA
1 ATTTTTTTTCA
* *
49809206 CTTTTTTTTGA
1 ATTTTTTTTCA
49809217 ATTTTTTTTCA
1 ATTTTTTTTCA
49809228 AT
1 AT
49809230 CAAAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:49809259 original size:17 final size:17
Alignment explanation
Indices: 49809216--49809258 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
49809206 CTTTTTTTTG
49809216 AATTTTTTTTCAATCAA
1 AATTTTTTTTCAATCAA
49809233 AATTTTTTTTCAATC-A
1 AATTTTTTTTCAATCAA
49809249 AATTTTTTTT
1 AATTTTTTTT
49809259 TGATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTTTTTTTCAATCAA
Found at i:49811380 original size:10 final size:10
Alignment explanation
Indices: 49811364--49811421 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
49811354 CAACTCCGAC
49811364 CAGCTCAATT
1 CAGCTCAATT
* *
49811374 GAGCTCATTT
1 CAGCTCAATT
49811384 CAGCTCAA-T
1 CAGCTCAATT
49811393 CGAGCTCAATT
1 C-AGCTCAATT
*
49811404 TAGCTACAATT
1 CAGCT-CAATT
49811415 CAGCTCA
1 CAGCTCA
49811422 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:49811387 original size:20 final size:20
Alignment explanation
Indices: 49811364--49811424 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
49811354 CAACTCCGAC
49811364 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
49811384 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
49811405 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
49811425 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:49812806 original size:9 final size:10
Alignment explanation
Indices: 49812785--49812817 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
49812775 AAGAGAGAAG
49812785 AAATTCAAAA
1 AAATTCAAAA
49812795 AAATTCAAAA
1 AAATTCAAAA
49812805 AAA-TCGAAAA
1 AAATTC-AAAA
49812815 AAA
1 AAA
49812818 AAGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 2 0.09
10 20 0.91
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:49812855 original size:38 final size:36
Alignment explanation
Indices: 49812800--49812873 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 36
49812790 CAAAAAAATT
49812800 CAAAAAAATCGAAAAAAAAAGAA-AAAAAAGAAGTGA
1 CAAAAAAATCGAAAAAAAAAGAAGAAAAAA-AAGTGA
*
49812836 CAAAAAAATCGAGTTAAAAAAAGAAGAAAAAAAAGTGA
1 CAAAAAAATCGA--AAAAAAAAGAAGAAAAAAAAGTGA
49812874 AAAGTCTTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 12 0.35
38 16 0.47
39 6 0.18
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.08
Consensus pattern (36 bp):
CAAAAAAATCGAAAAAAAAAGAAGAAAAAAAAGTGA
Found at i:49813883 original size:6 final size:6
Alignment explanation
Indices: 49813874--49813939 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
49813864 GAAAGAGATT
** * * **
49813874 GAAAAA GAAATT GAAAGAA AAAAAAA GAAAAC GAAAAA GAAAAA GAAATT
1 GAAAAA GAAAAA GAAA-AA GAA-AAA GAAAAA GAAAAA GAAAAA GAAAAA
*
49813924 GCAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAA
49813940 TCAAAATAGT
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
6 37 0.84
7 6 0.14
8 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (6 bp):
GAAAAA
Found at i:49813896 original size:18 final size:17
Alignment explanation
Indices: 49813875--49813940 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
49813865 AAAGAGATTG
49813875 AAAAAGAAATTGAAAGAAAA
1 AAAAAGAAATTG--A-AAAA
**
49813895 AAAAAGAAAACGAAAAA
1 AAAAAGAAATTGAAAAA
*
49813912 GAAAAAGAAATTGCAAAAG
1 -AAAAAGAAATTG-AAAAA
49813931 AAAAAGAAAT
1 AAAAAGAAAT
49813941 CAAAATAGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 4 0.10
18 21 0.54
19 4 0.10
20 10 0.26
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.08
Consensus pattern (17 bp):
AAAAAGAAATTGAAAAA
Found at i:49813911 original size:7 final size:6
Alignment explanation
Indices: 49813887--49813939 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
49813877 AAAGAAATTG
* ** *
49813887 AAAG-A AAA-AA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
49813933 AAAGAA A
1 AAAGAA A
49813940 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
5 7 0.18
6 31 0.82
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:49813999 original size:18 final size:18
Alignment explanation
Indices: 49813978--49814012 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
49813968 AGAAAAGAAA
49813978 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
49813996 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
49814013 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:49816087 original size:10 final size:10
Alignment explanation
Indices: 49816071--49816128 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
49816061 CAACTCCGAC
49816071 CAGCTCAATT
1 CAGCTCAATT
* *
49816081 GAGCTCATTT
1 CAGCTCAATT
49816091 CAGCTCAA-T
1 CAGCTCAATT
49816100 CGAGCTCAATT
1 C-AGCTCAATT
*
49816111 TAGCTACAATT
1 CAGCT-CAATT
49816122 CAGCTCA
1 CAGCTCA
49816129 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:49816094 original size:20 final size:20
Alignment explanation
Indices: 49816071--49816131 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
49816061 CAACTCCGAC
49816071 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
49816091 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
49816112 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
49816132 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:49825764 original size:24 final size:23
Alignment explanation
Indices: 49825710--49825787 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
49825700 GGATAATTAA
**
49825710 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
49825733 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
49825757 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
49825778 GAAATAGTAT
1 GAAATGGTAT
49825788 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:49825772 original size:21 final size:21
Alignment explanation
Indices: 49825746--49825812 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
49825736 TTGGTATTTG
49825746 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
49825767 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
49825788 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
49825811 GG
1 GG
49825813 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:49830076 original size:17 final size:17
Alignment explanation
Indices: 49830051--49830106 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
49830041 TCTCTTTTCA
*
49830051 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
49830068 TTCTTTTTTTTT-ATCATTT
1 TTCTTTTTTTTTGA--A-TT
* *
49830087 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
49830104 TTC
1 TTC
49830107 GTCTTTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 16 0.50
18 2 0.06
19 13 0.41
ACGTcount: A:0.09, C:0.12, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:49830098 original size:20 final size:18
Alignment explanation
Indices: 49830066--49830119 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
49830056 TTTTTTTGAA
49830066 TTTTCTTTT-TTTTTATCAT
1 TTTTCTTTTCTTTTTAT--T
49830085 TTTTCTTTTCTTTTGTATT
1 TTTTCTTTTCTTTT-TATT
*
49830104 TTCGTCTTTTCTTTTT
1 TT-TTCTTTTCTTTTT
49830120 CTCTCATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 13 0.42
20 15 0.48
21 3 0.10
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTATT
Found at i:49832351 original size:12 final size:14
Alignment explanation
Indices: 49832334--49832368 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
49832324 TATGCAATTT
49832334 TTTTTTTTTC-AA-
1 TTTTTTTTTCAAAC
49832346 TTTTTTTTTCAAAC
1 TTTTTTTTTCAAAC
49832360 TTTTTTTTT
1 TTTTTTTTT
49832369 ACGCACCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
13 2 0.10
14 9 0.43
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTTTCAAAC
Found at i:49832692 original size:21 final size:21
Alignment explanation
Indices: 49832666--49832732 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
49832656 TTGGTATTTG
49832666 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
49832687 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
49832708 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
49832731 GG
1 GG
49832733 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:49835382 original size:4 final size:4
Alignment explanation
Indices: 49835373--49835400 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
49835363 TATTTTTATT
49835373 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
49835401 CTTAGTTTAA
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:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:49837357 original size:12 final size:12
Alignment explanation
Indices: 49837308--49837354 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
49837298 GACCGTATGT
49837308 AATTTTTTTTTC
1 AATTTTTTTTTC
49837320 AATTTTTTTTTC
1 AATTTTTTTTTC
*
49837332 AATTTTTTTTTT
1 AATTTTTTTTTC
*
49837344 GATTTTTTTTT
1 AATTTTTTTTT
49837355 TGAATCTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (12 bp):
AATTTTTTTTTC
Found at i:49841334 original size:17 final size:18
Alignment explanation
Indices: 49841297--49841334 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
49841287 GATTGAGAGT
* *
49841297 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
49841315 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
49841332 GAA
1 GAA
49841335 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:49841347 original size:13 final size:12
Alignment explanation
Indices: 49841316--49841370 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
49841306 TGTGAAACAG
*
49841316 AAAAGAAATTGA
1 AAAAGAAGTTGA
49841328 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
49841340 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
49841352 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
49841364 AAAAGAA
1 AAAAGAA
49841371 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:49843994 original size:29 final size:29
Alignment explanation
Indices: 49843928--49843984 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
49843918 GATTCAAAGA
49843928 TGGGTTTATGGATATAAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
49843957 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
49843985 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:49845006 original size:14 final size:14
Alignment explanation
Indices: 49844964--49845008 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
49844954 TTAAAGAAGC
49844964 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
49844978 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
49844991 AACTCATTTAATTA
1 AACTCATTAAATTA
49845005 AACT
1 AACT
49845009 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:49848508 original size:9 final size:9
Alignment explanation
Indices: 49848494--49848518 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
49848484 TTGTTTGAAT
49848494 TTTTTTTCG
1 TTTTTTTCG
49848503 TTTTTTTCG
1 TTTTTTTCG
49848512 TTTTTTT
1 TTTTTTT
49848519 TGAAACTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (9 bp):
TTTTTTTCG
Found at i:49848804 original size:29 final size:29
Alignment explanation
Indices: 49848738--49848794 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
49848728 GATTCAAAGA
*
49848738 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
49848767 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
49848795 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:49849813 original size:14 final size:14
Alignment explanation
Indices: 49849770--49849815 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
49849760 ATTAAAGAAG
49849770 AAACTCATTAAATT
1 AAACTCATTAAATT
* *
49849784 AAATTCATCAAA-T
1 AAACTCATTAAATT
*
49849797 AAACTCATTTAATT
1 AAACTCATTAAATT
49849811 AAACT
1 AAACT
49849816 AAGATGAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
AAACTCATTAAATT
Found at i:49852735 original size:23 final size:22
Alignment explanation
Indices: 49852683--49852735 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
49852673 TCCACGTCTT
*
49852683 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
49852705 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
49852728 TTTCTTTT
1 TTTCTTTT
49852736 TCACACTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:49860381 original size:17 final size:18
Alignment explanation
Indices: 49860359--49860392 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49860349 TTTTTCTTTT
49860359 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
49860376 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
49860393 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:49860389 original size:6 final size:6
Alignment explanation
Indices: 49860380--49860484 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
49860370 TCAATCTCAA
* * * ** **
49860380 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
49860432 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
49860478 TTTCTT T
1 TTTCTT T
49860485 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:49860410 original size:27 final size:28
Alignment explanation
Indices: 49860350--49860416 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
49860340 TTCAACATCT
49860350 TTTTCTTTTTCAATTTTTTCTCAATCTCA
1 TTTTCTTTTTCAATTTTTTCTC-ATCTCA
* *
49860379 ATTTCTTTTTCAATTTTCTTTTC-T-TCA
1 TTTTCTTTTTCAATTTT-TTCTCATCTCA
49860406 TTTTCTTTTTC
1 TTTTCTTTTTC
49860417 TCTCACTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
29 16 0.47
30 4 0.12
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTCTTTTTCAATTTTTTCTCATCTCA
Found at i:49860497 original size:6 final size:6
Alignment explanation
Indices: 49860431--49860484 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
49860421 ACTATTTTGA
* ** * *
49860431 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
49860478 TTTCTT T
1 TTTCTT T
49860485 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:49861518 original size:11 final size:10
Alignment explanation
Indices: 49861503--49861527 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49861493 AGACTTTTCA
49861503 CTTTTTTTTT
1 CTTTTTTTTT
49861513 CTTTTTTTTT
1 CTTTTTTTTT
49861523 CTTTT
1 CTTTT
49861528 AACTCAATTT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:49873727 original size:30 final size:30
Alignment explanation
Indices: 49873693--49873789 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
49873683 TAAACTAAAA
*
49873693 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
49873723 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
49873753 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
49873783 TGAGCTA
1 TGAGCTA
49873790 GGAGCGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:49874760 original size:11 final size:11
Alignment explanation
Indices: 49874733--49874786 Score: 81
Period size: 11 Copynumber: 4.6 Consensus size: 11
49874723 CACAAATCAT
49874733 TTTTTTTTGAAA
1 TTTTTTTTG-AA
49874745 CTTTTTTTTGAA
1 -TTTTTTTTGAA
49874757 TTTTTTTTCGAA
1 TTTTTTTT-GAA
49874769 TTTTTTTTGAA
1 TTTTTTTTGAA
49874780 TTTTTTT
1 TTTTTTT
49874787 ATACTTGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.45
12 13 0.32
13 9 0.22
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.72
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:49874763 original size:23 final size:23
Alignment explanation
Indices: 49874731--49874786 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 23
49874721 TGCACAAATC
*
49874731 ATTTTTTTTTGAAACTTTTTTTTGA
1 ATTTTTTTTCG-AA-TTTTTTTTGA
49874756 ATTTTTTTTCGAATTTTTTTTGA
1 ATTTTTTTTCGAATTTTTTTTGA
49874779 ATTTTTTT
1 ATTTTTTT
49874787 ATACTTGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 18 0.60
24 2 0.07
25 10 0.33
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.71
Consensus pattern (23 bp):
ATTTTTTTTCGAATTTTTTTTGA
Found at i:49877220 original size:30 final size:30
Alignment explanation
Indices: 49877184--49877291 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 30
49877174 AGCTTACTCC
* *
49877184 TAGCTCATTTTCAACTCACGAGTTAAACCT
1 TAGCTCATTTTCAGCTCAAGAGTTAAACCT
** * * *
49877214 TAGCTCAACTTCAGCTTAGGAGTTTAACCT
1 TAGCTCATTTTCAGCTCAAGAGTTAAACCT
* * * *
49877244 CAGCTCAACTTT-AGCTCAAGAGCTAAAGCT
1 TAGCTC-ATTTTCAGCTCAAGAGTTAAACCT
49877274 TAGCTCATTTT-AGCTCAA
1 TAGCTCATTTTCAGCTCAA
49877292 ACCCTTTTTA
Statistics
Matches: 61, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
29 11 0.18
30 47 0.77
31 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (30 bp):
TAGCTCATTTTCAGCTCAAGAGTTAAACCT
Found at i:49878156 original size:6 final size:5
Alignment explanation
Indices: 49878132--49878188 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
49878122 ACGAGAAAAC
*
49878132 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATG- AAAGAA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AAAG-A
49878179 AAAGA AAAGA
1 AAAGA AAAGA
49878189 GAGGCAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 15 0.34
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:49878163 original size:15 final size:14
Alignment explanation
Indices: 49878132--49878188 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 14
49878122 ACGAGAAAAC
49878132 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
49878148 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
49878163 AAAGAAAATGAAAGAA
1 AAAGAAAA-G-AAGAA
49878179 AAAGAAAAGA
1 AAAGAAAAGA
49878189 GAGGCAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.13
15 11 0.29
16 17 0.45
17 5 0.13
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:49878278 original size:12 final size:12
Alignment explanation
Indices: 49878256--49878280 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49878246 TTTGAAAAAC
49878256 AAAAAGAAAATG
1 AAAAAGAAAATG
49878268 AAAAAGAAAATG
1 AAAAAGAAAATG
49878280 A
1 A
49878281 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:49878287 original size:18 final size:18
Alignment explanation
Indices: 49878247--49878300 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
49878237 GAAAAAGCCT
* *
49878247 TTGAAAAACAAAAAGAAA
1 TTGAAAAAGAAAATGAAA
* *
49878265 ATGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAATGAAA
*
49878283 TTGAAAAAGAGAATGAAA
1 TTGAAAAAGAAAATGAAA
49878301 AAGAGTTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.13
Consensus pattern (18 bp):
TTGAAAAAGAAAATGAAA
Found at i:49878312 original size:30 final size:30
Alignment explanation
Indices: 49878256--49878354 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
49878246 TTTGAAAAAC
**
49878256 AAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
* ***
49878286 AAAAAGAGAATGAAAAAGAGTTTGAGAGAG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
** * * *
49878316 AAAAAGAATGTGAATAAGAAAA-AAGAGTGG
1 AAAAAGAAAATGAAAAAGAAAATGAGAG-AG
49878346 AAAAAGAAA
1 AAAAAGAAA
49878355 TTGAGATAAA
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
29 4 0.08
30 48 0.92
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGAGAG
Found at i:49878352 original size:18 final size:19
Alignment explanation
Indices: 49878316--49878354 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
49878306 TTTGAGAGAG
*
49878316 AAAAAGAATGTGAATAAGA
1 AAAAAGAATGTGAAAAAGA
*
49878335 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
49878353 AA
1 AA
49878355 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:49880452 original size:30 final size:30
Alignment explanation
Indices: 49880418--49880474 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
49880408 ATCAACTCAC
*
49880418 GAGTTAAAACTTAGCTCAACTTCAGCTTAG
1 GAGTTAAAACTCAGCTCAACTTCAGCTTAG
* * *
49880448 GAGTTTAACCTCAGCTCAACTTTAGCT
1 GAGTTAAAACTCAGCTCAACTTCAGCT
49880475 CAAGGGCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (30 bp):
GAGTTAAAACTCAGCTCAACTTCAGCTTAG
Found at i:49886739 original size:8 final size:8
Alignment explanation
Indices: 49886726--49886751 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
49886716 TAAGGTGAAA
49886726 AGATGGAT
1 AGATGGAT
49886734 AGATGGAT
1 AGATGGAT
49886742 AGATGGAT
1 AGATGGAT
49886750 AG
1 AG
49886752 GTGAACGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (8 bp):
AGATGGAT
Found at i:49887776 original size:10 final size:10
Alignment explanation
Indices: 49887762--49887797 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
49887752 TAAGCTCGGT
49887762 TGAGCTCAAA
1 TGAGCTCAAA
* *
49887772 CGAGCTGAAA
1 TGAGCTCAAA
49887782 TGAGCTCAAA
1 TGAGCTCAAA
49887792 TGAGCT
1 TGAGCT
49887798 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.19
Consensus pattern (10 bp):
TGAGCTCAAA
Found at i:49887805 original size:20 final size:20
Alignment explanation
Indices: 49887760--49887807 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
49887750 AGTAAGCTCG
49887760 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
** *
49887780 AATGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
49887800 GTTGAGCT
1 GTTGAGCT
49887808 GGACGGAGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:49889505 original size:17 final size:17
Alignment explanation
Indices: 49889483--49889538 Score: 67
Period size: 17 Copynumber: 3.0 Consensus size: 17
49889473 CTTTTTCTCG
49889483 ATTTTCTTTTCTTTTTC
1 ATTTTCTTTTCTTTTTC
49889500 ATTTTCTTTTCTTTTTTCAC
1 ATTTTCTTTTC-TTTTT--C
49889520 ATTCATTCTTTTCTTTTTC
1 ATT--TTCTTTTCTTTTTC
49889539 TCTCAACTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.32
18 5 0.15
19 1 0.03
20 4 0.12
21 5 0.15
22 8 0.24
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTCTTTTCTTTTTC
Found at i:49891897 original size:40 final size:40
Alignment explanation
Indices: 49891814--49891890 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
49891804 ATTGATGAAC
49891814 ACTCCACTCGTGTTTGCACTCATTTTTAGGCTTTTTTAAA
1 ACTCCACTCGTGTTTGCACTCATTTTTAGGCTTTTTTAAA
49891854 ACTCCACTCGTGTTTGCACTCATTTTTAGGCTTTTTT
1 ACTCCACTCGTGTTTGCACTCATTTTTAGGCTTTTTT
49891891 TTAACTCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (40 bp):
ACTCCACTCGTGTTTGCACTCATTTTTAGGCTTTTTTAAA
Found at i:49892650 original size:8 final size:8
Alignment explanation
Indices: 49892637--49892662 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
49892627 TAAGGTGAAA
49892637 AGATGGAT
1 AGATGGAT
49892645 AGATGGAT
1 AGATGGAT
49892653 AGATGGAT
1 AGATGGAT
49892661 AG
1 AG
49892663 GTGAACGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (8 bp):
AGATGGAT
Found at i:49893817 original size:18 final size:19
Alignment explanation
Indices: 49893794--49893832 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
49893784 TTTATCTCAA
*
49893794 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
49893812 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
49893831 TT
1 TT
49893833 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:49893874 original size:13 final size:12
Alignment explanation
Indices: 49893838--49893876 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
49893828 TTTTTCTCTC
*
49893838 TCAAACTCTTTT
1 TCAATCTCTTTT
*
49893850 TCATTCTCTTTT
1 TCAATCTCTTTT
*
49893862 TCAATCTCATTT
1 TCAATCTCTTTT
49893874 TCA
1 TCA
49893877 TTTTCATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.54
Consensus pattern (12 bp):
TCAATCTCTTTT
Found at i:49893874 original size:24 final size:24
Alignment explanation
Indices: 49893838--49893887 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
49893828 TTTTTCTCTC
* *
49893838 TCAAACTCTTTTTCATTCTCTTTT
1 TCAAACTCATTTTCATTCTCATTT
* *
49893862 TCAATCTCATTTTCATTTTCATTT
1 TCAAACTCATTTTCATTCTCATTT
49893886 TC
1 TC
49893888 TTTTTGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (24 bp):
TCAAACTCATTTTCATTCTCATTT
Found at i:49893883 original size:12 final size:12
Alignment explanation
Indices: 49893847--49893887 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
49893837 CTCAAACTCT
*
49893847 TTTTCATTCTCT
1 TTTTCATTCTCA
*
49893859 TTTTCAATCTCA
1 TTTTCATTCTCA
*
49893871 TTTTCATTTTCA
1 TTTTCATTCTCA
49893883 TTTTC
1 TTTTC
49893888 TTTTTGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTCATTCTCA
Found at i:49893892 original size:12 final size:12
Alignment explanation
Indices: 49893843--49893878 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
49893833 CTCTCTCAAA
49893843 CTCTTTTTCATT
1 CTCTTTTTCATT
*
49893855 CTCTTTTTCAAT
1 CTCTTTTTCATT
*
49893867 CTCATTTTCATT
1 CTCTTTTTCATT
49893879 TTCATTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (12 bp):
CTCTTTTTCATT
Found at i:49893892 original size:18 final size:18
Alignment explanation
Indices: 49893847--49893900 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
49893837 CTCAAACTCT
*
49893847 TTTTCATTCTCTTTTTCA
1 TTTTCATTTTCTTTTTCA
* * *
49893865 ATCTCATTTTCATTTTCA
1 TTTTCATTTTCTTTTTCA
* *
49893883 TTTTCTTTTTGTTTTTCA
1 TTTTCATTTTCTTTTTCA
49893901 AAGGCTTTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.19, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTCATTTTCTTTTTCA
Found at i:49893989 original size:6 final size:5
Alignment explanation
Indices: 49893959--49894017 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
49893949 GCCTTTTGCC
49893959 TTTCT TTTCT TTT-T ATTTCAT TTTCT CTTTC- -TTCT TTTGCTT TTTCT
1 TTTCT TTTCT TTTCT -TTTC-T TTTCT -TTTCT TTTCT TTT-C-T TTTCT
49894006 TTTCT TTTCT TT
1 TTTCT TTTCT TT
49894018 GTTTTCTCGT
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
3 3 0.07
4 1 0.02
5 27 0.59
6 10 0.22
7 5 0.11
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTCT
Found at i:49894006 original size:15 final size:14
Alignment explanation
Indices: 49893960--49894017 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 14
49893950 CCTTTTGCCT
*
49893960 TTCTTTTCTTTTTAT
1 TTCTTTTCTTTTT-C
*
49893975 TTCATTTTCTCTTTC
1 TTC-TTTTCTTTTTC
49893990 TTCTTTTGCTTTTTC
1 TTCTTTT-CTTTTTC
49894005 TTTTCTTTTCTTT
1 --TTCTTTTCTTT
49894018 GTTTTCTCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 4 0.11
15 12 0.33
16 13 0.36
17 7 0.19
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (14 bp):
TTCTTTTCTTTTTC
Found at i:49896355 original size:11 final size:12
Alignment explanation
Indices: 49896328--49896353 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49896318 AAGCTGTAGC
49896328 AAACTAAATTAA
1 AAACTAAATTAA
49896340 AAACTAAATTAA
1 AAACTAAATTAA
49896352 AA
1 AA
49896354 CTTAGTTTAT
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAACTAAATTAA
Found at i:49897565 original size:10 final size:10
Alignment explanation
Indices: 49897552--49897600 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
49897542 AAGCTTGGTT
49897552 GAGCTCAAAC
1 GAGCTCAAAC
* *
49897562 GAGCTGAAAT
1 GAGCTCAAAC
*
49897572 GAACTCAAAC
1 GAGCTCAAAC
*
49897582 GAGCTGAAAC
1 GAGCTCAAAC
49897592 GAGCTCAAA
1 GAGCTCAAA
49897601 TAAGTTGAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:49897578 original size:20 final size:20
Alignment explanation
Indices: 49897555--49897600 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
49897545 CTTGGTTGAG
*
49897555 CTCAAACGAGCTGAAATGAA
1 CTCAAACGAGCTGAAACGAA
*
49897575 CTCAAACGAGCTGAAACGAG
1 CTCAAACGAGCTGAAACGAA
49897595 CTCAAA
1 CTCAAA
49897601 TAAGTTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.13
Consensus pattern (20 bp):
CTCAAACGAGCTGAAACGAA
Found at i:49901958 original size:28 final size:30
Alignment explanation
Indices: 49901926--49901996 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 30
49901916 TTTCAATCAC
*
49901926 TCTTTTTTTTCAATTTCG-A-TTTTTTTCT
1 TCTTTTTTTTCAATTCCGAATTTTTTTTCT
49901954 TC-TTTTTTT-AATTCCGAATTTTTTTTCT
1 TCTTTTTTTTCAATTCCGAATTTTTTTTCT
49901982 TCTTTTTTCTTCAAT
1 TCTTTTTT-TTCAAT
49901997 ACTAAATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 6 0.16
27 8 0.22
28 13 0.35
29 5 0.14
30 2 0.05
31 3 0.08
ACGTcount: A:0.13, C:0.15, G:0.03, T:0.69
Consensus pattern (30 bp):
TCTTTTTTTTCAATTCCGAATTTTTTTTCT
Found at i:49901959 original size:25 final size:27
Alignment explanation
Indices: 49901926--49901988 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
49901916 TTTCAATCAC
* *
49901926 TCTTTTTTTTCAATTTCG-A-TTTTTT
1 TCTTCTTTTTCAATTCCGAATTTTTTT
*
49901951 TCTTCTTTTTTTAATTCCGAATTTTTTT
1 TCTTC-TTTTTCAATTCCGAATTTTTTT
49901979 TCTTCTTTTT
1 TCTTCTTTTT
49901989 TCTTCAATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 4 0.12
26 11 0.34
27 6 0.19
28 11 0.34
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.71
Consensus pattern (27 bp):
TCTTCTTTTTCAATTCCGAATTTTTTT
Found at i:49902070 original size:13 final size:13
Alignment explanation
Indices: 49902033--49902076 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
49902023 GAATACAAAC
49902033 TTTTTTTGAATTT
1 TTTTTTTGAATTT
***
49902046 TTTTTCAAAATTT
1 TTTTTTTGAATTT
49902059 TTTTTTTGAATTT
1 TTTTTTTGAATTT
49902072 TTTTT
1 TTTTT
49902077 ATATATTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTTTTTGAATTT
Found at i:49902084 original size:13 final size:12
Alignment explanation
Indices: 49902041--49902088 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
49902031 ACTTTTTTTG
*
49902041 AATTTTTTTTCAA
1 AATTTTTTTT-AT
*
49902054 AATTTTTTTTTT
1 AATTTTTTTTAT
49902066 GAATTTTTTTTAT
1 -AATTTTTTTTAT
49902079 ATATTTTTTT
1 A-ATTTTTTT
49902089 ACAATACCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 1 0.03
13 29 0.97
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (12 bp):
AATTTTTTTTAT
Found at i:49905386 original size:26 final size:28
Alignment explanation
Indices: 49905356--49905416 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
49905346 TCAATCTCAA
49905356 TCTCAATCTCAAATTC-TTTTTCT-TTT
1 TCTCAATCTCAAATTCTTTTTTCTCTTT
* ** *
49905382 TCTCACTCTCATTTTCTTTTTTTTCTTT
1 TCTCAATCTCAAATTCTTTTTTCTCTTT
49905410 TCTCAAT
1 TCTCAAT
49905417 TTCATTCAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 13 0.46
27 6 0.21
28 9 0.32
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.61
Consensus pattern (28 bp):
TCTCAATCTCAAATTCTTTTTTCTCTTT
Found at i:49907092 original size:19 final size:19
Alignment explanation
Indices: 49907057--49907140 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 19
49907047 ATTGTAATTG
49907057 AAAAAAAAATC-AAAAAAA
1 AAAAAAAAATCGAAAAAAA
* * * *
49907075 GAAGAGAAATTGAAAAAAA
1 AAAAAAAAATCGAAAAAAA
49907094 AAAAAAAAATCGAAAAAAAA
1 AAAAAAAAATCG-AAAAAAA
49907114 ATTAAAAAAAATCGAAGATAAAA
1 A--AAAAAAAATCGAA-A-AAAA
49907137 AAAA
1 AAAA
49907141 GTGAAAAGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
18 7 0.13
19 15 0.29
20 8 0.15
21 5 0.10
22 12 0.23
23 5 0.10
ACGTcount: A:0.79, C:0.04, G:0.08, T:0.10
Consensus pattern (19 bp):
AAAAAAAAATCGAAAAAAA
Found at i:49907997 original size:16 final size:15
Alignment explanation
Indices: 49907976--49908042 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 15
49907966 TCTTGTAAAG
49907976 AGAAAAAAGAAAGAAA
1 AGAAAAAA-AAAGAAA
*
49907992 AGAAAAAGAAAA-AGCA
1 AGAAAAA-AAAAGA-AA
*
49908008 AGAGAAGAAAAAGAAA
1 AGA-AAAAAAAAGAAA
*
49908024 ATGAAATAAAAAGAAA
1 A-GAAAAAAAAAGAAA
49908040 AGA
1 AGA
49908043 GAGGCAAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.07
16 32 0.76
17 7 0.17
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03
Consensus pattern (15 bp):
AGAAAAAAAAAGAAA
Found at i:49908005 original size:21 final size:21
Alignment explanation
Indices: 49907979--49908040 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
49907969 TGTAAAGAGA
49907979 AAAAAGAAAGAAAAGAAAAAG
1 AAAAAGAAAGAAAAGAAAAAG
* *
49908000 AAAAAGCAAGAGAAGAAAAAG
1 AAAAAGAAAGAAAAGAAAAAG
* *
49908021 AAAATGAAATAAAAAGAAAA
1 AAAAAGAAA-GAAAAGAAAA
49908041 GAGAGGCAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 26 0.76
22 8 0.24
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAAAGAAAGAAAAGAAAAAG
Found at i:49908121 original size:11 final size:12
Alignment explanation
Indices: 49908089--49908119 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49908079 TTGAGAGAAC
49908089 TTGAAAAAGCCT
1 TTGAAAAAGCCT
49908101 TTGAAAAAGCCT
1 TTGAAAAAGCCT
49908113 TTGAAAA
1 TTGAAAA
49908120 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:49910264 original size:30 final size:30
Alignment explanation
Indices: 49910230--49910326 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
49910220 AGCTCACTCC
49910230 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
49910260 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
49910290 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
49910320 TAGCTCA
1 TAGCTCA
49910327 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:49914185 original size:30 final size:30
Alignment explanation
Indices: 49914151--49914224 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
49914141 TAAACTAAAA
* *
49914151 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
1 TGAGCTAAGCTTTAACTCCTAAGCTAAAGT
* * *
49914181 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAACTCCTAAGCTAAAGT
*
49914211 TGAGCTAAGGTTTA
1 TGAGCTAAGCTTTA
49914225 TGATACGAGC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
29 2 0.06
30 29 0.85
31 3 0.09
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAACTCCTAAGCTAAAGT
Found at i:49919875 original size:20 final size:20
Alignment explanation
Indices: 49919852--49919898 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
49919842 GGGTTAAGAT
*
49919852 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
49919872 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
49919892 TGAGCTG
1 TGAGCTG
49919899 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:49921624 original size:48 final size:48
Alignment explanation
Indices: 49921569--49921674 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
49921559 TTGTCTTTTC
*
49921569 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
49921617 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
49921665 TTTCTTTTTC
1 TTTCTTTTTC
49921675 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:49922713 original size:10 final size:9
Alignment explanation
Indices: 49922700--49922735 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
49922690 CTTTTCACTT
49922700 TTTTTTGTTC
1 TTTTTT-TTC
49922710 TTTTTTTTAC
1 TTTTTTTT-C
49922720 TTTTTTTTC
1 TTTTTTTTC
49922729 TTTTTTT
1 TTTTTTT
49922736 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:49922721 original size:22 final size:21
Alignment explanation
Indices: 49922691--49922750 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
49922681 CTCATAAGAC
*
49922691 TTTTCACTTTTTTTTGTTCTTT
1 TTTTCACTTTTTTTTCTT-TTT
*
49922713 TTTTTACTTTTTTTTCTTTTT
1 TTTTCACTTTTTTTTCTTTTT
*
49922734 TTGCTCACTTCTTTTTT
1 TT-TTCACTT-TTTTTT
49922751 TTTGAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 5 0.16
22 21 0.66
23 6 0.19
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTCACTTTTTTTTCTTTTT
Found at i:49924303 original size:20 final size:20
Alignment explanation
Indices: 49924280--49924326 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
49924270 GGGTTAAGAT
*
49924280 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
49924300 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
49924320 TGAGCTG
1 TGAGCTG
49924327 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:49935203 original size:24 final size:25
Alignment explanation
Indices: 49935150--49935203 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
49935140 AACAAATTCT
* *
49935150 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
49935175 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
49935198 TTTTTT
1 TTTTTT
49935204 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:49937479 original size:17 final size:17
Alignment explanation
Indices: 49937453--49937485 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49937443 CTAGACCGTA
*
49937453 TGCAATTTTTTTTTTTT
1 TGCAAATTTTTTTTTTT
49937470 TGCAAATTTTTTTTTT
1 TGCAAATTTTTTTTTT
49937486 CTTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (17 bp):
TGCAAATTTTTTTTTTT
Found at i:49940108 original size:15 final size:16
Alignment explanation
Indices: 49940089--49940123 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
49940079 AAAGTTGTAA
*
49940089 AAAAATAAAAGAAGAG
1 AAAAATAAAAGAAAAG
49940105 AAAAATAAAA-AAAAG
1 AAAAATAAAAGAAAAG
49940120 AAAA
1 AAAA
49940124 CAAAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAATAAAAGAAAAG
Found at i:49940128 original size:20 final size:21
Alignment explanation
Indices: 49940090--49940128 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
49940080 AAGTTGTAAA
* *
49940090 AAAATAAAAGAAGAGAAAAAT
1 AAAATAAAAGAAAACAAAAAT
49940111 AAAA-AAAAGAAAACAAAA
1 AAAATAAAAGAAAACAAAA
49940129 GAGAGTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (21 bp):
AAAATAAAAGAAAACAAAAAT
Found at i:49942051 original size:11 final size:11
Alignment explanation
Indices: 49942035--49942066 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
49942025 GGAAATTTGA
49942035 AAAAAAAATTC
1 AAAAAAAATTC
49942046 AAAAAAAATTC
1 AAAAAAAATTC
49942057 AAAAAAAATT
1 AAAAAAAATT
49942067 TTGAAGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:49951920 original size:14 final size:14
Alignment explanation
Indices: 49951898--49951945 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
49951888 ACCTAAACCG
* *
49951898 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
49951912 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
49951926 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
49951940 ACCATT
1 ACCATT
49951946 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:49954405 original size:37 final size:38
Alignment explanation
Indices: 49954337--49954410 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
49954327 GCAACTCAGC
* *
49954337 ATACGACTCGACTCTCCCCGAGGAGGTTCGTATCACTA
1 ATACGACTCCACTCTCCCCGAGGAGGATCGTATCACTA
* *
49954375 ATACGACTCCACTCT-TCCGAGGCGGATCGTATCACT
1 ATACGACTCCACTCTCCCCGAGGAGGATCGTATCACT
49954411 TTTCTTCTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 18 0.56
38 14 0.44
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.24
Consensus pattern (38 bp):
ATACGACTCCACTCTCCCCGAGGAGGATCGTATCACTA
Found at i:49957076 original size:11 final size:11
Alignment explanation
Indices: 49957062--49957162 Score: 70
Period size: 12 Copynumber: 9.2 Consensus size: 11
49957052 TCAAGTAAGT
49957062 TTCAAAAAAAA
1 TTCAAAAAAAA
49957073 TTC-AAAAAAA
1 TTCAAAAAAAA
49957083 TTCAAAAAAAA
1 TTCAAAAAAAA
49957094 GTTTCAAATAAAAA
1 --TTCAAA-AAAAA
*
49957108 TAT-GAAAAAAA
1 T-TCAAAAAAAA
*
49957119 TT--AAAAAAG
1 TTCAAAAAAAA
49957128 TT--AAAAAAA
1 TTCAAAAAAAA
*
49957137 TTTAGAAAAAAA
1 TTCA-AAAAAAA
*
49957149 TTAGAAAAAAAA
1 TT-CAAAAAAAA
49957161 TT
1 TT
49957163 TGAACATTGT
Statistics
Matches: 77, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
9 16 0.21
10 11 0.14
11 16 0.21
12 21 0.27
13 8 0.10
14 5 0.06
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:49957081 original size:10 final size:10
Alignment explanation
Indices: 49957066--49957138 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 10
49957056 GTAAGTTTCA
49957066 AAAAAAATTC
1 AAAAAAATTC
49957076 AAAAAAATTC
1 AAAAAAATTC
49957086 AAAAAAAAGTTTC
1 -AAAAAAA--TTC
*
49957099 AAATAAAAATATG
1 -AA-AAAAAT-TC
49957112 AAAAAAATT-
1 AAAAAAATTC
*
49957121 AAAAAAGTT-
1 AAAAAAATTC
49957130 AAAAAAATT
1 AAAAAAATT
49957139 TAGAAAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
9 16 0.29
10 11 0.20
11 13 0.24
12 3 0.05
13 7 0.13
14 5 0.09
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:49957101 original size:34 final size:35
Alignment explanation
Indices: 49957058--49957126 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
49957048 CTCATCAAGT
49957058 AAGTTTCAAA-AAAAAT-TCAAAAAAATTCAAAAAA
1 AAGTTTCAAATAAAAATATCAAAAAAATT-AAAAAA
*
49957092 AAGTTTCAAATAAAAATATGAAAAAAATTAAAAAA
1 AAGTTTCAAATAAAAATATCAAAAAAATTAAAAAA
49957127 GTTAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 10 0.31
35 12 0.38
36 10 0.31
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (35 bp):
AAGTTTCAAATAAAAATATCAAAAAAATTAAAAAA
Found at i:49957145 original size:12 final size:11
Alignment explanation
Indices: 49957066--49957159 Score: 63
Period size: 11 Copynumber: 8.6 Consensus size: 11
49957056 GTAAGTTTCA
*
49957066 AAAAAAATT-C
1 AAAAAAATTAG
49957076 AAAAAAATTCA-
1 AAAAAAATT-AG
**
49957087 AAAAAAAGTTTC
1 AAAAAAA-TTAG
*
49957099 AAATAAAAATATG
1 AAA-AAAATTA-G
49957112 AAAAAAATT--
1 AAAAAAATTAG
*
49957121 AAAAAAGTTA-
1 AAAAAAATTAG
*
49957131 AAAAAATTTAG
1 AAAAAAATTAG
49957142 AAAAAAATTAG
1 AAAAAAATTAG
49957153 AAAAAAA
1 AAAAAAA
49957160 ATTTGAACAT
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
9 8 0.12
10 18 0.26
11 24 0.35
12 11 0.16
13 7 0.10
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.20
Consensus pattern (11 bp):
AAAAAAATTAG
Found at i:49957158 original size:10 final size:9
Alignment explanation
Indices: 49957102--49957158 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
49957092 AAGTTTCAAA
*
49957102 TAAAAATAT
1 TAAAAAAAT
*
49957111 GAAAAAAAT
1 TAAAAAAAT
*
49957120 TAAAAAAGT
1 TAAAAAAAT
49957129 TAAAAAAATT
1 TAAAAAAA-T
49957139 TAGAAAAAAAT
1 T--AAAAAAAT
49957150 TAGAAAAAA
1 TA-AAAAAA
49957159 AATTTGAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 22 0.56
10 8 0.21
11 2 0.05
12 7 0.18
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:49960303 original size:21 final size:20
Alignment explanation
Indices: 49960269--49960318 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
49960259 ACATTCTTGT
49960269 AAAGAGAAAACAAAGAAAAG-A
1 AAAGA-AAAACAAA-AAAAGAA
*
49960290 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAA-CAAAAAAAGAA
49960311 AAAGAAAA
1 AAAGAAAA
49960319 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAGAAAAACAAAAAAAGAA
Found at i:49960311 original size:15 final size:14
Alignment explanation
Indices: 49960280--49960333 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 14
49960270 AAGAGAAAAC
49960280 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
49960296 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
49960311 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
49960327 AAAGAAA
1 AAAGAAA
49960334 GAGAGGCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 4 0.12
15 10 0.29
16 15 0.44
17 5 0.15
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:49960335 original size:26 final size:26
Alignment explanation
Indices: 49960275--49960335 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
49960265 TTGTAAAGAG
*
49960275 AAAACAAAG-AAAAGAAAAGAAAAAGC
1 AAAAGAAAGAAAAAGAAAAGAAAAA-C
*
49960301 AAAAG-AAGAAAAAGAAAATGAAATA-
1 AAAAGAAAGAAAAAGAAAA-GAAAAAC
49960326 AAAAGAAAGA
1 AAAAGAAAGA
49960336 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 8 0.27
26 17 0.57
27 5 0.17
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (26 bp):
AAAAGAAAGAAAAAGAAAAGAAAAAC
Found at i:49960438 original size:30 final size:30
Alignment explanation
Indices: 49960404--49960485 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
49960394 TTTGAAAAGC
*
49960404 AAAAAGAAAATGAAAATGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAA-GAAATATGAGAGTG
* * *
49960434 AAAAAGAGAACGAAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAGAAATATGAGAGTG
*
49960464 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATG-AAAAGAAAT
49960486 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 4 0.09
30 30 0.70
31 9 0.21
ACGTcount: A:0.63, C:0.01, G:0.22, T:0.13
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAGAAATATGAGAGTG
Found at i:49964728 original size:13 final size:14
Alignment explanation
Indices: 49964710--49964744 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
49964700 GGCTGAACCT
49964710 ACATAATTAAATA-
1 ACATAATTAAATAG
49964723 ACATAATTAAATAG
1 ACATAATTAAATAG
49964737 A-ATAATTA
1 ACATAATTA
49964745 TTCATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 20 0.95
14 1 0.05
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (14 bp):
ACATAATTAAATAG
Found at i:49964986 original size:21 final size:21
Alignment explanation
Indices: 49964962--49965002 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
49964952 GTAAAAGAAA
*
49964962 TGAGCTAAAACGAGCTAAATT
1 TGAGCTAAAACAAGCTAAATT
* *
49964983 TGAGCTCAAGCAAGCTAAAT
1 TGAGCTAAAACAAGCTAAAT
49965003 CGAGCTCAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (21 bp):
TGAGCTAAAACAAGCTAAATT
Found at i:49965009 original size:20 final size:21
Alignment explanation
Indices: 49964974--49965018 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
49964964 AGCTAAAACG
*
49964974 AGCTAAATTTGAGCTCAAGCA
1 AGCTAAATTCGAGCTCAAGCA
*
49964995 AGCTAAA-TCGAGCTCAAGCG
1 AGCTAAATTCGAGCTCAAGCA
49965015 AGCT
1 AGCT
49965019 GATTAGAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (21 bp):
AGCTAAATTCGAGCTCAAGCA
Found at i:49965027 original size:20 final size:20
Alignment explanation
Indices: 49964974--49965028 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
49964964 AGCTAAAACG
*
49964974 AGCTAAATTTGAGCTCAAGCA
1 AGCTAAA-TAGAGCTCAAGCA
* *
49964995 AGCTAAATCGAGCTCAAGCG
1 AGCTAAATAGAGCTCAAGCA
* *
49965015 AGCTGATTAGAGCT
1 AGCTAAATAGAGCT
49965029 GAATGACGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (20 bp):
AGCTAAATAGAGCTCAAGCA
Found at i:49967701 original size:17 final size:17
Alignment explanation
Indices: 49967681--49967718 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
49967671 CATATTAATA
49967681 ACAAATATTAATATAAG
1 ACAAATATTAATATAAG
49967698 ACAAATATTAATATAAG
1 ACAAATATTAATATAAG
49967715 ACAA
1 ACAA
49967719 GTTTAATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (17 bp):
ACAAATATTAATATAAG
Found at i:49967876 original size:30 final size:30
Alignment explanation
Indices: 49967791--49967887 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
49967781 TAAACTAAAA
* * *
49967791 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
* * * * *
49967821 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
49967851 TGAGCTAAGGTTTAGCTCGTAAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
49967880 ATGAGCTA
1 -TGAGCTA
49967888 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTAAGCTGAAGT
Found at i:49968585 original size:179 final size:179
Alignment explanation
Indices: 49968285--49968642 Score: 560
Period size: 179 Copynumber: 2.0 Consensus size: 179
49968275 CACGGAGTCT
* * *
49968285 TCAAGGCATTGTCCTTAGCTCCTCCAACGTCATGAACCTTGTTGTGATCCCAAATGCGTAACACC
1 TCAAGGCATTGTCCTTAGCTCCTCCAACGTCATGAACCTTGTTATCATCCCAAATGCGCAACACC
* * *
49968350 AATGCGGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCGATTCATGGGGCCTTTTGGAAGCTC
66 AAGGCGGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCAAGTCATGGGGCCTTTTGGAAGCTC
*
49968415 GATT-GATTCATGATTTGCATTCGAGGATGCCCCAGGCGTGCTCACATCA
131 AATTAG-TTCATGATTTGCATTCGAGGATGCCCCAGGCGTGCTCACATCA
*
49968464 TCAAGGCATTGTCCTTAGCTCGC-CCAACGT-ATTGGACCTTGTTATCATCCCAAATGCGCAACA
1 TCAAGGCATTGTCCTTAGCTC-CTCCAACGTCA-TGAACCTTGTTATCATCCCAAATGCGCAACA
* *
49968527 CCAAGGCTGATAAAGCATCTTGAATTTGCTTGGTTCGAGCTCAAGTCATGGGGCCTTTTGGAAGC
64 CCAAGGCGGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCAAGTCATGGGGCCTTTTGGAAGC
* *
49968592 TCAATTAGTTCTTGATTTGCATTCGAGGATGCCCCGGGCGTGCTCACATCA
129 TCAATTAGTTCATGATTTGCATTCGAGGATGCCCCAGGCGTGCTCACATCA
49968643 CCTACCTAAT
Statistics
Matches: 164, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
178 1 0.01
179 161 0.98
180 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (179 bp):
TCAAGGCATTGTCCTTAGCTCCTCCAACGTCATGAACCTTGTTATCATCCCAAATGCGCAACACC
AAGGCGGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCAAGTCATGGGGCCTTTTGGAAGCTC
AATTAGTTCATGATTTGCATTCGAGGATGCCCCAGGCGTGCTCACATCA
Done.