Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 134 of 190
Found at i:39618691 original size:30 final size:31
Alignment explanation
Indices: 39618652--39618711 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
39618642 GGAGGTGAGA
*
39618652 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
39618683 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
39618712 TAAATGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:39618927 original size:24 final size:23
Alignment explanation
Indices: 39618875--39618927 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
39618865 TGAGGGAAAA
39618875 GTAAAAAGGTTTAGGAGTTTGGG
1 GTAAAAAGGTTTAGGAGTTTGGG
39618898 GTAAAAAGGTTTAGGAGTTTGGG
1 GTAAAAAGGTTTAGGAGTTTGGG
39618921 GTAAAAA
1 GTAAAAA
39618928 TATAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (23 bp):
GTAAAAAGGTTTAGGAGTTTGGG
Found at i:39618971 original size:18 final size:18
Alignment explanation
Indices: 39618948--39618984 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39618938 TATAGTTTGA
39618948 TATTTGAATTATTCGAAT
1 TATTTGAATTATTCGAAT
*
39618966 TATTTGAGTTATTCGAAT
1 TATTTGAATTATTCGAAT
39618984 T
1 T
39618985 TGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (18 bp):
TATTTGAATTATTCGAAT
Found at i:39619054 original size:9 final size:9
Alignment explanation
Indices: 39619037--39619067 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39619027 TCGAGTTGAT
39619037 TCGAATAAC
1 TCGAATAAC
*
39619046 TCGATTAAC
1 TCGAATAAC
39619055 TCGAATAAC
1 TCGAATAAC
39619064 TCGA
1 TCGA
39619068 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:39626167 original size:48 final size:48
Alignment explanation
Indices: 39626111--39626245 Score: 218
Period size: 48 Copynumber: 2.8 Consensus size: 48
39626101 TTGATTTGTA
*
39626111 CAAAAATGGACAGCAATTAAGCA-TCAATTTGGACAGCATTAATATGCT
1 CAAAAATGGACAGCATTTAAGCACT-AATTTGGACAGCATTAATATGCT
*
39626159 CAAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATGCT
1 CAAAAATGGACAGCATTTAAGCACTAATTTGGACAGCATTAATATGCT
* *
39626207 AAAAAATGAACAGCATTTAAGCACTAATTTGGACAGCAT
1 CAAAAATGGACAGCATTTAAGCACTAATTTGGACAGCAT
39626246 CTTATCATCA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 80 0.99
49 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (48 bp):
CAAAAATGGACAGCATTTAAGCACTAATTTGGACAGCATTAATATGCT
Found at i:39626171 original size:25 final size:25
Alignment explanation
Indices: 39626140--39626223 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
39626130 AGCATCAATT
39626140 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
* * * **
39626165 TGGACAGCATT--TAAGCACTAATT
1 TGGACAGCATTAATATGCTCAAAAA
* *
39626188 TGGACAACATTAATATGCTAAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
*
39626213 TGAACAGCATT
1 TGGACAGCATT
39626224 TAAGCACTAA
Statistics
Matches: 43, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
23 17 0.40
25 26 0.60
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (25 bp):
TGGACAGCATTAATATGCTCAAAAA
Found at i:39627012 original size:43 final size:43
Alignment explanation
Indices: 39626931--39627012 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
39626921 ACTTATATAC
* * ***
39626931 GATGCCAATGTCCTAGACATGGCCTTACATGTTCTCACACTTT
1 GATGCCAACGTCCCAGACATGGCCTTACATGAAATCACACTTT
*
39626974 GATGCCAACGTCCCAGACATGGTCTTACATGAAATCACA
1 GATGCCAACGTCCCAGACATGGCCTTACATGAAATCACA
39627013 TCTCAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (43 bp):
GATGCCAACGTCCCAGACATGGCCTTACATGAAATCACACTTT
Found at i:39627901 original size:10 final size:9
Alignment explanation
Indices: 39627882--39627932 Score: 52
Period size: 8 Copynumber: 5.6 Consensus size: 9
39627872 AAGATGATAC
39627882 ATTTACTTA
1 ATTTACTTA
39627891 ATTTCACTTA
1 ATTT-ACTTA
*
39627901 ATTTATCATTT
1 ATTTA-C-TTA
39627912 ATTTAC-TA
1 ATTTACTTA
39627920 ATTTACTT-
1 ATTTACTTA
39627928 ATTTA
1 ATTTA
39627933 ACCATTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 12 0.33
9 6 0.17
10 11 0.31
11 7 0.19
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTACTTA
Found at i:39633728 original size:48 final size:48
Alignment explanation
Indices: 39633672--39633872 Score: 271
Period size: 48 Copynumber: 4.2 Consensus size: 48
39633662 AACAACATTC
* * *
39633672 GGACAGCATTGATTTG-TACAAAAATGGATAGCAATTAAGCA-TCAATTT
1 GGACAGCATTAATATGCT-CAAAAATGGACAGCAATTAAGCACT-AATTT
*
39633720 GGACAGCATTAATATGCTCAAAAATGGACAGCATTTAAGCACTAATTT
1 GGACAGCATTAATATGCTCAAAAATGGACAGCAATTAAGCACTAATTT
* * * * *
39633768 GGATAGCATTAATATGTTAAAAAATAGACAGCATTTAAGCACTAATTT
1 GGACAGCATTAATATGCTCAAAAATGGACAGCAATTAAGCACTAATTT
* *
39633816 CGATAGCATTAATATGCTCAAAAATGGACAGCAATTAAGCACTAATTT
1 GGACAGCATTAATATGCTCAAAAATGGACAGCAATTAAGCACTAATTT
39633864 GGACAGCAT
1 GGACAGCAT
39633873 CTTATCATCA
Statistics
Matches: 136, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
48 134 0.99
49 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (48 bp):
GGACAGCATTAATATGCTCAAAAATGGACAGCAATTAAGCACTAATTT
Found at i:39633748 original size:25 final size:25
Alignment explanation
Indices: 39633719--39633853 Score: 89
Period size: 25 Copynumber: 5.5 Consensus size: 25
39633709 AGCATCAATT
39633719 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
* * * **
39633744 TGGACAGCATT--TAAGCACTAATT
1 TGGACAGCATTAATATGCTCAAAAA
* * *
39633767 TGGATAGCATTAATATGTTAAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
* * * * **
39633792 TAGACAGCATT--TAAGCACTAATT
1 TGGACAGCATTAATATGCTCAAAAA
* *
39633815 TCGATAGCATTAATATGCTCAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
39633840 TGGACAGCAATTAA
1 TGGACAGC-ATTAA
39633854 GCACTAATTT
Statistics
Matches: 74, Mismatches: 31, Indels: 9
0.65 0.27 0.08
Matches are distributed among these distances:
23 31 0.42
25 38 0.51
26 5 0.07
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (25 bp):
TGGACAGCATTAATATGCTCAAAAA
Found at i:39634541 original size:43 final size:42
Alignment explanation
Indices: 39634476--39634629 Score: 120
Period size: 43 Copynumber: 3.7 Consensus size: 42
39634466 AGCTCATACA
*
39634476 ATGCCA-TATCCCAGATATGGTCTTACATGTTAACACATTTCG
1 ATGCCACTATCCCAGACATGGTCTTACATGTT-ACACATTTCG
* * * * * *
39634518 ATGCCACTGTCCCAGACAGGGTCTTATACG--ACTCATATACG
1 ATGCCACTATCCCAGACATGGTCTTACATGTTACACAT-TTCG
* * *
39634559 ATGCCAAC-ATCCCAGACATGGCCTTACATGTT-CTCTAACTTCG
1 ATGCC-ACTATCCCAGACATGGTCTTACATGTTACAC--ATTTCG
* *
39634602 ATGCCAATGTCCCAGACATGGTCTTACA
1 ATGCCACTATCCCAGACATGGTCTTACA
39634630 CGAAATCACA
Statistics
Matches: 87, Mismatches: 17, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
40 5 0.06
41 25 0.29
42 12 0.14
43 44 0.51
44 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (42 bp):
ATGCCACTATCCCAGACATGGTCTTACATGTTACACATTTCG
Found at i:39639841 original size:20 final size:22
Alignment explanation
Indices: 39639816--39639868 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
39639806 TATATGGTCA
* *
39639816 TTTTCTTTTTA-TT-TTTTTTC
1 TTTTCTTTCTAGTTCTTTGTTC
39639836 TTTTCTTTCTAGTTCTTTGTTC
1 TTTTCTTTCTAGTTCTTTGTTC
39639858 TTCTTCTTTCT
1 TT-TTCTTTCT
39639869 TTTATCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.36
21 2 0.07
22 8 0.29
23 8 0.29
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTTCTTTCTAGTTCTTTGTTC
Found at i:39640524 original size:42 final size:42
Alignment explanation
Indices: 39640506--39640587 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
39640496 GGTCGTGTGT
* *
39640506 GCCACACGGGCAAGGACATAGGCATGTGTCCAGGCCGTGTAA
1 GCCACACGGGAAAGGACATGGGCATGTGTCCAGGCCGTGTAA
* * *
39640548 GCCACACGGGAAAGGACATGGGCGTGTGTTCAGGCTGTGT
1 GCCACACGGGAAAGGACATGGGCATGTGTCCAGGCCGTGT
39640588 GGCATATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.37, T:0.17
Consensus pattern (42 bp):
GCCACACGGGAAAGGACATGGGCATGTGTCCAGGCCGTGTAA
Found at i:39641144 original size:22 final size:24
Alignment explanation
Indices: 39641101--39641165 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
39641091 TCTTTTTTGT
39641101 ATATGAAACTGAAATTGCTTCTGC
1 ATATGAAACTGAAATTGCTTCTGC
* * *
39641125 ATATGTAACT-AATTTG-TTCTGA
1 ATATGAAACTGAAATTGCTTCTGC
*
39641147 ATCTG-AACTGAAATTGCTT
1 ATATGAAACTGAAATTGCTT
39641166 TTGTTACCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 4 0.12
22 14 0.41
23 7 0.21
24 9 0.26
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (24 bp):
ATATGAAACTGAAATTGCTTCTGC
Found at i:39642780 original size:15 final size:17
Alignment explanation
Indices: 39642741--39642781 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
39642731 ATTGGAATGG
39642741 TGAATTGATGATGAAAT
1 TGAATTGATGATGAAAT
*
39642758 TGAGATTGAT-A-GAATT
1 TGA-ATTGATGATGAAAT
39642774 TGAATTGA
1 TGAATTGA
39642782 ACTGATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.23
16 7 0.32
17 4 0.18
18 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (17 bp):
TGAATTGATGATGAAAT
Found at i:39646381 original size:12 final size:12
Alignment explanation
Indices: 39646364--39646394 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39646354 TTGAGAAGGT
*
39646364 GGAGGTACCACA
1 GGAGGTACAACA
39646376 GGAGGTACAACA
1 GGAGGTACAACA
39646388 GGAGGTA
1 GGAGGTA
39646395 GAGGTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.39, T:0.10
Consensus pattern (12 bp):
GGAGGTACAACA
Found at i:39647806 original size:12 final size:12
Alignment explanation
Indices: 39647785--39647818 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39647775 TTATGCTCTC
*
39647785 TTCATCTTCATT
1 TTCATTTTCATT
39647797 TTCATTTTCATT
1 TTCATTTTCATT
39647809 TTCATCTTTC
1 TTCAT-TTTC
39647819 TTTGCCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCATTTTCATT
Found at i:39650675 original size:29 final size:30
Alignment explanation
Indices: 39650616--39650673 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39650606 TCCGAGCCTT
*
39650616 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
39650646 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
39650674 AGAGTCAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:39650904 original size:13 final size:13
Alignment explanation
Indices: 39650886--39650916 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39650876 TTCCAGCAAC
39650886 TATGAATTTATTT
1 TATGAATTTATTT
39650899 TATGAATTTATTT
1 TATGAATTTATTT
*
39650912 GATGA
1 TATGA
39650917 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:39651096 original size:56 final size:53
Alignment explanation
Indices: 39651010--39651160 Score: 189
Period size: 56 Copynumber: 2.8 Consensus size: 53
39651000 CATTTGGGTA
* *
39651010 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCAT
1 AAGAG-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC--AACATCAG
* * *
39651066 AAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCA-CCAACATGAG
1 AAGA-GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAACATCAG
* *
39651119 AACA-TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AAGAGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
39651161 GTTATTATCA
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
51 34 0.40
53 8 0.10
55 2 0.02
56 39 0.46
57 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (53 bp):
AAGAGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAACATCAG
Found at i:39662449 original size:6 final size:6
Alignment explanation
Indices: 39662438--39662470 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
39662428 GAGGGTAAGC
39662438 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
39662471 TTCATTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:39665919 original size:41 final size:41
Alignment explanation
Indices: 39665858--39665971 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
39665848 TTAATTTAAA
* * * *
39665858 CAGATTCAACGGCACTTAGCCTGCTAGGCTTATAGCTTGATT
1 CAGA-TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
39665900 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
39665941 CAGATCACCGGCACGTAGCCTGCTAGACTTA
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTA
39665972 AAGTCTGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 61 0.94
42 4 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
Found at i:39673377 original size:41 final size:41
Alignment explanation
Indices: 39673316--39673429 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
39673306 TTAATTTAAA
* * * *
39673316 CAGATTCAACGGCACTTAGCCTGCTAGGCTTATAGCTTGATT
1 CAGA-TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
39673358 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
39673399 CAGATCACCGGCACGTAGCCTGCTAGACTTA
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTA
39673430 AAGTCTGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 61 0.94
42 4 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
Found at i:39675685 original size:19 final size:20
Alignment explanation
Indices: 39675642--39675685 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
39675632 TGTGACCTCT
39675642 ATTTTCTAAAATTTTTAAGA
1 ATTTTCTAAAATTTTTAAGA
* *
39675662 TTTTTCTAAAA-TTTTATGA
1 ATTTTCTAAAATTTTTAAGA
39675681 ATTTT
1 ATTTT
39675686 TTTGTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTCTAAAATTTTTAAGA
Found at i:39676948 original size:23 final size:23
Alignment explanation
Indices: 39676886--39676932 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39676876 AGACACAATG
39676886 CACAAAGTCTCGAGACATGAACC
1 CACAAAGTCTCGAGACATGAACC
39676909 CACAAAGTCTCGAGACATGAACC
1 CACAAAGTCTCGAGACATGAACC
39676932 C
1 C
39676933 CTAATGTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.32, G:0.17, T:0.13
Consensus pattern (23 bp):
CACAAAGTCTCGAGACATGAACC
Found at i:39677850 original size:119 final size:119
Alignment explanation
Indices: 39677639--39677873 Score: 418
Period size: 119 Copynumber: 2.0 Consensus size: 119
39677629 TTTTACATGG
* *
39677639 TTTAGTTAAGGGCAAAGTGGTAAATGTTTAATTAAATTGTAATCAAATAAAAAAAACAAAGGCTA
1 TTTAGTTAAGGGCAAAGTGGTAAATATTTAATTAAATTATAATCAAATAAAAAAAACAAAGGCTA
39677704 TCATCTCTTTCCTTTTTTTTGGCCGAAAATGGGAAGAAAGAAACTGGGAGTTAA
66 TCATCTCTTTCCTTTTTTTTGGCCGAAAATGGGAAGAAAGAAACTGGGAGTTAA
* *
39677758 TTTAGTTAAGGGCAAAGTGGTAAATATTTAATTAAATTATAATCAAATAAAATAAACAAATGCTA
1 TTTAGTTAAGGGCAAAGTGGTAAATATTTAATTAAATTATAATCAAATAAAAAAAACAAAGGCTA
39677823 TCATCTCTTTCCTTTGTTTTT-GCCGAAAATGGGAAGAAAGAAACTGGGAGT
66 TCATCTCTTTCCTTT-TTTTTGGCCGAAAATGGGAAGAAAGAAACTGGGAGT
39677874 AGCTTAAGTG
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
119 106 0.95
120 5 0.05
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (119 bp):
TTTAGTTAAGGGCAAAGTGGTAAATATTTAATTAAATTATAATCAAATAAAAAAAACAAAGGCTA
TCATCTCTTTCCTTTTTTTTGGCCGAAAATGGGAAGAAAGAAACTGGGAGTTAA
Found at i:39681721 original size:25 final size:25
Alignment explanation
Indices: 39681693--39681745 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
39681683 ACATACCGCA
* *
39681693 GCTCTCATGAGCGTCCCGATATATG
1 GCTCGCATGAACGTCCCGATATATG
* * *
39681718 GCTCGCTTGAACTTCCTGATATATG
1 GCTCGCATGAACGTCCCGATATATG
39681743 GCT
1 GCT
39681746 ATCTGGAGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (25 bp):
GCTCGCATGAACGTCCCGATATATG
Found at i:39681757 original size:25 final size:25
Alignment explanation
Indices: 39681701--39681757 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
39681691 CAGCTCTCAT
* * *
39681701 GAGCGTCCCGATATATGGCTCGCTT
1 GAGCTTCCCGATATATGGCTAGCTG
* * *
39681726 GAACTTCCTGATATATGGCTATCTG
1 GAGCTTCCCGATATATGGCTAGCTG
39681751 GAGCTTC
1 GAGCTTC
39681758 TTAGTAATAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGATATATGGCTAGCTG
Found at i:39681852 original size:23 final size:23
Alignment explanation
Indices: 39681825--39681883 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 23
39681815 TCTTATGAGT
*
39681825 TTCCTGTTATAGCCCAGATAAGC
1 TTCCTGTTATAGCCCACATAAGC
* * *
39681848 TTCCTGTTACATGGCTCACATGAGC
1 TTCCTGTT--ATAGCCCACATAAGC
39681873 TTCCTGTTATA
1 TTCCTGTTATA
39681884 TGGCTCGAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 10 0.34
25 19 0.66
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (23 bp):
TTCCTGTTATAGCCCACATAAGC
Found at i:39685968 original size:14 final size:14
Alignment explanation
Indices: 39685946--39685978 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39685936 TTTTAAAATA
*
39685946 TTTTT-AAAATACT
1 TTTTTAAAAATAAT
39685959 TTTTTAAAAATAAT
1 TTTTTAAAAATAAT
39685973 TTTTTA
1 TTTTTA
39685979 GTGTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTTAAAAATAAT
Found at i:39692599 original size:11 final size:11
Alignment explanation
Indices: 39692583--39692623 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
39692573 GTTGCTGTGG
39692583 AAAAGAAGAGA
1 AAAAGAAGAGA
39692594 AAAAG-AGAGA
1 AAAAGAAGAGA
*
39692604 AAAAGAGGAGA
1 AAAAGAAGAGA
39692615 AAAAGAAGA
1 AAAAGAAGA
39692624 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:39692684 original size:19 final size:21
Alignment explanation
Indices: 39692646--39692684 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
39692636 AATAATTGAT
*
39692646 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
39692667 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
39692685 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:39692746 original size:3 final size:3
Alignment explanation
Indices: 39692730--39692803 Score: 121
Period size: 3 Copynumber: 24.3 Consensus size: 3
39692720 AAAATAATAG
*
39692730 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
39692776 TAT TAT TAT TAT TAT CAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
39692804 GTTGTTGTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:39692808 original size:3 final size:3
Alignment explanation
Indices: 39692802--39692845 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
39692792 ATTATTATTA
*
39692802 TTG TTG TTG TTG TTG TTG CTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
39692846 AGTATTAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.32, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:39693670 original size:18 final size:18
Alignment explanation
Indices: 39693626--39693670 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
39693616 TTGACATGGT
*
39693626 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
* *
39693644 TGCTAGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
39693662 TGGTGGCGA
1 TGGTGGCGA
39693671 TCATTGAGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.07, G:0.47, T:0.16
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:39698346 original size:22 final size:22
Alignment explanation
Indices: 39698321--39698362 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
39698311 AGGTTTTTTT
*
39698321 TATATATTTTGGTAAATAAATA
1 TATATATATTGGTAAATAAATA
39698343 TATATATATTGGTAAATAAA
1 TATATATATTGGTAAATAAA
39698363 AAAACTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (22 bp):
TATATATATTGGTAAATAAATA
Found at i:39699180 original size:4 final size:4
Alignment explanation
Indices: 39699151--39699322 Score: 101
Period size: 4 Copynumber: 42.8 Consensus size: 4
39699141 CCTCTTCTTC
* * * * *
39699151 TTCT TTTT TTTT TTCT CTTC- TCCT TTC- TT-T TTCT TCCC TTCT TTCT
1 TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
39699197 TTCT TT-T TTCT TCTCCT TTCCT TT-T CTTC- TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT T-T-CT TT-CT TTCT -TTCT TTCT TTCT TTCT TTCT
* * *
39699242 TTTT TTCT CTTC- TCCT TTCCTT TTCT TTCC TTC- TT-T TTCT TTCT TTCCT
1 TTCT TTCT -TTCT TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT TT-CT
* *
39699291 CTCCT CTCT TTCT TTCT TTCT TTCT TTCT TTC
1 -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
39699323 CCTCTCCTTC
Statistics
Matches: 133, Mismatches: 17, Indels: 36
0.72 0.09 0.19
Matches are distributed among these distances:
3 19 0.14
4 88 0.66
5 19 0.14
6 7 0.05
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:39699185 original size:33 final size:33
Alignment explanation
Indices: 39699122--39699241 Score: 91
Period size: 39 Copynumber: 3.4 Consensus size: 33
39699112 ATACATTTTC
* *
39699122 TTTTTTTTTTC-CTTCCTTCC-CTCTTCTTCTTCT
1 TTTTTTTTTTCTCTT-C-TCCTTTCTTTTTCTTCT
39699155 TTTTTTTTTTCTCTTCTCCTTTCTTTTTCTTCCCTT
1 TTTTTTTTTTCTCTTCTCCTTTCTTTTTCTT--C-T
* *
39699191 CTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTCT
1 -TTT-TTT-TTTTCTCTTCTCCTTTCTTTTTCTTCT
39699227 TCTTTCTTTCTTTCT
1 T-TTT-TTT-TTTCT
39699242 TTTTTTCTCT
Statistics
Matches: 71, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
32 3 0.04
33 21 0.30
34 3 0.04
35 4 0.06
36 10 0.14
37 4 0.06
38 3 0.04
39 23 0.32
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (33 bp):
TTTTTTTTTTCTCTTCTCCTTTCTTTTTCTTCT
Found at i:39699204 original size:23 final size:23
Alignment explanation
Indices: 39699147--39699249 Score: 74
Period size: 26 Copynumber: 4.6 Consensus size: 23
39699137 CTTCCCTCTT
*
39699147 CTTC-TTCTTT-TTTTTT-TTCT
1 CTTCTTTCTTTCTTTTTTCTTCC
*
39699167 CTTC-TCCTTTCTTTT-TCTTCC
1 CTTCTTTCTTTCTTTTTTCTTCC
39699188 CTTCTTTCTTTCTTTTTTCTTCTC
1 CTTCTTTCTTTCTTTTTTCTTC-C
* *
39699212 CTTTCCTTT-TCTTCTTCTTTCTTTC
1 C-TT-CTTTCT-TTCTTTTTTCTTCC
* *
39699237 TTTCTTTTTTTCT
1 CTTCTTTCTTTCT
39699250 CTTCTCCTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
20 10 0.15
21 11 0.16
22 10 0.15
23 13 0.19
24 5 0.07
25 4 0.06
26 15 0.22
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (23 bp):
CTTCTTTCTTTCTTTTTTCTTCC
Found at i:39699242 original size:49 final size:48
Alignment explanation
Indices: 39699175--39699288 Score: 140
Period size: 49 Copynumber: 2.4 Consensus size: 48
39699165 CTCTTCTCCT
* * * * *
39699175 TTCTTTTTCTTCCCTTCTTTCTTTCT-TTTTTCTTCTCCTTTCCTTTTC
1 TTCTTTTTCTTTCTTTCTTTCTTTCTCTTCTCCTT-TCCTTTCCTTTCC
* *
39699223 TTCTTCTTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCC
1 TTCTT-TTTCTTTCTTTCTTTCTTTCTCTTCTCCTTTCCTTTCCTTTCC
39699272 TTCTTTTTCTTTCTTTC
1 TTCTTTTTCTTTCTTTC
39699289 CTCTCCTCTC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 17 0.30
49 34 0.60
50 6 0.11
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (48 bp):
TTCTTTTTCTTTCTTTCTTTCTTTCTCTTCTCCTTTCCTTTCCTTTCC
Found at i:39699284 original size:44 final size:44
Alignment explanation
Indices: 39699144--39699287 Score: 185
Period size: 44 Copynumber: 3.4 Consensus size: 44
39699134 TTCCTTCCCT
* * * *
39699144 CTTCTTCTTCTTTTTTTTTTTCTCTTCTCCTTTCTTTTTCTTCC
1 CTTCTTTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
39699188 CTTC--TTTCTTTC--TTTTT-TCTTCTCCTTTCCTTTTC-TT-
1 CTTCTTTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
39699225 CTTCTTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTC-TT-TTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
39699271 CTTCTTTTTCTTTCTTT
1 CTTCTTTTTCTTTCTTT
39699288 CCTCTCCTCT
Statistics
Matches: 87, Mismatches: 4, Indels: 18
0.80 0.04 0.17
Matches are distributed among these distances:
37 4 0.05
38 1 0.01
39 17 0.20
40 5 0.06
41 8 0.09
42 6 0.07
43 5 0.06
44 33 0.38
45 4 0.05
46 4 0.05
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (44 bp):
CTTCTTTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:39699311 original size:44 final size:45
Alignment explanation
Indices: 39699203--39699321 Score: 123
Period size: 48 Copynumber: 2.5 Consensus size: 45
39699193 TTCTTTCTTT
* * * **
39699203 TTTCTTCTCCTTTCCTTTTCTTCTTCTTTCTTTCTTTCTTTTTTTCTC
1 TTTCTT-TCCTTT-CTTTCCTTCTT-TTTCTTTCTTTCCTCTCCTCTC
39699251 TTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTCTC
1 TT-T-CTTTCC-TTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTCTC
*
39699299 TTTCTTT-CTTTCTTTCTTTCTTT
1 TTTCTTTCCTTTCTTTCCTTCTTT
39699322 CCCTCTCCTT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
44 14 0.23
45 1 0.02
46 4 0.06
47 1 0.02
48 22 0.35
49 14 0.23
50 6 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (45 bp):
TTTCTTTCCTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTCTC
Found at i:39699415 original size:27 final size:27
Alignment explanation
Indices: 39699366--39699417 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
39699356 TCCTAATAAA
***
39699366 CATTGGTGCCGCCAATGGTATTGGCAC
1 CATTGGTGCCGCCAATCCCATTGGCAC
39699393 CATTGGTGCCGCCAATCCCATTGGC
1 CATTGGTGCCGCCAATCCCATTGGC
39699418 GTGACCAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.25
Consensus pattern (27 bp):
CATTGGTGCCGCCAATCCCATTGGCAC
Found at i:39699498 original size:24 final size:24
Alignment explanation
Indices: 39699471--39699518 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39699461 GGTTTTTTTT
39699471 TATATATTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
39699495 TATATATTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
39699519 AGTTATAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (24 bp):
TATATATTTTGGTAAATAAAAAAA
Found at i:39699531 original size:28 final size:24
Alignment explanation
Indices: 39699471--39699537 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 24
39699461 GGTTTTTTTT
*
39699471 TATATATTTTGGTAAATAAAAAAA
1 TATACATTTTGGTAAATAAAAAAA
*
39699495 TATATATTTTGGTAAATAAAAAAAA
1 TATACATTTTGGTAAAT-AAAAAAA
39699520 GTTATAACATTTTGGTAA
1 --TAT-ACATTTTGGTAA
39699538 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
24 17 0.45
25 7 0.18
27 3 0.08
28 11 0.29
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (24 bp):
TATACATTTTGGTAAATAAAAAAA
Found at i:39701244 original size:20 final size:20
Alignment explanation
Indices: 39701219--39701264 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
39701209 GTTGTTGCTA
*
39701219 TGTTTTGCTATTGTTTCCAC
1 TGTTTTGCTACTGTTTCCAC
* *
39701239 TGTTTTGTTACTGTTTCTAC
1 TGTTTTGCTACTGTTTCCAC
39701259 TGTTTT
1 TGTTTT
39701265 ATTGTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.61
Consensus pattern (20 bp):
TGTTTTGCTACTGTTTCCAC
Found at i:39701522 original size:19 final size:19
Alignment explanation
Indices: 39701476--39701532 Score: 87
Period size: 21 Copynumber: 2.9 Consensus size: 19
39701466 AATATTCAAG
*
39701476 GATATGCAATCTTGGATAT
1 GATATGCAATCTTGGAAAT
39701495 GATATATGCAATCTTGGAAAT
1 G--ATATGCAATCTTGGAAAT
39701516 GATATGCAATCTTGGAA
1 GATATGCAATCTTGGAA
39701533 GATATGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 17 0.49
21 18 0.51
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTGGAAAT
Found at i:39708571 original size:44 final size:44
Alignment explanation
Indices: 39708523--39709282 Score: 311
Period size: 44 Copynumber: 17.3 Consensus size: 44
39708513 AGATACCAGC
* * *
39708523 CTTGCCTCCCTGGGTTGTGGTGGAGCAGGTTGAAGACAGCAGAT
1 CTTGCCTCCCTGCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* * * * * ** * * * * *
39708567 CTTGCATTCCTGCATCGACAACGAAGCAGATCGAAGATACCAG-C
1 CTTGCCTCCCTGCGTTG-TAGTGGAGCAGGTTGAAGATAGCAGAT
* *
39708611 CTTGCCTCCCTAG-GTTGTAGTGGAGAAGGTTGAAGATAGCAAAT
1 CTTGCCTCCCT-GCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* * * * * * * * *
39708655 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATACCAG-T
1 CTTGCCTCCCTGCGTTG-TAGTGGAGCAGGTTGAAGATAGCAGAT
**
39708699 CTTGCCTCCCTATGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTGCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* *** * ** * * ** * *
39708743 CTTGCCTTCCTGCAACGACAACGAAGCAGATCAAAGATACCAG-C
1 CTTGCCTCCCTGCGTTG-TAGTGGAGCAGGTTGAAGATAGCAGAT
*
39708787 CTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTGCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* ***** * * * * * *
39708831 CTTGCCTTCCTATACCGACAGTGAAACAGATCGAAGATA-CTAG-C
1 CTTGCCTCCCTGCGTTG-TAGTGGAGCAGGTTGAAGATAGC-AGAT
* *
39708875 CTTGCCTTCCTAG-GTCGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCT-GCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* **** * * * ** *
39708919 CTTGCCTTCCTGTACCGACAGTGAAGCAGATCAAAGATACCAGA-
1 CTTGCCTCCCTGCGTTG-TAGTGGAGCAGGTTGAAGATAGCAGAT
* * *
39708963 CTTGCCTCCCTGGGTTGTCGTGGAGCAGGTTGAATATAGCAGAT
1 CTTGCCTCCCTGCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* * * * *** * * * * * *
39709007 CATGCTTTCCTGCATCAACAGCGAAGCAGATCGAAGATACCAG-C
1 CTTGCCTCCCTGCGT-TGTAGTGGAGCAGGTTGAAGATAGCAGAT
*
39709051 CTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTGCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* **** * * ** * * * *
39709095 CTTGCCTTCCTGTACCGACAATAAAGCAGATCGAAGATACCAG-C
1 CTTGCCTCCCTGCGTTG-TAGTGGAGCAGGTTGAAGATAGCAGAT
* * *
39709139 CTTGCCTCCCTGGGTCGTAGTGGAGCAGGTTAAAGATAGCAGAT
1 CTTGCCTCCCTGCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* * **** * * * * *
39709183 CTTGCCTTCTTGTAC-CAACAGTGAAGCAGATCGAAGATACCAG-C
1 CTTGCCTCCCTG--CGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
*
39709227 CTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTGCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
*
39709271 CTTGCCTTCCTG
1 CTTGCCTCCCTG
39709283 TACCGACAGT
Statistics
Matches: 488, Mismatches: 204, Indels: 48
0.66 0.28 0.06
Matches are distributed among these distances:
43 146 0.30
44 199 0.41
45 143 0.29
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (44 bp):
CTTGCCTCCCTGCGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
Found at i:39709362 original size:88 final size:88
Alignment explanation
Indices: 39708432--39709332 Score: 1280
Period size: 88 Copynumber: 10.2 Consensus size: 88
39708422 GAAATCACAA
* * * * * * * * *
39708432 AGCCTTGTCTTCCTGGTTTGCAGCGGAGCAGGTTGAAAATAACAGATCTTGCCTTCTTGTACTGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
* * *
39708497 CGGCGAAGTAGATCGAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* * * * *
39708520 AGCCTTGCCTCCCTGGGTTGTGGTGGAGCAGGTTGAAGACAGCAGATCTTGCATTCCTGCATCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
**
39708585 CAACGAAGCAGATCGAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* * * * *
39708608 AGCCTTGCCTCCCTAGGTTGTAGTGGAGAAGGTTGAAGATAGCAAATCTTGCCTTCCTGCATCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
*
39708673 CAGCGAAGCAGATCGAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* ** * *
39708696 AGTCTTGCCTCCCTATGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCAACGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
** *
39708761 CAACGAAGCAGATCAAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
*
39708784 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTATACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
* *
39708849 CAGTGAAACAGATCGAAGATACT
66 CAGTGAAGCAGATCGAAGATACC
* * *
39708872 AGCCTTGCCTTCCTAGGTCGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
*
39708937 CAGTGAAGCAGATCAAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* * * * * * * *
39708960 AGACTTGCCTCCCTGGGTTGTCGTGGAGCAGGTTGAATATAGCAGATCATGCTTTCCTGCATCAA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
*
39709025 CAGCGAAGCAGATCGAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
39709048 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
* *
39709113 CAATAAAGCAGATCGAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* * * *
39709136 AGCCTTGCCTCCCTGGGTCGTAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCTTGTACCAA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
39709201 CAGTGAAGCAGATCGAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
39709224 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
*
39709289 CAGTGAAGCAGATCAAAGATACC
66 CAGTGAAGCAGATCGAAGATACC
* *
39709312 AGACTTGCTTCCCTGGGTTGT
1 AGCCTTGCCTCCCTGGGTTGT
39709333 CGTGAAGTAG
Statistics
Matches: 727, Mismatches: 86, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 727 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (88 bp):
AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
CAGTGAAGCAGATCGAAGATACC
Found at i:39709383 original size:44 final size:44
Alignment explanation
Indices: 39709333--39709674 Score: 379
Period size: 44 Copynumber: 7.8 Consensus size: 44
39709323 CCTGGGTTGT
* *
39709333 CGTGAAGTAGATCGAAGAAAACAGATCTTGTTTTCATGTATTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * * *
39709377 CGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTC-TCATAATGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCAT-GTATTGG
* *
39709421 TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
1 -CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * *
39709466 CGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATATATTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * *** *
39709510 TGTGAAGTAGATCGAA-AATAGCAGTTCTTGTCTTCCCATACTGTG
1 CGTGAAGTAGATCGAAGAA-AGCAGATCTTGTCTTCATGTATTG-G
* *
39709555 -GTGAAGTATATCGAAGAAAGTAGATCTTGTCTTCATGTATTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
*
39709598 C--GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATCGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
** * * **
39709640 TATGAAATAGATCAAAGGTAGCAGATCTTGTCTTC
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
39709675 CCATACTAGT
Statistics
Matches: 250, Mismatches: 39, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
42 38 0.15
43 3 0.01
44 169 0.68
45 39 0.16
46 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (44 bp):
CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
Found at i:39709447 original size:89 final size:89
Alignment explanation
Indices: 39709336--39709702 Score: 444
Period size: 89 Copynumber: 4.2 Consensus size: 89
39709326 GGGTTGTCGT
* *
39709336 GAAGTAGATCGAAGAAAACAGATCTTGTTTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAG
39709401 ATCTTGTCTTCTCATAATGGTGGC
66 ATCTTGTCTTCTCATAATGGTGGC
39709425 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAG
* *
39709490 ATCTTGTCTTCAT-ATATTGGT-GT
66 ATCTTGTCTTC-TCATAATGGTGGC
* *** * * * * *
39709513 GAAGTAGATCGAA-AATAGCAGTTCTTGTCTTCCCATACTGTG-GTGAAGTATATCGAAGAAAGT
1 GAAGTAGATCGAAGAA-AGCAGATCTTGTCTTCATGTATTG-GCGTGAAGTAGATCAAAGATAGC
*
39709576 AGATCTTGTC-T-TCATGTAT--TGGC
64 AGATCTTGTCTTCTCAT-AATGGTGGC
* ** * *
39709599 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATCGGTATGAAATAGATCAAAGGTAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAG
* * *
39709664 ATCTTGTCTTCCCATACTAGTGGC
66 ATCTTGTCTTCTCATAATGGTGGC
39709688 GAAGTAGATCGAAGA
1 GAAGTAGATCGAAGA
39709703 TACAAGTCTT
Statistics
Matches: 234, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
85 3 0.01
86 58 0.25
87 8 0.03
88 63 0.27
89 101 0.43
90 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (89 bp):
GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAG
ATCTTGTCTTCTCATAATGGTGGC
Found at i:39713805 original size:43 final size:43
Alignment explanation
Indices: 39713744--39713906 Score: 222
Period size: 43 Copynumber: 3.8 Consensus size: 43
39713734 TTTCTAACAA
39713744 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
*
39713787 GTGTTTTCGTGTAAGACCACGTCTGAGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
* *
39713830 GTGTTTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATTGATTT
1 GTGTTTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACTT
* * * * *
39713873 GTGATTACATGTAAGACCACGTCTAGGACATTGG
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGG
39713907 TATTGTATGA
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
42 1 0.01
43 104 0.97
44 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.33
Consensus pattern (43 bp):
GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
Found at i:39716195 original size:63 final size:63
Alignment explanation
Indices: 39716060--39716180 Score: 179
Period size: 63 Copynumber: 1.9 Consensus size: 63
39716050 AAGGGAAGCA
* * * **
39716060 TGCTTGAAAACGCATTTCAGAATACGCATTTTCATCGAATAATAATAATGAAAGCTTCAGAGG
1 TGCTTGAAAACGCATTTCAGAAGACACATTTTCATCAAATAATAATAATGAAAGAGTCAGAGG
* *
39716123 TGCTTGAAAATGCATTTCAGCAGACACATTTTCATCAAATAATAATAATGAAAGAGTC
1 TGCTTGAAAACGCATTTCAGAAGACACATTTTCATCAAATAATAATAATGAAAGAGTC
39716181 TTCTGTGCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (63 bp):
TGCTTGAAAACGCATTTCAGAAGACACATTTTCATCAAATAATAATAATGAAAGAGTCAGAGG
Found at i:39717984 original size:51 final size:51
Alignment explanation
Indices: 39717901--39718017 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
39717891 CGGATCACAT
*
39717901 TTATCACTTGTCACTTGTCACTGATCCAATAAGTGTACCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTAATCCAATAAGTGTACCTAAAGCTACCAC
* *
39717952 TTATCACTTATCACTTGTCACTAAT-CAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTAATCCA-ATAAGTGTACCTAAAGCTACCAC
39718003 TTATCACTTGTCACT
1 TTATCACTTGTCACT
39718018 GATCAGAAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 2 0.03
51 59 0.97
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTAATCCAATAAGTGTACCTAAAGCTACCAC
Found at i:39725223 original size:18 final size:18
Alignment explanation
Indices: 39725187--39725230 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
39725177 CATTAAAAAC
*
39725187 TTTGGTAAAGTGACAAAT
1 TTTGGTAAAGTAACAAAT
39725205 TTTGGTAAAGGTAAC-AAT
1 TTTGGTAAA-GTAACAAAT
*
39725223 TTTAGTAA
1 TTTGGTAA
39725231 TTGTTAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (18 bp):
TTTGGTAAAGTAACAAAT
Found at i:39725405 original size:40 final size:38
Alignment explanation
Indices: 39725278--39725484 Score: 136
Period size: 40 Copynumber: 5.2 Consensus size: 38
39725268 TATCTTATAA
* *
39725278 ATTTTGGTAAAGT-TTTATAAATATTGATAATCGATAGAA
1 ATTTTGGTAAA-TCTTTAAAAATATTGATAATCG-TAGAT
*
39725317 ATTTTGGTAAATCTTTAAAAAAAATTG-TAAAT-GTTAGAT
1 ATTTTGGTAAATCTTT-AAAAATATTGAT-AATCG-TAGAT
** **
39725356 ATAATGGTAAATCTTTGGAAATATTGAATAATCGTCAGAT
1 ATTTTGGTAAATCTTTAAAAATATTG-ATAATCGT-AGAT
*
39725396 ATTTTGGTAAAT-TCTTAAAAATTTTGATAAATCGTTAGAT
1 ATTTTGGTAAATCT-TTAAAAATATTGAT-AATCG-TAGAT
* ** * * *
39725436 ATATTAATAAATCGTTAAATATATT-AGTAAGTCCTTAGAT
1 ATTTTGGTAAATCTTTAAAAATATTGA-TAA-T-CGTAGAT
39725476 ATTTTGGTA
1 ATTTTGGTA
39725485 GAGTCATAGA
Statistics
Matches: 130, Mismatches: 24, Indels: 27
0.72 0.13 0.15
Matches are distributed among these distances:
38 8 0.06
39 44 0.34
40 76 0.58
41 2 0.02
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (38 bp):
ATTTTGGTAAATCTTTAAAAATATTGATAATCGTAGAT
Found at i:39725445 original size:20 final size:20
Alignment explanation
Indices: 39725422--39725477 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
39725412 AAAAATTTTG
39725422 ATAAATCGTTAGATATATTA
1 ATAAATCGTTAGATATATTA
*
39725442 ATAAATCGTTAAATATATTA
1 ATAAATCGTTAGATATATTA
* * *
39725462 GTAAGTCCTTAGATAT
1 ATAAATCGTTAGATAT
39725478 TTTGGTAGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (20 bp):
ATAAATCGTTAGATATATTA
Found at i:39725604 original size:20 final size:20
Alignment explanation
Indices: 39725560--39725715 Score: 141
Period size: 20 Copynumber: 7.8 Consensus size: 20
39725550 TAAAAACTTG
* * *
39725560 GAAATTTTGGTAAAGTCTCA
1 GAAATTTTGGTAAATTGTTA
* * *
39725580 TAAATATTGGTAAATTGATA
1 GAAATTTTGGTAAATTGTTA
* ***
39725600 GAAATTTTAGTAAAACATTA
1 GAAATTTTGGTAAATTGTTA
39725620 GAAATTTTGGTAAATTGTTA
1 GAAATTTTGGTAAATTGTTA
* * * *
39725640 GATATCTTGATAAATTCTTA
1 GAAATTTTGGTAAATTGTTA
*
39725660 GAAATTTTGATAAATTGTTA
1 GAAATTTTGGTAAATTGTTA
* *
39725680 GATATATTGGTAAATTGTTA
1 GAAATTTTGGTAAATTGTTA
* *
39725700 GATATTTTGATAAATT
1 GAAATTTTGGTAAATT
39725716 CTTTAAAATA
Statistics
Matches: 107, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 107 1.00
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (20 bp):
GAAATTTTGGTAAATTGTTA
Found at i:39725654 original size:60 final size:58
Alignment explanation
Indices: 39725538--39725716 Score: 169
Period size: 60 Copynumber: 3.0 Consensus size: 58
39725528 TTAGAAAATT
* * * * * * * *
39725538 TAGAAATATTTGTAAAAACTTGGAAATTTTGGTAAAGTCTCATAAATATTGGTAAATTGA
1 TAGAAAT-TTTGTAAAAA-TTAGAAATTTTGGTAAATTGTTAGATATATTGATAAATTCA
* *
39725598 TAGAAATTTTAGTAAAACATTAGAAATTTTGGTAAATTGTTAGATATCTTGATAAATTCT
1 TAGAAATTTT-GTAAAA-ATTAGAAATTTTGGTAAATTGTTAGATATATTGATAAATTCA
** * * *
39725658 TAGAAATTTTGATAAATTGTTAGATATATTGGTAAATTGTTAGATATTTTGATAAATTC
1 TAGAAATTTTG-TAAA-AATTAGAAATTTTGGTAAATTGTTAGATATATTGATAAATTC
39725717 TTTAAAATAC
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.04
60 95 0.95
61 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (58 bp):
TAGAAATTTTGTAAAAATTAGAAATTTTGGTAAATTGTTAGATATATTGATAAATTCA
Found at i:39725773 original size:20 final size:20
Alignment explanation
Indices: 39725586--39725913 Score: 171
Period size: 20 Copynumber: 16.4 Consensus size: 20
39725576 CTCATAAATA
* * *
39725586 TTGGTAAATTGATAGAAATT
1 TTGGTAAATCGTTAGATATT
* * * *
39725606 TTAGTAAAACATTAGAAATT
1 TTGGTAAATCGTTAGATATT
* *
39725626 TTGGTAAATTGTTAGATATC
1 TTGGTAAATCGTTAGATATT
* *
39725646 TTGATAAATTC-TTAGAAATT
1 TTGGTAAA-TCGTTAGATATT
* * *
39725666 TTGATAAATTGTTAGATATA
1 TTGGTAAATCGTTAGATATT
*
39725686 TTGGTAAATTGTTAGATATT
1 TTGGTAAATCGTTAGATATT
* * * *
39725706 TTGATAAATTCTTTA-AAATA
1 TTGGTAAA-TCGTTAGATATT
* * * *
39725726 CTGGTAAACCGTTATATATA
1 TTGGTAAATCGTTAGATATT
**
39725746 TTATTAAATCGTTAGATATT
1 TTGGTAAATCGTTAGATATT
* *
39725766 TTGGTAAACCGATAG-T-TT
1 TTGGTAAATCGTTAGATATT
* * *
39725784 TCCTCGAAAATCGATAGATATTT
1 T--TGGTAAATCGTTAGATA-TT
* * * *
39725807 TTGATAAATCCTTAGAAATA
1 TTGGTAAATCGTTAGATATT
* * * *
39725827 TTAGCAAGTCGTTAGATATA
1 TTGGTAAATCGTTAGATATT
* * *
39725847 TTGGTAAATCCTTAAATTTT
1 TTGGTAAATCGTTAGATATT
*
39725867 TTGATAAATCGTTAGATATT
1 TTGGTAAATCGTTAGATATT
* *
39725887 TTGGTAAAGTC-ATAGAAATT
1 TTGGTAAA-TCGTTAGATATT
39725907 TTGGTAA
1 TTGGTAA
39725914 TTGTTAAGAC
Statistics
Matches: 228, Mismatches: 70, Indels: 20
0.72 0.22 0.06
Matches are distributed among these distances:
18 3 0.01
19 6 0.03
20 197 0.86
21 19 0.08
23 3 0.01
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (20 bp):
TTGGTAAATCGTTAGATATT
Found at i:39726000 original size:20 final size:20
Alignment explanation
Indices: 39725977--39726058 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
39725967 CTAAATATTA
39725977 GTAAAACGATAGAAATTTTG
1 GTAAAACGATAGAAATTTTG
** *
39725997 GTAACTC-ATTAGACATTTTG
1 GTAAAACGA-TAGAAATTTTG
* **
39726017 GTAAATCTTTAGAAATTTTG
1 GTAAAACGATAGAAATTTTG
* * *
39726037 GTAAGATGATAAAAATTTTG
1 GTAAAACGATAGAAATTTTG
39726057 GT
1 GT
39726059 GTTTGTCAAG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
19 1 0.02
20 47 0.98
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (20 bp):
GTAAAACGATAGAAATTTTG
Found at i:39726176 original size:20 final size:20
Alignment explanation
Indices: 39726153--39726269 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
39726143 AGTAAATAGA
* *
39726153 TAGAAATTTTGGTAACTTAT
1 TAGAAATTTTGGTAAATCAT
* * *
39726173 TAGATATTTTGATAAATCCT
1 TAGAAATTTTGGTAAATCAT
* *
39726193 TAGAAATATTGGTAAATCGT
1 TAGAAATTTTGGTAAATCAT
* *
39726213 TAGATATATTGGTAAATGC-T
1 TAGAAATTTTGGTAAAT-CAT
* *
39726233 TATAAATTTTGATAAAGTC-T
1 TAGAAATTTTGGTAAA-TCAT
* *
39726253 TATAAATATTGGTAAAT
1 TAGAAATTTTGGTAAAT
39726270 TGATATATTT
Statistics
Matches: 79, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.01
20 76 0.96
21 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (20 bp):
TAGAAATTTTGGTAAATCAT
Found at i:39726208 original size:60 final size:60
Alignment explanation
Indices: 39726096--39726274 Score: 166
Period size: 60 Copynumber: 3.0 Consensus size: 60
39726086 GAAAATTTAA
* * * * *
39726096 AAATATCGGTAAAATCA-TAGAAATTTTGGTAAAGT-TTCATAAATATTAGTAAATAGATAG
1 AAATATTGGT-AAATGATTAGAAATTTTGATAAAGTCTT-AGAAATATTGGTAAATAGATAG
* * * * * *
39726156 AAATTTTGGTAACTTATTAGATATTTTGATAAA-TCCTTAGAAATATTGGTAAATCGTTAG
1 AAATATTGGTAAATGATTAGAAATTTTGATAAAGT-CTTAGAAATATTGGTAAATAGATAG
* * * * *
39726216 ATATATTGGTAAATGCTTATAAATTTTGATAAAGTCTTATAAATATTGGTAAATTGATA
1 AAATATTGGTAAATGATTAGAAATTTTGATAAAGTCTTAGAAATATTGGTAAATAGATA
39726275 TATTTGTTTA
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
59 5 0.05
60 87 0.92
61 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (60 bp):
AAATATTGGTAAATGATTAGAAATTTTGATAAAGTCTTAGAAATATTGGTAAATAGATAG
Found at i:39726216 original size:40 final size:40
Alignment explanation
Indices: 39726153--39726248 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
39726143 AGTAAATAGA
* * *
39726153 TAGAAATTTTGGTAACTTATTAGATATTTTGATAAATCCT
1 TAGAAATTTTGGTAAATCATTAGATATATTGATAAATCCT
* * * *
39726193 TAGAAATATTGGTAAATCGTTAGATATATTGGTAAATGCT
1 TAGAAATTTTGGTAAATCATTAGATATATTGATAAATCCT
* *
39726233 TATAAATTTTGATAAA
1 TAGAAATTTTGGTAAA
39726249 GTCTTATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.42
Consensus pattern (40 bp):
TAGAAATTTTGGTAAATCATTAGATATATTGATAAATCCT
Found at i:39732633 original size:46 final size:46
Alignment explanation
Indices: 39732564--39732856 Score: 441
Period size: 46 Copynumber: 6.5 Consensus size: 46
39732554 TGATCAGTGA
39732564 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
39732610 CAAGTGAAAAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
39732656 CAAGTGACAAAGTGATAGGTGGTAGCTTTAGCTACACTTATCTAAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
39732702 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATTTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
39732747 CAAGTGACAAAGTGAGAAGTGGTAGCTTTAGCTACTCTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* * * *
39732793 CAAGTGACAAAGTGATAAGTGGTAGC-CTAACTACATTTATCTAAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
39732838 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
39732857 ATCATACGTA
Statistics
Matches: 225, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
43 12 0.05
44 5 0.02
45 56 0.25
46 152 0.68
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:39732787 original size:91 final size:91
Alignment explanation
Indices: 39732564--39732856 Score: 455
Period size: 91 Copynumber: 3.2 Consensus size: 91
39732554 TGATCAGTGA
* *
39732564 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAA
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
*
39732629 TGGTAGCTTTAGCTACACTTATCTGAT
66 TGGTAGC-CTAGCTACACTTATCTGAT
* *
39732656 CAAGTGACAAAGTGATAGGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
*
39732721 TGGTAGCCTAGCTACACTTATTTGAT
66 TGGTAGCCTAGCTACACTTATCTGAT
* *
39732747 CAAGTGACAAAGTGAGAAGTGGTAGCTTTAGCTACTCTTATCTGATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
* * *
39732812 TGGTAGCCTAACTACATTTATCTAAT
66 TGGTAGCCTAGCTACACTTATCTGAT
*
39732838 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
39732857 ATCATACGTA
Statistics
Matches: 185, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
89 11 0.06
90 5 0.03
91 101 0.55
92 68 0.37
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (91 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
TGGTAGCCTAGCTACACTTATCTGAT
Found at i:39732815 original size:137 final size:137
Alignment explanation
Indices: 39732564--39732856 Score: 457
Period size: 137 Copynumber: 2.2 Consensus size: 137
39732554 TGATCAGTGA
* *
39732564 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAA
1 CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGATCAAGTGAAAAAGTGAGAAA
* * *
39732629 TGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAGGTGGTAGCTTTAGCTACACT
66 TGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAACTACACT
39732694 TATCTAAT
130 TATCTAAT
* * *
39732702 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATTTGATCAAGTGACAAAGTGAGAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGATCAAGTGAAAAAGTGAGAAA
* *
39732766 TGGTAGCTTTAGCTACTCTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAACTACATTT
66 TGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAACTACACTT
39732831 ATCTAAT
131 ATCTAAT
*
39732838 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
39732857 ATCATACGTA
Statistics
Matches: 144, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
134 12 0.08
135 5 0.03
136 17 0.12
137 84 0.58
138 26 0.18
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (137 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGATCAAGTGAAAAAGTGAGAAA
TGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAACTACACTT
ATCTAAT
Found at i:39734987 original size:17 final size:17
Alignment explanation
Indices: 39734965--39735005 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
39734955 AATCATAATT
39734965 ATTTAATGTATAACCAA
1 ATTTAATGTATAACCAA
39734982 ATTTAATGTATAACCAA
1 ATTTAATGTATAACCAA
39734999 ATTTAAT
1 ATTTAAT
39735006 TCCATGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (17 bp):
ATTTAATGTATAACCAA
Found at i:39735709 original size:95 final size:91
Alignment explanation
Indices: 39735478--39735693 Score: 279
Period size: 91 Copynumber: 2.3 Consensus size: 91
39735468 TGAACATTTC
* * *
39735478 AGTTTGTGGATGAACCACCAGTGTTTGTAGGTTAATACGCTGCTAGTAGGTTATGAATGCACAAC
1 AGTTTGTGGATGAACCACCAGTGTTTGCAGGTTAATACGTTGCCAGTAGGTTATGAATGCACAAC
* * *
39735543 CTCTTTGCACATAAAAGTTGTCAGTA
66 CTATTTGCACATAAAAGCTGCCAGTA
* * * *
39735569 AGTTTATGGATGAACCACTAGCGTTTGCAGGTTAATACGTTGCCAGTAGGTTGTGAATGCACAGC
1 AGTTTGTGGATGAACCACCAGTGTTTGCAGGTTAATACGTTGCCAGTAGGTTATGAATG--CA-C
* *
39735634 ATACGTATTTGCAGATAAAAGCTGCCAGTA
63 A-ACCTATTTGCACATAAAAGCTGCCAGTA
*
39735664 AGTTTGTGGATAAACCACCAGTGTTTGCAG
1 AGTTTGTGGATGAACCACCAGTGTTTGCAG
39735694 ATTGTTAAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
91 52 0.50
93 2 0.02
94 2 0.02
95 49 0.47
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (91 bp):
AGTTTGTGGATGAACCACCAGTGTTTGCAGGTTAATACGTTGCCAGTAGGTTATGAATGCACAAC
CTATTTGCACATAAAAGCTGCCAGTA
Found at i:39735901 original size:38 final size:38
Alignment explanation
Indices: 39735782--39735907 Score: 128
Period size: 38 Copynumber: 3.3 Consensus size: 38
39735772 TACATAAAAC
* ** *
39735782 AGTAGACATGCTTTAATATGTATTATGTTCAACAATAAT
1 AGTAGACATGC-TTAACATGTATTCGGTTCAACAGTAAT
* * **
39735821 AGTAAACATGCTTAACATGTA-TCTGGTTCAATAGTAGC
1 AGTAGACATGCTTAACATGTATTC-GGTTCAACAGTAAT
* *
39735859 AGTAGACATGCTTAACATGTATTCGGTTCCACGGTAAT
1 AGTAGACATGCTTAACATGTATTCGGTTCAACAGTAAT
*
39735897 AGTAGGCATGC
1 AGTAGACATGC
39735908 AATCGATAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
37 1 0.01
38 57 0.81
39 12 0.17
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTCGGTTCAACAGTAAT
Found at i:39739479 original size:7 final size:7
Alignment explanation
Indices: 39739456--39739495 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
39739446 TTACTCCATA
39739456 TTTTTAT
1 TTTTTAT
*
39739463 TTTTAAAT
1 TTTT-TAT
39739471 TTTTTAT
1 TTTTTAT
39739478 TTTTTAT
1 TTTTTAT
39739485 TTTTTAT
1 TTTTTAT
39739492 TTTT
1 TTTT
39739496 CGAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTAT
Found at i:39740006 original size:29 final size:28
Alignment explanation
Indices: 39739973--39740030 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
39739963 TTTTTAAGAT
*
39739973 TTACATCAACATTTTATTTCAAAAAAAAA
1 TTACATCAACATTTTA-ATCAAAAAAAAA
* *
39740002 TTACATCAATATTTTAATCAAAATAAAA
1 TTACATCAACATTTTAATCAAAAAAAAA
39740030 T
1 T
39740031 ATTTGAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (28 bp):
TTACATCAACATTTTAATCAAAAAAAAA
Found at i:39743782 original size:52 final size:52
Alignment explanation
Indices: 39743725--39743828 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
39743715 ATAAATAAGA
39743725 GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
1 GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
39743777 GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
1 GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
39743829 ACCCATACTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (52 bp):
GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
Found at i:39744185 original size:31 final size:30
Alignment explanation
Indices: 39744146--39744209 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
39744136 TTTTCATAAA
*
39744146 TTTAGAATTTAGT-CTTTGTACTTTTTTATT
1 TTTAGAATTTAGTCCTTT-TACTTTTTTAGT
*
39744176 TTTAGGAATTTTGTCCTTTTACTTTTTTAGT
1 TTTA-GAATTTAGTCCTTTTACTTTTTTAGT
39744207 TTT
1 TTT
39744210 CAAAATTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 4 0.13
31 22 0.73
32 4 0.13
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.64
Consensus pattern (30 bp):
TTTAGAATTTAGTCCTTTTACTTTTTTAGT
Found at i:39746747 original size:10 final size:10
Alignment explanation
Indices: 39746729--39746769 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
39746719 AAATATTTAA
39746729 AATAATTTTT
1 AATAATTTTT
39746739 -ATAATTTTT
1 AATAATTTTT
39746748 AATAA-TTTT
1 AATAATTTTT
*
39746757 AATGATTTTT
1 AATAATTTTT
39746767 AAT
1 AAT
39746770 TTTTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 17 0.61
10 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
AATAATTTTT
Found at i:39746751 original size:19 final size:19
Alignment explanation
Indices: 39746729--39746769 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
39746719 AAATATTTAA
*
39746729 AATAATTTTTATAATTTTT
1 AATAATTTTAATAATTTTT
*
39746748 AATAATTTTAATGATTTTT
1 AATAATTTTAATAATTTTT
39746767 AAT
1 AAT
39746770 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
AATAATTTTAATAATTTTT
Found at i:39749043 original size:21 final size:21
Alignment explanation
Indices: 39748998--39749044 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
39748988 TATATCTCTC
*
39748998 GCAAAAATATTAATAATAATG
1 GCAAAAATATTAATAATAATA
*
39749019 GCAAGAATATTAATAACTAA-A
1 GCAAAAATATTAATAA-TAATA
39749040 GCAAA
1 GCAAA
39749045 TTAATAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (21 bp):
GCAAAAATATTAATAATAATA
Found at i:39758814 original size:24 final size:24
Alignment explanation
Indices: 39758782--39758830 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
39758772 GATCTTGAAA
39758782 ACTTAGGTTTAAGGGTAAGTTTGG
1 ACTTAGGTTTAAGGGTAAGTTTGG
*
39758806 ACTTAGGTTTAAGGGTAGGTTTGG
1 ACTTAGGTTTAAGGGTAAGTTTGG
39758830 A
1 A
39758831 TGGATGGCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.35, T:0.37
Consensus pattern (24 bp):
ACTTAGGTTTAAGGGTAAGTTTGG
Found at i:39761210 original size:32 final size:33
Alignment explanation
Indices: 39761155--39761221 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
39761145 CTTAATACTT
** *
39761155 TTTTTAATTTTTATATATTATTTACATT-TTTA
1 TTTTTAATTTTTATATAAAATTTAAATTATTTA
39761187 TTTTTAATATTTT-TATAAAATTTAAATTATTTA
1 TTTTTAAT-TTTTATATAAAATTTAAATTATTTA
39761220 TT
1 TT
39761222 GATGTATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (33 bp):
TTTTTAATTTTTATATAAAATTTAAATTATTTA
Found at i:39767379 original size:7 final size:7
Alignment explanation
Indices: 39767367--39767391 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39767357 TCTAATAAAA
39767367 ACATGCC
1 ACATGCC
39767374 ACATGCC
1 ACATGCC
39767381 ACATGCC
1 ACATGCC
39767388 ACAT
1 ACAT
39767392 TTTCATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.40, G:0.12, T:0.16
Consensus pattern (7 bp):
ACATGCC
Found at i:39768806 original size:13 final size:13
Alignment explanation
Indices: 39768770--39768806 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
39768760 CTCTTTCTAT
39768770 TTTTTATTTTTTA
1 TTTTTATTTTTTA
* *
39768783 TTTATAATTTTTA
1 TTTTTATTTTTTA
39768796 TTTTTATTTTT
1 TTTTTATTTTT
39768807 GGAAAGTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:39769800 original size:2 final size:2
Alignment explanation
Indices: 39769793--39769828 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39769783 CGGTTTCGTT
39769793 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
39769829 AACCTAACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39777054 original size:29 final size:29
Alignment explanation
Indices: 39777002--39777057 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
39776992 ATAGAGATTA
* *
39777002 GATTAAATTAGTCTTTTTACTATTAAATG
1 GATTAAATTAGTCTATGTACTATTAAATG
* *
39777031 GATTAATTTAGTCTATGTATTATTAAA
1 GATTAAATTAGTCTATGTACTATTAAA
39777058 AAAATCAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (29 bp):
GATTAAATTAGTCTATGTACTATTAAATG
Found at i:39777655 original size:26 final size:26
Alignment explanation
Indices: 39777608--39777657 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
39777598 AGGGGGAGCC
* *
39777608 TCGCGCCGCAACCAGGATCTTCACGT
1 TCGCGCCGCAACCACGACCTTCACGT
* *
39777634 TCGCGCCGCAGCCCCGACCTTCAC
1 TCGCGCCGCAACCACGACCTTCAC
39777658 CTGCAGCAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (26 bp):
TCGCGCCGCAACCACGACCTTCACGT
Found at i:39778774 original size:22 final size:23
Alignment explanation
Indices: 39778735--39778780 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
39778725 GATAATGTAA
*
39778735 AATTTTTTGTTATATATATATGT
1 AATTATTTGTTATATATATATGT
*
39778758 AATTATTT-TTATCTATATATGT
1 AATTATTTGTTATATATATATGT
39778780 A
1 A
39778781 TATATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (23 bp):
AATTATTTGTTATATATATATGT
Found at i:39778822 original size:17 final size:16
Alignment explanation
Indices: 39778800--39778832 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
39778790 TTGTTTTTTA
39778800 ATGAATATTTTCTATAT
1 ATGAATATTTT-TATAT
39778817 ATGAATATTTTTATAT
1 ATGAATATTTTTATAT
39778833 TTATACGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (16 bp):
ATGAATATTTTTATAT
Found at i:39778884 original size:3 final size:3
Alignment explanation
Indices: 39778876--39778906 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
39778866 AAATATTTAC
39778876 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
39778907 ATATAAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39779116 original size:15 final size:15
Alignment explanation
Indices: 39779093--39779126 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39779083 GTTTATTGAC
* *
39779093 TTATGTTTTTTTCAT
1 TTATATTTTGTTCAT
39779108 TTATATTTTGTTCAT
1 TTATATTTTGTTCAT
39779123 TTAT
1 TTAT
39779127 TTGATATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATATTTTGTTCAT
Found at i:39779248 original size:19 final size:20
Alignment explanation
Indices: 39779207--39779248 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
39779197 ATTTCTATGC
* *
39779207 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
39779227 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
39779246 CAT
1 CAT
39779249 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:39780562 original size:82 final size:82
Alignment explanation
Indices: 39780393--39780592 Score: 239
Period size: 82 Copynumber: 2.4 Consensus size: 82
39780383 NNNNAACATA
* * * *
39780393 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCAATCACCGGCACTTAGCCTGCTTGG
1 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCCAATCACCGGCACTTAGCCTGCTAGA
*
39780458 TTTATAACCTGATTCAG
66 CTTATAACCTGATTCAG
*
39780475 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGATCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCCA-ATCACCGGCACTTAGCCTGCTAG
* *
39780539 ACTTA-AAGTCTGAATT-AT
65 ACTTATAA-CCTG-ATTCAG
*
39780557 TTCACCGGC-CTTAAGCCTACTAGGTTT-TAAACCTGA
1 TTCACCGGCACTT-AGCCTGCTAGGTTTAT-AACCTGA
39780593 AAATTTCAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
81 8 0.08
82 92 0.89
83 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCCAATCACCGGCACTTAGCCTGCTAGA
CTTATAACCTGATTCAG
Found at i:39780565 original size:41 final size:41
Alignment explanation
Indices: 39780394--39780543 Score: 239
Period size: 41 Copynumber: 3.7 Consensus size: 41
39780384 NNNAACATAT
*
39780394 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT-CAGA
* *
39780435 TCACCGGCACTTAGCCTGCTTGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
39780476 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
39780517 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
39780544 AAGTCTGAAT
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 2 0.02
41 100 0.98
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:39780593 original size:41 final size:41
Alignment explanation
Indices: 39780394--39780593 Score: 214
Period size: 41 Copynumber: 4.9 Consensus size: 41
39780384 NNNAACATAT
* *
39780394 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG-ATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTA-AACCTGAATT-CAGA
*
39780435 TCACCGGCACTTAGCCTGCTTGGTTTATAACCTG-ATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTA-AACCTGAATTCAGA
39780476 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTG-ATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTA-AACCTGAATTCAGA
** * **
39780517 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCTGAATT-ATT
1 TCACCGGCACTTAGCCTGCTAGGTTTAAA-CCTGAATTCAGA
*
39780558 TCACCGGC-CTTAAGCCTACTAGGTTTTAAACCTGAA
1 TCACCGGCACTT-AGCCTGCTAGG-TTTAAACCTGAA
39780594 AATTTCAATT
Statistics
Matches: 141, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
40 7 0.05
41 126 0.89
42 8 0.06
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTAAACCTGAATTCAGA
Found at i:39782970 original size:23 final size:22
Alignment explanation
Indices: 39782910--39782970 Score: 52
Period size: 23 Copynumber: 2.7 Consensus size: 22
39782900 TTTTAATCTA
* * *
39782910 ATCACTTTCATTTTGGGTTTTG
1 ATCAGTTTAATTTTGGGGTTTG
*
39782932 ATCAGTTTAAGGTTTGGGGTTTG
1 ATCAGTTTAA-TTTTGGGGTTTG
39782955 AATC-GTTTAGATTTTG
1 -ATCAGTTTA-ATTTTG
39782971 ATTGTTTTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 8 0.26
23 19 0.61
24 4 0.13
ACGTcount: A:0.18, C:0.08, G:0.25, T:0.49
Consensus pattern (22 bp):
ATCAGTTTAATTTTGGGGTTTG
Found at i:39785411 original size:15 final size:17
Alignment explanation
Indices: 39785382--39785413 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
39785372 ATAAAGGGCT
39785382 AAAAATGATATTTTTAA
1 AAAAATGATATTTTTAA
39785399 AAAAAT-AT-TTTTTAA
1 AAAAATGATATTTTTAA
39785414 TTTTTAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AAAAATGATATTTTTAA
Found at i:39785460 original size:31 final size:31
Alignment explanation
Indices: 39785425--39785517 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 31
39785415 TTTTAGAGTT
*
39785425 AGAACTAAATTGATAGATTTTGTAAATATTG
1 AGAACTAAATTGATAAATTTTGTAAATATTG
* * * * *
39785456 AGAACCAAATTTATTACATTTTTTAGA-ATT-
1 AGAACTAAATTGA-TAAATTTTGTAAATATTG
*
39785486 AGAACTACAA-TGACAAATTTTGTAAATATTG
1 AGAACTA-AATTGATAAATTTTGTAAATATTG
39785517 A
1 A
39785518 AGGCTAATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
29 9 0.19
30 11 0.23
31 17 0.36
32 10 0.21
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (31 bp):
AGAACTAAATTGATAAATTTTGTAAATATTG
Found at i:39785530 original size:61 final size:61
Alignment explanation
Indices: 39785414--39785541 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 61
39785404 TATTTTTTAA
* * *
39785414 TTTTTAGAGTTAGAACTAAATTGATAGATTTTGTAAATATTGAGAACCAAATTTATT-ACAT
1 TTTTTAGAATTAGAACTAAATTGACAAATTTTGTAAATATTGAGAACCAAATTTATTGA-AT
* * *
39785475 TTTTTAGAATTAGAACTACAA-TGACAAATTTTGTAAATATTGA-AGGCTAATTTTATTGAAT
1 TTTTTAGAATTAGAACTA-AATTGACAAATTTTGTAAATATTGAGA-ACCAAATTTATTGAAT
39785536 TTTTTA
1 TTTTTA
39785542 TATTTTATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
60 1 0.02
61 54 0.93
62 3 0.05
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.43
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAATTGACAAATTTTGTAAATATTGAGAACCAAATTTATTGAAT
Found at i:39791726 original size:2 final size:2
Alignment explanation
Indices: 39791719--39791746 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39791709 CCTGTGTAAA
39791719 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
39791747 CTTTGGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39793460 original size:32 final size:32
Alignment explanation
Indices: 39793419--39793482 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
39793409 TCAATACTAG
*
39793419 TCAGAACGATAAAGTGAAGTTGATAGATGCTA
1 TCAGAACGATAAAGTGAAGTTGACAGATGCTA
*
39793451 TCAGAACGATAAAGTGAAGTTGGCAGATGCTA
1 TCAGAACGATAAAGTGAAGTTGACAGATGCTA
39793483 ACTCTGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (32 bp):
TCAGAACGATAAAGTGAAGTTGACAGATGCTA
Found at i:39801773 original size:2 final size:2
Alignment explanation
Indices: 39801754--39801800 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
39801744 ATTTAGTTTT
* *
39801754 TA TA TA TG TA TA TG 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
39801796 TA TA T
1 TA TA T
39801801 TATTTTTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39804531 original size:9 final size:9
Alignment explanation
Indices: 39804513--39804617 Score: 140
Period size: 9 Copynumber: 11.4 Consensus size: 9
39804503 TTTGGTTAAA
39804513 AATTACCCG
1 AATTACCCG
*
39804522 AATTATCCG
1 AATTACCCG
39804531 AATTACCCG
1 AATTACCCG
*
39804540 ACTTACCCG
1 AATTACCCG
39804549 AATTACCC-
1 AATTACCCG
39804557 AACTTACCCG
1 AA-TTACCCG
*
39804567 ACTTACCCG
1 AATTACCCG
*
39804576 AATTAACCG
1 AATTACCCG
39804585 AAAATTACCCG
1 --AATTACCCG
39804596 AATTACCCG
1 AATTACCCG
39804605 AATTACCCG
1 AATTACCCG
39804614 AATT
1 AATT
39804618 GACACTTTGA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
8 2 0.02
9 73 0.87
10 1 0.01
11 8 0.10
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:39805398 original size:16 final size:16
Alignment explanation
Indices: 39805377--39805416 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
39805367 GCCTAAGAGA
39805377 AAATTGGGCTGGATTT
1 AAATTGGGCTGGATTT
*
39805393 AAATTGGGCTGGGTTT
1 AAATTGGGCTGGATTT
39805409 AAATTGGG
1 AAATTGGG
39805417 AGGGAGTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.05, G:0.35, T:0.35
Consensus pattern (16 bp):
AAATTGGGCTGGATTT
Found at i:39812922 original size:20 final size:20
Alignment explanation
Indices: 39812884--39812922 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39812874 TTGTTTGTAA
* * *
39812884 CTTTTATGTTTTATTTTTTT
1 CTTTTATATTATATATTTTT
39812904 CTTTTATATTATATATTTT
1 CTTTTATATTATATATTTT
39812923 GAAAATGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (20 bp):
CTTTTATATTATATATTTTT
Found at i:39815217 original size:31 final size:29
Alignment explanation
Indices: 39815157--39815224 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
39815147 GTGATAGTTT
*
39815157 AAGTACCACATTAGACATTTTCAAAGTAC
1 AAGTACCACATTAGACATTATCAAAGTAC
*
39815186 AAGTACCACATTAGACATGTAATGAAAGTAC
1 AAGTACCACATTAGACAT-T-ATCAAAGTAC
*
39815217 AGGTACCA
1 AAGTACCA
39815225 AATAATATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 18 0.53
30 1 0.03
31 15 0.44
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (29 bp):
AAGTACCACATTAGACATTATCAAAGTAC
Found at i:39815312 original size:91 final size:91
Alignment explanation
Indices: 39815037--39815318 Score: 266
Period size: 91 Copynumber: 3.1 Consensus size: 91
39815027 TAACTCCAAA
* * * * * *
39815037 TACCATAATAATACACATATTGATAGTTCAAGTACCACCTT-GAATATTTTCAAAGTATAAGTAT
1 TACCA-AATAATACACAAAGTGATAGTTCAAGTACCACATTAG-ACATTTTCAAAGTACAAGTAC
** * * *
39815101 CATGTTGGACATTTCATGAAAGTACA--
64 CACATTAGACATGTAATGAAAGTACAGG
* *
39815127 AACCTTAAATAATACACAAAGTGATAGTTTAAGTACCACATTAGACATTTTCAAAGTACAAGTAC
1 TACC--AAATAATACACAAAGTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTACAAGTAC
39815192 CACATTAGACATGTAATGAAAGTACAGG
64 CACATTAGACATGTAATGAAAGTACAGG
* * * ** * *
39815220 TACCAAATAATATACAAATTGATGGTTCAAGTACGGCATTAGACATTTTTAAGGTACATA-TACC
1 TACCAAATAATACACAAAGTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTACA-AGTACC
* * * * *
39815284 ACATTGGATATTTTATGAAAGTATAGG
65 ACATTAGACATGTAATGAAAGTACAGG
39815311 TACCAAAT
1 TACCAAAT
39815319 GTGACATTAT
Statistics
Matches: 159, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
90 3 0.02
91 150 0.94
92 3 0.02
93 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (91 bp):
TACCAAATAATACACAAAGTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTACAAGTACCA
CATTAGACATGTAATGAAAGTACAGG
Found at i:39815784 original size:2 final size:2
Alignment explanation
Indices: 39815779--39815829 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
39815769 CCTAAATTTA
39815779 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
39815821 AT AT AT AT A
1 AT AT AT AT A
39815830 AAACAAGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39819842 original size:20 final size:20
Alignment explanation
Indices: 39819819--39819870 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
39819809 TGCATGAAGT
*
39819819 ATAAAATATTCACTAAATTA
1 ATAAAATATTCAATAAATTA
*
39819839 AT-AAATTTATCAATAAATTA
1 ATAAAATAT-TCAATAAATTA
*
39819859 ATAAAGTATTCA
1 ATAAAATATTCA
39819871 TTCATCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAAAATATTCAATAAATTA
Found at i:39827361 original size:3 final size:3
Alignment explanation
Indices: 39827353--39827398 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
39827343 TTTTACTAAC
39827353 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39827399 CTATAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39827724 original size:27 final size:27
Alignment explanation
Indices: 39827683--39827750 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
39827673 AACACGAGTA
* ** **
39827683 GTGCCGCCAATCTGGTTGGCAGGACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
*
39827710 GTGCCGCCAACCTGGTTCCCTCCACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
39827737 GTGCCGCCAACCTG
1 GTGCCGCCAACCTG
39827751 CTTCTCTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.13, C:0.37, G:0.29, T:0.21
Consensus pattern (27 bp):
GTGCCGCCAACCTGGTTCCCACCACTG
Found at i:39827765 original size:27 final size:27
Alignment explanation
Indices: 39827706--39827788 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
39827696 GGTTGGCAGG
*
39827706 ACTGGTGCCGCCAACCTGGTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
* *
39827733 ACTGGTGCCGCCAACCTGCTTCTCT-T
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
* **
39827759 ATTTGGTGCCGCCAACCCACTTCCCTCC
1 A-CTGGTGCCGCCAACCTGCTTCCCTCC
39827787 AC
1 AC
39827789 CCAAGGAGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
26 1 0.02
27 43 0.96
28 1 0.02
ACGTcount: A:0.13, C:0.43, G:0.18, T:0.25
Consensus pattern (27 bp):
ACTGGTGCCGCCAACCTGCTTCCCTCC
Found at i:39828066 original size:3 final size:3
Alignment explanation
Indices: 39828058--39828097 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
39828048 ATCCTATTCC
*
39828058 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
39828098 TGTTTTAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39829238 original size:13 final size:13
Alignment explanation
Indices: 39829222--39829274 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
39829212 TTTAAACCAA
39829222 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
39829235 ACTTTTCCACAA-T
1 ACTTTT-CAAAAGC
*
39829248 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
39829261 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
39829274 A
1 A
39829275 ATGATAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 26 0.76
14 4 0.12
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39840720 original size:26 final size:26
Alignment explanation
Indices: 39840691--39840751 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
39840681 TTTTTAAAAA
39840691 TTTTAAAAGTTT-AT-ATTTTTATATTT
1 TTTTAAAA-TTTAATCATTTTT-TATTT
*
39840717 TTTTATAATTTAATCATTTTTTATTT
1 TTTTAAAATTTAATCATTTTTTATTT
39840743 TTTTAAAAT
1 TTTTAAAAT
39840752 ATTTTGTCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 3 0.10
26 22 0.71
27 6 0.19
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTTAAAATTTAATCATTTTTTATTT
Found at i:39840723 original size:18 final size:18
Alignment explanation
Indices: 39840700--39840747 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
39840690 ATTTTAAAAG
39840700 TTTATATTTTTAT-ATTTT
1 TTTATATTTTTATCA-TTT
* *
39840718 TTTATAATTTAATCATTT
1 TTTATATTTTTATCATTT
*
39840736 TTTATTTTTTTA
1 TTTATATTTTTA
39840748 AAATATTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATATTTTTATCATTT
Found at i:39841573 original size:22 final size:23
Alignment explanation
Indices: 39841505--39841588 Score: 70
Period size: 23 Copynumber: 3.8 Consensus size: 23
39841495 CTTAAAAATA
* *
39841505 ATAAAAATT-TAATTTAATTCTC
1 ATAAAAATTATAATTTAACTATC
* *
39841527 -TAAAATATAAATTATTTAA--ATC
1 ATAAAA-AT-TATAATTTAACTATC
*
39841549 AT-AAAATTATATTTTAACTATC
1 ATAAAAATTATAATTTAACTATC
39841571 ATAAAAATTATAATTTAA
1 ATAAAAATTATAATTTAA
39841589 TTTTGATCTA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
20 7 0.15
21 7 0.15
22 12 0.25
23 15 0.31
24 7 0.15
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAAAATTATAATTTAACTATC
Found at i:39845964 original size:14 final size:14
Alignment explanation
Indices: 39845945--39845974 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39845935 CCCTCGTAGG
*
39845945 GTTATCGTATACTT
1 GTTATCATATACTT
39845959 GTTATCATATACTT
1 GTTATCATATACTT
39845973 GT
1 GT
39845975 GCACATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (14 bp):
GTTATCATATACTT
Found at i:39848021 original size:26 final size:26
Alignment explanation
Indices: 39847985--39848044 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
39847975 GAAGCTTCGG
39847985 AGAGCCATTAATC-AGAAAGCTCACAA
1 AGAGCCATTAATCGAG-AAGCTCACAA
* *
39848011 AGAGCCTTTAATCGAGAAGCTCACGA
1 AGAGCCATTAATCGAGAAGCTCACAA
39848037 AGAGCCAT
1 AGAGCCAT
39848045 ATATTGGGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (26 bp):
AGAGCCATTAATCGAGAAGCTCACAA
Found at i:39851555 original size:20 final size:19
Alignment explanation
Indices: 39851516--39851556 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
39851506 AATTTGTTTG
* *
39851516 TTTAGTTAATTAACCTTAA
1 TTTAGTTAAATAAACTTAA
39851535 TTTAGTTAAATAATACTTAA
1 TTTAGTTAAATAA-ACTTAA
39851555 TT
1 TT
39851557 AATTAAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTAGTTAAATAAACTTAA
Found at i:39857453 original size:14 final size:15
Alignment explanation
Indices: 39857434--39857466 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
39857424 AAATCGCAAC
39857434 AAACC-ATTTTGCTA
1 AAACCAATTTTGCTA
39857448 AAACCATATTTTGCTA
1 AAACCA-ATTTTGCTA
39857464 AAA
1 AAA
39857467 ATCAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
16 12 0.71
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (15 bp):
AAACCAATTTTGCTA
Found at i:39858695 original size:76 final size:76
Alignment explanation
Indices: 39858569--39858721 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 76
39858559 TCCATTTCGA
* *
39858569 CGGATTTAGTCTCTCGTTTTAGAATACTTAAAGTATTCACATAAATCACAAATCAAATAATAATA
1 CGGATTTAGTCTCTCATTTTAGAATACTTAAAGTATTCACATAAATCACAAATAAAATAATAATA
39858634 TTTTGTTTAGG
66 TTTTGTTTAGG
39858645 CGGATTTAGTCTCTCATTTTAGAATACTTAAAGTATTCACATAAATCACAAATAAAATAATAATA
1 CGGATTTAGTCTCTCATTTTAGAATACTTAAAGTATTCACATAAATCACAAATAAAATAATAATA
39858710 TTTTGTTTAGG
66 TTTTGTTTAGG
39858721 C
1 C
39858722 ATTATTAACG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (76 bp):
CGGATTTAGTCTCTCATTTTAGAATACTTAAAGTATTCACATAAATCACAAATAAAATAATAATA
TTTTGTTTAGG
Found at i:39865158 original size:9 final size:9
Alignment explanation
Indices: 39865144--39865243 Score: 101
Period size: 9 Copynumber: 10.4 Consensus size: 9
39865134 CTTCGGGGGA
39865144 ATGGGCGGC
1 ATGGGCGGC
*
39865153 ATGGGCGAC
1 ATGGGCGGC
39865162 ATGATGGGCGGC
1 ---ATGGGCGGC
39865174 ATGGGCGGC
1 ATGGGCGGC
39865183 ATGGGCGGC
1 ATGGGCGGC
39865192 ATGGGCGGC
1 ATGGGCGGC
* *
39865201 ATGGGTGAC
1 ATGGGCGGC
*
39865210 ATGATGGGTGGC
1 ---ATGGGCGGC
39865222 ATGGGCGGC
1 ATGGGCGGC
*
39865231 ATGGGTGGC
1 ATGGGCGGC
39865240 ATGG
1 ATGG
39865244 ATGAATTTGA
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
9 62 0.79
12 16 0.21
ACGTcount: A:0.15, C:0.17, G:0.52, T:0.16
Consensus pattern (9 bp):
ATGGGCGGC
Done.