Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_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: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1494976 original size:20 final size:20
Alignment explanation
Indices: 1494948--1495280 Score: 274
Period size: 20 Copynumber: 16.6 Consensus size: 20
1494938 TAAACGCGCT
*
1494948 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGTG
* *
1494968 TTGCAAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGTG
**
1494988 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGACTTTC-GTG
* * *
1495009 TTGTGAATTTGAAATTTAGTG
1 TTGCGAATTTG-ACTTTCGTG
* *
1495030 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
*
1495050 TTACGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
1495070 TTGCGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
* *
1495090 TTGCG-ATTT-ACAAATTCGCG
1 TTGCGAATTTGAC--TTTCGTG
*
1495110 TTGCG-ATTT-ACAGATTCGTG
1 TTGCGAATTTGAC--TTTCGTG
* *
1495130 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
* *
1495150 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
* *
1495170 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
1495190 TTGCGAATTTGACTTAT-GTG
1 TTGCGAATTTGACTT-TCGTG
1495210 TTGCGAATTTGACTTAT-GTG
1 TTGCGAATTTGACTT-TCGTG
*
1495230 TTGTGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
*
1495250 TTGCG-ATTT-ACATATTCGCG
1 TTGCGAATTTGAC-T-TTCGTG
1495270 TTGCGAATTTG
1 TTGCGAATTTG
1495281 GAAACTGGTT
Statistics
Matches: 267, Mismatches: 30, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.02
19 11 0.04
20 204 0.76
21 41 0.15
22 6 0.02
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGTG
Found at i:1495173 original size:100 final size:101
Alignment explanation
Indices: 1494948--1495280 Score: 323
Period size: 100 Copynumber: 3.3 Consensus size: 101
1494938 TAAACGCGCT
* * * * *
1494948 TTGCGAATTTGACTTTCGCGTTGCAAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTGTTGT
1 TTGCGAATTTGAC-TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTCAAATTCAGCGTTGC
1495013 GAATTTGAAATTTAGTGTTGCGAATTTGACTATCGCG
65 GAATTTGAAATTTAGTGTTGCGAATTTGACTATCGCG
* *
1495050 TTACGAATTTGACTTCTGTGTTGCGAATTTGACTTCTGTGTTGCG-ATTTACAAATTC-GCGTTG
1 TTGCGAATTTGACTTC-GCGTTGCGAATTTGACTTCTGTGTTGCGAATTT-CAAATTCAGCGTTG
*
1495113 CG-ATTT-ACAGA-TTCGTGTTGCGAATTTGACTATCGCG
64 CGAATTTGA-A-ATTTAGTGTTGCGAATTTGACTATCGCG
* * * *
1495150 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTT-GACTT-ATGTGTT
1 TTGCGAATTTGACT-TCGCGTTGCGAATTTGACT-TCTGTGTTGCGAATTTCAAATTCA-GCGTT
* * *
1495212 GCGAATTTG--ACTTATGTGTTGTGAATTTGACT-TCTGTG
63 GCGAATTTGAAATTTA-GTGTTGCGAATTTGACTATC-GCG
1495250 TTGCG-ATTT-ACATATTCGCGTTGCGAATTTG
1 TTGCGAATTTGAC---TTCGCGTTGCGAATTTG
1495281 GAAACTGGTT
Statistics
Matches: 197, Mismatches: 17, Indels: 36
0.79 0.07 0.14
Matches are distributed among these distances:
98 3 0.02
99 12 0.06
100 112 0.57
101 27 0.14
102 43 0.22
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.41
Consensus pattern (101 bp):
TTGCGAATTTGACTTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTCAAATTCAGCGTTGCG
AATTTGAAATTTAGTGTTGCGAATTTGACTATCGCG
Found at i:1497551 original size:37 final size:38
Alignment explanation
Indices: 1497468--1497563 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 38
1497458 AATTAAGACA
* * *
1497468 TATCAATTTATATTTATGAACGGACACAAATAAAAGTG
1 TATCCATTTATATTCATGAACGAACACAAATAAAAGTG
* * *
1497506 TATTCATTTATATTCATGAATGAACA-AAATTAAAGTG
1 TATCCATTTATATTCATGAACGAACACAAATAAAAGTG
1497543 TATCCATTTATATTCATGAAC
1 TATCCATTTATATTCATGAAC
1497564 AAGTTCATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
37 29 0.58
38 21 0.42
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.36
Consensus pattern (38 bp):
TATCCATTTATATTCATGAACGAACACAAATAAAAGTG
Found at i:1500879 original size:43 final size:43
Alignment explanation
Indices: 1500831--1500920 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
1500821 GTTTGAGGCT
1500831 TTGCGGGTCCAGGAATTAATGCCGTCACCCTTTTTGTGCAGAC
1 TTGCGGGTCCAGGAATTAATGCCGTCACCCTTTTTGTGCAGAC
1500874 TTGCGGGTCCAGGAATTAATGCCGTCACCCTTTTTGTGCAGAC
1 TTGCGGGTCCAGGAATTAATGCCGTCACCCTTTTTGTGCAGAC
1500917 TTGC
1 TTGC
1500921 TTACTCCTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (43 bp):
TTGCGGGTCCAGGAATTAATGCCGTCACCCTTTTTGTGCAGAC
Found at i:1506889 original size:12 final size:12
Alignment explanation
Indices: 1506872--1506896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1506862 ATTTAGCAGT
1506872 AATAAAGATTTC
1 AATAAAGATTTC
1506884 AATAAAGATTTC
1 AATAAAGATTTC
1506896 A
1 A
1506897 CTTATTGACT
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AATAAAGATTTC
Found at i:1511445 original size:34 final size:32
Alignment explanation
Indices: 1511392--1511461 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1511382 ACCTTACAAC
*
1511392 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1511424 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1511458 TCCC
1 TCCC
1511462 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1511694 original size:20 final size:22
Alignment explanation
Indices: 1511669--1511708 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1511659 TGTCGTATAT
1511669 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1511689 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1511709 TATATTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1511841 original size:21 final size:21
Alignment explanation
Indices: 1511815--1511857 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
1511805 CTGTTGAACA
1511815 GGGGGGGAATC-ATACACCCT
1 GGGGGGGAATCGATACACCCT
*
1511835 GGGGGGGAATCGATACCCCCT
1 GGGGGGGAATCGATACACCCT
1511856 GG
1 GG
1511858 ACATTCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.21, C:0.26, G:0.40, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGATACACCCT
Found at i:1511921 original size:18 final size:18
Alignment explanation
Indices: 1511891--1511928 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1511881 AAAACCTGCA
1511891 GGGGGTATCTGTACCCTGG
1 GGGGGTATCTGTACCC-GG
1511910 GGGGGTAT-TGTACCCGG
1 GGGGGTATCTGTACCCGG
1511927 GG
1 GG
1511929 TACTGTACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.11, C:0.18, G:0.47, T:0.24
Consensus pattern (18 bp):
GGGGGTATCTGTACCCGG
Found at i:1512101 original size:30 final size:31
Alignment explanation
Indices: 1512054--1512114 Score: 99
Period size: 29 Copynumber: 2.0 Consensus size: 31
1512044 AAACTTTGAA
1512054 TAAATTCAATTAAGTCC-AAAAAC-ATTTTG
1 TAAATTCAATTAAGTCCAAAAAACTATTTTG
1512083 TAAATTCAATTCAAGTCCAAAAAACTATTTTG
1 TAAATTCAATT-AAGTCCAAAAAACTATTTTG
1512115 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 11 0.38
30 6 0.21
31 6 0.21
32 6 0.21
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTAAGTCCAAAAAACTATTTTG
Found at i:1513303 original size:19 final size:19
Alignment explanation
Indices: 1513267--1513312 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1513257 CTAAATCCTT
*
1513267 TTTCAAAATTTCATTTTGGC
1 TTTCAAAATCTCATTTT-GC
*
1513287 TTTCAAAATCT-ATTTTGT
1 TTTCAAAATCTCATTTTGC
1513305 TTTCAAAA
1 TTTCAAAA
1513313 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:1514221 original size:34 final size:32
Alignment explanation
Indices: 1514168--1514237 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1514158 ACCTTACAAC
*
1514168 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1514200 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1514234 TCCC
1 TCCC
1514238 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1514473 original size:20 final size:22
Alignment explanation
Indices: 1514448--1514487 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1514438 AGTCGTATAT
1514448 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1514468 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1514488 TATATTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1514674 original size:21 final size:21
Alignment explanation
Indices: 1514649--1514728 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
1514639 AAAACCTGCA
1514649 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
1514670 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
1514686 -GGGGTATCTGTACCCCCTTGG
1 GGGGGTATCTGTACCCCC-TGG
* *
1514707 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
1514728 G
1 G
1514729 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 17 0.34
22 15 0.30
ACGTcount: A:0.12, C:0.28, G:0.36, T:0.24
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:1514690 original size:36 final size:37
Alignment explanation
Indices: 1514650--1514722 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 37
1514640 AAACCTGCAG
* *
1514650 GGGGTATCTGTACCCCC-TGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTTGGGGGGGAATCTATACCC
1514686 GGGGTATCTGTACCCCCTTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTTGGGGGGGAATCTATACCC
1514723 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 17 0.50
37 17 0.50
ACGTcount: A:0.14, C:0.27, G:0.34, T:0.25
Consensus pattern (37 bp):
GGGGTATCTGTACCCCCTTGGGGGGGAATCTATACCC
Found at i:1514691 original size:15 final size:15
Alignment explanation
Indices: 1514671--1514700 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1514661 ACCCCCTGGG
1514671 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1514686 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1514701 CCTTGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:1514849 original size:29 final size:31
Alignment explanation
Indices: 1514817--1514876 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
1514807 AAACTTTGAA
1514817 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1514846 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1514877 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1518248 original size:7 final size:6
Alignment explanation
Indices: 1518226--1518255 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1518216 ATTTTCGTTC
1518226 TTTTTA TTTTTA TTTTTA TTTTTGA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTT-A TTTTT
1518256 CGGAATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:1520301 original size:18 final size:18
Alignment explanation
Indices: 1520278--1520318 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1520268 GCTAAAAAAC
1520278 TCTTTTGAATTATTCTTA
1 TCTTTTGAATTATTCTTA
1520296 TCTTTTGAATTATTCTTA
1 TCTTTTGAATTATTCTTA
1520314 TCTTT
1 TCTTT
1520319 AGAAAAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.63
Consensus pattern (18 bp):
TCTTTTGAATTATTCTTA
Found at i:1521805 original size:21 final size:21
Alignment explanation
Indices: 1521781--1521820 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1521771 TCATACTCCT
1521781 CAACAACCGCCACACGATCCC
1 CAACAACCGCCACACGATCCC
1521802 CAACAACCGCCACACGATC
1 CAACAACCGCCACACGATC
1521821 AATCGACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.50, G:0.10, T:0.05
Consensus pattern (21 bp):
CAACAACCGCCACACGATCCC
Found at i:1528573 original size:14 final size:13
Alignment explanation
Indices: 1528539--1528584 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
1528529 AGCCAAGCCG
*
1528539 ACTGAGTCAACCTGC
1 ACTGAGTTAA-CT-C
1528554 ACTGAGTTAACTC
1 ACTGAGTTAACTC
1528567 GACTGAGTTAACTC
1 -ACTGAGTTAACTC
1528581 ACTG
1 ACTG
1528585 GGTCAACCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 5 0.17
14 15 0.52
15 9 0.31
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (13 bp):
ACTGAGTTAACTC
Found at i:1528665 original size:37 final size:37
Alignment explanation
Indices: 1528592--1528666 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
1528582 CTGGGTCAAC
* *
1528592 CCGTTGACTTTGACCGAGTCAACATGTTAGCTGTTGA
1 CCGTTGACTTTGACCGAGCCAACATGTTAGCCGTTGA
*
1528629 CCGTTGACTTTGACCGAGCCAACCTGTT-GACCGTTGA
1 CCGTTGACTTTGACCGAGCCAACATGTTAG-CCGTTGA
1528666 C
1 C
1528667 TTTGACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 1 0.03
37 33 0.97
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (37 bp):
CCGTTGACTTTGACCGAGCCAACATGTTAGCCGTTGA
Found at i:1530823 original size:24 final size:24
Alignment explanation
Indices: 1530796--1530880 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
1530786 TGAATTATGT
* * *
1530796 TATGATACCTGACCTGGATTCTAA
1 TATGATACTTGACATGGATTCTGA
*
1530820 TATGATATTTGACATGGATTCTGA
1 TATGATACTTGACATGGATTCTGA
* *
1530844 TCTGTTACTTGACATGGATTCTGA
1 TATGATACTTGACATGGATTCTGA
1530868 TATGATACTTGAC
1 TATGATACTTGAC
1530881 CTAAATTATG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
TATGATACTTGACATGGATTCTGA
Found at i:1545418 original size:19 final size:19
Alignment explanation
Indices: 1545394--1545430 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1545384 ATGACCAACA
*
1545394 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1545413 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1545431 CAGTATCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1545510 original size:21 final size:21
Alignment explanation
Indices: 1545464--1545517 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1545454 GATTTTTACT
*
1545464 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
1545485 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
1545506 ATCGCAATGCGA
1 ATCGCATTGCGA
1545518 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:1545732 original size:166 final size:166
Alignment explanation
Indices: 1545490--1545866 Score: 682
Period size: 166 Copynumber: 2.3 Consensus size: 166
1545480 CCAAATTCGC
*
1545490 GTTGCGATTTTAGAAAATCGCAATGCGAATATGTAAATCGCAACGCGATATTCAGTATCGCAAAT
1 GTTGCGATTTTAGAAAATCGCAATGCGAATATGTAAATCGCAACGCGATATCCAGTATCGCAAAT
* * * *
1545555 CAGTTTCCAGATTTGCAACGCGATTTTGACTATCGCATTGCGATTTTCCAAATTCGCGTTGTGAT
66 AAGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTGCAATTTTCCAAATTCGCGTTGCGAT
*
1545620 TCTGACTATCGCAACGCGATAATACAGAATCGCGTT
131 TCTGACTATCGCAACGCGATAATACAGAATCACGTT
* *
1545656 GTTGCGATTTTAGAAAATCACAATGCGAATATGTAAATCGCAACGCGATCTCCAGTATCGCAAAT
1 GTTGCGATTTTAGAAAATCGCAATGCGAATATGTAAATCGCAACGCGATATCCAGTATCGCAAAT
1545721 AAGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTGCAATTTTCCAAATTCGCGTTGCGAT
66 AAGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTGCAATTTTCCAAATTCGCGTTGCGAT
1545786 TCTGACTATCGCAACGCGATAATACAGAATCACGTT
131 TCTGACTATCGCAACGCGATAATACAGAATCACGTT
1545822 GTTGCGATTTTAGAAAATCGCAATGCGAATATGTAAATCGCAACG
1 GTTGCGATTTTAGAAAATCGCAATGCGAATATGTAAATCGCAACG
1545867 TGAATTTGGA
Statistics
Matches: 202, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
166 202 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (166 bp):
GTTGCGATTTTAGAAAATCGCAATGCGAATATGTAAATCGCAACGCGATATCCAGTATCGCAAAT
AAGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTGCAATTTTCCAAATTCGCGTTGCGAT
TCTGACTATCGCAACGCGATAATACAGAATCACGTT
Found at i:1545861 original size:20 final size:21
Alignment explanation
Indices: 1545834--1545890 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
1545824 TGCGATTTTA
1545834 GAAAATCGCAATGCGAATAT-
1 GAAAATCGCAATGCGAATATG
* * * *
1545854 GTAAATCGCAACGTGAATTTG
1 GAAAATCGCAATGCGAATATG
1545875 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1545891 TAGTCAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (21 bp):
GAAAATCGCAATGCGAATATG
Found at i:1545882 original size:21 final size:20
Alignment explanation
Indices: 1545834--1545903 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1545824 TGCGATTTTA
*
1545834 GAAAATCGCAATGCGAATAT
1 GAAAATCGCAACGCGAATAT
* * *
1545854 GTAAATCGCAACGTGAATTT
1 GAAAATCGCAACGCGAATAT
*
1545874 GGAAAATCGCAATGCG-ATAGT
1 -GAAAATCGCAACGCGAATA-T
*
1545895 CAAAATCGC
1 GAAAATCGC
1545904 GTTGCGAATC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 26 0.67
21 13 0.33
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGCGAATAT
Found at i:1545948 original size:20 final size:20
Alignment explanation
Indices: 1545925--1545971 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1545915 GGAAACTTAT
*
1545925 TTGCGATACT-GGAGATCGCG
1 TTGCGATACTCAGA-ATCGCG
*
1545945 TTGCGATAGTCAGAATCGCG
1 TTGCGATACTCAGAATCGCG
1545965 TTGCGAT
1 TTGCGAT
1545972 TTACATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (20 bp):
TTGCGATACTCAGAATCGCG
Found at i:1546055 original size:20 final size:20
Alignment explanation
Indices: 1546032--1546085 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1546022 TTATCGCGTT
1546032 GCGATAGTCAAAATCGCAAC
1 GCGATAGTCAAAATCGCAAC
* * *
1546052 GCGA-ATTTGGAAAATCGCAAT
1 GCGATA-GT-CAAAATCGCAAC
1546073 GCGATAGTCAAAA
1 GCGATAGTCAAAA
1546086 CCACGTTGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.04
20 9 0.35
21 15 0.58
22 1 0.04
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (20 bp):
GCGATAGTCAAAATCGCAAC
Found at i:1546095 original size:186 final size:186
Alignment explanation
Indices: 1545856--1546193 Score: 604
Period size: 186 Copynumber: 1.8 Consensus size: 186
1545846 GCGAATATGT
* * *
1545856 AAATCGCAACGTGAATTTGGAAAATCGCAATGCGATAGTCAAAATCGCGTTGCGAATCTGGAAAC
1 AAATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGTCAAAACCACGTTGCGAATCTGGAAAC
* *
1545921 TTATTTGCGATACTGGAGATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCAT
66 TGATTTACGATACTGGAGATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCAT
*
1545986 TGCGATTTTCTAAAATCGCAACAACGCGATTCTGTATTATCGCGTTGCGATAGTCA
131 TACGATTTTCTAAAATCGCAACAACGCGATTCTGTATTATCGCGTTGCGATAGTCA
1546042 AAATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGTCAAAACCACGTTGCGAATCTGGAAAC
1 AAATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGTCAAAACCACGTTGCGAATCTGGAAAC
* *
1546107 TGATTTACGATACTGGAGATCGCGTTGTGATAGTCAGAATCGTGTTGCGATTTACATATTCGCAT
66 TGATTTACGATACTGGAGATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCAT
1546172 TACGATTTTCTAAAATCGCAAC
131 TACGATTTTCTAAAATCGCAAC
1546194 GCGAATTTGG
Statistics
Matches: 144, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
186 144 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (186 bp):
AAATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGTCAAAACCACGTTGCGAATCTGGAAAC
TGATTTACGATACTGGAGATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCAT
TACGATTTTCTAAAATCGCAACAACGCGATTCTGTATTATCGCGTTGCGATAGTCA
Found at i:1546691 original size:19 final size:19
Alignment explanation
Indices: 1546616--1546720 Score: 102
Period size: 19 Copynumber: 5.2 Consensus size: 19
1546606 TATTTTGGAT
* **
1546616 TTTTCACTATCGCAACATT
1 TTTTAACTATCGCAACACA
*
1546635 TTTTCACTATCGCAACAACA
1 TTTTAACTATCGCAAC-ACA
*
1546655 CGTTTTTCAAACTCTCGCAACACA
1 ---TTTT--AACTATCGCAACACA
1546679 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
*
1546698 TTTTAACTATCACAACACA
1 TTTTAACTATCGCAACACA
1546717 TTTT
1 TTTT
1546721 TCAAAATCAC
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 52 0.70
20 1 0.01
21 4 0.05
23 4 0.05
24 3 0.04
25 10 0.14
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:1546922 original size:2 final size:2
Alignment explanation
Indices: 1546912--1546947 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1546902 TTTTTTCTTT
*
1546912 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1546948 GGGAAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1547101 original size:17 final size:17
Alignment explanation
Indices: 1547079--1547125 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
1547069 GGTTATTATG
1547079 CATCAGTGATTGTGCAA
1 CATCAGTGATTGTGCAA
1547096 CATCAGTGATTGTGCAA
1 CATCAGTGATTGTGCAA
1547113 CATCAGTGATTGT
1 CATCAGTGATTGT
1547126 AGTTTGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (17 bp):
CATCAGTGATTGTGCAA
Found at i:1547797 original size:18 final size:19
Alignment explanation
Indices: 1547774--1547813 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1547764 AAAAAAATTA
1547774 ATTTTTTATATTTT-AAAT
1 ATTTTTTATATTTTAAAAT
*
1547792 ATTTTTTATTTTTTAAAAT
1 ATTTTTTATATTTTAAAAT
1547811 ATT
1 ATT
1547814 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTTATATTTTAAAAT
Found at i:1551906 original size:48 final size:47
Alignment explanation
Indices: 1551853--1551987 Score: 157
Period size: 48 Copynumber: 2.8 Consensus size: 47
1551843 TAAATATATG
* * *
1551853 TATGTGAAATATTAATATTTACATCAGTGTAAGTATGTGTCTTTGT-AA
1 TATGTGAAATGTTCATATTTACATCAGTGTAAGTATGTG--TATGTAAA
* *
1551901 TATGTGAAATGTTCATATTTACATCCGTATAAGTATGTGTATGTAAA
1 TATGTGAAATGTTCATATTTACATCAGTGTAAGTATGTGTATGTAAA
* *
1551948 TATGTAGAAATGTTCATATCTACAGT-AGTGTAATTATGTG
1 TATGT-GAAATGTTCATATTTACA-TCAGTGTAAGTATGTG
1551988 AAATCTGTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 4 0.05
47 7 0.09
48 63 0.84
49 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.41
Consensus pattern (47 bp):
TATGTGAAATGTTCATATTTACATCAGTGTAAGTATGTGTATGTAAA
Found at i:1552381 original size:39 final size:38
Alignment explanation
Indices: 1552324--1552466 Score: 114
Period size: 39 Copynumber: 3.7 Consensus size: 38
1552314 TTGTATAGTG
* *
1552324 TGAGTATTAGGACATTCAGGTTCGTCCACTTAAATGGTA
1 TGAGTAGTGGGACATTCAGGTTCGTCCACTT-AATGGTA
* * *
1552363 TGAGTAGTGGGACCTTCAGGTTTTGTTCCA--T-ATGGTG
1 TGAGTAGTGGGACATTCAGG-TTCG-TCCACTTAATGGTA
* *** *
1552400 TGAGTATTCAAACCTTC-GAGTTCGTCCACCTTAATGGTA
1 TGAGTAGTGGGACATTCAG-GTTCGTCCA-CTTAATGGTA
*
1552439 TAAGTAGTGGGACATTCAGGTTCGTCCA
1 TGAGTAGTGGGACATTCAGGTTCGTCCA
1552467 TGCTACATGA
Statistics
Matches: 79, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
35 4 0.05
36 4 0.05
37 19 0.24
38 1 0.01
39 43 0.54
40 4 0.05
41 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (38 bp):
TGAGTAGTGGGACATTCAGGTTCGTCCACTTAATGGTA
Found at i:1552560 original size:93 final size:91
Alignment explanation
Indices: 1552392--1552636 Score: 258
Period size: 93 Copynumber: 2.6 Consensus size: 91
1552382 GTTTTGTTCC
* * * *
1552392 ATATGGTGTGAGTATTCAAACCTTCGAGTTCGTCCACCTTAATGGTATAAGTAGTGGGACATTCA
1 ATATGGTGTGAGTATT-GAACCTTCGAGTTCGTCCACCTTAATGGTGT-AGTATTGGGAAATTCA
* * * *
1552457 GGTTCGTCCATGCT-ACATGATTTATTTT
64 GATTCATCCAT-ATGACATGATTTATTCT
*
1552485 ATATGGTGTGAGTATTGGAACCTTCGAATTCGTCCACCTTAATGGTGTATGTATTGGGAAATTCA
1 ATATGGTGTGAGTATT-GAACCTTCGAGTTCGTCCACCTTAATGGTGTA-GTATTGGGAAATTCA
* ** *
1552550 GATTTATCCATATGATGTGATTTGTTCT
64 GATTCATCCATATGACATGATTTATTCT
* * * * *
1552578 CTATGGTATAAGTATTGAGACCTTCGAGTTCGTCTACCTTAATGATGTGAGTATTGGGA
1 ATATGGTGTGAGTATTGA-ACCTTCGAGTTCGTCCACCTTAATGGTGT-AGTATTGGGA
1552637 CTTTTAGATT
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
92 4 0.03
93 123 0.96
94 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (91 bp):
ATATGGTGTGAGTATTGAACCTTCGAGTTCGTCCACCTTAATGGTGTAGTATTGGGAAATTCAGA
TTCATCCATATGACATGATTTATTCT
Found at i:1561195 original size:125 final size:124
Alignment explanation
Indices: 1560875--1561178 Score: 466
Period size: 124 Copynumber: 2.4 Consensus size: 124
1560865 AAGTTGTGAT
* * * *
1560875 ATGTTGGGGCGCGACTGAACCCACATCATGTTGAGAAGACAAGATTCAGACCAAGGAGGTATTAA
1 ATGTTGGGGCGAGACTGAACCCACGTCATGTTGAGATGAAAAGATTCAGACCAAGGAGGTATTAA
* * *
1560940 GAATGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGATGCCCGTACCAGTATAAGATA
66 GAATGAGCCTCACAATTTGAGGTGATGGGGCATTTTGAGGCCCGTACCAGTATAAGATA
* *
1560999 ATGTTGGGGC-ATGACTGAACCCACGTCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATAA
1 ATGTTGGGGCGA-GACTGAACCCACGTCATGTTGAGATGAAAAGATTCAGACCAAGGAGGTATTA
* *
1561063 AGAATGAGCCTCACAATTTGAGGTGATGGGGCATTTTGAAGGCCCTTACCAGTGTAAGATA
65 AGAATGAGCCTCACAATTTGAGGTGATGGGGCATTTTG-AGGCCCGTACCAGTATAAGATA
**
1561124 ATGTTGGGGCGAGACCAAACCCACGTCATGTTGAGATGAAAAGATTCAGACCAAG
1 ATGTTGGGGCGAGACTGAACCCACGTCATGTTGAGATGAAAAGATTCAGACCAAG
1561179 AAATTATTGA
Statistics
Matches: 164, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
124 93 0.57
125 70 0.43
126 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (124 bp):
ATGTTGGGGCGAGACTGAACCCACGTCATGTTGAGATGAAAAGATTCAGACCAAGGAGGTATTAA
GAATGAGCCTCACAATTTGAGGTGATGGGGCATTTTGAGGCCCGTACCAGTATAAGATA
Found at i:1562067 original size:36 final size:36
Alignment explanation
Indices: 1561915--1562108 Score: 237
Period size: 36 Copynumber: 5.4 Consensus size: 36
1561905 GAGCAAGTCA
1561915 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * *
1561951 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCA
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
*
1561987 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * *
1562023 ATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
** * * *
1562059 ATCTTAAGTATTCACC-AAAAAGTAGTGAAGCAGATCC
1 ATCTTAAGCCTTCACCGGAGAA-TAGTGAAGCA-AACC
*
1562096 ATTTTAAGCCTTC
1 ATCTTAAGCCTTC
1562109 TCAGAAGAGT
Statistics
Matches: 137, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
35 2 0.01
36 122 0.89
37 13 0.09
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
Found at i:1562562 original size:51 final size:53
Alignment explanation
Indices: 1562478--1562723 Score: 277
Period size: 51 Copynumber: 4.6 Consensus size: 53
1562468 GTGAAGCAAA
* * *
1562478 TGAAGATATGCGAGTTCTATACTCCTTAGAGAAAGAAGGAGCGAACCC-GT-T
1 TGAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCAGTGT
* * *
1562529 TGAAGATGTTCGAGTTCTATACTCCGTAAAGAAAGAAGGAGCAAACCC-GT-T
1 TGAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCAGTGT
* * * *
1562580 TGAAGATATCCGAGATCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGT
1 TGAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCA-GTGT
* *
1562634 TGAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGT
1 TGAAGA-TATTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCA-GTGT
* * *
1562689 TGAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAA
1 TGAAGA-TATTCGAGTTC-TATACTCCCTAAAGAAA
1562724 TAGGGGGCAG
Statistics
Matches: 173, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
51 88 0.51
53 1 0.01
54 9 0.05
55 75 0.43
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (53 bp):
TGAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCAGTGT
Found at i:1562711 original size:55 final size:54
Alignment explanation
Indices: 1562597--1563356 Score: 738
Period size: 55 Copynumber: 14.0 Consensus size: 54
1562587 ATCCGAGATC
* * * * *
1562597 TATACTCCCTAAAGAAAGAGGGAGC-GAACCCATTTGTTGAAGATTATTCGAGT-T
1 TATACTCTCTGAAGAAATAGGGGGCAG-ACCCA-TTGTTGAAGATTGTTCGAGTCT
* * * *
1562651 CTATACTCCCTAAAGAAAGAGGGAGC-GAACCCATTTGTTGAAGATTGTTCGAGTCT
1 -TATACTCTCTGAAGAAATAGGGGGCAG-ACCCA-TTGTTGAAGATTGTTCGAGTCT
* * * *
1562707 TATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGAAATATT-GAGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAG-ATTGTTCGAGTCT
* * *
1562762 TATACTCTCTGAAGATATAGGGGGCAGACACGATCGTTGAAGATTGTTCGAGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGTCT
* * *
1562817 TATACTCTCT-AAGGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-GGGTCT
1 TATACTCTCTGAA-GAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGTCT
* * *
1562870 TATACTCTCTGAAGAAATAGAGGGCAGACGCAATAGTTGAAGATTGTTCGAGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGTCT
* * *
1562925 TATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATATATT-GAGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGAT-TGTTCGAGTCT
* * * *
1562980 TATACTCTCTGAAGATATAGGGGGCATACACGATCGTTGAAGATTGTTCGAGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGTCT
* * * *
1563035 TATACTCTCTGAAGAAATAGGGGGAAGACGCGATTGATGAAGATTG-T-GGGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGTCT
* * * *
1563088 TATACTCTCTGAAGAAATAGAGGGCAGACGCAATAGTTGAAGATTGTTCGGGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGTCT
* * * * *
1563143 TTTACTCTCTGAAGATATAGGGGGCAGACACAATCGTTGAAGATCGTTCGAGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGTCT
* * * * *
1563198 TATACTCCCTGAAGAAATAGGGGGCAGACGCGATTGATGAAAATTG-T-GGGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGTCT
* * * * *
1563251 TATACTCTCTAAAGATATAGGGGGCAGACGCGATTGATGAAGATTG-T-GGGTCT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGTCT
* * * *
1563304 TATACTCTCTGAAGAAATAGGGGGCAGACACGATTGGTAAAGATTATTCGAGT
1 TATACTCTCTGAAGAAATAGGGGGCAGAC-CCATTGTTGAAGATTGTTCGAGT
1563357 TCCATACTCC
Statistics
Matches: 619, Mismatches: 71, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
53 184 0.30
54 17 0.03
55 407 0.66
56 11 0.02
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (54 bp):
TATACTCTCTGAAGAAATAGGGGGCAGACCCATTGTTGAAGATTGTTCGAGTCT
Found at i:1562911 original size:163 final size:164
Alignment explanation
Indices: 1562632--1563356 Score: 900
Period size: 163 Copynumber: 4.4 Consensus size: 164
1562622 GAACCCATTT
* * * * * *
1562632 GTTGAAGATTATTCGAGT-TCTATACTCCCTAAAGAAAGAGGGAGC-GA-ACCCATTTGTTGAAG
1 GTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGGGCAGACA-CGA-TTGTTGAAG
* *
1562694 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGAAATAT-TGA
63 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAG-AAT-TGTGA
* *
1562758 GTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATC
126 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATC
* *
1562797 GTTGAAGATTGTTCGAGTCTTATACTCTCT-AAGGAAATAGGGGGCAGACGCGATTGATGAAGAT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAA-GAAATAGGGGGCAGACACGATTGTTGAAGAT
* * * * *
1562861 TG-T-GGGTCTTATACTCTCTGAAGAAATAGAGGGCAGACGCAATAGTTGAAG-ATTGTTCGAGT
65 TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGAATTG-T-GAGT
1562923 CTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATC
128 CTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATC
* * * *
1562960 GTTGAAGATATATT-GAGTCTTATACTCTCTGAAGATATAGGGGGCATACACGATCGTTGAAGAT
1 GTTGAAGAT-TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGAT
* *
1563024 TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGAAGACGCGATTGATGAAG-ATTGTGGGTCT
65 TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGAATTGTGAGTCT
* * *
1563088 TATACTCTCTGAAGAAATAGAGGGCAGACGCAATA
130 TATACTCTCTGAAGAAATAGGGGGCAGACGCGATC
* * * * * *
1563123 GTTGAAGATTGTTCGGGTCTTTTACTCTCTGAAGATATAGGGGGCAGACACAATCGTTGAAGATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATT
* *
1563188 GTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCAGACGCGATTGATGAA-AATTGTGGGTCTT
66 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGAATTGTGAGTCTT
* * *
1563252 ATACTCTCTAAAGATATAGGGGGCAGACGCGATT
131 ATACTCTCTGAAGAAATAGGGGGCAGACGCGATC
* * * *
1563286 GATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGGTAAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATT
*
1563349 ATTCGAGT
66 GTTCGAGT
1563357 TCCATACTCC
Statistics
Matches: 496, Mismatches: 51, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
160 1 0.00
161 53 0.11
162 5 0.01
163 328 0.66
164 10 0.02
165 94 0.19
166 5 0.01
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (164 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATT
GTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGAATTGTGAGTCTT
ATACTCTCTGAAGAAATAGGGGGCAGACGCGATC
Found at i:1562917 original size:218 final size:216
Alignment explanation
Indices: 1562687--1563332 Score: 1055
Period size: 218 Copynumber: 3.0 Consensus size: 216
1562677 GAACCCATTT
1562687 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGAAA
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAG-AA
1562752 TATTGAGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATCGTTGAAGATTGTTCGAGTCT
65 TATTGAGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATCGTTGAAGATTGTTCGAGTCT
1562817 TATACTCTCTAAGGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGGTCTTATACTCTCTGA
130 TATACTCTCTAA-GAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGGTCTTATACTCTCTGA
1562882 AGAAATAGAGGGCAGACGCAATA
194 AGAAATAGAGGGCAGACGCAATA
1562905 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATA
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGA-A
*
1562970 TATTGAGTCTTATACTCTCTGAAGATATAGGGGGCATACACGATCGTTGAAGATTGTTCGAGTCT
65 TATTGAGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATCGTTGAAGATTGTTCGAGTCT
*
1563035 TATACTCTCTGAAGAAATAGGGGGAAGACGCGATTGATGAAGATTGTGGGTCTTATACTCTCTGA
130 TATACTCTCT-AAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGGTCTTATACTCTCTGA
1563100 AGAAATAGAGGGCAGACGCAATA
194 AGAAATAGAGGGCAGACGCAATA
* * * * *
1563123 GTTGAAGATTGTTCGGGTCTTTTACTCTCTGAAGATATAGGGGGCAGACACAATCGTTGAAG-AT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGAAT
* * * * * * * *
1563187 CGTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCAGACGCGATTGATGAAAATTG-T-GGGTC
66 -ATT-GAGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATCGTTGAAGATTGTTCGAGTC
*
1563250 TTATACTCTCTAAAGATATAGGGGGCAGACGCGATTGATGAAGATTGTGGGTCTTATACTCTCTG
129 TTATACTCTCT-AAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGGTCTTATACTCTCTG
*
1563315 AAGAAATAGGGGGCAGAC
193 AAGAAATAGAGGGCAGAC
1563333 ACGATTGGTA
Statistics
Matches: 404, Mismatches: 20, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
216 85 0.21
217 4 0.01
218 313 0.77
219 2 0.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (216 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGAAT
ATTGAGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATCGTTGAAGATTGTTCGAGTCTT
ATACTCTCTAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGGTCTTATACTCTCTGAAG
AAATAGAGGGCAGACGCAATA
Found at i:1572344 original size:184 final size:183
Alignment explanation
Indices: 1572035--1572382 Score: 678
Period size: 184 Copynumber: 1.9 Consensus size: 183
1572025 ATGAAGTTAA
1572035 TAGTCATTTCACAATATGGAGTTAATTTATCTAGTTTTATGCCAAAAGTTAGTCATAAAGGACTT
1 TAGTCATTTCACAATATGGAGTTAATTTATCTAGTTTTATGCCAAAAGTTAGTCATAAAGGACTT
*
1572100 AATTTGCATCAGGCAGTCTAGCAAGTTTTCTGTATGCTATTCTAGAAAGAATAAGAATTCATTAA
66 AATTTGCATCAGGCAGTCCAGCAAGTTTTCTGTATGCTATTCTAGAAAGAATAAGAATTCA-TAA
1572165 TCAGAACTTTGTTTTTTTTGGCCCCTTCAACATCTAGAAAGTTAATTATGAAGT
130 TCAGAACTTTGTTTTTTTTGGCCCCTTCAACATCTAGAAAGTTAATTATGAAGT
1572219 TAGTCATTTCACAATATGGAGTTAATTTATCTAGTTTTATGCCAAAAGTTAGTCATAAAGGACTT
1 TAGTCATTTCACAATATGGAGTTAATTTATCTAGTTTTATGCCAAAAGTTAGTCATAAAGGACTT
1572284 AATTTGCATCAGGCAGTCCAGCAAGTTTTCTGTATGCTATTCTAGAAAGAATAAGAATTCATAAT
66 AATTTGCATCAGGCAGTCCAGCAAGTTTTCTGTATGCTATTCTAGAAAGAATAAGAATTCATAAT
1572349 CAGAACTTTGTTTTTTTTGGCCCCTTCAACATCT
131 CAGAACTTTGTTTTTTTTGGCCCCTTCAACATCT
1572383 TTATAGTTTG
Statistics
Matches: 163, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
183 38 0.23
184 125 0.77
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (183 bp):
TAGTCATTTCACAATATGGAGTTAATTTATCTAGTTTTATGCCAAAAGTTAGTCATAAAGGACTT
AATTTGCATCAGGCAGTCCAGCAAGTTTTCTGTATGCTATTCTAGAAAGAATAAGAATTCATAAT
CAGAACTTTGTTTTTTTTGGCCCCTTCAACATCTAGAAAGTTAATTATGAAGT
Found at i:1574959 original size:20 final size:20
Alignment explanation
Indices: 1574936--1574979 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1574926 GTTTCCAAAT
1574936 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* *
1574956 TCGCAACGTGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
1574976 TCGC
1 TCGC
1574980 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:1575082 original size:20 final size:20
Alignment explanation
Indices: 1574993--1575103 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
1574983 GCGATTTCCA
* **
1574993 AATTCGCAACACTGAATTTCA
1 AATTCGCAACTC-GAATTTTG
*
1575014 AATTCGTAACTCG-ATTTCTG
1 AATTCGCAACTCGAATTT-TG
*
1575034 AATTCGCAACGCGAATTTTG
1 AATTCGCAACTCGAATTTTG
* * *
1575054 -TTGTAGCAACTCGATTTTTG
1 AAT-TCGCAACTCGAATTTTG
*
1575074 AATTCGCAACACGAATTTT-
1 AATTCGCAACTCGAATTTTG
1575093 AATTTCGCAAC
1 AA-TTCGCAAC
1575104 AGGTTTTAGT
Statistics
Matches: 71, Mismatches: 14, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
19 7 0.10
20 49 0.69
21 15 0.21
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (20 bp):
AATTCGCAACTCGAATTTTG
Found at i:1575103 original size:40 final size:40
Alignment explanation
Indices: 1574984--1575103 Score: 134
Period size: 40 Copynumber: 3.0 Consensus size: 40
1574974 AATCGCGTTG
** * * *
1574984 CGATTTCCAAATTCGCAACACTGAATTTCAAATTCGTAACT
1 CGATTTCTGAATTCGCAACAC-GAATTTTAATTTCGCAACT
* * *
1575025 CGATTTCTGAATTCGCAACGCGAATTTT-GTTGTAGCAACT
1 CGATTTCTGAATTCGCAACACGAATTTTAATT-TCGCAACT
*
1575065 CGATTTTTGAATTCGCAACACGAATTTTAATTTCGCAAC
1 CGATTTCTGAATTCGCAACACGAATTTTAATTTCGCAAC
1575104 AGGTTTTAGT
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.02
40 44 0.68
41 20 0.31
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (40 bp):
CGATTTCTGAATTCGCAACACGAATTTTAATTTCGCAACT
Found at i:1575104 original size:20 final size:20
Alignment explanation
Indices: 1574995--1575123 Score: 72
Period size: 20 Copynumber: 6.5 Consensus size: 20
1574985 GATTTCCAAA
* *
1574995 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-GAATTTTAAT
* *
1575016 TTCGTAACTCG-ATTTCTGAA-
1 TTCGCAACACGAATTT-T-AAT
* *
1575036 TTCGCAACGCGAATTTT-GT
1 TTCGCAACACGAATTTTAAT
* * *
1575055 TGTAGCAACTCGATTTTTGAA-
1 T-TCGCAACACGAATTTT-AAT
1575076 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
* *
1575096 TTCGCAACA-G-GTTTTAGT
1 TTCGCAACACGAATTTTAAT
1575114 TTCGCAACAC
1 TTCGCAACAC
1575124 AAATGTTTTG
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
18 15 0.18
19 8 0.10
20 46 0.55
21 15 0.18
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:1575913 original size:12 final size:12
Alignment explanation
Indices: 1575892--1575925 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1575882 ACCACATTTT
*
1575892 CAATACCAAACA
1 CAATATCAAACA
1575904 CAATATCAAACA
1 CAATATCAAACA
*
1575916 CAATCTCAAA
1 CAATATCAAA
1575926 ACCCGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1578858 original size:13 final size:14
Alignment explanation
Indices: 1578842--1578874 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1578832 CATCAATTAA
1578842 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
1578855 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1578869 ACAAAT
1 ACAAAT
1578875 ATATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1582263 original size:16 final size:16
Alignment explanation
Indices: 1582235--1582268 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1582225 ATCTAATAAT
1582235 AATACAAAAAATTAAA
1 AATACAAAAAATTAAA
1582251 AATA-AAAATAATTAAA
1 AATACAAAA-AATTAAA
1582267 AA
1 AA
1582269 ACTAACCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
AATACAAAAAATTAAA
Found at i:1592170 original size:13 final size:14
Alignment explanation
Indices: 1592152--1592183 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1592142 TATTAATAAC
1592152 ATTATTA-TTTATT
1 ATTATTATTTTATT
1592165 ATTATTATTTTATT
1 ATTATTATTTTATT
1592179 -TTATT
1 ATTATT
1592184 TTGCAGGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTATTATTTTATT
Found at i:1596659 original size:22 final size:23
Alignment explanation
Indices: 1596634--1596698 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
1596624 AGATTCAATC
1596634 AAAACAAAAAGAAA-AAAGAGAA
1 AAAACAAAAAGAAACAAAGAGAA
*
1596656 AAAACAAAGAGAAAACAAAGAGAA
1 AAAACAAAAAG-AAACAAAGAGAA
1596680 AATAA-AAAAGAGAAACAAA
1 AA-AACAAAA-AGAAACAAA
1596699 AACAAAGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 10 0.27
23 3 0.08
24 20 0.54
25 4 0.11
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (23 bp):
AAAACAAAAAGAAACAAAGAGAA
Found at i:1596664 original size:13 final size:13
Alignment explanation
Indices: 1596648--1596694 Score: 62
Period size: 11 Copynumber: 3.7 Consensus size: 13
1596638 CAAAAAGAAA
1596648 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
1596661 AAAGAG--AAAAC
1 AAAGAGAAAAAAC
*
1596672 AAAGAGAAAATAAA
1 AAAGAGAAAA-AAC
1596686 AAAGAGAAA
1 AAAGAGAAA
1596695 CAAAAACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 11 0.37
13 8 0.27
14 11 0.37
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:1599508 original size:18 final size:18
Alignment explanation
Indices: 1599485--1599530 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1599475 AGGCATTTGA
* *
1599485 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
1599503 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
1599521 TCCTCGTGCT
1 TCCTC-TGCT
1599531 GTTCTGGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.00, C:0.30, G:0.24, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:1599540 original size:18 final size:19
Alignment explanation
Indices: 1599495--1599545 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
1599485 TCCTCTGGTT
*
1599495 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
1599513 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
1599531 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
1599546 CAGAGTCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:1601126 original size:19 final size:19
Alignment explanation
Indices: 1601115--1601163 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 19
1601105 GGGGTATCGA
1601115 TTCCCCTAGGGGGAATCAG
1 TTCCCCTAGGGGGAATCAG
1601134 TTCCCCTTCAAAGGGGGAATCAG
1 TTCCCC-T---AGGGGGAATCAG
1601157 TTCCCCT
1 TTCCCCT
1601164 GTAAGAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.23
20 1 0.04
22 1 0.04
23 18 0.69
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (19 bp):
TTCCCCTAGGGGGAATCAG
Found at i:1601408 original size:20 final size:19
Alignment explanation
Indices: 1601383--1601421 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1601373 AGCAATGAAT
1601383 GTAATCAGAAATTACTTTTA
1 GTAATCAGAAATTA-TTTTA
1601403 GTAATCAGAAATTATTTTA
1 GTAATCAGAAATTATTTTA
1601422 AACACTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (19 bp):
GTAATCAGAAATTATTTTA
Found at i:1604075 original size:202 final size:201
Alignment explanation
Indices: 1603719--1604116 Score: 746
Period size: 202 Copynumber: 2.0 Consensus size: 201
1603709 TAGAGTGTAG
1603719 TTTTTCGTTTTGGATTACTTAAAAAATGTGATGAAATTTTCTAATGCTTCTCTTAGTACTTAAGA
1 TTTTTCGTTTTGGATTACTTAAAAAATGTGATGAAATTTTCTAATGCTTCTCTTAGTACTTAAGA
1603784 ATATAACTCAAGTATATCTAGAATAGTCATCTACCAAGAAAAAATGCATATTGTTTTCCACCCAA
66 ATATAACTCAAGTATATCTAGAATAGTCATCTACCAAGAAAAAATGCATATTGTTTTCCACCCAA
1603849 GCTAGTAGTCCTAGTTGGCCAAAAAGATCTATATGGATCAATTGTAATA-CTACTAGTTGACACA
131 GCTAGTAGTCCTAGTTGGCCAAAAAGATCTATATGGATCAATTGTAATACCTACTAGTTGACACA
1603913 GTAACC
196 GTAACC
1603919 TTTTTCGTTTTGGATTACTTAAAAAATGTGATGAAATTTTCTAATGCTTCATCTTTAGTACTTAA
1 TTTTTCGTTTTGGATTACTTAAAAAATGTGATGAAATTTTCTAATGCTTC-TC-TTAGTACTTAA
1603984 GAATATAACTCAAGTATATCTAGAATAGTCATCTACCAAG-AAAAATGCATATTGTTTTCCACCC
64 GAATATAACTCAAGTATATCTAGAATAGTCATCTACCAAGAAAAAATGCATATTGTTTTCCACCC
1604048 AAGCTAGTAGTCCTAGTTGGCCCAAAAAGATCTATATGGATCAATTGTAATACTCTACTAGTTGA
129 AAGCTAGTAGTCCTAGTTGG-CCAAAAAGATCTATATGGATCAATTGTAATAC-CTACTAGTTGA
1604113 CACA
192 CACA
1604117 TCATTAATGG
Statistics
Matches: 193, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
200 50 0.26
201 46 0.24
202 82 0.42
204 15 0.08
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (201 bp):
TTTTTCGTTTTGGATTACTTAAAAAATGTGATGAAATTTTCTAATGCTTCTCTTAGTACTTAAGA
ATATAACTCAAGTATATCTAGAATAGTCATCTACCAAGAAAAAATGCATATTGTTTTCCACCCAA
GCTAGTAGTCCTAGTTGGCCAAAAAGATCTATATGGATCAATTGTAATACCTACTAGTTGACACA
GTAACC
Found at i:1607685 original size:43 final size:44
Alignment explanation
Indices: 1607594--1607715 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 44
1607584 AAAGGGCCAT
* * * ***
1607594 CCACGATTTCAACTCCATGACGGATGATATCGTACCCATGGATA
1 CCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACACATA
1607638 -CACGATTTCAACTCCACGACGGAGGATATCGTGCCCACACA-A
1 CCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACACATA
* * * *
1607680 CCACGATTTCAACTTCACAACGAAGGATATTGTGCC
1 CCACGATTTCAACTCCACGACGGAGGATATCGTGCC
1607716 AACTCTAGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.01
43 66 0.99
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (44 bp):
CCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACACATA
Found at i:1608093 original size:124 final size:124
Alignment explanation
Indices: 1607855--1608098 Score: 335
Period size: 124 Copynumber: 2.0 Consensus size: 124
1607845 TAATACAAGC
* * * **
1607855 TTGGATTTCAACTTCACGATGAAGGATATTCAAGTCAAGACTCAACTTCACGATGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGACTCAACTTCACAACAAAGGGGCCAT
* * * *
1607920 CCACGGTTTCAACTTCACGACGAATGAAATCATGCACACAAGCAGCATTCATCTTTAGA
66 CCACGATTTCAACTTCACGACGAAGGAAATCATACACACAAGCAACATTCATCTTTAGA
* *
1607979 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGACTCAACTTCACAACAAAGGGGCCAT
* * * * * *
1608044 CCACGATTTTAACTTCACGATGAAGGGAATCGTACCCACCAGCAACATTCATCTT
66 CCACGATTTCAACTTCACGACGAAGGAAATCATACACACAAGCAACATTCATCTT
1608099 CAGGAACAAG
Statistics
Matches: 103, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
124 103 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGACTCAACTTCACAACAAAGGGGCCAT
CCACGATTTCAACTTCACGACGAAGGAAATCATACACACAAGCAACATTCATCTTTAGA
Found at i:1608255 original size:36 final size:36
Alignment explanation
Indices: 1608215--1608490 Score: 300
Period size: 36 Copynumber: 7.8 Consensus size: 36
1608205 AAACAAATTC
*
1608215 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATATTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1608251 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA-----
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* * * *
1608282 AC-CT-TTGA-ATATGTTTTACATT-AAACAAATTTTG
1 TCTCTCTTGAGACA-G-TTTCCCTTGAAACAAATTTTG
* ** * *
1608316 TCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTG
* *
1608353 TCTCTCCTGAGACAGTTTCTCTTGAAACAAATTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* * *
1608389 TTTCTCTTGAGACAGTTTTCCTTGAAACAAATTTTA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1608425 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTTTG
* *
1608462 TCTCTGTTGAGACAGTTTCTCTTGAAACA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACA
1608491 CCAATCCTTG
Statistics
Matches: 200, Mismatches: 27, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 12 0.06
30 8 0.04
31 1 0.00
34 1 0.00
35 6 0.03
36 106 0.53
37 64 0.32
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (36 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
Found at i:1608458 original size:109 final size:102
Alignment explanation
Indices: 1608215--1608557 Score: 331
Period size: 109 Copynumber: 3.3 Consensus size: 102
1608205 AAACAAATTC
* *
1608215 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TATTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
* *
1608279 AAAACCTTTGAATATGTTTTACATTAAACAAATTTTG
66 AAAACCTTTGAACATGTTTTACATTAAACAAATTTTA
* ** * * *
1608316 TCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCCTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
** *
1608381 AAATTTTGTTTCTCTTGAGACA-GTTTT-CCTTGAAACAAATTTTA
66 AAA------ACCT-TTGA-ACATGTTTTACATT-AAACAAATTTTA
*
1608425 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTGTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
* * *
1608490 ACCAATCC-TTGAATATGTTTCT-C-TTGAAACAAAATTTTG
66 A--AAACCTTTGAACATGTTT-TACATT-AAAC-AAATTTTA
* *
1608529 CCTC-CTTTGAGACAGTTTCTCTTGAAACA
1 TCTCTC-TTGAGACAGTTTCCCTTGAAACA
1608558 CACAAAAAAA
Statistics
Matches: 201, Mismatches: 25, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
101 26 0.13
102 35 0.17
103 16 0.08
104 34 0.17
105 2 0.01
108 5 0.02
109 79 0.39
110 2 0.01
111 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (102 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
AAAACCTTTGAACATGTTTTACATTAAACAAATTTTA
Found at i:1609682 original size:35 final size:35
Alignment explanation
Indices: 1609636--1609705 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1609626 AATGTACAGG
1609636 GGGAACAGATTCCCCCCT-GGGGGTATCGATTCCCC
1 GGGAACAGATT-CCCCCTGGGGGGTATCGATTCCCC
1609671 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1609706 CTAAATGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 6 0.18
35 28 0.82
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
Found at i:1610331 original size:15 final size:15
Alignment explanation
Indices: 1610311--1610346 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1610301 TCGAGGGTAT
*
1610311 TGTAGTTCTTCGGGA
1 TGTAGTCCTTCGGGA
1610326 TGTAGTCCTTCGGGA
1 TGTAGTCCTTCGGGA
*
1610341 CGTAGT
1 TGTAGT
1610347 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.17, G:0.33, T:0.36
Consensus pattern (15 bp):
TGTAGTCCTTCGGGA
Found at i:1619448 original size:22 final size:24
Alignment explanation
Indices: 1619423--1619474 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
1619413 TTTTGTCCGA
1619423 ATTTTAAAAAAATTATT-TTT-TT
1 ATTTTAAAAAAATTATTATTTATT
* *
1619445 ATTTTAATAACATTATTATTTATT
1 ATTTTAAAAAAATTATTATTTATT
1619469 ATTTTA
1 ATTTTA
1619475 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 15 0.58
23 3 0.12
24 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTAAAAAAATTATTATTTATT
Found at i:1622878 original size:66 final size:66
Alignment explanation
Indices: 1622772--1622901 Score: 174
Period size: 66 Copynumber: 2.0 Consensus size: 66
1622762 GGTATGAAGA
*
1622772 CTCTGGCAGGTTCAGTCGCTGCGGGTAATTACTTGTATAGGTT-ATGCATCGACCGGTAATTCCT
1 CTCTGGCAGGTTCAGTCGCTGCGGGTAATTACTTGTATAGGTTCA-ACATCGACCGGTAATTCCT
1622836 AT
65 AT
* ** * *
1622838 CTCTGGTAGGTTCAGTCGCTGTTGGTAATT-CATTTTATAGGTTCAACATCGACTGGTAATTCCT
1 CTCTGGCAGGTTCAGTCGCTGCGGGTAATTAC-TTGTATAGGTTCAACATCGACCGGTAATTCCT
1622902 TATGGACCTA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
65 1 0.02
66 54 0.96
67 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (66 bp):
CTCTGGCAGGTTCAGTCGCTGCGGGTAATTACTTGTATAGGTTCAACATCGACCGGTAATTCCTA
T
Found at i:1623648 original size:19 final size:19
Alignment explanation
Indices: 1623624--1623665 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1623614 AATGTGACAC
1623624 CCCGGATTGGATCGGGTCA
1 CCCGGATTGGATCGGGTCA
1623643 CCCGGATTGGATCGGGTCA
1 CCCGGATTGGATCGGGTCA
1623662 CCCG
1 CCCG
1623666 CATCGGTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.19
Consensus pattern (19 bp):
CCCGGATTGGATCGGGTCA
Found at i:1625536 original size:20 final size:20
Alignment explanation
Indices: 1625511--1625551 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1625501 CAGCTCTGCA
1625511 GGTGGGGTAGGCAGGCTGAT
1 GGTGGGGTAGGCAGGCTGAT
*
1625531 GGTGGGGTGGGCAGGCTGAT
1 GGTGGGGTAGGCAGGCTGAT
1625551 G
1 G
1625552 AACTCTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.10, G:0.59, T:0.20
Consensus pattern (20 bp):
GGTGGGGTAGGCAGGCTGAT
Found at i:1625829 original size:2 final size:2
Alignment explanation
Indices: 1625822--1625847 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1625812 TCATAAAATT
1625822 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1625848 ATTTTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1625910 original size:14 final size:14
Alignment explanation
Indices: 1625891--1625935 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1625881 GTAAAATTTT
1625891 ATTTTAATTATTGA
1 ATTTTAATTATTGA
1625905 ATTTT-A-TA-TGA
1 ATTTTAATTATTGA
*
1625916 TATTTTAATTATAGA
1 -ATTTTAATTATTGA
1625931 ATTTT
1 ATTTT
1625936 TTATAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
11 3 0.12
12 7 0.27
13 2 0.08
14 12 0.46
15 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (14 bp):
ATTTTAATTATTGA
Found at i:1627345 original size:24 final size:24
Alignment explanation
Indices: 1627318--1627366 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1627308 CGTTCGTGAA
1627318 CGTTAGGTTATGTTCGTTTATGTT
1 CGTTAGGTTATGTTCGTTTATGTT
*
1627342 CGTTTGGTTATGTTCGTTTATGTT
1 CGTTAGGTTATGTTCGTTTATGTT
1627366 C
1 C
1627367 ATTCATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.10, G:0.24, T:0.55
Consensus pattern (24 bp):
CGTTAGGTTATGTTCGTTTATGTT
Found at i:1627376 original size:24 final size:24
Alignment explanation
Indices: 1627324--1627378 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1627314 TGAACGTTAG
* **
1627324 GTTATGTTCGTTTATGTTCGTTTG
1 GTTATGTTCGTTTATGTTCATTCA
1627348 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
1627372 TTTATGT
1 GTTATGT
1627379 CTAACCCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.13, C:0.09, G:0.20, T:0.58
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:1628476 original size:16 final size:16
Alignment explanation
Indices: 1628453--1628507 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
1628443 GGGTCTCCAA
1628453 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
1628469 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
1628485 CGTTTATGTTCGTATT
1 CGTTTATGTTCGTGTT
1628501 CGTTTAT
1 CGTTTAT
1628508 TTATTAAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.11, C:0.13, G:0.20, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:1628592 original size:16 final size:16
Alignment explanation
Indices: 1628571--1628603 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1628561 CAAAAAAATT
1628571 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1628587 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1628603 T
1 T
1628604 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1629032 original size:31 final size:31
Alignment explanation
Indices: 1628980--1629044 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1628970 GATACATGAT
* *
1628980 CCTAACGTTATTGATCTATTCGATTTTAATC
1 CCTAACATTACTGATCTATTCGATTTTAATC
*
1629011 CCTAACATTACTGAT-TCATTCGATTTTAGTC
1 CCTAACATTACTGATCT-ATTCGATTTTAATC
1629042 CCT
1 CCT
1629045 CAGCAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (31 bp):
CCTAACATTACTGATCTATTCGATTTTAATC
Found at i:1639608 original size:31 final size:32
Alignment explanation
Indices: 1639571--1639661 Score: 107
Period size: 31 Copynumber: 2.9 Consensus size: 32
1639561 AAATTAAGGG
1639571 GTTAAATTGATA-TTTGATCTAAAGTTCAAGA
1 GTTAAATTGATATTTTGATCTAAAGTTCAAGA
* * **
1639602 GTTAAATTGATATTTTAATC-AAAGTTTAATT
1 GTTAAATTGATATTTTGATCTAAAGTTCAAGA
*
1639633 GTCAAATTGATATTTTTG-TCTAAAGTTCA
1 GTTAAATTGATA-TTTTGATCTAAAGTTCA
1639662 TGTATCAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.66
32 17 0.34
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (32 bp):
GTTAAATTGATATTTTGATCTAAAGTTCAAGA
Found at i:1639670 original size:32 final size:32
Alignment explanation
Indices: 1639574--1639672 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 32
1639564 TTAAGGGGTT
* *
1639574 AAATTGATA--TTTGATCTAAAGTTCAAG-AGTT
1 AAATTGATATTTTTG-TCTAAAGTTCATGTA-TC
** * *
1639605 AAATTGATATTTTAATC-AAAGTTTAAT-TGTC
1 AAATTGATATTTTTGTCTAAAG-TTCATGTATC
1639636 AAATTGATATTTTTGTCTAAAGTTCATGTATC
1 AAATTGATATTTTTGTCTAAAGTTCATGTATC
1639668 AAATT
1 AAATT
1639673 AAAATTGGTG
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
31 33 0.63
32 17 0.33
33 2 0.04
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.43
Consensus pattern (32 bp):
AAATTGATATTTTTGTCTAAAGTTCATGTATC
Found at i:1643463 original size:17 final size:17
Alignment explanation
Indices: 1643443--1643480 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1643433 ATTATATAAG
1643443 TAAAATA-TTAAATAAAT
1 TAAAATACTT-AATAAAT
1643460 TAAAATACTTAATAAAT
1 TAAAATACTTAATAAAT
1643477 TAAA
1 TAAA
1643481 TACAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAATACTTAATAAAT
Found at i:1643489 original size:16 final size:17
Alignment explanation
Indices: 1643452--1643489 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1643442 GTAAAATATT
*
1643452 AAATAAATTAAAATACT
1 AAATAAATTAAAATACA
*
1643469 TAATAAATT-AAATACA
1 AAATAAATTAAAATACA
1643485 AAATA
1 AAATA
1643490 TTAAAAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAATTAAAATACA
Found at i:1643542 original size:10 final size:10
Alignment explanation
Indices: 1643519--1643568 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
1643509 TACCTTAAAC
* *
1643519 AGAGAATATA
1 AGAGAATTTG
*
1643529 AGAGTATTTG
1 AGAGAATTTG
*
1643539 AGAGAAGTTG
1 AGAGAATTTG
*
1643549 AGAGAAATTG
1 AGAGAATTTG
1643559 AGAGAATTTG
1 AGAGAATTTG
1643569 GTGTGATGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:1643990 original size:43 final size:43
Alignment explanation
Indices: 1643929--1644014 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1643919 TTTACATTAC
*
1643929 CTTTAACCTGTGTTAAATATATGTGCGAGTTTTATTAAAAAAA
1 CTTTAACCTATGTTAAATATATGTGCGAGTTTTATTAAAAAAA
1643972 CTTTAACCTATGTTAAATATATGTGCGAGTTTTATTAAAAAAA
1 CTTTAACCTATGTTAAATATATGTGCGAGTTTTATTAAAAAAA
1644015 AATTGGTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (43 bp):
CTTTAACCTATGTTAAATATATGTGCGAGTTTTATTAAAAAAA
Found at i:1645146 original size:30 final size:30
Alignment explanation
Indices: 1645112--1645178 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
1645102 CCCGAAGGAC
*
1645112 CTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1645142 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1645172 CTGTCCA
1 CTATCCA
1645179 TATCTCTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1647833 original size:24 final size:24
Alignment explanation
Indices: 1647806--1647905 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1647796 GATATCAAAA
*
1647806 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1647830 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1647854 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1647878 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1647902 ATCA
1 ATCA
1647906 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1647905 original size:48 final size:48
Alignment explanation
Indices: 1647799--1647907 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1647789 AAACGGAGAT
* * * * *
1647799 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1647847 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1647895 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1647908 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1649056 original size:18 final size:18
Alignment explanation
Indices: 1649035--1649070 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1649025 CTTCCATCCG
*
1649035 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1649053 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1649071 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1650389 original size:13 final size:13
Alignment explanation
Indices: 1650371--1650444 Score: 67
Period size: 13 Copynumber: 5.3 Consensus size: 13
1650361 TCCGGTCAAC
1650371 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1650384 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1650397 GGTCGGGTTAACGGGTCG
1 GGTC-----AACGGGTCG
* *
1650415 AGTCAACGGGTCC
1 GGTCAACGGGTCG
* *
1650428 AGTAAACGGGTCG
1 GGTCAACGGGTCG
1650441 GGTC
1 GGTC
1650445 GGGTTGTGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 38 0.76
18 12 0.24
ACGTcount: A:0.18, C:0.22, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1650400 original size:18 final size:18
Alignment explanation
Indices: 1650377--1650414 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1650367 CAACGGTCAA
1650377 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1650395 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
1650413 CG
1 CG
1650415 AGTCAACGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.50, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1652402 original size:2 final size:2
Alignment explanation
Indices: 1652395--1652423 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1652385 TTTTTAAAAC
1652395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1652424 CCCCCATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1652616 original size:24 final size:24
Alignment explanation
Indices: 1652589--1652688 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1652579 GATATCAAAA
*
1652589 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1652613 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1652637 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1652661 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1652685 ATCA
1 ATCA
1652689 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1652688 original size:48 final size:48
Alignment explanation
Indices: 1652582--1652690 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1652572 AAACGGAGAT
* * * * *
1652582 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1652630 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1652678 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1652691 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1653839 original size:18 final size:18
Alignment explanation
Indices: 1653818--1653853 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1653808 CTTCCATCCG
*
1653818 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1653836 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1653854 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1655173 original size:13 final size:13
Alignment explanation
Indices: 1655155--1655228 Score: 67
Period size: 13 Copynumber: 5.3 Consensus size: 13
1655145 TCCGGTCAAC
1655155 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1655168 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1655181 GGTCGGGTTAACGGGTCG
1 GGTC-----AACGGGTCG
* *
1655199 AGTCAACGGGTCC
1 GGTCAACGGGTCG
* *
1655212 AGTAAACGGGTCG
1 GGTCAACGGGTCG
1655225 GGTC
1 GGTC
1655229 GGGTTGTGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 38 0.76
18 12 0.24
ACGTcount: A:0.18, C:0.22, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1655184 original size:18 final size:18
Alignment explanation
Indices: 1655161--1655198 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1655151 CAACGGTCAA
1655161 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1655179 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
1655197 CG
1 CG
1655199 AGTCAACGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.50, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1655251 original size:9 final size:9
Alignment explanation
Indices: 1655237--1655285 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
1655227 TCGGGTTGTG
1655237 ACCGGTCAA
1 ACCGGTCAA
1655246 ACCGGTCAAA
1 ACCGGTC-AA
* *
1655256 ACAGTTCCAAA
1 ACCGGT-C-AA
1655267 ACCGGTCAA
1 ACCGGTCAA
1655276 ACCGGTCAA
1 ACCGGTCAA
1655285 A
1 A
1655286 ACAGTTCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 19 0.56
10 7 0.21
11 8 0.24
ACGTcount: A:0.39, C:0.31, G:0.18, T:0.12
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1655273 original size:30 final size:30
Alignment explanation
Indices: 1655237--1655298 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1655227 TCGGGTTGTG
1655237 ACCGGTCAAACCGGTCAAAACAGTTCCAAA
1 ACCGGTCAAACCGGTCAAAACAGTTCCAAA
1655267 ACCGGTCAAACCGGTCAAAACAGTTCCAAA
1 ACCGGTCAAACCGGTCAAAACAGTTCCAAA
1655297 AC
1 AC
1655299 AGTAGCCCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.31, G:0.16, T:0.13
Consensus pattern (30 bp):
ACCGGTCAAACCGGTCAAAACAGTTCCAAA
Found at i:1655848 original size:2 final size:2
Alignment explanation
Indices: 1655841--1655865 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1655831 TTTTTAAAAC
1655841 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1655866 CCCCCATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1656058 original size:24 final size:24
Alignment explanation
Indices: 1656031--1656130 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1656021 GATATCAAAA
*
1656031 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1656055 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1656079 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1656103 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1656127 ATCA
1 ATCA
1656131 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1656130 original size:48 final size:48
Alignment explanation
Indices: 1656024--1656132 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1656014 AAACGGAGAT
* * * * *
1656024 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1656072 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1656120 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1656133 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1658615 original size:13 final size:13
Alignment explanation
Indices: 1658597--1658670 Score: 67
Period size: 13 Copynumber: 5.3 Consensus size: 13
1658587 TCCGGTCAAC
1658597 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1658610 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1658623 GGTCGGGTTAACGGGTCG
1 GGTC-----AACGGGTCG
* *
1658641 AGTCAACGGGTCC
1 GGTCAACGGGTCG
* *
1658654 AGTAAACGGGTCG
1 GGTCAACGGGTCG
1658667 GGTC
1 GGTC
1658671 GGGTTGTGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 38 0.76
18 12 0.24
ACGTcount: A:0.18, C:0.22, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1658626 original size:18 final size:18
Alignment explanation
Indices: 1658603--1658640 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1658593 CAACGGTCAA
1658603 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1658621 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
1658639 CG
1 CG
1658641 AGTCAACGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.50, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1659740 original size:28 final size:28
Alignment explanation
Indices: 1659709--1659762 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1659699 CACCTTCTTG
*
1659709 TATCAACTTCTTCTCTCAACGACAACGA
1 TATCAACTTATTCTCTCAACGACAACGA
* *
1659737 TATCACCTTATTCTCTCAACGGCAAC
1 TATCAACTTATTCTCTCAACGACAAC
1659763 ACCTTCTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (28 bp):
TATCAACTTATTCTCTCAACGACAACGA
Found at i:1659756 original size:41 final size:41
Alignment explanation
Indices: 1659674--1659756 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
1659664 ATAGTAGCAC
* *
1659674 CTTCGTCTCTCAACGACAACGATAACACCTTCTTGTATCAA
1 CTTCGTCTCTCAACGACAACGATAACACCTTATTCTATCAA
* * *
1659715 CTTCTTCTCTCAACGACAACGATATCACCTTATTCTCTCAA
1 CTTCGTCTCTCAACGACAACGATAACACCTTATTCTATCAA
1659756 C
1 C
1659757 GGCAACACCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.34, G:0.07, T:0.31
Consensus pattern (41 bp):
CTTCGTCTCTCAACGACAACGATAACACCTTATTCTATCAA
Found at i:1668291 original size:2 final size:2
Alignment explanation
Indices: 1668284--1668314 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1668274 ACTTTGTATG
1668284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1668315 GAAAACTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1672237 original size:11 final size:11
Alignment explanation
Indices: 1672221--1672250 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1672211 AAATTAGGAA
1672221 GAAGAAAGATG
1 GAAGAAAGATG
1672232 GAAGAAAGATG
1 GAAGAAAGATG
1672243 GAAGAAAG
1 GAAGAAAG
1672251 GGAAACATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (11 bp):
GAAGAAAGATG
Found at i:1672480 original size:81 final size:81
Alignment explanation
Indices: 1672345--1672502 Score: 273
Period size: 81 Copynumber: 2.0 Consensus size: 81
1672335 TATAGGACGC
* *
1672345 TGCTTTGTTGGGTTCTTTAACTATTAAAAGTTACAAAATGATCATTTGATTATAGGGAGTTACTT
1 TGCTTTGTTGAGTTCTTCAACTATTAAAAGTTACAAAATGATCATTTGATTATAGGGAGTTACTT
1672410 TGTTGAGTCTCCAAGT
66 TGTTGAGTCTCCAAGT
*
1672426 TGCTTTGTTGAGTTCTTCAACTATTAAAAGTTACAAAATGATCCTCTT-ATTATAGGGAGTTACT
1 TGCTTTGTTGAGTTCTTCAACTATTAAAAGTTACAAAATGATCAT-TTGATTATAGGGAGTTACT
1672490 TTGTTGAGTCTCC
65 TTGTTGAGTCTCC
1672503 GACTATTTAA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
81 71 0.97
82 2 0.03
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (81 bp):
TGCTTTGTTGAGTTCTTCAACTATTAAAAGTTACAAAATGATCATTTGATTATAGGGAGTTACTT
TGTTGAGTCTCCAAGT
Found at i:1674491 original size:20 final size:20
Alignment explanation
Indices: 1674466--1674504 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1674456 GTAAATTGAC
1674466 GTGTTTTCCATTTAAATATT
1 GTGTTTTCCATTTAAATATT
*
1674486 GTGTTTTCCTTTTAAATAT
1 GTGTTTTCCATTTAAATAT
1674505 GTTTGTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (20 bp):
GTGTTTTCCATTTAAATATT
Found at i:1674611 original size:9 final size:9
Alignment explanation
Indices: 1674590--1674725 Score: 66
Period size: 10 Copynumber: 14.4 Consensus size: 9
1674580 TTTTGGTCCT
1674590 TTTTATTTA
1 TTTTATTTA
1674599 -TTTATTTA
1 TTTTATTTA
1674607 TTTTATTTA
1 TTTTATTTA
*
1674616 TTTTTATTATT
1 -TTTTATT-TA
* *
1674627 TTTTAATAA
1 TTTTATTTA
1674636 CTTTTATTTA
1 -TTTTATTTA
*
1674646 TCTTT-GTTA
1 T-TTTATTTA
*
1674655 -TCTATTTTA
1 TTTTA-TTTA
1674664 TTTTA-TTA
1 TTTTATTTA
1674672 TTATTATTATA
1 TT-TTATT-TA
*
1674683 TTAATATTT-
1 TT-TTATTTA
* *
1674692 TTTCTCTTTT
1 TTT-TATTTA
1674702 TTTATATTTA
1 TTT-TATTTA
1674712 TTTATATTTA
1 TTT-TATTTA
1674722 TTTT
1 TTTT
1674726 TCAATTTAAC
Statistics
Matches: 98, Mismatches: 16, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
7 2 0.02
8 13 0.13
9 25 0.26
10 48 0.49
11 10 0.10
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1677422 original size:99 final size:99
Alignment explanation
Indices: 1677311--1677508 Score: 297
Period size: 99 Copynumber: 2.0 Consensus size: 99
1677301 TAATATTATA
* ** * *
1677311 TATACATTAAAGCTTGAGCTGTTTCTCTAGAGCAATTGGTTAAACGTCCCGGCTTTATGGATAAG
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATAAG
1677376 ATTCAACTAACCTGATAAAGGTGATTATAATATC
66 ATTCAACTAACCTGATAAAGGTGATTATAATATC
* * * *
1677410 TATACAATAAAGCTTGAGTTGTCCCTGTAGAGCAATTGGTTAAACGCCCCAGTTTTATGGATAAT
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATAAG
* *
1677475 ATTCAGCTAGCCTGATAAAGGTGATTATAATATC
66 ATTCAACTAACCTGATAAAGGTGATTATAATATC
1677509 ATTGAGTTGT
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (99 bp):
TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATAAG
ATTCAACTAACCTGATAAAGGTGATTATAATATC
Found at i:1678479 original size:80 final size:80
Alignment explanation
Indices: 1678346--1678833 Score: 733
Period size: 80 Copynumber: 6.1 Consensus size: 80
1678336 TTAACAAAAA
* * *
1678346 ACCTTCAAGTTCAATTACACTCAGCTCAAAGGCACATTATTTGCAGCATAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
1678411 GGCTACCTGCCAAAG
66 GGCTACCTGCCAAAG
* * * *
1678426 ACCTTCGAGTTCAATTACACTCAGCTTAAAGGCACATCATTTGTAGTATAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
*
1678491 GGCTAGCTGCCAAAG
66 GGCTACCTGCCAAAG
* * *
1678506 ACATTTGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAACAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
1678571 GGCTACCTGCCAAAG
66 GGCTACCTGCCAAAG
*
1678586 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
*
1678651 GGTTACCTGCCAAAG
66 GGCTACCTGCCAAAG
* * * *
1678666 ACCTTCGAGTTCGATTACACTCAGCTCAAAAGCACATCATTTGCAGTATAACTTAAGGCAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
* * *
1678731 GGTTATCTACCAAAG
66 GGCTACCTGCCAAAG
* * *
1678746 ACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATTATTTGCAGCATAGCTCAAGGAAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
* * *
1678811 GGATATCTGCTAAAG
66 GGCTACCTGCCAAAG
*
1678826 ATCTTCGA
1 ACCTTCGA
1678834 AAGGCACATC
Statistics
Matches: 370, Mismatches: 38, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 370 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (80 bp):
ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
GGCTACCTGCCAAAG
Found at i:1678782 original size:240 final size:241
Alignment explanation
Indices: 1678346--1679369 Score: 991
Period size: 240 Copynumber: 4.3 Consensus size: 241
1678336 TTAACAAAAA
* * *
1678346 ACCTTCAAGTTCAATTACACTCAGCTCAAAGGCACATTATTTGCAGCATAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
* * *
1678411 GGCTACCTGCCAAAGACCTTCGAGTTCAATTACACTCAGCTTAAAGGCACATCATTTGTAGTATA
66 GGCTACCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATA
* * * * * *
1678476 GCTCAAGGCAAGAAGGGCTAGCT-GCCAAAGACATTTGAGTTCGATTACACTCAGCTCAAAGGCA
131 ACTCAAGGCAAGAAGGGTTATCTCACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
* * *
1678540 CATCATTTGCAGCATAGCTCAAGGCAACAAGGGCTACCTGCCAAAG
196 CATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTATCTGCCAAAG
*
1678586 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
* *
1678651 GGTTACCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAAGCACATCATTTGCAGTATA
66 GGCTACCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATA
* *
1678716 ACTTAAGGCAAGAAGGGTTATCT-ACCAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCA
131 ACTCAAGGCAAGAAGGGTTATCTCACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
* * *
1678780 CATTATTTGCAGCATAGCTCAAGGAAAGAAGGGATATCTGCTAAAG
196 CATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTATCTGCCAAAG
* ** ** ** ** * *
1678826 ATCTTCGA--AAG-GCACA-TCATTTGCAACA-TAAC-TCA--AG--GCA-AG---AAGGGCTA-
1 ACCTTCGAGTTCGATTACACTCAGCT-CAA-AGGCACATCATTTGCAGCATAGCTCAA-GGCAAG
* * ** * * *
1678876 TA----TGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGC
63 AAGGGCTACCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGT
* * * *
1678937 ATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTTAGCTTAA
128 ATAACTCAAGGCAAGAAGGGTTATC--TCACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAA
* * * * *
1679002 AAGCATATTATTTGCAGCATAGCTCAAGGAAAGAAAGGCTATATGCCAAAG
191 AGGCACATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTATCTGCCAAAG
* * * * *
1679053 ACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAACTCAGGGCAAGAAA
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
* ** * * *
1679118 GTCTATTTGCCAACAAAAAACCTTCGAGTTCGATTACACTCATCTCAAAGGCACATCATTTGTAG
66 GGCTACCTG-C--C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAG
* * * * *
1679183 TATAGCTCAATGCGAGAAGGGATATCTGCCAACAAAAGACCTTCGAGTTCGATT--A--CA-CT-
127 TATAACTCAAGGCAAGAAGGGTTATCT--C-ACCAAAGACCTTCGAGTTCGATTACACTCAGCTC
* ** *
1679242 -------CATCATTTGCAGCATAGCTCAATGCGAGAAGGGTTATCTGCCAACAAAAG
189 AAAGGCACATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTATCTG-C--C-AAAG
* ** *
1679292 AACTTCGAGTTCGATTACACTCAGCTCAAAGATACATCATTTGCAGCATAGCTCAAGGCGAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
*
1679357 GGCTATCTGCCAA
66 GGCTACCTGCCAA
1679370 CAAAAGACCT
Statistics
Matches: 643, Mismatches: 105, Indels: 77
0.78 0.13 0.09
Matches are distributed among these distances:
224 75 0.12
226 1 0.00
227 83 0.13
228 3 0.00
229 5 0.01
230 8 0.01
231 9 0.01
232 3 0.00
233 1 0.00
234 1 0.00
235 37 0.06
236 10 0.02
237 8 0.01
238 8 0.01
239 69 0.11
240 226 0.35
243 3 0.00
244 2 0.00
245 1 0.00
246 1 0.00
247 68 0.11
248 21 0.03
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (241 bp):
ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
GGCTACCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATA
ACTCAAGGCAAGAAGGGTTATCTCACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
CATCATTTGCAGCATAGCTCAAGGAAAGAAGGGCTATCTGCCAAAG
Found at i:1678954 original size:144 final size:140
Alignment explanation
Indices: 1678697--1678963 Score: 390
Period size: 144 Copynumber: 1.9 Consensus size: 140
1678687 CAGCTCAAAA
** * * * *
1678697 GCACATCATTTGCAGTATAACTTAAGGCAAGAAGGGTTATCTACCAAAGACCTTTGAGTTCGATT
1 GCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCAACAAAAGACCTTCGAGTTCGATT
* * *
1678762 ACACTCAGCTCAAAGGCACATTATTTGCAGCATAGCTCAAGGAAAGAAGGGATATCTGCTAAAGA
66 ACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGAAAGAAGGGATATCTGCTAAAGA
1678827 TCTTCGAAAG
131 TCTTCGAAAG
1678837 GCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGAGTTC
1 GCACATCATTTGCAACATAACTCAAGGCAAGAAGGG-T-TAT--CAACAAAAGACCTTCGAGTTC
** *
1678902 GATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
62 GATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGAAAGAAGGGATATCTG
1678964 TCAACAAAGA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
140 33 0.30
141 1 0.01
142 3 0.03
144 74 0.67
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (140 bp):
GCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCAACAAAAGACCTTCGAGTTCGATT
ACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGAAAGAAGGGATATCTGCTAAAGA
TCTTCGAAAG
Found at i:1679134 original size:163 final size:167
Alignment explanation
Indices: 1678837--1679386 Score: 609
Period size: 155 Copynumber: 3.4 Consensus size: 167
1678827 TCTTCGAAAG
* *
1678837 GCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGAGTTC
1 GCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATATGCC-ACAAAAGACCTTCGAGTTC
* * *
1678902 GATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
65 GATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGAGTTATCTGCCA
* * *
1678967 AC-AAAGACCTTCGAGTTCGATTACACTTAGCTTAAAA
130 ACAAAAAACCTTCGAGTTCGATTACACTCAGCTCAAAA
* * * * *
1679004 GCATATTATTTGCAGCATAGCTCAAGGAAAGAAAGGCTATATG-C-C-AAAGACCTTCAAGTTCG
1 GCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATATGCCACAAAAGACCTTCGAGTTCG
** * *
1679066 ATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAACTCAGGGCAAGAA-AGTCTATTTGCCA
66 ATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGAGT-TATCTGCCA
* *
1679130 ACAAAAAACCTTCGAGTTCGATTACACTCATCTCAAAG
130 ACAAAAAACCTTCGAGTTCGATTACACTCAGCTCAAAA
* * * * * *
1679168 GCACATCATTTGTAGTATAGCTCAATGCGAGAAGGGATATCTGCCAACAAAAGACCTTCGAGTTC
1 GCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATATGCC-ACAAAAGACCTTCGAGTTC
* * * * *
1679233 GATT--A--CA-CT--------CATCATTTGCAGCATAGCTCAATGCGAGAAGGGTTATCTGCCA
65 GATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGAGTTATCTGCCA
1679285 ACAAAAGAA-CTTCGAGTTCGATTACACTCAGCTC-AAA
130 ACAAAA-AACCTTCGAGTTCGATTACACTCAGCTCAAAA
* * *
1679322 GATACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTT
1 G-CACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATATGCC-ACAAAAGACCTTCGAGTT
1679387 ATCTACCAAC
Statistics
Matches: 330, Mismatches: 44, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
154 3 0.01
155 121 0.37
156 4 0.01
162 2 0.01
163 74 0.22
164 66 0.20
165 1 0.00
166 2 0.01
167 38 0.12
168 19 0.06
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (167 bp):
GCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATATGCCACAAAAGACCTTCGAGTTCG
ATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGAGTTATCTGCCAA
CAAAAAACCTTCGAGTTCGATTACACTCAGCTCAAAA
Found at i:1679245 original size:84 final size:84
Alignment explanation
Indices: 1678833--1679243 Score: 526
Period size: 84 Copynumber: 5.0 Consensus size: 84
1678823 AAGATCTTCG
*
1678833 AAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGA
1 AAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGA
1678898 GTTCGATTACACTCAGCTC
66 GTTCGATTACACTCAGCTC
* * * * *
1678917 AAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCGA
1 AAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGA
* *
1678981 GTTCGATTACACTTAGCTT
66 GTTCGATTACACTCAGCTC
* * * * * * *
1679000 AAAAGCATATTATTTGCAGCATAGCTCAAGGAAAGAAAGGCTATATG-C--C-AAAGACCTTCAA
1 AAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGA
1679061 GTTCGATTACACTCAGCTC
66 GTTCGATTACACTCAGCTC
* * * * * *
1679080 AAAGGCACATCATTTGTAGCATAACTCAGGGCAAGAAAGTCTATTTGCCAACAAAAAACCTTCGA
1 AAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGA
*
1679145 GTTCGATTACACTCATCTC
66 GTTCGATTACACTCAGCTC
* * * * * * *
1679164 AAAGGCACATCATTTGTAGTATAGCTCAATGCGAGAAGGGATATCTGCCAACAAAAGACCTTCGA
1 AAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGA
1679229 GTTCGATTACACTCA
66 GTTCGATTACACTCA
1679244 TCATTTGCAG
Statistics
Matches: 280, Mismatches: 43, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
80 67 0.24
81 1 0.00
82 1 0.00
83 67 0.24
84 144 0.51
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (84 bp):
AAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGA
GTTCGATTACACTCAGCTC
Found at i:1679287 original size:71 final size:71
Alignment explanation
Indices: 1679171--1679314 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 71
1679161 CTCAAAGGCA
* * *
1679171 CATCATTTGTAGTATAGCTCAATGCGAGAAGGGATATCTGCCAACAAAAGACCTTCGAGTTCGAT
1 CATCATTTGCAGCATAGCTCAATGCGAGAAGGGATATCTGCCAACAAAAGAACTTCGAGTTCGAT
1679236 TACACT
66 TACACT
*
1679242 CATCATTTGCAGCATAGCTCAATGCGAGAAGGGTTATCTGCCAACAAAAGAACTTCGAGTTCGAT
1 CATCATTTGCAGCATAGCTCAATGCGAGAAGGGATATCTGCCAACAAAAGAACTTCGAGTTCGAT
1679307 TACACT
66 TACACT
1679313 CA
1 CA
1679315 GCTCAAAGAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (71 bp):
CATCATTTGCAGCATAGCTCAATGCGAGAAGGGATATCTGCCAACAAAAGAACTTCGAGTTCGAT
TACACT
Found at i:1679396 original size:26 final size:26
Alignment explanation
Indices: 1679360--1679412 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1679350 CGAGAAGGGC
*
1679360 TATCTGCCAACAAAAGACCTTCGAGT
1 TATCTACCAACAAAAGACCTTCGAGT
1679386 TATCTACCAACAAAAGACCTTCGAGT
1 TATCTACCAACAAAAGACCTTCGAGT
1679412 T
1 T
1679413 CGATTACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (26 bp):
TATCTACCAACAAAAGACCTTCGAGT
Found at i:1679467 original size:110 final size:110
Alignment explanation
Indices: 1679274--1679496 Score: 392
Period size: 110 Copynumber: 2.0 Consensus size: 110
1679264 TGCGAGAAGG
* * *
1679274 GTTATCTGCCAACAAAAGAACTTCGAGTTCGATTACACTCAGCTCAAAGATACATCATTTGCAGC
1 GTTATCTACCAACAAAAGAACTTCGAGTTCGATTACACTCAACTCAAAGACACATCATTTGCAGC
1679339 ATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGA
66 ATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGA
* * *
1679384 GTTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGG
1 GTTATCTACCAACAAAAGAACTTCGAGTTCGATTACACTCAACTCAAAGACACATCATTTGCAGC
1679449 ATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGA
66 ATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGA
1679494 GTT
1 GTT
1679497 CGATTACACT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (110 bp):
GTTATCTACCAACAAAAGAACTTCGAGTTCGATTACACTCAACTCAAAGACACATCATTTGCAGC
ATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGA
Found at i:1679487 original size:84 final size:84
Alignment explanation
Indices: 1679384--1679711 Score: 410
Period size: 85 Copynumber: 3.9 Consensus size: 84
1679374 AGACCTTCGA
* * *
1679384 GTTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATC-ATTTGCAG
1 GTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAG
*
1679448 GATAGCTCAAGGCGAGAAGG
65 CATAGCTCAAGGCGAGAAGG
* **
1679468 GCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATGTCCAATTTACA
1 GTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CAATTTACA
*
1679533 GCATAACTCAAGGCGAGAAGG
64 GCATAGCTCAAGGCGAGAAGG
* * * *
1679554 GTTATCTGTCAACCAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCATATCAAATTTACAG
1 GTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-AATTTACAG
* *
1679619 CATAGCTCAA-GCTAGAGGG
65 CATAGCTCAAGGCGAGAAGG
* * * * * *
1679638 GTTATCTGTCATCAAAGACCCTTCGAGTTCGATTCCATTCAGCTCAAAGGCACATC-AGTTGCAG
1 GTTATCTGCCAACAAAGA-CCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAG
1679702 CATAGCTCAA
65 CATAGCTCAA
1679712 TGTAATAAGA
Statistics
Matches: 216, Mismatches: 24, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
83 16 0.07
84 74 0.34
85 90 0.42
86 36 0.17
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
GTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAGC
ATAGCTCAAGGCGAGAAGG
Found at i:1681175 original size:21 final size:21
Alignment explanation
Indices: 1681150--1681196 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1681140 TTTGTTTGCG
1681150 TAAATTGA-CGTGTTTTCCCTT
1 TAAATT-ATCGTGTTTTCCCTT
* *
1681171 TAAA-TATTGTGTTTTCCTTT
1 TAAATTATCGTGTTTTCCCTT
1681191 TAAATT
1 TAAATT
1681197 TGTTTGTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53
Consensus pattern (21 bp):
TAAATTATCGTGTTTTCCCTT
Done.