Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 127 of 185
Found at i:39030928 original size:16 final size:17
Alignment explanation
Indices: 39030898--39030930 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39030888 TATACAAGAG
*
39030898 AAAATTATTACTTCAAA
1 AAAATTAATACTTCAAA
39030915 AAAATTAATA-TTCAAA
1 AAAATTAATACTTCAAA
39030931 TATGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAATACTTCAAA
Found at i:39041802 original size:31 final size:31
Alignment explanation
Indices: 39041735--39041814 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
39041725 AAGTTTAAAT
** * *
39041735 TTTAATATGAAAATAATTGTCAAGTTGATGA
1 TTTAATATGAAAATAATTAACAAATTGAGGA
39041766 TTTAATATGAAAATAATTAACAAATTGAAGGA
1 TTTAATATGAAAATAATTAACAAATTG-AGGA
39041798 -TTAATATGGATAAATAA
1 TTTAATAT-GA-AAATAA
39041815 AATTTAAGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 31 0.74
32 5 0.12
33 6 0.14
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.35
Consensus pattern (31 bp):
TTTAATATGAAAATAATTAACAAATTGAGGA
Found at i:39056861 original size:15 final size:15
Alignment explanation
Indices: 39056836--39056870 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
39056826 GACTCTATTT
*
39056836 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
39056850 TAATTAATATTAAGA
1 TAATTAATATTAAGA
39056865 TAATTA
1 TAATTA
39056871 TTAAGGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:39060747 original size:7 final size:7
Alignment explanation
Indices: 39060731--39060807 Score: 72
Period size: 7 Copynumber: 11.0 Consensus size: 7
39060721 CAACACAATT
39060731 TTTATT-
1 TTTATTA
39060737 TTTATTA
1 TTTATTA
39060744 TTTATTA
1 TTTATTA
39060751 TTTATTA
1 TTTATTA
39060758 TTTATT-
1 TTTATTA
* *
39060764 TTTCTTTC
1 TTT-ATTA
39060772 TTTACTTTA
1 TTTA--TTA
39060781 TTTATTA
1 TTTATTA
39060788 CTTTA-T-
1 -TTTATTA
39060794 TTTATTA
1 TTTATTA
39060801 TTTATTA
1 TTTATTA
39060808 CTGATTTGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
5 4 0.07
6 10 0.17
7 33 0.55
8 7 0.12
9 6 0.10
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Found at i:39060790 original size:12 final size:12
Alignment explanation
Indices: 39060773--39060806 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
39060763 TTTTCTTTCT
39060773 TTACTTTATTTA
1 TTACTTTATTTA
39060785 TTACTTTATTTTA
1 TTACTTTA-TTTA
39060798 TTA-TTTATT
1 TTACTTTATT
39060807 ACTGATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:39061696 original size:101 final size:101
Alignment explanation
Indices: 39061511--39061702 Score: 228
Period size: 101 Copynumber: 1.9 Consensus size: 101
39061501 AAACGTGACT
* * * * *
39061511 GACTGAGTAATCGGGGTAGGGTGCTTGAGTTGTCATCCTATTTCGCGTCAAAAGGTTCAATGTGT
1 GACTGAGTAACCGAGGTAGGGTGCTTGAGCTGTCATCCTATTTCGCGTCAAAAGGTTCAATATAT
*
39061576 TCTTAAGAAAAAATTATAATAAATAAGGAATCCGCTG
66 TCTAAAGAAAAAA-TATAATAAATAAGGAATCCGCTG
* * * *
39061613 GACTGAGTAACCGAGGTGGGGTGCTTG-GCTGTTATCTCTCTTT-GCGTCAAAAGGTTCAGTATA
1 GACTGAGTAACCGAGGTAGGGTGCTTGAGCTGTCATC-CTATTTCGCGTCAAAAGGTTCAATATA
*
39061676 TTCCTAAAGCATAAAA-ATAATAAATAA
65 TT-CTAAAG-AAAAAATATAATAAATAA
39061703 ATAAAAATCA
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
101 37 0.49
102 34 0.45
103 5 0.07
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (101 bp):
GACTGAGTAACCGAGGTAGGGTGCTTGAGCTGTCATCCTATTTCGCGTCAAAAGGTTCAATATAT
TCTAAAGAAAAAATATAATAAATAAGGAATCCGCTG
Found at i:39061703 original size:4 final size:4
Alignment explanation
Indices: 39061690--39061735 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
39061680 TAAAGCATAA
39061690 AAAT -AAT AAAT AAAT -AA- AAAT CAAAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AAAT AAAT AAA
39061736 AAGAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 7 0.19
4 26 0.70
6 4 0.11
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:39061707 original size:24 final size:24
Alignment explanation
Indices: 39061686--39061731 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
39061676 TTCCTAAAGC
39061686 ATAAAAAT-AATAAATAAATAAAA
1 ATAAAAATAAATAAATAAATAAAA
*
39061709 ATCAAAATAAATAAATAAATAAA
1 ATAAAAATAAATAAATAAATAAA
39061732 TAAAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (24 bp):
ATAAAAATAAATAAATAAATAAAA
Found at i:39061708 original size:16 final size:17
Alignment explanation
Indices: 39061686--39061735 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 17
39061676 TTCCTAAAGC
39061686 ATAAAAATAATAAATAA
1 ATAAAAATAATAAATAA
*
39061703 ATAAAAATCA-AAATAA
1 ATAAAAATAATAAATAA
*
39061719 ATAAATA-AATAAATAA
1 ATAAAAATAATAAATAA
39061735 A
1 A
39061736 AAGAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.03
16 19 0.66
17 9 0.31
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
ATAAAAATAATAAATAA
Found at i:39061743 original size:28 final size:27
Alignment explanation
Indices: 39061690--39061752 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
39061680 TAAAGCATAA
**
39061690 AAATAATAAATAAATAAAAATCAAAAT
1 AAATAATAAATAAATAAAAAGAAAAAT
*
39061717 AAATAAATAAATAAATAAAAAGAAAAAG
1 AAAT-AATAAATAAATAAAAAGAAAAAT
39061745 AATATAAT
1 AA-ATAAT
39061753 TTGGTGACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 25 0.81
29 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.21
Consensus pattern (27 bp):
AAATAATAAATAAATAAAAAGAAAAAT
Found at i:39066539 original size:23 final size:23
Alignment explanation
Indices: 39066491--39066545 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
39066481 ATTTTATGCA
* *
39066491 TGCAAGTGTTAGTGGCACTACGG
1 TGCAAGTGATAGTGGCACTACAG
**
39066514 TGCAAGTGATAGTGGCACTTTAG
1 TGCAAGTGATAGTGGCACTACAG
39066537 TGCAAGTGA
1 TGCAAGTGA
39066546 CAGAAGCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (23 bp):
TGCAAGTGATAGTGGCACTACAG
Found at i:39070389 original size:18 final size:18
Alignment explanation
Indices: 39070368--39070402 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39070358 ATTCTGTAAT
39070368 TAGTTTAAATTTAATTTC
1 TAGTTTAAATTTAATTTC
*
39070386 TAGTTTAAATTTGATTT
1 TAGTTTAAATTTAATTT
39070403 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (18 bp):
TAGTTTAAATTTAATTTC
Found at i:39072991 original size:28 final size:29
Alignment explanation
Indices: 39072930--39072987 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
39072920 AAATATTTTT
* * *
39072930 AATTAATAATTCCTTTATTTATATAAATA
1 AATTAATAATTCATATAATTATATAAATA
39072959 AATTAATAATT-ATATAATTATAT-AATA
1 AATTAATAATTCATATAATTATATAAATA
39072986 AA
1 AA
39072988 ATTATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.23
28 9 0.35
29 11 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTAATAATTCATATAATTATATAAATA
Found at i:39072992 original size:13 final size:14
Alignment explanation
Indices: 39072948--39072995 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 14
39072938 ATTCCTTTAT
39072948 TTATATAA-ATAAA
1 TTATATAATATAAA
39072961 TTA-ATAATTATATAA
1 TTATATAA-TATA-AA
39072976 TTATATAATA-AAA
1 TTATATAATATAAA
39072989 TTATATA
1 TTATATA
39072996 TTTTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.13
13 12 0.39
14 4 0.13
15 7 0.23
16 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:39094217 original size:44 final size:44
Alignment explanation
Indices: 39094125--39094217 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
39094115 ATCTCAAGGT
* *
39094125 CCATATTTATAACATAGCAATTAAAGAAGAATTGACAGAAAAGT
1 CCATGTTTATAACATAGCAATTAAAGAAGAATTGACAGAAAAGA
* * *
39094169 CCATGTTTATAACATGGCAATT-AAGAAAGAATTGACGGAACAGA
1 CCATGTTTATAACATAGCAATTAAAG-AAGAATTGACAGAAAAGA
39094213 CCATG
1 CCATG
39094218 GTTGGACCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.07
44 40 0.93
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (44 bp):
CCATGTTTATAACATAGCAATTAAAGAAGAATTGACAGAAAAGA
Found at i:39094229 original size:44 final size:44
Alignment explanation
Indices: 39094135--39094231 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
39094125 CCATATTTAT
* * * *
39094135 AACATAGCAATTAAAGAAGAATTGACAGAAAAGTCCATGTTTAT
1 AACATGGCAATTAAAGAAGAATTGACAGAAAAGACCATGGTTAG
* * *
39094179 AACATGGCAATT-AAGAAAGAATTGACGGAACAGACCATGGTTGG
1 AACATGGCAATTAAAG-AAGAATTGACAGAAAAGACCATGGTTAG
*
39094223 ACCATGGCA
1 AACATGGCA
39094232 GTAAGTGTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 3 0.07
44 41 0.93
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (44 bp):
AACATGGCAATTAAAGAAGAATTGACAGAAAAGACCATGGTTAG
Found at i:39094299 original size:50 final size:51
Alignment explanation
Indices: 39094238--39094469 Score: 253
Period size: 50 Copynumber: 4.7 Consensus size: 51
39094228 GGCAGTAAGT
*
39094238 GTGCCAATGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGA-GGA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATGGA
* * *
39094288 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGACC-ATCGA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATGGA
* * * *
39094338 GTGCTAGTGTAAGACCATATCTGGGACATGGCATCGGCACGGACAGA-GAA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATGGA
* * * * * * *
39094388 GAGTCAGTGTAAGACCATGTATGGGACATGGCATCGACACCGA--TATGTGA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATG-GA
* *
39094438 -TCCCA-TGTAAGACCATATCTGGGATATGGCAT
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCAT
39094470 TGGCGTCCTA
Statistics
Matches: 152, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
48 25 0.16
49 4 0.03
50 122 0.80
51 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (51 bp):
GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATGGA
Found at i:39096106 original size:16 final size:17
Alignment explanation
Indices: 39096085--39096135 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
39096075 TTATTCTTAT
39096085 TTTTC-TCTTTTTTCCC
1 TTTTCATCTTTTTTCCC
*
39096101 TTTTCTTCTTCTTTT--C
1 TTTTCATCTT-TTTTCCC
39096117 TTTTCATCTTTTTTCCC
1 TTTTCATCTTTTTTCCC
39096134 TT
1 TT
39096136 CCAAACAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 15 0.50
17 7 0.23
18 4 0.13
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCATCTTTTTTCCC
Found at i:39097359 original size:6 final size:6
Alignment explanation
Indices: 39097348--39097383 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
39097338 GATTTTCTCC
39097348 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
39097384 GAGAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:39111621 original size:17 final size:16
Alignment explanation
Indices: 39111590--39111663 Score: 55
Period size: 17 Copynumber: 4.5 Consensus size: 16
39111580 TTATCAAATA
39111590 AATAAA-AATTT--TT
1 AATAAATAATTTAATT
39111603 AATATAATAATTTAATT
1 AATA-AATAATTTAATT
* *
39111620 AATAAATATCTTTATTTTT
1 AATAAATA-ATTTA--ATT
*
39111639 AATATATTAATTTAATT
1 AATA-AATAATTTAATT
39111656 AATAAATA
1 AATAAATA
39111664 TCTTTTACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
13 4 0.09
14 2 0.04
15 5 0.11
16 7 0.15
17 16 0.34
19 10 0.21
20 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (16 bp):
AATAAATAATTTAATT
Found at i:39111644 original size:36 final size:36
Alignment explanation
Indices: 39111597--39111668 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
39111587 ATAAATAAAA
39111597 ATTTTTAATATAATAATTTAATTAATAAATATCTTT
1 ATTTTTAATATAATAATTTAATTAATAAATATCTTT
*
39111633 ATTTTTAATATATTAATTTAATTAATAAATATCTTT
1 ATTTTTAATATAATAATTTAATTAATAAATATCTTT
39111669 TACTTAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (36 bp):
ATTTTTAATATAATAATTTAATTAATAAATATCTTT
Found at i:39111664 original size:19 final size:19
Alignment explanation
Indices: 39111610--39111664 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
39111600 TTTAATATAA
39111610 TAATTTAATTAATAAATATCT
1 TAATTTAATTAATAAATA--T
*
39111631 TTATTT--TTAAT--ATAT
1 TAATTTAATTAATAAATAT
39111646 TAATTTAATTAATAAATAT
1 TAATTTAATTAATAAATAT
39111665 CTTTTACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
15 6 0.21
17 8 0.29
19 9 0.32
21 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATTTAATTAATAAATAT
Found at i:39111806 original size:17 final size:16
Alignment explanation
Indices: 39111775--39111818 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
39111765 GATTTATTTA
39111775 ATAATATAATATCATT
1 ATAATATAATATCATT
*
39111791 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
39111808 AATTATATAAT
1 -ATAATATAAT
39111819 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:39117687 original size:46 final size:44
Alignment explanation
Indices: 39117583--39117690 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
39117573 TGTCTTTGAC
** * * *
39117583 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
39117627 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
39117673 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
39117691 TTTCTGCTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:39133804 original size:42 final size:42
Alignment explanation
Indices: 39133705--39133814 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
39133695 TCTCATAAGC
* * * * * *
39133705 TTCAGTTAA-CTCATATGAGTTTCTGTTTAACCCTATTGGTT
1 TTCAGTTAAGCACTTATGAGCTTCTGTTCAACCCTATCGGGT
*
39133746 TTCAGTTAAGCTCTTATGAGCTTCTGTTCAACCCT-TACGGGT
1 TTCAGTTAAGCACTTATGAGCTTCTGTTCAACCCTAT-CGGGT
* * *
39133788 TTCCGTTTAGCACTTATGTGCTTCTGT
1 TTCAGTTAAGCACTTATGAGCTTCTGT
39133815 GTAGCCTTCG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 10 0.17
42 48 0.83
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
TTCAGTTAAGCACTTATGAGCTTCTGTTCAACCCTATCGGGT
Found at i:39137375 original size:61 final size:61
Alignment explanation
Indices: 39137306--39137425 Score: 231
Period size: 61 Copynumber: 2.0 Consensus size: 61
39137296 AAAAATCAGC
*
39137306 TCAATTGAGAGGTTAATTGAGTAGGGATGGAATTATCATTTATTGAAAGCTTAGGGAAAAA
1 TCAATTGAGAGGTTAATTGAGTAGGGATGAAATTATCATTTATTGAAAGCTTAGGGAAAAA
39137367 TCAATTGAGAGGTTAATTGAGTAGGGATGAAATTATCATTTATTGAAAGCTTAGGGAAA
1 TCAATTGAGAGGTTAATTGAGTAGGGATGAAATTATCATTTATTGAAAGCTTAGGGAAA
39137426 GAATGGTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (61 bp):
TCAATTGAGAGGTTAATTGAGTAGGGATGAAATTATCATTTATTGAAAGCTTAGGGAAAAA
Found at i:39144877 original size:29 final size:30
Alignment explanation
Indices: 39144819--39144877 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
39144809 AATTTAGATT
* * *
39144819 AAATCAAAATTTCATGTATAAATTTGCACA
1 AAATCAAAATTTCATATATAAAATTACACA
*
39144849 AAATCAAAGTTT-ATATATAAAATTACACA
1 AAATCAAAATTTCATATATAAAATTACACA
39144878 TCAAACCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTACACA
Found at i:39150868 original size:3 final size:3
Alignment explanation
Indices: 39150860--39150894 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
39150850 AAAATGCACA
*
39150860 AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39150895 AAGGAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:39152508 original size:39 final size:40
Alignment explanation
Indices: 39152444--39152532 Score: 119
Period size: 39 Copynumber: 2.2 Consensus size: 40
39152434 TAAAAAATAT
* * *
39152444 TTATATTAAAAAAATAATCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAAAAAATCATAAATAAAATAAATATTTTA
39152484 TTATATTAAAAAATAAAAT-A-AAATAAAATAAATATTTTA
1 TTATATTAAAAAA-AAAATCATAAATAAAATAAATATTTTA
*
39152523 TTGTATTAAA
1 TTATATTAAA
39152533 TATAATATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 26 0.59
40 14 0.32
41 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAAAAAAATCATAAATAAAATAAATATTTTA
Found at i:39153989 original size:27 final size:27
Alignment explanation
Indices: 39153932--39153995 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
39153922 GGTCTGCCAT
* * ** *
39153932 AGGCGGCACCAAAGGTGCCAGTGGCAG
1 AGGCGACACCAAAGGTGCCACTACCAC
*
39153959 AGGCGACACCAAAGGTGCCTCTACCAC
1 AGGCGACACCAAAGGTGCCACTACCAC
39153986 AGGCGACACC
1 AGGCGACACC
39153996 TGTGCCATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.31, T:0.08
Consensus pattern (27 bp):
AGGCGACACCAAAGGTGCCACTACCAC
Found at i:39154197 original size:20 final size:19
Alignment explanation
Indices: 39154137--39154198 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
39154127 GGTGCCAAAA
39154137 AAAGA-AAAGAAAAAGAGAG
1 AAAGAGAAAGAAAAAGA-AG
*
39154156 AAAGAGAATAGAGAATAG-AG
1 AAAGAGAA-AGA-AAAAGAAG
*
39154176 AAAGGAGAAAGAAAGAGAAG
1 AAA-GAGAAAGAAAAAGAAG
39154196 AAA
1 AAA
39154199 AAAAATAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 9 0.25
20 15 0.42
21 8 0.22
22 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (19 bp):
AAAGAGAAAGAAAAAGAAG
Found at i:39154551 original size:37 final size:38
Alignment explanation
Indices: 39154509--39154607 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 38
39154499 TTTTACACTA
**
39154509 TATTATTGTTAGTTATTATTTTTAGTAAAACCCTA-AT
1 TATTATTGTTAGTTATTATTTTTAGTAAAAAACTATAT
39154546 TATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTAT
1 TATTATTGTTAG-T--TATTATTTTTAGTAAAAAACTA-TAT
39154588 TATTATTTTGTTAGTTATTA
1 TATTA--TTGTTAGTTATTA
39154608 GGATTAGTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
37 12 0.23
38 1 0.02
40 20 0.38
41 5 0.09
42 7 0.13
43 1 0.02
44 7 0.13
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (38 bp):
TATTATTGTTAGTTATTATTTTTAGTAAAAAACTATAT
Found at i:39154589 original size:76 final size:78
Alignment explanation
Indices: 39154384--39154615 Score: 229
Period size: 76 Copynumber: 2.9 Consensus size: 78
39154374 GTTTAGTTAT
* *
39154384 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTCTGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-TGGTTAGTTAT
39154449 TAGGATTAGTAAAAACCC
61 TAGGATTAGTAAAAACCC
* * *** * **
39154467 TAATTATAATT-TTAGTTAGTATGATTGTTAGTTTTTACACTA-TATTATT-GTTAGTTATTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGGTTAGTTATTAGG
*
39154529 TTTAGT-AAAACCC
65 ATTAGTAAAAACCC
* *
39154542 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATTATTTTGTTAGTTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-TTGGTTAGTTATT
39154607 AGGATTAGT
62 AGGATTAGT
39154616 GGTTAAATGT
Statistics
Matches: 120, Mismatches: 21, Indels: 18
0.75 0.13 0.11
Matches are distributed among these distances:
75 21 0.17
76 34 0.28
77 1 0.01
78 3 0.03
79 10 0.08
80 4 0.03
81 16 0.13
82 18 0.15
83 13 0.11
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.50
Consensus pattern (78 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGGTTAGTTATTAGGA
TTAGTAAAAACCC
Found at i:39159718 original size:157 final size:158
Alignment explanation
Indices: 39159362--39159743 Score: 617
Period size: 157 Copynumber: 2.4 Consensus size: 158
39159352 TTATTTTCGG
* * * * *
39159362 ATTTATCTTATTTTTGAATTTTATTGCTTTCAAAAAATATATTATTTTTGTATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
39159427 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTATTTTTTTATATAAATTTAGTA
66 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTG-ATTTTTTTATATAAATTTAGTA
*
39159492 AAAAACCCTTATTTTGACCATTTGTTCGT
130 AAAAACCCTTATTTTGACCATTTGTTCAT
* *
39159521 ATTTTTCTTATTTTCAGATTTTACTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
*
39159586 TATTATTTTAGTACATAATA-TTTGAAATGTATTATTTTAGTG-TTTTTTTATATAAATTTAGTA
66 TATTATTTTAGTACATAA-AGTTTGAAATGTATTAATTTAGTGATTTTTTTATATAAATTTAGTA
* *
39159649 AAAAACTCTTATTTTGGTCC-TTTGTTCAT
130 AAAAACCCTTATTTT-GACCATTTGTTCAT
39159678 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
39159743 T
66 T
39159744 TTGGTTCCGT
Statistics
Matches: 208, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
157 107 0.51
158 3 0.01
159 97 0.47
160 1 0.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (158 bp):
ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGATTTTTTTATATAAATTTAGTAA
AAAACCCTTATTTTGACCATTTGTTCAT
Found at i:39161925 original size:17 final size:16
Alignment explanation
Indices: 39161903--39161939 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
39161893 AAATATACTA
*
39161903 TTTTCGTTTTTTATTT
1 TTTTCGTATTTTATTT
39161919 CTTTTCGTATTTTATTT
1 -TTTTCGTATTTTATTT
39161936 TTTT
1 TTTT
39161940 AATAAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTCGTATTTTATTT
Found at i:39161932 original size:157 final size:157
Alignment explanation
Indices: 39161383--39161917 Score: 811
Period size: 157 Copynumber: 3.4 Consensus size: 157
39161373 TAATTTCAAT
* *
39161383 GTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* * *
39161448 TATATTATTTTAGTACAGAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAG
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTG--TTTTTATATAAATTTAG
** *
39161513 TAAAAAACCCTTATTTTGGCCCTTTGTTT
129 TAAAAAACCCTTATTTTGGCTATTTGTTC
* * *
39161542 GTAATTTTCTTATTTTCGAATTTTTTTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* *
39161607 TATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTGTTTTTATACAAATTTAGTA
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGTA
* * *
39161672 AAAAGCCCTTATTTTGACTGTTTGTTC
131 AAAAACCCTTATTTTGGCTATTTGTTC
* *
39161699 GTATTTTTCTTATTTTCGGATTTTATTACTTTTAAAAAATATACTATTTT-GATATTTTATTACT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCG-TATTTTATTATT
*
39161763 TTATATTATTTTAGTATATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGT
65 TTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGT
39161828 AAAAAAACCCTTATTTTGGCTATTTGTTC
130 -AAAAAACCCTTATTTTGGCTATTTGTTC
* * ** *
39161857 GTATTTTTATTTTTTTCGGATTTTATTACTTTCAGTAAATATACTATTTTCGTTTTTTATT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATT
39161918 TCTTTTCGTA
Statistics
Matches: 341, Mismatches: 32, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
156 1 0.00
157 159 0.47
158 78 0.23
159 103 0.30
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.55
Consensus pattern (157 bp):
GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGTA
AAAAACCCTTATTTTGGCTATTTGTTC
Found at i:39161965 original size:50 final size:50
Alignment explanation
Indices: 39161854--39161970 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 50
39161844 TGGCTATTTG
* *
39161854 TTCGTATTTTTATTTTTTTCGGATTTTATTACTTTCAGTAAATATACTATT
1 TTCGTA-TTTTATTTTTTTCGGATTTTATTACTTTCAATAAACATACTATT
* * * * * *
39161905 TTCGTTTTTTATTTCTTTTCGTATTTTATT-TTTTTAATAAACATATTTTT
1 TTCGTATTTTATTT-TTTTCGGATTTTATTACTTTCAATAAACATACTATT
*
39161955 TTGGTATTTTATTTTT
1 TTCGTATTTTATTTTT
39161971 AATACTATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
49 2 0.04
50 34 0.62
51 19 0.35
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.65
Consensus pattern (50 bp):
TTCGTATTTTATTTTTTTCGGATTTTATTACTTTCAATAAACATACTATT
Found at i:39162015 original size:69 final size:69
Alignment explanation
Indices: 39161941--39162082 Score: 243
Period size: 69 Copynumber: 2.1 Consensus size: 69
39161931 TATTTTTTTA
*
39161941 ATAAACATATTTTTTTGGTATTTTATTTTTAATACTA-TTTTTGTAAAAAAAAATCTCATTACAA
1 ATAAACATATTTTTTCGGTATTTTATTTTTAATACTATTTTTTGT-AAAAAAAATCTCATTACAA
39162005 CATGC
65 CATGC
*
39162010 ATAAACATATTTTTTCGGTATTTTATTTTTAATACTATTTTTTGTAAAAAAAATCTCATTATAAC
1 ATAAACATATTTTTTCGGTATTTTATTTTTAATACTATTTTTTGTAAAAAAAATCTCATTACAAC
39162075 ATGC
66 ATGC
39162079 -TAAA
1 ATAAA
39162083 TAAATTTCAT
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
68 4 0.06
69 59 0.84
70 7 0.10
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (69 bp):
ATAAACATATTTTTTCGGTATTTTATTTTTAATACTATTTTTTGTAAAAAAAATCTCATTACAAC
ATGC
Found at i:39162183 original size:12 final size:12
Alignment explanation
Indices: 39162166--39162198 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39162156 TAGAATGTAC
39162166 ATAACATAAATA
1 ATAACATAAATA
39162178 ATAACATAAATA
1 ATAACATAAATA
*
39162190 ATAAAATAA
1 ATAACATAA
39162199 TAAGACATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAACATAAATA
Found at i:39162553 original size:3 final size:3
Alignment explanation
Indices: 39162545--39162589 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
39162535 CCTCTTTCCC
* *
39162545 CTT CTT CTT CTT CTT CTT ATT C-T CTT CTT -TT CTT C-T CTT ATT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
39162590 TTTTCCTGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:39162559 original size:9 final size:9
Alignment explanation
Indices: 39162545--39162589 Score: 51
Period size: 8 Copynumber: 5.3 Consensus size: 9
39162535 CCTCTTTCCC
39162545 CTTCTTCTT
1 CTTCTTCTT
39162554 CTTCTTCTT
1 CTTCTTCTT
*
39162563 ATTC-TCTT
1 CTTCTTCTT
39162571 CTT-TTCTT
1 CTTCTTCTT
*
39162579 C-TCTTATT
1 CTTCTTCTT
39162587 CTT
1 CTT
39162590 TTTTCCTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
7 1 0.03
8 16 0.53
9 13 0.43
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (9 bp):
CTTCTTCTT
Found at i:39163315 original size:3 final size:3
Alignment explanation
Indices: 39163297--39163412 Score: 55
Period size: 3 Copynumber: 39.3 Consensus size: 3
39163287 AACAGCAGGA
*
39163297 AAG AAG AATG AGAG AAG AAG AA- AAG -AG AAA AAG -AG AAG -AG AAG
1 AAG AAG AA-G A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
** * ** * * *
39163340 -AG AAG AAG AAG AAG GGG AAG GAG GCG CAG AAGG AAG AAA AAGG AAA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AA-G AAG
* *
39163386 AAG AAA AAG -AG AAG GAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39163413 GGGAGGGAAG
Statistics
Matches: 84, Mismatches: 19, Indels: 20
0.68 0.15 0.16
Matches are distributed among these distances:
2 12 0.14
3 62 0.74
4 9 0.11
5 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.36, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:39163335 original size:18 final size:19
Alignment explanation
Indices: 39163309--39163353 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
39163299 GAAGAATGAG
39163309 AGAAGAAGAAAAGAGAAAA
1 AGAAGAAGAAAAGAGAAAA
* *
39163328 AG-AGAAGAGAAGAGAAGA
1 AGAAGAAGAAAAGAGAAAA
39163346 AGAAGAAG
1 AGAAGAAG
39163354 GGGAAGGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
AGAAGAAGAAAAGAGAAAA
Found at i:39163662 original size:16 final size:16
Alignment explanation
Indices: 39163641--39163691 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
39163631 TTTTAATTTT
39163641 TATGTTATGTACATTC
1 TATGTTATGTACATTC
*
39163657 TATGTT-T-TATTATT-
1 TATGTTATGTA-CATTC
*
39163671 TATGTTATGTACATAC
1 TATGTTATGTACATTC
39163687 TATGT
1 TATGT
39163692 CTTATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (16 bp):
TATGTTATGTACATTC
Found at i:39163665 original size:30 final size:29
Alignment explanation
Indices: 39163631--39163748 Score: 126
Period size: 30 Copynumber: 4.2 Consensus size: 29
39163621 CATAATTTAA
39163631 TTTTAATTTTTATGTTATGTACATTCTATG
1 TTTT-ATTTTTATGTTATGTACATTCTATG
*
39163661 TTTTATTATTTATGTTATGTACATACTATG
1 TTTTATT-TTTATGTTATGTACATTCTATG
* *
39163691 TCTTA---TTATTTTAT-T--ATT-TATG
1 TTTTATTTTTATGTTATGTACATTCTATG
39163713 TTTTATTATTTATGTTA-GTACATTCTATG
1 TTTTATT-TTTATGTTATGTACATTCTATG
39163742 TTTTATT
1 TTTTATT
39163749 ATTTTATTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 19
0.74 0.06 0.19
Matches are distributed among these distances:
22 8 0.11
23 2 0.03
25 1 0.01
26 16 0.22
28 3 0.04
29 14 0.19
30 29 0.40
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.62
Consensus pattern (29 bp):
TTTTATTTTTATGTTATGTACATTCTATG
Found at i:39163718 original size:14 final size:14
Alignment explanation
Indices: 39163699--39163761 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
39163689 TGTCTTATTA
39163699 TTTTATTATTTATG
1 TTTTATTATTTATG
39163713 TTTTATTATTTATG
1 TTTTATTATTTATG
* *
39163727 TTAGTA-CATTCTATG
1 TT-TTATTATT-TATG
*
39163742 TTTTATTATTT-TA
1 TTTTATTATTTATG
39163755 TTTTATT
1 TTTTATT
39163762 TAATTAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
13 8 0.20
14 22 0.54
15 11 0.27
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTATTATTTATG
Found at i:39163752 original size:51 final size:52
Alignment explanation
Indices: 39163657--39163756 Score: 175
Period size: 51 Copynumber: 1.9 Consensus size: 52
39163647 ATGTACATTC
39163657 TATGTTTTATTATTTATGTTATGTACATACTATGTCTTATTATTTTATTATT
1 TATGTTTTATTATTTATGTTATGTACATACTATGTCTTATTATTTTATTATT
* *
39163709 TATGTTTTATTATTTATGTTA-GTACATTCTATGTTTTATTATTTTATT
1 TATGTTTTATTATTTATGTTATGTACATACTATGTCTTATTATTTTATT
39163757 TTATTTAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 25 0.54
52 21 0.46
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (52 bp):
TATGTTTTATTATTTATGTTATGTACATACTATGTCTTATTATTTTATTATT
Found at i:39164216 original size:156 final size:157
Alignment explanation
Indices: 39163914--39164452 Score: 832
Period size: 156 Copynumber: 3.4 Consensus size: 157
39163904 TACGAAAAGA
* * ** *
39163914 AATAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAAC
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
* * *
39163979 AAAGGGCCAAAATAATGGTTTTTTACTAAATTTTTATAAAAATACACTAAAATAATACATTTCAA
66 AAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAACACACTAAAATAATACATTTCAA
*
39164044 ACATTATGTACTAAAATAATATAAAAT
131 ATATTATGTACTAAAATAATATAAAAT
*
39164071 AATAAAATACGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
*
39164136 AAAGGGCCAAAAT-AGGGGTTTTTACTAAATTTATATAAAAACACACTAAAATAATACATTTCAA
66 AAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAACACACTAAAATAATACATTTCAA
39164200 ATATTATGTACTAAAATAATATAAAAT
131 ATATTATGTACTAAAATAATATAAAAT
*
39164227 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATATGAAC
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
* * *
39164292 AAATGGCCAAAATAAGAGTTTTTTTACTAAATTTATATAAAAAACACACACACTAAATTAATACA
66 AAAGGGCCAAAATAAG-GGTTTTTTACTAAATTTATAT---AAA-A-ACACACTAAAATAATACA
39164357 TTTCAAACT-TTATGTACTAAAATAATATAAAAT
125 TTTCAAA-TATTATGTACTAAAATAATATAAAAT
* *
39164390 AATAAAATACGAAAATAATATATTTTTTGAAAGTAGTAAAA-TCTGAAAATAAGAAAAATACGA
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATTC-GAAAATAAGAAAAATACGA
39164453 TGAAAAAAAA
Statistics
Matches: 353, Mismatches: 20, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
156 148 0.42
157 74 0.21
158 19 0.05
161 3 0.01
162 3 0.01
163 105 0.30
164 1 0.00
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (157 bp):
AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
AAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAACACACTAAAATAATACATTTCAA
ATATTATGTACTAAAATAATATAAAAT
Found at i:39164592 original size:191 final size:195
Alignment explanation
Indices: 39164264--39164641 Score: 665
Period size: 191 Copynumber: 2.0 Consensus size: 195
39164254 TGAAAGTAAT
** * *
39164264 AAAATTCGAAAATAAGAAAAATATGAACAAATGGCCAAAATAAGAGTTTTTTTACTAAATTTATA
1 AAAATTCGAAAATAAGAAAAATACAAACAAAGGGCCAAAATAAGAGGTTTTTTACTAAATTTATA
39164329 TAAAAAACACACACACTAAATTAATACATTTCAAACTTTATGTACTAAAATAATATAAAATAATA
66 TAAAAAACACACACACTAAATTAATACATTTCAAACTTTATGTACTAAAATAATATAAAATAATA
*
39164394 AAATACGAAAATAATATATTTTTTGAAAGTAGTAAAATCTGAAAATAAGAAAAATACGATGAAAA
131 AAATACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAAATACGATGAAAA
*
39164459 AAAATTCGAAAATAAGAAAATTACAAACAAAGGGCCAAAATAAG-GGTTTTTTACTAAATTTATA
1 AAAATTCGAAAATAAGAAAAATACAAACAAAGGGCCAAAATAAGAGGTTTTTTACTAAATTTATA
*
39164523 T-AAAAA-A-ACACACTAAATTAATACATTTCAAACTTTCTGTACTAAAATAATATAAAATAATA
66 TAAAAAACACACACACTAAATTAATACATTTCAAACTTTATGTACTAAAATAATATAAAATAATA
39164585 AAATACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAAATAC
131 AAATACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAAATAC
39164642 ATTGAAATTA
Statistics
Matches: 176, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
191 110 0.62
192 1 0.01
193 5 0.03
194 20 0.11
195 40 0.23
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (195 bp):
AAAATTCGAAAATAAGAAAAATACAAACAAAGGGCCAAAATAAGAGGTTTTTTACTAAATTTATA
TAAAAAACACACACACTAAATTAATACATTTCAAACTTTATGTACTAAAATAATATAAAATAATA
AAATACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAAATACGATGAAAA
Found at i:39169788 original size:76 final size:76
Alignment explanation
Indices: 39169708--39169849 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 76
39169698 ATAGTTTTTT
39169708 ACTAAAAATAATACTAACTAACAATAATAATTAAGG-TTTTACTAAAAATAATAACTAACAATAA
1 ACTAAAAATAATACTAACTAA-AATAATAATTAAGGTTTTTACTAAAAATAATAACTAACAATAA
39169772 TATAGTGTAAAA
65 TATAGTGTAAAA
* * * *** *
39169784 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTTACTAATTCTAATAACTAACCATAAT
1 ACTAAAAATAATACTAACTAAAATAATAATTAAGGTTTTTACTAAAAATAATAACTAACAATAAT
39169849 A
66 A
39169850 ATAATATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 13 0.22
76 45 0.78
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (76 bp):
ACTAAAAATAATACTAACTAAAATAATAATTAAGGTTTTTACTAAAAATAATAACTAACAATAAT
ATAGTGTAAAA
Found at i:39170106 original size:20 final size:20
Alignment explanation
Indices: 39170083--39170136 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
39170073 TTCTATTTTT
39170083 TTTCTTCTCTTTCTTTCTC-C
1 TTTCTTCT-TTTCTTTCTCTC
*
39170103 TTTC-TCTATTCTTTTCTCTC
1 TTTCTTCTTTTC-TTTCTCTC
39170123 TTT-TTCTTTTCTTT
1 TTTCTTCTTTTCTTT
39170137 TTTCGGCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 14 0.48
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTCTTCTTTTCTTTCTCTC
Found at i:39173824 original size:32 final size:32
Alignment explanation
Indices: 39173788--39173853 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
39173778 TCATTCTATG
39173788 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
1 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
39173820 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
1 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
39173852 TT
1 TT
39173854 CATTTCATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (32 bp):
TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
Found at i:39178922 original size:20 final size:20
Alignment explanation
Indices: 39178876--39178923 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
39178866 TAAATCGAGC
*
39178876 CTTTGAAGCCCTAAAAATAG
1 CTTTGAGGCCCTAAAAATAG
*
39178896 CTTTGAGGCCTTAAAAATAG
1 CTTTGAGGCCCTAAAAATAG
*
39178916 TTTTGAGG
1 CTTTGAGG
39178924 TAATTCAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (20 bp):
CTTTGAGGCCCTAAAAATAG
Found at i:39181803 original size:16 final size:17
Alignment explanation
Indices: 39181782--39181813 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39181772 TATAAAACAA
39181782 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
39181798 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
39181814 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:39182765 original size:25 final size:25
Alignment explanation
Indices: 39182714--39182769 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
39182704 ACTTTAGCGC
* ***
39182714 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTACTAGCACGACAGT
39182739 GCTCTCTGATTACTAGCACGACAGT
1 GCTCTCTGATTACTAGCACGACAGT
39182764 GCTCTC
1 GCTCTC
39182770 CGTTTAGCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGACAGT
Found at i:39193908 original size:12 final size:12
Alignment explanation
Indices: 39193896--39193945 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
39193886 CTTGTTCTTG
*
39193896 TTATTGTTATTG
1 TTATTGTTATTA
*
39193908 TTGTTGTTATTA
1 TTATTGTTATTA
* *
39193920 CTATTATTATTA
1 TTATTGTTATTA
*
39193932 TTATTATTATTA
1 TTATTGTTATTA
39193944 TT
1 TT
39193946 TGTGGTTCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.66
Consensus pattern (12 bp):
TTATTGTTATTA
Found at i:39193927 original size:3 final size:3
Alignment explanation
Indices: 39193914--39193945 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
39193904 ATTGTTGTTG
*
39193914 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39193946 TGTGGTTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:39203139 original size:12 final size:12
Alignment explanation
Indices: 39203122--39203146 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39203112 GGTGTTCATT
39203122 CGGTTAACCGAC
1 CGGTTAACCGAC
39203134 CGGTTAACCGAC
1 CGGTTAACCGAC
39203146 C
1 C
39203147 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:39203318 original size:9 final size:9
Alignment explanation
Indices: 39203304--39203367 Score: 85
Period size: 9 Copynumber: 7.2 Consensus size: 9
39203294 TTTGGTTAAA
39203304 AATTACCCG
1 AATTACCCG
39203313 AATTACCCG
1 AATTACCCG
39203322 AATTACCCG
1 AATTACCCG
*
39203331 -ATTAACCG
1 AATTACCCG
* *
39203339 AATTAACTG
1 AATTACCCG
*
39203348 AATTAACCG
1 AATTACCCG
39203357 AATTACCCG
1 AATTACCCG
39203366 AA
1 AA
39203368 AATTACCCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
8 7 0.14
9 43 0.86
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:39203327 original size:18 final size:18
Alignment explanation
Indices: 39203304--39203367 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
39203294 TTTGGTTAAA
*
39203304 AATTACCCGAATTACCCG
1 AATTACCCGAATTAACCG
39203322 AATTACCCG-ATTAACCG
1 AATTACCCGAATTAACCG
* *
39203339 AATTAACTGAATTAACCG
1 AATTACCCGAATTAACCG
39203357 AATTACCCGAA
1 AATTACCCGAA
39203368 AATTACCCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
17 14 0.35
18 26 0.65
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:39204532 original size:3 final size:3
Alignment explanation
Indices: 39204524--39204563 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
39204514 GTATGTCAAT
39204524 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
39204564 CCTCTCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:39212239 original size:22 final size:22
Alignment explanation
Indices: 39212213--39212258 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
39212203 ATATGTTTCG
39212213 ATATATGCTAT-ATTAGATTGAA
1 ATATATGC-ATGATTAGATTGAA
*
39212235 ATATATGCATGATTATATTGAA
1 ATATATGCATGATTAGATTGAA
39212257 AT
1 AT
39212259 TTTAGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (22 bp):
ATATATGCATGATTAGATTGAA
Found at i:39213327 original size:4 final size:4
Alignment explanation
Indices: 39213318--39213359 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
39213308 ATAGTTTTAG
39213318 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
39213360 TCTCTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:39215096 original size:21 final size:22
Alignment explanation
Indices: 39215045--39215105 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
39215035 ATTCAATTAT
* *
39215045 TTTAAAAAAAATAAAGATCAAA
1 TTTAATAAAAATAAAAATCAAA
*
39215067 TTTAATAAAAATAAAAATTAAA
1 TTTAATAAAAATAAAAATCAAA
* *
39215089 -TTATTAAAAATATAAAT
1 TTTAATAAAAATAAAAAT
39215106 GTTAAGAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TTTAATAAAAATAAAAATCAAA
Found at i:39215124 original size:14 final size:14
Alignment explanation
Indices: 39215078--39215125 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
39215068 TTAATAAAAA
39215078 TAAAAATTAAATTAT
1 TAAAAATTAAATT-T
*
39215093 TAAAAATATAAATGT
1 TAAAAAT-TAAATTT
*
39215108 TAAGAATTAAATTT
1 TAAAAATTAAATTT
39215122 TAAA
1 TAAA
39215126 TTATACCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 9 0.32
15 14 0.50
16 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (14 bp):
TAAAAATTAAATTT
Found at i:39221012 original size:95 final size:95
Alignment explanation
Indices: 39220849--39221799 Score: 1893
Period size: 95 Copynumber: 10.0 Consensus size: 95
39220839 AATCTCCTTA
39220849 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39220914 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
39220944 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39221009 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
39221039 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39221104 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
39221134 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39221199 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
39221229 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39221294 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
39221324 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39221389 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
39221419 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39221484 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
39221514 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39221579 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
39221609 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39221674 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
*
39221704 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTGCATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
39221769 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
39221799 G
1 G
39221800 CTATTCCTTT
Statistics
Matches: 855, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 855 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (95 bp):
GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTACATTA
TCTCATGATGGCTTGCACCCCAATTGTTTT
Found at i:39225043 original size:35 final size:35
Alignment explanation
Indices: 39224997--39225067 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
39224987 ATCCCAAGAA
*
39224997 CTCGTGTATGTCAATCATGAGGCTCTCTTTCGCTC
1 CTCGTGTATGTCAATCATGAGGCTCTCTTTCACTC
39225032 CTCGTGTATGTCAATCATGAGGCTCTCTTTCACTC
1 CTCGTGTATGTCAATCATGAGGCTCTCTTTCACTC
39225067 C
1 C
39225068 CCCCCCCCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.37
Consensus pattern (35 bp):
CTCGTGTATGTCAATCATGAGGCTCTCTTTCACTC
Found at i:39231268 original size:19 final size:20
Alignment explanation
Indices: 39231225--39231268 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
39231215 CTTGGTACAA
39231225 ATACACATAAAATTGTGTGAAG
1 ATACACATAAAA-T-TGTGAAG
*
39231247 ATACACATAAAA-TGTGACG
1 ATACACATAAAATTGTGAAG
39231266 ATA
1 ATA
39231269 GACGAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
22 12 0.57
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (20 bp):
ATACACATAAAATTGTGAAG
Found at i:39237644 original size:31 final size:29
Alignment explanation
Indices: 39237608--39237678 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
39237598 ACTACCAAAA
* *
39237608 TAGTCACTTTTATTTGGCACATGTTACATTT
1 TAGTCACTTATATTT-G-AAATGTTACATTT
* *
39237639 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATATTTGAAATGTTACATTT
39237668 TAGTCACTTAT
1 TAGTCACTTAT
39237679 GTTATCACGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 22 0.61
30 1 0.03
31 13 0.36
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (29 bp):
TAGTCACTTATATTTGAAATGTTACATTT
Found at i:39237703 original size:31 final size:29
Alignment explanation
Indices: 39237628--39237704 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
39237618 TATTTGGCAC
* *
39237628 ATGTTACATTTTAGTCACTTATGTTTGAA
1 ATGTAACATTTTAGTCACTTATGTTTCAA
* * *
39237657 ATGTTACGTTTTAGTCACTTATGTTATCACG
1 ATGTAACATTTTAGTCACTTATGTT-TCA-A
*
39237688 TTGTAACATTTTAGTCA
1 ATGTAACATTTTAGTCA
39237705 TTGAGCCATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 24 0.60
30 2 0.05
31 14 0.35
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (29 bp):
ATGTAACATTTTAGTCACTTATGTTTCAA
Found at i:39238331 original size:31 final size:29
Alignment explanation
Indices: 39238267--39238335 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
39238257 ATGATAACGT
* *
39238267 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
39238296 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
39238327 AAGTGACTA
1 AAGTGACTA
39238336 TTTTGATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:39250456 original size:19 final size:20
Alignment explanation
Indices: 39250415--39250453 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
39250405 TTATTTTTAT
*
39250415 ATTTTTATACTTTTTAAATA
1 ATTTTTATACTTTTTAAAAA
39250435 ATTTTTA-A-TTTTTAAAAA
1 ATTTTTATACTTTTTAAAAA
39250453 A
1 A
39250454 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTATACTTTTTAAAAA
Found at i:39257507 original size:16 final size:16
Alignment explanation
Indices: 39257486--39257517 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39257476 TAATATCAGC
39257486 TTTTTTGGCAGCAGGA
1 TTTTTTGGCAGCAGGA
*
39257502 TTTTTTGGGAGCAGGA
1 TTTTTTGGCAGCAGGA
39257518 ATTGATGCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.09, G:0.34, T:0.38
Consensus pattern (16 bp):
TTTTTTGGCAGCAGGA
Found at i:39266520 original size:19 final size:19
Alignment explanation
Indices: 39266475--39266522 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
39266465 CTGAGGTCAA
39266475 TTTGAAACAAAATGGAAAAG
1 TTTGAAA-AAAATGGAAAAG
* *
39266495 TTAGAAAAAAGAT-GAAAAT
1 TTTGAAAAAA-ATGGAAAAG
39266514 TTTGAAAAA
1 TTTGAAAAA
39266523 TAAGGGACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.58, C:0.02, G:0.17, T:0.23
Consensus pattern (19 bp):
TTTGAAAAAAATGGAAAAG
Found at i:39269246 original size:17 final size:17
Alignment explanation
Indices: 39269221--39269254 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39269211 CAGAATATTC
*
39269221 ATTATCTAATCCACAAA
1 ATTAGCTAATCCACAAA
39269238 ATTAGCTAATCCACAAA
1 ATTAGCTAATCCACAAA
39269255 GCAAAGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (17 bp):
ATTAGCTAATCCACAAA
Found at i:39285827 original size:26 final size:26
Alignment explanation
Indices: 39285789--39285846 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
39285779 CATGAAATTC
*
39285789 TTATCATGAAACATTTACTTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
39285815 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
39285841 TTATCA
1 TTATCA
39285847 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:39306939 original size:14 final size:14
Alignment explanation
Indices: 39306916--39306955 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
39306906 AATGGCAGTA
39306916 CAAA-GAAGCAAAC
1 CAAATGAAGCAAAC
39306929 CAAATGAAGCAAAC
1 CAAATGAAGCAAAC
39306943 CAAATGAAGCAAA
1 CAAATGAAGCAAA
39306956 AAGAGAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.60, C:0.20, G:0.15, T:0.05
Consensus pattern (14 bp):
CAAATGAAGCAAAC
Found at i:39328429 original size:18 final size:18
Alignment explanation
Indices: 39328406--39328443 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39328396 TATTGGAGAT
39328406 AAATTATTACCCATGTAA
1 AAATTATTACCCATGTAA
* *
39328424 AAATTATTACTCGTGTAA
1 AAATTATTACCCATGTAA
39328442 AA
1 AA
39328444 GTATTTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (18 bp):
AAATTATTACCCATGTAA
Found at i:39330273 original size:13 final size:14
Alignment explanation
Indices: 39330240--39330270 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39330230 TGTTTAACTA
*
39330240 AAAATGATTTTTGG
1 AAAATGATTTATGG
39330254 AAAATGATTTATGG
1 AAAATGATTTATGG
39330268 AAA
1 AAA
39330271 TGACTTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.35
Consensus pattern (14 bp):
AAAATGATTTATGG
Found at i:39335275 original size:21 final size:21
Alignment explanation
Indices: 39335250--39335318 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
39335240 TATAATGATT
39335250 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
39335271 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
39335291 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
39335311 ATTATTAT
1 ATTATTAT
39335319 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:39335331 original size:15 final size:14
Alignment explanation
Indices: 39335305--39335335 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
39335295 TATGGTTTTA
39335305 TATTAGATTATTAT
1 TATTAGATTATTAT
39335319 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
39335334 TA
1 TA
39335336 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:39336857 original size:22 final size:22
Alignment explanation
Indices: 39336832--39336874 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
39336822 ATTGAAAAGT
39336832 ATGAGAAAGAATATATGAACTC
1 ATGAGAAAGAATATATGAACTC
39336854 ATGAGAAAGAATATATGAACT
1 ATGAGAAAGAATATATGAACT
39336875 AAATTATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (22 bp):
ATGAGAAAGAATATATGAACTC
Found at i:39338403 original size:14 final size:14
Alignment explanation
Indices: 39338384--39338412 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39338374 ATAAAAAGAT
39338384 TATCCAATGTTCAA
1 TATCCAATGTTCAA
39338398 TATCCAATGTTCAA
1 TATCCAATGTTCAA
39338412 T
1 T
39338413 CTTTCGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (14 bp):
TATCCAATGTTCAA
Found at i:39339963 original size:16 final size:16
Alignment explanation
Indices: 39339942--39339973 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39339932 TTTTCTTATA
39339942 TTTCATTGTTTAATTG
1 TTTCATTGTTTAATTG
39339958 TTTCATTGTTTAATTG
1 TTTCATTGTTTAATTG
39339974 AGTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTCATTGTTTAATTG
Found at i:39340342 original size:20 final size:20
Alignment explanation
Indices: 39340292--39340342 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
39340282 TTAATCGAGT
*
39340292 GGTTAATTAGGTTTTAATTAA
1 GGTTAATTA-GTTTAAATTAA
*
39340313 -GTGAATTTAGTTTAAATTAA
1 GGTTAA-TTAGTTTAAATTAA
39340333 GGTTAATTAG
1 GGTTAATTAG
39340343 GTATAAGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (20 bp):
GGTTAATTAGTTTAAATTAA
Found at i:39340506 original size:20 final size:22
Alignment explanation
Indices: 39340483--39340523 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
39340473 TTTATGTTTT
39340483 AAATATATTAT-TTA-ATTATA
1 AAATATATTATATTATATTATA
39340503 AAATATATTATATTATATTAT
1 AAATATATTATATTATATTAT
39340524 TATGTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATATATTATATTATATTATA
Found at i:39340616 original size:13 final size:14
Alignment explanation
Indices: 39340597--39340653 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 14
39340587 TTTTTGTAAA
39340597 ATATATATATTTATT
1 ATATATATA-TTATT
39340612 ATATAAGTATATTATT
1 ATAT-A-TATATTATT
*
39340628 AAAT-TATATTATT
1 ATATATATATTATT
39340641 ATA-ATATTATTAT
1 ATATATA-TATTAT
39340654 AAAATAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 13 0.36
14 6 0.17
15 4 0.11
16 9 0.25
17 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
ATATATATATTATT
Found at i:39340693 original size:18 final size:19
Alignment explanation
Indices: 39340663--39340709 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
39340653 TAAAATAAAT
39340663 GAAACAAATGAAATA-AAAA
1 GAAACAAA-GAAATAGAAAA
*
39340682 GAAATAAAGAAATAGAAAA
1 GAAACAAAGAAATAGAAAA
39340701 GAAACAAAG
1 GAAACAAAG
39340710 TAACAGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.72, C:0.04, G:0.15, T:0.09
Consensus pattern (19 bp):
GAAACAAAGAAATAGAAAA
Found at i:39340717 original size:19 final size:19
Alignment explanation
Indices: 39340663--39340717 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
39340653 TAAAATAAAT
*
39340663 GAAACAAATGAAATA-AAAA
1 GAAACAAA-GAAACAGAAAA
* *
39340682 GAAATAAAGAAATAGAAAA
1 GAAACAAAGAAACAGAAAA
*
39340701 GAAACAAAGTAACAGAA
1 GAAACAAAGAAACAGAA
39340718 TATGAAAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.71, C:0.05, G:0.15, T:0.09
Consensus pattern (19 bp):
GAAACAAAGAAACAGAAAA
Found at i:39342101 original size:18 final size:18
Alignment explanation
Indices: 39342086--39342176 Score: 83
Period size: 18 Copynumber: 5.1 Consensus size: 18
39342076 TGGCTGTTCT
*
39342086 TGAATAATTGATTGTTAC
1 TGAATAACTGATTGTTAC
*
39342104 TGAATAACTGATTGCTAC
1 TGAATAACTGATTGTTAC
* * *
39342122 TGAGTAAATGATTGTTGC
1 TGAATAACTGATTGTTAC
* * *
39342140 TGAACAACTAATTGCTAC
1 TGAATAACTGATTGTTAC
* * *
39342158 TGAATGATTGAATGTTAC
1 TGAATAACTGATTGTTAC
39342176 T
1 T
39342177 AAATGAAACT
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (18 bp):
TGAATAACTGATTGTTAC
Found at i:39342178 original size:28 final size:28
Alignment explanation
Indices: 39342164--39342227 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
39342154 CTACTGAATG
39342164 ATTGAATGTTACTAAATGAAACTGATAA
1 ATTGAATGTTACTAAATGAAACTGATAA
39342192 ATTGAATGTTACTAAATGAAACTGATAA
1 ATTGAATGTTACTAAATGAAACTGATAA
39342220 ATTGAATG
1 ATTGAATG
39342228 ACACTGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (28 bp):
ATTGAATGTTACTAAATGAAACTGATAA
Found at i:39346451 original size:17 final size:19
Alignment explanation
Indices: 39346409--39346452 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39346399 ACGAAATTTT
*
39346409 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
39346428 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
39346446 AA-TATTA
1 AATTATTA
39346453 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:39349945 original size:17 final size:19
Alignment explanation
Indices: 39349903--39349946 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39349893 ACGAAATTTT
*
39349903 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
39349922 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
39349940 AA-TATTA
1 AATTATTA
39349947 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:39351794 original size:8 final size:8
Alignment explanation
Indices: 39351781--39351811 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
39351771 CTAGATCGGC
39351781 AAAAGCCG
1 AAAAGCCG
39351789 AAAAGCCG
1 AAAAGCCG
*
39351797 AAATGCCG
1 AAAAGCCG
39351805 AAAAGCC
1 AAAAGCC
39351812 AGCATTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.26, G:0.23, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:39357889 original size:29 final size:31
Alignment explanation
Indices: 39357857--39357920 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
39357847 AATAAAATAA
*
39357857 TAAAATAATAAAAT-AATAA-AA-TATCTTAT
1 TAAAAT-ATAAAATAAATAATAATTATCTAAT
*
39357886 TAAAATATTAAATAAATAATAATTATCTAAT
1 TAAAATATAAAATAAATAATAATTATCTAAT
39357917 TAAA
1 TAAA
39357921 TAACTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 6 0.20
29 11 0.37
30 2 0.07
31 11 0.37
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (31 bp):
TAAAATATAAAATAAATAATAATTATCTAAT
Found at i:39357897 original size:8 final size:8
Alignment explanation
Indices: 39357847--39357879 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
39357837 ATATAGACTA
39357847 AATAAAAT
1 AATAAAAT
39357855 AATAAAAT
1 AATAAAAT
39357863 AATAAAAT
1 AATAAAAT
39357871 AATAAAAT
1 AATAAAAT
39357879 A
1 A
39357880 TCTTATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:39359942 original size:16 final size:17
Alignment explanation
Indices: 39359921--39359958 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
39359911 ATATGAAGAA
39359921 TATTATTTAAAA-TTAT
1 TATTATTTAAAATTTAT
39359937 TATTATTTAAAATTTAT
1 TATTATTTAAAATTTAT
39359954 TATTA
1 TATTA
39359959 AAATAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATTTAAAATTTAT
Found at i:39359991 original size:20 final size:20
Alignment explanation
Indices: 39359966--39360028 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
39359956 TTAAAATAAA
39359966 ATTAAAATATTAAATAATTT
1 ATTAAAATATTAAATAATTT
*
39359986 ATTAAAATAATAAAT--TTAT
1 ATTAAAATATTAAATAATT-T
*
39360005 ATTAATTATATT-AATAATTT
1 ATTAA-AATATTAAATAATTT
39360025 ATTA
1 ATTA
39360029 TATGAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.06
19 9 0.25
20 23 0.64
21 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTAAAATATTAAATAATTT
Found at i:39362275 original size:22 final size:21
Alignment explanation
Indices: 39362250--39362292 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
39362240 TAAGGGAATG
* *
39362250 TTTTCAACATGATTATTTTCAT
1 TTTTCAAAAAGATT-TTTTCAT
*
39362272 TTTTTAAAAAGATTTTTTCAT
1 TTTTCAAAAAGATTTTTTCAT
39362293 ATATTTTGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTCAAAAAGATTTTTTCAT
Found at i:39365463 original size:24 final size:24
Alignment explanation
Indices: 39365436--39365531 Score: 66
Period size: 24 Copynumber: 4.0 Consensus size: 24
39365426 TCCCTCCCGA
*
39365436 TGTTCCTGGACTCGTGGTTGTCCC
1 TGTTCCAGGACTCGTGGTTGTCCC
** * *
39365460 TGTTGGAGGAGTTGTGGTTGTCCC
1 TGTTCCAGGACTCGTGGTTGTCCC
** * *
39365484 TGTTGGAGGAGTTGTGGTTGTCCC
1 TGTTCCAGGACTCGTGGTTGTCCC
* ** * *
39365508 AGTTGGAGGAGTTGTGGTTGTCCC
1 TGTTCCAGGACTCGTGGTTGTCCC
39365532 AGTCGGAGGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.08, C:0.17, G:0.39, T:0.36
Consensus pattern (24 bp):
TGTTCCAGGACTCGTGGTTGTCCC
Found at i:39365549 original size:24 final size:24
Alignment explanation
Indices: 39365449--39365543 Score: 163
Period size: 24 Copynumber: 4.0 Consensus size: 24
39365439 TCCTGGACTC
*
39365449 GTGGTTGTCCCTGTTGGAGGAGTT
1 GTGGTTGTCCCAGTTGGAGGAGTT
*
39365473 GTGGTTGTCCCTGTTGGAGGAGTT
1 GTGGTTGTCCCAGTTGGAGGAGTT
39365497 GTGGTTGTCCCAGTTGGAGGAGTT
1 GTGGTTGTCCCAGTTGGAGGAGTT
*
39365521 GTGGTTGTCCCAGTCGGAGGAGT
1 GTGGTTGTCCCAGTTGGAGGAGT
39365544 CATGGTAGGG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.11, C:0.14, G:0.42, T:0.34
Consensus pattern (24 bp):
GTGGTTGTCCCAGTTGGAGGAGTT
Found at i:39365558 original size:48 final size:48
Alignment explanation
Indices: 39365461--39365573 Score: 145
Period size: 48 Copynumber: 2.4 Consensus size: 48
39365451 GGTTGTCCCT
* * ** * *
39365461 GTTGGAGGAGTTGTGGTTGTCCCTGTTGGAGGAGTTGTGGTTGTCCCA
1 GTTGGAGGAGTTGTGGTTGTCCCAGTCGGAGGAGTCATGGTAGGCCCA
*
39365509 GTTGGAGGAGTTGTGGTTGTCCCAGTCGGAGGAGTCATGGTAGGGCCA
1 GTTGGAGGAGTTGTGGTTGTCCCAGTCGGAGGAGTCATGGTAGGCCCA
* *
39365557 GTCGGAGGAGTCGTGGT
1 GTTGGAGGAGTTGTGGT
39365574 AGGGCCGGTG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (48 bp):
GTTGGAGGAGTTGTGGTTGTCCCAGTCGGAGGAGTCATGGTAGGCCCA
Found at i:39365587 original size:24 final size:24
Alignment explanation
Indices: 39365530--39365579 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
39365520 TGTGGTTGTC
39365530 CCAGTCGGAGGAGTCATGGTAGGG
1 CCAGTCGGAGGAGTCATGGTAGGG
*
39365554 CCAGTCGGAGGAGTCGTGGTAGGG
1 CCAGTCGGAGGAGTCATGGTAGGG
39365578 CC
1 CC
39365580 GGTGGGAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.20, G:0.46, T:0.16
Consensus pattern (24 bp):
CCAGTCGGAGGAGTCATGGTAGGG
Found at i:39369600 original size:13 final size:13
Alignment explanation
Indices: 39369582--39369613 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
39369572 TAACTTTTAA
39369582 AGTATAGGGATTT
1 AGTATAGGGATTT
39369595 AGTATAGGGATTT
1 AGTATAGGGATTT
39369608 AGTATA
1 AGTATA
39369614 TGGACTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (13 bp):
AGTATAGGGATTT
Found at i:39370614 original size:2 final size:2
Alignment explanation
Indices: 39370607--39370633 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39370597 GTGAAATCCA
39370607 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
39370634 TATATGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:39372609 original size:161 final size:156
Alignment explanation
Indices: 39372355--39372652 Score: 418
Period size: 161 Copynumber: 1.9 Consensus size: 156
39372345 AACCCCCATT
* * *
39372355 TGAACAAGCAAACTACTCCAAATTCTCAAATCTAATGACTTGATTAACTTGAACCTATATTTTAC
1 TGAACAAGCAAACAACTCAAAATTCTCAAATCTAATGACTTGATTAACTTAAACCTATATTTTAC
* ** * * * *
39372420 GTGTAAACAATCAGATCAAATGAAATGTTAAGAAAGCATTAACAGAAATGAAAACAATG-TCAAA
66 ATGTAAACAATCAGATCAAACAAAATGTTAAAAAAGCACTAACACAAACGAAAACAATGTTC-AA
39372484 AACAATACATCCAAGGAAAACCCTTTA
130 AACAATACATCCAAGGAAAACCCTTTA
* * *
39372511 TGAACAAGCAAACAACCTTCAAAATTCTCAAATCTAATGACTTGATTGACTTAAATCTACATGGT
1 TGAACAAGCAAACAA-C-TCAAAATTCTCAAATCTAATGACTTGATTAACTTAAACCT--AT-AT
39372576 TTTACATGTAAACAATCAGATCAAACAAAATGTTAAAAAAGCACTAACACAAACGAAAACAATGT
61 TTTACATGTAAACAATCAGATCAAACAAAATGTTAAAAAAGCACTAACACAAACGAAAACAATGT
39372641 TCAAAACAATAC
126 TCAAAACAATAC
39372653 TGTTGACGGG
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
156 14 0.11
157 1 0.01
158 36 0.29
160 2 0.02
161 68 0.55
162 2 0.02
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.24
Consensus pattern (156 bp):
TGAACAAGCAAACAACTCAAAATTCTCAAATCTAATGACTTGATTAACTTAAACCTATATTTTAC
ATGTAAACAATCAGATCAAACAAAATGTTAAAAAAGCACTAACACAAACGAAAACAATGTTCAAA
ACAATACATCCAAGGAAAACCCTTTA
Found at i:39377367 original size:3 final size:3
Alignment explanation
Indices: 39377359--39377396 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
39377349 AAACGATAAA
* *
39377359 AAG AAG AAG AAG AAG AAG AAG AAG AAG ATG ATG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
39377397 TTAATACCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.32, T:0.05
Consensus pattern (3 bp):
AAG
Found at i:39385966 original size:39 final size:40
Alignment explanation
Indices: 39385900--39385987 Score: 124
Period size: 39 Copynumber: 2.2 Consensus size: 40
39385890 ATATTTGACG
* * * *
39385900 TATATCCGGGCTTAAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGGTCCGCAGGCTACGTGCTAGAAA
39385940 TATATCCGGACTT-AAGGTCCGCAGGCTACGTGCTAGAAA
1 TATATCCGGACTTAAAGGTCCGCAGGCTACGTGCTAGAAA
*
39385979 TATGTCCGG
1 TATATCCGG
39385988 GCTACAGTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 31 0.72
40 12 0.28
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TATATCCGGACTTAAAGGTCCGCAGGCTACGTGCTAGAAA
Found at i:39391281 original size:51 final size:51
Alignment explanation
Indices: 39391205--39391360 Score: 303
Period size: 51 Copynumber: 3.1 Consensus size: 51
39391195 TGATACCCTT
*
39391205 AACATTGCAACACCAACCCGATAATTTTGAAAATATTACATTTAAGTCCTC
1 AACATCGCAACACCAACCCGATAATTTTGAAAATATTACATTTAAGTCCTC
39391256 AACATCGCAACACCAACCCGATAATTTTGAAAATATTACATTTAAGTCCTC
1 AACATCGCAACACCAACCCGATAATTTTGAAAATATTACATTTAAGTCCTC
39391307 AACATCGCAACACCAACCCGATAATTTTGAAAATATTACATTTAAGTCCTC
1 AACATCGCAACACCAACCCGATAATTTTGAAAATATTACATTTAAGTCCTC
39391358 AAC
1 AAC
39391361 TAACCTTGGT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 104 1.00
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.28
Consensus pattern (51 bp):
AACATCGCAACACCAACCCGATAATTTTGAAAATATTACATTTAAGTCCTC
Found at i:39391735 original size:16 final size:15
Alignment explanation
Indices: 39391714--39391744 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
39391704 TCCAAGAGCG
39391714 TCGCCTTCGATTGTA
1 TCGCCTTCGATTGTA
39391729 NTCGCCTTCGATTGTA
1 -TCGCCTTCGATTGTA
39391745 AAAGCGAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.39
Consensus pattern (15 bp):
TCGCCTTCGATTGTA
Found at i:39394228 original size:3 final size:3
Alignment explanation
Indices: 39394220--39394251 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39394210 AACGATAAAA
39394220 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
39394252 TTAATACCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39394676 original size:3 final size:3
Alignment explanation
Indices: 39394668--39394694 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39394658 ATGTAATTCT
39394668 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
39394695 AATATGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39397408 original size:17 final size:17
Alignment explanation
Indices: 39397388--39397420 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39397378 AAAATGTTTT
*
39397388 TAATATTTAAATTTTAA
1 TAATATTAAAATTTTAA
39397405 TAATATTAAAATTTTA
1 TAATATTAAAATTTTA
39397421 TCCTGATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATATTAAAATTTTAA
Found at i:39404417 original size:25 final size:25
Alignment explanation
Indices: 39404389--39404437 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39404379 GTCACTTCAA
39404389 TTCTAATAATCAAATGTCATTCTGG
1 TTCTAATAATCAAATGTCATTCTGG
* * *
39404414 TTCTGATAATGAAATGTTATTCTG
1 TTCTAATAATCAAATGTCATTCTG
39404438 ATTATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (25 bp):
TTCTAATAATCAAATGTCATTCTGG
Found at i:39404440 original size:74 final size:73
Alignment explanation
Indices: 39404274--39404440 Score: 171
Period size: 74 Copynumber: 2.3 Consensus size: 73
39404264 AAAAGTAAAT
* * * * *
39404274 TATGATATGACATTCTGATTTGATAATGAAATGTTTTCTTATTCTAATAAATAAATATCATATTG
1 TATGAAATGTCATTCTGATTTGATAATAAAATGTCTTCTAATTCTAATAAATAAATATCATATTG
39404339 ATTCTGAA
66 ATTCTGAA
* * *
39404347 TATGATATGTCATTTTGATTTGATAATAAAATGTCACTTC-AATTCTAAT-AATCAAATGTCAT-
1 TATGAAATGTCATTCTGATTTGATAATAAAATGT--CTTCTAATTCTAATAAAT-AAATATCATA
*
39404409 TCTGGTTCTG-A
63 T-TGATTCTGAA
*
39404420 TAATGAAATGTTATTCTGATT
1 T-ATGAAATGTCATTCTGATT
39404441 ATAAAATATG
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
73 37 0.47
74 39 0.49
75 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (73 bp):
TATGAAATGTCATTCTGATTTGATAATAAAATGTCTTCTAATTCTAATAAATAAATATCATATTG
ATTCTGAA
Found at i:39406270 original size:87 final size:88
Alignment explanation
Indices: 39406111--39406312 Score: 235
Period size: 87 Copynumber: 2.3 Consensus size: 88
39406101 TACAGTGCAT
* * * * * * * *
39406111 TGCGGTAAACTACTGCACAGATATGTTGCAGTTTAAACTGCTAGATTAGATAATAGTACGCAGCA
1 TGCGGTAAACTACTGTACCGATAAGTTACAGTTTAAACTACCAGATCAGATAATAGTACGCAACA
* * *
39406176 AAACTGACATACATGCGGTATAG
66 AAACTGACATACAAGCGGTACAA
* * *
39406199 TGCGGTAAACTGCTGTACCTATAAGTTACAG-TTAAACTACCAGATCAGATAATAGTATGCAACA
1 TGCGGTAAACTACTGTACCGATAAGTTACAGTTTAAACTACCAGATCAGATAATAGTACGCAACA
* * *
39406263 AAGCTGACGTACAAGTGGTACAA
66 AAACTGACATACAAGCGGTACAA
*
39406286 TGCGGTAAACCACTGTACCGATAAGTT
1 TGCGGTAAACTACTGTACCGATAAGTT
39406313 GAGATCAAAT
Statistics
Matches: 94, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
87 69 0.73
88 25 0.27
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (88 bp):
TGCGGTAAACTACTGTACCGATAAGTTACAGTTTAAACTACCAGATCAGATAATAGTACGCAACA
AAACTGACATACAAGCGGTACAA
Found at i:39413322 original size:53 final size:53
Alignment explanation
Indices: 39413258--39413362 Score: 133
Period size: 53 Copynumber: 2.0 Consensus size: 53
39413248 ATCCTTTTTA
* * *
39413258 AACTTACCATTGACATGTCTT-GACAT-GCTCTTACATGGTATCCTTGCCTTATG
1 AACTCACCATTGACATGCCTTGGA-ATAG-TCTTACATGGGATCCTTGCCTTATG
* *
39413311 AACTCACCATTGTCATGCCTTGGAATAGTCTTACATGGGATCTTTGCCTTAT
1 AACTCACCATTGACATGCCTTGGAATAGTCTTACATGGGATCCTTGCCTTAT
39413363 CGTAGTTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
53 42 0.93
54 3 0.07
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (53 bp):
AACTCACCATTGACATGCCTTGGAATAGTCTTACATGGGATCCTTGCCTTATG
Found at i:39415474 original size:13 final size:13
Alignment explanation
Indices: 39415456--39415483 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39415446 TCAACATCAT
39415456 TTAACATACATAA
1 TTAACATACATAA
39415469 TTAACATACATAA
1 TTAACATACATAA
39415482 TT
1 TT
39415484 CATACATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAACATACATAA
Found at i:39417098 original size:46 final size:46
Alignment explanation
Indices: 39416871--39417097 Score: 307
Period size: 46 Copynumber: 4.9 Consensus size: 46
39416861 TTTGACATAA
* * * * * * *
39416871 TGCCATAGTGTCTTTCAACTATTGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCACGT
*
39416917 TGCCATGGTATCTTTCAACCATGGTCTTATT-ATTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCACGT
*
39416963 TGCCATGGTATTTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
*
39417009 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
*
39417055 TGCCATGGTATCTTTCAACCATGGTCTTACAT-ATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTA-TTCATTTCATATCA
39417098 GAGAGCACAC
Statistics
Matches: 167, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
45 6 0.04
46 159 0.95
47 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
Found at i:39419238 original size:11 final size:11
Alignment explanation
Indices: 39419222--39419273 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
39419212 CTTTCTTTAT
39419222 ATAATAATAAA
1 ATAATAATAAA
39419233 ATAATAATAAA
1 ATAATAATAAA
*
39419244 ATATATTATTAAA
1 ATA-A-TAATAAA
*
39419257 ATATTAATAAA
1 ATAATAATAAA
39419268 ATAATA
1 ATAATA
39419274 TTTATCTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 25 0.71
12 1 0.03
13 9 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATAATAAA
Done.