Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 48 of 54
Found at i:19193825 original size:16 final size:17
Alignment explanation
Indices: 19193793--19193825 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19193783 CACATTTAAC
19193793 TAACTAAAACTATCAAAT
1 TAACTAAAAC-ATCAAAT
19193811 TAACTAAAA-ATCAAA
1 TAACTAAAACATCAAA
19193826 ACCTAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
TAACTAAAACATCAAAT
Found at i:19196625 original size:21 final size:20
Alignment explanation
Indices: 19196600--19196638 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19196590 CGGCCATAAG
19196600 GAGAGAACAAGAAAGAAAATA
1 GAGAGAA-AAGAAAGAAAATA
* *
19196621 GAGAGGAAAGGAAGAAAA
1 GAGAGAAAAGAAAGAAAA
19196639 GAGAAAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.03
Consensus pattern (20 bp):
GAGAGAAAAGAAAGAAAATA
Found at i:19198956 original size:20 final size:21
Alignment explanation
Indices: 19198931--19198975 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
19198921 ATCTTACTTT
19198931 TTTTCAC-TTGTTT-CCTTGAA
1 TTTTCACGTT-TTTCCCTTGAA
19198951 TTTTCACGTTTTTCCCTTGAA
1 TTTTCACGTTTTTCCCTTGAA
19198972 TTTT
1 TTTT
19198976 TCCACCTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.13, C:0.20, G:0.09, T:0.58
Consensus pattern (21 bp):
TTTTCACGTTTTTCCCTTGAA
Found at i:19200274 original size:5 final size:5
Alignment explanation
Indices: 19200264--19200289 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19200254 TATGTGTATA
19200264 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
19200290 TTATAGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:19200713 original size:34 final size:34
Alignment explanation
Indices: 19200667--19200749 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
19200657 TTCAAGAAGG
* *
19200667 GAAAGAGAGCCATTTAAGGGCTGGTTTTGGAGGCT
1 GAAA-AGAGCCATTTAACGGCTGGATTTGGAGGCT
** *
19200702 GAAAAGAGCCATTTTTCTGCTGGATTTGGAGGCT
1 GAAAAGAGCCATTTAACGGCTGGATTTGGAGGCT
* *
19200736 GGAAAGTGCCATTT
1 GAAAAGAGCCATTT
19200750 TTTTGCTGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 37 0.90
35 4 0.10
ACGTcount: A:0.25, C:0.13, G:0.33, T:0.29
Consensus pattern (34 bp):
GAAAAGAGCCATTTAACGGCTGGATTTGGAGGCT
Found at i:19200776 original size:34 final size:34
Alignment explanation
Indices: 19200686--19200778 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 34
19200676 CCATTTAAGG
* *
19200686 GCTGGTTTTGGAGGCTGAAAAGAGCCATTTTTCT
1 GCTGATTTTGGAGGCTGAAAAGTGCCATTTTTCT
* *
19200720 GCTGGA-TTTGGAGGCTGGAAAGTGCCATTTTTTT
1 GCT-GATTTTGGAGGCTGAAAAGTGCCATTTTTCT
**
19200754 GCTGATTTTGGAGGCCAAAAAGTGC
1 GCTGATTTTGGAGGCTGAAAAGTGC
19200779 AGAATTTTGC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 2 0.04
34 47 0.94
35 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (34 bp):
GCTGATTTTGGAGGCTGAAAAGTGCCATTTTTCT
Found at i:19200949 original size:34 final size:33
Alignment explanation
Indices: 19200856--19200955 Score: 105
Period size: 34 Copynumber: 3.0 Consensus size: 33
19200846 TTCAAATTTT
*
19200856 TTTGAAGG--AAAGGTGCAGCTTAGCTACTGAAA
1 TTTGAAGGAAAAAGGAGCAGCTTAGCTACTG-AA
* * * *
19200888 TTTGAAGGAAAAACAGAGCAGCATAGCTGCTGAT
1 TTTGAAGGAAAAA-GGAGCAGCTTAGCTACTGAA
*
19200922 TTTGAAGTAAAAAGGAGCAGCTTTAGCTACTGAA
1 TTTGAAGGAAAAAGGAGCAGC-TTAGCTACTGAA
19200956 AATTTCTAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
32 8 0.15
33 7 0.13
34 25 0.46
35 14 0.26
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (33 bp):
TTTGAAGGAAAAAGGAGCAGCTTAGCTACTGAA
Found at i:19201114 original size:10 final size:10
Alignment explanation
Indices: 19201101--19201161 Score: 68
Period size: 10 Copynumber: 5.9 Consensus size: 10
19201091 AGAAAGAAAG
19201101 AAAGAAAATA
1 AAAGAAAATA
*
19201111 AAAGAAATTA
1 AAAGAAAATA
*
19201121 AAAGAAAAGA
1 AAAGAAAATA
**
19201131 AAAGAAAGGA
1 AAAGAAAATA
19201141 AAAGAAAATA
1 AAAGAAAATA
19201151 ACAAGGAAAAT
1 A-AA-GAAAAT
19201162 GGGCATGGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
10 35 0.81
11 2 0.05
12 6 0.14
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.08
Consensus pattern (10 bp):
AAAGAAAATA
Found at i:19201126 original size:20 final size:20
Alignment explanation
Indices: 19201093--19201151 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
19201083 GAAGGAAGAG
19201093 AAAGAAA-G-AAAGAAAATA
1 AAAGAAAGGAAAAGAAAATA
** *
19201111 AAAGAAATTAAAAGAAAAGA
1 AAAGAAAGGAAAAGAAAATA
19201131 AAAGAAAGGAAAAGAAAATA
1 AAAGAAAGGAAAAGAAAATA
19201151 A
1 A
19201152 CAAGGAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 7 0.21
20 27 0.79
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AAAGAAAGGAAAAGAAAATA
Found at i:19201128 original size:5 final size:5
Alignment explanation
Indices: 19201088--19201148 Score: 63
Period size: 5 Copynumber: 12.4 Consensus size: 5
19201078 AGGAAGAAGG
* **
19201088 AAGAGA AAG-A AAG-A AAGAA AATAA AAGAA ATTAA AAGAA AAGAA AAGAA
1 AAGA-A AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
*
19201137 AGGAA AAGAA AA
1 AAGAA AAGAA AA
19201149 TAACAAGGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
4 8 0.17
5 35 0.76
6 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (5 bp):
AAGAA
Found at i:19201217 original size:25 final size:25
Alignment explanation
Indices: 19201180--19201228 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
19201170 CCCAACAAGC
*
19201180 AAGGAAAATTGGACATGATCCAATA
1 AAGGAAAATTGGACATGACCCAATA
19201205 AAGGAAGAA-TGGACATGACCCAAT
1 AAGGAA-AATTGGACATGACCCAAT
19201229 TAAAAAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.16
Consensus pattern (25 bp):
AAGGAAAATTGGACATGACCCAATA
Found at i:19201241 original size:25 final size:24
Alignment explanation
Indices: 19201189--19201241 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
19201179 CAAGGAAAAT
*
19201189 TGGACATGATCCAATAAAGGAAGAA
1 TGGACATGACCCAATAAA-GAAGAA
19201214 TGGACATGACCCAATTAAA-AAGACA
1 TGGACATGACCCAA-TAAAGAAGA-A
19201239 TGG
1 TGG
19201242 GAGAAGTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 4 0.16
25 17 0.68
26 4 0.16
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (24 bp):
TGGACATGACCCAATAAAGAAGAA
Found at i:19204027 original size:35 final size:34
Alignment explanation
Indices: 19203964--19204033 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 34
19203954 TACTACATTG
*
19203964 GGTTTTAGTTTAGCCCGTGAAAAACTATTGTGAAA
1 GGTTTTAGTTGAGCCCGTGAAAAACTATTGT-AAA
* *
19203999 GGTTTTAGTTGAGCCTG-GTAAAAGCTATTGTAAA
1 GGTTTTAGTTGAGCCCGTG-AAAAACTATTGTAAA
19204033 G
1 G
19204034 CTTGGTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 5 0.16
35 26 0.84
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (34 bp):
GGTTTTAGTTGAGCCCGTGAAAAACTATTGTAAA
Found at i:19210872 original size:19 final size:18
Alignment explanation
Indices: 19210824--19210872 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 18
19210814 AGTATAAATA
19210824 TCTTTCTTCCAGTAGCTTT
1 TCTTT-TTCCAGTAGCTTT
19210843 TCACATTTTTCCAGTAGCTTCT
1 T--C-TTTTTCCAGTAGCTT-T
19210865 TCTTTTTC
1 TCTTTTTC
19210873 TTCCTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
21 13 0.50
22 5 0.19
ACGTcount: A:0.12, C:0.27, G:0.08, T:0.53
Consensus pattern (18 bp):
TCTTTTTCCAGTAGCTTT
Found at i:19215655 original size:2 final size:2
Alignment explanation
Indices: 19215648--19215674 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19215638 TTTCTATGAC
19215648 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
19215675 CATTATCATG
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:19215783 original size:43 final size:42
Alignment explanation
Indices: 19215706--19215820 Score: 185
Period size: 43 Copynumber: 2.7 Consensus size: 42
19215696 AACACACTCC
* *
19215706 GCTCATGTGCACTCCCTACTCGCACATAGTTGGGTCATCATCA
1 GCTCATGTGCACTCCC-ACACGCACATAGCTGGGTCATCATCA
*
19215749 GCTCATGTGCACTCCCACACCGCATATAGCTGGGTCATCATCA
1 GCTCATGTGCACTCCCACA-CGCACATAGCTGGGTCATCATCA
19215792 GCTCATGTGCACTCCCACACGCACATAGC
1 GCTCATGTGCACTCCCACACGCACATAGC
19215821 GAGCTCATCA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
42 11 0.16
43 56 0.84
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
GCTCATGTGCACTCCCACACGCACATAGCTGGGTCATCATCA
Found at i:19217832 original size:7 final size:7
Alignment explanation
Indices: 19217822--19217873 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
19217812 CCTTTTTGTT
19217822 TTTCTTC
1 TTTCTTC
19217829 TTTCTTC
1 TTTCTTC
*
19217836 CTTC-TC
1 TTTCTTC
19217842 TTT-TATC
1 TTTCT-TC
19217849 TTTACTTC
1 TTT-CTTC
*
19217857 TTTCTCC
1 TTTCTTC
19217864 TTTCTTC
1 TTTCTTC
19217871 TTT
1 TTT
19217874 TCTCTTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 4 0.11
7 27 0.73
8 5 0.14
9 1 0.03
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTCTTC
Found at i:19217856 original size:28 final size:29
Alignment explanation
Indices: 19217825--19217880 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
19217815 TTTTGTTTTT
19217825 CTTCTTTCTTCC-TTC-TCTTTTATCTTTA
1 CTTCTTTC-TCCTTTCTTCTTTTATCTTTA
*
19217853 CTTCTTTCTCCTTTCTTCTTTTCTCTTT
1 CTTCTTTCTCCTTTCTTCTTTTATCTTT
19217881 TTGCTTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 11 0.44
29 11 0.44
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (29 bp):
CTTCTTTCTCCTTTCTTCTTTTATCTTTA
Found at i:19227006 original size:30 final size:28
Alignment explanation
Indices: 19226972--19227031 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
19226962 TTTTTGAAAT
* *
19226972 TTACACTTTTGCCCCCACAAAAGTGAAAAA
1 TTACACTTTTG--CCCAAAAAACTGAAAAA
*
19227002 TTACATTTTTGCCCAAAAAACTGAAAAA
1 TTACACTTTTGCCCAAAAAACTGAAAAA
19227030 TT
1 TT
19227032 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 17 0.63
30 10 0.37
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (28 bp):
TTACACTTTTGCCCAAAAAACTGAAAAA
Found at i:19228470 original size:64 final size:63
Alignment explanation
Indices: 19228334--19228481 Score: 181
Period size: 64 Copynumber: 2.3 Consensus size: 63
19228324 GTATTTAGAG
*** * *
19228334 GTTGTGCTTGATCCTTGAAAGGCATAAAGGTTATACGTTAGCCTTCAAAAGGTTGTGTGTAAG
1 GTTGTGCTTGATCCTTGAAAGGCATAAAGGTTATACGTTAGCCTTCAAAAGGTAAAGTGAAAA
* * *
19228397 GATTATGCTTGATCCTTGAAAGGCATAGAGGTTATATC-TTAGCCTTCAAAGGGTAAAGTGAAAA
1 G-TTGTGCTTGATCCTTGAAAGGCATAAAGGTTATA-CGTTAGCCTTCAAAAGGTAAAGTG-AAA
19228461 A
63 A
*
19228462 GTTGTGCTTGAACCTTGAAA
1 GTTGTGCTTGATCCTTGAAA
19228482 AATAGCTAGT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.01
64 67 0.93
65 4 0.06
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (63 bp):
GTTGTGCTTGATCCTTGAAAGGCATAAAGGTTATACGTTAGCCTTCAAAAGGTAAAGTGAAAA
Found at i:19228528 original size:20 final size:20
Alignment explanation
Indices: 19228499--19228536 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19228489 AGTTTGTGCA
19228499 CCAAACCTTCTCTAACTACT
1 CCAAACCTTCTCTAACTACT
*
19228519 CCAAAGCTTCTCTAACTA
1 CCAAACCTTCTCTAACTA
19228537 TAAAAAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.29
Consensus pattern (20 bp):
CCAAACCTTCTCTAACTACT
Found at i:19232023 original size:68 final size:69
Alignment explanation
Indices: 19231896--19232098 Score: 189
Period size: 69 Copynumber: 3.0 Consensus size: 69
19231886 TGGAATCATT
* * * * * * * * * *
19231896 ATCACATATATTTCAACTTAGCATTCATCATATACTCATTTTTATCTCTTATAGCATGTGG-TAT
1 ATCACATACATTACAACATAGCATACATCGTATGCTCATTCTCATCTCATATAGCATGTGGAAAT
19231960 CAA-C
66 -AAGC
* * * * *
19231964 ATCA-ATTACCTTACAACATAGCATATATCATTGTGCTCATTCTCATCTCAT-TAGTATGTGGAA
1 ATCACA-TACATTACAACATAGCATACATC-GTATGCTCATTCTCATCTCATATAGCATGTGGAA
19232027 ATAAGC
64 ATAAGC
* * *
19232033 ATCACATACATTACAACATAGTATACATCGTATGCTCATTCTCGTCTCATATAGCATGTGCAAAT
1 ATCACATACATTACAACATAGCATACATCGTATGCTCATTCTCATCTCATATAGCATGTGGAAAT
19232098 A
66 A
19232099 GCCAAACATG
Statistics
Matches: 107, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
67 1 0.01
68 50 0.47
69 55 0.51
70 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (69 bp):
ATCACATACATTACAACATAGCATACATCGTATGCTCATTCTCATCTCATATAGCATGTGGAAAT
AAGC
Found at i:19232113 original size:68 final size:69
Alignment explanation
Indices: 19231974--19232115 Score: 164
Period size: 68 Copynumber: 2.1 Consensus size: 69
19231964 ATCAATTACC
* * * * * *
19231974 TTACAACATAGCATATATCATTGTGCTCATTCTCATCTCATTAGTATGTGGAAATAAGCATCACA
1 TTACAACATAGCATACATCAGTATGCTCATTCTCATCTCATTAGCATGTGCAAATAAGCATAACA
19232039 TACA
66 TACA
* *
19232043 TTACAACATAGTATACATC-GTATGCTCATTCTCGTCTCATATAGCATGTGCAAAT-AGCCA-AA
1 TTACAACATAGCATACATCAGTATGCTCATTCTCATCTCAT-TAGCATGTGCAAATAAG-CATAA
*
19232105 CATGCA
64 CATACA
19232111 TTACA
1 TTACA
19232116 TTAGAACATA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
68 31 0.50
69 31 0.50
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (69 bp):
TTACAACATAGCATACATCAGTATGCTCATTCTCATCTCATTAGCATGTGCAAATAAGCATAACA
TACA
Found at i:19234984 original size:68 final size:68
Alignment explanation
Indices: 19234855--19235075 Score: 268
Period size: 68 Copynumber: 3.2 Consensus size: 68
19234845 AAAATGATGT
* **
19234855 TTCCAAGAAAGTTCGTAATTGCTTTTATATAGTACCACCAACAGCAAGTTTAGTGTTTATGTTGA
1 TTCCAAGAAAGTTCCTAATTG-TTTT-TATAGT---ACCAACAGCAAGTTTAGTGTTTATGTCAA
19234920 GATAATGC
61 GATAATGC
* * * *
19234928 TTCCAAGAACGTTCCTAATTGTTTTTATAGTACCAACAGCAAGTTTAGCGTGTATGTCAAGATGA
1 TTCCAAGAAAGTTCCTAATTGTTTTTATAGTACCAACAGCAAGTTTAGTGTTTATGTCAAGATAA
*
19234993 TGT
66 TGC
* *
19234996 TTCCAAGAAAGTTCCTAATTGCTTTTATAGTACCAACAACAAGTTTAGTGTTTATGTC--GATGA
1 TTCCAAGAAAGTTCCTAATTGTTTTTATAGTACCAACAGCAAGTTTAGTGTTTATGTCAAGAT-A
*
19235059 A-GT
65 ATGC
19235062 TTCCAAGAAAGTTC
1 TTCCAAGAAAGTTC
19235076 ATGCGAAGGG
Statistics
Matches: 133, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
66 19 0.14
67 1 0.01
68 84 0.63
71 6 0.05
72 4 0.03
73 19 0.14
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (68 bp):
TTCCAAGAAAGTTCCTAATTGTTTTTATAGTACCAACAGCAAGTTTAGTGTTTATGTCAAGATAA
TGC
Found at i:19238773 original size:2 final size:2
Alignment explanation
Indices: 19238762--19238831 Score: 112
Period size: 2 Copynumber: 37.0 Consensus size: 2
19238752 TAATAGTAAG
19238762 TA TA -A TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19238801 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19238832 CTCACATACA
Statistics
Matches: 64, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
1 4 0.06
2 60 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19239399 original size:2 final size:2
Alignment explanation
Indices: 19239392--19239462 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
19239382 GGTACCCTAN
19239392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19239434 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 A
19239463 ATGAGAGATC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19242009 original size:15 final size:16
Alignment explanation
Indices: 19241989--19242023 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19241979 TCCGATAGAA
*
19241989 AATTCTGTTGGAAAT-
1 AATTCTGTAGGAAATG
19242004 AATTCTGTAGGAAATG
1 AATTCTGTAGGAAATG
19242020 AATT
1 AATT
19242024 TCCAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (16 bp):
AATTCTGTAGGAAATG
Found at i:19244637 original size:30 final size:30
Alignment explanation
Indices: 19244603--19244670 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
19244593 TTCATCTTCA
* *
19244603 TCTTCATTTTCATCTCC-TTCCATGTCATTT
1 TCTTCATCTTCATC-CCTTTCCATGTCATCT
*
19244633 TCTTCATCTTCATCCCTTTGCATGTCATCT
1 TCTTCATCTTCATCCCTTTCCATGTCATCT
19244663 TCTTCATC
1 TCTTCATC
19244671 CTCAATCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.13, C:0.32, G:0.04, T:0.50
Consensus pattern (30 bp):
TCTTCATCTTCATCCCTTTCCATGTCATCT
Found at i:19244643 original size:21 final size:22
Alignment explanation
Indices: 19244593--19244643 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
19244583 CGTCTTCAAG
*
19244593 TTCATCTT-CATCTTCATTTTC
1 TTCATCTTCCATCGTCATTTTC
*
19244614 ATC-TCCTTCCAT-GTCATTTTC
1 TTCAT-CTTCCATCGTCATTTTC
19244635 TTCATCTTC
1 TTCATCTTC
19244644 ATCCCTTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.14, C:0.31, G:0.02, T:0.53
Consensus pattern (22 bp):
TTCATCTTCCATCGTCATTTTC
Found at i:19255912 original size:18 final size:18
Alignment explanation
Indices: 19255885--19255939 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 18
19255875 GTGAACAAGA
*
19255885 ATTTTATTATTTTTTACT
1 ATTTTTTTATTTTTTACT
*
19255903 ATTTTTTTATTTTTATATT
1 ATTTTTTTATTTTT-TACT
19255922 ATTTATTATATATTTTTT
1 ATTT-TT-T-TATTTTTT
19255940 TATATTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 13 0.42
19 7 0.23
20 2 0.06
21 2 0.06
22 7 0.23
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTTTTATTTTTTACT
Found at i:19255914 original size:26 final size:26
Alignment explanation
Indices: 19255885--19255976 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 26
19255875 GTGAACAAGA
*
19255885 ATTTTATTATTTTTTACTATTTTTTT
1 ATTTTATTATTTTTTATTATTTTTTT
* * *
19255911 ATTTT-TATATTATTTATTATATATTT
1 ATTTTAT-TATTTTTTATTATTTTTTT
* *
19255937 -TTTTA-TATTTTGATTATTATTATATT
1 ATTTTATTATTTT--TTATTATTTTTTT
19255963 ATTATTATT-TTTTT
1 ATT-TTATTATTTTT
19255977 GTTGTAAGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
24 5 0.10
25 5 0.10
26 30 0.60
27 2 0.04
28 7 0.14
29 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (26 bp):
ATTTTATTATTTTTTATTATTTTTTT
Found at i:19255954 original size:41 final size:40
Alignment explanation
Indices: 19255894--19255970 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
19255884 AATTTTATTA
* *
19255894 TTTTTTACTATTTTTTTATTTTTATATTATTTATTATATAT
1 TTTTTTACTATTTTATTATTATTATATTA-TTATTATATAT
19255935 TTTTTTA-TATTTTGATTATTATTATATTATTATTAT
1 TTTTTTACTATTTT-ATTATTATTATATTATTATTAT
19255971 TTTTTTGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 13 0.39
41 20 0.61
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (40 bp):
TTTTTTACTATTTTATTATTATTATATTATTATTATATAT
Found at i:19255963 original size:11 final size:11
Alignment explanation
Indices: 19255909--19255970 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
19255899 TACTATTTTT
*
19255909 TTATTTTTATA
1 TTATTATTATA
19255920 TTATTTATTATA
1 TTA-TTATTATA
19255932 -TATT-TT-T-
1 TTATTATTATA
*
19255939 TTA-TATTTTGA
1 TTATTATTAT-A
19255950 TTATTATTATA
1 TTATTATTATA
19255961 TTATTATTAT
1 TTATTATTAT
19255971 TTTTTTGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
7 1 0.02
8 5 0.12
9 3 0.07
10 2 0.05
11 19 0.45
12 12 0.29
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
TTATTATTATA
Found at i:19255971 original size:14 final size:14
Alignment explanation
Indices: 19255909--19255971 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
19255899 TACTATTTTT
*
19255909 TTATTTTTATATTA
1 TTATTATTATATTA
19255923 TTTATTA-TATATT-
1 -TTATTATTATATTA
* *
19255936 TTTTTA-TATTTTGA
1 TTATTATTATATT-A
19255950 TTATTATTATATTA
1 TTATTATTATATTA
19255964 TTATTATT
1 TTATTATT
19255972 TTTTTGTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.25
14 20 0.50
15 10 0.25
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:19266819 original size:15 final size:15
Alignment explanation
Indices: 19266799--19266844 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
19266789 TTCTTAAAAC
19266799 AACTTTAAAATCAAA
1 AACTTTAAAATCAAA
*
19266814 AACTTTAAAATCCAA
1 AACTTTAAAATCAAA
*
19266829 AGCTTTAAAATCAAA
1 AACTTTAAAATCAAA
19266844 A
1 A
19266845 TATCTTATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (15 bp):
AACTTTAAAATCAAA
Found at i:19272221 original size:37 final size:37
Alignment explanation
Indices: 19272101--19272342 Score: 295
Period size: 37 Copynumber: 6.5 Consensus size: 37
19272091 TTAATGAGAT
* * *
19272101 TCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAAT
1 TCCTCAAAACTGAGGCAACGAGACTTTT-AAAATGAAC
* * *
19272139 TCCTCAAAACTAAGGCAATGTGACTTTTAAAAATGAAC
1 TCCTCAAAACTGAGGCAACGAGACTTTT-AAAATGAAC
* **
19272177 TCTTCAAAGTTGAGGCAACGAGACTTTTAAAATGAAC
1 TCCTCAAAACTGAGGCAACGAGACTTTTAAAATGAAC
* * *
19272214 TCGTCAAAACTGAGGCAACGAAACTTTAAAAATGAAC
1 TCCTCAAAACTGAGGCAACGAGACTTTTAAAATGAAC
* * * *
19272251 TCCTCAAAGCTGAGGCAATGTGACTTTAAAAATGAAC
1 TCCTCAAAACTGAGGCAACGAGACTTTTAAAATGAAC
* *
19272288 TCCTCAAAATTGAGGCAACGAGACTTTGAAAATGAAC
1 TCCTCAAAACTGAGGCAACGAGACTTTTAAAATGAAC
*
19272325 TTCTCAAAACTGAGGCAA
1 TCCTCAAAACTGAGGCAA
19272343 TGAAACCTTT
Statistics
Matches: 175, Mismatches: 29, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
37 121 0.69
38 54 0.31
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (37 bp):
TCCTCAAAACTGAGGCAACGAGACTTTTAAAATGAAC
Found at i:19272320 original size:111 final size:113
Alignment explanation
Indices: 19272103--19272353 Score: 391
Period size: 111 Copynumber: 2.2 Consensus size: 113
19272093 AATGAGATTC
* *
19272103 CTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAATTCCTCAAAACTAAGGCAATGTGACTTTTA
1 CTCAAAACTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAACTAAGGCAATGTGACTTTTA
* * *
19272168 AAAATGAACTCTTCAAAGTTGAGGCAACGAGACTTTTAAAATGAAC-T
66 AAAATGAACTCCTCAAAATTGAGGCAACGAGACTTTGAAAATGAACTT
* *
19272215 CGTCAAAACTGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAGCTGAGGCAATGTGAC-TTT
1 C-TCAAAACTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAACTAAGGCAATGTGACTTTT
19272278 AAAAATGAACTCCTCAAAATTGAGGCAACGAGACTTTGAAAATGAACTT
65 AAAAATGAACTCCTCAAAATTGAGGCAACGAGACTTTGAAAATGAACTT
*
19272327 CTCAAAACTGAGGCAATGAAACCTTTT
1 CTCAAAACTGAGGCAACGAAA-CTTTT
19272354 TTCCTTTTTT
Statistics
Matches: 127, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
111 66 0.52
112 38 0.30
113 23 0.18
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (113 bp):
CTCAAAACTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAACTAAGGCAATGTGACTTTTA
AAAATGAACTCCTCAAAATTGAGGCAACGAGACTTTGAAAATGAACTT
Found at i:19274458 original size:16 final size:16
Alignment explanation
Indices: 19274437--19274468 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19274427 TTGAGATAAT
19274437 GCACAATATCATGGTA
1 GCACAATATCATGGTA
19274453 GCACAATATCATGGTA
1 GCACAATATCATGGTA
19274469 CCACGATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (16 bp):
GCACAATATCATGGTA
Found at i:19284590 original size:9 final size:10
Alignment explanation
Indices: 19284538--19284618 Score: 53
Period size: 10 Copynumber: 8.0 Consensus size: 10
19284528 TGAACAAGAA
19284538 TTTTATTATT
1 TTTTATTATT
*
19284548 TTTTACTATT
1 TTTTATTATT
19284558 TTTTA-T-TT
1 TTTTATTATT
*
19284566 TTATATTATT
1 TTTTATTATT
19284576 TATTT-TATATT
1 T-TTTAT-TATT
*
19284587 TTTTA-AATT
1 TTTTATTATT
19284596 TTGATTATTATAT
1 TT--TTATTAT-T
*
19284609 TATTATTATT
1 TTTTATTATT
19284619 ATTATTTGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
8 6 0.11
9 7 0.12
10 22 0.39
11 17 0.30
12 2 0.04
13 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (10 bp):
TTTTATTATT
Found at i:19284604 original size:40 final size:43
Alignment explanation
Indices: 19284537--19284618 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 43
19284527 GTGAACAAGA
*
19284537 ATTTTATTATTTTTTACTATTTTTTATT-T-TTA-TATTATTT
1 ATTTTATTATTTTTTACAATTTTTTATTATATTATTATTATTT
19284577 ATTTTA-TATTTTTTA-AATTTTGATTATTATATTATTATTATT
1 ATTTTATTATTTTTTACAATTTT--TTATTATATTATTATTATT
19284619 ATTATTTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
38 5 0.14
39 9 0.25
40 11 0.31
41 1 0.03
42 3 0.08
43 7 0.19
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (43 bp):
ATTTTATTATTTTTTACAATTTTTTATTATATTATTATTATTT
Found at i:19290267 original size:28 final size:29
Alignment explanation
Indices: 19290219--19290277 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
19290209 TTTTTGAAAT
** *
19290219 TTACATTTTTGCCTCGTAAAAGTGAAAAA
1 TTACATTTTTGCCTCAAAAAAGTAAAAAA
*
19290248 TTACATTTTTGCC-CAAAAAATTAAAAAA
1 TTACATTTTTGCCTCAAAAAAGTAAAAAA
19290276 TT
1 TT
19290278 GCCCATAGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (29 bp):
TTACATTTTTGCCTCAAAAAAGTAAAAAA
Found at i:19291994 original size:13 final size:13
Alignment explanation
Indices: 19291978--19292002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19291968 TTCTAGAAAA
19291978 TTTATAAAATCAT
1 TTTATAAAATCAT
19291991 TTTATAAAATCA
1 TTTATAAAATCA
19292003 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:19297011 original size:5 final size:5
Alignment explanation
Indices: 19297003--19297035 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
19296993 ACCTAACCTG
19297003 ACTTA ACTTA AC-TA ACTTA ACTTA ACTTA ACTT
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTT
19297036 GGGCCACGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
ACTTA
Found at i:19297022 original size:14 final size:15
Alignment explanation
Indices: 19297003--19297035 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
19296993 ACCTAACCTG
19297003 ACTTAACTTAAC-TA
1 ACTTAACTTAACTTA
19297017 ACTTAACTTAACTTA
1 ACTTAACTTAACTTA
19297032 ACTT
1 ACTT
19297036 GGGCCACGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (15 bp):
ACTTAACTTAACTTA
Found at i:19297090 original size:15 final size:15
Alignment explanation
Indices: 19297070--19297115 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
19297060 TTCTTAAAAC
19297070 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
19297085 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
* *
19297100 AGCTTTAAAATCAAA
1 AACTTTAAAACCAAA
19297115 A
1 A
19297116 TCTCTAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.89
16 2 0.07
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:19299939 original size:19 final size:19
Alignment explanation
Indices: 19299915--19299952 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19299905 CTGTCAAACC
*
19299915 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
19299934 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
19299953 AGTTAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:19303447 original size:10 final size:11
Alignment explanation
Indices: 19303423--19303466 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
19303413 TCTCTAGGGT
19303423 TTTTGTTCT-TC
1 TTTT-TTCTCTC
19303434 TTTTTTC-CTC
1 TTTTTTCTCTC
19303444 -TTTTTCTCTC
1 TTTTTTCTCTC
19303454 -TTTTTCTCTC
1 TTTTTTCTCTC
19303464 TTT
1 TTT
19303467 GGCCAACCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 6 0.20
10 18 0.60
11 6 0.20
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (11 bp):
TTTTTTCTCTC
Found at i:19305877 original size:18 final size:18
Alignment explanation
Indices: 19305843--19305877 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19305833 GAGACAATAC
*
19305843 AAAGCTTGATGTAAATTT
1 AAAGCTTGATGCAAATTT
*
19305861 AAAGCTTGATGCCAATT
1 AAAGCTTGATGCAAATT
19305878 GAGAATATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (18 bp):
AAAGCTTGATGCAAATTT
Found at i:19330296 original size:20 final size:20
Alignment explanation
Indices: 19330268--19330319 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
19330258 AAGTTTAGGG
*
19330268 TTAGTGTCCAACA-TACAAAC
1 TTAGGGTCCAA-AGTACAAAC
*
19330288 TTAGGGTCCAAAGTGCAAAC
1 TTAGGGTCCAAAGTACAAAC
*
19330308 TTAGGGTTCAAA
1 TTAGGGTCCAAA
19330320 TTGAAATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (20 bp):
TTAGGGTCCAAAGTACAAAC
Found at i:19332406 original size:13 final size:13
Alignment explanation
Indices: 19332388--19332412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19332378 GCACGAAGGA
19332388 AACCAATTTAAGC
1 AACCAATTTAAGC
19332401 AACCAATTTAAG
1 AACCAATTTAAG
19332413 GAAGCGAGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
AACCAATTTAAGC
Found at i:19337059 original size:54 final size:54
Alignment explanation
Indices: 19336982--19337321 Score: 308
Period size: 54 Copynumber: 6.1 Consensus size: 54
19336972 TCGGACTTAG
* *
19336982 TCTTGATCACGAACTAAACTTGATATCTTCGCTTCAAAGGG-CTTGACGACTTGA
1 TCTTGATCACGAACTATACTTGATATCTTCACTTC-AAGGGTCTTGACGACTTGA
* * * *
19337036 TTTTGATTACGAACTATATTTGATATCTTCACCTCAAGGGTCTTGATAACTTGATCTTGATA
1 TCTTGATCACGAACTATACTTGATATCTTCACTTCAAGGGTCTTG---AC--GA-CTTG--A
* * * * ***
19337098 GTCTTGGTTACGAGCTAAACTTGATATCTTCACTTCAAACATCTTGACGACTTGA
1 -TCTTGATCACGAACTATACTTGATATCTTCACTTCAAGGGTCTTGACGACTTGA
* * *
19337153 TCTTGATCACAAACTATATTTGATATCTCTGC-CTT-AAGGGTCTTGACAACTTGA
1 TCTTGATCACGAACTATACTTGATATCT-T-CACTTCAAGGGTCTTGACGACTTGA
* ** ** *
19337207 TCTTGATCATGAACTATGTTTGATATCTTTGCTTCAAGGGTCTTCACGACTTGA
1 TCTTGATCACGAACTATACTTGATATCTTCACTTCAAGGGTCTTGACGACTTGA
* * * *
19337261 TCTTGATCATGAACTATACTTGATATCTTCACCTCAAGGGTCTTCACGACTTAA
1 TCTTGATCACGAACTATACTTGATATCTTCACTTCAAGGGTCTTGACGACTTGA
*
19337315 TTTTGAT
1 TCTTGAT
19337322 GTCAAGCTCA
Statistics
Matches: 234, Mismatches: 38, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
53 9 0.04
54 166 0.71
55 5 0.02
56 1 0.00
57 6 0.03
58 2 0.01
59 2 0.01
60 6 0.03
62 1 0.00
63 36 0.15
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (54 bp):
TCTTGATCACGAACTATACTTGATATCTTCACTTCAAGGGTCTTGACGACTTGA
Found at i:19337134 original size:117 final size:114
Alignment explanation
Indices: 19336979--19337304 Score: 362
Period size: 117 Copynumber: 2.9 Consensus size: 114
19336969 AACTCGGACT
* * *
19336979 TAGTCTTGATCACGAACTAAACTTGATATCTTCGCTTCAAAGGGCTTGACGACTTGATTTTGATT
1 TAGTCTTGGT-ACG-ACTAAACTTGATATCTTCGCTTCAAAGGGCTTGACGACTTGATCTTGATC
*
19337044 ACGAACTATATTTGATATCTTCACCTCAAGGGTCTTGATAACTTGATCTTG
64 ACGAACTATATTTGATATCTTCACCTCAAGGGTCTTGACAACTTGATCTTG
* ***
19337095 ATAGTCTTGGTTACGAGCTAAACTTGATATCTTCACTTCAAACATCTTGACGACTTGATCTTGAT
1 -TAGTCTTGG-TACGA-CTAAACTTGATATCTTCGCTTCAAAGGGCTTGACGACTTGATCTTGAT
* * *
19337160 CACAAACTATATTTGATATC-TCTGCCTTAAGGGTCTTGACAACTTGATCTTG
63 CACGAACTATATTTGATATCTTC-ACCTCAAGGGTCTTGACAACTTGATCTTG
* *** * *
19337212 -A-TCAT-G-A--ACTATGTTTGATATCTTTGCTTC-AAGGGTCTTCACGACTTGATCTTGATCA
1 TAGTCTTGGTACGACTAAACTTGATATCTTCGCTTCAAAGGG-CTTGACGACTTGATCTTGATCA
* *
19337270 TGAACTATACTTGATATCTTCACCTCAAGGGTCTT
65 CGAACTATATTTGATATCTTCACCTCAAGGGTCTT
19337305 CACGACTTAA
Statistics
Matches: 178, Mismatches: 26, Indels: 19
0.80 0.12 0.09
Matches are distributed among these distances:
107 2 0.01
108 65 0.37
109 3 0.02
111 1 0.01
113 1 0.01
114 3 0.02
115 1 0.01
116 3 0.02
117 98 0.55
118 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.37
Consensus pattern (114 bp):
TAGTCTTGGTACGACTAAACTTGATATCTTCGCTTCAAAGGGCTTGACGACTTGATCTTGATCAC
GAACTATATTTGATATCTTCACCTCAAGGGTCTTGACAACTTGATCTTG
Found at i:19339663 original size:20 final size:20
Alignment explanation
Indices: 19339638--19339678 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
19339628 ATTAGCCTTG
*
19339638 TTGATTTTTATGAAATGAAA
1 TTGATTTATATGAAATGAAA
19339658 TTGATTTATATGAAATGAAA
1 TTGATTTATATGAAATGAAA
19339678 T
1 T
19339679 GAGATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGATTTATATGAAATGAAA
Found at i:19339694 original size:25 final size:25
Alignment explanation
Indices: 19339647--19339696 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
19339637 GTTGATTTTT
*
19339647 ATGAAATGAAATTGATTTATATGAA
1 ATGAAATGAAATTGATGTATATGAA
*
19339672 ATGAAATGAGATTTGATGT-TATGAA
1 ATGAAATGA-AATTGATGTATATGAA
19339697 TCATATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (25 bp):
ATGAAATGAAATTGATGTATATGAA
Found at i:19340906 original size:57 final size:57
Alignment explanation
Indices: 19340792--19340906 Score: 135
Period size: 57 Copynumber: 2.0 Consensus size: 57
19340782 AAGTTAAGTA
* * * **
19340792 TTATCTCTAAATCATCTTAATTTATTTGGAGATAAATTAAATAATAAAATTTGATTT
1 TTATCTCTAAATCATCATAATTTATTTAGAGATAAATTAAATAACAAAATTAAATTT
* *
19340849 TTATCTCTAAATTATCATAA-TTA-TTAGAGATAAATTAAATGACCAATAATTAAATTT
1 TTATCTCTAAATCATCATAATTTATTTAGAGATAAATTAAAT-AACAA-AATTAAATTT
19340906 T
1 T
19340907 GATTGGTCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
55 16 0.33
56 6 0.12
57 27 0.55
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (57 bp):
TTATCTCTAAATCATCATAATTTATTTAGAGATAAATTAAATAACAAAATTAAATTT
Found at i:19340976 original size:80 final size:77
Alignment explanation
Indices: 19340849--19341022 Score: 204
Period size: 80 Copynumber: 2.2 Consensus size: 77
19340839 AATTTGATTT
* * * *
19340849 TTATCTCTAAATTATCATAATTATTAGAGATAAATTAAATGACCAATAATTAAATTTTGATTGGT
1 TTATCTTTAAATTATCTTAATTATTAGAGACAAATTAAATGACCAATAATTAAATTTTAATTGGT
*
19340914 CAAAAATATGATA
66 CAAAAATA-AATA
* * * *
19340927 TTATCTTTAAATTATCTTGATTTATTTAGAGACAAATTAGATTATCAATAATTAAATTTTAATTG
1 TTATCTTTAAATTATCTT-AATTA-TTAGAGACAAATTAAATGACCAATAATTAAATTTTAATTG
* * *
19340992 TTCCAAATTAAATA
64 GTCAAAAATAAATA
*
19341006 TTATCTTCAAATTATCT
1 TTATCTTTAAATTATCT
19341023 CAAGGGATAA
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
78 16 0.20
79 23 0.28
80 42 0.52
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (77 bp):
TTATCTTTAAATTATCTTAATTATTAGAGACAAATTAAATGACCAATAATTAAATTTTAATTGGT
CAAAAATAAATA
Found at i:19343945 original size:18 final size:18
Alignment explanation
Indices: 19343909--19343946 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19343899 ATGTAAGATT
*
19343909 ATATTTTATTTAATTCTA
1 ATATTTTATTTAATGCTA
19343927 ATATTTTAATTT-ATGCTA
1 ATATTTT-ATTTAATGCTA
19343945 AT
1 AT
19343947 GAGTACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
ATATTTTATTTAATGCTA
Found at i:19345714 original size:13 final size:14
Alignment explanation
Indices: 19345698--19345750 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
19345688 ATCGGCATAT
*
19345698 TTAAC-AATTAAAT
1 TTAACAAATTAAAA
**
19345711 TTAACGATGTTAAAA
1 TTAAC-AAATTAAAA
19345726 TTAA-AAATTAAAA
1 TTAACAAATTAAAA
19345739 TTAACAAATTAA
1 TTAACAAATTAA
19345751 CAAAATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 16 0.50
14 7 0.22
15 9 0.28
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (14 bp):
TTAACAAATTAAAA
Found at i:19346234 original size:20 final size:20
Alignment explanation
Indices: 19346206--19346257 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
19346196 AAGTTTAGGG
* *
19346206 TTAGTGTCCAAAATACAAGC
1 TTAGGGTCCAAAATACAAAC
* *
19346226 TTAGGGTCCAAAGTGCAAAC
1 TTAGGGTCCAAAATACAAAC
*
19346246 TTAGGGTTCAAA
1 TTAGGGTCCAAA
19346258 TTGAAATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (20 bp):
TTAGGGTCCAAAATACAAAC
Found at i:19346689 original size:26 final size:26
Alignment explanation
Indices: 19346656--19346722 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
19346646 ATGTCATAAT
19346656 ACATGATGACATGGTATGTTAATGTG
1 ACATGATGACATGGTATGTTAATGTG
19346682 ACATGATGACATGGTATGTTAATGTG
1 ACATGATGACATGGTATGTTAATGTG
19346708 ACATGATGACATGGT
1 ACATGATGACATGGT
19346723 CATATCACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (26 bp):
ACATGATGACATGGTATGTTAATGTG
Found at i:19348982 original size:15 final size:16
Alignment explanation
Indices: 19348950--19348996 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
19348940 TAATTATTAA
*
19348950 TTAATTTATAATATCTT
1 TTAATATAT-ATATCTT
19348967 TTAATATATATA-CTT
1 TTAATATATATATCTT
19348982 TATATATATATATAT
1 T-TA-ATATATATAT
19348997 ATATTAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 17 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATATATATATCTT
Found at i:19352332 original size:19 final size:19
Alignment explanation
Indices: 19352308--19352345 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19352298 TTGTCAAACT
*
19352308 CTCAAATTATACCCCAATA
1 CTCAAATCATACCCCAATA
*
19352327 CTCAAATCATACTCCAATA
1 CTCAAATCATACCCCAATA
19352346 AGTTAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACCCCAATA
Found at i:19352930 original size:20 final size:20
Alignment explanation
Indices: 19352902--19352953 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
19352892 AAGTTTAGGG
*
19352902 TTAGTGTCCAAAATACAAAC
1 TTAGGGTCCAAAATACAAAC
* *
19352922 TTAGGGTCCAAAGTGCAAAC
1 TTAGGGTCCAAAATACAAAC
*
19352942 TTAGGGTTCAAA
1 TTAGGGTCCAAA
19352954 TTGATATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (20 bp):
TTAGGGTCCAAAATACAAAC
Found at i:19355719 original size:20 final size:20
Alignment explanation
Indices: 19355694--19355732 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19355684 TAGGGCTAGT
19355694 GTCCAAAATACAAACTTAGG
1 GTCCAAAATACAAACTTAGG
* *
19355714 GTCCAAAGTGCAAACTTAG
1 GTCCAAAATACAAACTTAG
19355733 AGTTCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
GTCCAAAATACAAACTTAGG
Found at i:19357825 original size:13 final size:13
Alignment explanation
Indices: 19357807--19357831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19357797 GCACGAAGGA
19357807 AACCAATTTAAGC
1 AACCAATTTAAGC
19357820 AACCAATTTAAG
1 AACCAATTTAAG
19357832 GAAGCGAGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
AACCAATTTAAGC
Found at i:19360594 original size:9 final size:9
Alignment explanation
Indices: 19360577--19360610 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
19360567 ATTTATTTTG
19360577 TTTTATTAT
1 TTTTATTAT
*
19360586 TTTTGTTAT
1 TTTTATTAT
19360595 TTTTATTAT
1 TTTTATTAT
*
19360604 TATTATT
1 TTTTATT
19360611 TATGCAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTATTAT
Found at i:19361893 original size:14 final size:14
Alignment explanation
Indices: 19361874--19361902 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19361864 ATTTAGATAA
19361874 GTTTAAGCATTAAT
1 GTTTAAGCATTAAT
19361888 GTTTAAGCATTAAT
1 GTTTAAGCATTAAT
19361902 G
1 G
19361903 ATATTCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (14 bp):
GTTTAAGCATTAAT
Found at i:19362154 original size:14 final size:14
Alignment explanation
Indices: 19362108--19362155 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
19362098 CATAAAACAA
*
19362108 AAAAAAAATAAAAT
1 AAAAATAATAAAAT
*
19362122 -AAAATAA-ATAAT
1 AAAAATAATAAAAT
19362134 AATAAATAATAAAAT
1 AA-AAATAATAAAAT
19362149 AAAAATA
1 AAAAATA
19362156 TAATGACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 7 0.25
14 11 0.39
15 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAATAATAAAAT
Found at i:19362653 original size:18 final size:18
Alignment explanation
Indices: 19362630--19362694 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
19362620 NNNNNNNNNN
19362630 AAAAATATAAAAATATAA
1 AAAAATATAAAAATATAA
* *
19362648 AAAAATACAAAAAGATAA
1 AAAAATATAAAAATATAA
19362666 AATATAA-AT-AAAATA-AA
1 AA-A-AATATAAAAATATAA
*
19362683 AAATATATAAAA
1 AAAAATATAAAA
19362695 TTTTTGTCAC
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 3 0.08
17 7 0.18
18 23 0.61
19 2 0.05
20 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAAATATAAAAATATAA
Found at i:19362667 original size:25 final size:26
Alignment explanation
Indices: 19362630--19362695 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
19362620 NNNNNNNNNN
*
19362630 AAAAATATAAAAATATAAA-AAAATAC
1 AAAAATAT-AAAATATAAATAAAATAA
*
19362656 AAAAAGATAAAATATAAATAAAATAA
1 AAAAATATAAAATATAAATAAAATAA
19362682 AAAATATATAAAAT
1 AAAA-ATATAAAAT
19362696 TTTTGTCACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 10 0.29
26 17 0.49
27 8 0.23
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (26 bp):
AAAAATATAAAATATAAATAAAATAA
Found at i:19362864 original size:29 final size:31
Alignment explanation
Indices: 19362807--19362866 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
19362797 AATTAGAAAG
19362807 AAAATAGAAAATATGATAATAAAAAATAAAAT
1 AAAATAGAAAATA-GATAATAAAAAATAAAAT
* *
19362839 AAAAT-GAAAATA-ATAATTAATAATAAAA
1 AAAATAGAAAATAGATAATAAAAAATAAAA
19362867 AATGGACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
31 7 0.27
32 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (31 bp):
AAAATAGAAAATAGATAATAAAAAATAAAAT
Found at i:19365951 original size:2 final size:2
Alignment explanation
Indices: 19365944--19365970 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19365934 AATAATACAA
19365944 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
19365971 ATGAGAGATC
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:19385381 original size:2 final size:2
Alignment explanation
Indices: 19385374--19385412 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19385364 CATTATGTTG
19385374 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
19385413 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19385518 original size:43 final size:43
Alignment explanation
Indices: 19385471--19385598 Score: 175
Period size: 43 Copynumber: 3.0 Consensus size: 43
19385461 GTAATGATAT
* * *
19385471 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGC
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCAGATGC
* * *
19385514 TGACCCAGCTATGTGCGAGTAGTGACTGCACATGAGCAGATGC
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCAGATGC
* * *
19385557 TGACCCAGCTATGTGCAAGTAGGGAGTGCACATGAGCTGATG
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCAGATG
19385599 ATGATGGGAT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.24, C:0.22, G:0.34, T:0.20
Consensus pattern (43 bp):
TGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCAGATGC
Found at i:19385633 original size:2 final size:2
Alignment explanation
Indices: 19385626--19385673 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
19385616 ATGATGACGG
19385626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
19385668 AG AT AT
1 AT AT AT
19385674 GTGTGTTACA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:19389257 original size:43 final size:43
Alignment explanation
Indices: 19389180--19389273 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
19389170 ACCATCCCGC
* * * *
19389180 CATCATCAACTCATGTGCATTCCCCACTCGCACATAGCTGGGT
1 CATCATCAACTCATGTACACTCCACACTCACACATAGCTGGGT
* *
19389223 CATCATCAACTCATGTACACTCTCACAC-CACACATGGTTGGGT
1 CATCATCAACTCATGTACACTC-CACACTCACACATAGCTGGGT
19389266 CATCATCA
1 CATCATCA
19389274 TCACACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 40 0.91
44 4 0.09
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.26
Consensus pattern (43 bp):
CATCATCAACTCATGTACACTCCACACTCACACATAGCTGGGT
Found at i:19392370 original size:60 final size:58
Alignment explanation
Indices: 19392266--19392379 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 58
19392256 ATTCTTGAAA
* * *
19392266 GGTTTTACCTCCTTGAAAAGGTAGATAGGTTATACTTGAGCCTTGAAAAAGTAAGCTT
1 GGTTATACCTCCTTGAAAAGGTAGATAAGTTATACTTGAACCTTGAAAAAGTAAGCTT
* * *
19392324 GGTTATACCTCCATTGTAAAAGGTAGATAAGTTGTGA-TTTAACCTTGAAAAGGTAA
1 GGTTATACCTCC-TTG-AAAAGGTAGATAAGTTAT-ACTTGAACCTTGAAAAAGTAA
19392380 TGACTTGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 11 0.23
59 3 0.06
60 32 0.68
61 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (58 bp):
GGTTATACCTCCTTGAAAAGGTAGATAAGTTATACTTGAACCTTGAAAAAGTAAGCTT
Found at i:19395169 original size:33 final size:34
Alignment explanation
Indices: 19395145--19395209 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
19395135 CACAACCTTT
19395145 ACAATGC-TTTTCACGTG-AGCAAGCATAACCCAC
1 ACAATGCATTTTCACG-GAAGCAAGCATAACCCAC
19395178 ACAATGCATTTTCACGGAAGCAAGCATAACCC
1 ACAATGCATTTTCACGGAAGCAAGCATAACCC
19395210 CTTGCCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.20
Consensus pattern (34 bp):
ACAATGCATTTTCACGGAAGCAAGCATAACCCAC
Found at i:19395242 original size:29 final size:29
Alignment explanation
Indices: 19395204--19395322 Score: 175
Period size: 29 Copynumber: 4.1 Consensus size: 29
19395194 GAAGCAAGCA
* * *
19395204 TAACCCCTTGCCTTTTCAAGGATTAGGTG
1 TAACCTCTTACCTTTTCAAGGATCAGGTG
*
19395233 TAACCTCTTGCCTTTTCAAGGATCAGGTG
1 TAACCTCTTACCTTTTCAAGGATCAGGTG
* *
19395262 TAACTTCTTACCTTTTCAAGGATTAGGTG
1 TAACCTCTTACCTTTTCAAGGATCAGGTG
*
19395291 TAACTTCTTACCTTTTCAAGGATCAGGTG
1 TAACCTCTTACCTTTTCAAGGATCAGGTG
19395320 TAA
1 TAA
19395323 ACTCATGACA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (29 bp):
TAACCTCTTACCTTTTCAAGGATCAGGTG
Found at i:19404283 original size:13 final size:14
Alignment explanation
Indices: 19404265--19404293 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19404255 TAATGATGTG
19404265 AAAATTAA-AAATT
1 AAAATTAACAAATT
19404278 AAAATTAACAAATT
1 AAAATTAACAAATT
19404292 AA
1 AA
19404294 CAAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTAACAAATT
Found at i:19404776 original size:20 final size:20
Alignment explanation
Indices: 19404748--19404799 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
19404738 AAGTTGAGGA
* *
19404748 TTAGTGTCCAAAATACAAGC
1 TTAGGGTCCAAAATACAAAC
* *
19404768 TTAGGGTCCAAAGTGCAAAC
1 TTAGGGTCCAAAATACAAAC
*
19404788 TTAGGGTTCAAA
1 TTAGGGTCCAAA
19404800 TTGAAATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (20 bp):
TTAGGGTCCAAAATACAAAC
Found at i:19408583 original size:20 final size:20
Alignment explanation
Indices: 19408555--19408606 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
19408545 AAGTTTAGGG
*
19408555 TTAGTGTCCAAAATACAAAC
1 TTAGGGTCCAAAATACAAAC
* *
19408575 TTAGGGTCCAAAGTGCAAAC
1 TTAGGGTCCAAAATACAAAC
*
19408595 TTAGGGTTCAAA
1 TTAGGGTCCAAA
19408607 TTGAAATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (20 bp):
TTAGGGTCCAAAATACAAAC
Found at i:19408766 original size:26 final size:25
Alignment explanation
Indices: 19408736--19408794 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
19408726 TTGATTCCAC
*
19408736 AAAATAAAGATAACA-AAAGCAAATAA
1 AAAATAAAGA-AAAAGAAAG-AAATAA
* *
19408762 AAAATCAGGAAAAAGAAAGAAATAA
1 AAAATAAAGAAAAAGAAAGAAATAA
19408787 AAAATAAA
1 AAAATAAA
19408795 AGGCCTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.75, C:0.05, G:0.10, T:0.10
Consensus pattern (25 bp):
AAAATAAAGAAAAAGAAAGAAATAA
Found at i:19409973 original size:2 final size:2
Alignment explanation
Indices: 19409966--19410009 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
19409956 CTGGTGTCAT
19409966 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19410008 TA
1 TA
19410010 GACAAGAGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19412881 original size:26 final size:25
Alignment explanation
Indices: 19412852--19412905 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
19412842 TTGGGTAAGC
* *
19412852 AATTAATTAAATAAGTAATATTATTT
1 AATTAATAAAATAAGTAA-ATTAATT
* *
19412878 AATTTATAAAATAATTAAATTAATT
1 AATTAATAAAATAAGTAAATTAATT
19412903 AAT
1 AAT
19412906 ATACTAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
AATTAATAAAATAAGTAAATTAATT
Found at i:19417325 original size:80 final size:78
Alignment explanation
Indices: 19417196--19417445 Score: 218
Period size: 80 Copynumber: 3.1 Consensus size: 78
19417186 TGTAACATTT
* * * *
19417196 TCATAAATCATCATCATATACTCAGCCCATAGTGTATATGACTA-GCTCAACACATACATCTCAT
1 TCATAAATCAT--TCA-ACACTTAGCCCATAGTGTACATGA-TATACTCAACACATACATCTCAT
*
19417260 GGCATGCATTTCATATTC
62 GGCAT-CATTTCATAATC
* ** *
19417278 TCATAAATCATTCACACACTTAGCCCATTGTGTACATGATATACTCAATGCATACAACTCATGGC
1 TCATAAATCATTCA-ACACTTAGCCCATAGTGTACATGATATACTCAACACATACATCTCATGGC
*
19417343 AT-ATCTGTTATAATC
65 ATCAT-T-TCATAATC
* * * * **
19417358 TCATAATTCA-TCAACATGCTTAGCCCATAATGGACATGACATTTTCAACACATACATCTCATGG
1 TCATAAATCATTCAACA--CTTAGCCCATAGTGTACATGATATACTCAACACATACATCTCATGG
**
19417422 CATACAGGTCATAATC
64 CAT-CATTTCATAATC
19417438 TCATAAAT
1 TCATAAAT
19417446 GGAACTCATG
Statistics
Matches: 136, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
78 5 0.04
79 6 0.04
80 113 0.83
82 12 0.09
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (78 bp):
TCATAAATCATTCAACACTTAGCCCATAGTGTACATGATATACTCAACACATACATCTCATGGCA
TCATTTCATAATC
Found at i:19423498 original size:26 final size:26
Alignment explanation
Indices: 19423469--19423527 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
19423459 ATTTTCTAGT
* *
19423469 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTTTTATT-C
*
19423495 TTTCCTCTCTATTTTCTCTTTTATTC
1 TTTCCTTTCTATTTTCTCTTTTATTC
19423521 TTTCCTT
1 TTTCCTT
19423528 ATGGCCGGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.03, C:0.27, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTTTTATTC
Found at i:19432100 original size:2 final size:2
Alignment explanation
Indices: 19432088--19432141 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
19432078 AAGCAATCTC
19432088 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19432129 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
19432142 GTGTGTGTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19433644 original size:14 final size:14
Alignment explanation
Indices: 19433625--19433655 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
19433615 AACTAAGGTT
19433625 TGCATCCCCAAACC
1 TGCATCCCCAAACC
19433639 TGCATCCCCAAACC
1 TGCATCCCCAAACC
19433653 TGC
1 TGC
19433656 TAAGCAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.48, G:0.10, T:0.16
Consensus pattern (14 bp):
TGCATCCCCAAACC
Found at i:19434248 original size:163 final size:160
Alignment explanation
Indices: 19434029--19434343 Score: 488
Period size: 163 Copynumber: 1.9 Consensus size: 160
19434019 TTATCCCTTG
19434029 AGATAATTTAAAAATAATATTTAAATTGGACCAATCAAAAAATTAGTTATTGGTCATTCAATTTA
1 AGATAATTTAAAAATAATATTTAAATTGGACCAATCAAAAAATTAGTTATTGGTCATTCAATTTA
* * *
19434094 TCTCTAAATAAATCAAGATAATTTAGAGATAATATTCATATTTTTTACCAATCAAAAAATTAGTT
66 TCTCTAAATAAATCAAAATAATTTAGAGATAATATTCATA-TTTTGACCAATC-AAAAATTAATT
19434159 ATTGGTCATCCAATTTATCTCTAAATAAATCA
129 ATTGGTCATCCAATTTATCTCTAAATAAATCA
* ** *
19434191 AGATAATTTAAAGATAATATTCATATTTTTGACCAATC-AAAAATTAGTTATTGGTCATTCAATT
1 AGATAATTTAAAAATAATATT--TAAATTGGACCAATCAAAAAATTAGTTATTGGTCATTCAATT
* *
19434255 TATCTCTAAATAAATCAAAATAATTTAGAGATAATATTTATATTTTGACCAATCAAAATTTAATT
64 TATCTCTAAATAAATCAAAATAATTTAGAGATAATATTCATATTTTGACCAATCAAAAATTAATT
**
19434320 ATTGGTCATTTAATTTATCTCTAA
129 ATTGGTCATCCAATTTATCTCTAA
19434344 TAATTATATT
Statistics
Matches: 140, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
161 31 0.22
162 31 0.22
163 66 0.47
164 12 0.09
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (160 bp):
AGATAATTTAAAAATAATATTTAAATTGGACCAATCAAAAAATTAGTTATTGGTCATTCAATTTA
TCTCTAAATAAATCAAAATAATTTAGAGATAATATTCATATTTTGACCAATCAAAAATTAATTAT
TGGTCATCCAATTTATCTCTAAATAAATCA
Found at i:19434270 original size:81 final size:82
Alignment explanation
Indices: 19434029--19434343 Score: 478
Period size: 82 Copynumber: 3.9 Consensus size: 82
19434019 TTATCCCTTG
* ** *
19434029 AGATAATTTAAAAATAATATT--TAAATTGGACCAATCAAAAAATTAGTTATTGGTCATTCAATT
1 AGATAATTTAAAGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATTCAATT
19434092 TATCTCTAAATAAATCA
66 TATCTCTAAATAAATCA
* * *
19434109 AGATAATTTAGAGATAATATTCATATTTTTTACCAATCAAAAAATTAGTTATTGGTCATCCAATT
1 AGATAATTTAAAGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATTCAATT
19434174 TATCTCTAAATAAATCA
66 TATCTCTAAATAAATCA
19434191 AGATAATTTAAAGATAATATTCATATTTTTGACCAATC-AAAAATTAGTTATTGGTCATTCAATT
1 AGATAATTTAAAGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATTCAATT
19434255 TATCTCTAAATAAATCA
66 TATCTCTAAATAAATCA
* * * * * *
19434272 AAATAATTTAGAGATAATATTTATA-TTTTGACCAATC-AAAATTTAATTATTGGTCATTTAATT
1 AGATAATTTAAAGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATTCAATT
19434335 TATCTCTAA
66 TATCTCTAA
19434344 TAATTATATT
Statistics
Matches: 217, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
80 63 0.29
81 64 0.29
82 90 0.41
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (82 bp):
AGATAATTTAAAGATAATATTCATATTTTTGACCAATCAAAAAATTAGTTATTGGTCATTCAATT
TATCTCTAAATAAATCA
Found at i:19434666 original size:17 final size:17
Alignment explanation
Indices: 19434644--19434677 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19434634 AGAGGTATTC
*
19434644 GAAGATTGGGAGCATTT
1 GAAGATTGAGAGCATTT
19434661 GAAGATTGAGAGCATTT
1 GAAGATTGAGAGCATTT
19434678 CAGAGATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.29
Consensus pattern (17 bp):
GAAGATTGAGAGCATTT
Found at i:19434738 original size:26 final size:25
Alignment explanation
Indices: 19434708--19434761 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
19434698 AGATTTTTTA
19434708 AGTGAAGATCAAGCAACAACGAAGTT
1 AGTG-AGATCAAGCAACAACGAAGTT
* *
19434734 CGT--GATCAAGCAGCAACGAAGTT
1 AGTGAGATCAAGCAACAACGAAGTT
19434757 AGTGA
1 AGTGA
19434762 TCAAGATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
23 21 0.91
26 2 0.09
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.17
Consensus pattern (25 bp):
AGTGAGATCAAGCAACAACGAAGTT
Found at i:19434786 original size:25 final size:25
Alignment explanation
Indices: 19434727--19434820 Score: 147
Period size: 25 Copynumber: 3.8 Consensus size: 25
19434717 CAAGCAACAA
* *
19434727 CGAAGTTCGTGATCAAG-CAGCAA-
1 CGAAGTTCGTGATCAAGATATCAAG
*
19434750 CGAAGTTAGTGATCAAGATATCAAG
1 CGAAGTTCGTGATCAAGATATCAAG
19434775 CGAAGTTCGTGATCAAGATATCAAG
1 CGAAGTTCGTGATCAAGATATCAAG
19434800 CGAAGTTCGTGATCAAGATAT
1 CGAAGTTCGTGATCAAGATAT
19434821 TGTGTTCGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
23 16 0.25
24 4 0.06
25 45 0.69
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (25 bp):
CGAAGTTCGTGATCAAGATATCAAG
Found at i:19434875 original size:49 final size:49
Alignment explanation
Indices: 19434822--19434993 Score: 272
Period size: 49 Copynumber: 3.5 Consensus size: 49
19434812 TCAAGATATT
* *
19434822 GTGTTCGTAATCAAGATTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
1 GTGTTCGTGATCAAGACTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
* * *
19434871 GTGTTCGTGATCAAGATTAACTCGTGAATACCCTTGAAGCGAAGATCAA
1 GTGTTCGTGATCAAGACTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
*
19434920 GTGTTCGTGATCAAGACTAAGTCGTGAAGACCCTTGACGCGAAGATCAA
1 GTGTTCGTGATCAAGACTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
19434969 GCATGTTCGTGATCAAGACTAAGTC
1 G--TGTTCGTGATCAAGACTAAGTC
19434994 CAAGTTTGCA
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
49 92 0.81
51 22 0.19
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (49 bp):
GTGTTCGTGATCAAGACTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
Found at i:19442711 original size:40 final size:40
Alignment explanation
Indices: 19442607--19442941 Score: 277
Period size: 36 Copynumber: 8.8 Consensus size: 40
19442597 ATACCATGGT
*
19442607 GATAATAAATTGTGTGCTATTTTAAAGAGCA-CCTCCCAAG
1 GATAATAAATTGTGTGCTATTATAAAGAGCACCCT-CCAAG
*
19442647 GAT--TAACA---AGTGCTATTATAAAGAGCACCCTCCAAG
1 GATAATAA-ATTGTGTGCTATTATAAAGAGCACCCTCCAAG
**
19442683 GATAATAAATTGTGTGCTAGAATAAAGAGCA-CCTCCCAAG
1 GATAATAAATTGTGTGCTATTATAAAGAGCACCCT-CCAAG
* *
19442723 GATCAA-CAA----GTGCTATGATAAAGAGCACCCTCCAAG
1 GAT-AATAAATTGTGTGCTATTATAAAGAGCACCCTCCAAG
* *
19442759 AATAATTAATTGTGTGCTATT-TAAAAGAGCA-CCTCCCAAG
1 GATAATAAATTGTGTGCTATTAT-AAAGAGCACCCT-CCAAG
* *
19442799 AATCAGT-AA----GTGCTATTATAAAGAGCACCCTCCAAG
1 GAT-AATAAATTGTGTGCTATTATAAAGAGCACCCTCCAAG
* *
19442835 GATAATAAATTGTGTGCTATTATGAAGAGCACCCCCCAAG
1 GATAATAAATTGTGTGCTATTATAAAGAGCACCCTCCAAG
* *
19442875 GATCAAT-AA----GTGCTATGATAAAGAGCACCCTCCGAG
1 GAT-AATAAATTGTGTGCTATTATAAAGAGCACCCTCCAAG
* **
19442911 GAAAATAAATTGCATGCTATTATAAAGAGCA
1 GATAATAAATTGTGTGCTATTATAAAGAGCA
19442942 TCACTTTAAA
Statistics
Matches: 241, Mismatches: 23, Indels: 62
0.74 0.07 0.19
Matches are distributed among these distances:
35 7 0.03
36 102 0.42
37 11 0.05
38 6 0.02
39 8 0.03
40 100 0.41
41 7 0.03
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (40 bp):
GATAATAAATTGTGTGCTATTATAAAGAGCACCCTCCAAG
Found at i:19442733 original size:76 final size:76
Alignment explanation
Indices: 19442607--19442941 Score: 492
Period size: 76 Copynumber: 4.4 Consensus size: 76
19442597 ATACCATGGT
* * *
19442607 GATAATAAATTGTGTGCTATTTTAAAGAGCACCTCCCAAGGATTAACAAGTGCTATTATAAAGAG
1 GATAATAAATTGTGTGCTATTATAAAGAGCACCTCCCAAGGATCAACAAGTGCTATGATAAAGAG
19442672 CACCCTCCAAG
66 CACCCTCCAAG
**
19442683 GATAATAAATTGTGTGCTAGAATAAAGAGCACCTCCCAAGGATCAACAAGTGCTATGATAAAGAG
1 GATAATAAATTGTGTGCTATTATAAAGAGCACCTCCCAAGGATCAACAAGTGCTATGATAAAGAG
19442748 CACCCTCCAAG
66 CACCCTCCAAG
* * * ** *
19442759 AATAATTAATTGTGTGCTATT-TAAAAGAGCACCTCCCAAGAATCAGTAAGTGCTATTATAAAGA
1 GATAATAAATTGTGTGCTATTAT-AAAGAGCACCTCCCAAGGATCAACAAGTGCTATGATAAAGA
19442823 GCACCCTCCAAG
65 GCACCCTCCAAG
* * *
19442835 GATAATAAATTGTGTGCTATTATGAAGAGCACCCCCCAAGGATCAATAAGTGCTATGATAAAGAG
1 GATAATAAATTGTGTGCTATTATAAAGAGCACCTCCCAAGGATCAACAAGTGCTATGATAAAGAG
*
19442900 CACCCTCCGAG
66 CACCCTCCAAG
* **
19442911 GAAAATAAATTGCATGCTATTATAAAGAGCA
1 GATAATAAATTGTGTGCTATTATAAAGAGCA
19442942 TCACTTTAAA
Statistics
Matches: 232, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
75 1 0.00
76 230 0.99
77 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (76 bp):
GATAATAAATTGTGTGCTATTATAAAGAGCACCTCCCAAGGATCAACAAGTGCTATGATAAAGAG
CACCCTCCAAG
Found at i:19443812 original size:60 final size:59
Alignment explanation
Indices: 19443719--19443838 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 59
19443709 CTTATAATTT
19443719 TGAGAAGATGAAAAAATCGATCTTGCTTGCTTATGGAATATCAGTAATGCTCAAGTTGA
1 TGAGAAGATGAAAAAATCGATCTTGCTTGCTTATGGAATATCAGTAATGCTCAAGTTGA
* *
19443778 NTGAGAAGATGAAAAAATCGGTCTTGCTTGCTTATGGAATATCCGTAATGCTCAAGTTGA
1 -TGAGAAGATGAAAAAATCGATCTTGCTTGCTTATGGAATATCAGTAATGCTCAAGTTGA
19443838 T
1 T
19443839 TTTGATGTGC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 1 0.02
60 57 0.98
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (59 bp):
TGAGAAGATGAAAAAATCGATCTTGCTTGCTTATGGAATATCAGTAATGCTCAAGTTGA
Found at i:19444025 original size:28 final size:28
Alignment explanation
Indices: 19443919--19444018 Score: 119
Period size: 28 Copynumber: 3.4 Consensus size: 28
19443909 TGTAATCCTA
*
19443919 ATTGCAATATACTTCTTTAAATAGTTTT
1 ATTGCAATATACTTCTTCAAATAGTTTT
* **
19443947 ATTGCAATATACCTCTTTCAAAATTATAGCCTT
1 ATTGCAATATACTTC-TTC--AA--ATAGTTTT
19443980 ATTGCAATATACTTCTTCAAATAGTTTT
1 ATTGCAATATACTTCTTCAAATAGTTTT
19444008 ATTGCAATATA
1 ATTGCAATATA
19444019 AATCTTCCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
28 31 0.52
29 2 0.03
30 2 0.03
31 2 0.03
32 3 0.05
33 20 0.33
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (28 bp):
ATTGCAATATACTTCTTCAAATAGTTTT
Found at i:19444034 original size:61 final size:61
Alignment explanation
Indices: 19443919--19444035 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
19443909 TGTAATCCTA
* ** *
19443919 ATTGCAATATACTTCTTTAAATAGTTTTATTGCAATATACCTCTTTCAAAATTATAGCCTT
1 ATTGCAATATACTTCTTCAAATAGTTTTATTGCAATATAAATCTTCCAAAATTATAGCCTT
*
19443980 ATTGCAATATACTTCTTCAAATAGTTTTATTGCAATATAAATCTTCCAATATTATA
1 ATTGCAATATACTTCTTCAAATAGTTTTATTGCAATATAAATCTTCCAAAATTATA
19444036 ATTCTCTTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (61 bp):
ATTGCAATATACTTCTTCAAATAGTTTTATTGCAATATAAATCTTCCAAAATTATAGCCTT
Found at i:19444605 original size:81 final size:82
Alignment explanation
Indices: 19444384--19444670 Score: 472
Period size: 82 Copynumber: 3.5 Consensus size: 82
19444374 ATTTAAATTA
* *
19444384 GACCAATCAAAAAATTAGTTATTGGTCATTCAATTTATCTCTAAATAAATCAAGATAACTTAGAA
1 GACCAATCAAAAAATTAGTTATTGGTCATTCAATTTATCTCTAAATAAATCAAGATAATTTAGAG
19444449 ATAATATTCATATTTTT
66 ATAATATTCATATTTTT
* *
19444466 GACCAATCAAAAAATTAGTTATTGGTCATCCAATTTATCTCTACATAAATCAAGATAATTTAGAG
1 GACCAATCAAAAAATTAGTTATTGGTCATTCAATTTATCTCTAAATAAATCAAGATAATTTAGAG
19444531 ATAATATTCATATTTTT
66 ATAATATTCATATTTTT
*
19444548 GACCAATC-AAAAATTAGTTATTGGTCATTCAATTTATCTCTAAATAAATCAAAATAATTTAGAG
1 GACCAATCAAAAAATTAGTTATTGGTCATTCAATTTATCTCTAAATAAATCAAGATAATTTAGAG
*
19444612 ATAATATTTATA-TTTT
66 ATAATATTCATATTTTT
* * *
19444628 GACCAATC-AAAATTTAATTATTGGTCATTTAATTTATCTCTAA
1 GACCAATCAAAAAATTAGTTATTGGTCATTCAATTTATCTCTAA
19444671 TAATTATATT
Statistics
Matches: 194, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
80 44 0.23
81 64 0.33
82 86 0.44
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (82 bp):
GACCAATCAAAAAATTAGTTATTGGTCATTCAATTTATCTCTAAATAAATCAAGATAATTTAGAG
ATAATATTCATATTTTT
Found at i:19444991 original size:17 final size:17
Alignment explanation
Indices: 19444947--19445004 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
19444937 CATTTTAGAG
*
19444947 GCATTTGAAGATTCAGA
1 GCATTTGAAGATTGAGA
* *
19444964 GGCATTCGAAGATTGGGA
1 -GCATTTGAAGATTGAGA
19444982 GCATTTGAAGATTGAGA
1 GCATTTGAAGATTGAGA
19444999 GCATTT
1 GCATTT
19445005 CAGAGATCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 21 0.60
18 14 0.40
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.29
Consensus pattern (17 bp):
GCATTTGAAGATTGAGA
Found at i:19445111 original size:25 final size:25
Alignment explanation
Indices: 19445055--19445172 Score: 186
Period size: 25 Copynumber: 4.8 Consensus size: 25
19445045 AAGCGACAAT
***
19445055 GAAGTTCGTGATCAAG-CGGCAA-C
1 GAAGTTCGTGATCAAGATATCAAGC
19445078 GAAGTTCGTGATCAAGATATCAAGC
1 GAAGTTCGTGATCAAGATATCAAGC
19445103 GAAGTTCGTGATCAAGATATCAAGC
1 GAAGTTCGTGATCAAGATATCAAGC
19445128 GAAGTTCGTGATCAAGATATCAAGC
1 GAAGTTCGTGATCAAGATATCAAGC
*
19445153 GAAGTTCATGATCAAGATAT
1 GAAGTTCGTGATCAAGATAT
19445173 TGTGTTCGTA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
23 16 0.18
24 3 0.03
25 70 0.79
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24
Consensus pattern (25 bp):
GAAGTTCGTGATCAAGATATCAAGC
Found at i:19445227 original size:49 final size:49
Alignment explanation
Indices: 19445174--19445345 Score: 263
Period size: 49 Copynumber: 3.5 Consensus size: 49
19445164 TCAAGATATT
* *
19445174 GTGTTCGTAATCAAGATTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
1 GTGTTCGTGATCAAGACTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
* *
19445223 GTGTTCGTGATCAAGATTAAGTCGTGAAGACCCTTGAAGCAAAGATCAA
1 GTGTTCGTGATCAAGACTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
* * *
19445272 GTGTTCATGATCAAGACTAAGTCGTGAAGACCCTTGACGTGAAGATCAA
1 GTGTTCGTGATCAAGACTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
19445321 GCATGTTCGTGATCAAGACTAAGTC
1 G--TGTTCGTGATCAAGACTAAGTC
19445346 CAAGTTTGCG
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
49 92 0.81
51 21 0.19
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (49 bp):
GTGTTCGTGATCAAGACTAAGTCGTGAAGACCCTTGAAGCGAAGATCAA
Found at i:19445600 original size:45 final size:44
Alignment explanation
Indices: 19445486--19445602 Score: 153
Period size: 45 Copynumber: 2.6 Consensus size: 44
19445476 TGTGTACAGT
*
19445486 CATGTACAAAAATATGTGATAAGCCATGATTAACGTATTACACG
1 CATGTACAAAAATATGTGATAAGTCATGATTAACGTATTACACG
* * *
19445530 CTATGTACAAAAATATGTGATAAGTCATGATTAGCTTGTTACACGG
1 C-ATGTACAAAAATATGTGATAAGTCATGATTAACGTATTACAC-G
* * *
19445576 CATGTATAAAAAAATGTGACAAGTCAT
1 CATGTACAAAAATATGTGATAAGTCAT
19445603 ATACAAAAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
44 1 0.02
45 61 0.95
46 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (44 bp):
CATGTACAAAAATATGTGATAAGTCATGATTAACGTATTACACG
Found at i:19445674 original size:45 final size:45
Alignment explanation
Indices: 19445618--19445762 Score: 200
Period size: 45 Copynumber: 3.2 Consensus size: 45
19445608 AAAACCTATG
* * *
19445618 ACAAGCTATGGTTAGCGTGTTACACGCTATGTACAAAAATATGTA
1 ACAAGCCATGGTTAGCTTGTTACACACTATGTACAAAAATATGTA
* * * *
19445663 ATAAGCCATGGTTAGCTTGTTACACATTATGTATAAAAATATGTG
1 ACAAGCCATGGTTAGCTTGTTACACACTATGTACAAAAATATGTA
* *
19445708 ACAAGCCATGGTTAGCTTGTTACACACCATGTACAAAAATATGTG
1 ACAAGCCATGGTTAGCTTGTTACACACTATGTACAAAAATATGTA
*
19445753 ACAAGTCATG
1 ACAAGCCATG
19445763 TACAAAAACC
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (45 bp):
ACAAGCCATGGTTAGCTTGTTACACACTATGTACAAAAATATGTA
Found at i:19445767 original size:24 final size:24
Alignment explanation
Indices: 19445734--19446010 Score: 89
Period size: 24 Copynumber: 12.0 Consensus size: 24
19445724 TTGTTACACA
*
19445734 CCATGTACAAAAATATGTGACAAG
1 CCATGTACAAAAACATGTGACAAG
* *
19445758 TCATGTACAAAAACCTGTGACAAG
1 CCATGTACAAAAACATGTGACAAG
* * * * *
19445782 CCATGGT----TAGCGTGTTACACG
1 CCAT-GTACAAAAACATGTGACAAG
* *
19445803 CTATGTACAAAAATATGTGACAAG
1 CCATGTACAAAAACATGTGACAAG
** * * * *
19445827 CCATG---ATTAGCTTGTTACACG
1 CCATGTACAAAAACATGTGACAAG
* *
19445848 CCATGTACAAAAATATGTAACAAG
1 CCATGTACAAAAACATGTGACAAG
* * * *
19445872 TCATATACAAAAACCTGTGACAAA
1 CCATGTACAAAAACATGTGACAAG
* * * * * *
19445896 CTATGGT----TAGCTTGTTACATG
1 CCAT-GTACAAAAACATGTGACAAG
*
19445917 CCATGTACAAAAACTTGTGACAAG
1 CCATGTACAAAAACATGTGACAAG
* * * *
19445941 CCATGGT----TAACGTGTTACACG
1 CCAT-GTACAAAAACATGTGACAAG
* *
19445962 CTATGTACAAAAATATGTGACAAG
1 CCATGTACAAAAACATGTGACAAG
* *
19445986 CCATGTACAAAAACCTGTAACAAG
1 CCATGTACAAAAACATGTGACAAG
19446010 C
1 C
19446011 TATGGTTAGC
Statistics
Matches: 170, Mismatches: 65, Indels: 36
0.63 0.24 0.13
Matches are distributed among these distances:
20 6 0.04
21 50 0.29
24 109 0.64
25 5 0.03
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
CCATGTACAAAAACATGTGACAAG
Found at i:19445779 original size:159 final size:159
Alignment explanation
Indices: 19445487--19445871 Score: 581
Period size: 159 Copynumber: 2.4 Consensus size: 159
19445477 GTGTACAGTC
* * * *
19445487 ATGTACAAAAATATGTGATAAGCCATGATTAACGTATTACACGCTATGTACAAAAATATGTGATA
1 ATGTACAAAAATATGTGATAAGCCATGATTAGCTTGTTACACGCTATGTACAAAAATATGTGACA
* ** *
19445552 AGTCATGATTAGCTTGTTACACGGCATGTATAAAAAAATGTGACAAGTCATATACAAAAACCTAT
66 AGCCATGATTAGCTTGTTACACACCATGTACAAAAAAATGTGACAAGTCATATACAAAAACCTAT
*
19445617 GACAAGCTATGGTTAGCGTGTTACACGCT
131 GACAAGCCATGGTTAGCGTGTTACACGCT
* * ** *
19445646 ATGTACAAAAATATGTAATAAGCCATGGTTAGCTTGTTACACATTATGTATAAAAATATGTGACA
1 ATGTACAAAAATATGTGATAAGCCATGATTAGCTTGTTACACGCTATGTACAAAAATATGTGACA
* * * *
19445711 AGCCATGGTTAGCTTGTTACACACCATGTACAAAAATATGTGACAAGTCATGTACAAAAACCTGT
66 AGCCATGATTAGCTTGTTACACACCATGTACAAAAAAATGTGACAAGTCATATACAAAAACCTAT
19445776 GACAAGCCATGGTTAGCGTGTTACACGCT
131 GACAAGCCATGGTTAGCGTGTTACACGCT
* * *
19445805 ATGTACAAAAATATGTGACAAGCCATGATTAGCTTGTTACACGCCATGTACAAAAATATGTAACA
1 ATGTACAAAAATATGTGATAAGCCATGATTAGCTTGTTACACGCTATGTACAAAAATATGTGACA
19445870 AG
66 AG
19445872 TCATATACAA
Statistics
Matches: 200, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
159 200 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (159 bp):
ATGTACAAAAATATGTGATAAGCCATGATTAGCTTGTTACACGCTATGTACAAAAATATGTGACA
AGCCATGATTAGCTTGTTACACACCATGTACAAAAAAATGTGACAAGTCATATACAAAAACCTAT
GACAAGCCATGGTTAGCGTGTTACACGCT
Found at i:19445811 original size:45 final size:45
Alignment explanation
Indices: 19445759--19445871 Score: 163
Period size: 45 Copynumber: 2.5 Consensus size: 45
19445749 TGTGACAAGT
* *
19445759 CATGTACAAAAACCTGTGACAAGCCATGGTTAGCGTGTTACACGC
1 CATGTACAAAAACATGTGACAAGCCATGATTAGCGTGTTACACGC
* * *
19445804 TATGTACAAAAATATGTGACAAGCCATGATTAGCTTGTTACACGC
1 CATGTACAAAAACATGTGACAAGCCATGATTAGCGTGTTACACGC
* *
19445849 CATGTACAAAAATATGTAACAAG
1 CATGTACAAAAACATGTGACAAG
19445872 TCATATACAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (45 bp):
CATGTACAAAAACATGTGACAAGCCATGATTAGCGTGTTACACGC
Found at i:19445922 original size:159 final size:157
Alignment explanation
Indices: 19445487--19445990 Score: 501
Period size: 159 Copynumber: 3.2 Consensus size: 157
19445477 GTGTACAGTC
* * * * * * * *
19445487 ATGTACAAAAATATGTGATAAGCCATGATTAACGTATTACACGCTATGTACAAAAATATGTGATA
1 ATGTACAAAAATATGTGACAAGCCATGATTAGCTTGTTACACACCATGTACAAAAATATGTAACA
* * * * * *** * * * *
19445552 AGTCATGATTAGCTTGTTACACGGCATGTATAAAAAAATGTGACAAGTCATATACAAAAACCTAT
66 AGCCATGATAAACCTGTGACAAACCATG--TAAAAATATGTGACAAGCCATGTACAAAAACCTGT
*
19445617 GACAAGCTATGGTTAGCGTGTTACACGCT
129 GACAAGCCATGGTTAGCGTGTTACACGCT
* * * ** * *
19445646 ATGTACAAAAATATGTAATAAGCCATGGTTAGCTTGTTACACATTATGTATAAAAATATGTGACA
1 ATGTACAAAAATATGTGACAAGCCATGATTAGCTTGTTACACACCATGTACAAAAATATGTAACA
* * * * * * *
19445711 AGCCATGGTTAGCTTGTTACACACCATGTACAAAAATATGTGACAAGTCATGTACAAAAACCTGT
66 AGCCATGATAAACCTGTGACAAACCATGT--AAAAATATGTGACAAGCCATGTACAAAAACCTGT
19445776 GACAAGCCATGGTTAGCGTGTTACACGCT
129 GACAAGCCATGGTTAGCGTGTTACACGCT
*
19445805 ATGTACAAAAATATGTGACAAGCCATGATTAGCTTGTTACACGCCATGTACAAAAATATGTAACA
1 ATGTACAAAAATATGTGACAAGCCATGATTAGCTTGTTACACACCATGTACAAAAATATGTAACA
* * * ** * * *
19445870 AGTCAT-ATACAAAAACCTGTGACAAACTATGGT-TAGCT-TGTTACATGCCATGTACAAAAACT
66 AGCCATGAT----AAACCTGTGACAAACCAT-GTAAAAATATGTGACAAGCCATGTACAAAAACC
*
19445932 TGTGACAAGCCATGGTTAACGTGTTACACGCT
126 TGTGACAAGCCATGGTTAGCGTGTTACACGCT
19445964 ATGTACAAAAATATGTGACAAGCCATG
1 ATGTACAAAAATATGTGACAAGCCATG
19445991 TACAAAAACC
Statistics
Matches: 297, Mismatches: 41, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
157 1 0.00
158 1 0.00
159 279 0.94
160 2 0.01
162 12 0.04
163 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (157 bp):
ATGTACAAAAATATGTGACAAGCCATGATTAGCTTGTTACACACCATGTACAAAAATATGTAACA
AGCCATGATAAACCTGTGACAAACCATGTAAAAATATGTGACAAGCCATGTACAAAAACCTGTGA
CAAGCCATGGTTAGCGTGTTACACGCT
Found at i:19445947 original size:45 final size:45
Alignment explanation
Indices: 19445877--19445990 Score: 149
Period size: 45 Copynumber: 2.5 Consensus size: 45
19445867 ACAAGTCATA
* * * * * *
19445877 TACAAAAACCTGTGACAAACTATGGTTAGCTTGTTACATGCCATG
1 TACAAAAACTTGTGACAAGCCATGGTTAACGTGTTACACGCCATG
*
19445922 TACAAAAACTTGTGACAAGCCATGGTTAACGTGTTACACGCTATG
1 TACAAAAACTTGTGACAAGCCATGGTTAACGTGTTACACGCCATG
19445967 TACAAAAA-TATGTGACAAGCCATG
1 TACAAAAACT-TGTGACAAGCCATG
19445991 TACAAAAACC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 1 0.02
45 60 0.98
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (45 bp):
TACAAAAACTTGTGACAAGCCATGGTTAACGTGTTACACGCCATG
Found at i:19445989 original size:69 final size:69
Alignment explanation
Indices: 19445916--19446059 Score: 225
Period size: 69 Copynumber: 2.1 Consensus size: 69
19445906 CTTGTTACAT
* * *
19445916 GCCATGTACAAAAACTTGTGACAAGCCATGGTTAACGTGTTACACGCTATGTACAAAAATATGTG
1 GCCATGTACAAAAACCTGTAACAAGCCATGGTTAACGTGTTACACGCCATGTACAAAAATATGTG
19445981 ACAA
66 ACAA
* * * *
19445985 GCCATGTACAAAAACCTGTAACAAGCTATGGTTAGCTTGTTACACGCCATGTACAAAAATTTGTG
1 GCCATGTACAAAAACCTGTAACAAGCCATGGTTAACGTGTTACACGCCATGTACAAAAATATGTG
19446050 ACAA
66 ACAA
19446054 GCCATG
1 GCCATG
19446060 GTTAGGTTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (69 bp):
GCCATGTACAAAAACCTGTAACAAGCCATGGTTAACGTGTTACACGCCATGTACAAAAATATGTG
ACAA
Found at i:19446034 original size:45 final size:45
Alignment explanation
Indices: 19445985--19446079 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
19445975 TATGTGACAA
*
19445985 GCCATGTACAAAAACCTGTAACAAGCTATGGTTAGCTTGTTACAC
1 GCCATGTACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACAC
** * *
19446030 GCCATGTACAAAAATTTGTGACAAGCCATGGTTAGGTTGTTACAC
1 GCCATGTACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACAC
*
19446075 ACCAT
1 GCCAT
19446080 ATTGAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (45 bp):
GCCATGTACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACAC
Found at i:19446088 original size:114 final size:114
Alignment explanation
Indices: 19445646--19446079 Score: 618
Period size: 114 Copynumber: 3.8 Consensus size: 114
19445636 GTTACACGCT
** * *** *
19445646 ATGTACAAAAATATGTAATAAGCCATGGTTAGCTTGTTACACATTATGTATAAAAATATGTGACA
1 ATGTACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCATGTACAAAAATATGTGACA
19445711 AGCCATGGTTAGCTTGTTACACACCATGTACAAAAATATGTGACAAGTC
66 AGCCATGGTTAGCTTGTTACACACCATGTACAAAAATATGTGACAAGTC
* * *
19445760 ATGTACAAAAACCTGTGACAAGCCATGGTTAGCGTGTTACACGCTATGTACAAAAATATGTGACA
1 ATGTACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCATGTACAAAAATATGTGACA
* * *
19445825 AGCCATGATTAGCTTGTTACACGCCATGTACAAAAATATGTAACAAGTC
66 AGCCATGGTTAGCTTGTTACACACCATGTACAAAAATATGTGACAAGTC
* * * * *
19445874 ATATACAAAAACCTGTGACAAACTATGGTTAGCTTGTTACATGCCATGTACAAAAACT-TGTGAC
1 ATGTACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCATGTACAAAAA-TATGTGAC
* * * * *
19445938 AAGCCATGGTTAACGTGTTACACGCTATGTACAAAAATATGTGACAAGCC
65 AAGCCATGGTTAGCTTGTTACACACCATGTACAAAAATATGTGACAAGTC
* *
19445988 ATGTACAAAAACCTGTAACAAGCTATGGTTAGCTTGTTACACGCCATGTACAAAAATTTGTGACA
1 ATGTACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCATGTACAAAAATATGTGACA
*
19446053 AGCCATGGTTAGGTTGTTACACACCAT
66 AGCCATGGTTAGCTTGTTACACACCAT
19446080 ATTGAAAAAA
Statistics
Matches: 286, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
113 1 0.00
114 284 0.99
115 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (114 bp):
ATGTACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCATGTACAAAAATATGTGACA
AGCCATGGTTAGCTTGTTACACACCATGTACAAAAATATGTGACAAGTC
Found at i:19446151 original size:26 final size:24
Alignment explanation
Indices: 19446096--19446154 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
19446086 AAAAAATATT
19446096 GTTGTTACACGTCATGTACAAAAA
1 GTTGTTACACGTCATGTACAAAAA
**
19446120 CATGTTACACGTCATAGTTA-AAAAA
1 GTTGTTACACGTCAT-G-TACAAAAA
19446145 GGTTGTTACA
1 -GTTGTTACA
19446155 TGCCATGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 13 0.46
25 6 0.21
26 9 0.32
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (24 bp):
GTTGTTACACGTCATGTACAAAAA
Found at i:19446214 original size:30 final size:30
Alignment explanation
Indices: 19446065--19446216 Score: 101
Period size: 30 Copynumber: 5.4 Consensus size: 30
19446055 CCATGGTTAG
* *
19446065 GTTGTTACACACCATATTGAAAAAAAATATT
1 GTTGTTACACGCCATGTTGAAAAAAAA-ATT
* * *
19446096 GTTGTTACACGTCATG-T-ACAAAAACA--
1 GTTGTTACACGCCATGTTGAAAAAAAAATT
* *
19446122 --TGTTACACGTCATAGTT----AAAAAA-G
1 GTTGTTACACGCCAT-GTTGAAAAAAAAATT
*
19446146 GTTGTTACATGCCATGTTGAAAAAAAAATT
1 GTTGTTACACGCCATGTTGAAAAAAAAATT
* * * *
19446176 ATTATTACACGCCATTTTGAAAAAAATATT
1 GTTGTTACACGCCATGTTGAAAAAAAAATT
19446206 GTTGTTACACG
1 GTTGTTACACG
19446217 ACATATTCAA
Statistics
Matches: 95, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
23 5 0.05
24 13 0.14
25 4 0.04
26 12 0.13
28 1 0.01
29 12 0.13
30 35 0.37
31 13 0.14
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (30 bp):
GTTGTTACACGCCATGTTGAAAAAAAAATT
Found at i:19449205 original size:2 final size:2
Alignment explanation
Indices: 19449198--19449230 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19449188 CTATATTAAT
*
19449198 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19449231 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:19449664 original size:15 final size:15
Alignment explanation
Indices: 19449639--19449677 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
19449629 TAACAAAACA
*
19449639 AAATAATAATAATATT
1 AAAT-ATAATAAAATT
19449655 AAATATAATAAAATT
1 AAATATAATAAAATT
*
19449670 TAATATAA
1 AAATATAA
19449678 ATAACATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATAATAAAATT
Found at i:19452711 original size:23 final size:22
Alignment explanation
Indices: 19452685--19452730 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
19452675 ATAAATATAA
19452685 TCATACAAAA-ATTAATGTAAAAC
1 TCATACAAAATA-TAATG-AAAAC
*
19452708 TCATGCAAAATATAATGAAAAC
1 TCATACAAAATATAATGAAAAC
19452730 T
1 T
19452731 ATTAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (22 bp):
TCATACAAAATATAATGAAAAC
Found at i:19452777 original size:28 final size:29
Alignment explanation
Indices: 19452730--19452799 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
19452720 TAATGAAAAC
19452730 TATTAATATAACTTATTATATAT-TA-AGT
1 TATTAATAT-ACTTATTATATATATATAGT
*
19452758 TATTAATATA-TTATACTATATATAGTATATT
1 TATTAATATACTTAT--TATATATA-TATAGT
19452789 TATTAATATAC
1 TATTAATATAC
19452800 AATAAATAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 4 0.11
27 1 0.03
28 16 0.46
30 2 0.06
31 12 0.34
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (29 bp):
TATTAATATACTTATTATATATATATAGT
Done.