Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007961.1 Hibiscus syriacus cultivar Beakdansim tig00110388_pilon, 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: 2700559
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1011043 original size:19 final size:19
Alignment explanation
Indices: 1011021--1011062 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1011011 AAATCACAAC
1011021 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
1011040 GCGATTTTTATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
1011059 GCGA
1 GCGA
1011063 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:1011095 original size:19 final size:19
Alignment explanation
Indices: 1011030--1011096 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
1011020 CGCGAATTTA
*
1011030 ATTTCGCGTTGCGATTTTT
1 ATTTCGCGTTGCGATTTTC
1011049 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
1011066 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
1011082 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
1011097 AGTACTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 2 0.05
19 24 0.62
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1011213 original size:14 final size:14
Alignment explanation
Indices: 1011194--1011230 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1011184 CATCAATTAA
1011194 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1011208 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1011222 ACAAATCAA
1 ACAAATCAA
1011231 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1012650 original size:21 final size:21
Alignment explanation
Indices: 1012584--1012650 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1012574 GTGAATCGGG
*
1012584 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * * *
1012604 CCTCTTCAACAATGGCAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1012626 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1012647 CTCT
1 CTCT
1012651 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1012669 original size:42 final size:42
Alignment explanation
Indices: 1012623--1012702 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1012613 CAATGGCAGT
* * *
1012623 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1012665 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
1012703 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1014735 original size:20 final size:19
Alignment explanation
Indices: 1014704--1014825 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 19
1014694 TCTTTTGGTT
1014704 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1014723 GATAATGAGAATCGCAACGCA
1 GA-AATGAAAATCGCAACG-A
** *
1014744 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
1014763 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
1014777 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
1014796 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1014810 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1014826 TGCGATTTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
14 18 0.23
16 4 0.05
17 4 0.05
19 21 0.27
20 28 0.36
21 3 0.04
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1014786 original size:33 final size:33
Alignment explanation
Indices: 1014729--1014827 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
1014719 ACGAGATAAT
1014729 GAGAATCGCAACGCAGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAATGA
* *
1014763 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAATGA
**
1014796 GAGAATCGCAACGCGAAATGAAAATCGCAATG
1 GAGAATCGCAACGCGAAATGACTATCGCAATG
1014828 CGATTTTTGT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAATGA
Found at i:1014848 original size:19 final size:20
Alignment explanation
Indices: 1014826--1014870 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1014816 AAAATCGCAA
*
1014826 TGCGATTTTT-GTTTCGCGT
1 TGCGATTTTTCATTTCGCGT
1014845 TGCG-TTTTTCATTTCGCGT
1 TGCGATTTTTCATTTCGCGT
1014864 TGCGATT
1 TGCGATT
1014871 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 16 0.70
20 2 0.09
ACGTcount: A:0.07, C:0.18, G:0.24, T:0.51
Consensus pattern (20 bp):
TGCGATTTTTCATTTCGCGT
Found at i:1015446 original size:20 final size:20
Alignment explanation
Indices: 1015421--1015473 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1015411 GCGCTATGTA
1015421 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1015441 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1015461 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1015474 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1015507 original size:20 final size:20
Alignment explanation
Indices: 1015482--1015535 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1015472 GATTTTGTAT
1015482 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
1015502 TATCGCATTGCTATAGTCAG
1 TATCGCATTGCGATAGTAAG
1015522 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1015536 TTTTCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1015520 original size:61 final size:61
Alignment explanation
Indices: 1015422--1015538 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1015412 CGCTATGTAA
* * * * *
1015422 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * * *
1015483 ATCGCATTGCGATAGTAAGTATCGCATTGCTATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1015539 TCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1015646 original size:21 final size:21
Alignment explanation
Indices: 1015606--1015646 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1015596 ACTGTAGACC
**
1015606 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1015627 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1015647 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1016604 original size:2 final size:2
Alignment explanation
Indices: 1016597--1016639 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1016587 TTGTATTTAT
1016597 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1016638 TA
1 TA
1016640 AATAAGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1025101 original size:14 final size:15
Alignment explanation
Indices: 1025082--1025112 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1025072 ATCGCATCAA
1025082 AAATATT-ATATTTT
1 AAATATTAATATTTT
1025096 AAATATTAATATTTT
1 AAATATTAATATTTT
1025111 AA
1 AA
1025113 TAATGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATATTAATATTTT
Found at i:1025114 original size:14 final size:14
Alignment explanation
Indices: 1025083--1025131 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
1025073 TCGCATCAAA
1025083 AATATT-ATATTTT
1 AATATTAATATTTT
1025096 AAATATTAATATTTT
1 -AATATTAATATTTT
*
1025111 AATAATGAA-A-TTT
1 AAT-ATTAATATTTT
1025124 AATATTAA
1 AATATTAA
1025132 AAGATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 4 0.13
13 6 0.19
14 10 0.32
15 11 0.35
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
AATATTAATATTTT
Found at i:1032130 original size:25 final size:25
Alignment explanation
Indices: 1032102--1032152 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1032092 AAAAAATTAG
1032102 AACTTTTGTTCCCAAGTAGAGATGC
1 AACTTTTGTTCCCAAGTAGAGATGC
1032127 AACTTTTGTTCCCAAGTAGAGATGC
1 AACTTTTGTTCCCAAGTAGAGATGC
1032152 A
1 A
1032153 TTTAATCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (25 bp):
AACTTTTGTTCCCAAGTAGAGATGC
Found at i:1040459 original size:13 final size:13
Alignment explanation
Indices: 1040441--1040466 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1040431 CTATTCTTTC
1040441 TACCTTGTACCAT
1 TACCTTGTACCAT
1040454 TACCTTGTACCAT
1 TACCTTGTACCAT
1040467 CATATTGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
TACCTTGTACCAT
Found at i:1049363 original size:348 final size:350
Alignment explanation
Indices: 1048722--1049728 Score: 1887
Period size: 348 Copynumber: 2.9 Consensus size: 350
1048712 CAAGAAATGG
1048722 TGCAACAAACTCGTAAAGCCTCATCTATCTTACCCATAACAACCATGAAATAAAAAACCGGATCC
1 TGCAACAAACTCGTAAAGCCTCATCTATCTTACCCATAACAACCATGAAATAAAAAACCGGATCC
*
1048787 GACTGACTAGTTTAACCGAAAAGCAACAGTTCAACTGATCAACCTTCAGTTCATAATTTTCAAAT
66 GACTGACTAGTTTAACCGAAAAGCAATAGTTCAACTGATCAACCTTCAGTTCATAATTTTCAAAT
1048852 TAGTTGCAGCAATATGCTCTCTTTTGCTTACTTTCCTTTATATGAAATCAAAACCCTAACTTTTT
131 TAGTTGCAGCAATATGCTCTCTTTTGCTT--TTTCCTTTATATGAAATCAAAACCCTAACTTTTT
1048917 CTACAAGTTAGGGAATAATATACCTCCGCAGTGATGTACAAGGAGCTCATACTCTAACCTCAGAA
194 CTACAAGTTAGGGAATAATATACCTCCGCAGTGATGTACAAGGAGCTCATACTCTAACCTCAGAA
*
1048982 AAATAAGTCGATGAGACAGCCAACCCCTCGGCGTCCTAAGTTCGACGCAGTGATCTTTGGAAGGC
259 AAATAAGTCGATGAGACAGCCAACCCCTCGGCGTCGTAAGTTCGACGCAGTGATCTTTGGAAGGC
1049047 ACTTAAATTTAATTGAAAATTTAAAAA
324 ACTTAAATTTAATTGAAAATTTAAAAA
1049074 TGCAACAAACTCGTAAAGCCTCATCTATCTTACCCATAACAACCATGAAATAAAAAA-CGGATCC
1 TGCAACAAACTCGTAAAGCCTCATCTATCTTACCCATAACAACCATGAAATAAAAAACCGGATCC
1049138 GACTGACTAGTTTAACCGAAAAGCAATAGTTCAACTGATCAACCTTCAGTTCATAATTTTCAAAT
66 GACTGACTAGTTTAACCGAAAAGCAATAGTTCAACTGATCAACCTTCAGTTCATAATTTTCAAAT
1049203 TAGTTGCAGCAATATGCTCTCTTTTGCTTTTTCCTTTATATGAAATCAAAACCCTAAC-TTTTCT
131 TAGTTGCAGCAATATGCTCTCTTTTGCTTTTTCCTTTATATGAAATCAAAACCCTAACTTTTTCT
1049267 ACAAGTTAGGGAATAATATACCTCCGCAGTGATGTACAAGGAGCTCATACTCTAACCTCAGAAAA
196 ACAAGTTAGGGAATAATATACCTCCGCAGTGATGTACAAGGAGCTCATACTCTAACCTCAGAAAA
1049332 ATAAGTCGATGAGACAGCCAACCCCTCGGCGTCGTAAGTTCGACGCAGTGATCTTTGGAAGGCAC
261 ATAAGTCGATGAGACAGCCAACCCCTCGGCGTCGTAAGTTCGACGCAGTGATCTTTGGAAGGCAC
*
1049397 TTAAATTTAGTTGAAAATTTAAAAA
326 TTAAATTTAATTGAAAATTTAAAAA
* *
1049422 TGCAACAAACTCGTAAAGCCTCGTCTATCTTACCCATAATAACCATGAAATAAAAAACCGGATCC
1 TGCAACAAACTCGTAAAGCCTCATCTATCTTACCCATAACAACCATGAAATAAAAAACCGGATCC
*
1049487 GACTGACTAGTTTAACCGAAAAGCAATAGTTCAACTGATCAACCTTCAGTTCATAATTTTAAAAT
66 GACTGACTAGTTTAACCGAAAAGCAATAGTTCAACTGATCAACCTTCAGTTCATAATTTTCAAAT
* *
1049552 TAGTTACAGTAATATGCTCTCTTTTGC--TTTCCTTTATATGAAATCAAAACCCTAACTTTTTCT
131 TAGTTGCAGCAATATGCTCTCTTTTGCTTTTTCCTTTATATGAAATCAAAACCCTAACTTTTTCT
1049615 ACAAGTTAGGGAATAATATACCTCCGCAGTGATGTACAAGGAGCTCATACTCTAACCTCAGAAAA
196 ACAAGTTAGGGAATAATATACCTCCGCAGTGATGTACAAGGAGCTCATACTCTAACCTCAGAAAA
*
1049680 ATAAGTCGATGAGACAGCCAACCCCTCGGCGTCGTAAGTTCGAAGCAGT
261 ATAAGTCGATGAGACAGCCAACCCCTCGGCGTCGTAAGTTCGACGCAGT
1049729 CTCTGTCTCT
Statistics
Matches: 644, Mismatches: 9, Indels: 8
0.97 0.01 0.01
Matches are distributed among these distances:
347 29 0.05
348 333 0.52
349 125 0.19
351 100 0.16
352 57 0.09
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (350 bp):
TGCAACAAACTCGTAAAGCCTCATCTATCTTACCCATAACAACCATGAAATAAAAAACCGGATCC
GACTGACTAGTTTAACCGAAAAGCAATAGTTCAACTGATCAACCTTCAGTTCATAATTTTCAAAT
TAGTTGCAGCAATATGCTCTCTTTTGCTTTTTCCTTTATATGAAATCAAAACCCTAACTTTTTCT
ACAAGTTAGGGAATAATATACCTCCGCAGTGATGTACAAGGAGCTCATACTCTAACCTCAGAAAA
ATAAGTCGATGAGACAGCCAACCCCTCGGCGTCGTAAGTTCGACGCAGTGATCTTTGGAAGGCAC
TTAAATTTAATTGAAAATTTAAAAA
Found at i:1053783 original size:59 final size:60
Alignment explanation
Indices: 1053669--1053785 Score: 148
Period size: 59 Copynumber: 2.0 Consensus size: 60
1053659 CGTACATTTC
* * * *
1053669 GGATAAAATTGGAATGTTCAAAAATTTTGGGGACCAATTTAGTATGAAGGTCATAGTTTG
1 GGATAAAATTGAAATGTTCAAAAAGTTTGAGGACCAATTTAGAATGAAGGTCATAGTTTG
* * *
1053729 GGATGAAATTGAAATGTTC-AGAAGTTTGAGGACTAATTTAGAATGACA-GTCATAGTT
1 GGATAAAATTGAAATGTTCAAAAAGTTTGAGGACCAATTTAGAATGA-AGGTCATAGTT
1053786 ATTTAGAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 31 0.63
60 18 0.37
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (60 bp):
GGATAAAATTGAAATGTTCAAAAAGTTTGAGGACCAATTTAGAATGAAGGTCATAGTTTG
Found at i:1057946 original size:28 final size:28
Alignment explanation
Indices: 1057913--1057969 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1057903 TTGTTGCTAC
*
1057913 TTTCAATCACTAACTCGACGATATAATA
1 TTTCAAGCACTAACTCGACGATATAATA
* *
1057941 TTTCAAGCACTGATTCGACGATATAATA
1 TTTCAAGCACTAACTCGACGATATAATA
1057969 T
1 T
1057970 AAACAGATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (28 bp):
TTTCAAGCACTAACTCGACGATATAATA
Found at i:1063499 original size:20 final size:21
Alignment explanation
Indices: 1063471--1063511 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1063461 AAACTTTTTT
*
1063471 TAAT-TTTTTCTTTTAAAAAA
1 TAATATTTTTATTTTAAAAAA
1063491 TAATATTTTTATTTTAAAAAA
1 TAATATTTTTATTTTAAAAAA
1063512 ATAAGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATATTTTTATTTTAAAAAA
Found at i:1070931 original size:21 final size:19
Alignment explanation
Indices: 1070898--1070958 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
1070888 TATCTAAATT
1070898 TAATTATAAAAATATATAA
1 TAATTATAAAAATATATAA
1070917 TAAGTTATACAAAATGTATATAA
1 TAA-TTATA-AAAA--TATATAA
1070940 -AATTA-AAAAATATA-AA
1 TAATTATAAAAATATATAA
1070956 TAA
1 TAA
1070959 ATCATAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.05
17 6 0.16
19 7 0.19
20 6 0.16
21 7 0.19
22 2 0.05
23 7 0.19
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (19 bp):
TAATTATAAAAATATATAA
Found at i:1070939 original size:20 final size:20
Alignment explanation
Indices: 1070901--1070958 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
1070891 CTAAATTTAA
1070901 TTATAAAAATATATAATAAG
1 TTATAAAAATATATAATAAG
1070921 TTATACAAAATGTATATAA-AA-
1 TTATA-AAAA--TATATAATAAG
1070942 TTA-AAAAATATA-AATAA
1 TTATAAAAATATATAATAA
1070959 ATCATAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.06
17 6 0.18
19 4 0.12
20 6 0.18
21 7 0.21
22 2 0.06
23 7 0.21
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (20 bp):
TTATAAAAATATATAATAAG
Found at i:1072359 original size:24 final size:24
Alignment explanation
Indices: 1072332--1072392 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
1072322 TTTGATAATT
*
1072332 AATTTTTCTTCTCTAAAA-TTTATA
1 AATTTGTCTTCT-TAAAATTTTATA
* *
1072356 AATTCGTCTTGTTAAAATTTTATA
1 AATTTGTCTTCTTAAAATTTTATA
1072380 AATTTGTC-TCTTA
1 AATTTGTCTTCTTA
1072393 GCCTACAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 9 0.29
24 22 0.71
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.52
Consensus pattern (24 bp):
AATTTGTCTTCTTAAAATTTTATA
Found at i:1081998 original size:64 final size:64
Alignment explanation
Indices: 1081928--1082083 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 64
1081918 ATGCACATGA
* ** *
1081928 AGTGCATCGATGCA-CTCTTTTAAAATACAAACATCGAAT-GCAATTAATGCATCGATGCATAAG
1 AGTGCATCGATGCATCCCCATT-AAATACAAACATCAAATAG-AATTAATGCATCGATGCATAAG
1081991 G
64 G
* * *
1081992 AGTGCATCGATGCATCCCCATTAAATACAAACATCAAATAGGATTTATGCATCGATGCAT-GGTG
1 AGTGCATCGATGCATCCCCATTAAATACAAACATCAAATAGAATTAATGCATCGATGCATAAG-G
*
1082056 TAGTGCATGGATGCATACCTCCATTAAA
1 -AGTGCATCGATGCAT-CC-CCATTAAA
1082084 AGATGAAAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 48 0.62
65 19 0.24
66 2 0.03
67 8 0.10
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
AGTGCATCGATGCATCCCCATTAAATACAAACATCAAATAGAATTAATGCATCGATGCATAAGG
Found at i:1082363 original size:25 final size:25
Alignment explanation
Indices: 1082308--1082365 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1082298 ATAAGTCTAG
* *
1082308 ATTCAATATTTTGATACATGATCGTA
1 ATTC-ATATTATGATACATGATCATA
*
1082334 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCAT-A
1082359 ATTCATA
1 ATTCATA
1082366 CCATATGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.07
25 22 0.81
26 3 0.11
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCATA
Found at i:1082729 original size:23 final size:23
Alignment explanation
Indices: 1082661--1082729 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1082651 TATTATTATA
*
1082661 TGGCACTCCGGTGCAATTCTACA
1 TGGCACTCCGGTGCAATTCTACG
* *
1082684 CGGCACTCCGGTGTAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
* *
1082707 TGGCACTTCGGTGCAATTATACG
1 TGGCACTCCGGTGCAATTCTACG
1082730 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTACG
Found at i:1088922 original size:64 final size:65
Alignment explanation
Indices: 1088852--1089007 Score: 192
Period size: 64 Copynumber: 2.4 Consensus size: 65
1088842 ATGCACATGA
* **
1088852 AGTGCATCGATGCA-CTCTTTTAAAATACAAACATCGAAT-GCAATTAATGCATCGATGCAT-AA
1 AGTGCATCGATGCATCCCCATT-AAATACAAACATCGAATAG-AATTAATGCATCGATGCATGAA
1088914 GG
64 GG
* * * *
1088916 AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGAGT
1 AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGAATTAATGCATCGATGCATGAAGG
1088981 AGTGCATCGATGCATACCTCCATTAAA
1 AGTGCATCGATGCAT-CC-CCATTAAA
1089008 AGATGAAAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
64 48 0.60
65 22 0.28
66 2 0.03
67 8 0.10
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (65 bp):
AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGAATTAATGCATCGATGCATGAAGG
Found at i:1089619 original size:23 final size:23
Alignment explanation
Indices: 1089588--1089655 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1089578 ATTATTATAT
*
1089588 GGCATTCCGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
1089611 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* * *
1089634 GGCACTTCGATGCAATTATACG
1 GGCACTCCGGTGCAATTCTACG
1089656 AGCTGCGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:1096414 original size:20 final size:20
Alignment explanation
Indices: 1096391--1096442 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1096381 AACGCGATCC
1096391 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1096411 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1096431 CCAAAATCGCAA
1 CCAGAATCGCAA
1096443 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1096459 original size:21 final size:20
Alignment explanation
Indices: 1096432--1096530 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1096422 AATCAGTTTC
1096432 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1096453 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1096474 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1096494 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1096515 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1096531 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1096559 original size:20 final size:20
Alignment explanation
Indices: 1096497--1096690 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1096487 CGATTTTCCA
* ** *
1096497 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1096517 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1096537 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1096557 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1096577 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1096597 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1096617 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1096637 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1096657 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1096678 AAATCGCAACGCG
1 AAATCGCAACGCG
1096691 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1096581 original size:60 final size:60
Alignment explanation
Indices: 1096497--1096690 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1096487 CGATTTTCCA
* ** * *
1096497 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1096557 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1096617 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1096678 AAATCGCAACGCG
1 AAATCGCAACGCG
1096691 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1097111 original size:33 final size:33
Alignment explanation
Indices: 1097072--1097142 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1097062 TTCACTTAGA
*
1097072 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1097105 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1097138 TTTCA
1 TTTCA
1097143 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1097282 original size:14 final size:14
Alignment explanation
Indices: 1097263--1097317 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1097253 AGAATGACTG
1097263 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1097277 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
1097296 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1097310 TCGCAACG
1 TCGCAACG
1097318 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1097330 original size:33 final size:33
Alignment explanation
Indices: 1097263--1097333 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1097253 AGAATGACTG
***
1097263 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1097296 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1097329 TCGCA
1 TCGCA
1097334 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1097351 original size:19 final size:19
Alignment explanation
Indices: 1097329--1097426 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1097319 GAAACCAAAA
*
1097329 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1097348 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1097362 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1097381 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1097395 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1097414 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1097427 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1097370 original size:14 final size:14
Alignment explanation
Indices: 1097351--1097440 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1097341 TTTCATTTCG
1097351 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1097365 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1097384 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1097398 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1097415 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1097431 CGTTGCGATT
1 CGTTGCGATT
1097441 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1097376 original size:33 final size:33
Alignment explanation
Indices: 1097334--1097448 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1097324 CAAAATCGCA
1097334 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1097367 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1097400 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1097433 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1097449 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1099376 original size:185 final size:185
Alignment explanation
Indices: 1099147--1099618 Score: 928
Period size: 185 Copynumber: 2.6 Consensus size: 185
1099137 TAGATTGCTT
1099147 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1099212 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1099277 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG-TTTGTCTTTTGGTTGAA
1099332 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1099397 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1099462 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAA
1099517 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1099582 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
1099619 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 274 0.96
186 12 0.04
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAA
Found at i:1099461 original size:93 final size:93
Alignment explanation
Indices: 1099147--1099618 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
1099137 TAGATTGCTT
1099147 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1099212 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1099240 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1099304 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1099332 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1099397 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1099425 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1099490 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1099517 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1099582 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1099610 AGTAAATTT
1 AGTAAATTT
1099619 ATCCATTCAA
Statistics
Matches: 377, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.49
93 193 0.51
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1099702 original size:19 final size:19
Alignment explanation
Indices: 1099662--1099790 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1099652 TAGTTTACTT
* *
1099662 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1099682 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1099701 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1099720 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1099734 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1099753 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1099767 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1099786 TCGCA
1 TCGCA
1099791 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1099741 original size:33 final size:32
Alignment explanation
Indices: 1099698--1099790 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1099688 CGCGAAACCA
**
1099698 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1099730 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1099763 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1099791 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1099788 original size:52 final size:52
Alignment explanation
Indices: 1099662--1099790 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1099652 TAGTTTACTT
**
1099662 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1099714 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1099767 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1099791 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1099808 original size:19 final size:19
Alignment explanation
Indices: 1099786--1099920 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1099776 GAAACCAAAA
*
1099786 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1099805 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1099821 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1099838 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1099854 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1099871 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1099890 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1099910 TCGTGTTGCGA
1 TCGCGTTGCGA
1099921 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1099827 original size:14 final size:14
Alignment explanation
Indices: 1099808--1099864 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1099798 TTTCATTTCG
1099808 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1099822 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1099839 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1099855 CGTTGCGATT
1 CGTTGCGATT
1099865 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1099833 original size:33 final size:33
Alignment explanation
Indices: 1099791--1099883 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1099781 CAAAATCGCA
*
1099791 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1099824 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1099857 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1099884 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1101846 original size:14 final size:14
Alignment explanation
Indices: 1101827--1101862 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1101817 ATTGTTTAAT
1101827 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1101841 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1101855 TGATTTGT
1 TGATTTGT
1101863 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1101985 original size:19 final size:19
Alignment explanation
Indices: 1101969--1102070 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1101959 AAAAATGACT
1101969 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1101988 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1102007 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1102021 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1102040 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1102060 ATCGCAATGCG
1 ATCGCAATGCG
1102071 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1102123 original size:19 final size:19
Alignment explanation
Indices: 1102099--1102404 Score: 340
Period size: 19 Copynumber: 17.4 Consensus size: 19
1102089 GATTATCTCG
1102099 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1102118 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1102137 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1102151 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1102170 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1102189 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
* *
1102208 TTGCGATTTTAATTTCGTA
1 TTGCGATTTTCATTTCGCA
* *
1102227 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
1102242 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1102260 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1102279 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1102293 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1102312 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1102330 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1102344 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1102364 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1102378 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1102397 TTGCGATT
1 TTGCGATT
1102405 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 12, Indels: 52
0.80 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.12
17 28 0.11
18 23 0.09
19 121 0.49
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1102260 original size:142 final size:135
Alignment explanation
Indices: 1102067--1102404 Score: 475
Period size: 142 Copynumber: 2.4 Consensus size: 135
1102057 AAAATCGCAA
*
1102067 TGCG-TTTATAATTTCGCATTACGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTAT-TCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
1102131 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCGA-
*
1102196 TTTCATTTCGTAT
127 -TTC-TCTCG--T
*
1102209 TGCGATTTTAATTTCGTATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTAT-TC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1102273 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATT
1102338 CTCTCGT
129 CTCTCGT
* * *
1102345 TGCGATTTTCATTTCCGCATTGCGATT-TTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATTC--GTTGCGATTTTCATTTCGCATTGCGATT
1102405 GTATTTTCCG
Statistics
Matches: 181, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
135 2 0.01
136 18 0.10
137 33 0.18
138 4 0.02
139 3 0.02
141 18 0.10
142 97 0.54
143 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (135 bp):
TGCGATTTTAATTTCGCATTGCGATTATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTCT
CTCGT
Found at i:1102364 original size:52 final size:52
Alignment explanation
Indices: 1102099--1102376 Score: 336
Period size: 52 Copynumber: 5.2 Consensus size: 52
1102089 GATTATCTCG
*
1102099 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
1102151 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * * *
1102208 TTGCGATTTTAATTTCGTATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
1102260 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1102312 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
1102364 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1102377 GTTGGGATTT
Statistics
Matches: 208, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
51 44 0.21
52 119 0.57
53 8 0.04
54 6 0.03
55 8 0.04
57 23 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:1104727 original size:12 final size:12
Alignment explanation
Indices: 1104710--1104734 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1104700 TCTTCGGGGA
1104710 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1104722 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1104734 C
1 C
1104735 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1104943 original size:24 final size:24
Alignment explanation
Indices: 1104909--1104955 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1104899 CTGAAACATC
1104909 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1104933 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1104956 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1105656 original size:20 final size:20
Alignment explanation
Indices: 1105628--1105996 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
1105618 AAATTTCAGT
* * * *
1105628 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1105648 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1105668 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1105688 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1105708 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1105728 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1105748 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1105768 GTTGCGATTTATGGATACGC
1 GTTGCGATTTACGGATACGC
*
1105788 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1105808 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1105828 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1105848 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1105868 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1105888 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1105908 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1105928 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1105948 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1105968 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1105988 GTTGCGATT
1 GTTGCGATT
1105997 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 297 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1106788 original size:10 final size:10
Alignment explanation
Indices: 1106769--1106802 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1106759 CATTTAAATG
*
1106769 ATAAATGAAC
1 ATAAACGAAC
1106779 ATAAACGAAC
1 ATAAACGAAC
*
1106789 GTAAACGAAC
1 ATAAACGAAC
1106799 ATAA
1 ATAA
1106803 TAAACGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.15
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1107106 original size:24 final size:26
Alignment explanation
Indices: 1107072--1107127 Score: 89
Period size: 24 Copynumber: 2.2 Consensus size: 26
1107062 TGTCATATGT
*
1107072 TCGAACATAAATGAACGATCATA-AA
1 TCGAACATAAATGAACGAACATATAA
1107097 T-GAACATAAATGAACGAACATATAA
1 TCGAACATAAATGAACGAACATATAA
1107122 TCGAAC
1 TCGAAC
1107128 GTTCACGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 20 0.71
25 4 0.14
26 4 0.14
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (26 bp):
TCGAACATAAATGAACGAACATATAA
Found at i:1107127 original size:16 final size:14
Alignment explanation
Indices: 1107073--1107128 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
1107063 GTCATATGTT
1107073 CGAACATAAATGAA
1 CGAACATAAATGAA
*
1107087 CGATCATAAAT---
1 CGAACATAAATGAA
1107098 -GAACATAAATGAA
1 CGAACATAAATGAA
1107111 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
1107127 CG
1 CG
1107129 TTCACGAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 9 0.26
14 17 0.50
15 3 0.09
16 5 0.15
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:1126496 original size:17 final size:16
Alignment explanation
Indices: 1126474--1126516 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
1126464 TTCAGAAGGA
1126474 AAAAATAATTAACTAAT
1 AAAAATAATTAA-TAAT
1126491 AAAAATAA--AATAAT
1 AAAAATAATTAATAAT
*
1126505 ATAAATAATTAA
1 AAAAATAATTAA
1126517 GTGACTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 2 0.09
17 8 0.35
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATAATTAATAAT
Found at i:1133002 original size:25 final size:23
Alignment explanation
Indices: 1132957--1133002 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
1132947 AAACACAATA
* *
1132957 ATTTGAAAATTAACAATTTTTTT
1 ATTTGAAAATTAAAAAATTTTTT
1132980 ATTTCGAAAATTTAAAAAATTTT
1 ATTT-GAAAA-TTAAAAAATTTT
1133003 GGAAAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 5 0.26
25 10 0.53
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
ATTTGAAAATTAAAAAATTTTTT
Found at i:1154667 original size:37 final size:37
Alignment explanation
Indices: 1154620--1154691 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
1154610 TGTCTAAAAC
*
1154620 AGACTTTCCCATGTTCTGCTTCATCCAGTCAATGTTG
1 AGACCTTCCCATGTTCTGCTTCATCCAGTCAATGTTG
1154657 AGACCTTCCCATGTTCTGCTTCATCCAGTCAATGT
1 AGACCTTCCCATGTTCTGCTTCATCCAGTCAATGT
1154692 AAGTCAACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.36
Consensus pattern (37 bp):
AGACCTTCCCATGTTCTGCTTCATCCAGTCAATGTTG
Found at i:1159915 original size:22 final size:21
Alignment explanation
Indices: 1159890--1159931 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1159880 GGATTCTACC
1159890 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
1159912 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
1159932 CATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:1165547 original size:16 final size:16
Alignment explanation
Indices: 1165528--1165568 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1165518 AAGATACATC
1165528 GCTACAGTAGAGATTT
1 GCTACAGTAGAGATTT
1165544 GCTACAGTAGAGATTT
1 GCTACAGTAGAGATTT
*
1165560 GTTACAGTA
1 GCTACAGTA
1165569 CCACGCCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (16 bp):
GCTACAGTAGAGATTT
Found at i:1166709 original size:21 final size:22
Alignment explanation
Indices: 1166665--1166709 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1166655 AAATGGTTAG
*
1166665 AAGATCTGATTGATAAAATTAA
1 AAGATCTGATTGATAAAATGAA
1166687 AAGATC-GA-TGATCAAAATGAA
1 AAGATCTGATTGAT-AAAATGAA
1166708 AA
1 AA
1166710 AGTATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.24
Consensus pattern (22 bp):
AAGATCTGATTGATAAAATGAA
Found at i:1174612 original size:8 final size:8
Alignment explanation
Indices: 1174599--1174626 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1174589 AAATATAATA
1174599 TTTTCTAT
1 TTTTCTAT
1174607 TTTTCTAT
1 TTTTCTAT
1174615 TTTTCTAT
1 TTTTCTAT
1174623 TTTT
1 TTTT
1174627 TTATGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCTAT
Found at i:1175299 original size:19 final size:20
Alignment explanation
Indices: 1175266--1175305 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1175256 AGATTCTAAC
1175266 ATATTAAAAAGTTAAA-AAA
1 ATATTAAAAAGTTAAAGAAA
1175285 ATATTAAAATA-TTAAAGAAA
1 ATATTAAAA-AGTTAAAGAAA
1175305 A
1 A
1175306 ACTATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
ATATTAAAAAGTTAAAGAAA
Found at i:1178065 original size:20 final size:19
Alignment explanation
Indices: 1178040--1178093 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1178030 GTGAAATAAA
1178040 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
1178060 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
1178080 AATCGCAACGCGAT
1 AATCGCAACGCGAT
1178094 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:1178141 original size:21 final size:21
Alignment explanation
Indices: 1178101--1178155 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1178091 GATTATGAAG
1178101 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAT
* **
1178121 AATTCGCATTGCGATTTTACAT
1 AA-TCGCAATGCGATAGTACAT
*
1178143 AATCGCAACGCGA
1 AATCGCAATGCGA
1178156 ACATATAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAT
Found at i:1178246 original size:81 final size:80
Alignment explanation
Indices: 1178143--1178373 Score: 236
Period size: 80 Copynumber: 2.9 Consensus size: 80
1178133 GATTTTACAT
* ** * *
1178143 AATCGCAACGCGAACATATAAATCGCAACGCGATTCTG-ACTATCGCAACGAGTAT-CTGTAAAA
1 AATCGCAACGCGAATACGTAAATCGCAACGCGATTCTGTA-AATCGCAACGAGAATAC-GT-AAA
* *
1178206 TCGCAACGCGTATCCGTA
63 TCACAACGCATATCCGTA
* *
1178224 AATCGCAACGAGAATACGTAAATCGCAACGCGTTTCTGTAAATCGCAACGAGAATACGTAAATCA
1 AATCGCAACGCGAATACGTAAATCGCAACGCGATTCTGTAAATCGCAACGAGAATACGTAAATCA
* *
1178289 CAATGCATATTCGTA
66 CAACGCATATCCGTA
* * * * *
1178304 AATCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GTAAATCGCAATGCGAAT-CTGTAAAT
1 AATCGCAACGCGAATACGTAAATCGCAACGCG-ATTCTGTAAATCGCAACGAGAATAC-GTAAAT
*
1178367 CGCAACG
64 CACAACG
1178374 AGATTCTGAC
Statistics
Matches: 126, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
79 1 0.01
80 73 0.58
81 50 0.40
82 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (80 bp):
AATCGCAACGCGAATACGTAAATCGCAACGCGATTCTGTAAATCGCAACGAGAATACGTAAATCA
CAACGCATATCCGTA
Found at i:1178265 original size:40 final size:39
Alignment explanation
Indices: 1178143--1178373 Score: 198
Period size: 40 Copynumber: 5.8 Consensus size: 39
1178133 GATTTTACAT
* * ** *
1178143 AATCGCAACGCGAACATATAAATCGCAACGCGATTC-TGA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTTTCGT-A
* * *
1178182 CTATCGCAACGAGTAT-CTGTAAAATCGCAACGCGTATCCGTA
1 -AATCGCAACGAGAATAC-GT-AAATCGCAACGCGT-TTCGTA
1178224 AATCGCAACGAGAATACGTAAATCGCAACGCGTTTCTGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTTTC-GTA
* * *
1178264 AATCGCAACGAGAATACGTAAATCACAATGCATATTCGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGT-TTCGTA
* * * * *
1178304 AATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCG-TTTCGTA
* *
1178344 AATCGCAATGCGAAT-CTGTAAATCGCAACG
1 AATCGCAACGAGAATAC-GTAAATCGCAACG
1178374 AGATTCTGAC
Statistics
Matches: 161, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
39 3 0.02
40 122 0.76
41 31 0.19
42 4 0.02
43 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (39 bp):
AATCGCAACGAGAATACGTAAATCGCAACGCGTTTCGTA
Found at i:1178304 original size:60 final size:59
Alignment explanation
Indices: 1178143--1178373 Score: 198
Period size: 60 Copynumber: 3.8 Consensus size: 59
1178133 GATTTTACAT
* ** * * * * *
1178143 AATCGCAACGCGAACATATAAATCGCAACGCGATTC-TGACTATCGCAACGAGTATCTGTAA
1 AATCGCAACGCGAATACGTAAATCGCAATGCAATTCGT-A-AATCGCAACGCGTTTCTGT-A
* * * * *
1178204 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGCGTTTCTGTA
1 AATCGCAACGCGAATACGTAAATCGCAATG-CAATTCGTAAATCGCAACGCGTTTCTGTA
* * * * *
1178264 AATCGCAACGAGAATACGTAAATCACAATGCATATTCGTAAATCGCAATGCGAATAC-GTA
1 AATCGCAACGCGAATACGTAAATCGCAATGCA-ATTCGTAAATCGCAACGCG-TTTCTGTA
*
1178324 AATCGCAATGCGAATACGTAAATCGCAATGCGAA-TCTGTAAATCGCAACG
1 AATCGCAACGCGAATACGTAAATCGCAATGC-AATTC-GTAAATCGCAACG
1178374 AGATTCTGAC
Statistics
Matches: 139, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
59 3 0.02
60 87 0.63
61 44 0.32
62 4 0.03
63 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (59 bp):
AATCGCAACGCGAATACGTAAATCGCAATGCAATTCGTAAATCGCAACGCGTTTCTGTA
Found at i:1178381 original size:20 final size:19
Alignment explanation
Indices: 1178161--1178379 Score: 131
Period size: 20 Copynumber: 10.9 Consensus size: 19
1178151 CGCGAACATA
*
1178161 TAAATCGCAACGCGATTC-
1 TAAATCGCAACGAGATTCG
*
1178179 TGACTATCGCAACGAG-TATCTG
1 T-A-AATCGCAACGAGAT-TC-G
* *
1178201 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGAG-ATTCG
*
1178222 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGAG-ATTCG
* *
1178242 TAAATCGCAACGCGTTTCTG
1 TAAATCGCAACGAGATTC-G
*
1178262 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGAG-ATTCG
* * *
1178282 TAAATCACAATGCATATTCG
1 TAAATCGCAACG-AGATTCG
*
1178302 TAAATCGCAATGCGA-ATACG
1 TAAATCGCAA--CGAGATTCG
*
1178322 TAAATCGCAATGCGA-ATACG
1 TAAATCGCAA--CGAGATTCG
* * *
1178342 TAAATCGCAATGCGAATCTG
1 TAAATCGCAACGAGATTC-G
1178362 TAAATCGCAACGAGATTC
1 TAAATCGCAACGAGATTC
1178380 TGACTATCAC
Statistics
Matches: 158, Mismatches: 29, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 129 0.82
21 16 0.10
22 4 0.03
23 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (19 bp):
TAAATCGCAACGAGATTCG
Found at i:1179260 original size:24 final size:24
Alignment explanation
Indices: 1179233--1179286 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1179223 GTATTCGAAA
1179233 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1179257 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1179281 TTTGAT
1 TTTGAT
1179287 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1181726 original size:20 final size:20
Alignment explanation
Indices: 1181701--1181754 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1181691 AGACATTCAT
**
1181701 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACACGGAA
1181721 TTGACTATCGCAACACGGAA
1 TTGACTATCGCAACACGGAA
*
1181741 ATGACTATCGCAAC
1 TTGACTATCGCAAC
1181755 GAGAGAATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACACGGAA
Found at i:1181815 original size:34 final size:33
Alignment explanation
Indices: 1181738--1181822 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
1181728 TCGCAACACG
**
1181738 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
1181771 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1181804 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
1181823 CAAAATTAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 31 0.65
34 17 0.35
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:1181897 original size:19 final size:19
Alignment explanation
Indices: 1181873--1181926 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
1181863 GATTCACTCG
1181873 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
*
1181892 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCACA
1181911 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1181927 CGCGTTGCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:1181899 original size:33 final size:35
Alignment explanation
Indices: 1181838--1181926 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 35
1181828 TTAGTTTCGT
* *
1181838 GTTGAGATTTTCATTTTCGCATTGCGA-TTCA-CTC
1 GTTGCGATTTTCA-TTTCACATTGCGATTTCATCTC
*
1181872 GTTGCGATTTTCATTTCACATTGCGATTTTCATTTC
1 GTTGCGATTTTCATTTCACATTGCGA-TTTCATCTC
1181908 GCATTGCGATTTTCATTTC
1 G--TTGCGATTTTCATTTC
1181927 CGCGTTGCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 12 0.26
34 12 0.26
35 4 0.09
36 3 0.06
38 16 0.34
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.47
Consensus pattern (35 bp):
GTTGCGATTTTCATTTCACATTGCGATTTCATCTC
Found at i:1182058 original size:14 final size:14
Alignment explanation
Indices: 1182039--1182075 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1182029 CATCAATTAA
1182039 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1182053 ACAAATCATCTTTT
1 ACAAATCAACATTT
1182067 ACAAATCAA
1 ACAAATCAA
1182076 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1183453 original size:21 final size:21
Alignment explanation
Indices: 1183387--1183453 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1183377 GTGAATCGGG
*
1183387 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1183407 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1183429 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1183450 CTCT
1 CTCT
1183454 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1183472 original size:42 final size:41
Alignment explanation
Indices: 1183387--1183509 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1183377 GTGAATCGGG
* * * *
1183387 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1183429 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1183471 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1183510 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1185506 original size:20 final size:20
Alignment explanation
Indices: 1185476--1185576 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 20
1185466 TTTTGGTTGA
1185476 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
** *
1185496 AATGACTATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
** *
1185515 AAATGACTATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
1185535 AATGAAAATCGCAACGAGA-
1 AATGAAAATCGCAACGAGAG
*
1185554 AATTAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1185574 AAT
1 AAT
1185577 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
19 35 0.49
20 36 0.51
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1185598 original size:19 final size:19
Alignment explanation
Indices: 1185474--1185605 Score: 121
Period size: 19 Copynumber: 7.1 Consensus size: 19
1185464 TCTTTTGGTT
*
1185474 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
1185493 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1185513 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
1185533 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1185552 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1185569 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
1185585 GAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1185604 GA
1 GA
1185606 TTTTGGTTTC
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 46 0.49
20 31 0.33
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1185701 original size:20 final size:19
Alignment explanation
Indices: 1185632--1185703 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
1185622 CGATTCTCTC
1185632 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
** *
1185652 CGTTGCGATAGTCAATTTCGT
1 -GTTGCGATTTTCATTTTC-T
1185673 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
1185693 GTTGCGATTTT
1 GTTGCGATTTT
1185704 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:1186296 original size:20 final size:21
Alignment explanation
Indices: 1186262--1186417 Score: 65
Period size: 20 Copynumber: 7.7 Consensus size: 21
1186252 CGCTTTAAAA
* *
1186262 ATCGCGTTGCGATTTACGGAT
1 ATCGCATTGCAATTTACGGAT
* * *
1186283 AT-GCGTTTCAATTTTACGTAT
1 ATCGCATTGCAA-TTTACGGAT
1186304 -TCGCATTGCAATTTACGGAT
1 ATCGCATTGCAATTTACGGAT
* * *
1186324 A-CACATTGCGATTTACGTAT
1 ATCGCATTGCAATTTACGGAT
* * * **
1186344 -TCTCGTTGCGATTTATAGAT
1 ATCGCATTGCAATTTACGGAT
* * *
1186364 AT-GCGTTGCGATTTACGTAT
1 ATCGCATTGCAATTTACGGAT
* * *
1186384 -TCTCGTTGCGATTTACGGAT
1 ATCGCATTGCAATTTACGGAT
* *
1186404 A-CGCGTTGCGATTT
1 ATCGCATTGCAATTT
1186418 TACGTATTGT
Statistics
Matches: 107, Mismatches: 21, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.01
20 88 0.82
21 18 0.17
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (21 bp):
ATCGCATTGCAATTTACGGAT
Found at i:1186345 original size:40 final size:40
Alignment explanation
Indices: 1186266--1186538 Score: 235
Period size: 40 Copynumber: 6.8 Consensus size: 40
1186256 TTAAAAATCG
* * * *
1186266 CGTTGCGATTTACGGATATGCGTTTCAATTTTACGTATTCG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* * * *
1186307 CATTGCAATTTACGGATACACATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
** *
1186347 CGTTGCGATTTATAGATATGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
1186387 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* ** * * *
1186428 CGTTGCGATTTATGGATACGTATTACGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* * ** * *
1186469 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTTACGTATTCT
* ** *
1186509 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGGATACGCGTTGCGATT
1186539 ATGTAAAATC
Statistics
Matches: 186, Mismatches: 41, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
39 1 0.01
40 100 0.54
41 84 0.45
42 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:1186432 original size:41 final size:41
Alignment explanation
Indices: 1186266--1186477 Score: 248
Period size: 41 Copynumber: 5.2 Consensus size: 41
1186256 TTAAAAATCG
* * * *
1186266 CGTTGCGATTTACGGATATGCGTTTCAATTTTACGTATTCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
1186307 CATTGCAATTTACGGATACACATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
** *
1186347 CGTTGCGATTTATAGATATGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1186387 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* ** * * *
1186428 CGTTGCGATTTATGGATACGTATTACGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
1186469 CGTTGCGAT
1 CGTTGCGAT
1186478 AGTCAGAATC
Statistics
Matches: 144, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
40 69 0.48
41 75 0.52
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1186509 original size:20 final size:20
Alignment explanation
Indices: 1186486--1186538 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1186476 ATAGTCAGAA
*
1186486 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1186506 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1186526 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1186539 ATGTAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1186556 original size:21 final size:20
Alignment explanation
Indices: 1186532--1186580 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1186522 ATATTCGCGT
1186532 TGCGATTATGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
1186553 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
1186574 TGCGATT
1 TGCGATT
1186581 CTGGGAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.75
22 3 0.12
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:1186616 original size:20 final size:20
Alignment explanation
Indices: 1186573--1186617 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1186563 TACTATCGCA
*
1186573 TTGCGATTCTGGGAACTGAT
1 TTGCGATTCTGGGAACTGAG
*
1186593 TTGCGATTCTGGAGATC-GAG
1 TTGCGATTCTGG-GAACTGAG
1186613 TTGCG
1 TTGCG
1186618 TTTTTATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.33
Consensus pattern (20 bp):
TTGCGATTCTGGGAACTGAG
Found at i:1204480 original size:29 final size:29
Alignment explanation
Indices: 1204442--1204497 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1204432 GAGGATCTTA
1204442 AGCTCTCTAAGACAATAACAGATGCTAAG
1 AGCTCTCTAAGACAATAACAGATGCTAAG
* *
1204471 AGCTCTCTAAGATAATAATAGATGCTA
1 AGCTCTCTAAGACAATAACAGATGCTA
1204498 CAAATGAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (29 bp):
AGCTCTCTAAGACAATAACAGATGCTAAG
Found at i:1207101 original size:26 final size:26
Alignment explanation
Indices: 1207072--1207124 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1207062 ATTAAGAGTG
* *
1207072 AACTTCTAAAGTTTTAGAGAGAGATA
1 AACTTCTAAAATTTTAGAGAGAAATA
*
1207098 AACTTCTAAAATTTTAGGGAGAAATA
1 AACTTCTAAAATTTTAGAGAGAAATA
1207124 A
1 A
1207125 TATTATCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (26 bp):
AACTTCTAAAATTTTAGAGAGAAATA
Found at i:1208500 original size:36 final size:37
Alignment explanation
Indices: 1208444--1208520 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 37
1208434 TCGTAGCCGC
* *
1208444 AACCTAATCAACTTGTGTTTCTTTGGAATACTTGATG
1 AACCTAATCAACTTGCGTTTCTTTGGAACACTTGATG
1208481 AACC-AATCAACTTGCGTTTCTTTGGAACACTTGATG
1 AACCTAATCAACTTGCGTTTCTTTGGAACACTTGATG
1208517 AACC
1 AACC
1208521 CCCTGAGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 34 0.89
37 4 0.11
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (37 bp):
AACCTAATCAACTTGCGTTTCTTTGGAACACTTGATG
Found at i:1210331 original size:64 final size:64
Alignment explanation
Indices: 1210261--1210419 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 64
1210251 TACACTTGGG
* * * **
1210261 GTGTATCGGTACACTAATTGCATTCGATGTTTTAATAAAGCCA-GAGTGTATCGATGCATAGGAT
1 GTGTATCGGTACACAAAATGCATTCGATGTTTCAATAAAAACAGGAGTGTATCGATGCAT-GGAT
* *
1210325 GTGTATCGGTACACAAAATGCATTCGATGTTTCAATAAAAATAGGAGTGTATCGATGCATGGTT
1 GTGTATCGGTACACAAAATGCATTCGATGTTTCAATAAAAACAGGAGTGTATCGATGCATGGAT
* *
1210389 GTGCATCGGTACATAAAATGGC-TTCGATGTT
1 GTGTATCGGTACACAAAAT-GCATTCGATGTT
1210420 GGGTGTGCAT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
64 66 0.79
65 18 0.21
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (64 bp):
GTGTATCGGTACACAAAATGCATTCGATGTTTCAATAAAAACAGGAGTGTATCGATGCATGGAT
Found at i:1217147 original size:21 final size:21
Alignment explanation
Indices: 1217110--1217149 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1217100 CCCCCTTTGA
*
1217110 AGGGGAACTGATTCCCCCCAC
1 AGGGGAACTGATACCCCCCAC
1217131 AGGGGAA-TCGATACCCCCC
1 AGGGGAACT-GATACCCCCC
1217150 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAACTGATACCCCCCAC
Found at i:1229293 original size:16 final size:16
Alignment explanation
Indices: 1229272--1229305 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1229262 TTACTATTCA
*
1229272 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1229288 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1229304 CG
1 CG
1229306 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1237524 original size:17 final size:17
Alignment explanation
Indices: 1237502--1237537 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1237492 GTGTATGTGA
1237502 AAATAAACATATAATTC
1 AAATAAACATATAATTC
1237519 AAATAAACATATAATTC
1 AAATAAACATATAATTC
1237536 AA
1 AA
1237538 CATGTTGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAAACATATAATTC
Found at i:1244644 original size:2 final size:2
Alignment explanation
Indices: 1244637--1244682 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1244627 ATATGAATGA
1244637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1244679 AT AT
1 AT AT
1244683 TTCCAATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1253417 original size:33 final size:33
Alignment explanation
Indices: 1253311--1253417 Score: 83
Period size: 33 Copynumber: 3.2 Consensus size: 33
1253301 CTTTAAAAAA
* * *
1253311 TAAAAAA-ATAAAAATAAAAGGCTATTTAAATTC
1 TAAAAAATTTAAAAATAAAAAGCT-TTTAAATTT
** ** * * *
1253344 TAAACTATTT-AAAATTTAAAGCCATTAAAATAT
1 TAAAAAATTTAAAAATAAAAAG-CTTTTAAATTT
*
1253377 TAGAAAATTTAAAAATAAAAAGCTTTTAAATTT
1 TAAAAAATTTAAAAATAAAAAGCTTTTAAATTT
1253410 TAAAAAAT
1 TAAAAAAT
1253418 AAATTAAAAA
Statistics
Matches: 52, Mismatches: 19, Indels: 6
0.68 0.25 0.08
Matches are distributed among these distances:
33 41 0.79
34 11 0.21
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.33
Consensus pattern (33 bp):
TAAAAAATTTAAAAATAAAAAGCTTTTAAATTT
Found at i:1254703 original size:7 final size:7
Alignment explanation
Indices: 1254691--1254724 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
1254681 CCCTCACCCT
1254691 CACCTCC
1 CACCTCC
1254698 CACCTCC
1 CACCTCC
1254705 CACCTCC
1 CACCTCC
1254712 CACCTCC
1 CACCTCC
1254719 CACCTC
1 CACCTC
1254725 GTCCCCCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.71, G:0.00, T:0.15
Consensus pattern (7 bp):
CACCTCC
Found at i:1254771 original size:23 final size:23
Alignment explanation
Indices: 1254745--1254789 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1254735 TCTCCTGCCT
1254745 CCCCTACAACAGCTCCCCCGCAG
1 CCCCTACAACAGCTCCCCCGCAG
*
1254768 CCCCTACAGCAGCTCCCCCGCA
1 CCCCTACAACAGCTCCCCCGCA
1254790 ACAGCTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.58, G:0.13, T:0.09
Consensus pattern (23 bp):
CCCCTACAACAGCTCCCCCGCAG
Found at i:1255135 original size:30 final size:31
Alignment explanation
Indices: 1255075--1255136 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
1255065 GGTTGAGAGA
* *
1255075 TGAAATGAAAGATTTTAGAATTTTAGGGATT
1 TGAAATGAAAGATTTTAGAATTTCAAGGATT
* *
1255106 TGAAAT-AAATATTTTAGAGTTTCAAGGATT
1 TGAAATGAAAGATTTTAGAATTTCAAGGATT
1255136 T
1 T
1255137 TTTTTGACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.40
Consensus pattern (31 bp):
TGAAATGAAAGATTTTAGAATTTCAAGGATT
Found at i:1264201 original size:24 final size:24
Alignment explanation
Indices: 1264174--1264219 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1264164 TATGTTTTTT
* *
1264174 ATTTTTTAAAATTTTATAAATTTA
1 ATTTTTGAAAATATTATAAATTTA
1264198 ATTTTTGAAAATATTATAAATT
1 ATTTTTGAAAATATTATAAATT
1264220 CGTTCATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTTTGAAAATATTATAAATTTA
Found at i:1271479 original size:69 final size:70
Alignment explanation
Indices: 1271364--1271496 Score: 196
Period size: 69 Copynumber: 1.9 Consensus size: 70
1271354 TGGTAATATA
* *
1271364 ATTAAAGCAAAATGATTAGGCATACTTGTTCTTTAAAACAAGAATCTTGCTTCATCATTCAAGCG
1 ATTAAAGCAAAATGATTAGCCATACTTGTTCCTTAAAACAAGAATCTTGCTTCATCATTCAAGCG
1271429 ACATG
66 ACATG
* * * * *
1271434 ATTAATGCACAATGATTAGCCATA-TTTTTCCTTAAAATAAGAATCTTTCTTCATCATTCAAGC
1 ATTAAAGCAAAATGATTAGCCATACTTGTTCCTTAAAACAAGAATCTTGCTTCATCATTCAAGC
1271497 AACAGAAAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
69 35 0.62
70 21 0.38
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (70 bp):
ATTAAAGCAAAATGATTAGCCATACTTGTTCCTTAAAACAAGAATCTTGCTTCATCATTCAAGCG
ACATG
Found at i:1277820 original size:31 final size:31
Alignment explanation
Indices: 1277778--1277837 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1277768 AACCTAGAAG
*
1277778 TGAAGTTCATTCTATGTGGAATGAATGAACA
1 TGAAGTACATTCTATGTGGAATGAATGAACA
* * *
1277809 TGAAGTACATTCTATTTGGTATGCATGAA
1 TGAAGTACATTCTATGTGGAATGAATGAA
1277838 ACATTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (31 bp):
TGAAGTACATTCTATGTGGAATGAATGAACA
Found at i:1279443 original size:30 final size:28
Alignment explanation
Indices: 1279407--1279487 Score: 108
Period size: 30 Copynumber: 2.8 Consensus size: 28
1279397 TGTACTTTGA
1279407 TTAAATATTGAATATAATATTTATATTTT
1 TTAAATATT-AATATAATATTTATATTTT
1279436 TTGAAATATTATATATAATATTTATATTTT
1 TT-AAATATTA-ATATAATATTTATATTTT
* *
1279466 TTTAATATTTAATATGATATTT
1 TTAAATA-TTAATATAATATTT
1279488 CTGTTTTGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 17 0.36
30 30 0.64
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
TTAAATATTAATATAATATTTATATTTT
Found at i:1281253 original size:20 final size:21
Alignment explanation
Indices: 1281216--1281255 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1281206 TTATATTTTT
*
1281216 TATAAAAATAAATTGAATAAA
1 TATAAAAATAAATAGAATAAA
*
1281237 TATAAAATTAAA-AGAATAA
1 TATAAAAATAAATAGAATAA
1281256 TACATTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
TATAAAAATAAATAGAATAAA
Found at i:1282077 original size:21 final size:20
Alignment explanation
Indices: 1282053--1282116 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1282043 AACTTTGAAA
1282053 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
1282074 AAATGTTTT-----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
1282088 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
1282109 AAATGTTT
1 AAATGTTT
1282117 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
20 11 0.32
21 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:1282091 original size:35 final size:36
Alignment explanation
Indices: 1282046--1282166 Score: 156
Period size: 35 Copynumber: 3.4 Consensus size: 36
1282036 GGTAACCAAC
1282046 TTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
1 TTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTTT
* *
1282083 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
* * *
1282118 TTTGAAAAATAGTTTTTCAAATTTTGGTAGATG-TTT
1 TTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTTT
*
1282154 GTTGAAAAATGAT
1 TTTGAAAAATGAT
1282167 AATGGGATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 35 0.47
36 16 0.22
37 23 0.31
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.45
Consensus pattern (36 bp):
TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
Found at i:1286712 original size:36 final size:37
Alignment explanation
Indices: 1286597--1286716 Score: 158
Period size: 35 Copynumber: 3.3 Consensus size: 37
1286587 TGGTAACCAA
1286597 CTTTGAAAAA-AGTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGT--TTTTCAAAGTTTGGTAAATGTTT
*
1286635 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
* *
1286670 CTTTGAAAAATAGTTTTTCAAATTTTGGTAGATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
1286707 -GTTGAAAAAT
1 CTTTGAAAAAT
1286717 GATAATGGGA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
35 28 0.38
36 14 0.19
37 27 0.36
38 5 0.07
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:1292960 original size:20 final size:19
Alignment explanation
Indices: 1292937--1292983 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1292927 CGATATAATA
1292937 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1292957 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1292977 GGTAAAA
1 GGTAAAA
1292984 CGCTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1292961 original size:180 final size:183
Alignment explanation
Indices: 1292544--1293016 Score: 718
Period size: 180 Copynumber: 2.6 Consensus size: 183
1292534 GATCTAAATT
* * **
1292544 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
1292609 AAACCGGTAAAGCGGTACCAGATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGATACTTC
66 AAACCGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * * ** *
1292674 GTTAATTTAAAAGAGAAGCATTTTTTAGCGTTTATAAAGTGTTGATACATTAA
131 GTGAATTTAAAAGAGAAGCATGTTATAGCGCCTATAAAGTGTCGATACATTAA
* *
1292727 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATAATAAAACCGGTATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
1292792 AAACCGGTAAAACGCTACCTGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
1292856 GTGAATTTAAAAGAGAAGCA-GTTATAGCGCCTATAAAGTGTCGATAC-TTTA
131 GTGAATTTAAAAGAGAAGCATGTTATAGCGCCTATAAAGTGTCGATACATTAA
* *
1292907 AAAAATGTATCGATCCACAGCGATATAATAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
1292972 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTTT
1293017 CGTAAGTACG
Statistics
Matches: 265, Mismatches: 25, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
180 108 0.41
181 22 0.08
182 36 0.14
183 99 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (183 bp):
AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCATGTTATAGCGCCTATAAAGTGTCGATACATTAA
Found at i:1295247 original size:21 final size:21
Alignment explanation
Indices: 1295221--1295285 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
1295211 AAGACAATTA
* *
1295221 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAAAAACTTGAG
1295242 AGAGTCGAAGAAAAACTTGAG
1 AGAGTCGAAGAAAAACTTGAG
* * *
1295263 AGAGTCGAATATACACTTGAG
1 AGAGTCGAAGAAAAACTTGAG
1295284 AG
1 AG
1295286 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAAAAACTTGAG
Found at i:1295361 original size:33 final size:33
Alignment explanation
Indices: 1295319--1295384 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1295309 AAATAGATGG
*
1295319 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
1295352 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1295385 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1295578 original size:16 final size:16
Alignment explanation
Indices: 1295539--1295579 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
1295529 GAGCTATGTA
*
1295539 AAGAAAAAATATGATG
1 AAGAAAAAATATGAAG
1295555 AACTGAAAAAATATGAAG
1 AA--GAAAAAATATGAAG
1295573 AAGAAAA
1 AAGAAAA
1295580 GAGGGAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.32
18 15 0.68
ACGTcount: A:0.66, C:0.02, G:0.17, T:0.15
Consensus pattern (16 bp):
AAGAAAAAATATGAAG
Found at i:1295623 original size:36 final size:33
Alignment explanation
Indices: 1295573--1295659 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1295563 AAATATGAAG
1295573 AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGA
1 AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGA
*
1295606 AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGG
1 AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGA
*
1295639 AAGAAATGA-GGAGGAAGGAAG
1 AAGAAAAGAGGGAGG-AGGAAG
1295660 TCGATGTCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 5 0.10
33 46 0.90
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (33 bp):
AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGA
Found at i:1297223 original size:19 final size:19
Alignment explanation
Indices: 1297199--1297247 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1297189 AATGTGGGGT
1297199 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1297218 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1297237 TAATTTTGTAT
1 TAATTTTGTAT
1297248 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1297820 original size:200 final size:200
Alignment explanation
Indices: 1297477--1298262 Score: 1367
Period size: 200 Copynumber: 3.9 Consensus size: 200
1297467 AATTTACAAT
*
1297477 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
* * *
1297542 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAGCATACCGATTTT
66 CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTT
* *
1297607 ATGAGAGATTAGGTATATAATATGTATCAACACTTTTTAATTTTATGTCGATACTATTGGTCCAG
131 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
1297672 AATGA
196 AATGA
* *
1297677 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTTGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1297742 CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTT
66 CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTT
* *
1297807 ATGAGATATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAA
131 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
1297872 AATGA
196 AATGA
* * *
1297877 ATGGCAAACAGGGTGCAACCATAAAGTGTTGATCCATATATAAAAGGTGTCAATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
* * *
1297942 CGAAACCCATAAGTTTAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTT
1298007 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
1298072 AATGA
196 AATGA
*
1298077 ATGGCAAACATGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
1298142 CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCAATTTT
66 CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTT
* * *
1298207 ATGAGATAATAGGTGTA-ATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
131 ATGAGAGATTAGGTATATA-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
1298263 ATTTAAATAT
Statistics
Matches: 556, Mismatches: 29, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
199 1 0.00
200 555 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATCTAACCGGTATAAGTATACCGATTTT
ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:1301374 original size:183 final size:183
Alignment explanation
Indices: 1301164--1301510 Score: 635
Period size: 183 Copynumber: 1.9 Consensus size: 183
1301154 ATATCAACAT
1301164 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTA
*
1301229 ATAGGTAATTTTGTAATATAACCGGTATATATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAAATATACC-GTTTTATGAGAGAATAGGTCTACAACC
1301294 TATATCGACAC-TTTTAATATTGTGTCGC-TACTTTATGTCCAGAATGGATGAAA
130 TATATCGACACTTTTTAATATTGTGTC-CATACTTTATGTCCAGAATGGATGAAA
*
1301347 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTA
*
1301412 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGTTTTATGAGAGAATAGGTCTATAACCT
66 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGTTTTATGAGAGAATAGGTCTACAACCT
1301477 ATATCGACACTTTTTAATATTGTGTCCATACTTT
131 ATATCGACACTTTTTAATATTGTGTCCATACTTT
1301511 TAAGTAACGC
Statistics
Matches: 159, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
182 38 0.24
183 121 0.76
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTAAAAAAACATCGGAACCCATAATTATAATGTA
ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGTTTTATGAGAGAATAGGTCTACAACCT
ATATCGACACTTTTTAATATTGTGTCCATACTTTATGTCCAGAATGGATGAAA
Found at i:1304570 original size:22 final size:22
Alignment explanation
Indices: 1304526--1304570 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1304516 ATTACATAAC
*
1304526 TTTAAAAAAAGTATCGATTCTT
1 TTTAAAAAAAGTATCGATACTT
* *
1304548 TTTACAAAAAGTATCTATACTT
1 TTTAAAAAAAGTATCGATACTT
1304570 T
1 T
1304571 CAACATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGATACTT
Found at i:1304831 original size:113 final size:113
Alignment explanation
Indices: 1304616--1304953 Score: 583
Period size: 112 Copynumber: 3.0 Consensus size: 113
1304606 ATAAAACTGA
* * *
1304616 TTTTGTCA-TTTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAAAGATCGATAC-T
1 TTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCAATCCTTTTTATAAAAGGATCGATACTT
*
1304679 TTAATATATCAGGTAAAGCGCTATCGGTTTTGTTATTTTTTTTACCGG
66 TTAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACCGG
1304727 TTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCAATCCTTTTTATAAAAGGATCGATACTT
1 TTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCAATCCTTTTTATAAAAGGATCGATACTT
*
1304792 TTAATATATCAGGTAAAGCGCTACCGGTTTTGTTA-TTTTTTTACCGA
66 TTAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACCGG
* *
1304839 TTTTGTTATTTTTTTACATGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCGATACTT
1 TTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCAATCCTTTTTATAAAAGGATCGATACTT
*
1304904 TCAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACCGG
66 TTAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACCGG
1304952 TT
1 TT
1304954 ATATTATCGA
Statistics
Matches: 215, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
111 7 0.03
112 160 0.74
113 48 0.22
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (113 bp):
TTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCAATCCTTTTTATAAAAGGATCGATACTT
TTAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACCGG
Done.