Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017249.1 Corchorus olitorius cultivar O-4 contig17282, 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: 95824
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:9210 original size:76 final size:76
Alignment explanation
Indices: 9084--9460 Score: 472
Period size: 76 Copynumber: 5.1 Consensus size: 76
9074 GAATGAGAAC
* * * *
9084 GAGCGTCCACGCAGACGTCATTCACGCAACGGCTGAGCGCTTAGACTGGCGCCCCCGTTCGTCTA
1 GAGCGTCCACGCAGACGCCACTCACACAACGGCTGAGCGCCTAGACTGGCGCCCCCGTTCGTCTA
*
9149 CCAGTGAGGCA
66 CAAGTGAGGCA
* ** * *
9160 GAGCGTTCGTGCAGACGCCACTCACACAACGGCTAAGCGCCTAGACTGGCGCTCCCGTTCGTCTA
1 GAGCGTCCACGCAGACGCCACTCACACAACGGCTGAGCGCCTAGACTGGCGCCCCCGTTCGTCTA
*
9225 TAAGTGAGGCA
66 CAAGTGAGGCA
* *
9236 GAGCGTCCACGCAGACGCCACTCATACAA---C--A--G-CT-GA---GCGCCCCCGTTCGTCCA
1 GAGCGTCCACGCAGACGCCACTCACACAACGGCTGAGCGCCTAGACTGGCGCCCCCGTTCGTCTA
9289 CAAGTGAGGCA
66 CAAGTGAGGCA
* * *
9300 GAGCGTCCACGCAAACGCCACTCACTCAACGGCTGAGCGCCCAGACTGGCGCCCCCGTTCGTCTA
1 GAGCGTCCACGCAGACGCCACTCACACAACGGCTGAGCGCCTAGACTGGCGCCCCCGTTCGTCTA
*
9365 CAAGTGATGCA
66 CAAGTGAGGCA
* * * *
9376 GAGCGTCCACGCAGACGCCATTCACTCAACGGTTGAGCGCCTAGACTGGCGCCCCCGTTCGTCCA
1 GAGCGTCCACGCAGACGCCACTCACACAACGGCTGAGCGCCTAGACTGGCGCCCCCGTTCGTCTA
9441 CCAAGTGAGGCA
66 -CAAGTGAGGCA
9453 GAGCGTCC
1 GAGCGTCC
9461 GTGCAGAACA
Statistics
Matches: 258, Mismatches: 30, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
64 51 0.20
67 3 0.01
68 2 0.01
69 2 0.01
71 2 0.01
72 1 0.00
73 3 0.01
76 176 0.68
77 18 0.07
ACGTcount: A:0.22, C:0.36, G:0.27, T:0.16
Consensus pattern (76 bp):
GAGCGTCCACGCAGACGCCACTCACACAACGGCTGAGCGCCTAGACTGGCGCCCCCGTTCGTCTA
CAAGTGAGGCA
Found at i:9295 original size:64 final size:64
Alignment explanation
Indices: 9208--9341 Score: 207
Period size: 64 Copynumber: 2.1 Consensus size: 64
9198 GCCTAGACTG
* * * *
9208 GCGCTCCCGTTCGTCTATAAGTGAGGCAGAGCGTCCACGCAGACGCCACTCA-TACAACAGCTGA
1 GCGCCCCCGTTCGTCCACAAGTGAGGCAGAGCGTCCACGCAAACGCCACTCACT-CAACAGCTGA
*
9272 GCGCCCCCGTTCGTCCACAAGTGAGGCAGAGCGTCCACGCAAACGCCACTCACTCAACGGCTGA
1 GCGCCCCCGTTCGTCCACAAGTGAGGCAGAGCGTCCACGCAAACGCCACTCACTCAACAGCTGA
9336 GCGCCC
1 GCGCCC
9342 AGACTGGCGC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 63 0.98
65 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.14
Consensus pattern (64 bp):
GCGCCCCCGTTCGTCCACAAGTGAGGCAGAGCGTCCACGCAAACGCCACTCACTCAACAGCTGA
Found at i:9416 original size:140 final size:140
Alignment explanation
Indices: 9132--9395 Score: 420
Period size: 140 Copynumber: 1.9 Consensus size: 140
9122 GCTTAGACTG
* * * ** *
9132 GCGCCCCCGTTCGTCTACCAGTGAGGCAGAGCGTTCGTGCAGACGCCACTCACACAACGGCTAAG
1 GCGCCCCCGTTCGTCCACAAGTGAGGCAGAGCGTCCACGCAAACGCCACTCACACAACGGCTAAG
* * *
9197 CGCCTAGACTGGCGCTCCCGTTCGTCTATAAGTGAGGCAGAGCGTCCACGCAGACGCCACTCATA
66 CGCCCAGACTGGCGCCCCCGTTCGTCTACAAGTGAGGCAGAGCGTCCACGCAGACGCCACTCATA
9262 CAACAGCTGA
131 CAACAGCTGA
* *
9272 GCGCCCCCGTTCGTCCACAAGTGAGGCAGAGCGTCCACGCAAACGCCACTCACTCAACGGCTGAG
1 GCGCCCCCGTTCGTCCACAAGTGAGGCAGAGCGTCCACGCAAACGCCACTCACACAACGGCTAAG
*
9337 CGCCCAGACTGGCGCCCCCGTTCGTCTACAAGTGATGCAGAGCGTCCACGCAGACGCCA
66 CGCCCAGACTGGCGCCCCCGTTCGTCTACAAGTGAGGCAGAGCGTCCACGCAGACGCCA
9396 TTCACTCAAC
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
140 112 1.00
ACGTcount: A:0.22, C:0.36, G:0.27, T:0.15
Consensus pattern (140 bp):
GCGCCCCCGTTCGTCCACAAGTGAGGCAGAGCGTCCACGCAAACGCCACTCACACAACGGCTAAG
CGCCCAGACTGGCGCCCCCGTTCGTCTACAAGTGAGGCAGAGCGTCCACGCAGACGCCACTCATA
CAACAGCTGA
Found at i:9508 original size:35 final size:35
Alignment explanation
Indices: 9467--9535 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
9457 GTCCGTGCAG
9467 AACAAATT-GAGAACCCTATGAGCGTCAAGGCTCAA
1 AACAAATTAG-GAACCCTATGAGCGTCAAGGCTCAA
9502 AACAAATTAGGAACCCTATGAGCGTCAAGGCTCA
1 AACAAATTAGGAACCCTATGAGCGTCAAGGCTCA
9536 GGGAATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (35 bp):
AACAAATTAGGAACCCTATGAGCGTCAAGGCTCAA
Found at i:12502 original size:21 final size:22
Alignment explanation
Indices: 12476--12517 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12466 TTATAGATAT
12476 ACTTAAACC-AAAAATCAAAAC
1 ACTTAAACCAAAAAATCAAAAC
*
12497 ACTTAATCCAAAAAATCAAAA
1 ACTTAAACCAAAAAATCAAAA
12518 TCCCCGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (22 bp):
ACTTAAACCAAAAAATCAAAAC
Found at i:14161 original size:46 final size:45
Alignment explanation
Indices: 14110--14198 Score: 151
Period size: 46 Copynumber: 2.0 Consensus size: 45
14100 CCTAAATTTA
*
14110 ACTCCTCCATCTCTAGGTAATTCATCAAAATAAAGCTAAATATTCT
1 ACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCT-AATATTCT
*
14156 ACTCCTCCATCTCTATATAATTCATCAAAATAAAGCTAATATT
1 ACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
14199 AATTGTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 6 0.15
46 35 0.85
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (45 bp):
ACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCT
Found at i:14373 original size:56 final size:56
Alignment explanation
Indices: 14287--14401 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
14277 GTTAAATTAA
* *
14287 TAGACTTGGGTAGGTGGAAGAATTTGGCTTCTGCGTAAGGAAGGCCTAATTTTTTG
1 TAGACTCGGGTAGGTGGAAGAATTTGGCTTCTGCATAAGGAAGGCCTAATTTTTTG
14343 TAGACTCGGGTAGGTGGAAGAATTTGGCTTCTGCATAAGGAAGGCCTAATTTTTTG
1 TAGACTCGGGTAGGTGGAAGAATTTGGCTTCTGCATAAGGAAGGCCTAATTTTTTG
14399 TAG
1 TAG
14402 TCAAGGAGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.33
Consensus pattern (56 bp):
TAGACTCGGGTAGGTGGAAGAATTTGGCTTCTGCATAAGGAAGGCCTAATTTTTTG
Found at i:14923 original size:12 final size:12
Alignment explanation
Indices: 14906--14933 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
14896 GAATTAAAAG
14906 TTATTTTTTATT
1 TTATTTTTTATT
14918 TTATTTTTTATT
1 TTATTTTTTATT
14930 TTAT
1 TTAT
14934 GTTAGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTTTATT
Found at i:16892 original size:160 final size:160
Alignment explanation
Indices: 16628--16950 Score: 583
Period size: 160 Copynumber: 2.0 Consensus size: 160
16618 GGGTTGGATC
* *
16628 AATTTGATGGGTTAAATTATTAGGGAAAACGGGTATCCATCAGAAATTTAATAAGATTGAAATGA
1 AATTTGATGGGTTAAATTACTAGGGAAAACGAGTATCCATCAGAAATTTAATAAGATTGAAATGA
16693 CAATAAAGCCCAATTCAATATAACACAAATCATTAAGGTGAAGTCTTTAGAACGGTTTTTAAGTA
66 CAATAAAGCCCAATTCAATATAACACAAATCATTAAGGTGAAGTCTTTAGAACGGTTTTTAAGTA
16758 CTTTCACTTCTCCTAATTATTCTTCTTAAT
131 CTTTCACTTCTCCTAATTATTCTTCTTAAT
16788 AATTTGATGGGTTAAATTACTAGGGAAAACGAGTATCCATCAGAAATTTAATAAGATTGAAATGA
1 AATTTGATGGGTTAAATTACTAGGGAAAACGAGTATCCATCAGAAATTTAATAAGATTGAAATGA
* *
16853 CAATAAAGCCCAATTCAGTATAACACAAATCATTAAGGTGAAGTCTTTAGAGCGGTTTTTAAGTA
66 CAATAAAGCCCAATTCAATATAACACAAATCATTAAGGTGAAGTCTTTAGAACGGTTTTTAAGTA
* * *
16918 CTTTTACTTCTCCTAATTATTGTTCTTTAT
131 CTTTCACTTCTCCTAATTATTCTTCTTAAT
16948 AAT
1 AAT
16951 ATCACATTTT
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
160 156 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (160 bp):
AATTTGATGGGTTAAATTACTAGGGAAAACGAGTATCCATCAGAAATTTAATAAGATTGAAATGA
CAATAAAGCCCAATTCAATATAACACAAATCATTAAGGTGAAGTCTTTAGAACGGTTTTTAAGTA
CTTTCACTTCTCCTAATTATTCTTCTTAAT
Found at i:19067 original size:12 final size:12
Alignment explanation
Indices: 19050--19104 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
19040 CCGTTTAATA
19050 ATTATATATATT
1 ATTATATATATT
* *
19062 ATTATATATGTA
1 ATTATATATATT
19074 ATTATATAT-TT
1 ATTATATATATT
* *
19085 AGTAT-TATTTT
1 ATTATATATATT
19096 A-TATATATA
1 ATTATATATA
19105 ATATACATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 6 0.17
11 11 0.31
12 19 0.53
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (12 bp):
ATTATATATATT
Found at i:20566 original size:25 final size:28
Alignment explanation
Indices: 20525--20586 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
20515 TCTTTTTTTC
20525 AAAAATATTTTTAAATTA-CCATTATTA
1 AAAAATATTTTTAAATTATCCATTATTA
*
20552 AAAAATA-TTTT-AATTATTCTATTATTA
1 AAAAATATTTTTAAATTA-TCCATTATTA
20579 AAATAATA
1 AAA-AATA
20587 AAAATTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 5 0.16
26 4 0.13
27 18 0.58
28 4 0.13
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAAATATTTTTAAATTATCCATTATTA
Found at i:22627 original size:21 final size:21
Alignment explanation
Indices: 22603--22812 Score: 350
Period size: 21 Copynumber: 10.0 Consensus size: 21
22593 GGTTTAATAT
*
22603 GGTTTGACTATCAAACTTTGG
1 GGTTTGACCATCAAACTTTGG
22624 GGTTTGACCATCAAACTTTGG
1 GGTTTGACCATCAAACTTTGG
22645 GGTTTGACCATCAAACTTTGG
1 GGTTTGACCATCAAACTTTGG
22666 GGTTTGACCATCAAACTTTGG
1 GGTTTGACCATCAAACTTTGG
22687 GGTTTGACCATCAAACTTTGG
1 GGTTTGACCATCAAACTTTGG
22708 GGTTTGACCATCAAACTTTGG
1 GGTTTGACCATCAAACTTTGG
*
22729 GGTTTGACCATCAAACTTTCG
1 GGTTTGACCATCAAACTTTGG
* *
22750 GGTTTGACTATCAAA-TTTTG
1 GGTTTGACCATCAAACTTTGG
* *
22770 GGTTTGACCATCAAATTTTAG
1 GGTTTGACCATCAAACTTTGG
*
22791 GGTTTGACCATCAAAATTTGG
1 GGTTTGACCATCAAACTTTGG
22812 G
1 G
22813 CTAAAACACA
Statistics
Matches: 180, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
20 18 0.10
21 162 0.90
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
GGTTTGACCATCAAACTTTGG
Found at i:22914 original size:21 final size:21
Alignment explanation
Indices: 22880--22954 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
22870 TGTTTTGATT
* *
22880 ATCAAACTTT-GGGTTTAACC
1 ATCAAAATTTGGGGTTTGACC
22900 ATCAAAATTTGGGGTTTGACC
1 ATCAAAATTTGGGGTTTGACC
* *
22921 ATCAAAATTTGGGGTTTGGCT
1 ATCAAAATTTGGGGTTTGACC
22942 ATCAAAATTTGGG
1 ATCAAAATTTGGG
22955 CAAAAACATA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 9 0.18
21 41 0.82
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (21 bp):
ATCAAAATTTGGGGTTTGACC
Found at i:22936 original size:142 final size:142
Alignment explanation
Indices: 22738--22996 Score: 412
Period size: 142 Copynumber: 1.8 Consensus size: 142
22728 GGGTTTGACC
* * * *
22738 ATCAAACTTTCGGGTTTGACTATCAAATTTTGGGTTTGACCATCAAATTTTAGGGTTTGACCATC
1 ATCAAACTTTCGGGTTTAACCATCAAATTTGGGGTTTGACCATCAAAATTTAGGGTTTGACCATC
* *
22803 AAAATTTGGGCTAAAACACAGTTTTGGGCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTCAA
66 AAAATTTGGGCAAAAACACAGTTTTGGGCAAAAATGTGGTGGATGCTTCAATTGATAAGGTTCAA
22868 CATGTTTTGATT
131 CATGTTTTGATT
* * *
22880 ATCAAACTTT-GGGTTTAACCATCAAAATTTGGGGTTTGACCATCAAAATTTGGGGTTTGGCTAT
1 ATCAAACTTTCGGGTTTAACCATC-AAATTTGGGGTTTGACCATCAAAATTTAGGGTTTGACCAT
*
22944 CAAAATTTGGGCAAAAACATAGTTTTGGGCAAAAATGTGGTGGATGCTTCAAT
65 CAAAATTTGGGCAAAAACACAGTTTTGGGCAAAAATGTGGTGGATGCTTCAAT
22997 AGACAACCAA
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
141 11 0.10
142 95 0.90
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (142 bp):
ATCAAACTTTCGGGTTTAACCATCAAATTTGGGGTTTGACCATCAAAATTTAGGGTTTGACCATC
AAAATTTGGGCAAAAACACAGTTTTGGGCAAAAATGTGGTGGATGCTTCAATTGATAAGGTTCAA
CATGTTTTGATT
Found at i:25651 original size:21 final size:18
Alignment explanation
Indices: 25627--25667 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
25617 TTTTTAAACA
25627 AAAATAAAATTAAAATATATT
1 AAAATAAAA--AAAATAT-TT
25648 AAAATAAAAAAAATATTT
1 AAAATAAAAAAAATATTT
25666 AA
1 AA
25668 TTTTTATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
21 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATAAAAAAAATATTT
Found at i:26027 original size:2 final size:2
Alignment explanation
Indices: 26020--26086 Score: 79
Period size: 2 Copynumber: 35.5 Consensus size: 2
26010 TCCAAAACCA
26020 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC -C TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
26060 TC CC TC TC T- TC CC CC TC -C TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
26087 ATGTAAAGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
1 4 0.07
2 53 0.93
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:26061 original size:26 final size:26
Alignment explanation
Indices: 26023--26086 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 26
26013 AAAACCATCT
* *
26023 CTCTCTCTCTCTCTCTCTCTCTCTCCTC
1 CTCTCTCTCTCCCTCTCT-TC-CCCCTC
26051 CTCTCTCTCTCCCTCTCTTCCCCCTC
1 CTCTCTCTCTCCCTCTCTTCCCCCTC
26077 CTCTCTCTCT
1 CTCTCTCTCT
26087 ATGTAAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 15 0.44
27 2 0.06
28 17 0.50
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (26 bp):
CTCTCTCTCTCCCTCTCTTCCCCCTC
Found at i:29484 original size:19 final size:19
Alignment explanation
Indices: 29438--29485 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
29428 GTGGGATCTA
* *
29438 TATATATATTGTTATTTAT
1 TATATTTATTGTTATATAT
*
29457 T-TTTATTATTGTTATATAT
1 TATAT-TTATTGTTATATAT
29476 TATATTTATT
1 TATATTTATT
29486 ATACAATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TATATTTATTGTTATATAT
Found at i:29948 original size:6 final size:6
Alignment explanation
Indices: 29904--29945 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
29894 AGGTGAGGCC
*
29904 GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG AAGCCG
1 GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG
29946 AAGTTGAAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.19, C:0.33, G:0.48, T:0.00
Consensus pattern (6 bp):
GAGCCG
Found at i:32059 original size:25 final size:24
Alignment explanation
Indices: 32013--32069 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
32003 GCCAGTCTTG
*
32013 AATTT-TTTAATGTTTAATTATTA
1 AATTTATTTAATATTTAATTATTA
*
32036 AATTTATTTAATATCTTTATTATTA
1 AATTTATTTAATAT-TTAATTATTA
*
32061 AAGTTATTT
1 AATTTATTT
32070 TACAATCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 7 0.24
25 17 0.59
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATATTTAATTATTA
Found at i:33579 original size:22 final size:22
Alignment explanation
Indices: 33554--33627 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
33544 TAAAAATCTC
*
33554 AATTTCATAAGGAGTTTATCAA
1 AATTTCATAAGGAGGTTATCAA
* * *
33576 AATTTAATAGGGAGGTTATCAG
1 AATTTCATAAGGAGGTTATCAA
* * * *
33598 AATTTTATAATGTGGTTATAAA
1 AATTTCATAAGGAGGTTATCAA
33620 AATTTCAT
1 AATTTCAT
33628 GAGGTTTCAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (22 bp):
AATTTCATAAGGAGGTTATCAA
Found at i:33902 original size:21 final size:22
Alignment explanation
Indices: 33863--33939 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
33853 TGGAGTAACC
**
33863 AAAATTTCGGAGGGAAGTTATT
1 AAAATTTCATAGGGAAGTTATT
* *
33885 AAAATTTCATA-TGAAGTTATC
1 AAAATTTCATAGGGAAGTTATT
* *
33906 AAAATTTTATAGGGAGGTTATT
1 AAAATTTCATAGGGAAGTTATT
33928 AAAATTTCATAG
1 AAAATTTCATAG
33940 TTTAGTTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 18 0.40
22 27 0.60
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGGGAAGTTATT
Found at i:33920 original size:43 final size:43
Alignment explanation
Indices: 33783--33938 Score: 126
Period size: 43 Copynumber: 3.7 Consensus size: 43
33773 AAAGTGTGGT
* * *
33783 ATTTCAGTGGG-AGATTATTAAAATTTCATAGTGTAGTTACC-AA
1 ATTTCAGAGGGAAG-TTATTAAAATTTCATA-TGAAGTAACCAAA
* * * *
33826 A-TT---AGGAAATTTATTAAAATTTTACTATGGAGTAACCAAA
1 ATTTCAGAGGGAAGTTATTAAAATTTCA-TATGAAGTAACCAAA
* * *
33866 ATTTCGGAGGGAAGTTATTAAAATTTCATATGAAGTTATCAAA
1 ATTTCAGAGGGAAGTTATTAAAATTTCATATGAAGTAACCAAA
* * *
33909 ATTTTATAGGGAGGTTATTAAAATTTCATA
1 ATTTCAGAGGGAAGTTATTAAAATTTCATA
33939 GTTTAGTTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
39 23 0.26
40 6 0.07
41 2 0.02
42 2 0.02
43 39 0.43
44 18 0.20
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (43 bp):
ATTTCAGAGGGAAGTTATTAAAATTTCATATGAAGTAACCAAA
Found at i:34036 original size:22 final size:22
Alignment explanation
Indices: 33879--34310 Score: 135
Period size: 22 Copynumber: 20.2 Consensus size: 22
33869 TCGGAGGGAA
* *
33879 GTTATTAAAATTTCATA-TGAA
1 GTTATCAAAATTTCATAGTGAG
* *
33900 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAGTGAG
* *
33922 GTTATTAAAATTTCATAGTTTA-
1 GTTATCAAAATTTCATAG-TGAG
* * *
33944 GTTTTTAGAATTTCATAGT--G
1 GTTATCAAAATTTCATAGTGAG
*
33964 G-T-TCAAATTTTCATAATGTGTA-
1 GTTATCAAAATTTCAT-A-GTG-AG
*
33986 G-T-TCAAATTTTCATAG-GAAG
1 GTTATCAAAATTTCATAGTG-AG
* *
34006 GCTAACAAAATTTCATAGTGAG
1 GTTATCAAAATTTCATAGTGAG
*** * *
34028 GTTATCAAAACAACAATAGGGAT
1 GTTATCAAAATTTC-ATAGTGAG
34051 GTTATCAAAA--T--TAGT--G
1 GTTATCAAAATTTCATAGTGAG
*
34067 GTTATCAAAATTTCATAAG-AAG
1 GTTATCAAAATTTCAT-AGTGAG
34089 GTTATCAAAATTT--TA-T-A-
1 GTTATCAAAATTTCATAGTGAG
* * **
34106 G-TGTGAAAATTT-ATAGGAAG
1 GTTATCAAAATTTCATAGTGAG
34126 GTTTATTATCAAAATTTCATAGTGAG
1 G----TTATCAAAATTTCATAGTGAG
* * *
34152 GTTTTCAAAATTCCATAGGGAG
1 GTTATCAAAATTTCATAGTGAG
* * * *
34174 GTTAACCAAATTTTAT-GGGAAG
1 GTTATCAAAATTTCATAGTG-AG
* * *
34196 CTTAACAAAATTTCATAGAT-TG
1 GTTATCAAAATTTCATAG-TGAG
* * * * *
34218 GTTCTCGAAATTACATAAT-ATT
1 GTTATCAAAATTTCATAGTGA-G
* **
34240 GTTATCAAAATTTTATAAAGAG
1 GTTATCAAAATTTCATAGTGAG
* *
34262 GTTATCAAAATTTCATAATGTG
1 GTTATCAAAATTTCATAGTGAG
* * *
34284 GTTATCACAATTTTATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
34306 GTTAT
1 GTTAT
34311 AGCTTGGGAC
Statistics
Matches: 309, Mismatches: 66, Indels: 71
0.69 0.15 0.16
Matches are distributed among these distances:
16 19 0.06
17 3 0.01
18 14 0.05
19 6 0.02
20 8 0.03
21 24 0.08
22 199 0.64
23 20 0.06
25 9 0.03
26 7 0.02
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAG
Found at i:34663 original size:2 final size:2
Alignment explanation
Indices: 34656--34687 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34646 TTAAAACTAG
34656 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34688 ATAAATCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36035 original size:27 final size:27
Alignment explanation
Indices: 35972--36039 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
35962 AAGGGATAAA
*
35972 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
*
35999 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
36026 GAGAG-GGAGGCTGC
1 GAG-GCGGAGGCTGC
36040 CGCTGGTGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.15, G:0.47, T:0.19
Consensus pattern (27 bp):
GAGGCGGAGGCTGCTCGGATGTATAGG
Found at i:36038 original size:33 final size:27
Alignment explanation
Indices: 35972--36028 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
35962 AAGGGATAAA
35972 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
35999 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
36026 GAG
1 GAG
36029 AGGGAGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.14, G:0.46, T:0.21
Consensus pattern (27 bp):
GAGGCTGAGGCTGCTCGGATGTATAGG
Found at i:36350 original size:20 final size:20
Alignment explanation
Indices: 36310--36351 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
36300 TATTATGTGA
**
36310 TATTATAAATTGAAATGAAT
1 TATTATAAATTGAAAAAAAT
36330 TATTATAAATTGAAAAAAAT
1 TATTATAAATTGAAAAAAAT
36350 TA
1 TA
36352 AATAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
TATTATAAATTGAAAAAAAT
Found at i:38162 original size:20 final size:20
Alignment explanation
Indices: 38133--38171 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38123 TATTTTGGGA
38133 TTTTTATGGATGTTTATGTC
1 TTTTTATGGATGTTTATGTC
* *
38153 TTTTTTTGGATTTTTATGT
1 TTTTTATGGATGTTTATGT
38172 ATATTGGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.18, T:0.67
Consensus pattern (20 bp):
TTTTTATGGATGTTTATGTC
Found at i:40396 original size:16 final size:13
Alignment explanation
Indices: 40373--40427 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 13
40363 CACCTGCGGC
40373 AATAATAAATGAAT
1 AATAATAAAT-AAT
40387 ACATTAATAAATAAT
1 A-A-TAATAAATAAT
40402 AATAATAAA-AAT
1 AATAATAAATAAT
*
40414 AAAAATAAA-AAT
1 AATAATAAATAAT
40426 AA
1 AA
40428 CTAAACTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
12 16 0.42
13 7 0.18
14 2 0.05
15 5 0.13
16 8 0.21
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:40407 original size:6 final size:6
Alignment explanation
Indices: 40392--40427 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
40382 TGAATACATT
*
40392 AATAAA TAATAAT AATAAA AATAAA AATAAA AATAA
1 AATAAA -AATAAA AATAAA AATAAA AATAAA AATAA
40428 CTAAACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:44088 original size:29 final size:31
Alignment explanation
Indices: 44020--44088 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
44010 ACGGCTTTGT
* *
44020 CTTGGACATTGGCACATGAACGACAAACGTC
1 CTTGGACATTGCCAAATGAACGACAAACGTC
* *
44051 C-TGAACATTGCCAAATGAAC-ACGAACG-C
1 CTTGGACATTGCCAAATGAACGACAAACGTC
44079 CTTGGACATT
1 CTTGGACATT
44089 ACCATCGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.06
29 13 0.41
30 16 0.50
31 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (31 bp):
CTTGGACATTGCCAAATGAACGACAAACGTC
Found at i:55326 original size:1 final size:1
Alignment explanation
Indices: 55322--55352 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
55312 AGCAAACATC
55322 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
55353 CTTGTGGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:58629 original size:5 final size:6
Alignment explanation
Indices: 58616--58645 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
58606 CAAATCTAAT
58616 AGAAAA AG-AAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
58646 TAAATCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:63544 original size:9 final size:9
Alignment explanation
Indices: 63530--63559 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
63520 GGTTTAATCG
63530 AAAAATAAA
1 AAAAATAAA
63539 AAAAAT-AA
1 AAAAATAAA
63547 AAAAATAAA
1 AAAAATAAA
63556 AAAA
1 AAAA
63560 TTTCGACCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:63548 original size:8 final size:8
Alignment explanation
Indices: 63530--63560 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
63520 GGTTTAATCG
63530 AAAAATAAA
1 AAAAAT-AA
63539 AAAAATAA
1 AAAAATAA
63547 AAAAATAA
1 AAAAATAA
63555 AAAAAT
1 AAAAAT
63561 TTCGACCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:65953 original size:40 final size:41
Alignment explanation
Indices: 65858--66408 Score: 583
Period size: 40 Copynumber: 13.6 Consensus size: 41
65848 ATAAATGTAG
*
65858 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTGAACTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAA
65899 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTT-A
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAA
*
65939 ACAACACCTTCCGATGAGG-AGGGTCAAACTGGTAAGCTTAA
1 ACAACACCTTCCGATGAGGAAGGG-CAAACTGGTAAACTTAA
* * * * * *
65980 ACAACATCTTCCGGTGGGGAAGGGCAAAATAGG--GATTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACT-GGTAAACTTAA
* *
66020 ACAACACCTTCCGATGAGG-AGGGTCAAACTAGTAAGCTTAA
1 ACAACACCTTCCGATGAGGAAGGG-CAAACTGGTAAACTTAA
* * * * *
66061 ACAAAACCTTCCGGTGGGGAAGGGCAAACTAGG--GATTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACT-GGTAAACTTAA
* *
66101 ACAACACCTTCCGGTGAGG-AGGGTCAAACTGGTAAGCTTAA
1 ACAACACCTTCCGATGAGGAAGGG-CAAACTGGTAAACTTAA
* * * * **
66142 ACGACACCTTCCGATGAGGAAGGGCAAACTAGTGAATTTGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAA
*
66183 ACAACACC-TCTCGATGAGGAAGGACAAACTGGTAAAC-TAA
1 ACAACACCTTC-CGATGAGGAAGGGCAAACTGGTAAACTTAA
* ** * *
66223 GCAACACCTTCTAATGAGGAAGGGCAAATTGGTGAA-TATAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACT-TAA
* * *
66264 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTGAAC-TAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAA
* * *
66304 GCAACACCTTCC-ATTGAGGAAGGGCAAACTGGGAAAC-TCA
1 ACAACACCTTCCGA-TGAGGAAGGGCAAACTGGTAAACTTAA
*
66344 TCAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAA
* *
66385 A-AACACCTTCCGGTGGGGAAGGGC
1 ACAACACCTTCCGATGAGGAAGGGC
66409 GAATTGGGAA
Statistics
Matches: 423, Mismatches: 66, Indels: 43
0.80 0.12 0.08
Matches are distributed among these distances:
39 16 0.04
40 205 0.48
41 187 0.44
42 15 0.04
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.18
Consensus pattern (41 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAA
Found at i:65956 original size:81 final size:81
Alignment explanation
Indices: 65816--66408 Score: 586
Period size: 81 Copynumber: 7.3 Consensus size: 81
65806 CAAGAATAAG
* * * * * * *
65816 AACAACACC-TCGCGATGAGGGAGGGTACATTGATAAATGTAGACAACACCTTCCGATGAGGAAG
1 AACAACACCTTC-CGATGAGGAAGGGCAAACTGGTAAATTTAAACAACACCTTCCGATGAGGAAG
65880 GGCAAACTGGTGAACTTA
65 GGCAAACTGGT-AACTTA
*
65898 AACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTT-AACAACACCTTCCGATGAGG-AGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAATTTAAACAACACCTTCCGATGAGGAAGG
65961 GTCAAACTGGTAAGCTTA
66 G-CAAACTGGTAA-CTTA
* * * * *
65979 AACAACATCTTCCGGTGGGGAAGGGCAAAATAGG--GATTTAAACAACACCTTCCGATGAGG-AG
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GGTAAATTTAAACAACACCTTCCGATGAGGAAG
*
66041 GGTCAAACTAGTAAGCTTA
65 GG-CAAACTGGTAA-CTTA
* * * * *
66060 AACAAAACCTTCCGGTGGGGAAGGGCAAACTAGG--GATTTAAACAACACCTTCCGGTGAGG-AG
1 AACAACACCTTCCGATGAGGAAGGGCAAACT-GGTAAATTTAAACAACACCTTCCGATGAGGAAG
66122 GGTCAAACTGGTAAGCTTA
65 GG-CAAACTGGTAA-CTTA
* * * **
66141 AACGACACCTTCCGATGAGGAAGGGCAAACTAGTGAATTTGGACAACACC-TCTCGATGAGGAAG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAATTTAAACAACACCTTC-CGATGAGGAAG
*
66205 GACAAACTGGTAAAC-TA
65 GGCAAACTGGT-AACTTA
* ** * * * *
66222 AGCAACACCTTCTAATGAGGAAGGGCAAATTGGTGAATATAAACAACACCTCCCGATGAGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAATTTAAACAACACCTTCCGATGAGGAAGG
*
66287 GCAAATTGGTGAAC-TA
66 GCAAACTGGT-AACTTA
* * * * *
66303 AGCAACACCTTCC-ATTGAGGAAGGGCAAACTGGGAAA-CTCATCAACACCTTCCGATGAGGAAG
1 AACAACACCTTCCGA-TGAGGAAGGGCAAACTGGTAAATTTAAACAACACCTTCCGATGAGGAAG
66366 GGCAAACTGGTAAACTTA
65 GGCAAACTGGT-AACTTA
* *
66384 AA-AACACCTTCCGGTGGGGAAGGGC
1 AACAACACCTTCCGATGAGGAAGGGC
66409 GAATTGGGAA
Statistics
Matches: 441, Mismatches: 56, Indels: 30
0.84 0.11 0.06
Matches are distributed among these distances:
80 66 0.15
81 306 0.69
82 62 0.14
83 7 0.02
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.18
Consensus pattern (81 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAATTTAAACAACACCTTCCGATGAGGAAGG
GCAAACTGGTAACTTA
Found at i:66125 original size:162 final size:162
Alignment explanation
Indices: 65858--66408 Score: 647
Period size: 162 Copynumber: 3.4 Consensus size: 162
65848 ATAAATGTAG
*
65858 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTGAACTTAAACAACACCTTCCGATGAGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAAACAACACCTTCCGATGAGGAAGGG
* * *
65923 CAAACTGGTAAACTT-AACAACACCTTCCGATGAGGAGGGTCAAACTGGTAAGCTTAAACAACAT
66 CAAACTGGT-GATTTAAACAACACCTTCCGATGAGGAGGGTCAAACTGGTAAGCTTAAACAACAC
* * *
65987 CTTCCGGTGGGGAAGGGCAAAATAGGGATTTAA
130 CTTCCGATGAGGAAGGGCAAACTAGGGATTTAA
* * * * *
66020 ACAACACCTTCCGATGAGG-AGGGTCAAACTAGTAAGCTTAAACAAAACCTTCCGGTGGGGAAGG
1 ACAACACCTTCCGATGAGGAAGGG-CAAACTGGTAAACTTAAACAACACCTTCCGATGAGGAAGG
* *
66084 GCAAACTAGG-GATTTAAACAACACCTTCCGGTGAGGAGGGTCAAACTGGTAAGCTTAAACGACA
65 GCAAACT-GGTGATTTAAACAACACCTTCCGATGAGGAGGGTCAAACTGGTAAGCTTAAACAACA
* **
66148 CCTTCCGATGAGGAAGGGCAAACTAGTGAATTTGG
129 CCTTCCGATGAGGAAGGGCAAACTAG-GGATTTAA
* * **
66183 ACAACACC-TCTCGATGAGGAAGGACAAACTGGTAAAC-TAAGCAACACCTTCTAATGAGGAAGG
1 ACAACACCTTC-CGATGAGGAAGGGCAAACTGGTAAACTTAAACAACACCTTCCGATGAGGAAGG
* * * * *
66246 GCAAATTGGTGAATATAAACAACACCTCCCGATGAGGAAGGG-CAAATTGGTGAA-C-TAAGCAA
65 GCAAACTGGTG-ATTTAAACAACACCTTCCGATGAGG-AGGGTCAAACTGGT-AAGCTTAAACAA
** *
66308 CACCTTCC-ATTGAGGAAGGGCAAACT-GGGAAACTCA
127 CACCTTCCGA-TGAGGAAGGGCAAACTAGGG-ATTTAA
* * *
66344 TCAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAAA-AACACCTTCCGGTGGGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAAACAACACCTTCCGATGAGGAAGGG
66408 C
66 C
66409 GAATTGGGAA
Statistics
Matches: 330, Mismatches: 45, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
160 1 0.00
161 64 0.19
162 191 0.58
163 65 0.20
164 9 0.03
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.18
Consensus pattern (162 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTAAACAACACCTTCCGATGAGGAAGGG
CAAACTGGTGATTTAAACAACACCTTCCGATGAGGAGGGTCAAACTGGTAAGCTTAAACAACACC
TTCCGATGAGGAAGGGCAAACTAGGGATTTAA
Found at i:69646 original size:13 final size:13
Alignment explanation
Indices: 69624--69656 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
69614 CTACTAACAA
69624 TTTTTCTTTTGAG
1 TTTTTCTTTTGAG
*
69637 TTTTTTTTTTGAG
1 TTTTTCTTTTGAG
69650 TTTTTCT
1 TTTTTCT
69657 AGGAAGCTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (13 bp):
TTTTTCTTTTGAG
Found at i:72295 original size:21 final size:21
Alignment explanation
Indices: 72269--72323 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
72259 CGGCCATTCA
**
72269 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
72290 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
72311 CCGTGCCATCACC
1 CCGTGCCACCACC
72324 ATTCCAAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:72683 original size:15 final size:14
Alignment explanation
Indices: 72663--72692 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
72653 ATCTTTTTAA
72663 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
72678 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
72692 T
1 T
72693 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:75611 original size:15 final size:15
Alignment explanation
Indices: 75581--75622 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
75571 TTACTCTGCT
75581 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
75597 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
75612 TTGCTTTCTGT
1 TTGTTTTCTGT
75623 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:85778 original size:22 final size:22
Alignment explanation
Indices: 85746--85790 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
85736 TCTAAAAACA
*
85746 GGACAAGTCCTGCCCAGGACTT
1 GGACAACTCCTGCCCAGGACTT
85768 GGACAACTCCTGCCCAGGACTT
1 GGACAACTCCTGCCCAGGACTT
85790 G
1 G
85791 TTGCGGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (22 bp):
GGACAACTCCTGCCCAGGACTT
Found at i:89295 original size:23 final size:23
Alignment explanation
Indices: 89269--89315 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
89259 TAGTCAATTG
89269 GCTAGTGACATGAGTGAGCTCAA
1 GCTAGTGACATGAGTGAGCTCAA
89292 GCTAGTGACATGAGTGAGCTCAA
1 GCTAGTGACATGAGTGAGCTCAA
89315 G
1 G
89316 ACACAAGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (23 bp):
GCTAGTGACATGAGTGAGCTCAA
Done.