Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 36 of 208
Found at i:13989496 original size:17 final size:17
Alignment explanation
Indices: 13989446--13989503 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
13989436 GGGTGAGATG
*
13989446 TAAAAGTTTAGGGGGAAAA
1 TAAAAGTTT-GAGGG-AAA
*
13989465 TAAAAAGTTT-TGGGAAA
1 T-AAAAGTTTGAGGGAAA
13989482 TAAAAGTTTGAGGGAAA
1 TAAAAGTTTGAGGGAAA
13989499 GTAAA
1 -TAAA
13989504 TAGGGGGAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.24
17 10 0.29
18 7 0.21
19 1 0.03
20 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (17 bp):
TAAAAGTTTGAGGGAAA
Found at i:13989867 original size:9 final size:9
Alignment explanation
Indices: 13989853--13989889 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
13989843 TATAGTTTGA
13989853 TATTCGAAT
1 TATTCGAAT
13989862 TATTCGAAT
1 TATTCGAAT
* *
13989871 TGTTCGAGT
1 TATTCGAAT
13989880 TATTCGAAT
1 TATTCGAAT
13989889 T
1 T
13989890 CGAAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:13998838 original size:3 final size:3
Alignment explanation
Indices: 13998823--13998925 Score: 71
Period size: 3 Copynumber: 34.0 Consensus size: 3
13998813 TTTAAGATTT
* * ** * * * * * *
13998823 TTA TTA TTG TTA TTA TTA TTA TTA ATA CCA TCA TCA TCA TCA TCA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** *
13998871 TGA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA CCA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
13998917 TTA TTA TTA
1 TTA TTA TTA
13998926 AATTTTTTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:14003709 original size:72 final size:72
Alignment explanation
Indices: 14003592--14003847 Score: 503
Period size: 72 Copynumber: 3.6 Consensus size: 72
14003582 ACAACTTGAC
*
14003592 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
14003657 ACTAACA
66 ACTAACA
14003664 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
14003729 ACTAACA
66 ACTAACA
14003736 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
14003801 ACTAACA
66 ACTAACA
14003808 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
14003848 AATAATAATA
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 183 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (72 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
ACTAACA
Found at i:14003856 original size:3 final size:3
Alignment explanation
Indices: 14003848--14003885 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
14003838 ATTACATCCA
14003848 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
14003886 AACATGTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:14008221 original size:72 final size:72
Alignment explanation
Indices: 14008104--14008359 Score: 494
Period size: 72 Copynumber: 3.6 Consensus size: 72
14008094 ACAACTTGAC
*
14008104 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
14008169 ACTAACA
66 ACTAACA
14008176 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
14008241 ACTAACA
66 ACTAACA
14008248 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
14008313 ACTAACA
66 ACTAACA
*
14008320 AACTTAGTTGGAATACAACTAAGTTATATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
14008360 AATAATAATA
Statistics
Matches: 182, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 182 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (72 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
ACTAACA
Found at i:14008368 original size:3 final size:3
Alignment explanation
Indices: 14008360--14008391 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
14008350 ATTACATCCA
14008360 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
14008392 AACATGTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:14008685 original size:28 final size:28
Alignment explanation
Indices: 14008645--14008701 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
14008635 AGAAAGAATG
14008645 ATATCTAGCATTATACTATAATCCTTTT
1 ATATCTAGCATTATACTATAATCCTTTT
14008673 ATATCTAGCATTATACTATAATCCTTTT
1 ATATCTAGCATTATACTATAATCCTTTT
14008701 A
1 A
14008702 CTCCATTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.46
Consensus pattern (28 bp):
ATATCTAGCATTATACTATAATCCTTTT
Found at i:14017541 original size:15 final size:15
Alignment explanation
Indices: 14017521--14017550 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14017511 CATCTTTTTC
14017521 TTGTTGCTTCCTATT
1 TTGTTGCTTCCTATT
14017536 TTGTTGCTTCCTATT
1 TTGTTGCTTCCTATT
14017551 AAAGCCACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.20, G:0.13, T:0.60
Consensus pattern (15 bp):
TTGTTGCTTCCTATT
Found at i:14027688 original size:15 final size:15
Alignment explanation
Indices: 14027668--14027697 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14027658 TAAATTAATT
14027668 TTTTTAGACAAGTTC
1 TTTTTAGACAAGTTC
14027683 TTTTTAGACAAGTTC
1 TTTTTAGACAAGTTC
14027698 AAGTCTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TTTTTAGACAAGTTC
Found at i:14028804 original size:20 final size:20
Alignment explanation
Indices: 14028757--14028811 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
14028747 TTTTTTATAG
* * *
14028757 TTTTATAATTTTTTTCATTT
1 TTTTATAATATTATTAATTT
**
14028777 TTAAATAATATTATTAATTT
1 TTTTATAATATTATTAATTT
*
14028797 TTTTATAATCTTATT
1 TTTTATAATATTATT
14028812 GTATTTTTGT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATAATATTATTAATTT
Found at i:14028850 original size:16 final size:15
Alignment explanation
Indices: 14028813--14028849 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
14028803 AATCTTATTG
* *
14028813 TATTTTTGTAAACTT
1 TATTTTTATAAACTA
14028828 TATTTTTATAAACTA
1 TATTTTTATAAACTA
14028843 TATTTTT
1 TATTTTT
14028850 TCTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTTTTATAAACTA
Found at i:14037005 original size:14 final size:14
Alignment explanation
Indices: 14036986--14037012 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14036976 TCAAAGCAGA
14036986 TCACTTTTGCAAAG
1 TCACTTTTGCAAAG
14037000 TCACTTTTGCAAA
1 TCACTTTTGCAAA
14037013 CAGTGTTCAA
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:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (14 bp):
TCACTTTTGCAAAG
Found at i:14049201 original size:21 final size:21
Alignment explanation
Indices: 14049175--14049215 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
14049165 ATCTGCTCAA
* *
14049175 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
14049196 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
14049216 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:14053159 original size:22 final size:22
Alignment explanation
Indices: 14053134--14053176 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
14053124 GAGTGACTAA
*
14053134 AATG-AAAATGTTGTAAAAATTG
1 AATGAAAAAT-TTATAAAAATTG
14053156 AATGAAAAATTTATAAAAATT
1 AATGAAAAATTTATAAAAATT
14053177 TTATTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (22 bp):
AATGAAAAATTTATAAAAATTG
Found at i:14058888 original size:27 final size:27
Alignment explanation
Indices: 14058850--14058913 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
14058840 CTTCAATGTT
14058850 CAATTTGGTATCTGAGTTTTTTTGTGC
1 CAATTTGGTATCTGAGTTTTTTTGTGC
14058877 CAATTTGGTATCTGAGTTTTTTTGTGC
1 CAATTTGGTATCTGAGTTTTTTTGTGC
14058904 CAATTTGGTA
1 CAATTTGGTA
14058914 CCTAATTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (27 bp):
CAATTTGGTATCTGAGTTTTTTTGTGC
Found at i:14059114 original size:22 final size:22
Alignment explanation
Indices: 14059088--14059132 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
14059078 TGAGATAAAG
* * *
14059088 AAAAGCTCAAGTATCAATTTGA
1 AAAAGATCAAGTACCAAATTGA
14059110 AAAAGATCAAGTACCAAATTGA
1 AAAAGATCAAGTACCAAATTGA
14059132 A
1 A
14059133 CATTAAAGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (22 bp):
AAAAGATCAAGTACCAAATTGA
Found at i:14059720 original size:10 final size:10
Alignment explanation
Indices: 14059700--14059813 Score: 71
Period size: 11 Copynumber: 11.3 Consensus size: 10
14059690 GCCCATTTTT
14059700 ATTTT-AAAA
1 ATTTTAAAAA
14059709 ATTTTAAAAA
1 ATTTTAAAAA
**
14059719 ATTAAAAAAA
1 ATTTTAAAAA
14059729 TATTTTAAAAA
1 -ATTTTAAAAA
*
14059740 TATTTTAAAAT
1 -ATTTTAAAAA
14059751 ATTTT--AAA
1 ATTTTAAAAA
14059759 A--TTAAAAA
1 ATTTTAAAAA
14059767 ATTTTTAAAAAAA
1 A-TTTT--AAAAA
14059780 GTATTTTAAAAA
1 --ATTTTAAAAA
14059792 TATTTT--AAA
1 -ATTTTAAAAA
*
14059801 ATTTAAAAAA
1 ATTTTAAAAA
14059811 ATT
1 ATT
14059814 AAAAAAGTAC
Statistics
Matches: 85, Mismatches: 7, Indels: 25
0.73 0.06 0.21
Matches are distributed among these distances:
6 2 0.02
8 11 0.13
9 8 0.09
10 23 0.27
11 26 0.31
12 5 0.06
13 5 0.06
14 4 0.05
15 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:14059738 original size:11 final size:11
Alignment explanation
Indices: 14059699--14059801 Score: 89
Period size: 10 Copynumber: 9.9 Consensus size: 11
14059689 GGCCCATTTT
14059699 TATTTT-AAAA
1 TATTTTAAAAA
14059709 -ATTTTAAAAA
1 TATTTTAAAAA
**
14059719 -ATTAAAAAAA
1 TATTTTAAAAA
14059729 TATTTTAAAAA
1 TATTTTAAAAA
14059740 TATTTT-AAAA
1 TATTTTAAAAA
14059750 TATTTT--AAA
1 TATTTTAAAAA
*
14059759 -A-TTAAAAAA
1 TATTTTAAAAA
14059768 T-TTTTAAAAAAA
1 TATTTT--AAAAA
14059780 GTATTTTAAAAA
1 -TATTTTAAAAA
14059792 TATTTTAAAA
1 TATTTTAAAA
14059802 TTTAAAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
7 2 0.03
8 1 0.01
9 11 0.14
10 24 0.31
11 24 0.31
12 10 0.13
13 1 0.01
14 4 0.05
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:14059760 original size:40 final size:41
Alignment explanation
Indices: 14059699--14059850 Score: 163
Period size: 40 Copynumber: 3.7 Consensus size: 41
14059689 GGCCCATTTT
14059699 TATTTTAAAA-ATTTTAAAAAATTAAAAAAATATTTTAAAAA-
1 TATTTTAAAATATTTT--AAAATTAAAAAAATATTTTAAAAAG
14059740 TATTTTAAAATATTTTAAAATT-AAAAAAT-TTTTAAAAAAAG
1 TATTTTAAAATATTTTAAAATTAAAAAAATATTTT--AAAAAG
* *
14059781 TATTTTAAAAATATTTTAAAATTTAAAAAA-A-TTAAAAAAG
1 TATTTT-AAAATATTTTAAAATTAAAAAAATATTTTAAAAAG
* **
14059821 TACGTAAAAAATATTTTAAAATTAAAAAAA
1 TA-TTTTAAAATATTTTAAAATTAAAAAAA
14059851 ATAAATATAT
Statistics
Matches: 98, Mismatches: 5, Indels: 17
0.82 0.04 0.14
Matches are distributed among these distances:
38 4 0.04
39 7 0.07
40 41 0.42
41 17 0.17
42 23 0.23
43 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (41 bp):
TATTTTAAAATATTTTAAAATTAAAAAAATATTTTAAAAAG
Found at i:14059765 original size:16 final size:16
Alignment explanation
Indices: 14059744--14059790 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
14059734 TAAAAATATT
14059744 TTAAAATATTTTAAAA
1 TTAAAATATTTTAAAA
*
14059760 TTAAAAAATTTTTAAAA
1 TTAAAATA-TTTTAAAA
*
14059777 --AAAGTATTTTAAAA
1 TTAAAATATTTTAAAA
14059791 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 8 0.30
15 4 0.15
16 7 0.26
17 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TTAAAATATTTTAAAA
Found at i:14059793 original size:52 final size:51
Alignment explanation
Indices: 14059720--14059841 Score: 158
Period size: 52 Copynumber: 2.4 Consensus size: 51
14059710 TTTTAAAAAA
**
14059720 TTAAAAAAATATTTTAAAAATATTTTAAAATATT-TTAAAATTAAAAAATTT
1 TTAAAAAAATATTTTAAAAATATTTTAAAAT-TTAAAAAAATTAAAAAATTT
**
14059771 TTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAGTAC
1 TTAAAAAAA-TATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAA-TTT
*
14059824 GT-AAAAAATATTTTAAAA
1 TTAAAAAAATATTTTAAAA
14059842 TTAAAAAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
51 21 0.33
52 40 0.63
53 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (51 bp):
TTAAAAAAATATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAATTT
Found at i:14059802 original size:82 final size:82
Alignment explanation
Indices: 14059699--14059849 Score: 200
Period size: 82 Copynumber: 1.8 Consensus size: 82
14059689 GGCCCATTTT
* * **
14059699 TATTTTAAAAATTTTAAAAAATTAAAAAAATATTTTAAAAA-TA-TTTTAAAATATTTTAAAATT
1 TATTTTAAAAATTTTAAAAAATTAAAAAAA-A-TTAAAAAAGTACGTAAAAAATATTTTAAAATT
14059762 AAAAAATTTTTAAAAAAAG
64 AAAAAATTTTTAAAAAAAG
* *
14059781 TATTTTAAAAATATTT-TAAAATTTAAAAAAATTAAAAAAGTACGTAAAAAATATTTTAAAATTA
1 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAATTAAAAAAGTACGTAAAAAATATTTTAAAATTA
14059845 AAAAA
65 AAAAA
14059850 AATAAATATA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
80 7 0.12
81 3 0.05
82 47 0.78
83 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (82 bp):
TATTTTAAAAATTTTAAAAAATTAAAAAAAATTAAAAAAGTACGTAAAAAATATTTTAAAATTAA
AAAATTTTTAAAAAAAG
Found at i:14061816 original size:16 final size:17
Alignment explanation
Indices: 14061785--14061817 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14061775 ATTAAAAAAT
*
14061785 AATAAATTATATTTTTG
1 AATAAAATATATTTTTG
14061802 AATAAAATA-ATTTTTG
1 AATAAAATATATTTTTG
14061818 GCTTCAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
AATAAAATATATTTTTG
Found at i:14065027 original size:18 final size:18
Alignment explanation
Indices: 14065004--14065076 Score: 110
Period size: 18 Copynumber: 4.1 Consensus size: 18
14064994 CGTTTATGGC
14065004 ACTATTCACGTATACAGT
1 ACTATTCACGTATACAGT
* * *
14065022 ACTATTCATGTATACGGC
1 ACTATTCACGTATACAGT
14065040 ACTATTCACGTATACAGT
1 ACTATTCACGTATACAGT
*
14065058 ACTGTTCACGTATACAGT
1 ACTATTCACGTATACAGT
14065076 A
1 A
14065077 GTTGGGATTG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (18 bp):
ACTATTCACGTATACAGT
Found at i:14065048 original size:36 final size:36
Alignment explanation
Indices: 14065001--14065072 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
14064991 GACCGTTTAT
*
14065001 GGCACTATTCACGTATACAGTACTATTCATGTATAC
1 GGCACTATTCACGTATACAGTACTATTCACGTATAC
*
14065037 GGCACTATTCACGTATACAGTACTGTTCACGTATAC
1 GGCACTATTCACGTATACAGTACTATTCACGTATAC
14065073 AGTAGTTGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (36 bp):
GGCACTATTCACGTATACAGTACTATTCACGTATAC
Found at i:14089019 original size:18 final size:18
Alignment explanation
Indices: 14088996--14089070 Score: 123
Period size: 18 Copynumber: 4.2 Consensus size: 18
14088986 CCCAACTACT
*
14088996 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
14089014 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
14089032 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
14089050 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
14089068 GTA
1 GTA
14089071 AACGGTCGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:14092733 original size:23 final size:24
Alignment explanation
Indices: 14092707--14092758 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
14092697 AGAATTAGAA
14092707 AAATTT-TGTAAATGTTAAAAATT-
1 AAATTTAT-TAAATGTTAAAAATTC
* *
14092730 AAATTTATTAAATTTTTAAAATTC
1 AAATTTATTAAATGTTAAAAATTC
14092754 AAATT
1 AAATT
14092759 CAAATGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTTATTAAATGTTAAAAATTC
Found at i:14097083 original size:21 final size:21
Alignment explanation
Indices: 14097059--14097098 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
14097049 AAAAAATTAT
14097059 ATTAAGTAAAAAATTAAAAAA
1 ATTAAGTAAAAAATTAAAAAA
* * *
14097080 ATTACGTACACAATTAAAA
1 ATTAAGTAAAAAATTAAAA
14097099 TATAAAATGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (21 bp):
ATTAAGTAAAAAATTAAAAAA
Found at i:14098201 original size:27 final size:25
Alignment explanation
Indices: 14098171--14098225 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
14098161 ATATTTGAAA
*
14098171 TTTAGTCATTTTATTTTTATTTTTATT
1 TTTAG-CAATTTATTTTT-TTTTTATT
* *
14098198 TTTAGGAATTTGTTTTTTTTTTATT
1 TTTAGCAATTTATTTTTTTTTTATT
14098223 TTT
1 TTT
14098226 CAGATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 9 0.36
27 5 0.20
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (25 bp):
TTTAGCAATTTATTTTTTTTTTATT
Found at i:14103668 original size:25 final size:25
Alignment explanation
Indices: 14103622--14103733 Score: 91
Period size: 25 Copynumber: 4.5 Consensus size: 25
14103612 ATGTATGCTT
* *
14103622 ATACAAGCATGTA-AACGAGAAGCTC
1 ATACGAGC-TGTATAACGGGAAGCTC
* *
14103647 TTCCGAGCTGTATAACGGGAAGCTC
1 ATACGAGCTGTATAACGGGAAGCTC
* *
14103672 ATACGAGCTGTATATCAGGAAGCTC
1 ATACGAGCTGTATAACGGGAAGCTC
* ** * *
14103697 ATGCGAGCCATTTATCGGGAAGCTC
1 ATACGAGCTGTATAACGGGAAGCTC
* *
14103722 ATAAGAGTTGTA
1 ATACGAGCTGTA
14103734 AATCAAGAAA
Statistics
Matches: 67, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
24 4 0.06
25 63 0.94
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (25 bp):
ATACGAGCTGTATAACGGGAAGCTC
Found at i:14103763 original size:50 final size:50
Alignment explanation
Indices: 14103662--14103782 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
14103652 AGCTGTATAA
* * * * * * **
14103662 CGGGAAGCTCATACGAGCTGTATATCAGGAAGCTCATGCGAGCCATTTAT
1 CGGGAAGCTCATAAGAGCTGTAAATCAAGAAACTCATGCAACCCAAATAT
*
14103712 CGGGAAGCTCATAAGAGTTGTAAATCAAGAAACTCATGCAACCCAAATAT
1 CGGGAAGCTCATAAGAGCTGTAAATCAAGAAACTCATGCAACCCAAATAT
*
14103762 CGAGAAGCTCA-AGAGAGCTGT
1 CGGGAAGCTCATA-AGAGCTGT
14103783 GGTGTGTCCA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 1 0.02
50 58 0.98
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (50 bp):
CGGGAAGCTCATAAGAGCTGTAAATCAAGAAACTCATGCAACCCAAATAT
Found at i:14106020 original size:20 final size:20
Alignment explanation
Indices: 14105997--14106060 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
14105987 AAAATTAGAA
14105997 AAAAAATTGTAAAAAAATTT
1 AAAAAATTGTAAAAAAATTT
*
14106017 AAAAAATTGT--AAAATTTT
1 AAAAAATTGTAAAAAAATTT
*
14106035 ATAAAAATCGTAAAAAAATTAT
1 A-AAAAATTGTAAAAAAATT-T
14106057 AAAA
1 AAAA
14106061 TTTTATAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 10 0.27
21 9 0.24
22 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAAAATTGTAAAAAAATTT
Found at i:14106040 original size:30 final size:30
Alignment explanation
Indices: 14105956--14106069 Score: 86
Period size: 30 Copynumber: 3.7 Consensus size: 30
14105946 TGAAAGGTAT
* *
14105956 AAAAATTATTAAATTTTAATAAAAAAA-TAT
1 AAAAATTATAAAATTTT-ATAAAAAAAGTAA
* * ** * * *
14105986 TAAAATTAGAAAAAAAATTGTAAAAAAATTTA
1 AAAAATT--ATAAAATTTTATAAAAAAAGTAA
* **
14106018 AAAAATTGTAAAATTTTATAAAAATCGTAA
1 AAAAATTATAAAATTTTATAAAAAAAGTAA
14106048 AAAAATTATAAAATTTTATAAA
1 AAAAATTATAAAATTTTATAAA
14106070 GCTATAAGAA
Statistics
Matches: 62, Mismatches: 19, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
30 41 0.66
31 8 0.13
32 13 0.21
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAAATTATAAAATTTTATAAAAAAAGTAA
Found at i:14106060 original size:10 final size:10
Alignment explanation
Indices: 14105997--14106132 Score: 58
Period size: 11 Copynumber: 14.0 Consensus size: 10
14105987 AAAATTAGAA
*
14105997 AAAAAATTGT
1 AAAAAATTAT
14106007 AAAAAAATT-T
1 -AAAAAATTAT
*
14106017 AAAAAATTGT
1 AAAAAATTAT
**
14106027 AAAATTTTAT
1 AAAAAATTAT
14106037 -AAAAATCGTA-
1 AAAAAAT--TAT
14106047 AAAAAATTAT
1 AAAAAATTAT
*
14106057 --AAAATTTT
1 AAAAAATTAT
* **
14106065 ATAAAGCTAT
1 AAAAAATTAT
14106075 AAGAAAATTAT
1 AA-AAAATTAT
14106086 AAAAAATGTA-
1 AAAAAAT-TAT
*
14106096 AAGAAA-TAT
1 AAAAAATTAT
14106105 --AAAATTCAT
1 AAAAAATT-AT
*
14106114 AAAAAAATAT
1 AAAAAATTAT
14106124 -AAAAATTAT
1 AAAAAATTAT
14106133 CTTACCAAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 30
0.67 0.11 0.21
Matches are distributed among these distances:
7 3 0.03
8 10 0.11
9 24 0.25
10 27 0.28
11 31 0.33
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:14106333 original size:19 final size:19
Alignment explanation
Indices: 14106309--14106390 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 19
14106299 CTTTTTGATA
14106309 CATTTTT-TAATTTTTTAT
1 CATTTTTATAATTTTTTAT
* **
14106327 GATTTTTATAAAATTTTA-
1 CATTTTTATAATTTTTTAT
* *
14106345 CAATTTTT-TATATATTTATAC
1 C-ATTTTTATA-AT-TTTTTAT
14106366 CATTTTTATAATTTTTTAT
1 CATTTTTATAATTTTTTAT
14106385 -ATTTTT
1 CATTTTT
14106391 CACTAAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
18 14 0.29
19 20 0.41
20 12 0.24
21 3 0.06
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (19 bp):
CATTTTTATAATTTTTTAT
Found at i:14106333 original size:29 final size:27
Alignment explanation
Indices: 14106300--14106390 Score: 101
Period size: 29 Copynumber: 3.2 Consensus size: 27
14106290 TTAAAAGGTC
14106300 TTTTTGATACATTTTTTAATTTTTTATGA
1 TTTTT-ATACATTTTTTAATTTTTTAT-A
* **
14106329 TTTTTATAAAATTTTACAATTTTTTATA
1 TTTTTAT-ACATTTTTTAATTTTTTATA
*
14106357 TATTTATACCATTTTTATAATTTTTTATA
1 TTTTTATA-CATTTTT-TAATTTTTTATA
14106386 TTTTT
1 TTTTT
14106391 CACTAAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
27 1 0.02
28 14 0.27
29 36 0.71
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTTATACATTTTTTAATTTTTTATA
Found at i:14106402 original size:29 final size:28
Alignment explanation
Indices: 14106316--14106411 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 28
14106306 ATACATTTTT
14106316 TAATTTTTTATGATTTTTA-TAAAATTTTA
1 TAATTTTTTAT-ATTTTTACTAAAA-TTTA
* * **
14106345 CAATTTTTTATATATTTATAC-CATTTTTA
1 TAATTTTTTATAT-TTT-TACTAAAATTTA
14106374 TAATTTTTTATATTTTTCACTAAAATTTAA
1 TAATTTTTTATATTTTT-ACTAAAATTT-A
14106404 TAATTTTT
1 TAATTTTT
14106412 ATAACTTGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.02
28 7 0.13
29 33 0.62
30 12 0.23
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (28 bp):
TAATTTTTTATATTTTTACTAAAATTTA
Found at i:14108058 original size:8 final size:8
Alignment explanation
Indices: 14108035--14108092 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
14108025 TACTTATATA
14108035 TATAATTT
1 TATAATTT
14108043 T-TATATTT
1 TATA-ATTT
14108051 TATAATTT
1 TATAATTT
*
14108059 TAT-ATATA
1 TATAAT-TT
**
14108067 TATCTTTT
1 TATAATTT
14108075 TATAATTT
1 TATAATTT
14108083 TAT-ATTT
1 TATAATTT
14108090 TAT
1 TAT
14108093 TCATTTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 11 0.27
8 27 0.66
9 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (8 bp):
TATAATTT
Found at i:14108083 original size:32 final size:29
Alignment explanation
Indices: 14108028--14108092 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 29
14108018 ATATACATAC
14108028 TTATATATATAATTTTTATATTTTATAATT
1 TTATATATATAATTTTTATATTTTAT-ATT
*
14108058 TTATATATATATCTTTTTATAATTTTATATT
1 TTATATATATA-ATTTTTAT-ATTTTATATT
14108089 TTAT
1 TTAT
14108093 TCATTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 11 0.34
31 14 0.44
32 7 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATATATATAATTTTTATATTTTATATT
Found at i:14108099 original size:24 final size:24
Alignment explanation
Indices: 14108047--14108101 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
14108037 TAATTTTTAT
14108047 ATTTTATAATTTTATATATATATC
1 ATTTTATAATTTTATATATATATC
* *
14108071 TTTTTATAATTTTATAT-TTTATTC
1 ATTTTATAATTTTATATATATA-TC
14108095 ATTTTAT
1 ATTTTAT
14108102 TTATTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTTATAATTTTATATATATATC
Found at i:14112179 original size:31 final size:29
Alignment explanation
Indices: 14112140--14112252 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
14112130 ATCTTAATCC
*
14112140 TAAAATTTTTAAGAAATATATAAAAATACG
1 TAAAATTTTTAA-AAATATATAAAAATACA
* *
14112170 TAAATATTTTCAAAAA-ATAT-ATAATA-A
1 TAAA-ATTTTTAAAAATATATAAAAATACA
*
14112197 TAAAA-TTTT-AAAATATATAAAAAATACT
1 TAAAATTTTTAAAAATATAT-AAAAATACA
14112225 TAAATATTTTT-AAAATATAATAATAAAT
1 TAAA-ATTTTTAAAAATAT-ATAA-AAAT
14112253 TTAAATTTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 17
0.75 0.07 0.19
Matches are distributed among these distances:
24 4 0.06
25 7 0.10
26 1 0.01
27 9 0.13
28 9 0.13
29 5 0.07
30 20 0.29
31 13 0.19
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (29 bp):
TAAAATTTTTAAAAATATATAAAAATACA
Found at i:14112294 original size:25 final size:25
Alignment explanation
Indices: 14112262--14112309 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
14112252 TTTAAATTTT
*
14112262 ATATTAATATTTAATAAAAATAATG
1 ATATTAATATTAAATAAAAATAATG
*
14112287 ATATTAATATTAAATAATAATAA
1 ATATTAATATTAAATAAAAATAA
14112310 AACCCTCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATTAATATTAAATAAAAATAATG
Found at i:14112898 original size:25 final size:25
Alignment explanation
Indices: 14112864--14112913 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
14112854 GGAGACGGGG
*
14112864 TTATTTTTATTTAATATGAATATAA
1 TTATTTTTATTAAATATGAATATAA
*
14112889 TTATTTTTATTAAATATTAATATAA
1 TTATTTTTATTAAATATGAATATAA
14112914 AATTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTTTTATTAAATATGAATATAA
Found at i:14113009 original size:37 final size:36
Alignment explanation
Indices: 14112921--14113001 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
14112911 TAAAATTTAA
* *
14112921 ATATATTATTATATTTTTAAAATATTTATGTATATTT
1 ATATATT-TTAAATTTTCAAAATATTTATGTATATTT
*
14112958 ATATATTTTAAATTTTCAATAATATTTCT-TAT-TTT
1 ATATATTTTAAATTTTCAA-AATATTTATGTATATTT
14112993 ATATATTTT
1 ATATATTTT
14113002 TAAAATTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
35 12 0.30
36 13 0.32
37 15 0.38
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (36 bp):
ATATATTTTAAATTTTCAAAATATTTATGTATATTT
Found at i:14113012 original size:22 final size:21
Alignment explanation
Indices: 14112986--14113045 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
14112976 ATAATATTTC
*
14112986 TTATTTTATATATTTTTAAAA
1 TTATTTTATATACTTTTAAAA
14113007 TTTATTATTATAT-CTTTTAAAA
1 -TTATT-TTATATACTTTTAAAA
*
14113029 ATA-TTTATATACTTTTA
1 TTATTTTATATACTTTTA
14113046 CATATTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 6 0.18
20 7 0.21
21 2 0.06
22 13 0.38
23 6 0.18
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTTTATATACTTTTAAAA
Found at i:14113034 original size:25 final size:22
Alignment explanation
Indices: 14112986--14113045 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
14112976 ATAATATTTC
*
14112986 TTATTTTATATATTTTTAAAAT
1 TTATTTTATATATTTTAAAAAT
*
14113008 TTATTATTATATCTTTTAAAAA-
1 TTATT-TTATATATTTTAAAAAT
14113030 -TA-TTTATATACTTTTA
1 TTATTTTATATA-TTTTA
14113046 CATATTGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.18
20 6 0.18
21 2 0.06
22 5 0.15
23 14 0.42
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTTTATATATTTTAAAAAT
Found at i:14116225 original size:15 final size:16
Alignment explanation
Indices: 14116185--14116225 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
14116175 ATATCGGGTG
*
14116185 TTCTAAACATAGTTAC
1 TTCTAAACATAATTAC
14116201 TT-TGAAACATAATTA-
1 TTCT-AAACATAATTAC
14116216 TTCTAAACAT
1 TTCTAAACAT
14116226 TAGTTGTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (16 bp):
TTCTAAACATAATTAC
Found at i:14118984 original size:16 final size:17
Alignment explanation
Indices: 14118963--14118995 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14118953 CGTGTAACTT
14118963 TTAAAAA-CAACTAAAA
1 TTAAAAATCAACTAAAA
*
14118979 TTAAAAATCAAGTAAAA
1 TTAAAAATCAACTAAAA
14118996 CCGAACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.67, C:0.09, G:0.03, T:0.21
Consensus pattern (17 bp):
TTAAAAATCAACTAAAA
Found at i:14119430 original size:13 final size:13
Alignment explanation
Indices: 14119399--14119446 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
14119389 GTTTACCATG
* *
14119399 TTAAAAAATGTTG
1 TTAAAAAATATTT
*
14119412 TGAAAAAA-ATCTT
1 TTAAAAAATAT-TT
14119425 TTAAAAAATATTT
1 TTAAAAAATATTT
14119438 TTAAAAAAT
1 TTAAAAAAT
14119447 TTGATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 1 0.03
13 26 0.90
14 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
TTAAAAAATATTT
Found at i:14119555 original size:6 final size:6
Alignment explanation
Indices: 14119544--14119572 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
14119534 ATTTGATCTT
14119544 CAAAAC CAAAAC CAAAAC CAAAAC CAAAA
1 CAAAAC CAAAAC CAAAAC CAAAAC CAAAA
14119573 GCTAAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAC
Found at i:14124985 original size:26 final size:25
Alignment explanation
Indices: 14124929--14124977 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
14124919 ATACACATTA
14124929 AAAAATATAAAAAAAATATAAATAT
1 AAAAATATAAAAAAAATATAAATAT
* *
14124954 ATAAAATCTAAAAAAAATCTAAAT
1 A-AAAATATAAAAAAAATATAAAT
14124978 TTTAAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAATATAAAAAAAATATAAATAT
Found at i:14125196 original size:20 final size:19
Alignment explanation
Indices: 14125166--14125226 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
14125156 GAAATTTAAA
*
14125166 TATAGATTTTTTTAATTTT
1 TATACATTTTTTTAATTTT
* *
14125185 TGTAGCATTTTTTAAATTTT
1 TATA-CATTTTTTTAATTTT
*
14125205 TATATATTATTTTTAATTTT
1 TATACATT-TTTTTAATTTT
14125225 TA
1 TA
14125227 AATTTTATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.18
20 28 0.82
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (19 bp):
TATACATTTTTTTAATTTT
Found at i:14125234 original size:20 final size:21
Alignment explanation
Indices: 14125193--14125234 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
14125183 TTTGTAGCAT
*
14125193 TTTTTAAATTTTTATATATTA
1 TTTTTAAATTTTTAAATATTA
*
14125214 TTTTT-AATTTTTAAATTTTA
1 TTTTTAAATTTTTAAATATTA
14125234 T
1 T
14125235 AATAAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTAAATTTTTAAATATTA
Found at i:14130418 original size:18 final size:18
Alignment explanation
Indices: 14130381--14130419 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
14130371 TTATTATTTT
*
14130381 TAAAATTTACTATTAGAA
1 TAAAATTTAATATTAGAA
14130399 TAAAATTTAAATATTA-AA
1 TAAAATTT-AATATTAGAA
14130417 TAA
1 TAA
14130420 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAATTTAATATTAGAA
Found at i:14132106 original size:17 final size:17
Alignment explanation
Indices: 14132065--14132106 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
14132055 ATTTGGTTCT
14132065 TATTTAT-AATATTAAA
1 TATTTATAAATATTAAA
14132081 TATTT-TAAATAATTAAA
1 TATTTATAAAT-ATTAAA
14132098 T-TTTATAAA
1 TATTTATAAA
14132107 AATATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 11 0.48
17 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTATAAATATTAAA
Found at i:14158484 original size:19 final size:20
Alignment explanation
Indices: 14158440--14158484 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
14158430 ATTAATTATT
*
14158440 TATAAAATTTAATTAGAATA
1 TATAAAATATAATTAGAATA
*
14158460 TATAAAATATATTTA-AATA
1 TATAAAATATAATTAGAATA
*
14158479 TTTAAA
1 TATAAA
14158485 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TATAAAATATAATTAGAATA
Found at i:14160438 original size:12 final size:12
Alignment explanation
Indices: 14160421--14160447 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
14160411 TATGTGTATA
14160421 ATTATTATAATT
1 ATTATTATAATT
14160433 ATTATTATAATT
1 ATTATTATAATT
14160445 ATT
1 ATT
14160448 TATTCAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATTATAATT
Found at i:14169210 original size:28 final size:28
Alignment explanation
Indices: 14169170--14169227 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
14169160 TAAAATAACC
14169170 ATTAATTCCAACAGGCAAGCATTTGTTA
1 ATTAATTCCAACAGGCAAGCATTTGTTA
14169198 ATTAATTCCAACAGGCAAGCATTTGTTA
1 ATTAATTCCAACAGGCAAGCATTTGTTA
14169226 AT
1 AT
14169228 CTCCTAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (28 bp):
ATTAATTCCAACAGGCAAGCATTTGTTA
Found at i:14170809 original size:16 final size:17
Alignment explanation
Indices: 14170788--14170819 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
14170778 TTCTTATAAT
14170788 TTTAAAAATTA-AAAAC
1 TTTAAAAATTAGAAAAC
14170804 TTTAAAAATTAGAAAA
1 TTTAAAAATTAGAAAA
14170820 TATTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
TTTAAAAATTAGAAAAC
Found at i:14170963 original size:17 final size:17
Alignment explanation
Indices: 14170937--14170978 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
14170927 ATAAAATTTA
*
14170937 TTTATTAAAATAATAAT
1 TTTATAAAAATAATAAT
14170954 TTTATAAAAATAATAAT
1 TTTATAAAAATAATAAT
*
14170971 CTTATAAA
1 TTTATAAA
14170979 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTATAAAAATAATAAT
Found at i:14171881 original size:11 final size:11
Alignment explanation
Indices: 14171861--14171967 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
14171851 CAAAAATTAA
14171861 AAAAAGTATTTT
1 AAAAA-TATTTT
14171873 AAAAATATTTT
1 AAAAATATTTT
14171884 --AAA-A--TT
1 AAAAATATTTT
* *
14171890 AAAAA-AATTA
1 AAAAATATTTT
14171900 AAAAAGTATTTT
1 AAAAA-TATTTT
*
14171912 AAAAAAATTTT
1 AAAAATATTTT
14171923 --AAA-A-TTT
1 AAAAATATTTT
*
14171930 AAAAAT-TTTAA
1 AAAAATATTT-T
14171941 AAAAAGTATTTT
1 AAAAA-TATTTT
*
14171953 AAAAGTATTTT
1 AAAAATATTTT
14171964 AAAA
1 AAAA
14171968 TTTAAAACAT
Statistics
Matches: 75, Mismatches: 7, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 6 0.08
9 9 0.12
10 8 0.11
11 26 0.35
12 18 0.24
13 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:14171918 original size:41 final size:40
Alignment explanation
Indices: 14171834--14171984 Score: 189
Period size: 39 Copynumber: 3.7 Consensus size: 40
14171824 ACCAAAAATT
14171834 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTTAAAAA
14171878 TATTTTAAAATTAAAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
* ** *
14171917 AATTTTAAAATTTAAAAATTTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAA
* *
14171958 TATTTTAAAATTTAAAACA-TAAAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAA
14171985 TAAAAATATT
Statistics
Matches: 97, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
39 35 0.36
40 22 0.23
41 28 0.29
43 6 0.06
44 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:14171934 original size:30 final size:29
Alignment explanation
Indices: 14171893--14171956 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
14171883 TAAAATTAAA
*
14171893 AAAATTAAAAAAGTATTTTAAAAAA-ATTTT
1 AAAATTAAAAAA-T-TTTAAAAAAAGATTTT
*
14171923 AAAATTTAAAAATTTTAAAAAAAGTATTTT
1 AAAATTAAAAAATTTTAAAAAAAG-ATTTT
14171953 AAAA
1 AAAA
14171957 GTATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 9 0.30
29 1 0.03
30 20 0.67
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTAAAAAATTTTAAAAAAAGATTTT
Found at i:14173783 original size:70 final size:71
Alignment explanation
Indices: 14173664--14173807 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 71
14173654 AAGCCAACTA
*
14173664 ACTGCTGTCTTGTTTTGATATATCTGTTGCTTGTTAAACATGATCTCATGTGTTGTAATGATGCT
1 ACTGCTGTCTTGTTTTGATATA-CTGTTGCTTGTTAAACATGATCTCATGTGTTGCAATGATGCT
14173729 TAATCCT
65 TAATCCT
14173736 ACTGCTGTCTTGTTTTGATATA-TGTTGCTTGTTAAACATGA-CTTCATGTGTTGCAATGATGCT
1 ACTGCTGTCTTGTTTTGATATACTGTTGCTTGTTAAACATGATC-TCATGTGTTGCAATGATGCT
14173799 TAATCCT
65 TAATCCT
14173806 AC
1 AC
14173808 CTTTGAATCT
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
69 1 0.01
70 47 0.67
72 22 0.31
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (71 bp):
ACTGCTGTCTTGTTTTGATATACTGTTGCTTGTTAAACATGATCTCATGTGTTGCAATGATGCTT
AATCCT
Found at i:14174418 original size:17 final size:17
Alignment explanation
Indices: 14174382--14174416 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
14174372 ATAAATTTAA
*
14174382 TTATTATTTAACATATT
1 TTATTATTTAAAATATT
14174399 TTATT-TTTAAAATATT
1 TTATTATTTAAAATATT
14174415 TT
1 TT
14174417 TAATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATTATTTAAAATATT
Found at i:14176028 original size:46 final size:46
Alignment explanation
Indices: 14175961--14176099 Score: 233
Period size: 46 Copynumber: 3.0 Consensus size: 46
14175951 ACATTGCTAT
* *
14175961 AACTCAGTATGGTTTTCTTCACGGAGATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
14176007 AACTCAGTATGGTTTTCTTCACTGAAACACCATATCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
14176053 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
14176099 A
1 A
14176100 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:14177359 original size:16 final size:17
Alignment explanation
Indices: 14177313--14177360 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
14177303 AAATTCTTTT
14177313 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
14177330 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
14177347 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
14177361 TTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:14177551 original size:24 final size:24
Alignment explanation
Indices: 14177517--14177562 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
14177507 TTGGCTTCGG
* **
14177517 TGAGATTGAAAATGTCAGTGGCGA
1 TGAGATCGAAAATCACAGTGGCGA
14177541 TGAGATCGAAAATCACAGTGGC
1 TGAGATCGAAAATCACAGTGGC
14177563 AGACTCAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (24 bp):
TGAGATCGAAAATCACAGTGGCGA
Found at i:14177727 original size:14 final size:14
Alignment explanation
Indices: 14177665--14177728 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
14177655 GTTGTTAAAA
*
14177665 ATAATTATCAATAT
1 ATAATTATTAATAT
*
14177679 ATAATAATTAAATTAAT
1 ATAATTATT-AA-T-AT
14177696 ATTAA-TATTAAT-T
1 A-TAATTATTAATAT
14177709 AATAATTATTAATAT
1 -ATAATTATTAATAT
14177724 ATAAT
1 ATAAT
14177729 AAAAATCTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
13 4 0.10
14 20 0.50
15 4 0.10
16 3 0.08
17 6 0.15
18 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAATTATTAATAT
Found at i:14177728 original size:17 final size:17
Alignment explanation
Indices: 14177664--14177730 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 17
14177654 AGTTGTTAAA
*
14177664 AATAATTATCAATATAT
1 AATAATTATTAATATAT
14177681 AATAATTA--AAT-TAAT
1 AATAATTATTAATAT-AT
*
14177696 ATTAA-TATT-A-AT-T
1 AATAATTATTAATATAT
14177709 AATAATTATTAATATAT
1 AATAATTATTAATATAT
14177726 AATAA
1 AATAA
14177731 AAATCTAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
13 5 0.12
14 7 0.17
15 12 0.30
16 2 0.05
17 14 0.35
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAATTATTAATATAT
Found at i:14193250 original size:23 final size:23
Alignment explanation
Indices: 14193224--14193276 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
14193214 ATAAGTGCAA
*
14193224 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
*
14193247 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
14193270 CACTGAT
1 CACTGAT
14193277 CAATAACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (23 bp):
CACTGATACGTAGCCGAAGCTAC
Found at i:14195660 original size:53 final size:53
Alignment explanation
Indices: 14195580--14195686 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
14195570 ACCGAACCTG
*
14195580 TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAATTTAAC
1 TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
*
14195633 TATAACCAAGATACACCCAAATATATTATTAATACAACCCGAATCAAATTAAC
1 TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
14195686 T
1 T
14195687 TACACTTCCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (53 bp):
TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
Found at i:14202376 original size:13 final size:13
Alignment explanation
Indices: 14202358--14202395 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
14202348 TGATATATGA
14202358 GTTTAATTTTTAT
1 GTTTAATTTTTAT
*
14202371 GTTTAA-TTTGAT
1 GTTTAATTTTTAT
*
14202383 ATTTAATTTTTAT
1 GTTTAATTTTTAT
14202396 CTGTTCAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (13 bp):
GTTTAATTTTTAT
Found at i:14202387 original size:25 final size:26
Alignment explanation
Indices: 14202359--14202409 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
14202349 GATATATGAG
*
14202359 TTTAATTTTTA-TGTTTAATTTGATA
1 TTTAATTTTTACTGTTCAATTTGATA
14202384 TTTAATTTTTATCTGTTCAATTTGAT
1 TTTAATTTTTA-CTGTTCAATTTGAT
14202410 GCTTAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
27 12 0.52
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.63
Consensus pattern (26 bp):
TTTAATTTTTACTGTTCAATTTGATA
Found at i:14202415 original size:27 final size:25
Alignment explanation
Indices: 14202360--14202415 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
14202350 ATATATGAGT
* *
14202360 TTAATTTTTATGTTTAATTTGATAT
1 TTAATTTTTATGTTCAATTTGATAC
*
14202385 TTAATTTTTATCTGTTCAATTTGATGC
1 TTAATTTTTA--TGTTCAATTTGATAC
14202412 TTAA
1 TTAA
14202416 GTCAAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 10 0.38
27 16 0.62
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (25 bp):
TTAATTTTTATGTTCAATTTGATAC
Found at i:14213776 original size:17 final size:17
Alignment explanation
Indices: 14213749--14213794 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
14213739 CCGATATAAT
* *
14213749 AAATATATTTATTTTTA
1 AAATATTTTTAATTTTA
*
14213766 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
14213783 AAATATTTTTAA
1 AAATATTTTTAA
14213795 AATACTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:14213813 original size:38 final size:38
Alignment explanation
Indices: 14213770--14213844 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
14213760 TTTTTAAAAT
14213770 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
14213808 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
14213845 TTAATTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (38 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:14213873 original size:22 final size:22
Alignment explanation
Indices: 14213824--14213884 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
14213814 AATTTTAAAA
** **
14213824 TATTTTTAAAATACTTTTTTTT
1 TATTTTTAAAATAAATTTTTGG
14213846 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTTGG
14213869 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
14213885 GGGCCGGGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 9 0.27
23 24 0.73
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (22 bp):
TATTTTTAAAATAAATTTTTGG
Found at i:14220279 original size:27 final size:27
Alignment explanation
Indices: 14220241--14220297 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
14220231 CTCATTTCGA
14220241 TTACTTCGGTGTTAAGATTTTTGAGTT
1 TTACTTCGGTGTTAAGATTTTTGAGTT
14220268 TTACTTCGGTGTTAAGATTTTTGAGTT
1 TTACTTCGGTGTTAAGATTTTTGAGTT
14220295 TTA
1 TTA
14220298 GTTTTGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.07, G:0.21, T:0.53
Consensus pattern (27 bp):
TTACTTCGGTGTTAAGATTTTTGAGTT
Found at i:14234864 original size:21 final size:20
Alignment explanation
Indices: 14234839--14234878 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
14234829 AAAATTACAA
14234839 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
* *
14234859 AAAAAATTCCAAATTTTTAT
1 AAAAAATTCAAAATATTTAT
14234879 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:14238565 original size:51 final size:48
Alignment explanation
Indices: 14238494--14238608 Score: 122
Period size: 51 Copynumber: 2.3 Consensus size: 48
14238484 TGGCCATTTG
* * *
14238494 TTCGTATTTTTCTTTTTTTTCGGATTTTATTACTTTCAGTAAATATACTATT
1 TTCGT-TTTTTATTTCTTTTCGGATTTTATT-CTTTCA-TAAACATA-TATT
* * *
14238546 TTCGTTTTTTATTTCTTTTCGTATTTTATTTTTTCATAAACATATTTT
1 TTCGTTTTTTATTTCTTTTCGGATTTTATTCTTTCATAAACATATATT
*
14238594 TTCGGTATTTTATTT
1 TTC-GTTTTTTATTT
14238609 TTAATACTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
48 6 0.11
49 17 0.31
50 5 0.09
51 22 0.40
52 5 0.09
ACGTcount: A:0.19, C:0.10, G:0.07, T:0.63
Consensus pattern (48 bp):
TTCGTTTTTTATTTCTTTTCGGATTTTATTCTTTCATAAACATATATT
Found at i:14238566 original size:17 final size:17
Alignment explanation
Indices: 14238544--14238576 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14238534 AAATATACTA
*
14238544 TTTTCGTTTTTTATTTC
1 TTTTCGTATTTTATTTC
14238561 TTTTCGTATTTTATTT
1 TTTTCGTATTTTATTT
14238577 TTTCATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTCGTATTTTATTTC
Found at i:14238573 original size:158 final size:158
Alignment explanation
Indices: 14238172--14238558 Score: 630
Period size: 158 Copynumber: 2.4 Consensus size: 158
14238162 TGGCACCCCA
* * *
14238172 CATTTGTTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATATTATTTTCGTGTT
1 CATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATT
* *
14238237 TTATTATTTTATATTATTTTATTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTATAT
66 TTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAATGTGTTTTTTATAT
*
14238302 AAATTTTGTAAAAAACCCTCATTTTGGC
131 AAATTTAGTAAAAAACCCTCATTTTGGC
14238330 CATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATT
1 CATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATT
* *
14238395 TTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAATGTGTTTTTTATAT
66 TTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAATGTGTTTTTTATAT
* * *
14238460 AAATTTAGTGAAAACCCCTTATTTTGGC
131 AAATTTAGTAAAAAACCCTCATTTTGGC
* ** *
14238488 CATTTGTTCGTATTTTTCTTTTTTTTCGGATTTTATTACTTTCAGTAAATATACTATTTTCGTTT
1 CATTTGTTCGTATTTTTC-TTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
14238553 TTTATT
65 TTTATT
14238559 TCTTTTCGTA
Statistics
Matches: 213, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
158 165 0.77
159 48 0.23
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (158 bp):
CATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATT
TTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAATGTGTTTTTTATAT
AAATTTAGTAAAAAACCCTCATTTTGGC
Found at i:14239144 original size:27 final size:27
Alignment explanation
Indices: 14239103--14239205 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
14239093 TAGTATTGGC
*
14239103 GCCTATCTGGAAGGCGCCAATGGTGGG
1 GCCTATCTGGGAGGCGCCAATGGTGGG
* *
14239130 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGG
*
14239157 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGG
**
14239184 GCC-ATACTGAAAGGCGCCAATG
1 GCCTAT-CTGGGAGGCGCCAATG
14239206 TTGTGATTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
26 2 0.03
27 67 0.97
ACGTcount: A:0.19, C:0.22, G:0.38, T:0.20
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGG
Found at i:14239309 original size:18 final size:20
Alignment explanation
Indices: 14239267--14239313 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
14239257 GAAACGGAAG
14239267 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
14239287 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
14239305 AAAGAAGAA
1 AAAGAAGAA
14239314 AAAAATTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:14239316 original size:22 final size:23
Alignment explanation
Indices: 14239263--14239316 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
14239253 TACAGAAACG
*
14239263 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
14239287 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
14239308 GAAGAAAAA
1 GAAGAAAAA
14239317 AATTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:14242819 original size:16 final size:15
Alignment explanation
Indices: 14242788--14242829 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
14242778 ACAAAATCAA
*
14242788 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
14242803 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
14242819 ATAAAAATTAA
1 ATAAAAGTTAA
14242830 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:14242892 original size:38 final size:38
Alignment explanation
Indices: 14242849--14242930 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 38
14242839 CAACAACTAT
14242849 ATGATTAAAAAGTCAGTTATAATTAAACTTTTAATAAA
1 ATGATTAAAAAGTCAGTTATAATTAAACTTTTAATAAA
*** * *** *
14242887 ATGATTTTTAATTTTTTTATAATTAAACTTTTAATGAA
1 ATGATTAAAAAGTCAGTTATAATTAAACTTTTAATAAA
14242925 ATGATT
1 ATGATT
14242931 TTTAATTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (38 bp):
ATGATTAAAAAGTCAGTTATAATTAAACTTTTAATAAA
Found at i:14242931 original size:38 final size:37
Alignment explanation
Indices: 14242865--14242945 Score: 144
Period size: 38 Copynumber: 2.2 Consensus size: 37
14242855 AAAAAGTCAG
14242865 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAA-TTTT
*
14242903 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
14242940 TTATAA
1 TTATAA
14242946 ACTTTATATG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 10 0.24
38 32 0.76
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (37 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
Found at i:14243163 original size:19 final size:19
Alignment explanation
Indices: 14243139--14243557 Score: 160
Period size: 19 Copynumber: 22.2 Consensus size: 19
14243129 ATATCCCCAC
14243139 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
14243158 ATTACAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
14243174 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
* *
14243188 ATTGCAATATTCATATAAA
1 ATTACAATATTCATACAAA
* *
14243207 ATTATAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
14243223 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
* *
14243237 ATTGCAATATTCATATAAA
1 ATTACAATATTCATACAAA
* *
14243256 ATTATAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
14243272 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
*
14243286 ATTATAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
14243305 ATTACAA-AAT--TACAAA
1 ATTACAATATTCATACAAA
14243321 ATTACAATATTCATACAAAAAAA
1 ATTACAATATTCATAC----AAA
*
14243344 ATTGCAATATTCATACAAAACTATAA
1 ATTACAATATTCAT-----AC-A-AA
14243370 TATTACAATATTCATACAAAAA
1 -ATTACAATATTCATAC--AAA
*
14243392 ATTTATAATATTCATACAAA
1 A-TTACAATATTCATACAAA
14243412 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
* * *
14243433 ATTACTAAT-CTAAAACTATAA
1 ATTAC-AATATTCATAC-A-AA
*
14243454 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
14243476 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAA
*
14243495 ATTACAATATTCATAAAAA
1 ATTACAATATTCATACAAA
*
14243514 ATTATAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
*
14243535 ATTTAAAATATTCATACAAA
1 A-TTACAATATTCATACAAA
14243555 ATT
1 ATT
14243558 CTAATCTAAA
Statistics
Matches: 304, Mismatches: 45, Indels: 102
0.67 0.10 0.23
Matches are distributed among these distances:
14 27 0.09
15 3 0.01
16 44 0.14
17 2 0.01
18 11 0.04
19 94 0.31
20 20 0.07
21 21 0.07
22 41 0.13
23 22 0.07
24 1 0.00
25 1 0.00
26 2 0.01
27 13 0.04
28 2 0.01
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:14243175 original size:27 final size:26
Alignment explanation
Indices: 14243139--14243422 Score: 242
Period size: 27 Copynumber: 11.1 Consensus size: 26
14243129 ATATCCCCAC
14243139 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
14243166 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
14243188 ATTGCAATATTCATATAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
14243215 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
14243237 ATTGCAATATTCATATAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
14243264 ATTACAATATTCATACAAAAAAATTATAAT
1 ATTACAATATTCATAC---AAAATTA-AAT
*** *
14243294 ATT-C-ATACAAAATTACAAAATTACAAA
1 ATTACAATA-TTCA-TACAAAATTA-AAT
14243321 ATTACAATATTCATACAAAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
14243344 ATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
14243371 ATTACAATATTCATAC-AAA--AAAT
1 ATTACAATATTCATACAAAATTAAAT
*
14243394 -TTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
14243420 ATT
1 ATT
14243423 CATACAAAAA
Statistics
Matches: 212, Mismatches: 19, Indels: 52
0.75 0.07 0.18
Matches are distributed among these distances:
22 42 0.20
23 35 0.17
24 5 0.02
25 5 0.02
26 18 0.08
27 80 0.38
28 5 0.02
29 5 0.02
30 17 0.08
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAT
Found at i:14243216 original size:49 final size:49
Alignment explanation
Indices: 14243086--14243422 Score: 385
Period size: 49 Copynumber: 6.7 Consensus size: 49
14243076 AATTAATTAT
* *
14243086 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATA-T-AT-C
1 AAAAAAATTGCAATATTCATAC--AAAATTACAATATTACAATATTCATAC
*** * *
14243134 -CCCACATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
14243182 AAAAAAATTGCAATATTCATATAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
14243231 AAAAAAATTGCAATATTCATATAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
**
14243280 AAAAAAATTATAATATTCATACAAAATTACAAAATTACAAAATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTAC--AA-T-----ATTACAATATTCATAC
* *
14243337 AAAAAAAATTGCAATATTCATACAAAACTATAATATTACAATATTCATAC
1 -AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
* **
14243387 AAAAAATTTATAATATTCATACAAAATTACAATATT
1 AAAAAAATTGCAATATTCATACAAAATTACAATATT
14243423 CATACAAAAA
Statistics
Matches: 251, Mismatches: 25, Indels: 25
0.83 0.08 0.08
Matches are distributed among these distances:
45 20 0.08
46 1 0.00
47 18 0.07
48 1 0.00
49 147 0.59
50 16 0.06
51 2 0.01
52 1 0.00
55 1 0.00
56 2 0.01
57 16 0.06
58 26 0.10
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (49 bp):
AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:14243309 original size:41 final size:41
Alignment explanation
Indices: 14243264--14243557 Score: 165
Period size: 41 Copynumber: 7.1 Consensus size: 41
14243254 AAATTATAAT
*
14243264 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
*
14243305 ATTACAA-AAT--TAC---AAAATTACAATATTCATACAAAAAAA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATAC----AAA
*
14243344 ATTGCAATATTCATACAAAACTATAATATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC-AAA--A-AA-ATTACAATATTCATAC--AAA
*
14243392 ATTTATAATATTCATAC---AAAATTACAATATTCATACAAAAA
1 A-TTACAATATTCATACAAAAAAATTACAATATTCATAC--AAA
* *
14243433 ATTAC--TAATC-TA-AAACTATAAA-TACAAATTTAATT-ATAAAATA
1 ATTACAATATTCATACAAA--A-AAATTAC-AA--T-ATTCATACAA-A
* *
14243476 ATTACAATATTCATAC---AACATTACAATATTCATAAAAA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
* * *
14243514 ATTATAATATTCATACAAAAAATTTAAAATATTCATACAAA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
14243555 ATT
1 ATT
14243558 CTAATCTAAA
Statistics
Matches: 201, Mismatches: 16, Indels: 72
0.70 0.06 0.25
Matches are distributed among these distances:
35 18 0.09
37 2 0.01
38 26 0.13
39 16 0.08
40 7 0.03
41 58 0.29
42 16 0.08
43 7 0.03
44 4 0.02
45 7 0.03
46 2 0.01
48 7 0.03
49 15 0.07
50 16 0.08
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (41 bp):
ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
Found at i:14243312 original size:8 final size:8
Alignment explanation
Indices: 14243299--14243327 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
14243289 ATAATATTCA
14243299 TACAAAAT
1 TACAAAAT
14243307 TACAAAAT
1 TACAAAAT
14243315 TACAAAAT
1 TACAAAAT
14243323 TACAA
1 TACAA
14243328 TATTCATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (8 bp):
TACAAAAT
Found at i:14243375 original size:58 final size:57
Alignment explanation
Indices: 14243250--14243412 Score: 189
Period size: 57 Copynumber: 3.0 Consensus size: 57
14243240 GCAATATTCA
* * * *
14243250 TATAAAATTATAATATTACAATATTCATACAAAAAAATTATAATATTCATACAAAAT
1 TATAAAATTACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAAC
* *
14243307 TACAAAATTACAAAATTACAATATTCATACAAAAAAAATTGCAATATTCATACAAAAC
1 TATAAAATTACAAAATTACAATATTCATAC-AAAAAAATTACAATATTCATACAAAAC
* *
14243365 TAT--AA-T-----ATTACAATATTCATACAAAAAATTTATAATATTCATACAAAA
1 TATAAAATTACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAA
14243413 TTACAATATT
Statistics
Matches: 95, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
49 23 0.24
50 16 0.17
55 1 0.01
56 2 0.02
57 27 0.28
58 26 0.27
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.32
Consensus pattern (57 bp):
TATAAAATTACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAAC
Found at i:14243380 original size:107 final size:106
Alignment explanation
Indices: 14243204--14243418 Score: 376
Period size: 107 Copynumber: 2.0 Consensus size: 106
14243194 ATATTCATAT
* * * *
14243204 AAAATTATAATATTACAATATTCATACAAAAAAATTGCAATATTCATATAAAATTATAATATTAC
1 AAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATTAC
14243269 AATATTCATACAAAAAAATTATAATATTCATACAAAATTAC
66 AATATTCATACAAAAAAATTATAATATTCATACAAAATTAC
14243310 AAAATTACAAAATTACAATATTCATACAAAAAAAATTGCAATATTCATACAAAACTATAATATTA
1 AAAATTACAAAATTACAATATTCATAC-AAAAAAATTGCAATATTCATACAAAACTATAATATTA
*
14243375 CAATATTCATACAAAAAATTTATAATATTCATACAAAATTAC
65 CAATATTCATACAAAAAAATTATAATATTCATACAAAATTAC
14243417 AA
1 AA
14243419 TATTCATACA
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
106 25 0.24
107 78 0.76
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (106 bp):
AAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATTAC
AATATTCATACAAAAAAATTATAATATTCATACAAAATTAC
Found at i:14243477 original size:107 final size:109
Alignment explanation
Indices: 14243215--14243555 Score: 302
Period size: 107 Copynumber: 3.2 Consensus size: 109
14243205 AAATTATAAT
* * * * *
14243215 ATTACAATATTCATAC-AAAAAAATTGCAATATTCATATAAAATTATAATATTACAATATTCATA
1 ATTAC-ATAATCATACAAAAAAAATTACAATATTAATACAAAA-CATAATATTACAATATTCATA
*
14243279 CAAAAAAATTATAATATTCATACAAAATTACAA-AAT--TAC--AAA
64 C-AAAAAATTATAATATTCATACAAAATTACAATATTCATACAAAAA
* * *
14243321 ATTACAATATTCATACAAAAAAAATTGCAATATTCATACAAAACTATAATATTACAATATTCATA
1 ATTAC-ATAATCATACAAAAAAAATTACAATATTAATACAAAAC-ATAATATTACAATATTCATA
14243386 CAAAAAATTTATAATATTCATACAAAATTACAATATTCATACAAAAA
64 CAAAAAA-TTATAATATTCATACAAAATTACAATATTCATACAAAAA
* *
14243433 ATTAC-TAATC-TA-AAACTATAAA-TACAA-ATTTAATTA-TAAA-AT-A-ATTACAATATTCA
1 ATTACATAATCATACAAA--AAAAATTACAATA-TTAA-TACAAAACATAATATTACAATATTCA
* * * *
14243489 TAC--AACATTACAATATTCATAAAAAATTATAATATTCATACAAAAA
62 TACAAAAAATTATAATATTCATACAAAATTACAATATTCATACAAAAA
* *
14243535 ATTTAAAATATTCATACAAAA
1 A-TT-ACATAATCATACAAAA
14243556 TTCTAATCTA
Statistics
Matches: 204, Mismatches: 14, Indels: 35
0.81 0.06 0.14
Matches are distributed among these distances:
102 37 0.18
103 5 0.02
104 1 0.00
105 21 0.10
106 25 0.12
107 76 0.37
108 6 0.03
109 12 0.06
110 13 0.06
112 8 0.04
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (109 bp):
ATTACATAATCATACAAAAAAAATTACAATATTAATACAAAACATAATATTACAATATTCATACA
AAAAATTATAATATTCATACAAAATTACAATATTCATACAAAAA
Found at i:14243485 original size:83 final size:85
Alignment explanation
Indices: 14243315--14243521 Score: 223
Period size: 83 Copynumber: 2.4 Consensus size: 85
14243305 ATTACAAAAT
*
14243315 TACAAAATTACAATATTCATACAAAAAAAATTGCAATATTCATACAAAACTATAATATTACAATA
1 TACAAAATTACAATATTCATAC--AAAAAATT---ATAATCATA-AAAACTATAATATTACAATA
* *
14243380 TTCATACAAAAAATTTATAATATTCA
60 TTAATACAAAAAATTTACAATATTCA
14243406 TACAAAATTACAATATTCATACAAAAAATTACTAATC-T-AAAACTATAA-A-TACAA-ATTTAA
1 TACAAAATTACAATATTCATACAAAAAATTA-TAATCATAAAAACTATAATATTACAATA-TTAA
*
14243466 TTATAAAATAA-TTACAATATTCA
64 -TACAAAA-AATTTACAATATTCA
*
14243489 TACAACATTACAATATTCAT--AAAAAATTATAAT
1 TACAAAATTACAATATTCATACAAAAAATTATAAT
14243522 ATTCATACAA
Statistics
Matches: 107, Mismatches: 5, Indels: 19
0.82 0.04 0.15
Matches are distributed among these distances:
80 4 0.04
81 10 0.09
82 8 0.07
83 37 0.35
84 12 0.11
86 2 0.02
87 4 0.04
89 8 0.07
91 22 0.21
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (85 bp):
TACAAAATTACAATATTCATACAAAAAATTATAATCATAAAAACTATAATATTACAATATTAATA
CAAAAAATTTACAATATTCA
Found at i:14243597 original size:7 final size:7
Alignment explanation
Indices: 14243587--14243618 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
14243577 CTAAATATAG
*
14243587 ATAATTT
1 ATAATTA
14243594 ATAATTA
1 ATAATTA
14243601 ATAATTA
1 ATAATTA
14243608 ATAATTA
1 ATAATTA
14243615 ATAA
1 ATAA
14243619 CAAAAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATAATTA
Found at i:14244028 original size:18 final size:18
Alignment explanation
Indices: 14243971--14244034 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
14243961 TTTGACCCCG
14243971 TATTTT-TTAAAAAAATAT
1 TATTTTATTAAAAAAA-AT
*** *
14243989 TAAAATATT-AAAAAATT
1 TATTTTATTAAAAAAAAT
14244006 ATATTTTATTAAAAAAAAT
1 -TATTTTATTAAAAAAAAT
14244025 TATTATTATT
1 TATT-TTATT
14244035 TTATTCATTG
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 1 0.03
18 19 0.56
19 14 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTTATTAAAAAAAAT
Found at i:14244111 original size:29 final size:28
Alignment explanation
Indices: 14244078--14244145 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
14244068 GAAAAGGTAA
*
14244078 CCTATTTTGGTAAATTTTTTTTCTGACAT
1 CCTATTTCGGTAAATTTTTTTTCT-ACAT
* *
14244107 CCTATTTCAGT-ATTTTTTTTTCTACAT
1 CCTATTTCGGTAAATTTTTTTTCTACAT
*
14244134 --TATTTGGGTAAA
1 CCTATTTCGGTAAA
14244146 AAACCCCTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
25 7 0.22
26 1 0.03
27 4 0.12
28 11 0.34
29 9 0.28
ACGTcount: A:0.22, C:0.13, G:0.10, T:0.54
Consensus pattern (28 bp):
CCTATTTCGGTAAATTTTTTTTCTACAT
Found at i:14244444 original size:2 final size:2
Alignment explanation
Indices: 14244437--14244485 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
14244427 TGTAAATATT
14244437 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
14244479 CA CA CA C
1 CA CA CA C
14244486 TACCAATCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:14250154 original size:22 final size:21
Alignment explanation
Indices: 14250128--14250187 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
14250118 ATCTAAATTC
*
14250128 AAATTAAATAATAAAATTATCT
1 AAATTAAAT-ATAAAATTATAT
*
14250150 AAATTTAAGTATAAAA-TATAT
1 AAA-TTAAATATAAAATTATAT
*
14250171 AAATATTAATATAAAAT
1 AAAT-TAAATATAAAAT
14250188 ATTTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 1 0.03
21 16 0.52
22 9 0.29
23 5 0.16
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATTAAATATAAAATTATAT
Found at i:14250183 original size:21 final size:21
Alignment explanation
Indices: 14250138--14250189 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
14250128 AAATTAAATA
*
14250138 ATAAAATTATCTAAATTTAAGT
1 ATAAAA-TATATAAATTTAAGT
14250160 ATAAAATATATAAATATTAA-T
1 ATAAAATATATAAAT-TTAAGT
14250181 ATAAAATAT
1 ATAAAATAT
14250190 TTTTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAAAATATATAAATTTAAGT
Found at i:14255191 original size:21 final size:21
Alignment explanation
Indices: 14255167--14255219 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
14255157 CATTGTTTCT
** *
14255167 AATCTCACTGCTACAGTATCC
1 AATCTCACCACTACAGTAACC
*
14255188 AATCTCACCACTACAGTAACT
1 AATCTCACCACTACAGTAACC
14255209 AATCTCACCAC
1 AATCTCACCAC
14255220 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.36, G:0.06, T:0.25
Consensus pattern (21 bp):
AATCTCACCACTACAGTAACC
Found at i:14255663 original size:25 final size:24
Alignment explanation
Indices: 14255629--14255676 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
14255619 ATGTATTAAA
* *
14255629 ATATTTTAATAGTTATATAATAAC
1 ATATTTTAATAATTAAATAATAAC
14255653 ATATATTTAATAATTAAATAATAA
1 ATAT-TTTAATAATTAAATAATAA
14255677 TTTGAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATTTTAATAATTAAATAATAAC
Found at i:14256708 original size:7 final size:7
Alignment explanation
Indices: 14256696--14256723 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
14256686 AGTAGTAGGC
14256696 AGTGGCA
1 AGTGGCA
14256703 AGTGGCA
1 AGTGGCA
14256710 AGTGGCA
1 AGTGGCA
14256717 AGTGGCA
1 AGTGGCA
14256724 TTTTATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.43, T:0.14
Consensus pattern (7 bp):
AGTGGCA
Found at i:14258347 original size:20 final size:18
Alignment explanation
Indices: 14258324--14258362 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
14258314 CATAAAAAAT
14258324 ATTTCAATTAAAAAATGTAA
1 ATTTC-ATTAAAAAAT-TAA
*
14258344 ATTTCCTTAAAAAATTAA
1 ATTTCATTAAAAAATTAA
14258362 A
1 A
14258363 AAAATGTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 9 0.50
20 5 0.28
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (18 bp):
ATTTCATTAAAAAATTAA
Found at i:14259276 original size:34 final size:35
Alignment explanation
Indices: 14259214--14259285 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 35
14259204 GGGGAGCTCA
14259214 ACTATAAATAGAGAGCCTCCCCCTCATTTGTACTC
1 ACTATAAATAGAGAGCCTCCCCCTCATTTGTACTC
14259249 ACTATAAATAGAGAGCCT-CCCCTCATTTGTACTC
1 ACTATAAATAGAGAGCCTCCCCCTCATTTGTACTC
14259283 ACT
1 ACT
14259286 CCTGAATTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 19 0.51
35 18 0.49
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.29
Consensus pattern (35 bp):
ACTATAAATAGAGAGCCTCCCCCTCATTTGTACTC
Found at i:14267624 original size:25 final size:26
Alignment explanation
Indices: 14267591--14267647 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
14267581 TATATATATT
* * *
14267591 ATAATAATAAATTAATGTATAATAAA
1 ATAATAATAAATAAATGAATAAAAAA
*
14267617 ATAA-AATAAGTAAATGAATAAAAAA
1 ATAATAATAAATAAATGAATAAAAAA
14267642 ATAATA
1 ATAATA
14267648 GAAAGCCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (26 bp):
ATAATAATAAATAAATGAATAAAAAA
Found at i:14268106 original size:19 final size:20
Alignment explanation
Indices: 14268082--14268122 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
14268072 GAATTTAGGA
*
14268082 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
14268101 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
14268121 AA
1 AA
14268123 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:14285873 original size:30 final size:31
Alignment explanation
Indices: 14285839--14285909 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
14285829 TATAATTTGA
** *
14285839 TCATTGAACTATTTGAAAG-TTTTCCTTAAG
1 TCATTGAACTATTCAAAAGTTTTTACTTAAG
*
14285869 TCATTGAACTATTCAAAAGTTTTTATTTAAG
1 TCATTGAACTATTCAAAAGTTTTTACTTAAG
14285900 TCATTGAACT
1 TCATTGAACT
14285910 TTTTTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 17 0.47
31 19 0.53
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (31 bp):
TCATTGAACTATTCAAAAGTTTTTACTTAAG
Found at i:14288056 original size:3 final size:3
Alignment explanation
Indices: 14288048--14288074 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
14288038 AAATAAACCC
14288048 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
14288075 TGAATGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:14296601 original size:41 final size:41
Alignment explanation
Indices: 14296544--14296634 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
14296534 GCATAGCGCT
*
14296544 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
* *
14296585 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
14296626 TAGCAGGCT
1 TAGCAGGCT
14296635 AAGTGCCAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
Found at i:14305780 original size:12 final size:12
Alignment explanation
Indices: 14305763--14305802 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
14305753 ATTAACCATC
*
14305763 ATATATACATGT
1 ATATATACATAT
*
14305775 ATATATAAATAT
1 ATATATACATAT
14305787 ATATATACATAT
1 ATATATACATAT
14305799 ATAT
1 ATAT
14305803 TCTTAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (12 bp):
ATATATACATAT
Found at i:14320444 original size:26 final size:26
Alignment explanation
Indices: 14320409--14320469 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
14320399 TATAATTTTT
*
14320409 TTTTTATAAATAAATATATTATAACA-
1 TTTTTATAAACAAATATATTATAA-AG
14320435 TTTTTATAAACAAATATATTATAAAG
1 TTTTTATAAACAAATATATTATAAAG
14320461 TTTTTATAA
1 TTTTTATAA
14320470 TATGTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTTATAAACAAATATATTATAAAG
Found at i:14322821 original size:16 final size:17
Alignment explanation
Indices: 14322796--14322827 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
14322786 AAAAAAATAT
14322796 AAATTAAAAAATTAAAA
1 AAATTAAAAAATTAAAA
14322813 AAATT-AAAAATTAAA
1 AAATTAAAAAATTAAA
14322828 TGAATGGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATTAAAAAATTAAAA
Found at i:14323473 original size:34 final size:34
Alignment explanation
Indices: 14323435--14323506 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
14323425 ATCCTGGTAA
* *
14323435 ATTTTTT-TTAATGATTTTTTGTTTCTTCTTTTAG
1 ATTTTTTCTGAATGA-TTTTTGTTTCTTATTTTAG
14323469 ATTTTTTCTGAATGATTTTTGTTTCTTATTTTAG
1 ATTTTTTCTGAATGATTTTTGTTTCTTATTTTAG
14323503 ATTT
1 ATTT
14323507 ATGATCTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 29 0.83
35 6 0.17
ACGTcount: A:0.17, C:0.06, G:0.10, T:0.68
Consensus pattern (34 bp):
ATTTTTTCTGAATGATTTTTGTTTCTTATTTTAG
Found at i:14346175 original size:3 final size:3
Alignment explanation
Indices: 14346167--14346191 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14346157 CTTTCTCCAA
14346167 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
14346192 CTTTGTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Done.