Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 121 of 190
Found at i:19061801 original size:9 final size:9
Alignment explanation
Indices: 19061761--19061819 Score: 79
Period size: 9 Copynumber: 6.8 Consensus size: 9
19061751 AACACCGTTT
19061761 TATTTATTTA
1 TATTT-TTTA
*
19061771 T-TTATTTA
1 TATTTTTTA
19061779 TA-TTTTTA
1 TATTTTTTA
19061787 TA-TTTTTA
1 TATTTTTTA
19061795 TATTTTTTA
1 TATTTTTTA
19061804 TATTTTTTA
1 TATTTTTTA
19061813 TATTTTT
1 TATTTTT
19061820 CTTTTTTCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
8 20 0.44
9 24 0.53
10 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TATTTTTTA
Found at i:19061833 original size:12 final size:12
Alignment explanation
Indices: 19061816--19061847 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
19061806 TTTTTTATAT
19061816 TTTTCTTTTTTC
1 TTTTCTTTTTTC
19061828 TTTTC-TTTTTC
1 TTTTCTTTTTTC
19061839 TTTT-TTTTT
1 TTTTCTTTTT
19061848 CCAGCACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:19062785 original size:15 final size:17
Alignment explanation
Indices: 19062752--19062792 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
19062742 TTTTTTTGAA
19062752 TTATTATTTTATATTATT
1 TTATTATTTTATA-TATT
19062770 TTATTATTTTA-A-ATT
1 TTATTATTTTATATATT
19062785 TTATTATT
1 TTATTATT
19062793 AGTATTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.48
17 1 0.04
18 11 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTATTTTATATATT
Found at i:19062793 original size:18 final size:19
Alignment explanation
Indices: 19062751--19062793 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
19062741 ATTTTTTTGA
*
19062751 ATTATTATTTTATATTATT
1 ATTATTATTTTAAATTATT
19062770 -TTATTATTTTAAATT-TT
1 ATTATTATTTTAAATTATT
19062787 ATTATTA
1 ATTATTA
19062794 GTATTTATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTATTATTTTAAATTATT
Found at i:19062876 original size:12 final size:12
Alignment explanation
Indices: 19062848--19062893 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
19062838 TTTGTTGTTT
*
19062848 TAATAATAATTAA
1 TAATAA-AATAAA
19062861 TAATAAAATAAA
1 TAATAAAATAAA
*
19062873 TAATAAAATACA
1 TAATAAAATAAA
19062885 TAATTAAAA
1 TAA-TAAAA
19062894 ATTTTGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATAAAATAAA
Found at i:19064729 original size:21 final size:21
Alignment explanation
Indices: 19064705--19064744 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19064695 ATGCATGAGA
19064705 ATGGATTAAGGGTTGGCTTTT
1 ATGGATTAAGGGTTGGCTTTT
* **
19064726 ATGGTTTGGGGGTTGGCTT
1 ATGGATTAAGGGTTGGCTT
19064745 AAGGTTTATT
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:0.12, C:0.05, G:0.40, T:0.42
Consensus pattern (21 bp):
ATGGATTAAGGGTTGGCTTTT
Found at i:19064836 original size:7 final size:7
Alignment explanation
Indices: 19064826--19064958 Score: 66
Period size: 7 Copynumber: 21.3 Consensus size: 7
19064816 TTTATCTTGG
19064826 TTAGGGT
1 TTAGGGT
19064833 TTAGGG-
1 TTAGGGT
19064839 TT--GGT
1 TTAGGGT
*
19064844 TTAGGAT
1 TTAGGGT
19064851 TT--GGT
1 TTAGGGT
19064856 TTAGGGT
1 TTAGGGT
*
19064863 TT--GTT
1 TTAGGGT
19064868 TTAGGGT
1 TTAGGGT
*
19064875 TTAGAGT
1 TTAGGGT
19064882 TT--GG-
1 TTAGGGT
*
19064886 TTAAGGT
1 TTAGGGT
*
19064893 TTAAGGT
1 TTAGGGT
19064900 TT--GGT
1 TTAGGGT
*
19064905 TTATGGT
1 TTAGGGT
19064912 TTAGGGT
1 TTAGGGT
*
19064919 TT--GAT
1 TTAGGGT
*
19064924 TTAGGGA
1 TTAGGGT
19064931 TTAGGGT
1 TTAGGGT
19064938 TT--GGT
1 TTAGGGT
19064943 TTAAGGGT
1 TT-AGGGT
19064951 TT-GGGT
1 TTAGGGT
19064957 TT
1 TT
19064959 TGCATTGTGG
Statistics
Matches: 98, Mismatches: 11, Indels: 35
0.68 0.08 0.24
Matches are distributed among these distances:
4 4 0.04
5 25 0.26
6 10 0.10
7 54 0.55
8 5 0.05
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (7 bp):
TTAGGGT
Found at i:19064856 original size:12 final size:11
Alignment explanation
Indices: 19064830--19064913 Score: 62
Period size: 12 Copynumber: 7.0 Consensus size: 11
19064820 TCTTGGTTAG
*
19064830 GGTTTAGGGTT
1 GGTTTAGGTTT
19064841 GGTTTAGGATTT
1 GGTTTAGG-TTT
19064853 GGTTTAGGGTTT
1 GGTTTA-GGTTT
*
19064865 GTTTTAGGGTTT
1 GGTTTA-GGTTT
*
19064877 AGAGTTT-GGTTAA
1 -G-GTTTAGGTT-T
19064890 GGTTTAAGGTTT
1 GGTTT-AGGTTT
19064902 GGTTTATGGTTT
1 GGTTTA-GGTTT
19064914 AGGGTTTGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
11 13 0.22
12 37 0.62
13 7 0.12
14 3 0.05
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (11 bp):
GGTTTAGGTTT
Found at i:19064875 original size:19 final size:19
Alignment explanation
Indices: 19064853--19064958 Score: 108
Period size: 19 Copynumber: 5.6 Consensus size: 19
19064843 TTTAGGATTT
19064853 GGTTTAGGGTTTGTTTTAG
1 GGTTTAGGGTTTGTTTTAG
* * *
19064872 GGTTTAGAGTTTG-GTTAA
1 GGTTTAGGGTTTGTTTTAG
* * *
19064890 GGTTTAAGGTTTGGTTTAT
1 GGTTTAGGGTTTGTTTTAG
*
19064909 GGTTTAGGGTTTGATTTAG
1 GGTTTAGGGTTTGTTTTAG
* *
19064928 GGATTAGGGTTTGGTTTAAG
1 GGTTTAGGGTTT-GTTTTAG
19064948 GGTTT-GGGTTT
1 GGTTTAGGGTTT
19064959 TGCATTGTGG
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.20
19 48 0.68
20 9 0.13
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (19 bp):
GGTTTAGGGTTTGTTTTAG
Found at i:19065008 original size:24 final size:24
Alignment explanation
Indices: 19064957--19065023 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 24
19064947 GGGTTTGGGT
* *
19064957 TTTGCATTGTGGTTTGGGGTTTATGG
1 TTTGCATTGTGGTTT--AGTTTAAGG
19064983 TTTGCATTGTGGTTTAGTTTAAGG
1 TTTGCATTGTGGTTTAGTTTAAGG
*
19065007 TTTGCATGGTGGTTTAG
1 TTTGCATTGTGGTTTAG
19065024 GGTTTGTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 23 0.61
26 15 0.39
ACGTcount: A:0.12, C:0.04, G:0.34, T:0.49
Consensus pattern (24 bp):
TTTGCATTGTGGTTTAGTTTAAGG
Found at i:19065036 original size:26 final size:26
Alignment explanation
Indices: 19064939--19065036 Score: 112
Period size: 26 Copynumber: 3.8 Consensus size: 26
19064929 GATTAGGGTT
*
19064939 TGGTTTAAGGGTTT-GGGTTTTGCATTG
1 TGGTTT-AGGGTTTATGG-TTTGCATTG
*
19064966 TGGTTTGGGGTTTATGGTTTGCATTG
1 TGGTTTAGGGTTTATGGTTTGCATTG
* *
19064992 TGGTTTA--GTTTAAGGTTTGCATGG
1 TGGTTTAGGGTTTATGGTTTGCATTG
*
19065016 TGGTTTAGGGTTTGTGGTTTG
1 TGGTTTAGGGTTTATGGTTTG
19065037 TATGAGCAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
24 22 0.36
26 31 0.51
27 8 0.13
ACGTcount: A:0.10, C:0.03, G:0.38, T:0.49
Consensus pattern (26 bp):
TGGTTTAGGGTTTATGGTTTGCATTG
Found at i:19066059 original size:22 final size:22
Alignment explanation
Indices: 19066015--19066059 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19066005 TAAATCAAAT
* *
19066015 AAAACTAATATGGAAAAGTATG
1 AAAACTAACATGGAAAAGCATG
19066037 AAAACTAACAT-GAAAATGCATG
1 AAAACTAACATGGAAAA-GCATG
19066059 A
1 A
19066060 GAGTATAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.20
Consensus pattern (22 bp):
AAAACTAACATGGAAAAGCATG
Found at i:19068154 original size:49 final size:49
Alignment explanation
Indices: 19068077--19068172 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
19068067 ACTTTAATTA
* *
19068077 TAGGTGTTTGAAAAAGAATGTGATTGTTGACAATAAAAACACTCATCAC
1 TAGGTGTTTGAAAAAGAATGTGACTGTTGACAATAAAAACACCCATCAC
*
19068126 TAGGTGTTTGAAAAAGAATGTGACTGTTGATAATAAAAACACCCATC
1 TAGGTGTTTGAAAAAGAATGTGACTGTTGACAATAAAAACACCCATC
19068173 TCTATTGTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (49 bp):
TAGGTGTTTGAAAAAGAATGTGACTGTTGACAATAAAAACACCCATCAC
Found at i:19072683 original size:3 final size:3
Alignment explanation
Indices: 19072675--19072702 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
19072665 TGGGCCAAGC
19072675 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19072703 ATGCATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19072729 original size:4 final size:4
Alignment explanation
Indices: 19072710--19072788 Score: 59
Period size: 4 Copynumber: 18.2 Consensus size: 4
19072700 TATATGCATA
* * * *
19072710 TATT TATT TTTAT TATT TATT TATT TTTGT TATT TATT TATT TTTT TATG
1 TATT TATT TAT-T TATT TATT TATT TAT-T TATT TATT TATT TATT TATT
*
19072760 TATTT TAATT TATAA TATTT TATT TATT T
1 TA-TT T-ATT TAT-T TA-TT TATT TATT T
19072789 TATAAATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
4 42 0.71
5 15 0.25
6 2 0.03
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:19072730 original size:17 final size:17
Alignment explanation
Indices: 19072710--19072789 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
19072700 TATATGCATA
19072710 TATTTATTTTTATTATT
1 TATTTATTTTTATTATT
*
19072727 TATTTATTTTTGTTATT
1 TATTTATTTTTATTATT
*
19072744 TATTTATTTTT-TTATG
1 TATTTATTTTTATTATT
* *
19072760 TATTTTAATTTATAATATTT
1 TA-TTT-ATTTTTATTA-TT
19072780 TATTTATTTT
1 TATTTATTTT
19072790 ATAAATTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
16 6 0.11
17 30 0.57
18 9 0.17
19 5 0.09
20 3 0.06
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TATTTATTTTTATTATT
Found at i:19072746 original size:21 final size:20
Alignment explanation
Indices: 19072722--19072764 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
19072712 TTTATTTTTA
19072722 TTATTTATTTATTTT-TGTTAT
1 TTATTTATTT-TTTTATG-TAT
19072743 TTATTTATTTTTTTATGTAT
1 TTATTTATTTTTTTATGTAT
19072763 TT
1 TT
19072765 TAATTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (20 bp):
TTATTTATTTTTTTATGTAT
Found at i:19072787 original size:9 final size:9
Alignment explanation
Indices: 19072710--19072791 Score: 59
Period size: 9 Copynumber: 9.3 Consensus size: 9
19072700 TATATGCATA
19072710 TATTTATTT
1 TATTTATTT
19072719 T-TATTA-TT
1 TAT-TTATTT
19072727 TATTTATTT
1 TATTTATTT
19072736 T-TGTTA-TT
1 TAT-TTATTT
19072744 TATTTATTT
1 TATTTATTT
*
19072753 T-TTTA-TG
1 TATTTATTT
*
19072760 TATTTTAATT
1 TA-TTTATTT
*
19072770 TATAATATTT
1 TAT-TTATTT
19072780 TATTTATTT
1 TATTTATTT
19072789 TAT
1 TAT
19072792 AAATTTTTAG
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
7 2 0.03
8 18 0.31
9 28 0.48
10 10 0.17
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (9 bp):
TATTTATTT
Found at i:19072800 original size:19 final size:19
Alignment explanation
Indices: 19072763--19072798 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19072753 TTTTATGTAT
19072763 TTTAATTTATAATATTTTA
1 TTTAATTTATAATATTTTA
*
19072782 TTTATTTTATAA-ATTTT
1 TTTAATTTATAATATTTT
19072799 TAGAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTAATTTATAATATTTTA
Found at i:19073222 original size:21 final size:20
Alignment explanation
Indices: 19073194--19073238 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
19073184 TCCTAAGAAA
*
19073194 ATTTTTTTATTTTGTGTTTT
1 ATTTTTTTATTCTGTGTTTT
19073214 ATTTGTTTTATTCTGT-TTTT
1 ATTT-TTTTATTCTGTGTTTT
19073234 -TTTTT
1 ATTTTT
19073239 CATTTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 3 0.13
20 8 0.35
21 10 0.43
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.80
Consensus pattern (20 bp):
ATTTTTTTATTCTGTGTTTT
Found at i:19073244 original size:6 final size:6
Alignment explanation
Indices: 19073235--19073279 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
19073225 TCTGTTTTTT
** *
19073235 TTTTCA TTTTTG TTTTCA TTTTCA TTTTCA TTTTCA ATTTC- TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
19073280 GTCTTTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
5 3 0.09
6 30 0.91
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:19073244 original size:12 final size:12
Alignment explanation
Indices: 19073229--19073268 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
19073219 TTTTATTCTG
*
19073229 TTTTTTTTTTCA
1 TTTTTATTTTCA
*
19073241 TTTTTGTTTTCA
1 TTTTTATTTTCA
*
19073253 TTTTCATTTTCA
1 TTTTTATTTTCA
19073265 TTTT
1 TTTT
19073269 CAATTTCTTT
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:0.10, C:0.10, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTTTATTTTCA
Found at i:19073250 original size:18 final size:18
Alignment explanation
Indices: 19073195--19073262 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
19073185 CCTAAGAAAA
19073195 TTTTTTT-ATTTTGTGTTT
1 TTTTTTTCATTTT-TGTTT
* *
19073213 TATTTGTTTTA-TTCTGTTT
1 T-TTT-TTTCATTTTTGTTT
19073232 TTTTTTTCATTTTTGTTT
1 TTTTTTTCATTTTTGTTT
**
19073250 TCATTTTCATTTT
1 TTTTTTTCATTTT
19073263 CATTTTCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 4 0.10
18 22 0.54
19 9 0.22
20 5 0.12
21 1 0.02
ACGTcount: A:0.09, C:0.06, G:0.07, T:0.78
Consensus pattern (18 bp):
TTTTTTTCATTTTTGTTT
Found at i:19073462 original size:22 final size:22
Alignment explanation
Indices: 19073437--19073531 Score: 73
Period size: 22 Copynumber: 4.3 Consensus size: 22
19073427 CACTAATCTC
*
19073437 GGCTTACATGCTAGCTAATTTA
1 GGCTTACATGCAAGCTAATTTA
* * *
19073459 GGCTTTCGTGCAAGCTAATTTG
1 GGCTTACATGCAAGCTAATTTA
* * * * *
19073481 GGTTTTCGTGCAAGGTAATTTTG
1 GGCTTACATGCAAGCTAA-TTTA
* **
19073504 GGCTTACATGCCAGCTAAACTA
1 GGCTTACATGCAAGCTAATTTA
19073526 GGCTTA
1 GGCTTA
19073532 AATTTCTATA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 41 0.71
23 17 0.29
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (22 bp):
GGCTTACATGCAAGCTAATTTA
Found at i:19073551 original size:32 final size:33
Alignment explanation
Indices: 19073512--19073601 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 33
19073502 TGGGCTTACA
19073512 TGCCAGCTAAACTAGGCTTAAATTTCTA-TAGG
1 TGCCAGCTAAACTAGGCTTAAATTTCTACTAGG
* * *
19073544 TGTCAGCTAAACTAGGCTCAAATTTTTACTAGG
1 TGCCAGCTAAACTAGGCTTAAATTTCTACTAGG
* ** *
19073577 TGCCAACTAATTTTGGCTTAAATTT
1 TGCCAGCTAAACTAGGCTTAAATTT
19073602 ACATTGAGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
32 25 0.52
33 23 0.48
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (33 bp):
TGCCAGCTAAACTAGGCTTAAATTTCTACTAGG
Found at i:19073600 original size:33 final size:32
Alignment explanation
Indices: 19073512--19073832 Score: 125
Period size: 33 Copynumber: 9.8 Consensus size: 32
19073502 TGGGCTTACA
*
19073512 TGCCAGCTAAACTAGGCTTAAATTTCTATAGG
1 TGCCAACTAAACTAGGCTTAAATTTCTATAGG
* * * *
19073544 TGTCAGCTAAACTAGGCTCAAATTTTTACTAGG
1 TGCCAACTAAACTAGGCTTAAATTTCTA-TAGG
** * *
19073577 TGCCAACTAATTTTGGCTTAAATTTAC-ATTGAG
1 TGCCAACTAAACTAGGCTTAAATTT-CTATAG-G
* * * * * * *
19073610 TGCTAGCTAAATTGGGCTAGAAACTTC-ATTAGA
1 TGCCAACTAAACTAGGCT-TAAATTTCTA-TAGG
* * * *
19073643 TGCTATCCAAACTAGGCTTAAAATTT-TAGTGGG
1 TGCCAACTAAACTAGGCTT-AAATTTCTA-TAGG
* *
19073676 TGCCAACTAATA-TAGACTTAAATTT-TCATTGG
1 TGCCAACTAA-ACTAGGCTTAAATTTCT-ATAGG
* * * * * *
19073708 ATGACAAATAATCTAAGCTTAAATTTTTATTGAG
1 -TGCCAACTAAACTAGGCTTAAATTTCTATAG-G
* * * *
19073742 TACCAACTAAATTAGGTTTAAAACTTC-ATTAGG
1 TGCCAACTAAACTAGGCTT-AAATTTCTA-TAGG
* *
19073775 TGCCAACCAAACTAAGCTTAAAATTTC-ACTAGG
1 TGCCAACTAAACTAGGCTT-AAATTTCTA-TAGG
* * *
19073808 TGCCAGCTAATCTGGGCTTAAATTT
1 TGCCAACTAAACTAGGCTTAAATTT
19073833 TCATTGGGTA
Statistics
Matches: 214, Mismatches: 60, Indels: 30
0.70 0.20 0.10
Matches are distributed among these distances:
32 43 0.20
33 154 0.72
34 17 0.08
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (32 bp):
TGCCAACTAAACTAGGCTTAAATTTCTATAGG
Found at i:19073704 original size:66 final size:66
Alignment explanation
Indices: 19073634--19073837 Score: 173
Period size: 66 Copynumber: 3.1 Consensus size: 66
19073624 GGCTAGAAAC
* * * *
19073634 TTCATTAGATGCTATCCAAACTAGGCTTAAAATTTTAGTGGGTGCCAACTAATATAGACTTAAAT
1 TTCATTAGATGCAATCCAAACTAAGCTTAAAATTTTACTGGGTGCCAACTAATATAGGCTTAAAT
19073699 T
66 T
* * * * * * *
19073700 TTCATTGGATGACAAAT--AATCTAAGCTTAAATTTTTATTGAGTACCAACTAA-ATTAGGTTTA
1 TTCATTAGATG-C-AATCCAAACTAAGCTTAAAATTTTACTGGGTGCCAACTAATA-TAGGCTTA
**
19073762 AAAC
63 AATT
* * * * * *
19073766 TTCATTAGGTGCCAA-CCAAACTAAGCTTAAAATTTCACTAGGTGCCAGCTAATCTGGGCTTAAA
1 TTCATTAGATG-CAATCCAAACTAAGCTTAAAATTTTACTGGGTGCCAACTAATATAGGCTTAAA
19073830 TT
65 TT
19073832 TTCATT
1 TTCATT
19073838 GGGTAACAGA
Statistics
Matches: 104, Mismatches: 28, Indels: 12
0.72 0.19 0.08
Matches are distributed among these distances:
65 3 0.03
66 98 0.94
67 1 0.01
68 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (66 bp):
TTCATTAGATGCAATCCAAACTAAGCTTAAAATTTTACTGGGTGCCAACTAATATAGGCTTAAAT
T
Found at i:19073766 original size:132 final size:131
Alignment explanation
Indices: 19073592--19073871 Score: 337
Period size: 132 Copynumber: 2.1 Consensus size: 131
19073582 ACTAATTTTG
* * * * ** * *
19073592 GCTTAAATTTACATTGAGTGCTAGCTAAATT-GGGCTAGAAACTTCATTAGATGCTATCCAAACT
1 GCTTAAATTTTCATTGAGTACCAACTAAATTAGGTTTA-AAACTTCATTAGATGCCAACCAAACT
* * * * *
19073656 AGGCTTAAAATTTTAGTGGGTGCCAACTAATATAGACTTAAATTTTCATTGGATGACAAATAATC
65 AAGCTTAAAATTTCACTAGGTGCCAACTAATATAGACTTAAATTTTCATTGGATAACAAATAATC
19073721 TAA
130 T-A
* *
19073724 GCTTAAATTTTTATTGAGTACCAACTAAATTAGGTTTAAAACTTCATTAGGTGCCAACCAAACTA
1 GCTTAAATTTTCATTGAGTACCAACTAAATTAGGTTTAAAACTTCATTAGATGCCAACCAAACTA
* * * * * *
19073789 AGCTTAAAATTTCACTAGGTGCCAGCTAATCTGGGCTTAAATTTTCATTGGGTAACAGATAATCT
66 AGCTTAAAATTTCACTAGGTGCCAACTAATATAGACTTAAATTTTCATTGGATAACAAATAATCT
19073854 A
131 A
*
19073855 GGTTAAATTTTCATTGA
1 GCTTAAATTTTCATTGA
19073872 TGCAAGATAA
Statistics
Matches: 124, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
131 16 0.13
132 104 0.84
133 4 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (131 bp):
GCTTAAATTTTCATTGAGTACCAACTAAATTAGGTTTAAAACTTCATTAGATGCCAACCAAACTA
AGCTTAAAATTTCACTAGGTGCCAACTAATATAGACTTAAATTTTCATTGGATAACAAATAATCT
A
Found at i:19073835 original size:33 final size:32
Alignment explanation
Indices: 19073654--19073959 Score: 122
Period size: 33 Copynumber: 9.4 Consensus size: 32
19073644 GCTATCCAAA
*
19073654 CTAGGCTTAAAATTTT-AGTGGGTGCCA-ACTAAT
1 CTAGGCTT-AAATTTTCA-TAGGTGCCAGA-TAAT
* * * * *
19073687 ATAGACTTAAATTTTCATTGGATGACAAATAAT
1 CTAGGCTTAAATTTTCATAGG-TGCCAGATAAT
* * * *
19073720 CTAAGCTTAAATTTTTATTGAGTACCA-ACTAAAT
1 CTAGGCTTAAATTTTCATAG-GTGCCAGA-T-AAT
* ** * *
19073754 -TAGGTTTAAAACTTCATTAGGTGCCA-ACCAAA
1 CTAGGCTTAAATTTTCA-TAGGTGCCAGA-TAAT
* * *
19073786 CTAAGCTTAAAATTTCACTAGGTGCCAGCTAAT
1 CTAGGCTTAAATTTTCA-TAGGTGCCAGATAAT
* * **
19073819 CTGGGCTTAAATTTTCATTGGGTAACAGATAAT
1 CTAGGCTTAAATTTTCA-TAGGTGCCAGATAAT
* * *
19073852 CTAGG-TTAAATTTTCATTGATGCAAGATAAT
1 CTAGGCTTAAATTTTCATAGGTGCCAGATAAT
* ** * * * *
19073883 CTTGGCTTAAAACTTCATTGGATGTCAGTTAAA
1 CTAGGCTTAAATTTTCATAGG-TGCCAGATAAT
* * *
19073916 CTAGGCTTAAA-TTTCATTGAGTGCTAGATAAG
1 CTAGGCTTAAATTTTCATAG-GTGCCAGATAAT
*
19073948 CTGGGCTTAAAT
1 CTAGGCTTAAAT
19073960 CTTTTCATGA
Statistics
Matches: 205, Mismatches: 55, Indels: 26
0.72 0.19 0.09
Matches are distributed among these distances:
31 14 0.07
32 60 0.29
33 124 0.60
34 7 0.03
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (32 bp):
CTAGGCTTAAATTTTCATAGGTGCCAGATAAT
Found at i:19073883 original size:64 final size:65
Alignment explanation
Indices: 19073783--19073962 Score: 186
Period size: 64 Copynumber: 2.8 Consensus size: 65
19073773 GGTGCCAACC
* * * * * *
19073783 AAACTAAGCTTAAAATTTCACT-AGGTGCCAGCTAATCTGGGCTTAAATTTTCATTGGGTAACAG
1 AAACTAGGCTT-AAATTTCATTGA-GTGCAAGATAATCTGGGCTTAAATCTTCATTGGATAACAG
19073847 AT
64 AT
* * * ** *
19073849 AATCTAGG-TTAAATTTTCATTGA-TGCAAGATAATCTTGGCTTAAAACTTCATTGGATGTCAGT
1 AAACTAGGCTTAAA-TTTCATTGAGTGCAAGATAATCTGGGCTTAAATCTTCATTGGATAACAGA
19073912 T
65 T
* *
19073913 AAACTAGGCTTAAATTTCATTGAGTGCTAGATAAGCTGGGCTTAAATCTT
1 AAACTAGGCTTAAATTTCATTGAGTGCAAGATAATCTGGGCTTAAATCTT
19073963 TTCATGAATG
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
64 51 0.55
65 35 0.38
66 7 0.08
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.35
Consensus pattern (65 bp):
AAACTAGGCTTAAATTTCATTGAGTGCAAGATAATCTGGGCTTAAATCTTCATTGGATAACAGAT
Found at i:19073893 original size:32 final size:33
Alignment explanation
Indices: 19073815--19073959 Score: 122
Period size: 32 Copynumber: 4.5 Consensus size: 33
19073805 AGGTGCCAGC
* * *
19073815 TAATCTGGGCTTAAATTTTCATTG-GGTAACAGA
1 TAATCTAGGCTTAAATTTTCATTGATGTCA-AGA
19073848 TAATCTAGG-TTAAATTTTCATTGATG-CAAGA
1 TAATCTAGGCTTAAATTTTCATTGATGTCAAGA
* ** *
19073879 TAATCTTGGCTTAAAACTTCATTGGATGTC-AGT
1 TAATCTAGGCTTAAATTTTCATT-GATGTCAAGA
* *
19073912 TAAACTAGGCTTAAA-TTTCATTGA-GTGCTAGA
1 TAATCTAGGCTTAAATTTTCATTGATGT-CAAGA
* *
19073944 TAAGCTGGGCTTAAAT
1 TAATCTAGGCTTAAAT
19073960 CTTTTCATGA
Statistics
Matches: 92, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
30 2 0.02
31 14 0.15
32 47 0.51
33 28 0.30
34 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (33 bp):
TAATCTAGGCTTAAATTTTCATTGATGTCAAGA
Found at i:19074307 original size:32 final size:32
Alignment explanation
Indices: 19074257--19074369 Score: 117
Period size: 32 Copynumber: 3.7 Consensus size: 32
19074247 AAAACCTAAG
* * *
19074257 TGCCAACTAAATTGGGCTTAAATTTTGATTGA
1 TGCCAGCTAAACTAGGCTTAAATTTTGATTGA
* * *
19074289 TGCTAGCTAAACTAGGCTTAAATTTTCATTGG
1 TGCCAGCTAAACTAGGCTTAAATTTTGATTGA
* *
19074321 TGCCAGCTAATCTAAGCTTAAATTTTG---G-
1 TGCCAGCTAAACTAGGCTTAAATTTTGATTGA
*
19074349 TGCCAGCTAAACTGGGCTTAA
1 TGCCAGCTAAACTAGGCTTAA
19074370 GACTTCATTA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
28 18 0.26
29 1 0.01
32 49 0.72
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (32 bp):
TGCCAGCTAAACTAGGCTTAAATTTTGATTGA
Found at i:19075368 original size:39 final size:36
Alignment explanation
Indices: 19075325--19075412 Score: 92
Period size: 39 Copynumber: 2.4 Consensus size: 36
19075315 ATTCATTTCA
19075325 TTTCATTTCTTTTTTTTTCTTTCTTTTA-CTTTATTCTT
1 TTTCATTTCTTTTTTTTT-TTTC-TTTACCTTT-TTCTT
19075363 CTTTCATTT-TTCCTTTTTTTTTTCTTTACCTTTTTCTT
1 -TTTCATTTCTT--TTTTTTTTTTCTTTACCTTTTTCTT
*
19075401 TTGCA-TTCTTTT
1 TTTCATTTCTTTT
19075413 ACTAAGTGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
35 2 0.05
36 2 0.05
37 6 0.14
38 11 0.25
39 16 0.36
40 7 0.16
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (36 bp):
TTTCATTTCTTTTTTTTTTTTCTTTACCTTTTTCTT
Found at i:19076606 original size:8 final size:9
Alignment explanation
Indices: 19076593--19076617 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19076583 TCCTTTTTCC
19076593 CTTTTTTGT
1 CTTTTTTGT
19076602 CTTTTTTGT
1 CTTTTTTGT
19076611 CTTTTTT
1 CTTTTTT
19076618 TCACTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (9 bp):
CTTTTTTGT
Found at i:19079949 original size:21 final size:21
Alignment explanation
Indices: 19079893--19079949 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
19079883 TGTATGTAAC
* * *
19079893 AAAATTAAATACTATATACAT
1 AAAAATAAATAATATATACAA
*
19079914 AAAAATGAATCAATA-ATACAA
1 AAAAATAAAT-AATATATACAA
19079935 AACAAATAAATAATA
1 AA-AAATAAATAATA
19079950 GAAATAGCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAAATAAATAATATATACAA
Found at i:19081624 original size:19 final size:19
Alignment explanation
Indices: 19081600--19081653 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
19081590 AAGTTCAGGA
* *
19081600 TTTCACATAAGGTTTCGGG
1 TTTCACATAGGGTTTCGAG
*
19081619 TTTCACTTAGGGCTTTCGAG
1 TTTCACATAGGG-TTTCGAG
19081639 TTTCACATAGGGTTT
1 TTTCACATAGGGTTT
19081654 TAGTTTAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.41
Consensus pattern (19 bp):
TTTCACATAGGGTTTCGAG
Found at i:19116911 original size:174 final size:175
Alignment explanation
Indices: 19116607--19116954 Score: 488
Period size: 174 Copynumber: 2.0 Consensus size: 175
19116597 TTGAGGGCAA
*
19116607 TTATTAAAGGCATTTACAAGCTGTCCTACTTACACCTCTAAGTTCCTTATAGATGTTGCTCAATT
1 TTATTAAAGGCATTTACAAGCTATCCTACTTACACCTCTAAGTTCCTTATAGATGTTGCTCAATT
* *
19116672 TTGTAAATTTTGAGAAAACATCTCTTCAATAGACGGTTTCTTTTCTTGTGGTAGTGGAAGTGGAT
66 TTGTAAAATTTGAGAAAACATCTCTTCAATAGACGGTTTCTTTTCTTGTGGTAGTGAAAGTGGAT
* *
19116737 GGTAATGTTATGGTTG-GGAAACCAAGTGGGTTAATAAGTCTAAG
131 GGTAATATTATGGTTGAGGAAACCAAATGGGTTAATAAGTCTAAG
* * * * *
19116781 TTATTAAGGGCATTTGCAAGCTATCCTACTTGCACCTCTAAGTTTCTTATAGATGTTGC-CTACT
1 TTATTAAAGGCATTTACAAGCTATCCTACTTACACCTCTAAGTTCCTTATAGATGTTGCTC-AAT
* * *
19116845 TTTGTAAAATTTGAGAAAACATCTCTTCAATGGATGGTTTCTTTTCTTAG-GGTGGT-AAAGGTG
65 TTTGTAAAATTTGAGAAAACATCTCTTCAATAGACGGTTTCTTTTCTT-GTGGTAGTGAAA-GTG
* * *
19116908 GATGGTATTATTATGGTTGATGGAAACTAAATGGGTTAATAGGTCTA
128 GATGGTAATATTATGGTTGA-GGAAACCAAATGGGTTAATAAGTCTA
19116955 TTGTAGGAAT
Statistics
Matches: 153, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
173 3 0.02
174 126 0.82
175 1 0.01
176 23 0.15
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (175 bp):
TTATTAAAGGCATTTACAAGCTATCCTACTTACACCTCTAAGTTCCTTATAGATGTTGCTCAATT
TTGTAAAATTTGAGAAAACATCTCTTCAATAGACGGTTTCTTTTCTTGTGGTAGTGAAAGTGGAT
GGTAATATTATGGTTGAGGAAACCAAATGGGTTAATAAGTCTAAG
Found at i:19119085 original size:21 final size:20
Alignment explanation
Indices: 19119061--19119099 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
19119051 AAAAAAGACT
*
19119061 TAAAGATAGAATCACAAATAA
1 TAAAGATAAAATC-CAAATAA
19119082 TAAAGATAAAATCCAAAT
1 TAAAGATAAAATCCAAAT
19119100 TGATTGCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.21
Consensus pattern (20 bp):
TAAAGATAAAATCCAAATAA
Found at i:19121987 original size:16 final size:16
Alignment explanation
Indices: 19121968--19122002 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19121958 ATACAAGCTC
*
19121968 ATACCAATTGTTAAGG
1 ATACCAATTGTTAAAG
19121984 ATACCAATTGTTAAAG
1 ATACCAATTGTTAAAG
19122000 ATA
1 ATA
19122003 TGTTATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (16 bp):
ATACCAATTGTTAAAG
Found at i:19125470 original size:14 final size:15
Alignment explanation
Indices: 19125451--19125492 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
19125441 ACAATTTAGA
*
19125451 ATCAATCAAG-ATAT
1 ATCAATAAAGCATAT
19125465 ATCAATAAAGCATAT
1 ATCAATAAAGCATAT
* *
19125480 AGCAATTAAGCAT
1 ATCAATAAAGCAT
19125493 TTCAACATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (15 bp):
ATCAATAAAGCATAT
Found at i:19137733 original size:114 final size:114
Alignment explanation
Indices: 19137600--19137834 Score: 434
Period size: 114 Copynumber: 2.1 Consensus size: 114
19137590 AAACTAGAAA
19137600 AAAATGTAAATGCATGCCATAAAATGAAAATATAGTAGCTAAATCAAAGTAAAAACAAATTTGAA
1 AAAAT-TAAATGCATGCCATAAAATGAAAATATAGTAGCTAAATCAAAGTAAAAACAAATTTGAA
* *
19137665 GTAAAATTGAACTGATAAAAATGCAAGATACAAATAACATTGCAAAATTG
65 GTAAAATTGAAATGATAAAAATGCAAGATACAAATAACATTGCAAAATCG
19137715 AAAATTAAATGCATGCCATAAAATGAAAATATAGTAGCTAAATCAAAGTAAAAACAAATTTGAAG
1 AAAATTAAATGCATGCCATAAAATGAAAATATAGTAGCTAAATCAAAGTAAAAACAAATTTGAAG
*
19137780 TAAAATTGAAATGATAAAAATGCAAGATACAAATATCATTGCAAAATCG
66 TAAAATTGAAATGATAAAAATGCAAGATACAAATAACATTGCAAAATCG
19137829 AAAATT
1 AAAATT
19137835 CTCGACTAAC
Statistics
Matches: 117, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
114 112 0.96
115 5 0.04
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.24
Consensus pattern (114 bp):
AAAATTAAATGCATGCCATAAAATGAAAATATAGTAGCTAAATCAAAGTAAAAACAAATTTGAAG
TAAAATTGAAATGATAAAAATGCAAGATACAAATAACATTGCAAAATCG
Found at i:19157785 original size:18 final size:18
Alignment explanation
Indices: 19157749--19157787 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19157739 ATCAAGGTTT
*
19157749 TCAAAATTCTAAAAGTCA
1 TCAAAATTATAAAAGTCA
19157767 TCAAATATTATAAAA-TCA
1 TCAAA-ATTATAAAAGTCA
19157785 TCA
1 TCA
19157788 TCTAAAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (18 bp):
TCAAAATTATAAAAGTCA
Found at i:19163503 original size:19 final size:20
Alignment explanation
Indices: 19163458--19163510 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
19163448 TTTGACAAAC
**
19163458 AAGAAAAAAAAATTGAAAATT
1 AAGAAAAAAAAAGAGAAAA-T
19163479 AA-AAAAAAAAAGAGAAAA-
1 AAGAAAAAAAAAGAGAAAAT
*
19163497 AAGAAAAGAAAAGA
1 AAGAAAAAAAAAGA
19163511 AACAAAGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 14 0.50
21 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (20 bp):
AAGAAAAAAAAAGAGAAAAT
Found at i:19163555 original size:29 final size:28
Alignment explanation
Indices: 19163479--19163555 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 28
19163469 ATTGAAAATT
*
19163479 AAAA-AAAAAAAG-AGAAAAAAGAAAAG
1 AAAAGAAACAAAGCAGAAAAAAGAAAAG
* * *
19163505 AAAAGAAACAAAGTAGTGAAAAAGCAAAG
1 AAAAGAAACAAAGCAG-AAAAAAGAAAAG
19163534 AAAAGAAGA-AAAGACAGAAAAA
1 AAAAGAA-ACAAAG-CAGAAAAA
19163556 TGTGCACAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
26 4 0.10
27 7 0.17
28 2 0.05
29 25 0.61
30 3 0.07
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.03
Consensus pattern (28 bp):
AAAAGAAACAAAGCAGAAAAAAGAAAAG
Found at i:19166910 original size:20 final size:18
Alignment explanation
Indices: 19166885--19166938 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 18
19166875 TGTTGAAAGA
19166885 TTTTTTTTATTTTTTTGGT
1 TTTTTTTTATTTTTTT-GT
19166904 TTTTTTTTACTTTTTTTGT
1 TTTTTTTTA-TTTTTTTGT
19166923 TTTTGTTTT-TTTTTTT
1 TTTT-TTTTATTTTTTT
19166939 AAAAGAGCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.21
19 15 0.45
20 11 0.33
ACGTcount: A:0.04, C:0.02, G:0.07, T:0.87
Consensus pattern (18 bp):
TTTTTTTTATTTTTTTGT
Found at i:19166918 original size:26 final size:26
Alignment explanation
Indices: 19166887--19166937 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
19166877 TTGAAAGATT
*
19166887 TTTTTTATTTTTTTGGTTTTTTTTTAC
1 TTTTTT-TGTTTTTGGTTTTTTTTTAC
*
19166914 TTTTTTTGTTTTTGTTTTTTTTTT
1 TTTTTTTGTTTTTGGTTTTTTTTT
19166938 TAAAAGAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.04, C:0.02, G:0.08, T:0.86
Consensus pattern (26 bp):
TTTTTTTGTTTTTGGTTTTTTTTTAC
Found at i:19167157 original size:50 final size:49
Alignment explanation
Indices: 19167083--19167268 Score: 198
Period size: 48 Copynumber: 3.8 Consensus size: 49
19167073 ATTTATTTGA
* *
19167083 AAAATGGCTCCTATAAAATAGGCATCAAACTTTAAAAAAAAATCTGTCTGG
1 AAAAGGGCTTCTATAAAATAGGCATCAAACTTTAAAAAAAAA--TGTCTGG
* ** * *
19167134 AAAA-GGCTTCTATCAAATAGGCATCAAACTTTTTAGAAAAATGTCTAG
1 AAAAGGGCTTCTATAAAATAGGCATCAAACTTTAAAAAAAAATGTCTGG
** * * *
19167182 AAAAAAGCTTTTATAAAATAGGTATCAAACTTTAAAAAAAAA-ATCTGG
1 AAAAGGGCTTCTATAAAATAGGCATCAAACTTTAAAAAAAAATGTCTGG
* *
19167230 AAAAGGGC-TCATATCAAATAGGCATCAAACTTTAGAAAA
1 AAAAGGGCTTC-TATAAAATAGGCATCAAACTTTAAAAAA
19167269 TCTCTATTTG
Statistics
Matches: 112, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
47 1 0.01
48 45 0.40
49 30 0.27
50 32 0.29
51 4 0.04
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (49 bp):
AAAAGGGCTTCTATAAAATAGGCATCAAACTTTAAAAAAAAATGTCTGG
Found at i:19167223 original size:49 final size:48
Alignment explanation
Indices: 19167045--19167268 Score: 184
Period size: 48 Copynumber: 4.6 Consensus size: 48
19167035 GAAAAAACTC
* * *** *
19167045 ATATGAAATAGGCATCAAAATTTTAAAAATTTAT-T-TGAAAAATGGCTC
1 ATATAAAATAGGCATC-AAACTTTAAAAAAAAATGTCTGAAAAA-GGCTT
* *
19167093 CTATAAAATAGGCATCAAACTTTAAAAAAAAATCTGTCTGGAAAAGGCTT
1 ATATAAAATAGGCATCAAACTTTAAAAAAAAA--TGTCTGAAAAAGGCTT
* * ** * *
19167143 CTATCAAATAGGCATCAAACTTTTTAGAAAAATGTCTAGAAAAAAGCTT
1 ATATAAAATAGGCATCAAACTTTAAAAAAAAATGTCT-GAAAAAGGCTT
* * * * *
19167192 TTATAAAATAGGTATCAAACTTTAAAAAAAAA-ATCTGGAAAAGGGCTC
1 ATATAAAATAGGCATCAAACTTTAAAAAAAAATGTCT-GAAAAAGGCTT
* *
19167240 ATATCAAATAGGCATCAAACTTTAGAAAA
1 ATATAAAATAGGCATCAAACTTTAAAAAA
19167269 TCTCTATTTG
Statistics
Matches: 142, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
47 12 0.08
48 55 0.39
49 36 0.25
50 33 0.23
51 6 0.04
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (48 bp):
ATATAAAATAGGCATCAAACTTTAAAAAAAAATGTCTGAAAAAGGCTT
Found at i:19167344 original size:31 final size:31
Alignment explanation
Indices: 19167284--19167391 Score: 85
Period size: 31 Copynumber: 3.5 Consensus size: 31
19167274 ATTTGATGCC
* *
19167284 AACTAATCTAGGCTTAATCCTCCTTGGTGCA
1 AACTAAACTAGGCTTAATCCTCCTAGGTGCA
* *
19167315 AACTAAACT-GGCTTAATTCTCCATAGGTGCC
1 AACTAAACTAGGCTTAATCCTCC-TAGGTGCA
* * * * ** *
19167346 ATCTAATCAAGACTTAATTTTCCTCA-GTGCC
1 AACTAAACTAGGCTTAATCCTCCT-AGGTGCA
19167377 AACTAAACTAGGCTT
1 AACTAAACTAGGCTT
19167392 GATTCTCTTC
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
30 12 0.20
31 37 0.61
32 12 0.20
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (31 bp):
AACTAAACTAGGCTTAATCCTCCTAGGTGCA
Found at i:19167522 original size:61 final size:62
Alignment explanation
Indices: 19167279--19167522 Score: 164
Period size: 62 Copynumber: 4.0 Consensus size: 62
19167269 TCTCTATTTG
* * * * * * * *
19167279 ATGCCAACTAATCTAGGCTTAATCCTCCTTGGTGCAAACTAAACT-GGCTTAATTCTCCAT-A
1 ATGCCAACTAAT-TTGGATTAATTCTTCTTAGTGCCAACTAAACTAGGCTTAATTCTTCTTCA
* * *** * *
19167340 GGTGCCATCTAATCAAGACTTAATT-TTCCTCAGTGCCAACTAAACTAGGCTTGATTC-TCTTCA
1 -ATGCCAACTAATTTGGA-TTAATTCTT-CTTAGTGCCAACTAAACTAGGCTTAATTCTTCTTCA
* *
19167403 ATGCCAACTAATTTGGATTATTTCTTCTTAGTGCCAACTAAACTGAGG-TTAA-TATTCTTCA
1 ATGCCAACTAATTTGGATTAATTCTTCTTAGTGCCAACTAAACT-AGGCTTAATTCTTCTTCA
* * * * *
19167464 GTGCTAGCTAAATTAT-GCTTAATTCTT-TTTGTGCCAACT-AACTAGGCTTAATTCTTCTT
1 ATGCCAACT-AATT-TGGATTAATTCTTCTTAGTGCCAACTAAACTAGGCTTAATTCTTCTT
19167523 GTACTAGTTA
Statistics
Matches: 142, Mismatches: 29, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
59 3 0.02
60 9 0.06
61 57 0.40
62 62 0.44
63 11 0.08
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (62 bp):
ATGCCAACTAATTTGGATTAATTCTTCTTAGTGCCAACTAAACTAGGCTTAATTCTTCTTCA
Found at i:19167724 original size:20 final size:20
Alignment explanation
Indices: 19167685--19167724 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19167675 TTTATAGGTC
*
19167685 CTCATTTTTCTTTTCTTTTT
1 CTCATTTTTCTTTTCGTTTT
* *
19167705 CTCATTTTTTTTTTGGTTTT
1 CTCATTTTTCTTTTCGTTTT
19167725 TTATGGGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (20 bp):
CTCATTTTTCTTTTCGTTTT
Found at i:19169180 original size:26 final size:26
Alignment explanation
Indices: 19169142--19169196 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
19169132 TCTTTCTTCA
19169142 TTTTCTTTCCCTTTCCTTATTTTCTC
1 TTTTCTTTCCCTTTCCTTATTTTCTC
* * *
19169168 TTTT-TTTCACCTTTCTTTTTTTTTTC
1 TTTTCTTTC-CCTTTCCTTATTTTCTC
19169194 TTT
1 TTT
19169197 GAGTGAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTCTTTCCCTTTCCTTATTTTCTC
Found at i:19169628 original size:11 final size:10
Alignment explanation
Indices: 19169613--19169667 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
19169603 TATAACCAAA
19169613 TTTTTTTCTC
1 TTTTTTTCTC
*
19169623 ATTTTTTC-C
1 TTTTTTTCTC
19169632 TTTTTTT-TC
1 TTTTTTTCTC
19169641 TTTTTTTCTTC
1 TTTTTTTC-TC
*
19169652 TTTTTTTTTC
1 TTTTTTTCTC
19169662 TTTTTT
1 TTTTTT
19169668 ACTTTGCATG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
9 15 0.38
10 15 0.38
11 9 0.23
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:19169655 original size:18 final size:19
Alignment explanation
Indices: 19169613--19169672 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
19169603 TATAACCAAA
19169613 TTTTTTTCTCATTTTTTCCT
1 TTTTTTTCT-ATTTTTTCCT
19169633 TTTTTTTCT-TTTTTTCTTCT
1 TTTTTTTCTATTTTTTC--CT
* *
19169653 TTTTTTT-TCTTTTTTACT
1 TTTTTTTCTATTTTTTCCT
19169671 TT
1 TT
19169673 GCATGTCCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 11 0.31
19 1 0.03
20 24 0.67
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTCTATTTTTTCCT
Found at i:19169663 original size:21 final size:20
Alignment explanation
Indices: 19169613--19169667 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
19169603 TATAACCAAA
**
19169613 TTTTTTTCTCATTTTTTCCT
1 TTTTTTTCTTTTTTTTTCCT
*
19169633 TTTTTTTCTTTTTTTCTTCTT
1 TTTTTTTCTTTTTTT-TTCCT
19169654 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
19169668 ACTTTGCATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTTTCCT
Found at i:19172394 original size:37 final size:37
Alignment explanation
Indices: 19172353--19172433 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
19172343 GTGCATCTAT
*
19172353 TATCTATTGAA-ATGTTCACGAAATGGAATACAGGTAC
1 TATCTATT-AAGATGTACACGAAATGGAATACAGGTAC
* * * * *
19172390 TATCTATTAAGATGTACATGAAATTGAATGCATGTAT
1 TATCTATTAAGATGTACACGAAATGGAATACAGGTAC
19172427 TATCTAT
1 TATCTAT
19172434 CAGGATGTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCTATTAAGATGTACACGAAATGGAATACAGGTAC
Found at i:19172441 original size:37 final size:37
Alignment explanation
Indices: 19172372--19172452 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
19172362 AAATGTTCAC
*
19172372 GAAATGGAATACAGGTACTATCTATTAAGATGTACAT
1 GAAATGGAATACAGGTACTATCTATCAAGATGTACAT
* * * * * *
19172409 GAAATTGAATGCATGTATTATCTATCAGGATGTGCAT
1 GAAATGGAATACAGGTACTATCTATCAAGATGTACAT
*
19172446 GAGATGG
1 GAAATGG
19172453 GGTACATGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (37 bp):
GAAATGGAATACAGGTACTATCTATCAAGATGTACAT
Found at i:19172697 original size:125 final size:125
Alignment explanation
Indices: 19172462--19172713 Score: 405
Period size: 125 Copynumber: 2.0 Consensus size: 125
19172452 GGGTACATGT
* *
19172462 ATTATCTTGCTATTTCTAATCATAATAAAAATGCATGAAAGAATGAAATATGAAATATGAAACAA
1 ATTATCTTACTATTTCTAATCATAATAAAAATGCATGAAAGAATGAAATATGAAACATGAAACAA
** *
19172527 CCTTCAAACTCAAAGCCTTTTTTTTAAGGAAGAAAATTTCAAAAAACACATATGAAATGC
66 AATTCAAACTCAAAGCCTTTTTTTTAAGGAAGAAAAATTCAAAAAACACATATGAAATGC
* * *
19172587 ATTATCTTATTATTTCTAATCATGATAAAAATGTATGAAAGAATGAAATATGAAACATGAAACAA
1 ATTATCTTACTATTTCTAATCATAATAAAAATGCATGAAAGAATGAAATATGAAACATGAAACAA
* *
19172652 AATTCAAACTCAAATCTTTTTTTTTAAAGGAAGAAAAATTCAAAAAACACATATGAAATGC
66 AATTCAAACTCAAAGCCTTTTTTTT-AAGGAAGAAAAATTCAAAAAACACATATGAAATGC
19172713 A
1 A
19172714 ATCACATAGA
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
125 81 0.70
126 35 0.30
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (125 bp):
ATTATCTTACTATTTCTAATCATAATAAAAATGCATGAAAGAATGAAATATGAAACATGAAACAA
AATTCAAACTCAAAGCCTTTTTTTTAAGGAAGAAAAATTCAAAAAACACATATGAAATGC
Found at i:19173578 original size:30 final size:25
Alignment explanation
Indices: 19173542--19173621 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
19173532 AATATATAAT
* * *
19173542 AAATGATATAATTAAAATATTCATG
1 AAATGACATGATTAAAATATGCATG
19173567 AAATGACATGATTAAAATATGCATG
1 AAATGACATGATTAAAATATGCATG
* *
19173592 AAATGACATAATTAAAAAATGCATG
1 AAATGACATGATTAAAATATGCATG
19173617 AAATG
1 AAATG
19173622 TAAGACACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (25 bp):
AAATGACATGATTAAAATATGCATG
Found at i:19173763 original size:20 final size:20
Alignment explanation
Indices: 19173718--19173783 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
19173708 AATCAAAACT
*
19173718 TTTTTTTTCATATTTTT-AAA
1 TTTTTTTT-ATTTTTTTCAAA
*
19173738 TATTTTTTTATTTTTTTCTAA
1 T-TTTTTTTATTTTTTTCAAA
19173759 TTTTTCTTT-TTTTTTTCAACA
1 TTTTT-TTTATTTTTTTCAA-A
19173780 TTTT
1 TTTT
19173784 CACTTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 21 0.54
21 18 0.46
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTTTATTTTTTTCAAA
Found at i:19174291 original size:11 final size:11
Alignment explanation
Indices: 19174275--19174300 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19174265 ATGGTCCTAT
19174275 TTTACTTAAAG
1 TTTACTTAAAG
19174286 TTTACTTAAAG
1 TTTACTTAAAG
19174297 TTTA
1 TTTA
19174301 AAATTAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTACTTAAAG
Found at i:19174331 original size:18 final size:18
Alignment explanation
Indices: 19174308--19174354 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
19174298 TTAAAATTAA
19174308 TTCCTTTTCTTCTTT-TTT
1 TTCCTTTT-TTCTTTCTTT
*
19174326 TTCCTTTTTTTTTTCTTT
1 TTCCTTTTTTCTTTCTTT
19174344 TTCCCTTTTTT
1 TT-CCTTTTTT
19174355 GTCATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 13 0.50
19 8 0.31
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTCCTTTTTTCTTTCTTT
Found at i:19174335 original size:12 final size:11
Alignment explanation
Indices: 19174312--19174345 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
19174302 AATTAATTCC
19174312 TTTTCTTCTTTT
1 TTTTCTT-TTTT
19174324 TTTTCCTTTTTT
1 TTTT-CTTTTTT
19174336 TTTTCTTTTT
1 TTTTCTTTTT
19174346 CCCTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.29
12 12 0.57
13 3 0.14
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:19176230 original size:17 final size:17
Alignment explanation
Indices: 19176182--19176239 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
19176172 CTAAACTCAA
19176182 ACCCTAAACC--CCT-G
1 ACCCTAAACCAACCTAG
*
19176196 ACCATAAACCCTAACCTAG
1 ACCCTAAA-CC-AACCTAG
*
19176215 ACCCTAAACCAACCTAA
1 ACCCTAAACCAACCTAG
19176232 ACCCTAAA
1 ACCCTAAA
19176240 ATCATTCTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.19
15 2 0.06
17 14 0.39
18 5 0.14
19 8 0.22
ACGTcount: A:0.41, C:0.41, G:0.03, T:0.14
Consensus pattern (17 bp):
ACCCTAAACCAACCTAG
Found at i:19184073 original size:1 final size:1
Alignment explanation
Indices: 19184067--19184098 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
19184057 CATCAATTAC
19184067 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19184099 CTTATTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19189646 original size:18 final size:19
Alignment explanation
Indices: 19189623--19189676 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
19189613 ATATCAAATT
19189623 TCTTAAAAT-TTAAAAAAA
1 TCTTAAAATATTAAAAAAA
19189641 TCTT-AAATATTAAAAAAA
1 TCTTAAAATATTAAAAAAA
* *
19189659 TCCTAAAAAATCTAAAAA
1 TCTTAAAATAT-TAAAAA
19189677 TTTAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 16 0.52
19 5 0.16
20 6 0.19
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (19 bp):
TCTTAAAATATTAAAAAAA
Found at i:19189667 original size:28 final size:27
Alignment explanation
Indices: 19189635--19189694 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
19189625 TTAAAATTTA
*
19189635 AAAAAATCT-TAAATATTAAAAAAATCC
1 AAAAAATCTAAAAAT-TTAAAAAAATCC
*
19189662 TAAAAAATCTAAAAATTTAAAATAATCC
1 -AAAAAATCTAAAAATTTAAAAAAATCC
19189690 AAAAA
1 AAAAA
19189695 CTACGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 20 0.69
29 4 0.14
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (27 bp):
AAAAAATCTAAAAATTTAAAAAAATCC
Found at i:19189703 original size:28 final size:27
Alignment explanation
Indices: 19189635--19189712 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
19189625 TTAAAATTTA
** *
19189635 AAAAAATCTTAAATATTAAAAAAATCCT
1 AAAAAATCGAAAAT-TTAAAATAATCCT
*
19189663 AAAAAATCTAAAAATTTAAAATAATCC-
1 AAAAAATC-GAAAATTTAAAATAATCCT
* *
19189690 AAAAACTACGAAAATTGAAAATA
1 AAAAAAT-CGAAAATTTAAAATA
19189713 TTAGTTTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 18 0.43
28 20 0.48
29 4 0.10
ACGTcount: A:0.63, C:0.10, G:0.03, T:0.24
Consensus pattern (27 bp):
AAAAAATCGAAAATTTAAAATAATCCT
Found at i:19189798 original size:19 final size:19
Alignment explanation
Indices: 19189739--19189800 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
19189729 TTTGGGAAGA
* *
19189739 TTTTAATTTTTATATATTT
1 TTTTAATTTTTTTAGATTT
* * *
19189758 TTTGAA-ATATTTAGGA-TT
1 TTTTAATTTTTTTA-GATTT
19189776 TTTTAATTTTTTTAGATTT
1 TTTTAATTTTTTTAGATTT
19189795 TTTTAA
1 TTTTAA
19189801 ATTTGTATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 13 0.41
19 19 0.59
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.66
Consensus pattern (19 bp):
TTTTAATTTTTTTAGATTT
Found at i:19189963 original size:25 final size:27
Alignment explanation
Indices: 19189935--19189985 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
19189925 TTTTAAAAAA
19189935 AATTGGTTTT-TATTTTA-AT-TTTTTG
1 AATT-GTTTTATATTTTATATATTTTTG
*
19189960 AATTTTTTTATATTTTATATATTTTT
1 AATTGTTTTATATTTTATATATTTTT
19189986 TCATTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 4 0.18
25 11 0.50
26 2 0.09
27 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (27 bp):
AATTGTTTTATATTTTATATATTTTTG
Found at i:19189965 original size:9 final size:8
Alignment explanation
Indices: 19189947--19190030 Score: 51
Period size: 8 Copynumber: 9.6 Consensus size: 8
19189937 TTGGTTTTTA
19189947 TTTTAATT
1 TTTTAATT
19189955 TTTTGAATTT
1 TTTT-AA-TT
19189965 TTTTATATT
1 TTTTA-ATT
*
19189974 TTATATATT
1 TTTTA-ATT
*
19189983 TTTTCATT
1 TTTTAATT
*
19189991 TTTCATATT
1 TTTTA-ATT
**
19190000 TTTTAAGC
1 TTTTAATT
19190008 TTTTACGATT
1 TTTTA--ATT
*
19190018 TTTTAAAT
1 TTTTAATT
19190026 TTTTA
1 TTTTA
19190031 TTATAATTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
8 23 0.39
9 23 0.39
10 13 0.22
ACGTcount: A:0.24, C:0.05, G:0.04, T:0.68
Consensus pattern (8 bp):
TTTTAATT
Found at i:19189983 original size:19 final size:19
Alignment explanation
Indices: 19189961--19190003 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
19189951 AATTTTTTGA
*
19189961 ATTTTTTTATATTTT-ATAT
1 ATTTTTTCAT-TTTTCATAT
19189980 ATTTTTTCATTTTTCATAT
1 ATTTTTTCATTTTTCATAT
19189999 -TTTTT
1 ATTTTT
19190004 AAGCTTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTTTTTCATTTTTCATAT
Found at i:19190040 original size:12 final size:12
Alignment explanation
Indices: 19190023--19190090 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
19190013 CGATTTTTTA
19190023 AATTTTTATTAT
1 AATTTTTATTAT
19190035 AATTTTTATT-T
1 AATTTTTATTAT
* *
19190046 TATTTTTGTT-T
1 AATTTTTATTAT
* * *
19190057 ATTTTATTTTTTAG
1 A-ATT-TTTATTAT
*
19190071 AATTTTTATTAA
1 AATTTTTATTAT
19190083 AATTTTTA
1 AATTTTTA
19190091 GATTTTATGA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 10 0.23
12 26 0.59
13 7 0.16
14 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
AATTTTTATTAT
Found at i:19190059 original size:15 final size:15
Alignment explanation
Indices: 19190039--19190067 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19190029 TATTATAATT
19190039 TTTATTTTATTTTTG
1 TTTATTTTATTTTTG
19190054 TTTATTTTATTTTT
1 TTTATTTTATTTTT
19190068 TAGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTATTTTATTTTTG
Found at i:19191504 original size:18 final size:17
Alignment explanation
Indices: 19191479--19191515 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
19191469 CTCCTTAGCC
*
19191479 TTTACCTAAGCCTTTAT
1 TTTACCTAAACCTTTAT
19191496 TTTATCCTAAACCTTTAT
1 TTTA-CCTAAACCTTTAT
19191514 TT
1 TT
19191516 GATTTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.24, C:0.22, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTACCTAAACCTTTAT
Found at i:19193194 original size:26 final size:28
Alignment explanation
Indices: 19193165--19193226 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 28
19193155 TATTCTAAGC
* *
19193165 TTTCTTTAAGTTCTCTTGTT-TT-AGTT
1 TTTCTTTAAGTTCTCATGTTCTTAAGGT
*
19193191 TTTCTTT-AGTTTTCATGTTCTTAAGGT
1 TTTCTTTAAGTTCTCATGTTCTTAAGGT
19193218 TTTCTTTAA
1 TTTCTTTAA
19193227 ATTGTTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 10 0.33
26 9 0.30
27 10 0.33
28 1 0.03
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.63
Consensus pattern (28 bp):
TTTCTTTAAGTTCTCATGTTCTTAAGGT
Found at i:19193224 original size:27 final size:25
Alignment explanation
Indices: 19193165--19193225 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
19193155 TATTCTAAGC
* *
19193165 TTTCTTTAAGTTCTCTTGTTTTAGTT
1 TTTCTTT-AGTTCTCATGTTTTAGGT
*
19193191 TTTCTTTAGTTTTCATGTTCTTAAGGT
1 TTTCTTTAGTTCTCATGTT-TT-AGGT
19193218 TTTCTTTA
1 TTTCTTTA
19193226 AATTGTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 10 0.33
26 9 0.30
27 11 0.37
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.64
Consensus pattern (25 bp):
TTTCTTTAGTTCTCATGTTTTAGGT
Found at i:19201763 original size:67 final size:67
Alignment explanation
Indices: 19201655--19201789 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
19201645 TATCAAAAAG
**
19201655 GGGGAGATTGTTAGCCTTGAATTGATCCTTATTTTGAAATGACAAAATGTTAAAGATAAATAAAC
1 GGGGAGATTGTTAGCCTTGAATTGATCCTTATTTTGAAATGACAAAACATTAAAGATAAATAAAC
19201720 TT
66 TT
*
19201722 GGGGAGATTGTTAGCCTTGAATTGATCCTTGTTTTGAAATGACAAAACATTAAAGATAAATAAAC
1 GGGGAGATTGTTAGCCTTGAATTGATCCTTATTTTGAAATGACAAAACATTAAAGATAAATAAAC
19201787 TT
66 TT
19201789 G
1 G
19201790 ATCAAAATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (67 bp):
GGGGAGATTGTTAGCCTTGAATTGATCCTTATTTTGAAATGACAAAACATTAAAGATAAATAAAC
TT
Found at i:19206506 original size:14 final size:16
Alignment explanation
Indices: 19206482--19206513 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19206472 AGAATATAAT
19206482 AATATATT-AAAATTA
1 AATATATTAAAAATTA
19206497 AATA-ATTAAAAATTA
1 AATATATTAAAAATTA
19206512 AA
1 AA
19206514 AAAATTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.19
15 13 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATATTAAAAATTA
Found at i:19211023 original size:145 final size:145
Alignment explanation
Indices: 19210847--19211127 Score: 526
Period size: 145 Copynumber: 1.9 Consensus size: 145
19210837 AAGTAGGCTT
* *
19210847 AACTCTATTTTTTATACCCTTGCTTATTTATTTATCTCAAATAAGTTAAATTTAGAATTATTAAA
1 AACTATATTTTTTATACCCTTGCTTATTTATTTATCTCAAATAAATTAAATTTAGAATTATTAAA
*
19210912 GGATACTGTACAACTTTTGAATTTTATGAATTATTATTATGCATCTTAATTGAAATATTAATTAG
66 GGATACTGTACAACTTTTGAATTTTATGAATTATTATTAAGCATCTTAATTGAAATATTAATTAG
19210977 TTTTCAAAAAAAAAA
131 TTTTCAAAAAAAAAA
19210992 AACTATATTTTTTATACCCTTGCTTATTTATTTATCTCAAATAAATTAAATTTAGAATTATTAAA
1 AACTATATTTTTTATACCCTTGCTTATTTATTTATCTCAAATAAATTAAATTTAGAATTATTAAA
*
19211057 GGATACTGTACAACTTTTGAATTTTATGAATTATTGTTAAGCATCTTAATTGAAATATTAATTAG
66 GGATACTGTACAACTTTTGAATTTTATGAATTATTATTAAGCATCTTAATTGAAATATTAATTAG
19211122 TTTTCA
131 TTTTCA
19211128 TAAACAAATA
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 132 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (145 bp):
AACTATATTTTTTATACCCTTGCTTATTTATTTATCTCAAATAAATTAAATTTAGAATTATTAAA
GGATACTGTACAACTTTTGAATTTTATGAATTATTATTAAGCATCTTAATTGAAATATTAATTAG
TTTTCAAAAAAAAAA
Found at i:19223734 original size:13 final size:13
Alignment explanation
Indices: 19223718--19223742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19223708 AATTTGTGAT
19223718 AAAAATTTATCAA
1 AAAAATTTATCAA
19223731 AAAAATTTATCA
1 AAAAATTTATCA
19223743 CAGATAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTTATCAA
Found at i:19224140 original size:234 final size:235
Alignment explanation
Indices: 19223719--19224781 Score: 1082
Period size: 235 Copynumber: 4.5 Consensus size: 235
19223709 ATTTGTGATA
* * * *
19223719 AAAATTTATCAAAAAAATTTATCACAGATAAAATTCTAAATTGGTGACAAAATTATAACATCACC
1 AAAATCTATAAAAAAAATTTATCACAGATAAAATTTTAAATTAGTGACAAAATTATAACATCACC
*
19223784 TAAA-ATAAAAAATGTCATAAAAAAATTT-TCACCAAATAAATTTGAT-GGTAAAAGTTTGTGAC
66 TAAATAAAAAAAATGTCAT-AAAAAATTTCTCACCAAATAAATTTG-TCGGTAAAAGTTTGTGAC
* * * * * ** *
19223846 ATTTATGTTATCGTAATATAACATCA-AACATTAATGTGACAAAATTATAATGTCATTAATAGTT
129 ATTTATGTTATCATCATATAACACCATAA-ATTGATATGATGAAATTACAATGTCATTAATAGTT
* * *
19223910 AAC-AAAGTGTTGAATTTGTGACAAAAATTAATAACATTACCT
193 AACTAAAGTGTTCAATTTGTGACAAAAATTAATAATATCACCT
* * * * * * *
19223952 -AAGTCTATCAAAAAAATTTGTCACAAATAAAAATTTAAATTCGTGACAAAATTATAACATCACA
1 AAAATCTATAAAAAAAATTTATCACAGATAAAATTTTAAATTAGTGACAAAATTATAACATCACC
* * * * *
19224016 TAAGATAAAAAAAATGTCATAAAAAATTTCCCATCAAATAAAATTGTCGGTAAAAGTTTATGAAA
66 TAA-ATAAAAAAAATGTCATAAAAAATTTCTCACCAAATAAATTTGTCGGTAAAAGTTTGTGACA
* * * *
19224081 TTTATGTTATCATCATATAACACTATAAATTGACATAATGAAATTACAATGTTATTAATAGTTAA
130 TTTATGTTATCATCATATAACACCATAAATTGATATGATGAAATTACAATGTCATTAATAGTTAA
* * *
19224146 CTAGAGTATTCAATTTGTGACAAAAATTAATAATGTCACCT
195 CTAAAGTGTTCAATTTGTGACAAAAATTAATAATATCACCT
* * * * *
19224187 AAAATCTATAAAAAAACATTTGTCAAAGATAAAATTTTAAATTAGTGAC--ACTTGTAACGTCAC
1 AAAATCTATAAAAAAA-ATTTATCACAGATAAAATTTTAAATTAGTGACAAAATTATAACATCAC
* * * * * **
19224250 TTAAAT-TAAAAAATGTCACAAACAAATTTTTCACCAAATAAATTTGACAATAAAAGTTTGTGAC
65 CTAAATAAAAAAAATGTCATAAA-AAATTTCTCACCAAATAAATTTGTCGGTAAAAGTTTGTGAC
** * * * *
19224314 ATTTATGTTATTGTCATATAATACCATAAAAT-AAAGGTGATGAAATTGCAATGTCATTAATAGT
129 ATTTATGTTATCATCATATAACACCATAAATTGATA--TGATGAAATTACAATGTCATTAATAGT
* * * * *
19224378 TAAATAAAGTGTT-ACATTTATGACAAAAATTGATAATATTAACT
192 TAACTAAAGTGTTCA-ATTTGTGACAAAAATTAATAATATCACCT
* * * * *
19224422 AAAATCTATTAGAAAAATTCATTACAGATAAAATTTTAAATTAGCGACAAAATT-TAA-AGGTCA
1 AAAATCTATAAAAAAAATTTATCACAGATAAAATTTTAAATTAGTGACAAAATTATAACA--TCA
* ** * * * * *
19224485 CCTAAAATAAAAAACATCACA-AAAAAATTTTTCACCTAATAATTTTGGCGATAAAAGTTTGTGA
64 CCT-AAATAAAAAAAATGTCATAAAAAATTTCTCACCAAATAAATTTGTCGGTAAAAGTTTGTGA
* * * * * *
19224549 CATTTATATTATTATCATATAACACCACACATTGATGTGATGAAATTGCAATGTCATTAATAGTT
128 CATTTATGTTATCATCATATAACACCATAAATTGATATGATGAAATTACAATGTCATTAATAGTT
**
19224614 AACTAAAGTGTTCAATTTGTGACAAAAATTAATAATGCCACCT
193 AACTAAAGTGTTCAATTTGTGACAAAAATTAATAATATCACCT
* * ** *
19224657 AAAATTTATAAAAAAAAATTCATCACAGATAAAATTTTAAATT-GACAACAAAATTATAACATCT
1 AAAATCTAT-AAAAAAAATTTATCACAGATAAAATTTTAAATTAG-TGACAAAATTATAACATCA
*
19224721 CCTAAA-ATAAAAAAATGTCATAAAAATATTTCCCACCAAATAAATTTGGT-GGTAAAA-TTTG
64 CCTAAATA-AAAAAAATGTCATAAAAA-ATTTCTCACCAAATAAATTT-GTCGGTAAAAGTTTG
19224782 GTAGCAAGAT
Statistics
Matches: 684, Mismatches: 118, Indels: 53
0.80 0.14 0.06
Matches are distributed among these distances:
232 59 0.09
233 27 0.04
234 182 0.27
235 207 0.30
236 138 0.20
237 61 0.09
238 10 0.01
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.32
Consensus pattern (235 bp):
AAAATCTATAAAAAAAATTTATCACAGATAAAATTTTAAATTAGTGACAAAATTATAACATCACC
TAAATAAAAAAAATGTCATAAAAAATTTCTCACCAAATAAATTTGTCGGTAAAAGTTTGTGACAT
TTATGTTATCATCATATAACACCATAAATTGATATGATGAAATTACAATGTCATTAATAGTTAAC
TAAAGTGTTCAATTTGTGACAAAAATTAATAATATCACCT
Found at i:19224610 original size:470 final size:467
Alignment explanation
Indices: 19223719--19224768 Score: 1239
Period size: 470 Copynumber: 2.2 Consensus size: 467
19223709 ATTTGTGATA
* * *
19223719 AAAATTTATCAAAAAAATTTATCACAGATAAAATTCTAAATTGGTGACAAAATTATAACATCACC
1 AAAATTTATAAAAAAAATTTATCACAGATAAAATTTTAAATTAGTGAC-AAATTATAACATCACC
* ***
19223784 TAAAATAAAAAATGTCATAAAAAAATTTTCACCAAATAAATTTGATGGTAAAAGTTTGTGACATT
65 TAAAATAAAAAATGTCACAAAAAAATTTTCACCAAATAAATTTGACAATAAAAGTTTGTGACATT
* * * * *
19223849 TATGTTATCGTAATATAACATCAAACATTAATGTGACAAAATTATAATGTCATTAATAGTTAACA
130 TATGTTATCGTAATATAACACCAAAAATAAAGGTGACAAAATTACAATGTCATTAATAGTTAACA
* * * **
19223914 AAGTGTTGAATTTGTGACAAAAATTAATAACATTACCTAAGTCTATCAAAAAAATTTGTCACAAA
195 AAGTGTTGAATTTATGACAAAAATTAATAACATTAACTAAATCTATCAAAAAAATTCATCACAAA
* * * **
19223979 TAAAAATTTAAATTCGTGACAAAATTATAACATCACATAAGATAAAAAAAATGTCATAAAAAATT
260 TAAAAATTTAAATTAGCGACAAAATTATAACATCACATAAAATAAAAAAAATCACATAAAAAATT
* * * * * *
19224044 TCCCATCAAATAAAATTGTCGGTAAAAGTTTATGAAATTTATGTTATCATCATATAACACTATAA
325 TCCCACCAAATAAAATTGGCGATAAAAGTTTATGAAATTTATATTATCATCATATAACACCACAA
* *
19224109 ATTGACATAATGAAATTACAATGTTATTAATAGTTAACTAGAGTATTCAATTTGTGACAAAAATT
390 ATTGACATAATGAAATTACAATGTCATTAATAGTTAACTAAAGTATTCAATTTGTGACAAAAATT
*
19224174 AATAATGTCACCT
455 AATAATGCCACCT
* * * * * * *
19224187 AAAATCTATAAAAAAACATTTGTCAAAGATAAAATTTTAAATTAGTGAC-ACTTGTAACGTCACT
1 AAAATTTATAAAAAAA-ATTTATCACAGATAAAATTTTAAATTAGTGACAAATTATAACATCACC
* *
19224251 TAAATTAAAAAATGTCACAAACAAATTTTTCACCAAATAAATTTGACAATAAAAGTTTGTGACAT
65 TAAAATAAAAAATGTCACAAA-AAAATTTTCACCAAATAAATTTGACAATAAAAGTTTGTGACAT
* * * ** *
19224316 TTATGTTATTGTCATATAATACCATAAAATAAAGGTGATGAAATTGCAATGTCATTAATAGTTAA
129 TTATGTTATCGTAATATAACACCA-AAAATAAAGGTGACAAAATTACAATGTCATTAATAGTT-A
* * * * * *
19224381 ATAAAGTGTT-ACATTTATGACAAAAATTGATAATATTAACTAAAATCTATTAGAAAAATTCATT
192 ACAAAGTGTTGA-ATTTATGACAAAAATTAATAACATTAACT-AAATCTATCAAAAAAATTCATC
* * * *
19224445 ACAGATAAAATTTTAAATTAGCGACAAAATT-TAA-AGGTCACCTAAAATAAAAAACATCACA-A
255 ACAAATAAAAATTTAAATTAGCGACAAAATTATAACA--TCACATAAAATAAAAAAAATCACATA
** * ** * * *
19224507 AAAAATTTTTCACCTAATAATTTTGGCGATAAAAGTTTGTGACATTTATATTATTATCATATAAC
318 AAAAATTTCCCACCAAATAAAATTGGCGATAAAAGTTTATGAAATTTATATTATCATCATATAAC
* ** * * *
19224572 ACCACACATTGATGTGATGAAATTGCAATGTCATTAATAGTTAACTAAAGTGTTCAATTTGTGAC
383 ACCACAAATTGACATAATGAAATTACAATGTCATTAATAGTTAACTAAAGTATTCAATTTGTGAC
19224637 AAAAATTAATAATGCCACCT
448 AAAAATTAATAATGCCACCT
* ** *
19224657 AAAATTTATAAAAAAAAATTCATCACAGATAAAATTTTAAATT-GACAACAAAATTATAACATCT
1 AAAATTTAT-AAAAAAAATTTATCACAGATAAAATTTTAAATTAG-TGAC-AAATTATAACATCA
* * *
19224721 CCTAAAATAAAAAAATGTCATAAAAATATTTCCCACCAAATAAATTTG
63 CCTAAAAT-AAAAAATGTCACAAAAAAATTT-TCACCAAATAAATTTG
19224769 GTGGTAAAAT
Statistics
Matches: 482, Mismatches: 86, Indels: 23
0.82 0.15 0.04
Matches are distributed among these distances:
467 30 0.06
468 73 0.15
469 62 0.13
470 199 0.41
471 69 0.14
472 20 0.04
473 29 0.06
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (467 bp):
AAAATTTATAAAAAAAATTTATCACAGATAAAATTTTAAATTAGTGACAAATTATAACATCACCT
AAAATAAAAAATGTCACAAAAAAATTTTCACCAAATAAATTTGACAATAAAAGTTTGTGACATTT
ATGTTATCGTAATATAACACCAAAAATAAAGGTGACAAAATTACAATGTCATTAATAGTTAACAA
AGTGTTGAATTTATGACAAAAATTAATAACATTAACTAAATCTATCAAAAAAATTCATCACAAAT
AAAAATTTAAATTAGCGACAAAATTATAACATCACATAAAATAAAAAAAATCACATAAAAAATTT
CCCACCAAATAAAATTGGCGATAAAAGTTTATGAAATTTATATTATCATCATATAACACCACAAA
TTGACATAATGAAATTACAATGTCATTAATAGTTAACTAAAGTATTCAATTTGTGACAAAAATTA
ATAATGCCACCT
Found at i:19227386 original size:7 final size:7
Alignment explanation
Indices: 19227374--19227399 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19227364 GGGATTAAAT
19227374 TTTATGA
1 TTTATGA
19227381 TTTATGA
1 TTTATGA
19227388 TTTATGA
1 TTTATGA
19227395 TTTAT
1 TTTAT
19227400 TGCAATCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TTTATGA
Found at i:19234029 original size:23 final size:23
Alignment explanation
Indices: 19234001--19234046 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
19233991 AAGCTATTGA
19234001 GACTAGCACATGGTTATGCTCTT
1 GACTAGCACATGGTTATGCTCTT
19234024 GACTAGCACATGGTTATGCTCTT
1 GACTAGCACATGGTTATGCTCTT
19234047 ACTTATGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (23 bp):
GACTAGCACATGGTTATGCTCTT
Found at i:19241655 original size:24 final size:23
Alignment explanation
Indices: 19241628--19241678 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
19241618 TTAAGCCGTT
*
19241628 TTTTACTTTTTATTTTTTCTTTTC
1 TTTTACTGTTTATTTTTT-TTTTC
* *
19241652 TTTTGCTGTTTCTTTTTTTTTTC
1 TTTTACTGTTTATTTTTTTTTTC
19241675 TTTT
1 TTTT
19241679 TCACTTCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTACTGTTTATTTTTTTTTTC
Found at i:19241680 original size:17 final size:17
Alignment explanation
Indices: 19241641--19241680 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
19241631 TACTTTTTAT
19241641 TTTTTCTTTTCTTTTGC
1 TTTTTCTTTTCTTTTGC
* * *
19241658 TGTTTCTTTTTTTTTTC
1 TTTTTCTTTTCTTTTGC
19241675 TTTTTC
1 TTTTTC
19241681 ACTTCCTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTGC
Found at i:19244470 original size:13 final size:13
Alignment explanation
Indices: 19244452--19244490 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
19244442 CCACATTGAT
19244452 AGTTGTTGGCTGC
1 AGTTGTTGGCTGC
19244465 AGTTGTTGGCTGC
1 AGTTGTTGGCTGC
*
19244478 GGTTGTTGGCTGC
1 AGTTGTTGGCTGC
19244491 CATAACTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.05, C:0.15, G:0.41, T:0.38
Consensus pattern (13 bp):
AGTTGTTGGCTGC
Found at i:19244709 original size:13 final size:12
Alignment explanation
Indices: 19244684--19244731 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
19244674 CTGTTTGTTA
19244684 TTTTATTTTATT
1 TTTTATTTTATT
19244696 TTTTATTCTTATT
1 TTTTATT-TTATT
*
19244709 TTTTATTTTGAGT
1 TTTTATTTT-ATT
19244722 TTTTATTTTA
1 TTTTATTTTA
19244732 AGATAATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
12 10 0.30
13 23 0.70
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:19244727 original size:20 final size:18
Alignment explanation
Indices: 19244684--19244731 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
19244674 CTGTTTGTTA
19244684 TTTTATTTTATTTTTTAT
1 TTTTATTTTATTTTTTAT
*
19244702 TCTTATTTT-TTATTTTGAGT
1 TTTTATTTTATT-TTTT-A-T
19244722 TTTTATTTTA
1 TTTTATTTTA
19244732 AGATAATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 2 0.08
18 12 0.50
19 1 0.04
20 9 0.38
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTATTTTATTTTTTAT
Found at i:19246053 original size:52 final size:52
Alignment explanation
Indices: 19245952--19246053 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
19245942 AAACAAAAAG
* * * *
19245952 AATTTCTAAATAGGCCCAAATAGTGAAAAATTTAGAAATTTCGAGAAAAACA
1 AATTTCTAAATAGACCCAAATAGTGAAAAATTTAGAAATTCCAAAAAAAACA
* *
19246004 AATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAA-TCCAACAAAAAA
1 AATTTCTAAATAGACCCAAATAGTGAAAAATTTAGAAATTCCAA-AAAAAA
19246054 AAAAAGAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 3 0.07
52 40 0.93
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.25
Consensus pattern (52 bp):
AATTTCTAAATAGACCCAAATAGTGAAAAATTTAGAAATTCCAAAAAAAACA
Found at i:19249992 original size:8 final size:7
Alignment explanation
Indices: 19249981--19250085 Score: 52
Period size: 9 Copynumber: 13.3 Consensus size: 7
19249971 TGAATGAATG
19249981 AAAGAAGA
1 AAAGAA-A
19249989 AAAGAAA
1 AAAGAAA
*
19249996 AGAGAAA
1 AAAGAAA
19250003 ATAAGAAAA
1 A-AAG-AAA
19250012 AAAGATGAA
1 AAAGA--AA
19250021 AAA-AAA
1 AAAGAAA
19250027 GGAAA-AAA
1 --AAAGAAA
19250035 AAAGAAA
1 AAAGAAA
19250042 AAATGAAA
1 AAA-GAAA
*
19250050 GAATAAAAA
1 -AA-AGAAA
19250059 AAAGATGAA
1 AAAGA--AA
19250068 AAAGAAA
1 AAAGAAA
19250075 GGAAAGAAA
1 --AAAGAAA
19250084 AA
1 AA
19250086 CTCAAATTGA
Statistics
Matches: 79, Mismatches: 4, Indels: 29
0.71 0.04 0.26
Matches are distributed among these distances:
6 5 0.06
7 21 0.27
8 24 0.30
9 28 0.35
10 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (7 bp):
AAAGAAA
Found at i:19249995 original size:12 final size:11
Alignment explanation
Indices: 19249980--19250075 Score: 56
Period size: 10 Copynumber: 8.5 Consensus size: 11
19249970 ATGAATGAAT
19249980 GAAAGAAGAAAA
1 GAAAGAA-AAAA
*
19249992 GAAAAGAGAAAA
1 G-AAAGAAAAAA
*
19250004 -TAAGAAAAAA
1 GAAAGAAAAAA
*
19250014 -AGATGAAAAAA
1 GA-AAGAAAAAA
*
19250025 -AAGGAAAAAA
1 GAAAGAAAAAA
19250035 -AAAGAAAAAA
1 GAAAGAAAAAA
19250045 TGAAAGAATAAAA
1 -GAAAGAA-AAAA
*
19250058 AAAAGATGAAAAA
1 GAAAGA--AAAAA
19250071 GAAAG
1 GAAAG
19250076 GAAAGAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 25 0.37
11 9 0.13
12 16 0.24
13 17 0.25
14 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (11 bp):
GAAAGAAAAAA
Found at i:19250016 original size:31 final size:31
Alignment explanation
Indices: 19249981--19250059 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
19249971 TGAATGAATG
* *
19249981 AAAGAAGAAAAGAAAA-GAGAAAATAAGAAAA
1 AAAGAAGAAAA-AAAAGGAAAAAAAAAGAAAA
*
19250012 AAAGATGAAAAAAAAGGAAAAAAAAAGAAAA
1 AAAGAAGAAAAAAAAGGAAAAAAAAAGAAAA
*
19250043 AATGAAAGAATAAAAAA
1 AAAG-AAGAA-AAAAAA
19250060 AAGATGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 4 0.10
31 26 0.65
32 4 0.10
33 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (31 bp):
AAAGAAGAAAAAAAAGGAAAAAAAAAGAAAA
Found at i:19250021 original size:11 final size:10
Alignment explanation
Indices: 19249985--19250060 Score: 71
Period size: 10 Copynumber: 7.2 Consensus size: 10
19249975 TGAATGAAAG
*
19249985 AAGAAAAGAA
1 AAGAAAAAAA
* *
19249995 AAGAGAAAAT
1 AAGAAAAAAA
19250005 AAGAAAAAAA
1 AAGAAAAAAA
*
19250015 GATGAAAAAAA
1 -AAGAAAAAAA
*
19250026 AGGAAAAAAA
1 AAGAAAAAAA
19250036 AAGAAAAAATGA
1 AAGAAAAAA--A
19250048 AAGAATAAAAA
1 AAGAA-AAAAA
19250059 AA
1 AA
19250061 AGATGAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
10 32 0.59
11 12 0.22
12 6 0.11
13 4 0.07
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:19250061 original size:19 final size:17
Alignment explanation
Indices: 19250019--19250070 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
19250009 AAAAAAGATG
*
19250019 AAAAAAAAGGAAAAAAA
1 AAAAAAAATGAAAAAAA
19250036 AAGAAAAAATGAAAGAATAA
1 AA-AAAAAATGAAA-AA-AA
*
19250056 AAAAAAGATGAAAAA
1 AAAAAAAATGAAAAA
19250071 GAAAGGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 2 0.07
18 12 0.40
19 12 0.40
20 4 0.13
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (17 bp):
AAAAAAAATGAAAAAAA
Found at i:19251182 original size:21 final size:22
Alignment explanation
Indices: 19251153--19251259 Score: 128
Period size: 21 Copynumber: 4.7 Consensus size: 22
19251143 AAGTCCTAAA
19251153 TTTTCAAATGAGAATCTTTGAG
1 TTTTCAAATGAGAATCTTTGAG
19251175 TTTT-AAATGAGAATCTTTAAGATG
1 TTTTCAAATGAGAATCTTT--GA-G
19251199 TTTTCAAATGAGAATCTTTGAG
1 TTTTCAAATGAGAATCTTTGAG
* *
19251221 TCTTC-AATGAGAATCTTTAAAATG
1 TTTTCAAATGAGAATCTTT--GA-G
19251245 TTTTCAAATGAGAAT
1 TTTTCAAATGAGAAT
19251260 TTTTAAGACT
Statistics
Matches: 74, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
21 27 0.36
22 9 0.12
23 5 0.07
24 10 0.14
25 23 0.31
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (22 bp):
TTTTCAAATGAGAATCTTTGAG
Found at i:19251206 original size:46 final size:46
Alignment explanation
Indices: 19251153--19251289 Score: 202
Period size: 46 Copynumber: 3.0 Consensus size: 46
19251143 AAGTCCTAAA
*
19251153 TTTTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGATG
1 TTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGATG
* *
19251199 TTTTCAAATGAGAATCTTTGAGTCTTCAATGAGAATCTTTAAAATG
1 TTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGATG
* * * * *
19251245 TTTTCAAATGAGAATTTTTAAGACTTAGATGAAAATCTTTAAGAT
1 TTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAT
19251290 ATTATTTGAG
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (46 bp):
TTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGATG
Found at i:19251208 original size:25 final size:24
Alignment explanation
Indices: 19251153--19251267 Score: 143
Period size: 25 Copynumber: 5.0 Consensus size: 24
19251143 AAGTCCTAAA
19251153 TTTTCAAATGAGAATCTTT--GAG
1 TTTTCAAATGAGAATCTTTAAGAG
19251175 TTTT-AAATGAGAATCTTTAAGATG
1 TTTTCAAATGAGAATCTTTAAGA-G
19251199 TTTTCAAATGAGAATCTTT--GAG
1 TTTTCAAATGAGAATCTTTAAGAG
* *
19251221 TCTTC-AATGAGAATCTTTAAAATG
1 TTTTCAAATGAGAATCTTTAAGA-G
*
19251245 TTTTCAAATGAGAATTTTTAAGA
1 TTTTCAAATGAGAATCTTTAAGA
19251268 CTTAGATGAA
Statistics
Matches: 80, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
21 27 0.34
22 9 0.11
23 5 0.06
24 10 0.12
25 29 0.36
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.41
Consensus pattern (24 bp):
TTTTCAAATGAGAATCTTTAAGAG
Found at i:19251363 original size:21 final size:21
Alignment explanation
Indices: 19251294--19251366 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
19251284 TAAGATATTA
19251294 TTTGAGTCTTAAATGAGAATCT
1 TTTGAGTCTTAAATGAGAAT-T
* * * * * *
19251316 TTAAGACATTTTCAAATAAGGACT
1 TT-TGA-GTCTT-AAATGAGAATT
19251340 TTTGAGTCTTAAATGAGAATT
1 TTTGAGTCTTAAATGAGAATT
19251361 TTTGAG
1 TTTGAG
19251367 ATGTGAAACC
Statistics
Matches: 36, Mismatches: 12, Indels: 7
0.65 0.22 0.13
Matches are distributed among these distances:
21 14 0.39
22 5 0.14
23 4 0.11
24 6 0.17
25 7 0.19
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (21 bp):
TTTGAGTCTTAAATGAGAATT
Found at i:19252155 original size:13 final size:12
Alignment explanation
Indices: 19252116--19252166 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
19252106 CTGTTTGTTA
*
19252116 TTTT-ATTTTAC
1 TTTTAATTTTAT
19252127 TTTT-ATTCTTAT
1 TTTTAATT-TTAT
19252139 TTTTAATTTTAAT
1 TTTTAATTTT-AT
19252152 TTTTAATTTTAT
1 TTTTAATTTTAT
19252164 TTT
1 TTT
19252167 AAGATAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
11 7 0.19
12 14 0.39
13 15 0.42
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTAATTTTAT
Found at i:19252168 original size:18 final size:18
Alignment explanation
Indices: 19252116--19252168 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
19252106 CTGTTTGTTA
19252116 TTTT-ATTTTACTTTT-AT
1 TTTTAATTTTA-TTTTAAT
* *
19252133 TCTTATTTTTAATTTTAAT
1 TTTTAATTTT-ATTTTAAT
19252152 TTTTAATTTTATTTTAA
1 TTTTAATTTTATTTTAA
19252169 GATAATATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 3 0.10
18 15 0.52
19 11 0.38
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTAATTTTATTTTAAT
Found at i:19252931 original size:8 final size:8
Alignment explanation
Indices: 19252920--19252971 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
19252910 CTATTTTTCG
19252920 TATTTTTT
1 TATTTTTT
19252928 TATTTTTT
1 TATTTTTT
19252936 TATTTATTT
1 TATTT-TTT
19252945 TA-TTTTT
1 TATTTTTT
*
19252952 TATGTATTT
1 TAT-TTTTT
*
19252961 TACTTTTT
1 TATTTTTT
19252969 TAT
1 TAT
19252972 GTATTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 5 0.14
8 21 0.57
9 11 0.30
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (8 bp):
TATTTTTT
Found at i:19252933 original size:17 final size:17
Alignment explanation
Indices: 19252911--19252978 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
19252901 GCTGTTTCAC
19252911 TATTTTTCGTATTT-TTT
1 TATTTTT-GTATTTATTT
*
19252928 TATTTTTTTATTTATTT
1 TATTTTTGTATTTATTT
*
19252945 TATTTTT-TATGTATTT
1 TATTTTTGTATTTATTT
*
19252961 TACTTTTT-TATGTATTT
1 TA-TTTTTGTATTTATTT
19252978 T
1 T
19252979 TTTGCATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
16 15 0.32
17 32 0.68
ACGTcount: A:0.16, C:0.03, G:0.04, T:0.76
Consensus pattern (17 bp):
TATTTTTGTATTTATTT
Found at i:19252961 original size:9 final size:8
Alignment explanation
Indices: 19252920--19252978 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 8
19252910 CTATTTTTCG
*
19252920 TATTTTTT
1 TATTATTT
*
19252928 TATTTTTT
1 TATTATTT
19252936 TATTTATTT
1 TA-TTATTT
19252945 TATT-TTT
1 TATTATTT
19252952 TATGTATTT
1 TAT-TATTT
19252961 TACTT-TTT
1 TA-TTATTT
19252969 TATGTATTT
1 TAT-TATTT
19252978 T
1 T
19252979 TTTGCATGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
7 7 0.16
8 19 0.43
9 17 0.39
10 1 0.02
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (8 bp):
TATTATTT
Found at i:19253003 original size:11 final size:11
Alignment explanation
Indices: 19252987--19253029 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
19252977 TTTTTGCATG
19252987 AAAAAAATTAA
1 AAAAAAATTAA
19252998 AAAAAAA-TAA
1 AAAAAAATTAA
*
19253008 AAAAAAAGTAA
1 AAAAAAATTAA
19253019 TAAAATAAATT
1 -AAAA-AAATT
19253030 TTGGGAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 10 0.36
11 10 0.36
12 4 0.14
13 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:19264101 original size:22 final size:22
Alignment explanation
Indices: 19264073--19264116 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19264063 CATCCAACAC
* *
19264073 TTGCTTAAATATTGTCAATGGA
1 TTGCTTAAAGATTATCAATGGA
19264095 TTGCTTAAAGATTATCAATGGA
1 TTGCTTAAAGATTATCAATGGA
19264117 CGTGCAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
TTGCTTAAAGATTATCAATGGA
Found at i:19268141 original size:20 final size:22
Alignment explanation
Indices: 19268092--19268143 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
19268082 TTATTACGGA
19268092 TCAGAT-TCCGATAAAACATAAC
1 TCAGATATCC-ATAAAACATAAC
19268114 TCAG--ATCCATAAAAC-TAAC
1 TCAGATATCCATAAAACATAAC
19268133 -CAGATATCCAT
1 TCAGATATCCAT
19268144 CATCATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 3 0.11
19 4 0.15
20 13 0.48
21 3 0.11
22 4 0.15
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (22 bp):
TCAGATATCCATAAAACATAAC
Found at i:19271642 original size:18 final size:17
Alignment explanation
Indices: 19271621--19271660 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
19271611 TCAAAGGATC
19271621 CCAAAAGCCCAACAAAGT
1 CCAAAAGCCCAA-AAAGT
* *
19271639 CCAAAAGCTCTAAAAGT
1 CCAAAAGCCCAAAAAGT
19271656 CCAAA
1 CCAAA
19271661 TTTTTATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.50, C:0.30, G:0.10, T:0.10
Consensus pattern (17 bp):
CCAAAAGCCCAAAAAGT
Found at i:19273094 original size:44 final size:44
Alignment explanation
Indices: 19273044--19273134 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 44
19273034 ACAATTAGAC
* * * *
19273044 TTTAAAGTATTAGATGTTTAAAGACAACATCAACAAAACATCAT
1 TTTAAAGTATGAGATGTTCAAAGACAACAGCAACAAAACACCAT
* * *
19273088 TTTAAAGTCTGAGATGTTCAAAGACAATAGCAACATAACACCAT
1 TTTAAAGTATGAGATGTTCAAAGACAACAGCAACAAAACACCAT
19273132 TTT
1 TTT
19273135 TAAACTCTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (44 bp):
TTTAAAGTATGAGATGTTCAAAGACAACAGCAACAAAACACCAT
Found at i:19273476 original size:32 final size:32
Alignment explanation
Indices: 19273435--19273499 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
19273425 TCACATCTCC
19273435 TTGTTTTTAATTATTACTGGTGCTTTCTTGAT
1 TTGTTTTTAATTATTACTGGTGCTTTCTTGAT
19273467 TTGTTTTTAATTATTACTGGTGCTTTCTTGAT
1 TTGTTTTTAATTATTACTGGTGCTTTCTTGAT
19273499 T
1 T
19273500 CTTGGCAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.60
Consensus pattern (32 bp):
TTGTTTTTAATTATTACTGGTGCTTTCTTGAT
Found at i:19276677 original size:47 final size:47
Alignment explanation
Indices: 19276608--19276702 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
19276598 AAAACTGTTT
19276608 TAACTCAAACATCTAAGCCTCGATATTTAGTTATATTTCTATCACTC
1 TAACTCAAACATCTAAGCCTCGATATTTAGTTATATTTCTATCACTC
*
19276655 TAACTCAAACATCTATGCCTCGATATTTAGTTATATTTCTATCACTC
1 TAACTCAAACATCTAAGCCTCGATATTTAGTTATATTTCTATCACTC
19276702 T
1 T
19276703 TTCTCTTATC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (47 bp):
TAACTCAAACATCTAAGCCTCGATATTTAGTTATATTTCTATCACTC
Found at i:19280187 original size:15 final size:16
Alignment explanation
Indices: 19280167--19280207 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
19280157 GTTTTTTTAG
19280167 AAAGAAA-ATTAATTT
1 AAAGAAATATTAATTT
*
19280182 AAAGAAATATTTATTT
1 AAAGAAATATTAATTT
19280198 --AGAAATATTA
1 AAAGAAATATTA
19280208 TGAACATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 7 0.30
16 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (16 bp):
AAAGAAATATTAATTT
Found at i:19280963 original size:14 final size:14
Alignment explanation
Indices: 19280941--19280996 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
19280931 CGATTTCCCC
*
19280941 TAGGGTTTTTATTT
1 TAGGGTTTTAATTT
*
19280955 TAGGTTTTTAATTT
1 TAGGGTTTTAATTT
*
19280969 TAGGGTTTCAATTT
1 TAGGGTTTTAATTT
* *
19280983 TAAGGTTTCAATTT
1 TAGGGTTTTAATTT
19280997 AAAGATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.21, C:0.04, G:0.18, T:0.57
Consensus pattern (14 bp):
TAGGGTTTTAATTT
Found at i:19281146 original size:21 final size:21
Alignment explanation
Indices: 19281116--19281165 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
19281106 TTAAAAATTT
19281116 TATTATTATTATCATT-TATTAA
1 TATT-TTATTATCATTAT-TTAA
*
19281138 TATTTTATTATTATTATTTAA
1 TATTTTATTATCATTATTTAA
19281159 TAATTTT
1 T-ATTTT
19281166 TCAACATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTATTATCATTATTTAA
Found at i:19281150 original size:24 final size:23
Alignment explanation
Indices: 19281118--19281166 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
19281108 AAAAATTTTA
*
19281118 TTATTATTATCATTTATTAATATT
1 TTATTATTATCATTTAATAAT-TT
*
19281142 TTATTATTATTATTTAATAATTT
1 TTATTATTATCATTTAATAATTT
19281165 TT
1 TT
19281167 CAACATCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATTATTATCATTTAATAATTT
Found at i:19281226 original size:51 final size:52
Alignment explanation
Indices: 19281129--19281230 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 52
19281119 TATTATTATC
* * *
19281129 ATTTATTAATATTTTATTATTATTATTTAATAATTTTTCAACATCTAGGCAG
1 ATTTATTAATATTTTATAAATATGATTTAATAATTTTTCAACATCTAGGCAG
*
19281181 ATTTATTAAT-TTTTA-AAATATGATTT-ATAATTCTTTCCAATATCTAGGCA
1 ATTTATTAATATTTTATAAATATGATTTAATAATT-TTT-CAACATCTAGGCA
19281231 AGAATTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
49 6 0.14
50 11 0.25
51 17 0.39
52 10 0.23
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (52 bp):
ATTTATTAATATTTTATAAATATGATTTAATAATTTTTCAACATCTAGGCAG
Found at i:19281425 original size:3 final size:3
Alignment explanation
Indices: 19281417--19281448 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19281407 AAGCATGATT
19281417 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
19281449 TATTATTATT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:19281453 original size:3 final size:3
Alignment explanation
Indices: 19281447--19281493 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
19281437 AATAATAATA
19281447 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19281494 GCAACAAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19281552 original size:13 final size:14
Alignment explanation
Indices: 19281534--19281563 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
19281524 TAAAGTTTTA
19281534 TTTATTTA-TATAT
1 TTTATTTATTATAT
19281547 TTTATTTATTATAT
1 TTTATTTATTATAT
19281561 TTT
1 TTT
19281564 TTGTTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTTATTATAT
Done.