Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 39 of 91
Found at i:13461210 original size:26 final size:26
Alignment explanation
Indices: 13461181--13461239 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
13461171 ATTTTCTAGT
* *
13461181 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
13461207 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
13461233 TTTCCTT
1 TTTCCTT
13461240 ATGGCCAGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:13468857 original size:26 final size:26
Alignment explanation
Indices: 13468828--13468886 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
13468818 ATTTTCTAGT
* *
13468828 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
13468854 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
13468880 TTTCCTT
1 TTTCCTT
13468887 ATTGCCGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:13470014 original size:38 final size:40
Alignment explanation
Indices: 13469972--13470074 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 40
13469962 ATAGTGCCCG
* *
13469972 TGTGCATGATGTGGGGGGATGTACACGAT-G-ACACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGTAC-CGGATA
* * *
13470010 TGTGCACGATGTGGGGGGATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTACCGGATA
13470050 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
13470075 TGAGCGGGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
38 27 0.48
39 4 0.07
40 25 0.45
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTACCGGATA
Found at i:13471723 original size:29 final size:29
Alignment explanation
Indices: 13471653--13471733 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
13471643 AGAATTATAT
* *
13471653 CATTGATCGGAGTAAACTCCCTATGGTGGG
1 CATTGCTCGGAGTAATCTCCC-ATGGTGGG
* * *
13471683 CATCT-CTTGGAGTAATCTCCCATTGTTGG
1 CAT-TGCTCGGAGTAATCTCCCATGGTGGG
13471712 CATTGCTCGGAGTAATCTCCCA
1 CATTGCTCGGAGTAATCTCCCA
13471734 AAGGGCAGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.02
29 25 0.58
30 16 0.37
31 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (29 bp):
CATTGCTCGGAGTAATCTCCCATGGTGGG
Found at i:13474963 original size:2 final size:2
Alignment explanation
Indices: 13474956--13474984 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13474946 NNNNNNNNNN
13474956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13474985 CAATCATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13475085 original size:42 final size:41
Alignment explanation
Indices: 13475032--13475142 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 41
13475022 TATGCAACAG
*
13475032 CTTATGCGCACTACCACTCGCACATAGCCT-GGTCAGCAACGA
1 CTTATGTGCACT-CCACTCGCACATAG-CTAGGTCAGCAACGA
* * *
13475074 CTTATGTGCACTCCCACTGGCATATAGCTAGGTCAGCAACGT
1 CTTATGTGCACT-CCACTCGCACATAGCTAGGTCAGCAACGA
*
13475116 CTTATGTGCACTCTTACTCGCACATAG
1 CTTATGTGCACTC-CACTCGCACATAG
13475143 TCGGGTCCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 3 0.05
42 56 0.95
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (41 bp):
CTTATGTGCACTCCACTCGCACATAGCTAGGTCAGCAACGA
Found at i:13478819 original size:21 final size:21
Alignment explanation
Indices: 13478785--13478839 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
13478775 CTCTTTAATT
*
13478785 TATCGATGCATTTTGACAATG
1 TATCGATACATTTTGACAATG
*
13478806 TATTGATACATTTTGACAATG
1 TATCGATACATTTTGACAATG
13478827 TATCGATACATTT
1 TATCGATACATTT
13478840 CAAGCAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (21 bp):
TATCGATACATTTTGACAATG
Found at i:13480278 original size:35 final size:35
Alignment explanation
Indices: 13480209--13480280 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
13480199 CCCCCAGCTT
* * *
13480209 ATGTTCACTCCTACACCGCACATAGCTAGGTCATC
1 ATGTGCACTCCTACACCGCACATAGCAAGATCATC
*
13480244 ATGTGCACTCCTACACCGCACATTA-CAATATCATC
1 ATGTGCACTCCTACACCGCACA-TAGCAAGATCATC
13480279 AT
1 AT
13480281 CAGCATCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 30 0.94
36 2 0.06
ACGTcount: A:0.29, C:0.33, G:0.11, T:0.26
Consensus pattern (35 bp):
ATGTGCACTCCTACACCGCACATAGCAAGATCATC
Found at i:13480304 original size:44 final size:42
Alignment explanation
Indices: 13480240--13480348 Score: 116
Period size: 44 Copynumber: 2.6 Consensus size: 42
13480230 ATAGCTAGGT
* * *
13480240 CATCATGTGCACTCCTACACCGCACATTACAATATCATCATCAG
1 CATCATGTGCTCTCCCACACCGCACATGAC-ATAT-ATCATCAG
* * *
13480284 CATCATGTGCTTTCCCACACCTCACATGGCATATATCATCAG
1 CATCATGTGCTCTCCCACACCGCACATGACATATATCATCAG
*
13480326 ---CGTGTGCTCTCCCACACCGCACA
1 CATCATGTGCTCTCCCACACCGCACA
13480349 CTACCGGCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
39 20 0.36
42 8 0.14
43 4 0.07
44 24 0.43
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.25
Consensus pattern (42 bp):
CATCATGTGCTCTCCCACACCGCACATGACATATATCATCAG
Found at i:13482220 original size:20 final size:20
Alignment explanation
Indices: 13482183--13482225 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
13482173 GATATAAATA
*
13482183 TCTAATTTCCAGCAGCTTCT
1 TCTAACTTCCAGCAGCTTCT
* *
13482203 TCTAACTTCTAGCGGCTTCT
1 TCTAACTTCCAGCAGCTTCT
13482223 TCT
1 TCT
13482226 TCTTCCTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.12, T:0.42
Consensus pattern (20 bp):
TCTAACTTCCAGCAGCTTCT
Found at i:13482558 original size:70 final size:68
Alignment explanation
Indices: 13482446--13482583 Score: 222
Period size: 70 Copynumber: 2.0 Consensus size: 68
13482436 TAGTGGACGT
* * *
13482446 AGCCCACTAAGCCCAAGCAAGCCTCTTTACGTAATCTCGTTCACCATCCCTTCAATTTTTCATCA
1 AGCCCACTAAGCCCAAGCAAGCCTCTTTACGTAACCCCGTTCACCATCCCATCAATTTTTCATCA
13482511 CCA
66 CCA
*
13482514 NAGCCCACTAAAGCCCAAGCAAGCCTCTTTACGTAACCCCGTTCACTATCCCATCAATTTTTCAT
1 -AGCCCACT-AAGCCCAAGCAAGCCTCTTTACGTAACCCCGTTCACCATCCCATCAATTTTTCAT
13482579 CACCA
64 CACCA
13482584 TTACTAGACC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 8 0.12
70 56 0.88
ACGTcount: A:0.28, C:0.37, G:0.09, T:0.26
Consensus pattern (68 bp):
AGCCCACTAAGCCCAAGCAAGCCTCTTTACGTAACCCCGTTCACCATCCCATCAATTTTTCATCA
CCA
Found at i:13483746 original size:38 final size:38
Alignment explanation
Indices: 13483686--13483761 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
13483676 CACACTCAGC
*
13483686 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
1 TCATGTCCACTCCCTACACGCACAAGGCAATATCATCA
* * ***
13483724 TCATGTCCACTCCTTACTCGCACATTTCAATATCATCA
1 TCATGTCCACTCCCTACACGCACAAGGCAATATCATCA
13483762 CACACACTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.28
Consensus pattern (38 bp):
TCATGTCCACTCCCTACACGCACAAGGCAATATCATCA
Found at i:13485428 original size:42 final size:43
Alignment explanation
Indices: 13485341--13485471 Score: 133
Period size: 43 Copynumber: 3.1 Consensus size: 43
13485331 GTAATTATAT
* ** *
13485341 TGACTCAGCTATGTGCGAGTAAAGAGTGAGCATAAGCC-GAG-GA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAA-CCTG-GTGA
*
13485384 TGACCC-GGTATGTGCGAGTAGGGAGTGCGCATAACCTGGTGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACCTGGTGA
* * * * *
13485426 TGACCCAGCCATGTGTGAATAGGGAGTGCGCATGAGCTGGTGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACCTGGTGA
13485469 TGA
1 TGA
13485472 TGATGATGGG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.04
42 33 0.45
43 38 0.51
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.21
Consensus pattern (43 bp):
TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACCTGGTGA
Found at i:13487302 original size:22 final size:21
Alignment explanation
Indices: 13487277--13487317 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
13487267 AGGAAGAAGA
*
13487277 AGAAGAAGCTGCTGGAAAAATG
1 AGAAGAAGCTACT-GAAAAATG
13487299 AGAAGAAGCTACTGAAAAA
1 AGAAGAAGCTACTGAAAAA
13487318 CGATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.51, C:0.10, G:0.27, T:0.12
Consensus pattern (21 bp):
AGAAGAAGCTACTGAAAAATG
Found at i:13489291 original size:42 final size:42
Alignment explanation
Indices: 13489245--13489327 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
13489235 ACTCTGTCTT
13489245 AGCTTATGTGCACTACC-ACACCGCACATGGCTGGGTCAGCAC
1 AGCTTATGTGCACT-CCTACACCGCACATGGCTGGGTCAGCAC
13489287 AGCTTATGTGCACTCCTACACCGCACATGGCTGGGTCAGCA
1 AGCTTATGTGCACTCCTACACCGCACATGGCTGGGTCAGCA
13489328 TTATCACACA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 2 0.05
42 38 0.95
ACGTcount: A:0.23, C:0.33, G:0.24, T:0.20
Consensus pattern (42 bp):
AGCTTATGTGCACTCCTACACCGCACATGGCTGGGTCAGCAC
Found at i:13490659 original size:10 final size:10
Alignment explanation
Indices: 13490644--13490668 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13490634 AAGGAGTTGC
13490644 TGGAAGCTGG
1 TGGAAGCTGG
13490654 TGGAAGCTGG
1 TGGAAGCTGG
13490664 TGGAA
1 TGGAA
13490669 AAAAAGTGAG
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:0.24, C:0.08, G:0.48, T:0.20
Consensus pattern (10 bp):
TGGAAGCTGG
Found at i:13513743 original size:27 final size:28
Alignment explanation
Indices: 13513713--13514015 Score: 266
Period size: 27 Copynumber: 11.2 Consensus size: 28
13513703 TTGTTTAACA
* **
13513713 CCATGTTGAAAAATGTAG-TATTACATT
1 CCATGTTGAAAAATGTAGTTGTTACACG
** * *
13513740 CCATGTTCTAAAATTTAGTTGTTACACA
1 CCATGTTGAAAAATGTAGTTGTTACACG
* *
13513768 CCATGTTG-GAAA--TAATTGTTACACG
1 CCATGTTGAAAAATGTAGTTGTTACACG
13513793 CCATGTTG-AAAATGTAGTTGTTACACG
1 CCATGTTGAAAAATGTAGTTGTTACACG
* *
13513820 CCATGTTGAAAAATGTAGTTATTACACA
1 CCATGTTGAAAAATGTAGTTGTTACACG
* * *
13513848 TCATGTTG-AAAATTTAGTTGTTACATG
1 CCATGTTGAAAAATGTAGTTGTTACACG
* * * *
13513875 CCTTGTTGAAAAATTTAATTG-TACACA
1 CCATGTTGAAAAATGTAGTTGTTACACG
* *
13513902 CCATGTT-AAAGATTTAGTTGTTACACG
1 CCATGTTGAAAAATGTAGTTGTTACACG
* * * *
13513929 CTATGTTG-AAGATTTAGTTGTTACATG
1 CCATGTTGAAAAATGTAGTTGTTACACG
* * *
13513956 CCATTTTGAAAAATATAGTTGTTACACA
1 CCATGTTGAAAAATGTAGTTGTTACACG
* * *
13513984 CCATGTTG-AAGATTTAGTTGTTACATG
1 CCATGTTGAAAAATGTAGTTGTTACACG
13514011 CCATG
1 CCATG
13514016 ATGATAAAGT
Statistics
Matches: 227, Mismatches: 41, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
25 22 0.10
26 11 0.05
27 124 0.55
28 70 0.31
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (28 bp):
CCATGTTGAAAAATGTAGTTGTTACACG
Found at i:13513959 original size:136 final size:135
Alignment explanation
Indices: 13513710--13514015 Score: 393
Period size: 136 Copynumber: 2.3 Consensus size: 135
13513700 ATCTTGTTTA
* * * * *
13513710 ACACCATGTTGAAAAATGTAG-TATTACATTCCATGTTCTAAAATTTAGTTGTTACACACCATGT
1 ACACCATGTTG-AAAATTTAGTTGTTACATGCCATGTTCAAAAATTTAATTGTTACACACCATGT
* *
13513774 TGGAAATAATTGTTACACGCCATGTTGAAAATGTAGTTGTTACACGCCATGTTGAAAAATGTAGT
65 TGAAAATAATTGTTACACGCCATGTTGAAAATGTAGTTGTTACACGCCATGTTGAAAAATATAGT
13513839 TATTAC
130 TATTAC
* * *
13513845 ACATCATGTTGAAAATTTAGTTGTTACATGCCTTGTTGAAAAATTTAATTG-TACACACCATGTT
1 ACACCATGTTGAAAATTTAGTTGTTACATGCCATGTTCAAAAATTTAATTGTTACACACCATGTT
* * * * * *
13513909 -AAAGATTTAGTTGTTACACGCTATGTTGAAGATTTAGTTGTTACATGCCATTTTGAAAAATATA
66 GAAA-A--TAATTGTTACACGCCATGTTGAAAATGTAGTTGTTACACGCCATGTTGAAAAATATA
*
13513973 GTTGTTAC
128 GTTATTAC
*
13513981 ACACCATGTTGAAGATTTAGTTGTTACATGCCATG
1 ACACCATGTTGAAAATTTAGTTGTTACATGCCATG
13514016 ATGATAAAGT
Statistics
Matches: 147, Mismatches: 20, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
133 2 0.01
134 22 0.15
135 34 0.23
136 89 0.61
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (135 bp):
ACACCATGTTGAAAATTTAGTTGTTACATGCCATGTTCAAAAATTTAATTGTTACACACCATGTT
GAAAATAATTGTTACACGCCATGTTGAAAATGTAGTTGTTACACGCCATGTTGAAAAATATAGTT
ATTAC
Found at i:13513994 original size:55 final size:54
Alignment explanation
Indices: 13513713--13514037 Score: 297
Period size: 55 Copynumber: 6.1 Consensus size: 54
13513703 TTGTTTAACA
* * ** * *
13513713 CCATGTTGAAAAATGTAG-TATTACATTCCATGTTCTAAAATTTAGTTGTTACACA
1 CCATGTTG-AAAATTTAGTTGTTACACGCCATGTT-GAAAATTTAGTTGTTACACG
* * *
13513768 CCATGTTGGAAA--TAATTGTTACACGCCATGTTGAAAATGTAGTTGTTACACG
1 CCATGTTGAAAATTTAGTTGTTACACGCCATGTTGAAAATTTAGTTGTTACACG
* * ** *
13513820 CCATGTTGAAAAATGTAGTTATTACACATCATGTTGAAAATTTAGTTGTTACATG
1 CCATGTTG-AAAATTTAGTTGTTACACGCCATGTTGAAAATTTAGTTGTTACACG
* * *
13513875 CCTTGTTGAAAAATTTAATTG-TACACACCATGTT-AAAGATTTAGTTGTTACACG
1 CCATGTTG-AAAATTTAGTTGTTACACGCCATGTTGAAA-ATTTAGTTGTTACACG
* * * * * *
13513929 CTATGTTGAAGATTTAGTTGTTACATGCCATTTTGAAAAATATAGTTGTTACACA
1 CCATGTTGAAAATTTAGTTGTTACACGCCATGTTG-AAAATTTAGTTGTTACACG
* * * *
13513984 CCATGTTGAAGATTTAGTTGTTACATGCCATGATGATAA---AGTTGTTACACG
1 CCATGTTGAAAATTTAGTTGTTACACGCCATGTTGAAAATTTAGTTGTTACACG
13514035 CCA
1 CCA
13514038 CGCCATGTTG
Statistics
Matches: 227, Mismatches: 35, Indels: 20
0.80 0.12 0.07
Matches are distributed among these distances:
51 14 0.06
52 27 0.12
53 29 0.13
54 49 0.22
55 105 0.46
56 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (54 bp):
CCATGTTGAAAATTTAGTTGTTACACGCCATGTTGAAAATTTAGTTGTTACACG
Found at i:13518329 original size:2 final size:2
Alignment explanation
Indices: 13518310--13518371 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
13518300 GAGTTGACAA
* **
13518310 AT AT AT AC AT AT GC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13518352 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
13518372 TGAACTATCA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13525080 original size:15 final size:14
Alignment explanation
Indices: 13525043--13525088 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
13525033 ACCAAGCTTG
*
13525043 TTCTTCCTTTCTCT
1 TTCTTTCTTTCTCT
13525057 TGT-TTTCTTTCTCCT
1 T-TCTTTCTTTCT-CT
13525072 TTCTTTCTTTC-CT
1 TTCTTTCTTTCTCT
13525085 TTCT
1 TTCT
13525089 CCTTTCTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 6 0.21
14 10 0.36
15 12 0.43
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.67
Consensus pattern (14 bp):
TTCTTTCTTTCTCT
Found at i:13525088 original size:20 final size:20
Alignment explanation
Indices: 13525047--13525096 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
13525037 AGCTTGTTCT
* *
13525047 TCCTTTCTCTTGTTTTCTTTC
1 TCCTTTCT-TTCTTTCCTTTC
13525068 TCCTTTCTTTCTTTCCTTTC
1 TCCTTTCTTTCTTTCCTTTC
13525088 TCCTTTCTT
1 TCCTTTCTT
13525097 CCAACTGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (20 bp):
TCCTTTCTTTCTTTCCTTTC
Found at i:13533061 original size:18 final size:18
Alignment explanation
Indices: 13533038--13533072 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13533028 AACCAAAATT
13533038 ATTTCTTAGC-TTTTAAAA
1 ATTTC-TAGCATTTTAAAA
13533056 ATTTCTAGCATTTTAAA
1 ATTTCTAGCATTTTAAA
13533073 CTAGGCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (18 bp):
ATTTCTAGCATTTTAAAA
Found at i:13538353 original size:2 final size:2
Alignment explanation
Indices: 13538346--13538375 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13538336 CATTATGATG
13538346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13538376 GTTGTGCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13538469 original size:38 final size:40
Alignment explanation
Indices: 13538427--13538529 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 40
13538417 ATAGTGCTCG
* * *
13538427 TGTGCACGATGCGGGGGGATGTACACGATGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGCACACGATGGCGACAGATA
* * * *
13538465 TGTGCACGATGTGGGAGGATGCACATGATGGCGGCAGCTA
1 TGTGCACGATGTGGGGGGATGCACACGATGGCGACAGATA
13538505 TGTGCACGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
13538530 TGAGCTGAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 28 0.51
39 3 0.05
40 24 0.44
ACGTcount: A:0.21, C:0.17, G:0.41, T:0.20
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACACGATGGCGACAGATA
Found at i:13539168 original size:22 final size:22
Alignment explanation
Indices: 13539140--13539184 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
13539130 GATTGATCAT
*
13539140 GGGTTTGTGAAACACTATGAGG
1 GGGTTTGTGAAAAACTATGAGG
13539162 GGGTTTGTGAAAAACTATGAGG
1 GGGTTTGTGAAAAACTATGAGG
13539184 G
1 G
13539185 CATTAATCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.07, G:0.38, T:0.27
Consensus pattern (22 bp):
GGGTTTGTGAAAAACTATGAGG
Found at i:13542873 original size:56 final size:56
Alignment explanation
Indices: 13542811--13542927 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
13542801 TATTTCCTTA
* * *
13542811 GCCACCCTCATGAGCCAATCAAATCACATGCATTCTTATTCTTCTTATTTCATTTG
1 GCCACCCTCATGAACCAATCAAAACACATGCATTCTTATTCTTCTCATTTCATTTG
13542867 GCCACCCTCATGAACCAATCAAAACACATGCATTCTTATTCTTCTCATTTCATTTG
1 GCCACCCTCATGAACCAATCAAAACACATGCATTCTTATTCTTCTCATTTCATTTG
13542923 GCCAC
1 GCCAC
13542928 TTTGCCATCT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (56 bp):
GCCACCCTCATGAACCAATCAAAACACATGCATTCTTATTCTTCTCATTTCATTTG
Found at i:13546622 original size:22 final size:23
Alignment explanation
Indices: 13546565--13546622 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
13546555 TGCTCCAAAC
13546565 TTGCATTTTAAATAATTTAACAA
1 TTGCATTTTAAATAATTTAACAA
*
13546588 TTGGATTTTAAATAATTTAACAA
1 TTGCATTTTAAATAATTTAACAA
13546611 TTGCA-TTTAAAT
1 TTGCATTTTAAAT
13546623 TATGCATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 7 0.21
23 26 0.79
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (23 bp):
TTGCATTTTAAATAATTTAACAA
Found at i:13547706 original size:20 final size:21
Alignment explanation
Indices: 13547664--13547718 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
13547654 AACGAAGCTT
*
13547664 TTTCTTCCTTTCTCTCTTTTCC
1 TTTC-TCCTTTCTTTCTTTTCC
13547686 TTTCTCCTTTCTTTC-TTTCC
1 TTTCTCCTTTCTTTCTTTTCC
*
13547706 TTTCTTCTTTCTT
1 TTTCTCCTTTCTT
13547719 CCAACTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 17 0.55
21 10 0.32
22 4 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTCTCCTTTCTTTCTTTTCC
Found at i:13547831 original size:19 final size:19
Alignment explanation
Indices: 13547807--13547843 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13547797 GGTGGCAAGG
13547807 TGAAAATGGCATGGAAGCT
1 TGAAAATGGCATGGAAGCT
*
13547826 TGAAAATGGCGTGGAAGC
1 TGAAAATGGCATGGAAGC
13547844 ATAAAGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.11, G:0.35, T:0.19
Consensus pattern (19 bp):
TGAAAATGGCATGGAAGCT
Found at i:13549480 original size:4 final size:4
Alignment explanation
Indices: 13549471--13549538 Score: 100
Period size: 4 Copynumber: 17.0 Consensus size: 4
13549461 NNNNNNNNNN
*
13549471 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
13549519 ACAT ATAT ACAT ACAT ATAT
1 ATAT ATAT ATAT ATAT ATAT
13549539 GGTAAATGGT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:13551881 original size:20 final size:20
Alignment explanation
Indices: 13551858--13551902 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
13551848 AGGAAAGGAA
13551858 GAAAAGAGAAAAACCAAAGG
1 GAAAAGAGAAAAACCAAAGG
** *
13551878 GAAACTAGAAAAATCAAAGG
1 GAAAAGAGAAAAACCAAAGG
13551898 GAAAA
1 GAAAA
13551903 TCGTGTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.09, G:0.22, T:0.04
Consensus pattern (20 bp):
GAAAAGAGAAAAACCAAAGG
Found at i:13565145 original size:27 final size:30
Alignment explanation
Indices: 13565097--13565151 Score: 89
Period size: 27 Copynumber: 1.9 Consensus size: 30
13565087 ATGTGTCGTT
13565097 CACTCCTCTCTTTTTTTCAGCCGTTTTCCA
1 CACTCCTCTCTTTTTTTCAGCCGTTTTCCA
13565127 CACTCCT-T-TTTTTTT-AGCCGTTTTC
1 CACTCCTCTCTTTTTTTCAGCCGTTTTC
13565152 ACTCTCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 10 0.40
28 7 0.28
29 1 0.04
30 7 0.28
ACGTcount: A:0.09, C:0.33, G:0.07, T:0.51
Consensus pattern (30 bp):
CACTCCTCTCTTTTTTTCAGCCGTTTTCCA
Found at i:13565343 original size:35 final size:35
Alignment explanation
Indices: 13565304--13565557 Score: 255
Period size: 35 Copynumber: 7.3 Consensus size: 35
13565294 TTAATTGTTT
* * *
13565304 AATTTAATCGATTAGGCCTAAAAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
13565339 AATTTAATTAATTAAGCCCAACAATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
*
13565374 AATTTTAATCAATTAGGCCCAATGACTTAATTAAAC
1 AA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * ****
13565410 AAATTTAATCAATTATGCCCTATAACTTAATTGTTT
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
13565446 AATTT-ATTAATTAGGCCCAATGACTTAATTAAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* *
13565480 AATTTAATTAATTAGGTCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
13565515 AATTTAGTTAATTAGG--C-ACAACTTAATTAAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
13565547 AATTTAATCAA
1 AATTTAATCAA
13565558 GTGCTTGAGA
Statistics
Matches: 183, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
32 22 0.12
33 1 0.01
34 27 0.15
35 77 0.42
36 54 0.30
37 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:13565474 original size:141 final size:137
Alignment explanation
Indices: 13565290--13565557 Score: 358
Period size: 141 Copynumber: 1.9 Consensus size: 137
13565280 GAAGCCCAAT
* *
13565290 TAACTTAATTGTTTAATTTAATCGATTAGGCCTAAAAACTTAATTAAACAATTTAATTAATTAAG
1 TAACTTAATTGTTTAATTTAATCAATTAGGCCCAAAAACTTAATTAAACAATTTAATTAATTAAG
* *
13565355 CCCAACAATTTAATTAAACAATTTTAATCAATTAGGCCCAATGACTTAATTAAACAAATTTAATC
66 CCCAACAACTTAATTAAACAA-TTTAATCAATTAGGCAC-A--ACTTAATTAAA-AAATTTAATC
13565420 AATTATGCCCTA
126 AATTATGCCCTA
* ** * *
13565432 TAACTTAATTGTTTAATTT-ATTAATTAGGCCCAATGACTTAATTAAATAATTTAATTAATTAGG
1 TAACTTAATTGTTTAATTTAATCAATTAGGCCCAAAAACTTAATTAAACAATTTAATTAATTAAG
* * * * *
13565496 TCCAATAACTTAATTAAACAATTTAGTTAATTAGGCACAACTTAATTAAATAATTTAATCAA
66 CCCAACAACTTAATTAAACAATTTAATCAATTAGGCACAACTTAATTAAAAAATTTAATCAA
13565558 GTGCTTGAGA
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
136 11 0.10
137 11 0.10
139 1 0.01
140 14 0.12
141 56 0.50
142 19 0.17
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.38
Consensus pattern (137 bp):
TAACTTAATTGTTTAATTTAATCAATTAGGCCCAAAAACTTAATTAAACAATTTAATTAATTAAG
CCCAACAACTTAATTAAACAATTTAATCAATTAGGCACAACTTAATTAAAAAATTTAATCAATTA
TGCCCTA
Found at i:13572943 original size:41 final size:42
Alignment explanation
Indices: 13572866--13572948 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 42
13572856 GTAATGATAT
* * *
13572866 TGACCCGGCTATGTGCAAGTGGGAGTGCGCATAAGCCGTTGC
1 TGACCAGGCTATGTGCAAGTGGGAGTGCGCACAAGCCATTGC
13572908 TGACCAGGCTATGTGCAAG-GGGAGTGCGCACAAGCCATTGC
1 TGACCAGGCTATGTGCAAGTGGGAGTGCGCACAAGCCATTGC
13572949 ATATGAGCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 20 0.53
42 18 0.47
ACGTcount: A:0.22, C:0.24, G:0.35, T:0.19
Consensus pattern (42 bp):
TGACCAGGCTATGTGCAAGTGGGAGTGCGCACAAGCCATTGC
Found at i:13578424 original size:26 final size:26
Alignment explanation
Indices: 13578368--13578426 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
13578358 GGCCGACCAT
* *
13578368 AAGGAAAGAACAAGAGAGAAAATAGA
1 AAGGAAAGAACAAAAGAGAAAATACA
* *
13578394 GAGGAAAGGAAGAAAAGAGAAAA-ACA
1 AAGGAAA-GAACAAAAGAGAAAATACA
13578420 AAGGAAA
1 AAGGAAA
13578427 ACTAGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.02
Consensus pattern (26 bp):
AAGGAAAGAACAAAAGAGAAAATACA
Found at i:13587982 original size:36 final size:36
Alignment explanation
Indices: 13587920--13587999 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
13587910 TCCAATACTA
* *
13587920 TTTTATCTTAAGACAATAATTATCTTAATAAACATT
1 TTTTATTTTAAGACAATAATTATCTTAAAAAACATT
* * *
13587956 TTTTATTTTAAGACAACT-CTTGTCTTAAAAAATATT
1 TTTTATTTTAAGACAA-TAATTATCTTAAAAAACATT
13587992 TATTTATT
1 T-TTTATT
13588000 AAGAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 30 0.81
37 7 0.19
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTTATTTTAAGACAATAATTATCTTAAAAAACATT
Found at i:13588094 original size:21 final size:21
Alignment explanation
Indices: 13588031--13588158 Score: 85
Period size: 21 Copynumber: 5.6 Consensus size: 21
13588021 AAAATAATGT
*
13588031 AATTAAGACAACTCTTGTCTTA
1 AATTAAGACAATTCTTGTC-TA
** * *
13588053 AAACAACACATATACTCTTGTCGA
1 AATTAAGACA-AT--TCTTGTCTA
*
13588077 AATTAAGACAATTCTTGTCTT
1 AATTAAGACAATTCTTGTCTA
13588098 AATTAAGACAACATATGTACTTTGTCTA
1 AATTAAG---ACA-AT-T-C-TTGTCTA
* *
13588126 AATTAAGACAACTCTTGTCTT
1 AATTAAGACAATTCTTGTCTA
13588147 AATTAAGACAAT
1 AATTAAGACAAT
13588159 ATCTAAAGTT
Statistics
Matches: 82, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
21 31 0.38
22 8 0.10
23 4 0.05
24 12 0.15
25 12 0.15
26 1 0.01
27 1 0.01
28 13 0.16
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (21 bp):
AATTAAGACAATTCTTGTCTA
Found at i:13588133 original size:49 final size:50
Alignment explanation
Indices: 13588031--13588157 Score: 183
Period size: 49 Copynumber: 2.6 Consensus size: 50
13588021 AAAATAATGT
13588031 AATTAAGACAACTCTTGTCTT-A--AA-ACAACACATATACTCTTGTCGA
1 AATTAAGACAACTCTTGTCTTAATTAAGACAACACATATACTCTTGTCGA
* * * *
13588077 AATTAAGACAATTCTTGTCTTAATTAAGACAACATATGTACT-TTGTCTA
1 AATTAAGACAACTCTTGTCTTAATTAAGACAACACATATACTCTTGTCGA
13588126 AATTAAGACAACTCTTGTCTTAATTAAGACAA
1 AATTAAGACAACTCTTGTCTTAATTAAGACAA
13588158 TATCTAAAGT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
46 20 0.28
47 1 0.01
49 39 0.54
50 12 0.17
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (50 bp):
AATTAAGACAACTCTTGTCTTAATTAAGACAACACATATACTCTTGTCGA
Found at i:13593056 original size:18 final size:18
Alignment explanation
Indices: 13593035--13593069 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13593025 TCGCTTGTTC
13593035 TAGTTGTTCCATGTGAAG
1 TAGTTGTTCCATGTGAAG
13593053 TAGTTGTTCCATGTGAA
1 TAGTTGTTCCATGTGAA
13593070 ACAATTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (18 bp):
TAGTTGTTCCATGTGAAG
Found at i:13600134 original size:3 final size:3
Alignment explanation
Indices: 13600126--13600153 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13600116 ACTTAGACCT
13600126 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
13600154 GTTAATGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:13601106 original size:71 final size:71
Alignment explanation
Indices: 13601021--13601155 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 71
13601011 TTTAATGGTT
* * *
13601021 GAAAATCATTTGTTCCTAAAGAAAAATGAATTTAAAGCTTGGAA-ATGAGTTGAGAGAGTGAAAA
1 GAAAATCACTTGTTCCTAAAGAAAAATGAATTTAAAGCTTGGAAGA-GAGTTGAAAGACTGAAAA
13601085 GTAGAGG
65 GTAGAGG
* * * *
13601092 GAAAATCACTTGTTCTTGAAGAAAAATGAGTTTGAAGCTTGGAAGAGAGTTGAAAGACTGAAAA
1 GAAAATCACTTGTTCCTAAAGAAAAATGAATTTAAAGCTTGGAAGAGAGTTGAAAGACTGAAAA
13601156 ATAAAGGGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 55 0.98
72 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.25
Consensus pattern (71 bp):
GAAAATCACTTGTTCCTAAAGAAAAATGAATTTAAAGCTTGGAAGAGAGTTGAAAGACTGAAAAG
TAGAGG
Found at i:13606099 original size:43 final size:43
Alignment explanation
Indices: 13606029--13606160 Score: 160
Period size: 43 Copynumber: 3.1 Consensus size: 43
13606019 GTAATTATAT
* * *
13606029 TGACTCAGCTATGTGCAAGTAGGGAGTGCGCATAAGTCAAG-GA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAA-CCAAGTGA
* *
13606072 TGACCC-GATTATGTGCGAGTAGGGAGTGCGCATAACCCAGTGA
1 TGACCCAG-CTATGTGCGAGTAGGGAGTGCGCATAACCAAGTGA
* **
13606115 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACCAAGTGA
13606158 TGA
1 TGA
13606161 TGATGATGGG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
42 4 0.05
43 73 0.94
44 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (43 bp):
TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACCAAGTGA
Found at i:13606602 original size:38 final size:38
Alignment explanation
Indices: 13606541--13606614 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
13606531 ACATTCTCAC
* * *
13606541 TGCAGCGAGAAACTTTCTATTTCTAGGTTGCAATTTGT
1 TGCAGCGAGAAACATTATATTTCTAGGTTACAATTTGT
* *
13606579 TGCAGCGAGAAACATTATGTTTCTGGGTTACAATTT
1 TGCAGCGAGAAACATTATATTTCTAGGTTACAATTT
13606615 CACTGCACCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (38 bp):
TGCAGCGAGAAACATTATATTTCTAGGTTACAATTTGT
Found at i:13608431 original size:33 final size:33
Alignment explanation
Indices: 13608388--13608456 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
13608378 CTGAGAAAAT
* * *
13608388 TGCATGTTCTAAATATGTTTTGGATTATGCAAA
1 TGCATATTCTAAATATGTTCTAGATTATGCAAA
* *
13608421 TGCATATTCTAAATGTGTTCTAGATTATGCATA
1 TGCATATTCTAAATATGTTCTAGATTATGCAAA
13608454 TGC
1 TGC
13608457 TAAATATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (33 bp):
TGCATATTCTAAATATGTTCTAGATTATGCAAA
Found at i:13614020 original size:80 final size:80
Alignment explanation
Indices: 13613879--13614041 Score: 283
Period size: 80 Copynumber: 2.0 Consensus size: 80
13613869 GGAGTTTTGA
* * *
13613879 TTTGAAATAGGCTAGGCCAACTGGTTGAGGAATTTGTTTGAAGTGAACAGGATTTTTCTGAAGGA
1 TTTGAAATAGGCTAAGCCAACTGGTTGAAGAATTGGTTTGAAGTGAACAGGATTTTTCTGAAGGA
13613944 AAAGTACAACTTTTC
66 AAAGTACAACTTTTC
13613959 TTTGAAATAGGCTAAGCCAACTGGTTGAAGAATTGGTTTGAAGTGAACAGG-TTTTTGCTGAAGG
1 TTTGAAATAGGCTAAGCCAACTGGTTGAAGAATTGGTTTGAAGTGAACAGGATTTTT-CTGAAGG
13614023 AAAAGTACAACTTTTC
65 AAAAGTACAACTTTTC
13614039 TTT
1 TTT
13614042 CTAACTCTAA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
79 5 0.06
80 74 0.94
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (80 bp):
TTTGAAATAGGCTAAGCCAACTGGTTGAAGAATTGGTTTGAAGTGAACAGGATTTTTCTGAAGGA
AAAGTACAACTTTTC
Found at i:13625736 original size:31 final size:32
Alignment explanation
Indices: 13625649--13625749 Score: 161
Period size: 32 Copynumber: 3.2 Consensus size: 32
13625639 AAGCATTAAT
* *
13625649 ATTAATACTTTGTATTAATGCA-GCTCAGCAAC
1 ATTAATGCTTTGTATTAATG-ATGCTTAGCAAC
13625681 ATTAATGCTTTGTATTAATGATGCTTAGCAAC
1 ATTAATGCTTTGTATTAATGATGCTTAGCAAC
13625713 ATTAATGCTTTGTATT-ATGATGCTTAGCAAC
1 ATTAATGCTTTGTATTAATGATGCTTAGCAAC
13625744 ATTAAT
1 ATTAAT
13625750 CCAAAGCATG
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
31 22 0.33
32 44 0.67
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (32 bp):
ATTAATGCTTTGTATTAATGATGCTTAGCAAC
Found at i:13632845 original size:3 final size:3
Alignment explanation
Indices: 13632837--13632862 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13632827 TAAATATAGT
13632837 TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TA
13632863 GAGATAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:13646787 original size:27 final size:27
Alignment explanation
Indices: 13646736--13646787 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
13646726 ATATCCTGGG
*
13646736 GGTGGAAAATTACAATTTTGCCCCTAA
1 GGTGGAAAATTACAATTTTGACCCTAA
*
13646763 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
13646788 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAA
Found at i:13646861 original size:20 final size:20
Alignment explanation
Indices: 13646831--13646876 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
13646821 ACTTTTAAAC
13646831 TCAAATCATACTTC-AATAAG
1 TCAAATCATAC-TCAAATAAG
* *
13646851 TTAAATTATACTCAAATAAG
1 TCAAATCATACTCAAATAAG
13646871 TCAAAT
1 TCAAAT
13646877 GGGGCAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCAAATAAG
Found at i:13649129 original size:30 final size:29
Alignment explanation
Indices: 13649056--13649156 Score: 100
Period size: 30 Copynumber: 3.5 Consensus size: 29
13649046 AAGAAAATTC
* *
13649056 AAATAAGTCCTTATATTTTTATTATG-TT
1 AAATAAGTCTTTATATTTTTATTTTGATT
* *
13649084 CAATCAAGTC--TATATTTGTATTTTGTATT
1 AAAT-AAGTCTTTATATTTTTATTTTG-ATT
*
13649113 AAATAAGTCTTTATATTTTTATTTTGAGTC
1 AAATAAGTCTTTATATTTTTATTTTGA-TT
*
13649143 AAATAAGTATTTAT
1 AAATAAGTCTTTAT
13649157 GATTAATAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
27 13 0.22
28 8 0.13
29 11 0.18
30 28 0.47
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (29 bp):
AAATAAGTCTTTATATTTTTATTTTGATT
Found at i:13649270 original size:33 final size:33
Alignment explanation
Indices: 13649228--13649290 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
13649218 GCATGTTAAC
*
13649228 ATATCATAATTGATGATGATGTGTCATGCTGAG
1 ATATCATAATTGATGATGATGTGACATGCTGAG
13649261 ATATCATAATTGATGATGATGTGACATGCT
1 ATATCATAATTGATGATGATGTGACATGCT
13649291 AATTTGGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATCATAATTGATGATGATGTGACATGCTGAG
Found at i:13650254 original size:30 final size:29
Alignment explanation
Indices: 13650216--13650273 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
13650206 GCCAATGTAC
13650216 TTTTATTTTAAACCAAATAAGTTTTTATA
1 TTTTATTTTAAACCAAATAAGTTTTTATA
* *
13650245 TTTTAATTTTGAATCAAATAAGTTTTTAT
1 TTTT-ATTTTAAACCAAATAAGTTTTTAT
13650274 GACTAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTTATTTTAAACCAAATAAGTTTTTATA
Found at i:13658749 original size:90 final size:90
Alignment explanation
Indices: 13658596--13658774 Score: 290
Period size: 90 Copynumber: 2.0 Consensus size: 90
13658586 TTCATATCAA
* *
13658596 ATAAGGAAAATATTTAACTTCAAAATTTTTTTAAATATTTTATTTATTATATATTTAAAACATTA
1 ATAAGGAAAATATTTAACTTCAAAATTTTTTAAAATATTTTATATATTATATATTTAAAACATTA
13658661 ATTAATA-CAATCATTATGAGAATAG
66 ATTAATATC-ATCATTATGAGAATAG
13658686 ATAAGGAAAATATTTAATCTTCAAAA-TTTTTAAAATATTTTATATATTATATATTTAAAACATT
1 ATAAGGAAAATATTTAA-CTTCAAAATTTTTTAAAATATTTTATATATTATATATTTAAAACATT
* *
13658750 AATTCATATCATTATTATGAGAATA
65 AATTAATATCATCATTATGAGAATA
13658775 CAAATTGTGC
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
90 74 0.89
91 9 0.11
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (90 bp):
ATAAGGAAAATATTTAACTTCAAAATTTTTTAAAATATTTTATATATTATATATTTAAAACATTA
ATTAATATCATCATTATGAGAATAG
Found at i:13661235 original size:21 final size:21
Alignment explanation
Indices: 13661193--13661239 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
13661183 GGAGTCTATC
* *
13661193 TATTGATAGATGGCTCCCATT
1 TATTGATAGATGGATCCAATT
13661214 TATTGATAGAT-GATACCAATT
1 TATTGATAGATGGAT-CCAATT
13661235 T-TTGA
1 TATTGA
13661240 AAAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (21 bp):
TATTGATAGATGGATCCAATT
Found at i:13680425 original size:57 final size:57
Alignment explanation
Indices: 13680356--13680486 Score: 174
Period size: 57 Copynumber: 2.3 Consensus size: 57
13680346 GATATCTCTT
** * * *
13680356 TTAAATTTAAATA-AACTAAATTAAAATGTAGTTAATTCTTATTTAAATTTAATCAAA
1 TTAAATTTAAATATAA-TAAATTAAAACATAGATAATCCTTATTTAAATTTAAACAAA
* **
13680413 TTAAATTTAAATATAATAGATTATTACATAGATAATCCTTATTTAAATTTAAACAAA
1 TTAAATTTAAATATAATAAATTAAAACATAGATAATCCTTATTTAAATTTAAACAAA
13680470 TTAAATTTAAATATAAT
1 TTAAATTTAAATATAAT
13680487 GGATAGATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
57 63 0.97
58 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (57 bp):
TTAAATTTAAATATAATAAATTAAAACATAGATAATCCTTATTTAAATTTAAACAAA
Found at i:13682700 original size:63 final size:63
Alignment explanation
Indices: 13682596--13682753 Score: 235
Period size: 63 Copynumber: 2.5 Consensus size: 63
13682586 ACATCATAGT
* * * * *
13682596 CGGCATGTGCACTTCCCACTCCACACATGCACGATTGTAATTGTCACAACATTTTCATTCAAC
1 CGGCATGTGCACTGCCCACTCCGCACATGCACAATTATAATTGTCACAACATTGTCATTCAAC
* * *
13682659 CGGTATGTGCACTGCCCACTCCGCACATGCACAATTATAATTGTCACAATATTGTCATTTAAC
1 CGGCATGTGCACTGCCCACTCCGCACATGCACAATTATAATTGTCACAACATTGTCATTCAAC
*
13682722 CGGCGTGTGCACTGCCCACTCCGCACATGCAC
1 CGGCATGTGCACTGCCCACTCCGCACATGCAC
13682754 GGTTACATCA
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 85 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (63 bp):
CGGCATGTGCACTGCCCACTCCGCACATGCACAATTATAATTGTCACAACATTGTCATTCAAC
Found at i:13691401 original size:3 final size:3
Alignment explanation
Indices: 13691393--13691420 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13691383 AATAAATATG
13691393 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
13691421 ATATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13691849 original size:124 final size:125
Alignment explanation
Indices: 13691601--13691850 Score: 371
Period size: 125 Copynumber: 2.0 Consensus size: 125
13691591 TATATATATA
* * *
13691601 TAGGTTTGAAGGCTAAAAAATCTAGAAAGGGTAAGAAAACTAAAATTTTCTGTTACAGACTCTAT
1 TAGGTTTGAAGGCAAAAAAATCTAAAAAAGGTAAGAAAACTAAAATTTTCTGTTACAGACTCTAT
* *
13691666 TCCTAATGCCTAAAGGACTGAAAAGATAATGTTAAGACACTTATTTACATCTTATTAAGC
66 TACTAATGCCTAAAGGACTGAAAAGAAAATGTTAAGACACTTATTTACATCTTATTAAGC
* *
13691726 TAGGTTTGGAA-GCAAAAAAATCTAAAAAAGGTAAGAAAACTAACATTTGT-TGTTACTGACTCT
1 TAGGTTT-GAAGGCAAAAAAATCTAAAAAAGGTAAGAAAACTAAAATTT-TCTGTTACAGACTCT
* * *
13691789 ATTACTAATG-CTTAAGGACTTAAAAGAAAATGTTAAGACACTTATTTGCATCTTATTAAGC
64 ATTACTAATGCCTAAAGGACTGAAAAGAAAATGTTAAGACACTTATTTACATCTTATTAAGC
13691850 T
1 T
13691851 GTTAGAAAAT
Statistics
Matches: 113, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
124 48 0.42
125 61 0.54
126 4 0.04
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (125 bp):
TAGGTTTGAAGGCAAAAAAATCTAAAAAAGGTAAGAAAACTAAAATTTTCTGTTACAGACTCTAT
TACTAATGCCTAAAGGACTGAAAAGAAAATGTTAAGACACTTATTTACATCTTATTAAGC
Found at i:13704468 original size:20 final size:20
Alignment explanation
Indices: 13704425--13704468 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
13704415 ACTGGTAAAG
*
13704425 TCGAGTAGAAAATTTTGTAG
1 TCGAGTAGAAAATTTTGTAA
*
13704445 TCGAGTAG-CAATTTGTGTAA
1 TCGAGTAGAAAATTT-TGTAA
13704465 TCGA
1 TCGA
13704469 TTAGTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (20 bp):
TCGAGTAGAAAATTTTGTAA
Found at i:13705191 original size:20 final size:21
Alignment explanation
Indices: 13705166--13705208 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13705156 AAGTCTGAGT
* *
13705166 GTTG-AAAGCTTGAGGATTGA
1 GTTGAAAAGCTTAAGGATCGA
13705186 GTTGAAAAGCTTAAGGATCGA
1 GTTGAAAAGCTTAAGGATCGA
13705207 GT
1 GT
13705209 AGTTGAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (21 bp):
GTTGAAAAGCTTAAGGATCGA
Found at i:13705280 original size:358 final size:355
Alignment explanation
Indices: 13704467--13705849 Score: 1725
Period size: 357 Copynumber: 3.9 Consensus size: 355
13704457 TTGTGTAATC
* * * *
13704467 GATT-AGTTG-AAAGCTTGAGGATCGAGTAGTTGAAGTTCAAGTGTCAATATGCTTGATTTTCCT
1 GATTGAGTTGAAAAGCTTAAGGATCGAGTAGTTGAAGTTCAAGTGTCAATACGCTTGGTTCTCCT
* * * * * *
13704530 ATCGTTTTAGTTTTTCTTCTTTGTTTTAGTAAGACATTTAAATGTTGTGTCGTGTTATCTTCTTT
66 ATCGTTTTAGTTTTTCTTCTTTGTTTTAGTAAAACGTTTAAATGCTGTGTCGTTTTATCAT-TTC
* ** * **
13704595 TATTGTTTGTAGTGGTAACTAAATGTTACCGTTTAGTTCATCTTTGTCAAATTAGTTTGTTAATT
130 TATTGTTTGTATTGGTAACTAAACATTACCATTTAGTTCATCTTTGTCAAATTAGTTTGTTAACC
* * * *
13704660 GTTGGAAAGCACAATGTTCAATGCACAGCTTACAGCGTTCTTCCAACATTTCAAGAGTTCATTTC
195 ATTGGAAAGCACAGTGTTCAATGCACAGCTTACAGTGTTTTTCCAACATTTCAAGAGTTCATTTC
* * * ** *
13704725 TTTTGATGCTACACTTAAGCATTTTTAGTTTGTTATCATGTATTTTGATATAAATAAAAACTTAA
260 -TTTGATGCTACACCTAAGCATTTTCAATTTGTTATCATGTATTTTGATATAAATACCAGCTTAA
* ** *
13704790 ATGAATAAAAGAATAAGTGTTGAAAGCTTGAG
324 ATGAATACAAGTCTGAGTGTTGAAAGCTTGAG
*
13704822 GATTGAGCTGAAAAGCTTAAGGATCGAGTAGTTGAAGTTCAAGTGTCAATACGCTTGGTTCTCCT
1 GATTGAGTTGAAAAGCTTAAGGATCGAGTAGTTGAAGTTCAAGTGTCAATACGCTTGGTTCTCCT
*
13704887 GTCGTTTTAGTTTTTCTTCTTTGTTTTAGTAAAACGTTTAAATGCTGTGTCGTTTTATCATATTC
66 ATCGTTTTAGTTTTTCTTCTTTGTTTTAGTAAAACGTTTAAATGCTGTGTCGTTTTATCAT-TTC
*
13704952 TATTGTTTGTATTGGTAACTAAACATTACCATTTAGTTCATCTTTATCAAATTAGTTTGTTAACC
130 TATTGTTTGTATTGGTAACTAAACATTACCATTTAGTTCATCTTTGTCAAATTAGTTTGTTAACC
* * * *
13705017 ATTAGAGAGCACAGTGTTCAATGCACATCTTACAATGTTTTTCCAACATTTCAAGAGTTCATTTC
195 ATTGGAAAGCACAGTGTTCAATGCACAGCTTACAGTGTTTTTCCAACATTTCAAGAGTTCATTTC
* * *
13705082 TTAGGATGCTACACCTCAGCATTTTCAA-TTGTTTATCATGTATTGTTGATATAAATGCCAGCTT
260 TT-TGATGCTACACCTAAGCATTTTCAATTTG-TTATCATGTATT-TTGATATAAATACCAGCTT
13705146 AAATGAATACAAGTCTGAGTGTTGAAAGCTTGAG
322 AAATGAATACAAGTCTGAGTGTTGAAAGCTTGAG
*
13705180 GATTGAGTTGAAAAGCTTAAGGATCGAGTAGTTGAAGTTCAAGTGTCAATACGCTTGGTGCTCCT
1 GATTGAGTTGAAAAGCTTAAGGATCGAGTAGTTGAAGTTCAAGTGTCAATACGCTTGGTTCTCCT
*
13705245 GTCGTTTTAGTTTTTCTTCTTTGTTTTAGTAAAACGTTTAAATGCTGTGTCGTTTTATCATTTTC
66 ATCGTTTTAGTTTTTCTTCTTTGTTTTAGTAAAACGTTTAAATGCTGTGTCGTTTTATCA-TTTC
*
13705310 TATTGTTTGTATTGGTAACTAAACATTAACATTTAGTTCATCTTTGTC-AATTAGTTTGTTAACC
130 TATTGTTTGTATTGGTAACTAAACATTACCATTTAGTTCATCTTTGTCAAATTAGTTTGTTAACC
* *
13705374 ATTGGAGAGCACAGTGTTCAATGCACATCTTACAGTGTTTTT----C----C----G-TC-TTTC
195 ATTGGAAAGCACAGTGTTCAATGCACAGCTTACAGTGTTTTTCCAACATTTCAAGAGTTCATTTC
*
13705425 ---GATGCTACACCTACGCATTTTCAATTTGTTATCATGTATTTTTGATATAAATACCAGCTTAA
260 TTTGATGCTACACCTAAGCATTTTCAATTTGTTATCATGTA-TTTTGATATAAATACCAGCTTAA
13705487 ATGAATACAAGTCTGAGTGTTGAAAGCTTGAG
324 ATGAATACAAGTCTGAGTGTTGAAAGCTTGAG
13705519 GATTGAGTTGAAAAGCTTAAGGATCGAGTTGAAAGCTTGAGGATCGAGTGGTTGAGGTTCAAGTG
1 GATTGAGTTGAAAAGCTTAAGGATCGAG-T---AG--T-----T-GA-------A-GTTCAAGTG
* * * * *
13705584 TCAATACACTTGGTTCTCATATTGTTTTAGTTTTTCCTCTTTGTTTTAGTAGAACGTTTAAATGC
46 TCAATACGCTTGGTTCTCCTATCGTTTTAGTTTTTCTTCTTTGTTTTAGTAAAACGTTTAAATGC
* * * * *
13705649 TGTGTCG--TT-TCATTTGTATTGTTTGCATTGGTAACTAAACGTTATCGTTTAGTTCATCTTTG
111 TGTGTCGTTTTATCATTTCTATTGTTTGTATTGGTAACTAAACATTACCATTTAGTTCATCTTTG
* * * * **
13705711 TCAAATTAGTTTGCTAACCGTTGGAAAGCACACTGTTCAATGCATAGCTTATGGTGTTTTTCCAA
176 TCAAATTAGTTTGTTAACCATTGGAAAGCACAGTGTTCAATGCACAGCTTACAGTGTTTTTCCAA
* * * * *
13705776 CATTTCAGGAGTTAATTTCTTTCGAGGCTACATCTAAGCATTTTCAGTTTGTTATCATGTATTTT
241 CATTTCAAGAGTTCATTTCTTT-GATGCTACACCTAAGCATTTTCAATTTGTTATCATGTATTTT
*
13705841 GAAATAAAT
305 GATATAAAT
13705850 GAATATAAGT
Statistics
Matches: 905, Mismatches: 76, Indels: 76
0.86 0.07 0.07
Matches are distributed among these distances:
339 112 0.12
340 6 0.01
343 6 0.01
344 2 0.00
345 2 0.00
349 1 0.00
350 1 0.00
351 2 0.00
353 1 0.00
355 51 0.06
356 62 0.07
357 312 0.34
358 218 0.24
359 75 0.08
360 1 0.00
364 1 0.00
368 1 0.00
369 1 0.00
370 4 0.00
373 12 0.01
374 34 0.04
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (355 bp):
GATTGAGTTGAAAAGCTTAAGGATCGAGTAGTTGAAGTTCAAGTGTCAATACGCTTGGTTCTCCT
ATCGTTTTAGTTTTTCTTCTTTGTTTTAGTAAAACGTTTAAATGCTGTGTCGTTTTATCATTTCT
ATTGTTTGTATTGGTAACTAAACATTACCATTTAGTTCATCTTTGTCAAATTAGTTTGTTAACCA
TTGGAAAGCACAGTGTTCAATGCACAGCTTACAGTGTTTTTCCAACATTTCAAGAGTTCATTTCT
TTGATGCTACACCTAAGCATTTTCAATTTGTTATCATGTATTTTGATATAAATACCAGCTTAAAT
GAATACAAGTCTGAGTGTTGAAAGCTTGAG
Found at i:13705535 original size:21 final size:20
Alignment explanation
Indices: 13705505--13705567 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
13705495 AAGTCTGAGT
*
13705505 GTTGAAAGCTTGAGGATTGA
1 GTTGAAAGCTTGAGGATCGA
*
13705525 GTTGAAAAGCTTAAGGATCGA
1 GTTG-AAAGCTTGAGGATCGA
13705546 GTTGAAAGCTTGAGGATCGA
1 GTTGAAAGCTTGAGGATCGA
13705566 GT
1 GT
13705568 GGTTGAGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 21 0.54
21 18 0.46
ACGTcount: A:0.32, C:0.08, G:0.33, T:0.27
Consensus pattern (20 bp):
GTTGAAAGCTTGAGGATCGA
Found at i:13710648 original size:16 final size:15
Alignment explanation
Indices: 13710603--13710660 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
13710593 GTGTAGACAC
* *
13710603 TAAAAATCATAAACA
1 TAAAAATAATAAAAA
13710618 -AAAAATGAATTAAAAA
1 TAAAAAT-AA-TAAAAA
13710634 TAAAAATAATAAAAA
1 TAAAAATAATAAAAA
*
13710649 TTAAAA-AATAAA
1 TAAAAATAATAAA
13710661 GAAATAATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 12 0.32
15 12 0.32
16 7 0.19
17 6 0.16
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (15 bp):
TAAAAATAATAAAAA
Found at i:13710650 original size:22 final size:26
Alignment explanation
Indices: 13710625--13710674 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
13710615 ACAAAAAATG
13710625 AATT-AAAAAT-AA-AAATAAT-AAA
1 AATTAAAAAATAAAGAAATAATGAAA
13710647 AATTAAAAAATAAAGAAATAATGAAA
1 AATTAAAAAATAAAGAAATAATGAAA
13710673 AA
1 AA
13710675 GGGTGGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.17
23 6 0.25
24 2 0.08
25 7 0.29
26 5 0.21
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (26 bp):
AATTAAAAAATAAAGAAATAATGAAA
Found at i:13710656 original size:17 final size:17
Alignment explanation
Indices: 13710617--13710659 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
13710607 AATCATAAAC
13710617 AAAAAATGAATTAAAAAT
1 AAAAAAT-AATTAAAAAT
13710635 -AAAAATAA-TAAAAATT
1 AAAAAATAATTAAAAA-T
13710651 AAAAAATAA
1 AAAAAATAA
13710660 AGAAATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.26
16 3 0.13
17 14 0.61
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAAATAATTAAAAAT
Found at i:13711210 original size:94 final size:93
Alignment explanation
Indices: 13711097--13711296 Score: 301
Period size: 94 Copynumber: 2.1 Consensus size: 93
13711087 GAAGAAGCAG
* *
13711097 AGAGAGGAGAGAGTTTGGTTCGAGCGGCGCCGACGAGGGGAGCAAAGCCAGATCTGGGCGACGAA
1 AGAGA-GAGAGAGTTTGGTTCGAGCAGCGCCGACGAGGGGAGCAAAGCCAGATCTGGCCGACGAA
13711162 AGTAAAAAAAGGCTTCGGTGGCCGACGGGA
65 AGT-AAAAAAGGCTTCGGTGGCCGACGGGA
* * * * * *
13711192 AGAGAGAGAGAGTTTGGTTTGAGCAGTGCCGGCGAGGGGAGGAAAGCTAGATTTGGCCGACGAAA
1 AGAGAGAGAGAGTTTGGTTCGAGCAGCGCCGACGAGGGGAGCAAAGCCAGATCTGGCCGACGAAA
*
13711257 GTAAAAAAGGCTTCGGTGGCCGATGGGA
66 GTAAAAAAGGCTTCGGTGGCCGACGGGA
13711285 AGAGAGAGAGAG
1 AGAGAGAGAGAG
13711297 GGTGAGAGGC
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 37 0.39
94 54 0.56
95 5 0.05
ACGTcount: A:0.30, C:0.14, G:0.41, T:0.14
Consensus pattern (93 bp):
AGAGAGAGAGAGTTTGGTTCGAGCAGCGCCGACGAGGGGAGCAAAGCCAGATCTGGCCGACGAAA
GTAAAAAAGGCTTCGGTGGCCGACGGGA
Found at i:13711417 original size:31 final size:32
Alignment explanation
Indices: 13711374--13711456 Score: 141
Period size: 33 Copynumber: 2.6 Consensus size: 32
13711364 GGTTTTACCA
13711374 ACCACCGATGAAAGGAGA-GAGAGAGATCTTG
1 ACCACCGATGAAAGGAGATGAGAGAGATCTTG
*
13711405 ACCACCGGTGAAAGGAGAATGAGAGAGATCTTG
1 ACCACCGATGAAAGGAG-ATGAGAGAGATCTTG
13711438 ACCACCGATGAAAGGAGAT
1 ACCACCGATGAAAGGAGAT
13711457 CTTGAGATCG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
31 16 0.33
32 3 0.06
33 29 0.60
ACGTcount: A:0.39, C:0.17, G:0.31, T:0.13
Consensus pattern (32 bp):
ACCACCGATGAAAGGAGATGAGAGAGATCTTG
Found at i:13712035 original size:20 final size:20
Alignment explanation
Indices: 13711991--13712036 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
13711981 TTTAATTAGA
* * *
13711991 ATAAAAGATAAAATATATAT
1 ATAAAAAATAAAATAAAAAT
13712011 ATAAAAAATAAAATAAAAAT
1 ATAAAAAATAAAATAAAAAT
*
13712031 TTAAAA
1 ATAAAA
13712037 TTATCAGATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
ATAAAAAATAAAATAAAAAT
Found at i:13712563 original size:14 final size:14
Alignment explanation
Indices: 13712546--13712572 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13712536 CTGAAAAAAT
13712546 AATAAATAAATAAA
1 AATAAATAAATAAA
13712560 AATAAATAAATAA
1 AATAAATAAATAA
13712573 GAAAAATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAATAAATAAA
Found at i:13712578 original size:18 final size:17
Alignment explanation
Indices: 13712538--13712578 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
13712528 AAAAACTACT
13712538 GAAAAAATAATAAATAA
1 GAAAAAATAATAAATAA
13712555 -ATAAAAATAAATAAATAA
1 GA-AAAAAT-AATAAATAA
13712573 GAAAAA
1 GAAAAA
13712579 TGATAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 6 0.29
18 13 0.62
19 1 0.05
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (17 bp):
GAAAAAATAATAAATAA
Found at i:13712883 original size:17 final size:16
Alignment explanation
Indices: 13712863--13712900 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
13712853 TTGCTTATGA
*
13712863 AAAAATATAATAATAAT
1 AAAAATATAAAAAT-AT
13712880 AAAAATATAAAAATAT
1 AAAAATATAAAAATAT
13712896 AAAAA
1 AAAAA
13712901 AGGATAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATATAAAAATAT
Found at i:13712889 original size:8 final size:8
Alignment explanation
Indices: 13712863--13712900 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
13712853 TTGCTTATGA
13712863 AAAAATAT
1 AAAAATAT
*
13712871 AATAATAAT
1 AAAAAT-AT
13712880 AAAAATAT
1 AAAAATAT
13712888 AAAAATAT
1 AAAAATAT
13712896 AAAAA
1 AAAAA
13712901 AGGATAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAATAT
Found at i:13713057 original size:27 final size:27
Alignment explanation
Indices: 13713008--13713079 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
13712998 AGTAACTTAA
* *
13713008 AATAAAAAATGTAAAGTATAAAAAAT-ATT
1 AATAAAAAA--TAAAATAGAAAAAATGA-T
* * *
13713037 AATTAGAAATAAAATAGAAAATATGAT
1 AATAAAAAATAAAATAGAAAAAATGAT
13713064 AATAAAAAATAAAATA
1 AATAAAAAATAAAATA
13713080 AATGAAAGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
27 27 0.77
28 1 0.03
29 7 0.20
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (27 bp):
AATAAAAAATAAAATAGAAAAAATGAT
Found at i:13715044 original size:4 final size:4
Alignment explanation
Indices: 13715035--13715099 Score: 58
Period size: 4 Copynumber: 16.2 Consensus size: 4
13715025 AGTGTTTTAT
** * * * * *
13715035 ACAC ACAC ACAC TTAC ATAC AGAC ATAG ACAC AAAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
*
13715083 ACAC ACAC ACAT ACAC A
1 ACAC ACAC ACAC ACAC A
13715100 TATAAGGTAC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.51, C:0.38, G:0.03, T:0.08
Consensus pattern (4 bp):
ACAC
Found at i:13715101 original size:6 final size:6
Alignment explanation
Indices: 13715035--13715099 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
13715025 AGTGTTTTAT
** * * * * *
13715035 ACACAC ACACAC TTACAT ACAGAC ATAGAC ACAAAC ACACAC ACACAC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
*
13715083 ACACAC ACACAT ACACA
1 ACACAC ACACAC ACACA
13715100 TATAAGGTAC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.51, C:0.38, G:0.03, T:0.08
Consensus pattern (6 bp):
ACACAC
Found at i:13715272 original size:42 final size:42
Alignment explanation
Indices: 13715213--13715321 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
13715203 ACCCATTTAC
13715213 CAACAATATCCATTAATATGCATATCTCTTAAGAAATCAAAT
1 CAACAATATCCATTAATATGCATATCTCTTAAGAAATCAAAT
* *
13715255 CAACAATATCCATTAATATGCATATCTTTTAAGGAATCAAAT
1 CAACAATATCCATTAATATGCATATCTCTTAAGAAATCAAAT
*
13715297 CAACAATATCCATTTATATGCATAT
1 CAACAATATCCATTAATATGCATAT
13715322 TTATTAAGGA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (42 bp):
CAACAATATCCATTAATATGCATATCTCTTAAGAAATCAAAT
Found at i:13717334 original size:12 final size:11
Alignment explanation
Indices: 13717317--13717350 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
13717307 ATTACAATGG
13717317 AAATAAAAATAA
1 AAATAAAAA-AA
13717329 AAATAAAAAAA
1 AAATAAAAAAA
13717340 AAA-AAAAAAA
1 AAATAAAAAAA
13717350 A
1 A
13717351 GGCAATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:13725778 original size:133 final size:132
Alignment explanation
Indices: 13725513--13725781 Score: 346
Period size: 133 Copynumber: 2.0 Consensus size: 132
13725503 ATATATTATT
* * *
13725513 TTTTAACAATGACTATTTGACTTAATGGGTTTTGAAATCTAGAGTTCAGATTTATCCCGACGCTT
1 TTTTAGCAATGACTATTAGACTTAATAGGTTTTGAAATCTAGAGTTCAGATTTATCCCGACGCTT
* *
13725578 CGGTGAAAATTCGTCTCGAACTTCGCACCCGAAAAACATCCAAACGAAAAAGGCAACTCTTTGCC
66 CGGTGAAAATCCGTCTCGAACTTCACACCCGAAAAACATCCAAACGAAAAAGGCAACTCTTTGCC
13725643 CC
131 CC
* * * * * *
13725645 TTTTAGNCAATGATTATTAGGCTTAATAGGTTTTGGAGTTTAGAGTTCGGATTTATCCCGACGCT
1 TTTTAG-CAATGACTATTAGACTTAATAGGTTTTGAAATCTAGAGTTCAGATTTATCCCGACGCT
* * * *
13725710 TCGGTGAAAATCCGTCTCTG-ACTTCATACCCG-AAAATATCC-ACCGGAAAGAGGCAACTCTTT
65 TCGGTGAAAATCCGTCTC-GAACTTCACACCCGAAAAACATCCAAAC-GAAAAAGGCAACTCTTT
13725772 GCCCCC
128 G-CCCC
13725778 TTTT
1 TTTT
13725782 TGGTGGTAAT
Statistics
Matches: 118, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
131 2 0.02
132 30 0.25
133 85 0.72
134 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
TTTTAGCAATGACTATTAGACTTAATAGGTTTTGAAATCTAGAGTTCAGATTTATCCCGACGCTT
CGGTGAAAATCCGTCTCGAACTTCACACCCGAAAAACATCCAAACGAAAAAGGCAACTCTTTGCC
CC
Found at i:13726561 original size:1 final size:1
Alignment explanation
Indices: 13726557--13726602 Score: 92
Period size: 1 Copynumber: 46.0 Consensus size: 1
13726547 TAAACCCCCC
13726557 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13726603 GTGGCTAGGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13743451 original size:20 final size:20
Alignment explanation
Indices: 13743426--13743465 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13743416 GGCATATGAA
13743426 GTTTATCTCTAATGCCATTG
1 GTTTATCTCTAATGCCATTG
13743446 GTTTATCTCTAATGCCATTG
1 GTTTATCTCTAATGCCATTG
13743466 AAACTCTCAC
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:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (20 bp):
GTTTATCTCTAATGCCATTG
Found at i:13757146 original size:40 final size:38
Alignment explanation
Indices: 13757055--13757159 Score: 131
Period size: 40 Copynumber: 2.7 Consensus size: 38
13757045 ATAGTGCCCG
* *
13757055 TGTGCACGATGT-GGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACGGAT
* * * *
13757092 TGTGCATGATGTGGGGGGATGCACATGATGGCGCCGGCT
1 TGTGCACGATGTGGGGGGATGTACATGATGGC-ACGGAT
13757131 ATGTGCACGATGTGGGGGGATGTACATGA
1 -TGTGCACGATGTGGGGGGATGTACATGA
13757160 GCCGGGTGTG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 11 0.19
38 17 0.30
39 3 0.05
40 26 0.46
ACGTcount: A:0.20, C:0.15, G:0.41, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACGGAT
Found at i:13760957 original size:13 final size:12
Alignment explanation
Indices: 13760933--13760968 Score: 63
Period size: 13 Copynumber: 2.9 Consensus size: 12
13760923 ATGCTTAAAG
13760933 GTATAAAGAATA
1 GTATAAAGAATA
13760945 GTATAAGAGAATA
1 GTATAA-AGAATA
13760958 GTATAAAGAAT
1 GTATAAAGAAT
13760969 GATTAAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (12 bp):
GTATAAAGAATA
Found at i:13762753 original size:66 final size:65
Alignment explanation
Indices: 13762580--13762780 Score: 231
Period size: 66 Copynumber: 3.0 Consensus size: 65
13762570 AAGTTAATTG
** * *
13762580 TTGGGTTTTGGTTGATCCCGTGGAAAAACCATTGTTGTAGGTTATGGTTGAGCCTTGGAAAAATC
1 TTGGGTTTTGGTTGATCCCGT-GAAAAACCATTG-TAAAGGTTGTGGTTGAGCCTT-GAAAAACC
*
13762645 ACT
63 ATT
* * * * *
13762648 TTGGGTTTTAGTTTAACCCGTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAT
1 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGT-AAAGGTTGTGGTTGAGCCTTGAAAAACCAT
13762713 T
65 T
* * *
13762714 TTGGATTTTGGTTGATCCCGTGAAAAACCATTGCTAAAGGTTGTGGCTGAGCCTGTGAAAAGCCA
1 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTG-TAAAGGTTGTGGTTGAGCCT-TGAAAAACCA
13762779 TT
64 TT
13762781 GTAAAAGCTT
Statistics
Matches: 112, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
66 55 0.49
67 39 0.35
68 18 0.16
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (65 bp):
TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTAAAGGTTGTGGTTGAGCCTTGAAAAACCATT
Found at i:13769016 original size:11 final size:11
Alignment explanation
Indices: 13769000--13769030 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
13768990 TAGAGTTTTG
13769000 GGTTTAAAGTT
1 GGTTTAAAGTT
13769011 GGTTTAAAGTT
1 GGTTTAAAGTT
*
13769022 GTTTTAAAG
1 GGTTTAAAG
13769031 CTATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (11 bp):
GGTTTAAAGTT
Found at i:13769105 original size:5 final size:5
Alignment explanation
Indices: 13769070--13769104 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
13769060 CCCCAAGTCT
* *
13769070 AGTTA AGTTA AGATA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
13769105 GATTCAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (5 bp):
AGTTA
Found at i:13778317 original size:66 final size:66
Alignment explanation
Indices: 13778229--13778480 Score: 319
Period size: 66 Copynumber: 3.8 Consensus size: 66
13778219 AAGTTAGTTG
* * * ***
13778229 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTGCAGGTTGTGGTTGA-CCTTAGAAAAACCA
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTT-GAAAAACCA
13778293 CT
65 CT
* * * *
13778295 TTGGGTTTTAGTTTAGCTCGTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAATCAC
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
13778360 T
66 T
* * *
13778361 TTGGGTTTTAGTTTAGCCTGTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
13778426 T
66 T
* * * *
13778427 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGCT-AAAGGTTGTGGCTGAGCCT
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTG-TAAAAGGTTGTGGTTGAGCCT
13778481 GCGAAAAGCC
Statistics
Matches: 164, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
66 159 0.97
67 5 0.03
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.34
Consensus pattern (66 bp):
TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
T
Found at i:13778419 original size:34 final size:34
Alignment explanation
Indices: 13778315--13778422 Score: 116
Period size: 34 Copynumber: 3.2 Consensus size: 34
13778305 GTTTAGCTCG
13778315 TGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
1 TGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
* ** * * *
13778349 TGAAAAA-TCACT-T--TGGGTTTTAGTTTAGCCT
1 TGAAAAACT-AGTGTAAAAGGTTGTGGTTGAGCCT
13778380 GTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
1 -TGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
13778415 TGAAAAAC
1 TGAAAAAC
13778423 CACTTTGGGT
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
31 13 0.23
32 9 0.16
33 4 0.07
34 17 0.30
35 13 0.23
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.31
Consensus pattern (34 bp):
TGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
Found at i:13780219 original size:23 final size:24
Alignment explanation
Indices: 13780183--13780228 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
13780173 ATGAAATCAA
13780183 GTTTTCTTCACTTTCCTT-TCCAT
1 GTTTTCTTCACTTTCCTTCTCCAT
** *
13780206 GTTTTCTTTTCTTTTCTTCTCCA
1 GTTTTCTTCACTTTCCTTCTCCA
13780229 AACTTCTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.07, C:0.28, G:0.04, T:0.61
Consensus pattern (24 bp):
GTTTTCTTCACTTTCCTTCTCCAT
Found at i:13781575 original size:84 final size:84
Alignment explanation
Indices: 13781453--13781622 Score: 241
Period size: 84 Copynumber: 2.0 Consensus size: 84
13781443 AAGAGTGTGC
* ** * * * *
13781453 ATAAGTCGATGCTGACCCGACTATGTGCGAGGGGGAGTGCGCATAAGTCGATGCTGACTCAGCTA
1 ATAAGTCGATGCTGACCCGACTATGTGCAAGGAAGAGTGCGCATAAGCCAATGCTGACCCAGCCA
13781518 TGTGCGAGAGGGAGTGCAT
66 TGTGCGAGAGGGAGTGCAT
* *
13781537 ATAAGTCGATGCTGACCTGACTATGTGCAAGTAAGAGTGCGCATAAGCCAATGCTGACCCAGCCA
1 ATAAGTCGATGCTGACCCGACTATGTGCAAGGAAGAGTGCGCATAAGCCAATGCTGACCCAGCCA
* *
13781602 TGTGCTAGTGGGAGTGCAT
66 TGTGCGAGAGGGAGTGCAT
13781621 AT
1 AT
13781623 GAGCTGATGG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (84 bp):
ATAAGTCGATGCTGACCCGACTATGTGCAAGGAAGAGTGCGCATAAGCCAATGCTGACCCAGCCA
TGTGCGAGAGGGAGTGCAT
Found at i:13781617 original size:42 final size:43
Alignment explanation
Indices: 13781423--13781618 Score: 195
Period size: 42 Copynumber: 4.7 Consensus size: 43
13781413 GTAATGATAT
* * ** *
13781423 TGACCTAG-CTATGTGTGAGTAAGAGTGTGCATAAGTCGATGC
1 TGACCCAGACTATGTGCGAGTGGGAGTGCGCATAAGTCGATGC
*
13781465 TGACCC-GACTATGTGCGAGGGGGAGTGCGCATAAGTCGATGC
1 TGACCCAGACTATGTGCGAGTGGGAGTGCGCATAAGTCGATGC
* * **
13781507 TGACTCAG-CTATGTGCGAGAGGGAGTGCATATAAGTCGATGC
1 TGACCCAGACTATGTGCGAGTGGGAGTGCGCATAAGTCGATGC
* * ** * *
13781549 TGA-CCTGACTATGTGCAAGTAAGAGTGCGCATAAGCCAATGC
1 TGACCCAGACTATGTGCGAGTGGGAGTGCGCATAAGTCGATGC
* *
13781591 TGACCCAG-CCATGTGCTAGTGGGAGTGC
1 TGACCCAGACTATGTGCGAGTGGGAGTGC
13781619 ATATGAGCTG
Statistics
Matches: 125, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
41 3 0.02
42 118 0.94
43 4 0.03
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (43 bp):
TGACCCAGACTATGTGCGAGTGGGAGTGCGCATAAGTCGATGC
Found at i:13781666 original size:2 final size:2
Alignment explanation
Indices: 13781659--13781696 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
13781649 ATGGTGATGG
* *
13781659 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13781697 GTGTGTTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13783510 original size:262 final size:262
Alignment explanation
Indices: 13783045--13783569 Score: 1016
Period size: 262 Copynumber: 2.0 Consensus size: 262
13783035 CAAGATTTTT
13783045 GGTGCCGTGTTCTCTCCTCAACCCTAAGAAGTTGCCAAAGTTCACTTTTAAGCTTTCTTATCTCA
1 GGTGCCGTGTTCTCTCCTCAACCCTAAGAAGTTGCCAAAGTTCACTTTTAAGCTTTCTTATCTCA
13783110 TTCCAAGATTGCTCATTAGACCCATTTTGCTACATCTCATCAGTGAGATGTTGAATTTTAGCACC
66 TTCCAAGATTGCTCATTAGACCCATTTTGCTACATCTCATCAGTGAGATGTTGAATTTTAGCACC
13783175 AAGATAGTGGATTCAACTTAACAAATTACCAAACTTTTGTTGCTGCTAGTTTTTTATATGTCCTT
131 AAGATAGTGGATTCAACTTAACAAATTACCAAACTTTTGTTGCTGCTAGTTTTTTATATGTCCTT
*
13783240 TAGTGTCTCTGAGCCAATGCCTAATGGCAGCCCATTTGCTGC-AATGGCCTCAATCTCATTCCAA
196 TAGTGTCTCTGAGCCAATGCCTAATGGCAGCCCATTTGCTCCTAATGGCCTCAATCTCATTCCAA
13783304 AA
261 AA
13783306 NGGTGCCGTGTTCTCTCCTCAACCCTAAGAAGTTGCCAAAGTTCACTTTTAAGCTTTCTTATCTC
1 -GGTGCCGTGTTCTCTCCTCAACCCTAAGAAGTTGCCAAAGTTCACTTTTAAGCTTTCTTATCTC
13783371 ATTCCAAGATTGCTCATTAGACCCATTTTGCTACATCTCATCAGTGAGATGTTGAATTTTAGCAC
65 ATTCCAAGATTGCTCATTAGACCCATTTTGCTACATCTCATCAGTGAGATGTTGAATTTTAGCAC
13783436 CAAGATAGTGGATTCAACTTAACAAATTACCAAACTTTTGTTGCTGCTAGTTTTTTATATGTCCT
130 CAAGATAGTGGATTCAACTTAACAAATTACCAAACTTTTGTTGCTGCTAGTTTTTTATATGTCCT
*
13783501 TTAGTGTCTCTGAGCCAGTGCCTAATGGCAGCCCATTTGCTCCTAATGGCCTCAATCTCATTCCA
195 TTAGTGTCTCTGAGCCAATGCCTAATGGCAGCCCATTTGCTCCTAATGGCCTCAATCTCATTCCA
13783566 AAA
260 AAA
13783569 G
1 G
13783570 AGGCAAACAT
Statistics
Matches: 260, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
262 236 0.91
263 24 0.09
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (262 bp):
GGTGCCGTGTTCTCTCCTCAACCCTAAGAAGTTGCCAAAGTTCACTTTTAAGCTTTCTTATCTCA
TTCCAAGATTGCTCATTAGACCCATTTTGCTACATCTCATCAGTGAGATGTTGAATTTTAGCACC
AAGATAGTGGATTCAACTTAACAAATTACCAAACTTTTGTTGCTGCTAGTTTTTTATATGTCCTT
TAGTGTCTCTGAGCCAATGCCTAATGGCAGCCCATTTGCTCCTAATGGCCTCAATCTCATTCCAA
AA
Found at i:13785602 original size:2 final size:2
Alignment explanation
Indices: 13785595--13785627 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13785585 GCATAAAATA
13785595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13785628 CACCATTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13785881 original size:34 final size:33
Alignment explanation
Indices: 13785843--13785935 Score: 150
Period size: 34 Copynumber: 2.7 Consensus size: 33
13785833 CCATTTAAGG
13785843 GCTGGTTTTGGAGGCTAAATAGTGCCATTTTTTT
1 GCTGGTTTTGGAGGCTAAA-AGTGCCATTTTTTT
13785877 GCTGGTTTTGGAGGCTGAAAAGTGCCATTTTTTT
1 GCTGGTTTTGGAGGCT-AAAAGTGCCATTTTTTT
*
13785911 GCTGGTTTTGGAGGCCAAAAAGTGC
1 GCTGGTTTTGGAGG-CTAAAAGTGC
13785936 AAAATTTTGC
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
34 52 0.93
35 4 0.07
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (33 bp):
GCTGGTTTTGGAGGCTAAAAGTGCCATTTTTTT
Found at i:13786072 original size:35 final size:35
Alignment explanation
Indices: 13786027--13786113 Score: 117
Period size: 34 Copynumber: 2.5 Consensus size: 35
13786017 AGGGAAAGGT
*
13786027 GCAGCTTAGCTGCTGAAATTTT-AAGGAAAAATAAA
1 GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAAT-AA
*
13786062 GCAGCATAGCTGCTG--ATTTTGAAGCAAAAATAA
1 GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAATAA
13786095 GCAGCCTTAGCTGCTGAAA
1 GCAG-CTTAGCTGCTGAAA
13786114 AATTAAAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
33 11 0.24
34 19 0.42
35 14 0.31
36 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (35 bp):
GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAATAA
Found at i:13786258 original size:5 final size:5
Alignment explanation
Indices: 13786248--13786306 Score: 93
Period size: 5 Copynumber: 11.8 Consensus size: 5
13786238 GAGAAAGAAA
*
13786248 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA- AAAGAG AAAAG AAACG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG
13786298 AAAAG AAAA
1 AAAAG AAAA
13786307 TAACAAGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
4 3 0.06
5 44 0.88
6 3 0.06
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:13786397 original size:25 final size:24
Alignment explanation
Indices: 13786341--13786397 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
13786331 AACAAGCAAC
*
13786341 AAAATGTACATGGTCTAATAAAGA
1 AAAATGGACATGGTCTAATAAAGA
13786365 AAATATGGACATGGTCTAATTAAA-A
1 AAA-ATGGACATGGTCTAA-TAAAGA
13786390 AGAAATGG
1 A-AAATGG
13786398 GAGAAGTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.10
25 20 0.69
26 6 0.21
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (24 bp):
AAAATGGACATGGTCTAATAAAGA
Found at i:13788447 original size:22 final size:22
Alignment explanation
Indices: 13788407--13788470 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
13788397 GATTGGTATT
13788407 AGAGATTTTGGTTTTTAAAGATC
1 AGAGATTTTGG-TTTTAAAGATC
*
13788430 AGAGCTTTTGGTTTTAAAGATC
1 AGAGATTTTGGTTTTAAAGATC
* *
13788452 AGAGTTTTTGGGTTTAAAG
1 AGAGATTTTGGTTTTAAAG
13788471 TTTGTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 28 0.74
23 10 0.26
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (22 bp):
AGAGATTTTGGTTTTAAAGATC
Found at i:13788561 original size:5 final size:5
Alignment explanation
Indices: 13788521--13788560 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
13788511 CCCCAAGTCT
** *
13788521 AGTTA AGTTA AAATA AGTTA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
13788561 GATTGAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (5 bp):
AGTTA
Found at i:13792647 original size:2 final size:2
Alignment explanation
Indices: 13792640--13792666 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13792630 GCATAAAATA
13792640 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 A
13792667 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13794599 original size:15 final size:15
Alignment explanation
Indices: 13794576--13794611 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
13794566 GAGACAAAAA
*
13794576 TTTTTAATTTATCTG
1 TTTTAAATTTATCTG
13794591 TTTTAAATTTATCTG
1 TTTTAAATTTATCTG
13794606 TTTTAA
1 TTTTAA
13794612 GTTGGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTAAATTTATCTG
Found at i:13796644 original size:11 final size:11
Alignment explanation
Indices: 13796628--13796657 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
13796618 TATTATTATG
13796628 TTTGTTTTGTT
1 TTTGTTTTGTT
13796639 TTTGTTTTGTT
1 TTTGTTTTGTT
*
13796650 TTTATTTT
1 TTTGTTTT
13796658 TATTTTCTAA
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:0.03, C:0.00, G:0.13, T:0.83
Consensus pattern (11 bp):
TTTGTTTTGTT
Found at i:13799381 original size:47 final size:47
Alignment explanation
Indices: 13799295--13799568 Score: 277
Period size: 47 Copynumber: 5.8 Consensus size: 47
13799285 TGTGACAAAG
* * * * * *
13799295 CTGTGACACGCCAGCGTTCAAAGTTAGTGAGATGCCATGGAGGGAAT
1 CTGTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
* * * *
13799342 ATGTGACACGCTAGGGTTAAGAGTTGGTGACACGTCATGGTA-GGAAT
1 CTGTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATGG-AGGGAAT
* * * * * *
13799389 CTGTGACATGCCA-ACATTCAAAGTTGGTGAGACGCCATAGAGGGAAT
1 CTGTGACACGCTAGA-GTTCAGAGTTGGTGACACGCCATGGAGGGAAT
* * *
13799436 CTGTGACACG-TCAGAGTTCAGAGTTGGTAACATGGCATGGAGGGAAT
1 CTGTGACACGCT-AGAGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
* * *
13799483 CTGTGACACG-TCAGCGTTCAGAGTTCGTGAGACGCCATGGAGGGAAT
1 CTGTGACACGCT-AGAGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
*
13799530 CTGTGACACGCTAGAGTTCAGAGTTGGTGACATGCCATG
1 CTGTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATG
13799569 TTTAGAGTGT
Statistics
Matches: 183, Mismatches: 38, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
46 1 0.01
47 179 0.98
48 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (47 bp):
CTGTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
Found at i:13799563 original size:94 final size:94
Alignment explanation
Indices: 13799295--13799568 Score: 372
Period size: 94 Copynumber: 2.9 Consensus size: 94
13799285 TGTGACAAAG
* * *
13799295 CTGTGACACGCCAGCGTTCAAAGTTAGTGAGATGCCATGGAGGGAATATGTGACACGCTAGGGTT
1 CTGTGACACGCCAGCGTTCAAAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTT
* * *
13799360 AAGAGTTGGTGACACGTCATGGTAGGAAT
66 CAGAGTTGGTGACATGCCATGGTAGGAAT
* * * * *
13799389 CTGTGACATGCCAACATTCAAAGTTGGTGAGACGCCATAGAGGGAATCTGTGACACG-TCAGAGT
1 CTGTGACACGCCAGCGTTCAAAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCT-AGAGT
* *
13799453 TCAGAGTTGGTAACATGGCATGG-AGGGAAT
65 TCAGAGTTGGTGACATGCCATGGTA-GGAAT
* * *
13799483 CTGTGACACGTCAGCGTTCAGAGTTCGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTT
1 CTGTGACACGCCAGCGTTCAAAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTT
13799548 CAGAGTTGGTGACATGCCATG
66 CAGAGTTGGTGACATGCCATG
13799569 TTTAGAGTGT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
93 2 0.01
94 153 0.98
95 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (94 bp):
CTGTGACACGCCAGCGTTCAAAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTT
CAGAGTTGGTGACATGCCATGGTAGGAAT
Found at i:13799567 original size:141 final size:141
Alignment explanation
Indices: 13799295--13799567 Score: 327
Period size: 141 Copynumber: 1.9 Consensus size: 141
13799285 TGTGACAAAG
* * * *
13799295 CTGTGACACGCCAGCGTTCAAAGTTAGTGAGATGCCATGGAGGGAATATGTGACACGCTAGGGTT
1 CTGTGACACGCCAGAGTTCAAAGTTAGTAACATGCCATGGAGGGAATATGTGACACGCTAGCGTT
* * * *
13799360 AAGAGTTGGTGACACGTCATGGTAGGAATCTGTGACATGCCAACATTCAAAGTTGGTGAGACGCC
66 AAGAGTTCGTGACACGCCATGGTAGGAATCTGTGACACGCCAACATTCAAAGTTGGTGACACGCC
13799425 ATAGAGGGAAT
131 ATAGAGGGAAT
* * * * *
13799436 CTGTGACACGTCAGAGTTCAGAGTTGGTAACATGGCATGGAGGGAATCTGTGACACG-TCAGCGT
1 CTGTGACACGCCAGAGTTCAAAGTTAGTAACATGCCATGGAGGGAATATGTGACACGCT-AGCGT
* * * * * *
13799500 TCAGAGTTCGTGAGACGCCATGG-AGGGAATCTGTGACACGCTAGA-GTTCAGAGTTGGTGACAT
65 TAAGAGTTCGTGACACGCCATGGTA-GGAATCTGTGACACGCCA-ACATTCAAAGTTGGTGACAC
13799563 GCCAT
128 GCCAT
13799568 GTTTAGAGTG
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
140 2 0.02
141 107 0.97
142 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (141 bp):
CTGTGACACGCCAGAGTTCAAAGTTAGTAACATGCCATGGAGGGAATATGTGACACGCTAGCGTT
AAGAGTTCGTGACACGCCATGGTAGGAATCTGTGACACGCCAACATTCAAAGTTGGTGACACGCC
ATAGAGGGAAT
Found at i:13799582 original size:23 final size:23
Alignment explanation
Indices: 13799556--13799633 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
13799546 TTCAGAGTTG
*
13799556 GTGACATGCCATGTTTAGAGTGT
1 GTGACATGCCATGTTTAGAATGT
* * * *
13799579 GTGACACGACATTGCTTA-AACAG-
1 GTGACATGCCA-TGTTTAGAA-TGT
*
13799602 CTGACATGCCATGGTTTAGAATGT
1 GTGACATGCCAT-GTTTAGAATGT
13799626 GTGACATG
1 GTGACATG
13799634 GCATTGAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 9
0.66 0.19 0.15
Matches are distributed among these distances:
22 1 0.03
23 23 0.59
24 15 0.38
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (23 bp):
GTGACATGCCATGTTTAGAATGT
Found at i:13799619 original size:47 final size:47
Alignment explanation
Indices: 13799557--13799709 Score: 158
Period size: 47 Copynumber: 3.4 Consensus size: 47
13799547 TCAGAGTTGG
* *
13799557 TGACATGCCAT-GTTTAGAGTGTGTGACACGACATTGCTTAAACAGC
1 TGACATGCCATGGTTTAGAGTGTGTGACATGGCATTGCTTAAACAGC
*
13799603 TGACATGCCATGGTTTAGAATGTGTGACATGGCATTG---AAA-AGC
1 TGACATGCCATGGTTTAGAGTGTGTGACATGGCATTGCTTAAACAGC
* ** * * *
13799646 TGATACACCATGGTTTAAAGTGTGTGAGATGGCATTGCTTGAACAGC
1 TGACATGCCATGGTTTAGAGTGTGTGACATGGCATTGCTTAAACAGC
13799693 TAAGACAT--CATGGTTTA
1 T--GACATGCCATGGTTTA
13799710 AAATAGAGAG
Statistics
Matches: 88, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
43 34 0.39
44 3 0.03
46 13 0.15
47 35 0.40
49 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (47 bp):
TGACATGCCATGGTTTAGAGTGTGTGACATGGCATTGCTTAAACAGC
Found at i:13800228 original size:31 final size:31
Alignment explanation
Indices: 13800180--13800343 Score: 195
Period size: 31 Copynumber: 5.3 Consensus size: 31
13800170 TTAGCATGTG
13800180 ACAACATTTGACTCGATATGCATGGCGTGTC
1 ACAACATTTGACTCGATATGCATGGCGTGTC
* *
13800211 ACAATATTTGACCCGATATGCATGGCGTGTC
1 ACAACATTTGACTCGATATGCATGGCGTGTC
* * *
13800242 CCAACATTTTACTCAATATGCATGGCGTGTC
1 ACAACATTTGACTCGATATGCATGGCGTGTC
* * * *
13800273 ACAACATTTTACTTGTTATGCATGGCATGTC
1 ACAACATTTGACTCGATATGCATGGCGTGTC
* * *
13800304 ACAACATTTTG-CTTGCTATGCATGGCATGTC
1 ACAACA-TTTGACTCGATATGCATGGCGTGTC
*
13800335 ACATCATTT
1 ACAACATTT
13800344 ATTCCTTAAT
Statistics
Matches: 117, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
30 3 0.03
31 111 0.95
32 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (31 bp):
ACAACATTTGACTCGATATGCATGGCGTGTC
Found at i:13802577 original size:31 final size:31
Alignment explanation
Indices: 13802528--13802795 Score: 329
Period size: 31 Copynumber: 8.6 Consensus size: 31
13802518 GTCAGTGTTA
*
13802528 GCGTGTGACAACATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
13802559 GCGTGTCAGAACAATTTACTTATTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
13802590 GCGTGTCACAACCTTTAACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * * **
13802621 TCGTGTCAGAACATTTTGCTTATTACCCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
13802652 GCATGTCACAACATTTTGCTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
13802683 GCGTGTCAAAACATTTTGCTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
13802714 GCGTGTCATAACGTTTTACTTGTTATCCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
** **
13802745 ATGTGTCACAATGTTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
13802776 GCGTGTCACAACATTTTACT
1 GCGTGTCACAACATTTTACT
13802796 GGTTGTGGTT
Statistics
Matches: 199, Mismatches: 38, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 199 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (31 bp):
GCGTGTCACAACATTTTACTTGTTATGCATG
Found at i:13804396 original size:17 final size:18
Alignment explanation
Indices: 13804374--13804410 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
13804364 CAATTAATTT
*
13804374 TATACATAATTT-TTTTA
1 TATACACAATTTATTTTA
13804391 TATACACAATTTATTTTA
1 TATACACAATTTATTTTA
13804409 TA
1 TA
13804411 CAATTCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (18 bp):
TATACACAATTTATTTTA
Found at i:13804408 original size:47 final size:47
Alignment explanation
Indices: 13804329--13804513 Score: 149
Period size: 52 Copynumber: 3.8 Consensus size: 47
13804319 GACCCTTGTC
* * *
13804329 TATACAT--TTTTTTTGTATATAGAATTAATTTTATACAATTAATTT
1 TATACATAATTTTTTTGTATACACAATTTATTTTATACAATTAATTT
* ** *
13804374 TATACATAATTTTTTTATATACACAATTTATTTTATACAATTCGTTG
1 TATACATAATTTTTTTGTATACACAATTTATTTTATACAATTAATTT
* * * *
13804421 TATACAGAATTAATTCTTATTGTATACATAATATATTTTATATAATTAATTT
1 TATAC---A-TAATT-TTTTTGTATACACAATTTATTTTATACAATTAATTT
* *
13804473 TTTACATAATTAATTTTTTGCCTATACACAATTAATTTTAT
1 TATACATAA-T--TTTTTTG--TATACACAATTTATTTTAT
13804514 CCAAGAATTT
Statistics
Matches: 108, Mismatches: 20, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
45 7 0.06
47 36 0.33
48 3 0.03
49 2 0.02
50 6 0.06
51 6 0.06
52 48 0.44
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (47 bp):
TATACATAATTTTTTTGTATACACAATTTATTTTATACAATTAATTT
Found at i:13804415 original size:14 final size:14
Alignment explanation
Indices: 13804346--13804379 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
13804336 TTTTTTTGTA
*
13804346 TATAGAATTAATTT
1 TATACAATTAATTT
13804360 TATACAATTAATTT
1 TATACAATTAATTT
13804374 TATACA
1 TATACA
13804380 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (14 bp):
TATACAATTAATTT
Found at i:13804484 original size:52 final size:50
Alignment explanation
Indices: 13804356--13804513 Score: 153
Period size: 52 Copynumber: 3.1 Consensus size: 50
13804346 TATAGAATTA
*
13804356 ATTTTATACAATTAATTTTATACATAA-T--TTTTTTATATACACAATTT
1 ATTTTATACAATTAATTTTATACATAATTAATTTTTTATATACACAATAT
** * * * *
13804403 ATTTTATACAATTCGTTGTATACAGAATTAATTCTTATTGTATACATAATAT
1 ATTTTATACAATTAATTTTATACATAATTAATT-TT-TTATATACACAATAT
* * *
13804455 ATTTTATATAATTAATTTTTTACATAATTAATTTTTTGCCTATACACAAT-T
1 ATTTTATACAATTAATTTTATACATAATTAATTTTTT--ATATACACAATAT
13804506 AATTTTAT
1 -ATTTTAT
13804514 CCAAGAATTT
Statistics
Matches: 88, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
47 23 0.26
48 1 0.01
50 4 0.05
51 5 0.06
52 55 0.62
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (50 bp):
ATTTTATACAATTAATTTTATACATAATTAATTTTTTATATACACAATAT
Found at i:13804490 original size:16 final size:16
Alignment explanation
Indices: 13804456--13804491 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
13804446 ACATAATATA
*
13804456 TTTTATATAATTAATT
1 TTTTACATAATTAATT
13804472 TTTTACATAATTAATT
1 TTTTACATAATTAATT
13804488 TTTT
1 TTTT
13804492 GCCTATACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTACATAATTAATT
Found at i:13805549 original size:31 final size:31
Alignment explanation
Indices: 13805510--13805771 Score: 326
Period size: 31 Copynumber: 8.5 Consensus size: 31
13805500 TGGCGTGTCA
* * *
13805510 GTGTGACAACATTTCACTTGATATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * * *
13805541 ATGTGACAACATTTGACTTGTTATGCATGAC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
13805572 GTGTCAAAACATTTTACTTGTTATGCATGAC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * * * *
13805603 ATGTCACAAAAATTTACGTGTTATGCATGCC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
13805634 ATGTCACTACATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * * * *
13805665 GTGTCAGAATAGTTTACTTGTTATGCACGAC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
13805696 GTGTCACAACATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
*
13805727 GTGTCACAACATTTTGCTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
13805758 GTGTCACAACATTT
1 GTGTCACAACATTT
13805772 ATTCCTTATT
Statistics
Matches: 199, Mismatches: 32, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 199 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (31 bp):
GTGTCACAACATTTTACTTGTTATGCATGGC
Found at i:13810082 original size:31 final size:31
Alignment explanation
Indices: 13810034--13810276 Score: 267
Period size: 31 Copynumber: 7.8 Consensus size: 31
13810024 TTTGTCAGTC
* *
13810034 ATGTTGTTACACACCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
13810065 ATGTAGTAACACGCCATGCATAAAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* * *
13810096 ATG-TGCTAACACGCCATGTAAATAACATAAA
1 ATGTTG-TAACACGCCATGCATATAACGTAAA
* *
13810127 ATATTGTAACACGCCATGCATATAATAG-AAA
1 ATGTTGTAACACGCCATGCATATAA-CGTAAA
* * * *
13810158 ATG-CGATAACATGCCATGCATATAATGTTAA
1 ATGTTG-TAACACGCCATGCATATAACGTAAA
* * * *
13810189 ATGCTGTAGCACGCCATGCATATAACATTAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
13810220 ATGTTGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
13810251 ATATTGTAGCACGCCATGCATATAAC
1 ATGTTGTAACACGCCATGCATATAAC
13810277 CAATGTCGTG
Statistics
Matches: 176, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
30 3 0.02
31 170 0.97
32 3 0.02
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (31 bp):
ATGTTGTAACACGCCATGCATATAACGTAAA
Found at i:13811905 original size:18 final size:18
Alignment explanation
Indices: 13811878--13811913 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13811868 CCTATTTTAC
* *
13811878 CTTATTTTATTTTATTTT
1 CTTATCTTATTTCATTTT
13811896 CTTATCTTATTTCATTTT
1 CTTATCTTATTTCATTTT
13811914 TAGTTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTATCTTATTTCATTTT
Found at i:13812141 original size:10 final size:10
Alignment explanation
Indices: 13812123--13812174 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
13812113 AAATTCAAGT
13812123 AAAAAAAAAG
1 AAAAAAAAAG
*
13812133 AAAATAAAAG
1 AAAAAAAAAG
13812143 AAAGAAACAAA-
1 AAA-AAA-AAAG
*
13812154 AAAAAAAAAA
1 AAAAAAAAAG
13812164 AAACAAAAAAG
1 AAA-AAAAAAG
13812175 GAAAGGAACC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
9 3 0.09
10 18 0.51
11 11 0.31
12 3 0.09
ACGTcount: A:0.87, C:0.04, G:0.08, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Done.